From 2fb3f0673377c4676bd1e50289fd2bae4eb038cc Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Tue, 23 Dec 2025 22:27:34 +0530 Subject: [PATCH 01/23] Fix --version-id -> --versionid in CLI --- databusclient/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/databusclient/cli.py b/databusclient/cli.py index 4e97470..0dc7047 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -16,7 +16,7 @@ def app(): @app.command() @click.option( - "--version-id", "version_id", + "--versionid", "version_id", required=True, help="Target databus version/dataset identifier of the form " "", From d4bb454af8fc7011ee652aa82394f1273bfe0407 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Tue, 23 Dec 2025 22:28:36 +0530 Subject: [PATCH 02/23] Fix --version-id -> --versionid in test script --- test.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test.sh b/test.sh index f590198..0a4c096 100755 --- a/test.sh +++ b/test.sh @@ -1,7 +1,7 @@ #!/usr/bin/env bash databusclient deploy \ - --version-id "https://d8lr.tools.dbpedia.org/hopver/testGroup/testArtifact/1.0-alpha/" \ + --versionid "https://d8lr.tools.dbpedia.org/hopver/testGroup/testArtifact/1.0-alpha/" \ --title "Test Title" \ --abstract "Test Abstract" \ --description "Test Description" \ From 189458ec1f673c55f66b97d43b5507c648230f47 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Fri, 26 Dec 2025 19:42:42 +0530 Subject: [PATCH 03/23] cli: add mkdist validations, completion helper, tests and docs --- README.md | 54 ++++++++++++++++++++++++++++++++++++++++---- databusclient/cli.py | 47 ++++++++++++++++++++++++++++++++++++++ tests/test_cli.py | 42 ++++++++++++++++++++++++++++++++++ 3 files changed, 138 insertions(+), 5 deletions(-) create mode 100644 tests/test_cli.py diff --git a/README.md b/README.md index 0b65641..a828d75 100644 --- a/README.md +++ b/README.md @@ -90,6 +90,8 @@ Options: Commands: deploy download + mkdist + completion ``` @@ -183,7 +185,7 @@ Arguments: - Metdata mode: None Options: - --version-id TEXT Target databus version/dataset identifier of the form [required] --title TEXT Dataset title [required] @@ -202,11 +204,11 @@ Options: #### Examples of using deploy command ##### Mode 1: Classic Deploy (Distributions) ``` -databusclient deploy --version-id https://databus.dbpedia.org/user1/group1/artifact1/2022-05-18 --title title1 --abstract abstract1 --description description1 --license http://dalicc.net/licenselibrary/AdaptivePublicLicense10 --apikey MYSTERIOUS 'https://raw.githubusercontent.com/dbpedia/databus/master/server/app/api/swagger.yml|type=swagger' +databusclient deploy --versionid https://databus.dbpedia.org/user1/group1/artifact1/2022-05-18 --title title1 --abstract abstract1 --description description1 --license http://dalicc.net/licenselibrary/AdaptivePublicLicense10 --apikey MYSTERIOUS 'https://raw.githubusercontent.com/dbpedia/databus/master/server/app/api/swagger.yml|type=swagger' ``` ``` -databusclient deploy --version-id https://dev.databus.dbpedia.org/denis/group1/artifact1/2022-05-18 --title "Client Testing" --abstract "Testing the client...." --description "Testing the client...." --license http://dalicc.net/licenselibrary/AdaptivePublicLicense10 --apikey MYSTERIOUS 'https://raw.githubusercontent.com/dbpedia/databus/master/server/app/api/swagger.yml|type=swagger' +databusclient deploy --versionid https://dev.databus.dbpedia.org/denis/group1/artifact1/2022-05-18 --title "Client Testing" --abstract "Testing the client...." --description "Testing the client...." --license http://dalicc.net/licenselibrary/AdaptivePublicLicense10 --apikey MYSTERIOUS 'https://raw.githubusercontent.com/dbpedia/databus/master/server/app/api/swagger.yml|type=swagger' ``` A few more notes for CLI usage: @@ -223,7 +225,7 @@ All files referenced there will be registered on the Databus. ```bash databusclient deploy \ --metadata /home/metadata.json \ - --version-id https://databus.org/user/dataset/version/1.0 \ + --versionid https://databus.org/user/dataset/version/1.0 \ --title "Metadata Deploy Example" \ --abstract "This is a short abstract of the dataset." \ --description "This dataset was uploaded using metadata.json." \ @@ -261,7 +263,7 @@ databusclient deploy \ --webdav-url https://cloud.example.com/remote.php/webdav \ --remote nextcloud \ --path datasets/mydataset \ - --version-id https://databus.org/user/dataset/version/1.0 \ + --versionid https://databus.org/user/dataset/version/1.0 \ --title "Test Dataset" \ --abstract "Short abstract of dataset" \ --description "This dataset was uploaded for testing the Nextcloud → Databus pipeline." \ @@ -296,6 +298,48 @@ docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://d ``` +### mkdist command + +Create a distribution string from components. + +Usage: +``` +databusclient mkdist URL --cv key=value --cv key2=value2 --format ttl --compression gz --sha-length : +``` + +Example: +``` +python -m databusclient mkdist "https://example.org/file.ttl" --cv lang=en --cv part=sorted --format ttl --compression gz --sha-length aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa:12345 +``` + +## Completion + +Enable shell completion (bash example): +``` +eval "$(_DATABUSCLIENT_COMPLETE=source_bash python -m databusclient)" +``` + +### mkdist command + +Create a distribution string from components. + +Usage: +``` +databusclient mkdist URL --cv key=value --cv key2=value2 --format ttl --compression gz --sha-length : +``` + +Example: +``` +python -m databusclient mkdist "https://example.org/file.ttl" --cv lang=en --cv part=sorted --format ttl --compression gz --sha-length aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa:12345 +``` + +## Completion + +Enable shell completion (bash example): +``` +eval "$(_DATABUSCLIENT_COMPLETE=source_bash python -m databusclient)" +``` + ## Module Usage ### Step 1: Create lists of distributions for the dataset diff --git a/databusclient/cli.py b/databusclient/cli.py index 0dc7047..d900c0f 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -3,6 +3,7 @@ import os import click +import re from typing import List from databusclient import client @@ -111,5 +112,51 @@ def download(databusuris: List[str], localdir, databus, token, authurl, clientid ) +@app.command() +@click.argument("url") +@click.option("--cv", "cvs", multiple=True, help="Content variant like key=value (repeatable). Keys must not contain '|' or '_'") +@click.option("--format", "file_format", help="Format extension (e.g. ttl)") +@click.option("--compression", help="Compression (e.g. gzip)") +@click.option("--sha-length", help="sha256:length (64 hex chars followed by ':' and integer length)") +@click.option("--json-output", is_flag=True, help="Output JSON distribution object instead of plain string") +def mkdist(url, cvs, file_format, compression, sha_length, json_output): + """Create a distribution string from components.""" + # Validate CVs + cvs_dict = {} + for cv in cvs: + if "=" not in cv: + raise click.BadParameter(f"Invalid content variant '{cv}': expected key=value") + key, val = cv.split("=", 1) + if any(ch in key for ch in ("|", "_")): + raise click.BadParameter("Invalid characters in content-variant key (forbidden: '|' and '_')") + if key in cvs_dict: + raise click.BadParameter(f"Duplicate content-variant key '{key}'") + cvs_dict[key] = val + + # Validate sha-length + sha_tuple = None + if sha_length: + if not re.match(r'^[A-Fa-f0-9]{64}:\d+$', sha_length): + raise click.BadParameter("Invalid --sha-length; expected SHA256HEX:length") + sha, length = sha_length.split(":", 1) + sha_tuple = (sha, int(length)) + + # Deterministic ordering + sorted_cvs = {k: cvs_dict[k] for k in sorted(cvs_dict)} + + dist = client.create_distribution(url=url, cvs=sorted_cvs, file_format=file_format, compression=compression, sha256_length_tuple=sha_tuple) + if json_output: + import json as _json + click.echo(_json.dumps({"distribution": dist})) + else: + click.echo(dist) + + +@app.command() +@click.argument("shell", type=click.Choice(["bash","zsh","fish","powershell"]), required=False) +def completion(shell="bash"): + click.echo(f"Run: eval \"$(_DATABUSCLIENT_COMPLETE=source_{shell} python -m databusclient)\"") + + if __name__ == "__main__": app() diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..3dfd3eb --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,42 @@ +from click.testing import CliRunner +from databusclient import cli + + +def test_mkdist_multiple_cv(): + runner = CliRunner() + sha = 'a' * 64 + res = runner.invoke(cli.app, [ + 'mkdist', + 'https://example.org/file', + '--cv', 'b=2', + '--cv', 'a=1', + '--format', 'ttl', + '--compression', 'gz', + '--sha-length', f'{sha}:42' + ]) + assert res.exit_code == 0, res.output + # keys should be sorted alphabetically: a then b + assert res.output.strip() == f'https://example.org/file|a=1_b=2|ttl|gz|{sha}:42' + + +def test_mkdist_invalid_cv(): + runner = CliRunner() + res = runner.invoke(cli.app, ['mkdist', 'https://example.org/file', '--cv', 'badcv']) + assert res.exit_code != 0 + assert 'Invalid content variant' in res.output + + +def test_mkdist_invalid_sha(): + runner = CliRunner() + res = runner.invoke(cli.app, [ + 'mkdist', 'https://example.org/file', '--cv', 'k=v', '--sha-length', 'abc:123' + ]) + assert res.exit_code != 0 + assert 'Invalid --sha-length' in res.output + + +def test_completion_output(): + runner = CliRunner() + res = runner.invoke(cli.app, ['completion', 'bash']) + assert res.exit_code == 0 + assert '_DATABUSCLIENT_COMPLETE' in res.output From f6f67c015b9411bd06a3125685093f05da7e1492 Mon Sep 17 00:00:00 2001 From: Fabian Hofer <57919013+Integer-Ctrl@users.noreply.github.com> Date: Thu, 4 Dec 2025 17:10:35 +0100 Subject: [PATCH 04/23] chore: refactored readme --- README.md | 569 +++++++++++++++++++++++++++++----------- databusclient/cli.py | 8 +- databusclient/client.py | 52 ++-- 3 files changed, 463 insertions(+), 166 deletions(-) diff --git a/README.md b/README.md index a828d75..fa0ad36 100644 --- a/README.md +++ b/README.md @@ -1,189 +1,333 @@ -# Databus Client Python +# Databus Python Client -## Quickstart Example -Commands to download the DBpedia Knowledge Graphs generated by Live Fusion. -DBpedia Live Fusion publishes two different kinds of KGs: +Command-line and Python client for downloading and deploying datasets on DBpedia Databus. -1. Open Core Knowledge Graphs under CC-BY-SA license, open with copyleft/share-alike, no registration needed -2. Industry Knowledge Graphs under BUSL 1.1 license, unrestricted for research and experimentation, commercial license for productive use, free registration needed. - -### Registration (Access Token) +## Table of Contents +- [Quickstart](#quickstart) + - [Python](#python) + - [Docker](#docker) +- [DBpedia](#dbpedia) + - [Registration (Access Token)](#registration-access-token) + - [DBpedia Knowledge Graphs](#dbpedia-knowledge-graphs) + - [Download Live Fusion KG Dump (BUSL 1.1, registration needed)](#download-live-fusion-kg-dump-busl-11-registration-needed) + - [Download Enriched Knowledge Graphs (BUSL 1.1, registration needed)](#download-enriched-knowledge-graphs-busl-11-registration-needed) + - [Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikipedia-knowledge-graphs-cc-by-sa-no-registration-needed) + - [Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikidata-knowledge-graphs-cc-by-sa-no-registration-needed) +- [CLI Usage](#cli-usage) + - [Download](#cli-download) + - [Deploy](#cli-deploy) + - [Delete](#cli-delete) +- [Module Usage](#module-usage) + - [Deploy](#module-deploy) +- [Development & Contributing](#development--contributing) + - [Linting](#linting) + - [Testing](#testing) + + +## Quickstart + +The client supports two main workflows: downloading datasets from the Databus and deploying datasets to the Databus. Below you can choose how to run it (Python or Docker), then follow the sections on [DBpedia downloads](#dbpedia-knowledge-graphs), [CLI usage](#cli-usage), or [module usage](#module-usage). + +You can use either **Python** or **Docker**. Both methods support all client features. The Docker image is available at [dbpedia/databus-python-client](https://hub.docker.com/r/dbpedia/databus-python-client). + +### Python + +Requirements: [Python 3.11+](https://www.python.org/downloads/) and [pip](https://pip.pypa.io/en/stable/installation/) -1. If you do not have a DBpedia Account yet (Forum/Databus), please register at https://account.dbpedia.org -2. Login at https://account.dbpedia.org and create your token. -3. Save the token to a file `vault-token.dat`. +Before using the client, install it via pip: -### Docker vs. Python -The databus-python-client comes as **docker** or **python** with these patterns. -`$DOWNLOADTARGET` can be any Databus URI including collections OR SPARQL query (or several thereof). Details are documented below. ```bash -# Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOADTARGET --token vault-token.dat -# Python python3 -m pip install databusclient -databusclient download $DOWNLOADTARGET --token vault-token.dat ``` -### Download Live Fusion KG Snapshot (BUSL 1.1, registration needed) -TODO One slogan sentence. [More information](https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-snapshot) +Note: the PyPI release was updated and this repository prepares version `0.15`. If you previously installed `databusclient` via `pip` and observe different CLI behavior, upgrade to the latest release: + ```bash -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-snapshot --token vault-token.dat +python3 -m pip install --upgrade databusclient==0.15 ``` -### Download Enriched Knowledge Graphs (BUSL 1.1, registration needed) -**DBpedia Wikipedia Extraction Enriched** -TODO One slogan sentence and link -Currently EN DBpedia only. +**Help and further general information:** ```bash -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-snapshot --token vault-token.dat +# Python +databusclient --help +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client --help + +# Output: +Usage: databusclient [OPTIONS] COMMAND [ARGS]... + + Databus Client CLI + +Options: + --help Show this message and exit. + +Commands: + deploy Flexible deploy to Databus command supporting three modes: + download Download datasets from databus, optionally using vault access... ``` -**DBpedia Wikidata Extraction Enriched** -TODO One slogan sentence and link + + +### Download + +With the download command, you can download datasets or parts thereof from the Databus. The download command expects one or more Databus URIs or a SPARQL query as arguments. The URIs can point to files, versions, artifacts, groups, or collections. If a SPARQL query is provided, the query must return download URLs from the Databus which will be downloaded. ```bash -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikidata-kg-enriched-snapshot --token vault-token.dat +# Python +databusclient download $DOWNLOADTARGET +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOADTARGET ``` -### Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed) -TODO One slogan sentence and link +- `$DOWNLOADTARGET` + - Can be any Databus URI including collections OR SPARQL query (or several thereof). +- `--localdir` + - If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the Databus layout, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. +- `--vault-token` + - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. +- `--databus-key` + - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. +**Help and further information on download command:** ```bash -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-snapshot +# Python +databusclient download --help +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download --help + +### Docker + +Requirements: [Docker](https://docs.docker.com/get-docker/) + +```bash +docker run --rm -v $(pwd):/data dbpedia/databus-python-client --help +docker run --rm -v $(pwd):/data dbpedia/databus-python-client deploy --help +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download --help ``` -### Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed) -TODO One slogan sentence and link +## DBpedia + +Commands to download the [DBpedia Knowledge Graphs](#dbpedia-knowledge-graphs) generated by Live Fusion. DBpedia Live Fusion publishes two kinds of KGs: + +1. Open Core Knowledge Graphs under CC-BY-SA license, open with copyleft/share-alike, no registration needed. +2. Industry Knowledge Graphs under BUSL 1.1 license, unrestricted for research and experimentation, commercial license for productive use, free [registration](#registration-access-token) needed. + +### Registration (Access Token) + +To download BUSL 1.1 licensed datasets, you need to register and get an access token. + +1. If you do not have a DBpedia Account yet (Forum/Databus), please register at [https://account.dbpedia.org](https://account.dbpedia.org) +2. Log in at [https://account.dbpedia.org](https://account.dbpedia.org) and create your token. +3. Save the token to a file, e.g. `vault-token.dat`. + +### DBpedia Knowledge Graphs + +#### Download Live Fusion KG Dump (BUSL 1.1, registration needed) +High-frequency, conflict-resolved knowledge graph that merges Live Wikipedia and Wikidata signals into a single, queryable dump for enterprise consumption. [More information](https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump) ```bash -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-snapshot +# Python +databusclient download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat ``` -## Docker Image Usage +#### Download Enriched Knowledge Graphs (BUSL 1.1, registration needed) -A docker image is available at [dbpedia/databus-python-client](https://hub.docker.com/r/dbpedia/databus-python-client). See [download section](#usage-of-docker-image) for details. +**DBpedia Wikipedia Extraction Enriched** +DBpedia-based enrichment of structured Wikipedia extractions (currently EN DBpedia only). [More information](https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump) -## CLI Usage +```bash +# Python +databusclient download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +``` + +#### Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed) + +Original extraction of structured Wikipedia data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump) -**Installation** ```bash -python3 -m pip install databusclient +# Python +databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump ``` -**Running** +#### Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed) + +Original extraction of structured Wikidata data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump) + ```bash -databusclient --help +# Python +databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump ``` -```man +## CLI Usage + +To get started with the command-line interface (CLI) of the databus-python-client, you can use either the Python installation or the Docker image. The examples below show both methods. + +**Help and further general information:** + +```bash +# Python +databusclient --help +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client --help + +# Output: Usage: databusclient [OPTIONS] COMMAND [ARGS]... + Databus Client CLI + Options: - --install-completion [bash|zsh|fish|powershell|pwsh] - Install completion for the specified shell. - --show-completion [bash|zsh|fish|powershell|pwsh] - Show completion for the specified shell, to - copy it or customize the installation. - --help Show this message and exit. + --help Show this message and exit. Commands: - deploy - download - mkdist - completion + deploy Flexible deploy to Databus command supporting three modes: + download Download datasets from databus, optionally using vault access... ``` + +### Download +With the download command, you can download datasets or parts thereof from the Databus. The download command expects one or more Databus URIs or a SPARQL query as arguments. The URIs can point to files, versions, artifacts, groups, or collections. If a SPARQL query is provided, the query must return download URLs from the Databus which will be downloaded. -### Download command +```bash +# Python +databusclient download $DOWNLOADTARGET +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOADTARGET ``` + +- `$DOWNLOADTARGET` + - Can be any Databus URI including collections OR SPARQL query (or several thereof). +- `--localdir` + - If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the Databus layout, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. +- `--vault-token` + - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. + + Note: Vault tokens are only required for certain protected Databus hosts (for example: `data.dbpedia.io`, `data.dev.dbpedia.link`). The client now detects those hosts and will fail early with a clear message if a token is required but not provided. Do not pass `--vault-token` for public downloads. +- `--databus-key` + - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. + +**Help and further information on download command:** +```bash +# Python databusclient download --help -``` +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download --help -``` +# Output: Usage: databusclient download [OPTIONS] DATABUSURIS... -Arguments: - DATABUSURIS... databus uris to download from https://databus.dbpedia.org, - or a query statement that returns databus uris from https://databus.dbpedia.org/sparql - to be downloaded [required] - Download datasets from databus, optionally using vault access if vault options are provided. Options: - --localdir TEXT Local databus folder (if not given, databus folder - structure is created in current working directory) - --databus TEXT Databus URL (if not given, inferred from databusuri, e.g. - https://databus.dbpedia.org/sparql) - --token TEXT Path to Vault refresh token file - --authurl TEXT Keycloak token endpoint URL [default: - https://auth.dbpedia.org/realms/dbpedia/protocol/openid- - connect/token] - --clientid TEXT Client ID for token exchange [default: vault-token- - exchange] - --help Show this message and exit. Show this message and exit. + --localdir TEXT Local databus folder (if not given, databus folder + structure is created in current working directory) + --databus TEXT Databus URL (if not given, inferred from databusuri, + e.g. https://databus.dbpedia.org/sparql) + --vault-token TEXT Path to Vault refresh token file + --databus-key TEXT Databus API key to download from protected databus + --all-versions When downloading artifacts, download all versions + instead of only the latest + --authurl TEXT Keycloak token endpoint URL [default: + https://auth.dbpedia.org/realms/dbpedia/protocol/openid- + connect/token] + --clientid TEXT Client ID for token exchange [default: vault-token- + exchange] + --help Show this message and exit. ``` -Examples of using download command +#### Examples of using the download command -**File**: download of a single file -``` +**Download File**: download of a single file +```bash +# Python databusclient download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01/mappingbased-literals_lang=az.ttl.bz2 +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01/mappingbased-literals_lang=az.ttl.bz2 ``` -**Version**: download of all files of a specific version -``` +**Download Version**: download of all files of a specific version +```bash +# Python databusclient download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01 +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01 ``` -**Artifact**: download of all files with latest version of an artifact -``` +**Download Artifact**: download of all files with the latest version of an artifact +```bash +# Python databusclient download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals -``` - -**Group**: download of all files with lates version of all artifacts of a group +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals ``` + +**Download Group**: download of all files with the latest version of all artifacts of a group +```bash +# Python databusclient download https://databus.dbpedia.org/dbpedia/mappings +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/mappings ``` -If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the databus structure, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. - -**Collection**: download of all files within a collection -``` +**Download Collection**: download of all files within a collection +```bash +# Python databusclient download https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12 +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12 ``` -**Query**: download of all files returned by a query (sparql endpoint must be provided with `--databus`) -``` +**Download Query**: download of all files returned by a query (SPARQL endpoint must be provided with `--databus`) +```bash +# Python databusclient download 'PREFIX dcat: SELECT ?x WHERE { ?sub dcat:downloadURL ?x . } LIMIT 10' --databus https://databus.dbpedia.org/sparql +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download 'PREFIX dcat: SELECT ?x WHERE { ?sub dcat:downloadURL ?x . } LIMIT 10' --databus https://databus.dbpedia.org/sparql ``` -### Deploy command + +### Deploy + +With the deploy command, you can deploy datasets to the Databus. The deploy command supports three modes: +1. Classic dataset deployment via list of distributions +2. Metadata-based deployment via metadata JSON file +3. Upload & deploy via Nextcloud/WebDAV + +```bash +# Python +databusclient deploy [OPTIONS] [DISTRIBUTIONS]... +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client deploy [OPTIONS] [DISTRIBUTIONS]... ``` + +**Help and further information on deploy command:** +```bash +# Python databusclient deploy --help -``` -``` +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client deploy --help + +# Output: Usage: databusclient deploy [OPTIONS] [DISTRIBUTIONS]... - Flexible deploy to databus command: + Flexible deploy to Databus command supporting three modes: - - Classic dataset deployment + - Classic deploy (distributions as arguments) - - Metadata-based deployment + - Metadata-based deploy (--metadata ) - - Upload & deploy via Nextcloud + - Upload & deploy via Nextcloud (--webdav-url, --remote, --path) -Arguments: - DISTRIBUTIONS... Depending on mode: - - Classic mode: List of distributions in the form - URL|CV|fileext|compression|sha256sum:contentlength - (where URL is the download URL and CV the key=value pairs, - separated by underscores) - - Upload mode: List of local file or folder paths (must exist) - - Metdata mode: None - Options: --versionid TEXT Target databus version/dataset identifier of the form +### Delete -For downloading files from the vault, you need to provide a vault token. See [getting-the-access-refresh-token](https://github.com/dbpedia/databus-vault-access?tab=readme-ov-file#step-1-getting-the-access-refresh-token) for details. You can come back here once you have a `vault-token.dat` file. To use it, just provide the path to the file with `--token /path/to/vault-token.dat`. +With the delete command you can delete collections, groups, artifacts, and versions from the Databus. Deleting files is not supported via API. -Example: -``` -databusclient download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-snapshots/fusion/2025-08-23 --token vault-token.dat +**Note**: Deleting datasets will recursively delete all data associated with the dataset below the specified level. Please use this command with caution. As security measure, the delete command will prompt you for confirmation before proceeding with any deletion. + +```bash +# Python +databusclient delete [OPTIONS] DATABUSURIS... +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete [OPTIONS] DATABUSURIS... ``` -If vault authentication is required for downloading a file, the client will use the token. If no vault authentication is required, the token will not be used. +**Help and further information on delete command:** +```bash +# Python +databusclient delete --help +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete --help + +# Output: +Usage: databusclient delete [OPTIONS] DATABUSURIS... -#### Usage of docker image + Delete a dataset from the databus. -A docker image is available at [dbpedia/databus-python-client](https://hub.docker.com/r/dbpedia/databus-python-client). You can use it like this: + Delete a group, artifact, or version identified by the given databus URI. + Will recursively delete all data associated with the dataset. +Options: + --databus-key TEXT Databus API key to access protected databus [required] + --dry-run Perform a dry run without actual deletion + --force Force deletion without confirmation prompt + --help Show this message and exit. ``` -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01 + +To authenticate the delete request, you need to provide an API key with `--databus-key YOUR_API_KEY`. + +If you want to perform a dry run without actual deletion, use the `--dry-run` option. This will show you what would be deleted without making any changes. + +As security measure, the delete command will prompt you for confirmation before proceeding with the deletion. If you want to skip this prompt, you can use the `--force` option. + +#### Examples of using the delete command + +**Delete Version**: delete a specific version +```bash +# Python +databusclient delete https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01 --databus-key YOUR_API_KEY +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals/2022.12.01 --databus-key YOUR_API_KEY ``` -If using vault authentication, make sure the token file is available in the container, e.g. by placing it in the current working directory. + +**Delete Artifact**: delete an artifact and all its versions +```bash +# Python +databusclient delete https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals --databus-key YOUR_API_KEY +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete https://databus.dbpedia.org/dbpedia/mappings/mappingbased-literals --databus-key YOUR_API_KEY ``` -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-snapshots/fusion/2025-08-23/fusion_props=all_subjectns=commons-wikimedia-org_vocab=all.ttl.gz --token vault-token.dat + +**Delete Group**: delete a group and all its artifacts and versions +```bash +# Python +databusclient delete https://databus.dbpedia.org/dbpedia/mappings --databus-key YOUR_API_KEY +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete https://databus.dbpedia.org/dbpedia/mappings --databus-key YOUR_API_KEY ``` +**Delete Collection**: delete collection +```bash +# Python +databusclient delete https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12 --databus-key YOUR_API_KEY +# Docker +docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12 --databus-key YOUR_API_KEY +``` ### mkdist command @@ -339,9 +569,12 @@ Enable shell completion (bash example): ``` eval "$(_DATABUSCLIENT_COMPLETE=source_bash python -m databusclient)" ``` - ## Module Usage -### Step 1: Create lists of distributions for the dataset + + +### Deploy + +#### Step 1: Create lists of distributions for the dataset ```python from databusclient import create_distribution @@ -360,10 +593,10 @@ distributions.append( # will just place parameters correctly, nothing will be downloaded or inferred distributions.append( create_distribution( - url="https://example.org/some/random/file.csv.bz2", - cvs={"type": "example", "realfile": "false"}, - file_format="csv", - compression="bz2", + url="https://example.org/some/random/file.csv.bz2", + cvs={"type": "example", "realfile": "false"}, + file_format="csv", + compression="bz2", sha256_length_tuple=("7a751b6dd5eb8d73d97793c3c564c71ab7b565fa4ba619e4a8fd05a6f80ff653", 367116) ) ) @@ -374,7 +607,7 @@ A few notes: * The dict for content variants can be empty ONLY IF there is just one distribution * There can be no compression if there is no file format -### Step 2: Create dataset +#### Step 2: Create dataset ```python from databusclient import create_dataset @@ -403,14 +636,56 @@ dataset = create_dataset( ) ``` -NOTE: To be used you need to set all group parameters, or it will be ignored +NOTE: Group metadata is applied only if all group parameters are set. -### Step 3: Deploy to databus +#### Step 3: Deploy to Databus ```python from databusclient import deploy -# to deploy something you just need the dataset from the previous step and an APIO key +# to deploy something you just need the dataset from the previous step and an API key # API key can be found (or generated) at https://$$DATABUS_BASE$$/$$USER$$#settings -deploy(dataset, "mysterious api key") +deploy(dataset, "mysterious API key") +``` + +## Development & Contributing + +Install development dependencies yourself or via [Poetry](https://python-poetry.org/): + +```bash +poetry install --with dev +``` + +### Linting + +The used linter is [Ruff](https://ruff.rs/). Ruff is configured in `pyproject.toml` and is enforced in CI (`.github/workflows/ruff.yml`). + +For development, you can run linting locally with `ruff check .` and optionally auto-format with `ruff format .`. + +To ensure compatibility with the `pyproject.toml` configured dependencies, run Ruff via Poetry: + +```bash +# To check for linting issues: +poetry run ruff check . + +# To auto-format code: +poetry run ruff format . +``` + +### Testing + +When developing new features please make sure to add appropriate tests and ensure that all tests pass. Tests are under `tests/` and use [pytest](https://docs.pytest.org/en/7.4.x/) as test framework. + +When fixing bugs or refactoring existing code, please make sure to add tests that cover the affected functionality. The current test coverage is very low, so any additional tests are highly appreciated. + +To run tests locally, use: + +```bash +pytest tests/ +``` + +Or to ensure compatibility with the `pyproject.toml` configured dependencies, run pytest via Poetry: + +```bash +poetry run pytest tests/ ``` \ No newline at end of file diff --git a/databusclient/cli.py b/databusclient/cli.py index d900c0f..d2e9007 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -95,10 +95,11 @@ def deploy(version_id, title, abstract, description, license_url, apikey, @click.argument("databusuris", nargs=-1, required=True) @click.option("--localdir", help="Local databus folder (if not given, databus folder structure is created in current working directory)") @click.option("--databus", help="Databus URL (if not given, inferred from databusuri, e.g. https://databus.dbpedia.org/sparql)") -@click.option("--token", help="Path to Vault refresh token file") +@click.option("--vault-token", help="Path to Vault refresh token file") +@click.option("--databus-key", help="Databus API key to donwload from protected databus") @click.option("--authurl", default="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", show_default=True, help="Keycloak token endpoint URL") @click.option("--clientid", default="vault-token-exchange", show_default=True, help="Client ID for token exchange") -def download(databusuris: List[str], localdir, databus, token, authurl, clientid): +def download(databusuris: List[str], localdir, databus, vault_token, databus_key, authurl, clientid): """ Download datasets from databus, optionally using vault access if vault options are provided. """ @@ -106,7 +107,8 @@ def download(databusuris: List[str], localdir, databus, token, authurl, clientid localDir=localdir, endpoint=databus, databusURIs=databusuris, - token=token, + token=vault_token, + databus_key=databus_key, auth_url=authurl, client_id=clientid, ) diff --git a/databusclient/client.py b/databusclient/client.py index 358f1a6..8138a84 100644 --- a/databusclient/client.py +++ b/databusclient/client.py @@ -491,7 +491,7 @@ def deploy_from_metadata( print(f" - {entry['url']}") -def __download_file__(url, filename, vault_token_file=None, auth_url=None, client_id=None) -> None: +def __download_file__(url, filename, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: """ Download a file from the internet with a progress bar using tqdm. @@ -520,10 +520,11 @@ def __download_file__(url, filename, vault_token_file=None, auth_url=None, clien print("Redirects url: ", url) # --- 2. Try direct GET --- - response = requests.get(url, stream=True, allow_redirects=False) # no redirects here, we want to see if auth is required + response = requests.get(url, stream=True, allow_redirects=True) www = response.headers.get('WWW-Authenticate', '') # get WWW-Authenticate header if present to check for Bearer auth - if (response.status_code == 401 or "bearer" in www.lower()): + # Vault token required if 401 Unauthorized with Bearer challenge + if (response.status_code == 401 and "bearer" in www.lower()): print(f"Authentication required for {url}") if not (vault_token_file): raise ValueError("Vault token file not given for protected download") @@ -534,6 +535,15 @@ def __download_file__(url, filename, vault_token_file=None, auth_url=None, clien # --- 4. Retry with token --- response = requests.get(url, headers=headers, stream=True) + + # Databus API key required if only 401 Unauthorized + elif response.status_code == 401: + print(f"API key required for {url}") + if not databus_key: + raise ValueError("Databus API key not given for protected download") + + headers = {"X-API-KEY": databus_key} + response = requests.get(url, headers=headers, stream=True) try: response.raise_for_status() # Raise if still failing @@ -554,8 +564,10 @@ def __download_file__(url, filename, vault_token_file=None, auth_url=None, clien file.write(data) progress_bar.close() + # TODO: could be a problem of github raw / openflaas if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - raise IOError("Downloaded size does not match Content-Length header") + # raise IOError("Downloaded size does not match Content-Length header") + print(f"Warning: Downloaded size does not match Content-Length header:\nExpected {total_size_in_bytes}, got {progress_bar.n}") def __get_vault_access__(download_url: str, @@ -702,31 +714,38 @@ def wsha256(raw: str): return sha256(raw.encode('utf-8')).hexdigest() -def __handle_databus_collection__(uri: str) -> str: +def __handle_databus_collection__(uri: str, databus_key: str = None) -> str: headers = {"Accept": "text/sparql"} + if databus_key is not None: + headers["X-API-KEY"] = databus_key + return requests.get(uri, headers=headers).text -def __get_json_ld_from_databus__(uri: str) -> str: +def __get_json_ld_from_databus__(uri: str, databus_key: str = None) -> str: headers = {"Accept": "application/ld+json"} + if databus_key is not None: + headers["X-API-KEY"] = databus_key return requests.get(uri, headers=headers).text def __download_list__(urls: List[str], localDir: str, vault_token_file: str = None, + databus_key: str = None, auth_url: str = None, client_id: str = None) -> None: + fileLocalDir = localDir for url in urls: if localDir is None: host, account, group, artifact, version, file = __get_databus_id_parts__(url) - localDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") - print(f"Local directory not given, using {localDir}") + fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") + print(f"Local directory not given, using {fileLocalDir}") file = url.split("/")[-1] - filename = os.path.join(localDir, file) + filename = os.path.join(fileLocalDir, file) print("\n") - __download_file__(url=url, filename=filename, vault_token_file=vault_token_file, auth_url=auth_url, client_id=client_id) + __download_file__(url=url, filename=filename, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) print("\n") @@ -742,6 +761,7 @@ def download( endpoint: str, databusURIs: List[str], token=None, + databus_key=None, auth_url=None, client_id=None ) -> None: @@ -771,15 +791,15 @@ def download( if "/collections/" in databusURI: # TODO "in" is not safe! there could be an artifact named collections, need to check for the correct part position in the URI query = __handle_databus_collection__(databusURI) res = __handle_databus_file_query__(endpoint, query) - __download_list__(res, localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus file elif file is not None: - __download_list__([databusURI], localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__([databusURI], localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus artifact version elif version is not None: json_str = __get_json_ld_from_databus__(databusURI) res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus artifact elif artifact is not None: json_str = __get_json_ld_from_databus__(databusURI) @@ -787,7 +807,7 @@ def download( print(f"No version given, using latest version: {latest}") json_str = __get_json_ld_from_databus__(latest) res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus group elif group is not None: @@ -800,7 +820,7 @@ def download( print(f"No version given, using latest version: {latest}") json_str = __get_json_ld_from_databus__(latest) res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus account elif account is not None: @@ -816,4 +836,4 @@ def download( if endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") res = __handle_databus_file_query__(endpoint, databusURI) - __download_list__(res, localDir, vault_token_file=token, auth_url=auth_url, client_id=client_id) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) From 49fa461eb9390cd061032ae9d444362e4baf660e Mon Sep 17 00:00:00 2001 From: Fabian Hofer <57919013+Integer-Ctrl@users.noreply.github.com> Date: Thu, 4 Dec 2025 19:09:42 +0100 Subject: [PATCH 05/23] cli: delete datasets (#38) * feat: databus api key for downloading * refactored README.md * feat: cli delete to delete datasets from databus --- README.md | 176 ++++----------------------------- databusclient/api/delete.py | 190 ++++++++++++++++++++++++++++++++++++ databusclient/api/utils.py | 37 +++++++ databusclient/cli.py | 23 ++++- databusclient/client.py | 63 +++++------- 5 files changed, 295 insertions(+), 194 deletions(-) create mode 100644 databusclient/api/delete.py create mode 100644 databusclient/api/utils.py diff --git a/README.md b/README.md index fa0ad36..8add7c5 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Command-line and Python client for downloading and deploying datasets on DBpedia - [DBpedia](#dbpedia) - [Registration (Access Token)](#registration-access-token) - [DBpedia Knowledge Graphs](#dbpedia-knowledge-graphs) - - [Download Live Fusion KG Dump (BUSL 1.1, registration needed)](#download-live-fusion-kg-dump-busl-11-registration-needed) + - [Download Live Fusion KG Snapshot (BUSL 1.1, registration needed)](#download-live-fusion-kg-snapshot-busl-11-registration-needed) - [Download Enriched Knowledge Graphs (BUSL 1.1, registration needed)](#download-enriched-knowledge-graphs-busl-11-registration-needed) - [Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikipedia-knowledge-graphs-cc-by-sa-no-registration-needed) - [Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikidata-knowledge-graphs-cc-by-sa-no-registration-needed) @@ -20,9 +20,6 @@ Command-line and Python client for downloading and deploying datasets on DBpedia - [Delete](#cli-delete) - [Module Usage](#module-usage) - [Deploy](#module-deploy) -- [Development & Contributing](#development--contributing) - - [Linting](#linting) - - [Testing](#testing) ## Quickstart @@ -33,7 +30,7 @@ You can use either **Python** or **Docker**. Both methods support all client fea ### Python -Requirements: [Python 3.11+](https://www.python.org/downloads/) and [pip](https://pip.pypa.io/en/stable/installation/) +Requirements: [Python](https://www.python.org/downloads/) and [pip](https://pip.pypa.io/en/stable/installation/) Before using the client, install it via pip: @@ -41,60 +38,13 @@ Before using the client, install it via pip: python3 -m pip install databusclient ``` -Note: the PyPI release was updated and this repository prepares version `0.15`. If you previously installed `databusclient` via `pip` and observe different CLI behavior, upgrade to the latest release: +You can then use the client in the command line: ```bash -python3 -m pip install --upgrade databusclient==0.15 -``` - -**Help and further general information:** - -```bash -# Python databusclient --help -# Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client --help - -# Output: -Usage: databusclient [OPTIONS] COMMAND [ARGS]... - - Databus Client CLI - -Options: - --help Show this message and exit. - -Commands: - deploy Flexible deploy to Databus command supporting three modes: - download Download datasets from databus, optionally using vault access... -``` - - -### Download - -With the download command, you can download datasets or parts thereof from the Databus. The download command expects one or more Databus URIs or a SPARQL query as arguments. The URIs can point to files, versions, artifacts, groups, or collections. If a SPARQL query is provided, the query must return download URLs from the Databus which will be downloaded. - -```bash -# Python -databusclient download $DOWNLOADTARGET -# Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOADTARGET -``` - -- `$DOWNLOADTARGET` - - Can be any Databus URI including collections OR SPARQL query (or several thereof). -- `--localdir` - - If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the Databus layout, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. -- `--vault-token` - - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. -- `--databus-key` - - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. - -**Help and further information on download command:** -```bash -# Python +databusclient deploy --help databusclient download --help -# Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download --help +``` ### Docker @@ -123,48 +73,48 @@ To download BUSL 1.1 licensed datasets, you need to register and get an access t ### DBpedia Knowledge Graphs -#### Download Live Fusion KG Dump (BUSL 1.1, registration needed) -High-frequency, conflict-resolved knowledge graph that merges Live Wikipedia and Wikidata signals into a single, queryable dump for enterprise consumption. [More information](https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump) +#### Download Live Fusion KG Snapshot (BUSL 1.1, registration needed) +High-frequency, conflict-resolved knowledge graph that merges Live Wikipedia and Wikidata signals into a single, queryable snapshot for enterprise consumption. [More information](https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump) ```bash # Python -databusclient download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat +databusclient download https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump --vault-token vault-token.dat # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump --vault-token vault-token.dat ``` #### Download Enriched Knowledge Graphs (BUSL 1.1, registration needed) **DBpedia Wikipedia Extraction Enriched** -DBpedia-based enrichment of structured Wikipedia extractions (currently EN DBpedia only). [More information](https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump) +DBpedia-based enrichment of structured Wikipedia extractions (currently EN DBpedia only). [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump) ```bash # Python -databusclient download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat ``` #### Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed) -Original extraction of structured Wikipedia data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump) +Original extraction of structured Wikipedia data before enrichment. [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump) ```bash # Python -databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump +databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump ``` #### Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed) -Original extraction of structured Wikidata data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump) +Original extraction of structured Wikidata data before enrichment. [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump) ```bash # Python -databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump +databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump ``` ## CLI Usage @@ -210,8 +160,6 @@ docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOAD - If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the Databus layout, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. - `--vault-token` - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. - - Note: Vault tokens are only required for certain protected Databus hosts (for example: `data.dbpedia.io`, `data.dev.dbpedia.link`). The client now detects those hosts and will fail early with a clear message if a token is required but not provided. Do not pass `--vault-token` for public downloads. - `--databus-key` - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. @@ -235,8 +183,6 @@ Options: e.g. https://databus.dbpedia.org/sparql) --vault-token TEXT Path to Vault refresh token file --databus-key TEXT Databus API key to download from protected databus - --all-versions When downloading artifacts, download all versions - instead of only the latest --authurl TEXT Keycloak token endpoint URL [default: https://auth.dbpedia.org/realms/dbpedia/protocol/openid- connect/token] @@ -329,7 +275,7 @@ Usage: databusclient deploy [OPTIONS] [DISTRIBUTIONS]... - Upload & deploy via Nextcloud (--webdav-url, --remote, --path) Options: - --versionid TEXT Target databus version/dataset identifier of the form [required] --title TEXT Dataset title [required] @@ -451,7 +397,6 @@ docker run --rm -v $(pwd):/data dbpedia/databus-python-client deploy \ ./data_folder ``` - ### Delete @@ -528,47 +473,6 @@ databusclient delete https://databus.dbpedia.org/dbpedia/collections/dbpedia-sna docker run --rm -v $(pwd):/data dbpedia/databus-python-client delete https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12 --databus-key YOUR_API_KEY ``` -### mkdist command - -Create a distribution string from components. - -Usage: -``` -databusclient mkdist URL --cv key=value --cv key2=value2 --format ttl --compression gz --sha-length : -``` - -Example: -``` -python -m databusclient mkdist "https://example.org/file.ttl" --cv lang=en --cv part=sorted --format ttl --compression gz --sha-length aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa:12345 -``` - -## Completion - -Enable shell completion (bash example): -``` -eval "$(_DATABUSCLIENT_COMPLETE=source_bash python -m databusclient)" -``` - -### mkdist command - -Create a distribution string from components. - -Usage: -``` -databusclient mkdist URL --cv key=value --cv key2=value2 --format ttl --compression gz --sha-length : -``` - -Example: -``` -python -m databusclient mkdist "https://example.org/file.ttl" --cv lang=en --cv part=sorted --format ttl --compression gz --sha-length aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa:12345 -``` - -## Completion - -Enable shell completion (bash example): -``` -eval "$(_DATABUSCLIENT_COMPLETE=source_bash python -m databusclient)" -``` ## Module Usage @@ -647,45 +551,3 @@ from databusclient import deploy # API key can be found (or generated) at https://$$DATABUS_BASE$$/$$USER$$#settings deploy(dataset, "mysterious API key") ``` - -## Development & Contributing - -Install development dependencies yourself or via [Poetry](https://python-poetry.org/): - -```bash -poetry install --with dev -``` - -### Linting - -The used linter is [Ruff](https://ruff.rs/). Ruff is configured in `pyproject.toml` and is enforced in CI (`.github/workflows/ruff.yml`). - -For development, you can run linting locally with `ruff check .` and optionally auto-format with `ruff format .`. - -To ensure compatibility with the `pyproject.toml` configured dependencies, run Ruff via Poetry: - -```bash -# To check for linting issues: -poetry run ruff check . - -# To auto-format code: -poetry run ruff format . -``` - -### Testing - -When developing new features please make sure to add appropriate tests and ensure that all tests pass. Tests are under `tests/` and use [pytest](https://docs.pytest.org/en/7.4.x/) as test framework. - -When fixing bugs or refactoring existing code, please make sure to add tests that cover the affected functionality. The current test coverage is very low, so any additional tests are highly appreciated. - -To run tests locally, use: - -```bash -pytest tests/ -``` - -Or to ensure compatibility with the `pyproject.toml` configured dependencies, run pytest via Poetry: - -```bash -poetry run pytest tests/ -``` \ No newline at end of file diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py new file mode 100644 index 0000000..a3d7625 --- /dev/null +++ b/databusclient/api/delete.py @@ -0,0 +1,190 @@ +import json +import requests +from typing import List + +from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus + +def _confirm_delete(databusURI: str) -> str: + """ + Confirm deletion of a Databus resource with the user. + + Parameters: + - databusURI: The full databus URI of the resource to delete + + Returns: + - "confirm" if the user confirms deletion + - "skip" if the user chooses to skip deletion + - "cancel" if the user chooses to cancel the entire deletion process + """ + print(f"Are you sure you want to delete: {databusURI}?") + print("\nThis action is irreversible and will permanently remove the resource and all its data.") + while True: + choice = input("Type 'yes'/'y' to confirm, 'skip'/'s' to skip this resource, or 'cancel'/'c' to abort: ").strip().lower() + if choice in ("yes", "y"): + return "confirm" + elif choice in ("skip", "s"): + return "skip" + elif choice in ("cancel", "c"): + return "cancel" + else: + print("Invalid input. Please type 'yes'/'y', 'skip'/'s', or 'cancel'/'c'.") + + +def _delete_resource(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): + """ + Delete a single Databus resource (version, artifact, group). + + Equivalent to: + curl -X DELETE "" -H "accept: */*" -H "X-API-KEY: " + + Parameters: + - databusURI: The full databus URI of the resource to delete + - databus_key: Databus API key to authenticate the deletion request + - dry_run: If True, do not perform the deletion but only print what would be deleted + - force: If True, skip confirmation prompt and proceed with deletion + """ + + # Confirm the deletion request, skip the request or cancel deletion process + if not (dry_run or force): + action = _confirm_delete(databusURI) + if action == "skip": + print(f"Skipping: {databusURI}\n") + return + if action == "cancel": + raise KeyboardInterrupt("Deletion cancelled by user.") + + if databus_key is None: + raise ValueError("Databus API key must be provided for deletion") + + headers = { + "accept": "*/*", + "X-API-KEY": databus_key + } + + if dry_run: + print(f"[DRY RUN] Would delete: {databusURI}") + return + + response = requests.delete(databusURI, headers=headers, timeout=30) + + if response.status_code in (200, 204): + print(f"Successfully deleted: {databusURI}") + else: + raise Exception(f"Failed to delete {databusURI}: {response.status_code} - {response.text}") + + +def _delete_list(databusURIs: List[str], databus_key: str, dry_run: bool = False, force: bool = False): + """ + Delete a list of Databus resources. + + Parameters: + - databusURIs: List of full databus URIs of the resources to delete + - databus_key: Databus API key to authenticate the deletion requests + """ + for databusURI in databusURIs: + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + + +def _delete_artifact(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): + """ + Delete an artifact and all its versions. + + This function first retrieves all versions of the artifact and then deletes them one by one. + Finally, it deletes the artifact itself. + + Parameters: + - databusURI: The full databus URI of the artifact to delete + - databus_key: Databus API key to authenticate the deletion requests + - dry_run: If True, do not perform the deletion but only print what would be deleted + """ + artifact_body = get_json_ld_from_databus(databusURI, databus_key) + + json_dict = json.loads(artifact_body) + versions = json_dict.get("databus:hasVersion") + + # Single version case {} + if isinstance(versions, dict): + versions = [versions] + # Multiple versions case [{}, {}] + + # If versions is None or empty skip + if versions is None: + print(f"No versions found for artifact: {databusURI}") + else: + version_uris = [v["@id"] for v in versions if "@id" in v] + if not version_uris: + print(f"No version URIs found in artifact JSON-LD for: {databusURI}") + else: + # Delete all versions + _delete_list(version_uris, databus_key, dry_run=dry_run, force=force) + + # Finally, delete the artifact itself + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + +def _delete_group(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): + """ + Delete a group and all its artifacts and versions. + + This function first retrieves all artifacts of the group, then deletes each artifact (which in turn deletes its versions). + Finally, it deletes the group itself. + + Parameters: + - databusURI: The full databus URI of the group to delete + - databus_key: Databus API key to authenticate the deletion requests + - dry_run: If True, do not perform the deletion but only print what would be deleted + """ + group_body = get_json_ld_from_databus(databusURI, databus_key) + + json_dict = json.loads(group_body) + artifacts = json_dict.get("databus:hasArtifact", []) + + artifact_uris = [] + for item in artifacts: + uri = item.get("@id") + if not uri: + continue + _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) + if version is None: + artifact_uris.append(uri) + + # Delete all artifacts (which deletes their versions) + for artifact_uri in artifact_uris: + _delete_artifact(artifact_uri, databus_key, dry_run=dry_run, force=force) + + # Finally, delete the group itself + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + +def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool): + """ + Delete a dataset from the databus. + + Delete a group, artifact, or version identified by the given databus URI. + Will recursively delete all data associated with the dataset. + + Parameters: + - databusURIs: List of full databus URIs of the resources to delete + - databus_key: Databus API key to authenticate the deletion requests + - dry_run: If True, will only print what would be deleted without performing actual deletions + - force: If True, skip confirmation prompt and proceed with deletion + """ + + for databusURI in databusURIs: + _host, _account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) + + if group == "collections" and artifact is not None: + print(f"Deleting collection: {databusURI}") + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + elif file is not None: + print(f"Deleting file is not supported via API: {databusURI}") + continue # skip file deletions + elif version is not None: + print(f"Deleting version: {databusURI}") + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + elif artifact is not None: + print(f"Deleting artifact and all its versions: {databusURI}") + _delete_artifact(databusURI, databus_key, dry_run=dry_run, force=force) + elif group is not None and group != "collections": + print(f"Deleting group and all its artifacts and versions: {databusURI}") + _delete_group(databusURI, databus_key, dry_run=dry_run, force=force) + else: + print(f"Deleting {databusURI} is not supported.") diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py new file mode 100644 index 0000000..1ffe421 --- /dev/null +++ b/databusclient/api/utils.py @@ -0,0 +1,37 @@ +import requests +from typing import Tuple, Optional + +def get_databus_id_parts_from_uri(uri: str) -> Tuple[Optional[str], Optional[str], Optional[str], Optional[str], Optional[str], Optional[str]]: + """ + Extract databus ID parts from a given databus URI. + + Parameters: + - uri: The full databus URI + + Returns: + A tuple containing (host, accountId, groupId, artifactId, versionId, fileId). + Each element is a string or None if not present. + """ + uri = uri.removeprefix("https://").removeprefix("http://") + parts = uri.strip("/").split("/") + parts += [None] * (6 - len(parts)) # pad with None if less than 6 parts + return tuple(parts[:6]) # return only the first 6 parts + +def get_json_ld_from_databus(uri: str, databus_key: str | None = None) -> str: + """ + Retrieve JSON-LD representation of a databus resource. + + Parameters: + - uri: The full databus URI + - databus_key: Optional Databus API key for authentication on protected resources + + Returns: + JSON-LD string representation of the databus resource. + """ + headers = {"Accept": "application/ld+json"} + if databus_key is not None: + headers["X-API-KEY"] = databus_key + response = requests.get(uri, headers=headers, timeout=30) + response.raise_for_status() + + return response.text diff --git a/databusclient/cli.py b/databusclient/cli.py index d2e9007..74b18b4 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -8,6 +8,7 @@ from databusclient import client from databusclient.rclone_wrapper import upload +from databusclient.api.delete import delete as api_delete @click.group() def app(): @@ -96,7 +97,7 @@ def deploy(version_id, title, abstract, description, license_url, apikey, @click.option("--localdir", help="Local databus folder (if not given, databus folder structure is created in current working directory)") @click.option("--databus", help="Databus URL (if not given, inferred from databusuri, e.g. https://databus.dbpedia.org/sparql)") @click.option("--vault-token", help="Path to Vault refresh token file") -@click.option("--databus-key", help="Databus API key to donwload from protected databus") +@click.option("--databus-key", help="Databus API key to download from protected databus") @click.option("--authurl", default="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", show_default=True, help="Keycloak token endpoint URL") @click.option("--clientid", default="vault-token-exchange", show_default=True, help="Client ID for token exchange") def download(databusuris: List[str], localdir, databus, vault_token, databus_key, authurl, clientid): @@ -113,6 +114,26 @@ def download(databusuris: List[str], localdir, databus, vault_token, databus_key client_id=clientid, ) +@app.command() +@click.argument("databusuris", nargs=-1, required=True) +@click.option("--databus-key", help="Databus API key to access protected databus", required=True) +@click.option("--dry-run", is_flag=True, help="Perform a dry run without actual deletion") +@click.option("--force", is_flag=True, help="Force deletion without confirmation prompt") +def delete(databusuris: List[str], databus_key: str, dry_run: bool, force: bool): + """ + Delete a dataset from the databus. + + Delete a group, artifact, or version identified by the given databus URI. + Will recursively delete all data associated with the dataset. + """ + + api_delete( + databusURIs=databusuris, + databus_key=databus_key, + dry_run=dry_run, + force=force, + ) + @app.command() @click.argument("url") diff --git a/databusclient/client.py b/databusclient/client.py index 8138a84..994e731 100644 --- a/databusclient/client.py +++ b/databusclient/client.py @@ -8,6 +8,8 @@ from hashlib import sha256 import os +from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus + __debug = False @@ -520,7 +522,7 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au print("Redirects url: ", url) # --- 2. Try direct GET --- - response = requests.get(url, stream=True, allow_redirects=True) + response = requests.get(url, stream=True, allow_redirects=True, timeout=30) www = response.headers.get('WWW-Authenticate', '') # get WWW-Authenticate header if present to check for Bearer auth # Vault token required if 401 Unauthorized with Bearer challenge @@ -534,7 +536,7 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au headers = {"Authorization": f"Bearer {vault_token}"} # --- 4. Retry with token --- - response = requests.get(url, headers=headers, stream=True) + response = requests.get(url, headers=headers, stream=True, timeout=30) # Databus API key required if only 401 Unauthorized elif response.status_code == 401: @@ -543,7 +545,7 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au raise ValueError("Databus API key not given for protected download") headers = {"X-API-KEY": databus_key} - response = requests.get(url, headers=headers, stream=True) + response = requests.get(url, headers=headers, stream=True, timeout=30) try: response.raise_for_status() # Raise if still failing @@ -566,8 +568,7 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au # TODO: could be a problem of github raw / openflaas if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - # raise IOError("Downloaded size does not match Content-Length header") - print(f"Warning: Downloaded size does not match Content-Length header:\nExpected {total_size_in_bytes}, got {progress_bar.n}") + raise IOError("Downloaded size does not match Content-Length header") def __get_vault_access__(download_url: str, @@ -620,13 +621,14 @@ def __get_vault_access__(download_url: str, return vault_token -def __query_sparql__(endpoint_url, query) -> dict: +def __query_sparql__(endpoint_url, query, databus_key=None) -> dict: """ Query a SPARQL endpoint and return results in JSON format. Parameters: - endpoint_url: the URL of the SPARQL endpoint - query: the SPARQL query string + - databus_key: Optional API key for authentication Returns: - Dictionary containing the query results @@ -635,12 +637,14 @@ def __query_sparql__(endpoint_url, query) -> dict: sparql.method = 'POST' sparql.setQuery(query) sparql.setReturnFormat(JSON) + if databus_key is not None: + sparql.setCustomHttpHeaders({"X-API-KEY": databus_key}) results = sparql.query().convert() return results -def __handle_databus_file_query__(endpoint_url, query) -> List[str]: - result_dict = __query_sparql__(endpoint_url, query) +def __handle_databus_file_query__(endpoint_url, query, databus_key=None) -> List[str]: + result_dict = __query_sparql__(endpoint_url, query, databus_key=databus_key) for binding in result_dict['results']['bindings']: if len(binding.keys()) > 1: print("Error multiple bindings in query response") @@ -704,7 +708,7 @@ def __get_databus_artifacts_of_group__(json_str: str) -> List[str]: uri = item.get("@id") if not uri: continue - _, _, _, _, version, _ = __get_databus_id_parts__(uri) + _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) if version is None: result.append(uri) return result @@ -714,19 +718,12 @@ def wsha256(raw: str): return sha256(raw.encode('utf-8')).hexdigest() -def __handle_databus_collection__(uri: str, databus_key: str = None) -> str: +def __handle_databus_collection__(uri: str, databus_key: str | None = None) -> str: headers = {"Accept": "text/sparql"} if databus_key is not None: headers["X-API-KEY"] = databus_key - return requests.get(uri, headers=headers).text - - -def __get_json_ld_from_databus__(uri: str, databus_key: str = None) -> str: - headers = {"Accept": "application/ld+json"} - if databus_key is not None: - headers["X-API-KEY"] = databus_key - return requests.get(uri, headers=headers).text + return requests.get(uri, headers=headers, timeout=30).text def __download_list__(urls: List[str], @@ -738,7 +735,7 @@ def __download_list__(urls: List[str], fileLocalDir = localDir for url in urls: if localDir is None: - host, account, group, artifact, version, file = __get_databus_id_parts__(url) + _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") print(f"Local directory not given, using {fileLocalDir}") @@ -749,13 +746,6 @@ def __download_list__(urls: List[str], print("\n") -def __get_databus_id_parts__(uri: str) -> Tuple[Optional[str], Optional[str], Optional[str], Optional[str], Optional[str], Optional[str]]: - uri = uri.removeprefix("https://").removeprefix("http://") - parts = uri.strip("/").split("/") - parts += [None] * (6 - len(parts)) # pad with None if less than 6 parts - return tuple(parts[:6]) # return only the first 6 parts - - def download( localDir: str, endpoint: str, @@ -772,13 +762,14 @@ def download( endpoint: the databus endpoint URL databusURIs: identifiers to access databus registered datasets token: Path to Vault refresh token file + databus_key: Databus API key for protected downloads auth_url: Keycloak token endpoint URL client_id: Client ID for token exchange """ # TODO: make pretty for databusURI in databusURIs: - host, account, group, artifact, version, file = __get_databus_id_parts__(databusURI) + host, account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) # dataID or databus collection if databusURI.startswith("http://") or databusURI.startswith("https://"): @@ -788,8 +779,8 @@ def download( print(f"SPARQL endpoint {endpoint}") # databus collection - if "/collections/" in databusURI: # TODO "in" is not safe! there could be an artifact named collections, need to check for the correct part position in the URI - query = __handle_databus_collection__(databusURI) + if group == "collections": + query = __handle_databus_collection__(databusURI, databus_key=databus_key) res = __handle_databus_file_query__(endpoint, query) __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus file @@ -797,28 +788,28 @@ def download( __download_list__([databusURI], localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus artifact version elif version is not None: - json_str = __get_json_ld_from_databus__(databusURI) + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) res = __handle_databus_artifact_version__(json_str) __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus artifact elif artifact is not None: - json_str = __get_json_ld_from_databus__(databusURI) + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) latest = __get_databus_latest_version_of_artifact__(json_str) print(f"No version given, using latest version: {latest}") - json_str = __get_json_ld_from_databus__(latest) + json_str = get_json_ld_from_databus(latest, databus_key=databus_key) res = __handle_databus_artifact_version__(json_str) __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) # databus group elif group is not None: - json_str = __get_json_ld_from_databus__(databusURI) + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) artifacts = __get_databus_artifacts_of_group__(json_str) for artifact_uri in artifacts: print(f"Processing artifact {artifact_uri}") - json_str = __get_json_ld_from_databus__(artifact_uri) + json_str = get_json_ld_from_databus(artifact_uri, databus_key=databus_key) latest = __get_databus_latest_version_of_artifact__(json_str) print(f"No version given, using latest version: {latest}") - json_str = __get_json_ld_from_databus__(latest) + json_str = get_json_ld_from_databus(latest, databus_key=databus_key) res = __handle_databus_artifact_version__(json_str) __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) @@ -835,5 +826,5 @@ def download( print("QUERY {}", databusURI.replace("\n", " ")) if endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") - res = __handle_databus_file_query__(endpoint, databusURI) + res = __handle_databus_file_query__(endpoint, databusURI, databus_key=databus_key) __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) From 0303454b43b44f57396a1724ffd4821e22608c62 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Fri, 5 Dec 2025 15:27:54 +0100 Subject: [PATCH 06/23] refactor: split client into deploy and download --- databusclient/{client.py => api/deploy.py} | 343 --------------------- databusclient/api/download.py | 331 ++++++++++++++++++++ databusclient/cli.py | 14 +- 3 files changed, 339 insertions(+), 349 deletions(-) rename databusclient/{client.py => api/deploy.py} (53%) create mode 100644 databusclient/api/download.py diff --git a/databusclient/client.py b/databusclient/api/deploy.py similarity index 53% rename from databusclient/client.py rename to databusclient/api/deploy.py index 994e731..ed8b931 100644 --- a/databusclient/client.py +++ b/databusclient/api/deploy.py @@ -3,12 +3,6 @@ import requests import hashlib import json -from tqdm import tqdm -from SPARQLWrapper import SPARQLWrapper, JSON -from hashlib import sha256 -import os - -from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus __debug = False @@ -491,340 +485,3 @@ def deploy_from_metadata( print(f"Deployed {len(metadata)} file(s):") for entry in metadata: print(f" - {entry['url']}") - - -def __download_file__(url, filename, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: - """ - Download a file from the internet with a progress bar using tqdm. - - Parameters: - - url: the URL of the file to download - - filename: the local file path where the file should be saved - - vault_token_file: Path to Vault refresh token file - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - Steps: - 1. Try direct GET without Authorization header. - 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized) or url starts with "https://data.dbpedia.io/databus.dbpedia.org", - then fetch Vault access token and retry with Authorization header. - """ - - print(f"Download file: {url}") - dirpath = os.path.dirname(filename) - if dirpath: - os.makedirs(dirpath, exist_ok=True) # Create the necessary directories - # --- 1. Get redirect URL by requesting HEAD --- - response = requests.head(url, stream=True) - # Check for redirect and update URL if necessary - if response.headers.get("Location") and response.status_code in [301, 302, 303, 307, 308]: - url = response.headers.get("Location") - print("Redirects url: ", url) - - # --- 2. Try direct GET --- - response = requests.get(url, stream=True, allow_redirects=True, timeout=30) - www = response.headers.get('WWW-Authenticate', '') # get WWW-Authenticate header if present to check for Bearer auth - - # Vault token required if 401 Unauthorized with Bearer challenge - if (response.status_code == 401 and "bearer" in www.lower()): - print(f"Authentication required for {url}") - if not (vault_token_file): - raise ValueError("Vault token file not given for protected download") - - # --- 3. Fetch Vault token --- - vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) - headers = {"Authorization": f"Bearer {vault_token}"} - - # --- 4. Retry with token --- - response = requests.get(url, headers=headers, stream=True, timeout=30) - - # Databus API key required if only 401 Unauthorized - elif response.status_code == 401: - print(f"API key required for {url}") - if not databus_key: - raise ValueError("Databus API key not given for protected download") - - headers = {"X-API-KEY": databus_key} - response = requests.get(url, headers=headers, stream=True, timeout=30) - - try: - response.raise_for_status() # Raise if still failing - except requests.exceptions.HTTPError as e: - if response.status_code == 404: - print(f"WARNING: Skipping file {url} because it was not found (404).") - return - else: - raise e - - total_size_in_bytes = int(response.headers.get('content-length', 0)) - block_size = 1024 # 1 KiB - - progress_bar = tqdm(total=total_size_in_bytes, unit='iB', unit_scale=True) - with open(filename, 'wb') as file: - for data in response.iter_content(block_size): - progress_bar.update(len(data)) - file.write(data) - progress_bar.close() - - # TODO: could be a problem of github raw / openflaas - if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - raise IOError("Downloaded size does not match Content-Length header") - - -def __get_vault_access__(download_url: str, - token_file: str, - auth_url: str, - client_id: str) -> str: - """ - Get Vault access token for a protected databus download. - """ - # 1. Load refresh token - refresh_token = os.environ.get("REFRESH_TOKEN") - if not refresh_token: - if not os.path.exists(token_file): - raise FileNotFoundError(f"Vault token file not found: {token_file}") - with open(token_file, "r") as f: - refresh_token = f.read().strip() - if len(refresh_token) < 80: - print(f"Warning: token from {token_file} is short (<80 chars)") - - # 2. Refresh token -> access token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "refresh_token", - "refresh_token": refresh_token - }) - resp.raise_for_status() - access_token = resp.json()["access_token"] - - # 3. Extract host as audience - # Remove protocol prefix - if download_url.startswith("https://"): - host_part = download_url[len("https://"):] - elif download_url.startswith("http://"): - host_part = download_url[len("http://"):] - else: - host_part = download_url - audience = host_part.split("/")[0] # host is before first "/" - - # 4. Access token -> Vault token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", - "subject_token": access_token, - "audience": audience - }) - resp.raise_for_status() - vault_token = resp.json()["access_token"] - - print(f"Using Vault access token for {download_url}") - return vault_token - - -def __query_sparql__(endpoint_url, query, databus_key=None) -> dict: - """ - Query a SPARQL endpoint and return results in JSON format. - - Parameters: - - endpoint_url: the URL of the SPARQL endpoint - - query: the SPARQL query string - - databus_key: Optional API key for authentication - - Returns: - - Dictionary containing the query results - """ - sparql = SPARQLWrapper(endpoint_url) - sparql.method = 'POST' - sparql.setQuery(query) - sparql.setReturnFormat(JSON) - if databus_key is not None: - sparql.setCustomHttpHeaders({"X-API-KEY": databus_key}) - results = sparql.query().convert() - return results - - -def __handle_databus_file_query__(endpoint_url, query, databus_key=None) -> List[str]: - result_dict = __query_sparql__(endpoint_url, query, databus_key=databus_key) - for binding in result_dict['results']['bindings']: - if len(binding.keys()) > 1: - print("Error multiple bindings in query response") - break - else: - value = binding[next(iter(binding.keys()))]['value'] - yield value - - -def __handle_databus_artifact_version__(json_str: str) -> List[str]: - """ - Parse the JSON-LD of a databus artifact version to extract download URLs. - Don't get downloadURLs directly from the JSON-LD, but follow the "file" links to count access to databus accurately. - - Returns a list of download URLs. - """ - - databusIdUrl = [] - json_dict = json.loads(json_str) - graph = json_dict.get("@graph", []) - for node in graph: - if node.get("@type") == "Part": - id = node.get("file") - databusIdUrl.append(id) - return databusIdUrl - - -def __get_databus_latest_version_of_artifact__(json_str: str) -> str: - """ - Parse the JSON-LD of a databus artifact to extract URLs of the latest version. - - Returns download URL of latest version of the artifact. - """ - json_dict = json.loads(json_str) - versions = json_dict.get("databus:hasVersion") - - # Single version case {} - if isinstance(versions, dict): - versions = [versions] - # Multiple versions case [{}, {}] - - version_urls = [v["@id"] for v in versions if "@id" in v] - if not version_urls: - raise ValueError("No versions found in artifact JSON-LD") - - version_urls.sort(reverse=True) # Sort versions in descending order - return version_urls[0] # Return the latest version URL - - -def __get_databus_artifacts_of_group__(json_str: str) -> List[str]: - """ - Parse the JSON-LD of a databus group to extract URLs of all artifacts. - - Returns a list of artifact URLs. - """ - json_dict = json.loads(json_str) - artifacts = json_dict.get("databus:hasArtifact", []) - - result = [] - for item in artifacts: - uri = item.get("@id") - if not uri: - continue - _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) - if version is None: - result.append(uri) - return result - - -def wsha256(raw: str): - return sha256(raw.encode('utf-8')).hexdigest() - - -def __handle_databus_collection__(uri: str, databus_key: str | None = None) -> str: - headers = {"Accept": "text/sparql"} - if databus_key is not None: - headers["X-API-KEY"] = databus_key - - return requests.get(uri, headers=headers, timeout=30).text - - -def __download_list__(urls: List[str], - localDir: str, - vault_token_file: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: - fileLocalDir = localDir - for url in urls: - if localDir is None: - _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) - fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") - print(f"Local directory not given, using {fileLocalDir}") - - file = url.split("/")[-1] - filename = os.path.join(fileLocalDir, file) - print("\n") - __download_file__(url=url, filename=filename, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - print("\n") - - -def download( - localDir: str, - endpoint: str, - databusURIs: List[str], - token=None, - databus_key=None, - auth_url=None, - client_id=None -) -> None: - """ - Download datasets to local storage from databus registry. If download is on vault, vault token will be used for downloading protected files. - ------ - localDir: the local directory - endpoint: the databus endpoint URL - databusURIs: identifiers to access databus registered datasets - token: Path to Vault refresh token file - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange - """ - - # TODO: make pretty - for databusURI in databusURIs: - host, account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) - - # dataID or databus collection - if databusURI.startswith("http://") or databusURI.startswith("https://"): - # Auto-detect sparql endpoint from databusURI if not given -> no need to specify endpoint (--databus) - if endpoint is None: - endpoint = f"https://{host}/sparql" - print(f"SPARQL endpoint {endpoint}") - - # databus collection - if group == "collections": - query = __handle_databus_collection__(databusURI, databus_key=databus_key) - res = __handle_databus_file_query__(endpoint, query) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus file - elif file is not None: - __download_list__([databusURI], localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus artifact version - elif version is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus artifact - elif artifact is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - latest = __get_databus_latest_version_of_artifact__(json_str) - print(f"No version given, using latest version: {latest}") - json_str = get_json_ld_from_databus(latest, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - # databus group - elif group is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - artifacts = __get_databus_artifacts_of_group__(json_str) - for artifact_uri in artifacts: - print(f"Processing artifact {artifact_uri}") - json_str = get_json_ld_from_databus(artifact_uri, databus_key=databus_key) - latest = __get_databus_latest_version_of_artifact__(json_str) - print(f"No version given, using latest version: {latest}") - json_str = get_json_ld_from_databus(latest, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - # databus account - elif account is not None: - print("accountId not supported yet") # TODO - else: - print("dataId not supported yet") # TODO add support for other DatabusIds - # query in local file - elif databusURI.startswith("file://"): - print("query in file not supported yet") - # query as argument - else: - print("QUERY {}", databusURI.replace("\n", " ")) - if endpoint is None: # endpoint is required for queries (--databus) - raise ValueError("No endpoint given for query") - res = __handle_databus_file_query__(endpoint, databusURI, databus_key=databus_key) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) diff --git a/databusclient/api/download.py b/databusclient/api/download.py new file mode 100644 index 0000000..d8dd4b3 --- /dev/null +++ b/databusclient/api/download.py @@ -0,0 +1,331 @@ +from typing import List +import requests +import os +from tqdm import tqdm +import json +from SPARQLWrapper import SPARQLWrapper, JSON + +from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus + +def __handle_databus_collection__(uri: str, databus_key: str | None = None) -> str: + headers = {"Accept": "text/sparql"} + if databus_key is not None: + headers["X-API-KEY"] = databus_key + + return requests.get(uri, headers=headers, timeout=30).text + +def __get_vault_access__(download_url: str, + token_file: str, + auth_url: str, + client_id: str) -> str: + """ + Get Vault access token for a protected databus download. + """ + # 1. Load refresh token + refresh_token = os.environ.get("REFRESH_TOKEN") + if not refresh_token: + if not os.path.exists(token_file): + raise FileNotFoundError(f"Vault token file not found: {token_file}") + with open(token_file, "r") as f: + refresh_token = f.read().strip() + if len(refresh_token) < 80: + print(f"Warning: token from {token_file} is short (<80 chars)") + + # 2. Refresh token -> access token + resp = requests.post(auth_url, data={ + "client_id": client_id, + "grant_type": "refresh_token", + "refresh_token": refresh_token + }) + resp.raise_for_status() + access_token = resp.json()["access_token"] + + # 3. Extract host as audience + # Remove protocol prefix + if download_url.startswith("https://"): + host_part = download_url[len("https://"):] + elif download_url.startswith("http://"): + host_part = download_url[len("http://"):] + else: + host_part = download_url + audience = host_part.split("/")[0] # host is before first "/" + + # 4. Access token -> Vault token + resp = requests.post(auth_url, data={ + "client_id": client_id, + "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", + "subject_token": access_token, + "audience": audience + }) + resp.raise_for_status() + vault_token = resp.json()["access_token"] + + print(f"Using Vault access token for {download_url}") + return vault_token + +def __download_file__(url, filename, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: + """ + Download a file from the internet with a progress bar using tqdm. + + Parameters: + - url: the URL of the file to download + - filename: the local file path where the file should be saved + - vault_token_file: Path to Vault refresh token file + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + + Steps: + 1. Try direct GET without Authorization header. + 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized) or url starts with "https://data.dbpedia.io/databus.dbpedia.org", + then fetch Vault access token and retry with Authorization header. + """ + + print(f"Download file: {url}") + dirpath = os.path.dirname(filename) + if dirpath: + os.makedirs(dirpath, exist_ok=True) # Create the necessary directories + # --- 1. Get redirect URL by requesting HEAD --- + response = requests.head(url, stream=True) + # Check for redirect and update URL if necessary + if response.headers.get("Location") and response.status_code in [301, 302, 303, 307, 308]: + url = response.headers.get("Location") + print("Redirects url: ", url) + + # --- 2. Try direct GET --- + response = requests.get(url, stream=True, allow_redirects=True, timeout=30) + www = response.headers.get('WWW-Authenticate', '') # get WWW-Authenticate header if present to check for Bearer auth + + # Vault token required if 401 Unauthorized with Bearer challenge + if (response.status_code == 401 and "bearer" in www.lower()): + print(f"Authentication required for {url}") + if not (vault_token_file): + raise ValueError("Vault token file not given for protected download") + + # --- 3. Fetch Vault token --- + vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) + headers = {"Authorization": f"Bearer {vault_token}"} + + # --- 4. Retry with token --- + response = requests.get(url, headers=headers, stream=True, timeout=30) + + # Databus API key required if only 401 Unauthorized + elif response.status_code == 401: + print(f"API key required for {url}") + if not databus_key: + raise ValueError("Databus API key not given for protected download") + + headers = {"X-API-KEY": databus_key} + response = requests.get(url, headers=headers, stream=True, timeout=30) + + try: + response.raise_for_status() # Raise if still failing + except requests.exceptions.HTTPError as e: + if response.status_code == 404: + print(f"WARNING: Skipping file {url} because it was not found (404).") + return + else: + raise e + + total_size_in_bytes = int(response.headers.get('content-length', 0)) + block_size = 1024 # 1 KiB + + progress_bar = tqdm(total=total_size_in_bytes, unit='iB', unit_scale=True) + with open(filename, 'wb') as file: + for data in response.iter_content(block_size): + progress_bar.update(len(data)) + file.write(data) + progress_bar.close() + + # TODO: could be a problem of github raw / openflaas + if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: + raise IOError("Downloaded size does not match Content-Length header") + +def __download_list__(urls: List[str], + localDir: str, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None) -> None: + fileLocalDir = localDir + for url in urls: + if localDir is None: + _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) + fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") + print(f"Local directory not given, using {fileLocalDir}") + + file = url.split("/")[-1] + filename = os.path.join(fileLocalDir, file) + print("\n") + __download_file__(url=url, filename=filename, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + print("\n") + +def __query_sparql__(endpoint_url, query, databus_key=None) -> dict: + """ + Query a SPARQL endpoint and return results in JSON format. + + Parameters: + - endpoint_url: the URL of the SPARQL endpoint + - query: the SPARQL query string + - databus_key: Optional API key for authentication + + Returns: + - Dictionary containing the query results + """ + sparql = SPARQLWrapper(endpoint_url) + sparql.method = 'POST' + sparql.setQuery(query) + sparql.setReturnFormat(JSON) + if databus_key is not None: + sparql.setCustomHttpHeaders({"X-API-KEY": databus_key}) + results = sparql.query().convert() + return results + +def __handle_databus_file_query__(endpoint_url, query, databus_key=None) -> List[str]: + result_dict = __query_sparql__(endpoint_url, query, databus_key=databus_key) + for binding in result_dict['results']['bindings']: + if len(binding.keys()) > 1: + print("Error multiple bindings in query response") + break + else: + value = binding[next(iter(binding.keys()))]['value'] + yield value + +def __get_databus_latest_version_of_artifact__(json_str: str) -> str: + """ + Parse the JSON-LD of a databus artifact to extract URLs of the latest version. + + Returns download URL of latest version of the artifact. + """ + json_dict = json.loads(json_str) + versions = json_dict.get("databus:hasVersion") + + # Single version case {} + if isinstance(versions, dict): + versions = [versions] + # Multiple versions case [{}, {}] + + version_urls = [v["@id"] for v in versions if "@id" in v] + if not version_urls: + raise ValueError("No versions found in artifact JSON-LD") + + version_urls.sort(reverse=True) # Sort versions in descending order + return version_urls[0] # Return the latest version URL + +def __handle_databus_artifact_version__(json_str: str) -> List[str]: + """ + Parse the JSON-LD of a databus artifact version to extract download URLs. + Don't get downloadURLs directly from the JSON-LD, but follow the "file" links to count access to databus accurately. + + Returns a list of download URLs. + """ + + databusIdUrl = [] + json_dict = json.loads(json_str) + graph = json_dict.get("@graph", []) + for node in graph: + if node.get("@type") == "Part": + id = node.get("file") + databusIdUrl.append(id) + return databusIdUrl + +def __get_databus_artifacts_of_group__(json_str: str) -> List[str]: + """ + Parse the JSON-LD of a databus group to extract URLs of all artifacts. + + Returns a list of artifact URLs. + """ + json_dict = json.loads(json_str) + artifacts = json_dict.get("databus:hasArtifact", []) + + result = [] + for item in artifacts: + uri = item.get("@id") + if not uri: + continue + _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) + if version is None: + result.append(uri) + return result + +def download( + localDir: str, + endpoint: str, + databusURIs: List[str], + token=None, + databus_key=None, + auth_url=None, + client_id=None +) -> None: + """ + Download datasets to local storage from databus registry. If download is on vault, vault token will be used for downloading protected files. + ------ + localDir: the local directory + endpoint: the databus endpoint URL + databusURIs: identifiers to access databus registered datasets + token: Path to Vault refresh token file + databus_key: Databus API key for protected downloads + auth_url: Keycloak token endpoint URL + client_id: Client ID for token exchange + """ + + # TODO: make pretty + for databusURI in databusURIs: + host, account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) + + # dataID or databus collection + if databusURI.startswith("http://") or databusURI.startswith("https://"): + # Auto-detect sparql endpoint from databusURI if not given -> no need to specify endpoint (--databus) + if endpoint is None: + endpoint = f"https://{host}/sparql" + print(f"SPARQL endpoint {endpoint}") + + # databus collection + if group == "collections": + query = __handle_databus_collection__(databusURI, databus_key=databus_key) + res = __handle_databus_file_query__(endpoint, query) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + # databus file + elif file is not None: + __download_list__([databusURI], localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + # databus artifact version + elif version is not None: + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) + res = __handle_databus_artifact_version__(json_str) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + # databus artifact + elif artifact is not None: + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) + latest = __get_databus_latest_version_of_artifact__(json_str) + print(f"No version given, using latest version: {latest}") + json_str = get_json_ld_from_databus(latest, databus_key=databus_key) + res = __handle_databus_artifact_version__(json_str) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + # databus group + elif group is not None: + json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) + artifacts = __get_databus_artifacts_of_group__(json_str) + for artifact_uri in artifacts: + print(f"Processing artifact {artifact_uri}") + json_str = get_json_ld_from_databus(artifact_uri, databus_key=databus_key) + latest = __get_databus_latest_version_of_artifact__(json_str) + print(f"No version given, using latest version: {latest}") + json_str = get_json_ld_from_databus(latest, databus_key=databus_key) + res = __handle_databus_artifact_version__(json_str) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + # databus account + elif account is not None: + print("accountId not supported yet") # TODO + else: + print("dataId not supported yet") # TODO add support for other DatabusIds + # query in local file + elif databusURI.startswith("file://"): + print("query in file not supported yet") + # query as argument + else: + print("QUERY {}", databusURI.replace("\n", " ")) + if endpoint is None: # endpoint is required for queries (--databus) + raise ValueError("No endpoint given for query") + res = __handle_databus_file_query__(endpoint, databusURI, databus_key=databus_key) + __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) \ No newline at end of file diff --git a/databusclient/cli.py b/databusclient/cli.py index 74b18b4..41d1c8a 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -5,10 +5,12 @@ import click import re from typing import List -from databusclient import client from databusclient.rclone_wrapper import upload + from databusclient.api.delete import delete as api_delete +import databusclient.api.deploy as api_deploy +from databusclient.api.download import download as api_download @click.group() def app(): @@ -56,8 +58,8 @@ def deploy(version_id, title, abstract, description, license_url, apikey, click.echo("[MODE] Classic deploy with distributions") click.echo(f"Deploying dataset version: {version_id}") - dataid = client.create_dataset(version_id, title, abstract, description, license_url, distributions) - client.deploy(dataid=dataid, api_key=apikey) + dataid = api_deploy.create_dataset(version_id, title, abstract, description, license_url, distributions) + api_deploy.deploy(dataid=dataid, api_key=apikey) return # === Mode 2: Metadata File === @@ -65,7 +67,7 @@ def deploy(version_id, title, abstract, description, license_url, apikey, click.echo(f"[MODE] Deploy from metadata file: {metadata_file}") with open(metadata_file, 'r') as f: metadata = json.load(f) - client.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) + api_deploy.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) return # === Mode 3: Upload & Deploy (Nextcloud) === @@ -81,7 +83,7 @@ def deploy(version_id, title, abstract, description, license_url, apikey, click.echo("[MODE] Upload & Deploy to DBpedia Databus via Nextcloud") click.echo(f"→ Uploading to: {remote}:{path}") metadata = upload.upload_to_nextcloud(distributions, remote, path, webdav_url) - client.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) + api_deploy.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) return raise click.UsageError( @@ -104,7 +106,7 @@ def download(databusuris: List[str], localdir, databus, vault_token, databus_key """ Download datasets from databus, optionally using vault access if vault options are provided. """ - client.download( + api_download( localDir=localdir, endpoint=databus, databusURIs=databusuris, From 525ba7505c10fe685b6925bfef02ec59ce7339d7 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Fri, 5 Dec 2025 17:08:22 +0100 Subject: [PATCH 07/23] refactor: iteration over download.py --- README.md | 2 + databusclient/__init__.py | 2 +- databusclient/api/delete.py | 6 +- databusclient/api/download.py | 422 +++++++++++++++++++++++----------- databusclient/api/utils.py | 2 +- databusclient/cli.py | 4 +- tests/test_databusclient.py | 2 +- tests/test_download.py | 6 +- 8 files changed, 298 insertions(+), 148 deletions(-) diff --git a/README.md b/README.md index 8add7c5..c652275 100644 --- a/README.md +++ b/README.md @@ -183,6 +183,8 @@ Options: e.g. https://databus.dbpedia.org/sparql) --vault-token TEXT Path to Vault refresh token file --databus-key TEXT Databus API key to download from protected databus + --latest-only When downloading artifacts, only download the latest + version --authurl TEXT Keycloak token endpoint URL [default: https://auth.dbpedia.org/realms/dbpedia/protocol/openid- connect/token] diff --git a/databusclient/__init__.py b/databusclient/__init__.py index fbb1463..3e053b5 100644 --- a/databusclient/__init__.py +++ b/databusclient/__init__.py @@ -1,5 +1,5 @@ from databusclient import cli -from databusclient.client import create_dataset, deploy, create_distribution +from databusclient.api.deploy import create_dataset, deploy, create_distribution __all__ = ["create_dataset", "deploy", "create_distribution"] diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index a3d7625..5db8ab2 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -2,7 +2,7 @@ import requests from typing import List -from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus +from databusclient.api.utils import get_databus_id_parts_from_uri, fetch_databus_jsonld def _confirm_delete(databusURI: str) -> str: """ @@ -97,7 +97,7 @@ def _delete_artifact(databusURI: str, databus_key: str, dry_run: bool = False, f - databus_key: Databus API key to authenticate the deletion requests - dry_run: If True, do not perform the deletion but only print what would be deleted """ - artifact_body = get_json_ld_from_databus(databusURI, databus_key) + artifact_body = fetch_databus_jsonld(databusURI, databus_key) json_dict = json.loads(artifact_body) versions = json_dict.get("databus:hasVersion") @@ -133,7 +133,7 @@ def _delete_group(databusURI: str, databus_key: str, dry_run: bool = False, forc - databus_key: Databus API key to authenticate the deletion requests - dry_run: If True, do not perform the deletion but only print what would be deleted """ - group_body = get_json_ld_from_databus(databusURI, databus_key) + group_body = fetch_databus_jsonld(databusURI, databus_key) json_dict = json.loads(group_body) artifacts = json_dict.get("databus:hasArtifact", []) diff --git a/databusclient/api/download.py b/databusclient/api/download.py index d8dd4b3..859e35f 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -1,84 +1,36 @@ -from typing import List +from typing import List, Iterator import requests import os from tqdm import tqdm import json from SPARQLWrapper import SPARQLWrapper, JSON -from databusclient.api.utils import get_databus_id_parts_from_uri, get_json_ld_from_databus +from databusclient.api.delete import _delete_group, _delete_resource +from databusclient.api.utils import get_databus_id_parts_from_uri, fetch_databus_jsonld -def __handle_databus_collection__(uri: str, databus_key: str | None = None) -> str: - headers = {"Accept": "text/sparql"} - if databus_key is not None: - headers["X-API-KEY"] = databus_key - return requests.get(uri, headers=headers, timeout=30).text - -def __get_vault_access__(download_url: str, - token_file: str, - auth_url: str, - client_id: str) -> str: - """ - Get Vault access token for a protected databus download. - """ - # 1. Load refresh token - refresh_token = os.environ.get("REFRESH_TOKEN") - if not refresh_token: - if not os.path.exists(token_file): - raise FileNotFoundError(f"Vault token file not found: {token_file}") - with open(token_file, "r") as f: - refresh_token = f.read().strip() - if len(refresh_token) < 80: - print(f"Warning: token from {token_file} is short (<80 chars)") - - # 2. Refresh token -> access token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "refresh_token", - "refresh_token": refresh_token - }) - resp.raise_for_status() - access_token = resp.json()["access_token"] - - # 3. Extract host as audience - # Remove protocol prefix - if download_url.startswith("https://"): - host_part = download_url[len("https://"):] - elif download_url.startswith("http://"): - host_part = download_url[len("http://"):] - else: - host_part = download_url - audience = host_part.split("/")[0] # host is before first "/" - - # 4. Access token -> Vault token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", - "subject_token": access_token, - "audience": audience - }) - resp.raise_for_status() - vault_token = resp.json()["access_token"] - - print(f"Using Vault access token for {download_url}") - return vault_token - -def __download_file__(url, filename, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: +def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: """ Download a file from the internet with a progress bar using tqdm. Parameters: - url: the URL of the file to download - - filename: the local file path where the file should be saved + - localDir: Local directory to download file to. If None, the databus folder structure is created in the current working directory. - vault_token_file: Path to Vault refresh token file - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange Steps: 1. Try direct GET without Authorization header. - 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized) or url starts with "https://data.dbpedia.io/databus.dbpedia.org", - then fetch Vault access token and retry with Authorization header. + 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized), then fetch Vault access token and retry with Authorization header. """ + if localDir is None: + _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) + fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") + print(f"Local directory not given, using {fileLocalDir}") + + file = url.split("/")[-1] + filename = os.path.join(fileLocalDir, file) print(f"Download file: {url}") dirpath = os.path.dirname(filename) @@ -102,6 +54,7 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au raise ValueError("Vault token file not given for protected download") # --- 3. Fetch Vault token --- + # TODO: cache token vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) headers = {"Authorization": f"Bearer {vault_token}"} @@ -140,26 +93,46 @@ def __download_file__(url, filename, vault_token_file=None, databus_key=None, au if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: raise IOError("Downloaded size does not match Content-Length header") -def __download_list__(urls: List[str], + +def _download_files(urls: List[str], localDir: str, vault_token_file: str = None, databus_key: str = None, auth_url: str = None, client_id: str = None) -> None: - fileLocalDir = localDir + """ + Download multiple files from the databus. + + Parameters: + - urls: List of file download URLs + - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + - vault_token_file: Path to Vault refresh token file + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + """ for url in urls: - if localDir is None: - _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) - fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") - print(f"Local directory not given, using {fileLocalDir}") - - file = url.split("/")[-1] - filename = os.path.join(fileLocalDir, file) - print("\n") - __download_file__(url=url, filename=filename, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - print("\n") - -def __query_sparql__(endpoint_url, query, databus_key=None) -> dict: + _download_file(url=url, localDir=localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + +def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> str: + """ + Get SPARQL query of collection members from databus collection URI. + + Parameters: + - uri: The full databus collection URI + - databus_key: Optional Databus API key for authentication on protected resources + + Returns: + SPARQL query string to get download URLs of all files in the collection. + """ + headers = {"Accept": "text/sparql"} + if databus_key is not None: + headers["X-API-KEY"] = databus_key + + return requests.get(uri, headers=headers, timeout=30).text + + +def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: """ Query a SPARQL endpoint and return results in JSON format. @@ -180,21 +153,178 @@ def __query_sparql__(endpoint_url, query, databus_key=None) -> dict: results = sparql.query().convert() return results -def __handle_databus_file_query__(endpoint_url, query, databus_key=None) -> List[str]: - result_dict = __query_sparql__(endpoint_url, query, databus_key=databus_key) - for binding in result_dict['results']['bindings']: - if len(binding.keys()) > 1: - print("Error multiple bindings in query response") - break - else: - value = binding[next(iter(binding.keys()))]['value'] - yield value -def __get_databus_latest_version_of_artifact__(json_str: str) -> str: +def _get_file_download_urls_from_sparql_query(endpoint_url, query, databus_key=None) -> List[str]: + """ + Execute a SPARQL query to get databus file download URLs. + + Parameters: + - endpoint_url: the URL of the SPARQL endpoint + - query: the SPARQL query string + - databus_key: Optional API key for authentication + + Returns: + - List of file download URLs """ - Parse the JSON-LD of a databus artifact to extract URLs of the latest version. + result_dict = _query_sparql_endpoint(endpoint_url, query, databus_key=databus_key) + + bindings = result_dict.get("results", {}).get("bindings") + if not isinstance(bindings, list): + raise ValueError("Invalid SPARQL response: 'bindings' missing or not a list") + + urls: List[str] = [] + + for binding in bindings: + if not isinstance(binding, dict) or len(binding) != 1: + raise ValueError(f"Invalid SPARQL binding structure: {binding}") + + value_dict = next(iter(binding.values())) + value = value_dict.get("value") + + if not isinstance(value, str): + raise ValueError(f"Invalid SPARQL value field: {value_dict}") - Returns download URL of latest version of the artifact. + urls.append(value) + + return urls + +def __get_vault_access__(download_url: str, + token_file: str, + auth_url: str, + client_id: str) -> str: + """ + Get Vault access token for a protected databus download. + """ + # 1. Load refresh token + refresh_token = os.environ.get("REFRESH_TOKEN") + if not refresh_token: + if not os.path.exists(token_file): + raise FileNotFoundError(f"Vault token file not found: {token_file}") + with open(token_file, "r") as f: + refresh_token = f.read().strip() + if len(refresh_token) < 80: + print(f"Warning: token from {token_file} is short (<80 chars)") + + # 2. Refresh token -> access token + resp = requests.post(auth_url, data={ + "client_id": client_id, + "grant_type": "refresh_token", + "refresh_token": refresh_token + }) + resp.raise_for_status() + access_token = resp.json()["access_token"] + + # 3. Extract host as audience + # Remove protocol prefix + if download_url.startswith("https://"): + host_part = download_url[len("https://"):] + elif download_url.startswith("http://"): + host_part = download_url[len("http://"):] + else: + host_part = download_url + audience = host_part.split("/")[0] # host is before first "/" + + # 4. Access token -> Vault token + resp = requests.post(auth_url, data={ + "client_id": client_id, + "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", + "subject_token": access_token, + "audience": audience + }) + resp.raise_for_status() + vault_token = resp.json()["access_token"] + + print(f"Using Vault access token for {download_url}") + return vault_token + + +def _download_collection(uri: str, + endpoint: str, + localDir: str, + vault_token: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None) -> None: + """ + Download all files in a databus collection. + + Parameters: + - uri: The full databus collection URI + - endpoint: the databus SPARQL endpoint URL + - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + - vault_token: Path to Vault refresh token file for protected downloads + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + """ + query = _get_sparql_query_of_collection(uri, databus_key=databus_key) + file_urls = _get_file_download_urls_from_sparql_query(endpoint, query, databus_key=databus_key) + _download_files(list(file_urls), localDir, vault_token_file=vault_token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + +def _download_version(uri: str, + localDir: str, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None) -> None: + """ + Download all files in a databus artifact version. + + Parameters: + - uri: The full databus artifact version URI + - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + - vault_token_file: Path to Vault refresh token file for protected downloads + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + """ + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) + _download_files(file_urls, localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + +def _download_artifact(uri: str, + localDir: str, + all_versions: bool = False, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None) -> None: + """ + Download files in a databus artifact. + + Parameters: + - uri: The full databus artifact URI + - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + - all_versions: If True, download all versions of the artifact; otherwise, only download the latest version + - vault_token_file: Path to Vault refresh token file for protected downloads + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + """ + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + versions = _get_databus_versions_of_artifact(json_str, all_versions=all_versions) + if isinstance(versions, str): + versions = [versions] + for version_uri in versions: + print(f"Downloading version: {version_uri}") + json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key) + file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) + _download_files(file_urls, localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + +def _get_databus_versions_of_artifact(json_str: str, all_versions: bool) -> str | List[str]: + """ + Parse the JSON-LD of a databus artifact to extract URLs of its versions. + + Parameters: + - json_str: JSON-LD string of the databus artifact + - all_versions: If True, return all version URLs; otherwise, return only the latest version URL + + Returns: + - If all_versions is True: List of all version URLs + - If all_versions is False: URL of the latest version """ json_dict = json.loads(json_str) versions = json_dict.get("databus:hasVersion") @@ -209,14 +339,21 @@ def __get_databus_latest_version_of_artifact__(json_str: str) -> str: raise ValueError("No versions found in artifact JSON-LD") version_urls.sort(reverse=True) # Sort versions in descending order - return version_urls[0] # Return the latest version URL -def __handle_databus_artifact_version__(json_str: str) -> List[str]: + if all_versions: + return version_urls + return version_urls[0] + +def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: """ Parse the JSON-LD of a databus artifact version to extract download URLs. Don't get downloadURLs directly from the JSON-LD, but follow the "file" links to count access to databus accurately. - Returns a list of download URLs. + Parameters: + - json_str: JSON-LD string of the databus artifact version + + Returns: + List of all file download URLs in the artifact version. """ databusIdUrl = [] @@ -228,7 +365,35 @@ def __handle_databus_artifact_version__(json_str: str) -> List[str]: databusIdUrl.append(id) return databusIdUrl -def __get_databus_artifacts_of_group__(json_str: str) -> List[str]: + +def _download_group(uri: str, + localDir: str, + all_versions: bool = False, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None) -> None: + """ + Download files in a databus group. + + Parameters: + - uri: The full databus group URI + - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + - all_versions: If True, download all versions of each artifact in the group; otherwise, only download the latest version + - vault_token_file: Path to Vault refresh token file for protected downloads + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL + - client_id: Client ID for token exchange + """ + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + artifacts = _get_databus_artifacts_of_group(json_str) + for artifact_uri in artifacts: + print(f"Download artifact: {artifact_uri}") + _download_artifact(artifact_uri, localDir, all_versions=all_versions, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + + + +def _get_databus_artifacts_of_group(json_str: str) -> List[str]: """ Parse the JSON-LD of a databus group to extract URLs of all artifacts. @@ -253,68 +418,49 @@ def download( databusURIs: List[str], token=None, databus_key=None, + all_versions=None, auth_url=None, client_id=None ) -> None: """ - Download datasets to local storage from databus registry. If download is on vault, vault token will be used for downloading protected files. - ------ - localDir: the local directory - endpoint: the databus endpoint URL - databusURIs: identifiers to access databus registered datasets - token: Path to Vault refresh token file - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + Download datasets from databus. + + Download of files, versions, artifacts, groups or databus collections by ther databus URIs or user-defined SPARQL queries that return file download URLs. + + Parameters: + - localDir: Local directory to download datasets to. If None, the databus folder structure is created in the current working directory. + - endpoint: the databus endpoint URL. If None, inferred from databusURI. Required for user-defined SPARQL queries. + - databusURIs: databus identifiers to specify datasets to download. + - token: Path to Vault refresh token file for protected downloads + - databus_key: Databus API key for protected downloads + - auth_url: Keycloak token endpoint URL. Default is "https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token". + - client_id: Client ID for token exchange. Default is "vault-token-exchange". """ - - # TODO: make pretty for databusURI in databusURIs: host, account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) # dataID or databus collection if databusURI.startswith("http://") or databusURI.startswith("https://"): - # Auto-detect sparql endpoint from databusURI if not given -> no need to specify endpoint (--databus) + # Auto-detect sparql endpoint from host if not given if endpoint is None: endpoint = f"https://{host}/sparql" print(f"SPARQL endpoint {endpoint}") - # databus collection - if group == "collections": - query = __handle_databus_collection__(databusURI, databus_key=databus_key) - res = __handle_databus_file_query__(endpoint, query) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus file + if group == "collections" and artifact is not None: + print(f"Downloading collection: {databusURI}") + _download_collection(databusURI, endpoint, localDir, token, databus_key, auth_url, client_id) elif file is not None: - __download_list__([databusURI], localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus artifact version + print(f"Downloading file: {databusURI}") + _download_file(databusURI, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) elif version is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - # databus artifact + print(f"Downloading version: {databusURI}") + _download_version(databusURI, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) elif artifact is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - latest = __get_databus_latest_version_of_artifact__(json_str) - print(f"No version given, using latest version: {latest}") - json_str = get_json_ld_from_databus(latest, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - # databus group - elif group is not None: - json_str = get_json_ld_from_databus(databusURI, databus_key=databus_key) - artifacts = __get_databus_artifacts_of_group__(json_str) - for artifact_uri in artifacts: - print(f"Processing artifact {artifact_uri}") - json_str = get_json_ld_from_databus(artifact_uri, databus_key=databus_key) - latest = __get_databus_latest_version_of_artifact__(json_str) - print(f"No version given, using latest version: {latest}") - json_str = get_json_ld_from_databus(latest, databus_key=databus_key) - res = __handle_databus_artifact_version__(json_str) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - # databus account + print(f"Downloading {'all' if all_versions else 'latest'} version(s) of artifact: {databusURI}") + _download_artifact(databusURI, localDir, all_versions=all_versions, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + elif group is not None and group != "collections": + print(f"Downloading group and all its artifacts and versions: {databusURI}") + _download_group(databusURI, localDir, all_versions=all_versions, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) elif account is not None: print("accountId not supported yet") # TODO else: @@ -327,5 +473,5 @@ def download( print("QUERY {}", databusURI.replace("\n", " ")) if endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") - res = __handle_databus_file_query__(endpoint, databusURI, databus_key=databus_key) - __download_list__(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) \ No newline at end of file + res = _get_file_download_urls_from_sparql_query(endpoint, databusURI, databus_key=databus_key) + _download_files(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) \ No newline at end of file diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index 1ffe421..5c0fd3f 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -17,7 +17,7 @@ def get_databus_id_parts_from_uri(uri: str) -> Tuple[Optional[str], Optional[str parts += [None] * (6 - len(parts)) # pad with None if less than 6 parts return tuple(parts[:6]) # return only the first 6 parts -def get_json_ld_from_databus(uri: str, databus_key: str | None = None) -> str: +def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: """ Retrieve JSON-LD representation of a databus resource. diff --git a/databusclient/cli.py b/databusclient/cli.py index 41d1c8a..ab1a5ac 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -100,9 +100,10 @@ def deploy(version_id, title, abstract, description, license_url, apikey, @click.option("--databus", help="Databus URL (if not given, inferred from databusuri, e.g. https://databus.dbpedia.org/sparql)") @click.option("--vault-token", help="Path to Vault refresh token file") @click.option("--databus-key", help="Databus API key to download from protected databus") +@click.option("--all-versions", is_flag=True, help="When downloading artifacts, download all versions instead of only the latest") @click.option("--authurl", default="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", show_default=True, help="Keycloak token endpoint URL") @click.option("--clientid", default="vault-token-exchange", show_default=True, help="Client ID for token exchange") -def download(databusuris: List[str], localdir, databus, vault_token, databus_key, authurl, clientid): +def download(databusuris: List[str], localdir, databus, vault_token, databus_key, all_versions, authurl, clientid): """ Download datasets from databus, optionally using vault access if vault options are provided. """ @@ -112,6 +113,7 @@ def download(databusuris: List[str], localdir, databus, vault_token, databus_key databusURIs=databusuris, token=vault_token, databus_key=databus_key, + all_versions=all_versions, auth_url=authurl, client_id=clientid, ) diff --git a/tests/test_databusclient.py b/tests/test_databusclient.py index 202ac16..ef965be 100644 --- a/tests/test_databusclient.py +++ b/tests/test_databusclient.py @@ -1,6 +1,6 @@ """Client tests""" import pytest -from databusclient.client import create_dataset, create_distribution, __get_file_info +from databusclient.api.deploy import create_dataset, create_distribution, __get_file_info from collections import OrderedDict diff --git a/tests/test_download.py b/tests/test_download.py index 6a1a72e..19dd3bc 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -1,6 +1,6 @@ """Download Tests""" import pytest -import databusclient.client as cl +from databusclient.api.download import download as api_download DEFAULT_ENDPOINT="https://databus.dbpedia.org/sparql" TEST_QUERY=""" @@ -17,7 +17,7 @@ TEST_COLLECTION="https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12" def test_with_query(): - cl.download("tmp",DEFAULT_ENDPOINT,[TEST_QUERY]) + api_download("tmp",DEFAULT_ENDPOINT,[TEST_QUERY]) def test_with_collection(): - cl.download("tmp",DEFAULT_ENDPOINT,[TEST_COLLECTION]) \ No newline at end of file + api_download("tmp",DEFAULT_ENDPOINT,[TEST_COLLECTION]) \ No newline at end of file From 9a95550e669b33ffec2d89537b175cc4e5b89127 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Sun, 7 Dec 2025 16:41:56 +0100 Subject: [PATCH 08/23] refactor: iteration over deploy.py --- databusclient/api/deploy.py | 30 +++++++++++++++--------------- databusclient/api/download.py | 7 +++---- tests/test_databusclient.py | 4 ++-- 3 files changed, 20 insertions(+), 21 deletions(-) diff --git a/databusclient/api/deploy.py b/databusclient/api/deploy.py index ed8b931..b8147c0 100644 --- a/databusclient/api/deploy.py +++ b/databusclient/api/deploy.py @@ -23,7 +23,7 @@ class DeployLogLevel(Enum): debug = 2 -def __get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: +def _get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: args = distribution_str.split("|") # cv string is ALWAYS at position 1 after the URL @@ -41,7 +41,7 @@ def __get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: return cvs -def __get_filetype_definition( +def _get_filetype_definition( distribution_str: str, ) -> Tuple[Optional[str], Optional[str]]: file_ext = None @@ -80,9 +80,9 @@ def __get_filetype_definition( return file_ext, compression -def __get_extensions(distribution_str: str) -> Tuple[str, str, str]: +def _get_extensions(distribution_str: str) -> Tuple[str, str, str]: extension_part = "" - format_extension, compression = __get_filetype_definition(distribution_str) + format_extension, compression = _get_filetype_definition(distribution_str) if format_extension is not None: # build the format extension (only append compression if not none) @@ -119,7 +119,7 @@ def __get_extensions(distribution_str: str) -> Tuple[str, str, str]: return extension_part, format_extension, compression -def __get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int]]: +def _get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int]]: metadata_list = distribution_str.split("|")[1:] # check whether there is the shasum:length tuple separated by : if len(metadata_list) == 0 or ":" not in metadata_list[-1]: @@ -139,7 +139,7 @@ def __get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int return sha256sum, content_length -def __load_file_stats(url: str) -> Tuple[str, int]: +def _load_file_stats(url: str) -> Tuple[str, int]: resp = requests.get(url) if resp.status_code > 400: raise requests.exceptions.RequestException(response=resp) @@ -149,20 +149,20 @@ def __load_file_stats(url: str) -> Tuple[str, int]: return sha256sum, content_length -def __get_file_info(distribution_str: str) -> Tuple[Dict[str, str], str, str, str, int]: - cvs = __get_content_variants(distribution_str) - extension_part, format_extension, compression = __get_extensions(distribution_str) +def get_file_info(distribution_str: str) -> Tuple[Dict[str, str], str, str, str, int]: + cvs = _get_content_variants(distribution_str) + extension_part, format_extension, compression = _get_extensions(distribution_str) content_variant_part = "_".join([f"{key}={value}" for key, value in cvs.items()]) if __debug: print("DEBUG", distribution_str, extension_part) - sha256sum, content_length = __get_file_stats(distribution_str) + sha256sum, content_length = _get_file_stats(distribution_str) if sha256sum is None or content_length is None: __url = str(distribution_str).split("|")[0] - sha256sum, content_length = __load_file_stats(__url) + sha256sum, content_length = _load_file_stats(__url) return cvs, format_extension, compression, sha256sum, content_length @@ -200,7 +200,7 @@ def create_distribution( return f"{url}|{meta_string}" -def create_distributions_from_metadata(metadata: List[Dict[str, Union[str, int]]]) -> List[str]: +def _create_distributions_from_metadata(metadata: List[Dict[str, Union[str, int]]]) -> List[str]: """ Create distributions from metadata entries. @@ -313,7 +313,7 @@ def create_dataset( compression, sha256sum, content_length, - ) = __get_file_info(dst_string) + ) = get_file_info(dst_string) if not cvs and len(distributions) > 1: raise BadArgumentException( @@ -453,7 +453,7 @@ def deploy_from_metadata( Parameters ---------- metadata : List[Dict[str, Union[str, int]]] - List of file metadata entries (see create_distributions_from_metadata) + List of file metadata entries (see _create_distributions_from_metadata) version_id : str Dataset version ID in the form $DATABUS_BASE/$ACCOUNT/$GROUP/$ARTIFACT/$VERSION title : str @@ -467,7 +467,7 @@ def deploy_from_metadata( apikey : str API key for authentication """ - distributions = create_distributions_from_metadata(metadata) + distributions = _create_distributions_from_metadata(metadata) dataset = create_dataset( version_id=version_id, diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 859e35f..0fa7dce 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -26,12 +26,11 @@ def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_ """ if localDir is None: _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) - fileLocalDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") - print(f"Local directory not given, using {fileLocalDir}") + localDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") + print(f"Local directory not given, using {localDir}") file = url.split("/")[-1] - filename = os.path.join(fileLocalDir, file) - + filename = os.path.join(localDir, file) print(f"Download file: {url}") dirpath = os.path.dirname(filename) if dirpath: diff --git a/tests/test_databusclient.py b/tests/test_databusclient.py index ef965be..4c65e19 100644 --- a/tests/test_databusclient.py +++ b/tests/test_databusclient.py @@ -1,6 +1,6 @@ """Client tests""" import pytest -from databusclient.api.deploy import create_dataset, create_distribution, __get_file_info +from databusclient.api.deploy import create_dataset, create_distribution, get_file_info from collections import OrderedDict @@ -47,7 +47,7 @@ def test_distribution_cases(): compression, sha256sum, content_length, - ) = __get_file_info(artifact_name, dst_string) + ) = get_file_info(artifact_name, dst_string) created_dst_str = create_distribution( uri, cvs, formatExtension, compression, (sha256sum, content_length) From 0cd8c5e012bcefe601474011398ce02e4442bb3d Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Sun, 7 Dec 2025 19:17:50 +0100 Subject: [PATCH 09/23] refactor: webdav --- databusclient/api/__init__.py | 1 + databusclient/api/download.py | 3 +-- databusclient/cli.py | 4 ++-- databusclient/consume/download.py | 4 ---- databusclient/extensions/__init__.py | 1 + .../{rclone_wrapper/upload.py => extensions/webdav.py} | 2 +- 6 files changed, 6 insertions(+), 9 deletions(-) create mode 100644 databusclient/api/__init__.py delete mode 100644 databusclient/consume/download.py create mode 100644 databusclient/extensions/__init__.py rename databusclient/{rclone_wrapper/upload.py => extensions/webdav.py} (96%) diff --git a/databusclient/api/__init__.py b/databusclient/api/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/databusclient/api/__init__.py @@ -0,0 +1 @@ + diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 0fa7dce..eb03d5f 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -1,11 +1,10 @@ -from typing import List, Iterator +from typing import List import requests import os from tqdm import tqdm import json from SPARQLWrapper import SPARQLWrapper, JSON -from databusclient.api.delete import _delete_group, _delete_resource from databusclient.api.utils import get_databus_id_parts_from_uri, fetch_databus_jsonld diff --git a/databusclient/cli.py b/databusclient/cli.py index ab1a5ac..19702ef 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -6,7 +6,7 @@ import re from typing import List -from databusclient.rclone_wrapper import upload +from databusclient.extensions import webdav from databusclient.api.delete import delete as api_delete import databusclient.api.deploy as api_deploy @@ -82,7 +82,7 @@ def deploy(version_id, title, abstract, description, license_url, apikey, click.echo("[MODE] Upload & Deploy to DBpedia Databus via Nextcloud") click.echo(f"→ Uploading to: {remote}:{path}") - metadata = upload.upload_to_nextcloud(distributions, remote, path, webdav_url) + metadata = webdav.upload_to_webdav(distributions, remote, path, webdav_url) api_deploy.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) return diff --git a/databusclient/consume/download.py b/databusclient/consume/download.py deleted file mode 100644 index a1bbd8a..0000000 --- a/databusclient/consume/download.py +++ /dev/null @@ -1,4 +0,0 @@ -### All kind of download functionalities for Databus ### - -class Downloder: - pass diff --git a/databusclient/extensions/__init__.py b/databusclient/extensions/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/databusclient/extensions/__init__.py @@ -0,0 +1 @@ + diff --git a/databusclient/rclone_wrapper/upload.py b/databusclient/extensions/webdav.py similarity index 96% rename from databusclient/rclone_wrapper/upload.py rename to databusclient/extensions/webdav.py index f0d3328..cac7027 100644 --- a/databusclient/rclone_wrapper/upload.py +++ b/databusclient/extensions/webdav.py @@ -26,7 +26,7 @@ def get_all_files(path): files.append(os.path.join(root, name)) return files -def upload_to_nextcloud(source_paths: list[str], remote_name: str, remote_path: str, webdav_url: str): +def upload_to_webdav(source_paths: list[str], remote_name: str, remote_path: str, webdav_url: str): result = [] for path in source_paths: if not os.path.exists(path): From 634ffd4612174f1d74fa0cd985e562e5a7bd6593 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Sun, 7 Dec 2025 19:34:03 +0100 Subject: [PATCH 10/23] feat: ruff linter & formatter --- .github/workflows/python-CI.yml | 25 +- README.md | 27 ++ databusclient/__init__.py | 3 +- databusclient/api/delete.py | 51 +++- databusclient/api/deploy.py | 36 ++- databusclient/api/download.py | 331 +++++++++++++++------- databusclient/api/utils.py | 18 +- databusclient/cli.py | 189 +++++++------ databusclient/extensions/webdav.py | 33 ++- poetry.lock | 430 ++++++++++++++++++----------- pyproject.toml | 9 +- tests/test_databusclient.py | 10 +- tests/test_download.py | 18 +- 13 files changed, 763 insertions(+), 417 deletions(-) diff --git a/.github/workflows/python-CI.yml b/.github/workflows/python-CI.yml index 547f7e8..f0cbee0 100644 --- a/.github/workflows/python-CI.yml +++ b/.github/workflows/python-CI.yml @@ -18,24 +18,17 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.10 - uses: actions/setup-python@v3 + - uses: actions/checkout@v4 + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.11" - uses: Gr1N/setup-poetry@v8 #install poetry - - name: Install parts of toolchain - run: | - python -m pip install --upgrade pip - pip install flake8 pytest + - name: Upgrade pip + run: python -m pip install --upgrade pip - name: Install requirements with poetry run: poetry install - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - name: Lint with Ruff + run: poetry run ruff check --output-format=github . - name: Test with pytest - run: | - poetry run pytest + run: poetry run pytest diff --git a/README.md b/README.md index c652275..6eba86e 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,8 @@ Command-line and Python client for downloading and deploying datasets on DBpedia - [Delete](#cli-delete) - [Module Usage](#module-usage) - [Deploy](#module-deploy) +- [Contributing](#contributing) + - [Linting](#linting) ## Quickstart @@ -43,6 +45,7 @@ You can then use the client in the command line: ```bash databusclient --help databusclient deploy --help +databusclient delete --help databusclient download --help ``` @@ -553,3 +556,27 @@ from databusclient import deploy # API key can be found (or generated) at https://$$DATABUS_BASE$$/$$USER$$#settings deploy(dataset, "mysterious API key") ``` + +## Development + +Install development dependencies yourself or via [Poetry](https://python-poetry.org/): + +```bash +poetry install --with dev +``` + +### Linting + +The used linter is [Ruff](https://ruff.rs/). Ruff is configured in `pyproject.toml` and is enforced in CI (`.github/workflows/ruff.yml`). + +For development, you can run linting locally with `ruff check . ` and optionally auto-format with `ruff format .`. + +To ensuere compatibility with the `pyproject.toml` configured dependencies, run Ruff via Poetry: + +```bash +# To check for linting issues: +poetry run ruff check . + +# To auto-format code: +poetry run ruff format . +``` \ No newline at end of file diff --git a/databusclient/__init__.py b/databusclient/__init__.py index 3e053b5..d15edb6 100644 --- a/databusclient/__init__.py +++ b/databusclient/__init__.py @@ -1,7 +1,8 @@ from databusclient import cli -from databusclient.api.deploy import create_dataset, deploy, create_distribution +from databusclient.api.deploy import create_dataset, create_distribution, deploy __all__ = ["create_dataset", "deploy", "create_distribution"] + def run(): cli.app() diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index 5db8ab2..828644f 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -1,8 +1,10 @@ import json -import requests from typing import List -from databusclient.api.utils import get_databus_id_parts_from_uri, fetch_databus_jsonld +import requests + +from databusclient.api.utils import fetch_databus_jsonld, get_databus_id_parts_from_uri + def _confirm_delete(databusURI: str) -> str: """ @@ -17,9 +19,17 @@ def _confirm_delete(databusURI: str) -> str: - "cancel" if the user chooses to cancel the entire deletion process """ print(f"Are you sure you want to delete: {databusURI}?") - print("\nThis action is irreversible and will permanently remove the resource and all its data.") + print( + "\nThis action is irreversible and will permanently remove the resource and all its data." + ) while True: - choice = input("Type 'yes'/'y' to confirm, 'skip'/'s' to skip this resource, or 'cancel'/'c' to abort: ").strip().lower() + choice = ( + input( + "Type 'yes'/'y' to confirm, 'skip'/'s' to skip this resource, or 'cancel'/'c' to abort: " + ) + .strip() + .lower() + ) if choice in ("yes", "y"): return "confirm" elif choice in ("skip", "s"): @@ -30,7 +40,9 @@ def _confirm_delete(databusURI: str) -> str: print("Invalid input. Please type 'yes'/'y', 'skip'/'s', or 'cancel'/'c'.") -def _delete_resource(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): +def _delete_resource( + databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False +): """ Delete a single Databus resource (version, artifact, group). @@ -56,10 +68,7 @@ def _delete_resource(databusURI: str, databus_key: str, dry_run: bool = False, f if databus_key is None: raise ValueError("Databus API key must be provided for deletion") - headers = { - "accept": "*/*", - "X-API-KEY": databus_key - } + headers = {"accept": "*/*", "X-API-KEY": databus_key} if dry_run: print(f"[DRY RUN] Would delete: {databusURI}") @@ -70,10 +79,14 @@ def _delete_resource(databusURI: str, databus_key: str, dry_run: bool = False, f if response.status_code in (200, 204): print(f"Successfully deleted: {databusURI}") else: - raise Exception(f"Failed to delete {databusURI}: {response.status_code} - {response.text}") + raise Exception( + f"Failed to delete {databusURI}: {response.status_code} - {response.text}" + ) -def _delete_list(databusURIs: List[str], databus_key: str, dry_run: bool = False, force: bool = False): +def _delete_list( + databusURIs: List[str], databus_key: str, dry_run: bool = False, force: bool = False +): """ Delete a list of Databus resources. @@ -85,7 +98,9 @@ def _delete_list(databusURIs: List[str], databus_key: str, dry_run: bool = False _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) -def _delete_artifact(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): +def _delete_artifact( + databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False +): """ Delete an artifact and all its versions. @@ -121,7 +136,10 @@ def _delete_artifact(databusURI: str, databus_key: str, dry_run: bool = False, f # Finally, delete the artifact itself _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) -def _delete_group(databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False): + +def _delete_group( + databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False +): """ Delete a group and all its artifacts and versions. @@ -154,13 +172,14 @@ def _delete_group(databusURI: str, databus_key: str, dry_run: bool = False, forc # Finally, delete the group itself _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool): """ Delete a dataset from the databus. Delete a group, artifact, or version identified by the given databus URI. Will recursively delete all data associated with the dataset. - + Parameters: - databusURIs: List of full databus URIs of the resources to delete - databus_key: Databus API key to authenticate the deletion requests @@ -169,7 +188,9 @@ def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool) """ for databusURI in databusURIs: - _host, _account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) + _host, _account, group, artifact, version, file = get_databus_id_parts_from_uri( + databusURI + ) if group == "collections" and artifact is not None: print(f"Deleting collection: {databusURI}") diff --git a/databusclient/api/deploy.py b/databusclient/api/deploy.py index b8147c0..4c7eb27 100644 --- a/databusclient/api/deploy.py +++ b/databusclient/api/deploy.py @@ -1,8 +1,9 @@ -from enum import Enum -from typing import List, Dict, Tuple, Optional, Union -import requests import hashlib import json +from enum import Enum +from typing import Dict, List, Optional, Tuple, Union + +import requests __debug = False @@ -153,7 +154,7 @@ def get_file_info(distribution_str: str) -> Tuple[Dict[str, str], str, str, str, cvs = _get_content_variants(distribution_str) extension_part, format_extension, compression = _get_extensions(distribution_str) - content_variant_part = "_".join([f"{key}={value}" for key, value in cvs.items()]) + # content_variant_part = "_".join([f"{key}={value}" for key, value in cvs.items()]) if __debug: print("DEBUG", distribution_str, extension_part) @@ -200,7 +201,10 @@ def create_distribution( return f"{url}|{meta_string}" -def _create_distributions_from_metadata(metadata: List[Dict[str, Union[str, int]]]) -> List[str]: + +def _create_distributions_from_metadata( + metadata: List[Dict[str, Union[str, int]]], +) -> List[str]: """ Create distributions from metadata entries. @@ -233,11 +237,16 @@ def _create_distributions_from_metadata(metadata: List[Dict[str, Union[str, int] size = entry["size"] url = entry["url"] if not isinstance(size, int) or size <= 0: - raise ValueError(f"Invalid size for {url}: expected positive integer, got {size}") + raise ValueError( + f"Invalid size for {url}: expected positive integer, got {size}" + ) # Validate SHA-256 hex digest (64 hex chars) - if not isinstance(checksum, str) or len(checksum) != 64 or not all( - c in '0123456789abcdefABCDEF' for c in checksum): - raise ValueError(f"Invalid checksum for {url}") + if ( + not isinstance(checksum, str) + or len(checksum) != 64 + or not all(c in "0123456789abcdefABCDEF" for c in checksum) + ): + raise ValueError(f"Invalid checksum for {url}") distributions.append( create_distribution( @@ -245,12 +254,13 @@ def _create_distributions_from_metadata(metadata: List[Dict[str, Union[str, int] cvs={"count": f"{counter}"}, file_format=entry.get("file_format"), compression=entry.get("compression"), - sha256_length_tuple=(checksum, size) + sha256_length_tuple=(checksum, size), ) ) counter += 1 return distributions + def create_dataset( version_id: str, title: str, @@ -361,7 +371,7 @@ def create_dataset( "@type": "Artifact", "title": title, "abstract": abstract, - "description": description + "description": description, } graphs.append(artifact_graph) @@ -445,7 +455,7 @@ def deploy_from_metadata( abstract: str, description: str, license_url: str, - apikey: str + apikey: str, ) -> None: """ Deploy a dataset from metadata entries. @@ -475,7 +485,7 @@ def deploy_from_metadata( abstract=abstract, description=description, license_url=license_url, - distributions=distributions + distributions=distributions, ) print(f"Deploying dataset version: {version_id}") diff --git a/databusclient/api/download.py b/databusclient/api/download.py index eb03d5f..5f5877a 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -1,14 +1,22 @@ +import json +import os from typing import List + import requests -import os +from SPARQLWrapper import JSON, SPARQLWrapper from tqdm import tqdm -import json -from SPARQLWrapper import SPARQLWrapper, JSON -from databusclient.api.utils import get_databus_id_parts_from_uri, fetch_databus_jsonld +from databusclient.api.utils import fetch_databus_jsonld, get_databus_id_parts_from_uri -def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_url=None, client_id=None) -> None: +def _download_file( + url, + localDir, + vault_token_file=None, + databus_key=None, + auth_url=None, + client_id=None, +) -> None: """ Download a file from the internet with a progress bar using tqdm. @@ -24,8 +32,16 @@ def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_ 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized), then fetch Vault access token and retry with Authorization header. """ if localDir is None: - _host, account, group, artifact, version, file = get_databus_id_parts_from_uri(url) - localDir = os.path.join(os.getcwd(), account, group, artifact, version if version is not None else "latest") + _host, account, group, artifact, version, file = get_databus_id_parts_from_uri( + url + ) + localDir = os.path.join( + os.getcwd(), + account, + group, + artifact, + version if version is not None else "latest", + ) print(f"Local directory not given, using {localDir}") file = url.split("/")[-1] @@ -37,16 +53,24 @@ def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_ # --- 1. Get redirect URL by requesting HEAD --- response = requests.head(url, stream=True) # Check for redirect and update URL if necessary - if response.headers.get("Location") and response.status_code in [301, 302, 303, 307, 308]: + if response.headers.get("Location") and response.status_code in [ + 301, + 302, + 303, + 307, + 308, + ]: url = response.headers.get("Location") print("Redirects url: ", url) # --- 2. Try direct GET --- response = requests.get(url, stream=True, allow_redirects=True, timeout=30) - www = response.headers.get('WWW-Authenticate', '') # get WWW-Authenticate header if present to check for Bearer auth + www = response.headers.get( + "WWW-Authenticate", "" + ) # get WWW-Authenticate header if present to check for Bearer auth # Vault token required if 401 Unauthorized with Bearer challenge - if (response.status_code == 401 and "bearer" in www.lower()): + if response.status_code == 401 and "bearer" in www.lower(): print(f"Authentication required for {url}") if not (vault_token_file): raise ValueError("Vault token file not given for protected download") @@ -58,7 +82,7 @@ def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_ # --- 4. Retry with token --- response = requests.get(url, headers=headers, stream=True, timeout=30) - + # Databus API key required if only 401 Unauthorized elif response.status_code == 401: print(f"API key required for {url}") @@ -77,27 +101,29 @@ def _download_file(url, localDir, vault_token_file=None, databus_key=None, auth_ else: raise e - total_size_in_bytes = int(response.headers.get('content-length', 0)) + total_size_in_bytes = int(response.headers.get("content-length", 0)) block_size = 1024 # 1 KiB - progress_bar = tqdm(total=total_size_in_bytes, unit='iB', unit_scale=True) - with open(filename, 'wb') as file: + progress_bar = tqdm(total=total_size_in_bytes, unit="iB", unit_scale=True) + with open(filename, "wb") as file: for data in response.iter_content(block_size): progress_bar.update(len(data)) file.write(data) progress_bar.close() # TODO: could be a problem of github raw / openflaas - if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - raise IOError("Downloaded size does not match Content-Length header") + # if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: + # raise IOError("Downloaded size does not match Content-Length header") -def _download_files(urls: List[str], - localDir: str, - vault_token_file: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: +def _download_files( + urls: List[str], + localDir: str, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None, +) -> None: """ Download multiple files from the databus. @@ -110,7 +136,15 @@ def _download_files(urls: List[str], - client_id: Client ID for token exchange """ for url in urls: - _download_file(url=url, localDir=localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + _download_file( + url=url, + localDir=localDir, + vault_token_file=vault_token_file, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) + def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> str: """ @@ -143,7 +177,7 @@ def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: - Dictionary containing the query results """ sparql = SPARQLWrapper(endpoint_url) - sparql.method = 'POST' + sparql.method = "POST" sparql.setQuery(query) sparql.setReturnFormat(JSON) if databus_key is not None: @@ -152,7 +186,9 @@ def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: return results -def _get_file_download_urls_from_sparql_query(endpoint_url, query, databus_key=None) -> List[str]: +def _get_file_download_urls_from_sparql_query( + endpoint_url, query, databus_key=None +) -> List[str]: """ Execute a SPARQL query to get databus file download URLs. @@ -186,10 +222,10 @@ def _get_file_download_urls_from_sparql_query(endpoint_url, query, databus_key=N return urls -def __get_vault_access__(download_url: str, - token_file: str, - auth_url: str, - client_id: str) -> str: + +def __get_vault_access__( + download_url: str, token_file: str, auth_url: str, client_id: str +) -> str: """ Get Vault access token for a protected databus download. """ @@ -204,31 +240,37 @@ def __get_vault_access__(download_url: str, print(f"Warning: token from {token_file} is short (<80 chars)") # 2. Refresh token -> access token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "refresh_token", - "refresh_token": refresh_token - }) + resp = requests.post( + auth_url, + data={ + "client_id": client_id, + "grant_type": "refresh_token", + "refresh_token": refresh_token, + }, + ) resp.raise_for_status() access_token = resp.json()["access_token"] # 3. Extract host as audience # Remove protocol prefix if download_url.startswith("https://"): - host_part = download_url[len("https://"):] + host_part = download_url[len("https://") :] elif download_url.startswith("http://"): - host_part = download_url[len("http://"):] + host_part = download_url[len("http://") :] else: host_part = download_url audience = host_part.split("/")[0] # host is before first "/" # 4. Access token -> Vault token - resp = requests.post(auth_url, data={ - "client_id": client_id, - "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", - "subject_token": access_token, - "audience": audience - }) + resp = requests.post( + auth_url, + data={ + "client_id": client_id, + "grant_type": "urn:ietf:params:oauth:grant-type:token-exchange", + "subject_token": access_token, + "audience": audience, + }, + ) resp.raise_for_status() vault_token = resp.json()["access_token"] @@ -236,13 +278,15 @@ def __get_vault_access__(download_url: str, return vault_token -def _download_collection(uri: str, - endpoint: str, - localDir: str, - vault_token: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: +def _download_collection( + uri: str, + endpoint: str, + localDir: str, + vault_token: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None, +) -> None: """ Download all files in a databus collection. @@ -256,16 +300,27 @@ def _download_collection(uri: str, - client_id: Client ID for token exchange """ query = _get_sparql_query_of_collection(uri, databus_key=databus_key) - file_urls = _get_file_download_urls_from_sparql_query(endpoint, query, databus_key=databus_key) - _download_files(list(file_urls), localDir, vault_token_file=vault_token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - -def _download_version(uri: str, - localDir: str, - vault_token_file: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: + file_urls = _get_file_download_urls_from_sparql_query( + endpoint, query, databus_key=databus_key + ) + _download_files( + list(file_urls), + localDir, + vault_token_file=vault_token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) + + +def _download_version( + uri: str, + localDir: str, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None, +) -> None: """ Download all files in a databus artifact version. @@ -279,16 +334,25 @@ def _download_version(uri: str, """ json_str = fetch_databus_jsonld(uri, databus_key=databus_key) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) - _download_files(file_urls, localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - -def _download_artifact(uri: str, - localDir: str, - all_versions: bool = False, - vault_token_file: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: + _download_files( + file_urls, + localDir, + vault_token_file=vault_token_file, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) + + +def _download_artifact( + uri: str, + localDir: str, + all_versions: bool = False, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None, +) -> None: """ Download files in a databus artifact. @@ -309,10 +373,19 @@ def _download_artifact(uri: str, print(f"Downloading version: {version_uri}") json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) - _download_files(file_urls, localDir, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - - -def _get_databus_versions_of_artifact(json_str: str, all_versions: bool) -> str | List[str]: + _download_files( + file_urls, + localDir, + vault_token_file=vault_token_file, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) + + +def _get_databus_versions_of_artifact( + json_str: str, all_versions: bool +) -> str | List[str]: """ Parse the JSON-LD of a databus artifact to extract URLs of its versions. @@ -342,6 +415,7 @@ def _get_databus_versions_of_artifact(json_str: str, all_versions: bool) -> str return version_urls return version_urls[0] + def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: """ Parse the JSON-LD of a databus artifact version to extract download URLs. @@ -364,13 +438,15 @@ def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: return databusIdUrl -def _download_group(uri: str, - localDir: str, - all_versions: bool = False, - vault_token_file: str = None, - databus_key: str = None, - auth_url: str = None, - client_id: str = None) -> None: +def _download_group( + uri: str, + localDir: str, + all_versions: bool = False, + vault_token_file: str = None, + databus_key: str = None, + auth_url: str = None, + client_id: str = None, +) -> None: """ Download files in a databus group. @@ -387,8 +463,15 @@ def _download_group(uri: str, artifacts = _get_databus_artifacts_of_group(json_str) for artifact_uri in artifacts: print(f"Download artifact: {artifact_uri}") - _download_artifact(artifact_uri, localDir, all_versions=all_versions, vault_token_file=vault_token_file, databus_key=databus_key, auth_url=auth_url, client_id=client_id) - + _download_artifact( + artifact_uri, + localDir, + all_versions=all_versions, + vault_token_file=vault_token_file, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) def _get_databus_artifacts_of_group(json_str: str) -> List[str]: @@ -410,6 +493,7 @@ def _get_databus_artifacts_of_group(json_str: str) -> List[str]: result.append(uri) return result + def download( localDir: str, endpoint: str, @@ -418,13 +502,13 @@ def download( databus_key=None, all_versions=None, auth_url=None, - client_id=None + client_id=None, ) -> None: """ Download datasets from databus. - + Download of files, versions, artifacts, groups or databus collections by ther databus URIs or user-defined SPARQL queries that return file download URLs. - + Parameters: - localDir: Local directory to download datasets to. If None, the databus folder structure is created in the current working directory. - endpoint: the databus endpoint URL. If None, inferred from databusURI. Required for user-defined SPARQL queries. @@ -435,7 +519,9 @@ def download( - client_id: Client ID for token exchange. Default is "vault-token-exchange". """ for databusURI in databusURIs: - host, account, group, artifact, version, file = get_databus_id_parts_from_uri(databusURI) + host, account, group, artifact, version, file = get_databus_id_parts_from_uri( + databusURI + ) # dataID or databus collection if databusURI.startswith("http://") or databusURI.startswith("https://"): @@ -446,23 +532,67 @@ def download( if group == "collections" and artifact is not None: print(f"Downloading collection: {databusURI}") - _download_collection(databusURI, endpoint, localDir, token, databus_key, auth_url, client_id) + _download_collection( + databusURI, + endpoint, + localDir, + token, + databus_key, + auth_url, + client_id, + ) elif file is not None: print(f"Downloading file: {databusURI}") - _download_file(databusURI, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + _download_file( + databusURI, + localDir, + vault_token_file=token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) elif version is not None: print(f"Downloading version: {databusURI}") - _download_version(databusURI, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + _download_version( + databusURI, + localDir, + vault_token_file=token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) elif artifact is not None: - print(f"Downloading {'all' if all_versions else 'latest'} version(s) of artifact: {databusURI}") - _download_artifact(databusURI, localDir, all_versions=all_versions, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + print( + f"Downloading {'all' if all_versions else 'latest'} version(s) of artifact: {databusURI}" + ) + _download_artifact( + databusURI, + localDir, + all_versions=all_versions, + vault_token_file=token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) elif group is not None and group != "collections": - print(f"Downloading group and all its artifacts and versions: {databusURI}") - _download_group(databusURI, localDir, all_versions=all_versions, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) + print( + f"Downloading group and all its artifacts and versions: {databusURI}" + ) + _download_group( + databusURI, + localDir, + all_versions=all_versions, + vault_token_file=token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) elif account is not None: print("accountId not supported yet") # TODO else: - print("dataId not supported yet") # TODO add support for other DatabusIds + print( + "dataId not supported yet" + ) # TODO add support for other DatabusIds # query in local file elif databusURI.startswith("file://"): print("query in file not supported yet") @@ -471,5 +601,14 @@ def download( print("QUERY {}", databusURI.replace("\n", " ")) if endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") - res = _get_file_download_urls_from_sparql_query(endpoint, databusURI, databus_key=databus_key) - _download_files(res, localDir, vault_token_file=token, databus_key=databus_key, auth_url=auth_url, client_id=client_id) \ No newline at end of file + res = _get_file_download_urls_from_sparql_query( + endpoint, databusURI, databus_key=databus_key + ) + _download_files( + res, + localDir, + vault_token_file=token, + databus_key=databus_key, + auth_url=auth_url, + client_id=client_id, + ) diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index 5c0fd3f..0c6f342 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -1,10 +1,21 @@ +from typing import Optional, Tuple + import requests -from typing import Tuple, Optional -def get_databus_id_parts_from_uri(uri: str) -> Tuple[Optional[str], Optional[str], Optional[str], Optional[str], Optional[str], Optional[str]]: + +def get_databus_id_parts_from_uri( + uri: str, +) -> Tuple[ + Optional[str], + Optional[str], + Optional[str], + Optional[str], + Optional[str], + Optional[str], +]: """ Extract databus ID parts from a given databus URI. - + Parameters: - uri: The full databus URI @@ -17,6 +28,7 @@ def get_databus_id_parts_from_uri(uri: str) -> Tuple[Optional[str], Optional[str parts += [None] * (6 - len(parts)) # pad with None if less than 6 parts return tuple(parts[:6]) # return only the first 6 parts + def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: """ Retrieve JSON-LD representation of a databus resource. diff --git a/databusclient/cli.py b/databusclient/cli.py index 19702ef..abb0f03 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -1,16 +1,15 @@ #!/usr/bin/env python3 import json import os - -import click -import re from typing import List -from databusclient.extensions import webdav +import click -from databusclient.api.delete import delete as api_delete import databusclient.api.deploy as api_deploy +from databusclient.api.delete import delete as api_delete from databusclient.api.download import download as api_download +from databusclient.extensions import webdav + @click.group() def app(): @@ -20,26 +19,46 @@ def app(): @app.command() @click.option( - "--versionid", "version_id", + "--version-id", + "version_id", required=True, help="Target databus version/dataset identifier of the form " - "", + "", ) @click.option("--title", required=True, help="Dataset title") @click.option("--abstract", required=True, help="Dataset abstract max 200 chars") @click.option("--description", required=True, help="Dataset description") -@click.option("--license", "license_url", required=True, help="License (see dalicc.net)") +@click.option( + "--license", "license_url", required=True, help="License (see dalicc.net)" +) @click.option("--apikey", required=True, help="API key") - -@click.option("--metadata", "metadata_file", type=click.Path(exists=True), - help="Path to metadata JSON file (for metadata mode)") -@click.option("--webdav-url", "webdav_url", help="WebDAV URL (e.g., https://cloud.example.com/remote.php/webdav)") +@click.option( + "--metadata", + "metadata_file", + type=click.Path(exists=True), + help="Path to metadata JSON file (for metadata mode)", +) +@click.option( + "--webdav-url", + "webdav_url", + help="WebDAV URL (e.g., https://cloud.example.com/remote.php/webdav)", +) @click.option("--remote", help="rclone remote name (e.g., 'nextcloud')") @click.option("--path", help="Remote path on Nextcloud (e.g., 'datasets/mydataset')") - @click.argument("distributions", nargs=-1) -def deploy(version_id, title, abstract, description, license_url, apikey, - metadata_file, webdav_url, remote, path, distributions: List[str]): +def deploy( + version_id, + title, + abstract, + description, + license_url, + apikey, + metadata_file, + webdav_url, + remote, + path, + distributions: List[str], +): """ Flexible deploy to Databus command supporting three modes:\n - Classic deploy (distributions as arguments)\n @@ -49,41 +68,55 @@ def deploy(version_id, title, abstract, description, license_url, apikey, # Sanity checks for conflicting options if metadata_file and any([distributions, webdav_url, remote, path]): - raise click.UsageError("Invalid combination: when using --metadata, do not provide --webdav-url, --remote, --path, or distributions.") + raise click.UsageError( + "Invalid combination: when using --metadata, do not provide --webdav-url, --remote, --path, or distributions." + ) if any([webdav_url, remote, path]) and not all([webdav_url, remote, path]): - raise click.UsageError("Invalid combination: when using WebDAV/Nextcloud mode, please provide --webdav-url, --remote, and --path together.") + raise click.UsageError( + "Invalid combination: when using WebDAV/Nextcloud mode, please provide --webdav-url, --remote, and --path together." + ) # === Mode 1: Classic Deploy === if distributions and not (metadata_file or webdav_url or remote or path): click.echo("[MODE] Classic deploy with distributions") click.echo(f"Deploying dataset version: {version_id}") - dataid = api_deploy.create_dataset(version_id, title, abstract, description, license_url, distributions) + dataid = api_deploy.create_dataset( + version_id, title, abstract, description, license_url, distributions + ) api_deploy.deploy(dataid=dataid, api_key=apikey) return # === Mode 2: Metadata File === if metadata_file: click.echo(f"[MODE] Deploy from metadata file: {metadata_file}") - with open(metadata_file, 'r') as f: + with open(metadata_file, "r") as f: metadata = json.load(f) - api_deploy.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) + api_deploy.deploy_from_metadata( + metadata, version_id, title, abstract, description, license_url, apikey + ) return - + # === Mode 3: Upload & Deploy (Nextcloud) === if webdav_url and remote and path: if not distributions: - raise click.UsageError("Please provide files to upload when using WebDAV/Nextcloud mode.") + raise click.UsageError( + "Please provide files to upload when using WebDAV/Nextcloud mode." + ) - #Check that all given paths exist and are files or directories.# + # Check that all given paths exist and are files or directories.# invalid = [f for f in distributions if not os.path.exists(f)] if invalid: - raise click.UsageError(f"The following input files or folders do not exist: {', '.join(invalid)}") + raise click.UsageError( + f"The following input files or folders do not exist: {', '.join(invalid)}" + ) click.echo("[MODE] Upload & Deploy to DBpedia Databus via Nextcloud") click.echo(f"→ Uploading to: {remote}:{path}") metadata = webdav.upload_to_webdav(distributions, remote, path, webdav_url) - api_deploy.deploy_from_metadata(metadata, version_id, title, abstract, description, license_url, apikey) + api_deploy.deploy_from_metadata( + metadata, version_id, title, abstract, description, license_url, apikey + ) return raise click.UsageError( @@ -96,14 +129,45 @@ def deploy(version_id, title, abstract, description, license_url, apikey, @app.command() @click.argument("databusuris", nargs=-1, required=True) -@click.option("--localdir", help="Local databus folder (if not given, databus folder structure is created in current working directory)") -@click.option("--databus", help="Databus URL (if not given, inferred from databusuri, e.g. https://databus.dbpedia.org/sparql)") +@click.option( + "--localdir", + help="Local databus folder (if not given, databus folder structure is created in current working directory)", +) +@click.option( + "--databus", + help="Databus URL (if not given, inferred from databusuri, e.g. https://databus.dbpedia.org/sparql)", +) @click.option("--vault-token", help="Path to Vault refresh token file") -@click.option("--databus-key", help="Databus API key to download from protected databus") -@click.option("--all-versions", is_flag=True, help="When downloading artifacts, download all versions instead of only the latest") -@click.option("--authurl", default="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", show_default=True, help="Keycloak token endpoint URL") -@click.option("--clientid", default="vault-token-exchange", show_default=True, help="Client ID for token exchange") -def download(databusuris: List[str], localdir, databus, vault_token, databus_key, all_versions, authurl, clientid): +@click.option( + "--databus-key", help="Databus API key to download from protected databus" +) +@click.option( + "--all-versions", + is_flag=True, + help="When downloading artifacts, download all versions instead of only the latest", +) +@click.option( + "--authurl", + default="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", + show_default=True, + help="Keycloak token endpoint URL", +) +@click.option( + "--clientid", + default="vault-token-exchange", + show_default=True, + help="Client ID for token exchange", +) +def download( + databusuris: List[str], + localdir, + databus, + vault_token, + databus_key, + all_versions, + authurl, + clientid, +): """ Download datasets from databus, optionally using vault access if vault options are provided. """ @@ -118,11 +182,18 @@ def download(databusuris: List[str], localdir, databus, vault_token, databus_key client_id=clientid, ) + @app.command() @click.argument("databusuris", nargs=-1, required=True) -@click.option("--databus-key", help="Databus API key to access protected databus", required=True) -@click.option("--dry-run", is_flag=True, help="Perform a dry run without actual deletion") -@click.option("--force", is_flag=True, help="Force deletion without confirmation prompt") +@click.option( + "--databus-key", help="Databus API key to access protected databus", required=True +) +@click.option( + "--dry-run", is_flag=True, help="Perform a dry run without actual deletion" +) +@click.option( + "--force", is_flag=True, help="Force deletion without confirmation prompt" +) def delete(databusuris: List[str], databus_key: str, dry_run: bool, force: bool): """ Delete a dataset from the databus. @@ -136,53 +207,7 @@ def delete(databusuris: List[str], databus_key: str, dry_run: bool, force: bool) databus_key=databus_key, dry_run=dry_run, force=force, - ) - - -@app.command() -@click.argument("url") -@click.option("--cv", "cvs", multiple=True, help="Content variant like key=value (repeatable). Keys must not contain '|' or '_'") -@click.option("--format", "file_format", help="Format extension (e.g. ttl)") -@click.option("--compression", help="Compression (e.g. gzip)") -@click.option("--sha-length", help="sha256:length (64 hex chars followed by ':' and integer length)") -@click.option("--json-output", is_flag=True, help="Output JSON distribution object instead of plain string") -def mkdist(url, cvs, file_format, compression, sha_length, json_output): - """Create a distribution string from components.""" - # Validate CVs - cvs_dict = {} - for cv in cvs: - if "=" not in cv: - raise click.BadParameter(f"Invalid content variant '{cv}': expected key=value") - key, val = cv.split("=", 1) - if any(ch in key for ch in ("|", "_")): - raise click.BadParameter("Invalid characters in content-variant key (forbidden: '|' and '_')") - if key in cvs_dict: - raise click.BadParameter(f"Duplicate content-variant key '{key}'") - cvs_dict[key] = val - - # Validate sha-length - sha_tuple = None - if sha_length: - if not re.match(r'^[A-Fa-f0-9]{64}:\d+$', sha_length): - raise click.BadParameter("Invalid --sha-length; expected SHA256HEX:length") - sha, length = sha_length.split(":", 1) - sha_tuple = (sha, int(length)) - - # Deterministic ordering - sorted_cvs = {k: cvs_dict[k] for k in sorted(cvs_dict)} - - dist = client.create_distribution(url=url, cvs=sorted_cvs, file_format=file_format, compression=compression, sha256_length_tuple=sha_tuple) - if json_output: - import json as _json - click.echo(_json.dumps({"distribution": dist})) - else: - click.echo(dist) - - -@app.command() -@click.argument("shell", type=click.Choice(["bash","zsh","fish","powershell"]), required=False) -def completion(shell="bash"): - click.echo(f"Run: eval \"$(_DATABUSCLIENT_COMPLETE=source_{shell} python -m databusclient)\"") + ) if __name__ == "__main__": diff --git a/databusclient/extensions/webdav.py b/databusclient/extensions/webdav.py index cac7027..c0747f6 100644 --- a/databusclient/extensions/webdav.py +++ b/databusclient/extensions/webdav.py @@ -1,14 +1,14 @@ import hashlib import os -import subprocess import posixpath -from urllib.parse import urljoin, quote +import subprocess +from urllib.parse import quote, urljoin def compute_sha256_and_length(filepath): sha256 = hashlib.sha256() total_length = 0 - with open(filepath, 'rb') as f: + with open(filepath, "rb") as f: while True: chunk = f.read(4096) if not chunk: @@ -17,6 +17,7 @@ def compute_sha256_and_length(filepath): total_length += len(chunk) return sha256.hexdigest(), total_length + def get_all_files(path): if os.path.isfile(path): return [path] @@ -26,7 +27,10 @@ def get_all_files(path): files.append(os.path.join(root, name)) return files -def upload_to_webdav(source_paths: list[str], remote_name: str, remote_path: str, webdav_url: str): + +def upload_to_webdav( + source_paths: list[str], remote_name: str, remote_path: str, webdav_url: str +): result = [] for path in source_paths: if not os.path.exists(path): @@ -40,7 +44,7 @@ def upload_to_webdav(source_paths: list[str], remote_name: str, remote_path: str tmp_results = [] for file in files: - checksum,size = compute_sha256_and_length(file) + checksum, size = compute_sha256_and_length(file) if os.path.isdir(path): rel_file = os.path.relpath(file, abs_path) @@ -51,15 +55,20 @@ def upload_to_webdav(source_paths: list[str], remote_name: str, remote_path: str remote_webdav_path = posixpath.join(remote_path, os.path.basename(file)) # Preserve scheme/host and percent-encode path segments - url = urljoin(webdav_url.rstrip("/") + "/", quote(remote_webdav_path.lstrip("/"), safe="/")) + url = urljoin( + webdav_url.rstrip("/") + "/", + quote(remote_webdav_path.lstrip("/"), safe="/"), + ) filename = os.path.basename(file) - tmp_results.append({ - "filename": filename, - "checksum": checksum, - "size": size, - "url": url, - }) + tmp_results.append( + { + "filename": filename, + "checksum": checksum, + "size": size, + "url": url, + } + ) dest_subpath = posixpath.join(remote_path.lstrip("/"), basename) if os.path.isdir(path): diff --git a/poetry.lock b/poetry.lock index b4b80af..f772e40 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. 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"6f798ca5bc7629dc0668179934c9889c0d971743c1b162ae1387bd0c5a349d94" +content-hash = "5961c30b6d27c388e50a2a08a598b37160f14e38719937c86faeb7d56ed770ec" diff --git a/pyproject.toml b/pyproject.toml index 0d32ee1..27bfca2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "databusclient" -version = "0.12" -description = "A simple client for submitting data to the DBpedia Databus" +version = "0.14" +description = "A simple client for submitting, downloading, and deleting data on the DBpedia Databus" authors = ["DBpedia Association"] license = "Apache-2.0 License" readme = "README.md" @@ -17,10 +17,15 @@ rdflib = "^7.2.1" [tool.poetry.group.dev.dependencies] black = "^22.6.0" pytest = "^7.1.3" +ruff = "^0.5.5" [tool.poetry.scripts] databusclient = "databusclient.cli:app" +[tool.ruff] +target-version = "py39" +src = ["databusclient", "tests"] + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" diff --git a/tests/test_databusclient.py b/tests/test_databusclient.py index 4c65e19..2a559d4 100644 --- a/tests/test_databusclient.py +++ b/tests/test_databusclient.py @@ -1,14 +1,16 @@ """Client tests""" -import pytest -from databusclient.api.deploy import create_dataset, create_distribution, get_file_info + from collections import OrderedDict +import pytest + +from databusclient.api.deploy import create_dataset, create_distribution, get_file_info EXAMPLE_URL = "https://raw.githubusercontent.com/dbpedia/databus/608482875276ef5df00f2360a2f81005e62b58bd/server/app/api/swagger.yml" + @pytest.mark.skip(reason="temporarily disabled since code needs fixing") def test_distribution_cases(): - metadata_args_with_filler = OrderedDict() metadata_args_with_filler["type=config_source=databus"] = "" @@ -24,7 +26,6 @@ def test_distribution_cases(): parameters = list(metadata_args_with_filler.keys()) for i in range(0, len(metadata_args_with_filler.keys())): - if i == 1: continue @@ -58,7 +59,6 @@ def test_distribution_cases(): @pytest.mark.skip(reason="temporarily disabled since code needs fixing") def test_empty_cvs(): - dst = [create_distribution(url=EXAMPLE_URL, cvs={})] dataset = create_dataset( diff --git a/tests/test_download.py b/tests/test_download.py index 19dd3bc..56dc6b6 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -1,9 +1,9 @@ """Download Tests""" -import pytest + from databusclient.api.download import download as api_download -DEFAULT_ENDPOINT="https://databus.dbpedia.org/sparql" -TEST_QUERY=""" +DEFAULT_ENDPOINT = "https://databus.dbpedia.org/sparql" +TEST_QUERY = """ PREFIX dcat: SELECT ?file WHERE { @@ -14,10 +14,14 @@ } LIMIT 10 """ -TEST_COLLECTION="https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12" +TEST_COLLECTION = ( + "https://databus.dbpedia.org/dbpedia/collections/dbpedia-snapshot-2022-12" +) + def test_with_query(): - api_download("tmp",DEFAULT_ENDPOINT,[TEST_QUERY]) - + api_download("tmp", DEFAULT_ENDPOINT, [TEST_QUERY]) + + def test_with_collection(): - api_download("tmp",DEFAULT_ENDPOINT,[TEST_COLLECTION]) \ No newline at end of file + api_download("tmp", DEFAULT_ENDPOINT, [TEST_COLLECTION]) From c1b8430b086c34299529361f9449211ac8b21b9a Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Tue, 9 Dec 2025 09:53:18 +0100 Subject: [PATCH 11/23] feat: python 3.11 migration --- Dockerfile | 2 +- README.md | 33 ++++-- databusclient/api/delete.py | 11 +- databusclient/api/deploy.py | 39 +++++-- databusclient/api/download.py | 96 +++++++++++----- databusclient/api/utils.py | 5 +- databusclient/cli.py | 2 +- poetry.lock | 107 +----------------- pyproject.toml | 4 +- .../{test_databusclient.py => test_deploy.py} | 32 +++++- tests/test_download.py | 2 + 11 files changed, 171 insertions(+), 162 deletions(-) rename tests/{test_databusclient.py => test_deploy.py} (81%) diff --git a/Dockerfile b/Dockerfile index b44f7b8..7cc4829 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.10-slim +FROM python:3.11-slim WORKDIR /data diff --git a/README.md b/README.md index 6eba86e..dc9991f 100644 --- a/README.md +++ b/README.md @@ -20,8 +20,9 @@ Command-line and Python client for downloading and deploying datasets on DBpedia - [Delete](#cli-delete) - [Module Usage](#module-usage) - [Deploy](#module-deploy) -- [Contributing](#contributing) +- [Development & Contributing](#development--contributing) - [Linting](#linting) + - [Testing](#testing) ## Quickstart @@ -32,7 +33,7 @@ You can use either **Python** or **Docker**. Both methods support all client fea ### Python -Requirements: [Python](https://www.python.org/downloads/) and [pip](https://pip.pypa.io/en/stable/installation/) +Requirements: [Python 3.11+](https://www.python.org/downloads/) and [pip](https://pip.pypa.io/en/stable/installation/) Before using the client, install it via pip: @@ -186,8 +187,8 @@ Options: e.g. https://databus.dbpedia.org/sparql) --vault-token TEXT Path to Vault refresh token file --databus-key TEXT Databus API key to download from protected databus - --latest-only When downloading artifacts, only download the latest - version + --all-versions When downloading artifacts, download all versions + instead of only the latest --authurl TEXT Keycloak token endpoint URL [default: https://auth.dbpedia.org/realms/dbpedia/protocol/openid- connect/token] @@ -557,7 +558,7 @@ from databusclient import deploy deploy(dataset, "mysterious API key") ``` -## Development +## Development & Contributing Install development dependencies yourself or via [Poetry](https://python-poetry.org/): @@ -569,9 +570,9 @@ poetry install --with dev The used linter is [Ruff](https://ruff.rs/). Ruff is configured in `pyproject.toml` and is enforced in CI (`.github/workflows/ruff.yml`). -For development, you can run linting locally with `ruff check . ` and optionally auto-format with `ruff format .`. +For development, you can run linting locally with `ruff check .` and optionally auto-format with `ruff format .`. -To ensuere compatibility with the `pyproject.toml` configured dependencies, run Ruff via Poetry: +To ensure compatibility with the `pyproject.toml` configured dependencies, run Ruff via Poetry: ```bash # To check for linting issues: @@ -579,4 +580,22 @@ poetry run ruff check . # To auto-format code: poetry run ruff format . +``` + +### Testing + +When developing new features please make sure to add appropriate tests and ensure that all tests pass. Tests are under `tests/` and use [pytest](https://docs.pytest.org/en/7.4.x/) as test framework. + +When fixing bugs or refactoring existing code, please make sure to add tests that cover the affected functionality. The current test coverage is very low, so any additional tests are highly appreciated. + +To run tests locally, use: + +```bash +pytest tests/ +``` + +Or to ensure compatibility with the `pyproject.toml` configured dependencies, run pytest via Poetry: + +```bash +poetry run pytest tests/ ``` \ No newline at end of file diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index 828644f..41bb119 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -3,7 +3,10 @@ import requests -from databusclient.api.utils import fetch_databus_jsonld, get_databus_id_parts_from_uri +from databusclient.api.utils import ( + fetch_databus_jsonld, + get_databus_id_parts_from_file_url, +) def _confirm_delete(databusURI: str) -> str: @@ -161,7 +164,7 @@ def _delete_group( uri = item.get("@id") if not uri: continue - _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) + _, _, _, _, version, _ = get_databus_id_parts_from_file_url(uri) if version is None: artifact_uris.append(uri) @@ -188,8 +191,8 @@ def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool) """ for databusURI in databusURIs: - _host, _account, group, artifact, version, file = get_databus_id_parts_from_uri( - databusURI + _host, _account, group, artifact, version, file = ( + get_databus_id_parts_from_file_url(databusURI) ) if group == "collections" and artifact is not None: diff --git a/databusclient/api/deploy.py b/databusclient/api/deploy.py index 4c7eb27..ef8ebf5 100644 --- a/databusclient/api/deploy.py +++ b/databusclient/api/deploy.py @@ -5,7 +5,7 @@ import requests -__debug = False +_debug = False class DeployError(Exception): @@ -36,6 +36,11 @@ def _get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: cvs = {} for kv in cv_str.split("_"): + if "=" not in kv: + raise BadArgumentException( + f"Invalid content variant format: '{kv}'. Expected 'key=value' format." + ) + key, value = kv.split("=") cvs[key] = value @@ -141,8 +146,8 @@ def _get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int] def _load_file_stats(url: str) -> Tuple[str, int]: - resp = requests.get(url) - if resp.status_code > 400: + resp = requests.get(url, timeout=30) + if resp.status_code >= 400: raise requests.exceptions.RequestException(response=resp) sha256sum = hashlib.sha256(bytes(resp.content)).hexdigest() @@ -156,7 +161,7 @@ def get_file_info(distribution_str: str) -> Tuple[Dict[str, str], str, str, str, # content_variant_part = "_".join([f"{key}={value}" for key, value in cvs.items()]) - if __debug: + if _debug: print("DEBUG", distribution_str, extension_part) sha256sum, content_length = _get_file_stats(distribution_str) @@ -306,7 +311,13 @@ def create_dataset( """ _versionId = str(version_id).strip("/") - _, account_name, group_name, artifact_name, version = _versionId.rsplit("/", 4) + parts = _versionId.rsplit("/", 4) + if len(parts) < 5: + raise BadArgumentException( + f"Invalid version_id format: '{version_id}'. " + f"Expected format: ////" + ) + _, _account_name, _group_name, _artifact_name, version = parts # could be build from stuff above, # was not sure if there are edge cases BASE=http://databus.example.org/"base"/... @@ -428,22 +439,30 @@ def deploy( headers = {"X-API-KEY": f"{api_key}", "Content-Type": "application/json"} data = json.dumps(dataid) - base = "/".join(dataid["@graph"][0]["@id"].split("/")[0:3]) + + try: + base = "/".join(dataid["@graph"][0]["@id"].split("/")[0:3]) + except (KeyError, IndexError, TypeError) as e: + raise DeployError(f"Invalid dataid structure: {e}") + api_uri = ( base + f"/api/publish?verify-parts={str(verify_parts).lower()}&log-level={log_level.name}" ) - resp = requests.post(api_uri, data=data, headers=headers) + resp = requests.post(api_uri, data=data, headers=headers, timeout=30) - if debug or __debug: - dataset_uri = dataid["@graph"][0]["@id"] + if debug or _debug: + try: + dataset_uri = dataid["@graph"][0]["@id"] + except (KeyError, IndexError, TypeError) as e: + raise DeployError(f"Invalid dataid structure: {e}") print(f"Trying submitting data to {dataset_uri}:") print(data) if resp.status_code != 200: raise DeployError(f"Could not deploy dataset to databus. Reason: '{resp.text}'") - if debug or __debug: + if debug or _debug: print("---------") print(resp.text) diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 5f5877a..190fada 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -6,7 +6,10 @@ from SPARQLWrapper import JSON, SPARQLWrapper from tqdm import tqdm -from databusclient.api.utils import fetch_databus_jsonld, get_databus_id_parts_from_uri +from databusclient.api.utils import ( + fetch_databus_jsonld, + get_databus_id_parts_from_file_url, +) def _download_file( @@ -32,8 +35,8 @@ def _download_file( 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized), then fetch Vault access token and retry with Authorization header. """ if localDir is None: - _host, account, group, artifact, version, file = get_databus_id_parts_from_uri( - url + _host, account, group, artifact, version, file = ( + get_databus_id_parts_from_file_url(url) ) localDir = os.path.join( os.getcwd(), @@ -51,7 +54,7 @@ def _download_file( if dirpath: os.makedirs(dirpath, exist_ok=True) # Create the necessary directories # --- 1. Get redirect URL by requesting HEAD --- - response = requests.head(url, stream=True) + response = requests.head(url, stream=True, timeout=30) # Check for redirect and update URL if necessary if response.headers.get("Location") and response.status_code in [ 301, @@ -111,9 +114,12 @@ def _download_file( file.write(data) progress_bar.close() - # TODO: could be a problem of github raw / openflaas - # if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - # raise IOError("Downloaded size does not match Content-Length header") + # TODO: keep check or remove? + if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: + localsize = os.path.getsize(filename) + print(f"\nHeaders: {response.headers}") + print(f"\n[WARNING]: Downloaded size {progress_bar.n} does not match Content-Length header {total_size_in_bytes} ( local file size: {localsize})") + # raise IOError("Downloaded size does not match Content-Length header") def _download_files( @@ -161,7 +167,9 @@ def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> if databus_key is not None: headers["X-API-KEY"] = databus_key - return requests.get(uri, headers=headers, timeout=30).text + response = requests.get(uri, headers=headers, timeout=30) + response.raise_for_status() + return response.text def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: @@ -247,6 +255,7 @@ def __get_vault_access__( "grant_type": "refresh_token", "refresh_token": refresh_token, }, + timeout=30, ) resp.raise_for_status() access_token = resp.json()["access_token"] @@ -270,6 +279,7 @@ def __get_vault_access__( "subject_token": access_token, "audience": audience, }, + timeout=30, ) resp.raise_for_status() vault_token = resp.json()["access_token"] @@ -400,12 +410,20 @@ def _get_databus_versions_of_artifact( json_dict = json.loads(json_str) versions = json_dict.get("databus:hasVersion") - # Single version case {} + if versions is None: + raise ValueError("No 'databus:hasVersion' field in artifact JSON-LD") + if isinstance(versions, dict): versions = [versions] - # Multiple versions case [{}, {}] + elif not isinstance(versions, list): + raise ValueError( + f"Unexpected type for 'databus:hasVersion': {type(versions).__name__}" + ) + + version_urls = [ + v["@id"] for v in versions if isinstance(v, dict) and "@id" in v + ] - version_urls = [v["@id"] for v in versions if "@id" in v] if not version_urls: raise ValueError("No versions found in artifact JSON-LD") @@ -428,13 +446,16 @@ def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: List of all file download URLs in the artifact version. """ - databusIdUrl = [] + databusIdUrl: List[str] = [] + json_dict = json.loads(json_str) graph = json_dict.get("@graph", []) for node in graph: if node.get("@type") == "Part": - id = node.get("file") - databusIdUrl.append(id) + file_uri = node.get("file") + if not isinstance(file_uri, str): + continue + databusIdUrl.append(file_uri) return databusIdUrl @@ -481,14 +502,28 @@ def _get_databus_artifacts_of_group(json_str: str) -> List[str]: Returns a list of artifact URLs. """ json_dict = json.loads(json_str) - artifacts = json_dict.get("databus:hasArtifact", []) + artifacts = json_dict.get("databus:hasArtifact") - result = [] - for item in artifacts: + if artifacts is None: + return [] + + if isinstance(artifacts, dict): + artifacts_iter = [artifacts] + elif isinstance(artifacts, list): + artifacts_iter = artifacts + else: + raise ValueError( + f"Unexpected type for 'databus:hasArtifact': {type(artifacts).__name__}" + ) + + result: List[str] = [] + for item in artifacts_iter: + if not isinstance(item, dict): + continue uri = item.get("@id") if not uri: continue - _, _, _, _, version, _ = get_databus_id_parts_from_uri(uri) + _, _, _, _, version, _ = get_databus_id_parts_from_file_url(uri) if version is None: result.append(uri) return result @@ -501,13 +536,13 @@ def download( token=None, databus_key=None, all_versions=None, - auth_url=None, - client_id=None, + auth_url="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", + client_id="vault-token-exchange", ) -> None: """ Download datasets from databus. - Download of files, versions, artifacts, groups or databus collections by ther databus URIs or user-defined SPARQL queries that return file download URLs. + Download of files, versions, artifacts, groups or databus collections via their databus URIs or user-defined SPARQL queries that return file download URLs. Parameters: - localDir: Local directory to download datasets to. If None, the databus folder structure is created in the current working directory. @@ -519,22 +554,25 @@ def download( - client_id: Client ID for token exchange. Default is "vault-token-exchange". """ for databusURI in databusURIs: - host, account, group, artifact, version, file = get_databus_id_parts_from_uri( - databusURI + host, account, group, artifact, version, file = ( + get_databus_id_parts_from_file_url(databusURI) ) + # Determine endpoint per-URI if not explicitly provided + uri_endpoint = endpoint + # dataID or databus collection if databusURI.startswith("http://") or databusURI.startswith("https://"): # Auto-detect sparql endpoint from host if not given - if endpoint is None: - endpoint = f"https://{host}/sparql" - print(f"SPARQL endpoint {endpoint}") + if uri_endpoint is None: + uri_endpoint = f"https://{host}/sparql" + print(f"SPARQL endpoint {uri_endpoint}") if group == "collections" and artifact is not None: print(f"Downloading collection: {databusURI}") _download_collection( databusURI, - endpoint, + uri_endpoint, localDir, token, databus_key, @@ -599,10 +637,10 @@ def download( # query as argument else: print("QUERY {}", databusURI.replace("\n", " ")) - if endpoint is None: # endpoint is required for queries (--databus) + if uri_endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") res = _get_file_download_urls_from_sparql_query( - endpoint, databusURI, databus_key=databus_key + uri_endpoint, databusURI, databus_key=databus_key ) _download_files( res, diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index 0c6f342..7e27ff3 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -3,7 +3,7 @@ import requests -def get_databus_id_parts_from_uri( +def get_databus_id_parts_from_file_url( uri: str, ) -> Tuple[ Optional[str], @@ -17,7 +17,8 @@ def get_databus_id_parts_from_uri( Extract databus ID parts from a given databus URI. Parameters: - - uri: The full databus URI + - uri: The full databus URI of the form + "http(s)://host/accountId/groupId/artifactId/versionId/fileId" Returns: A tuple containing (host, accountId, groupId, artifactId, versionId, fileId). diff --git a/databusclient/cli.py b/databusclient/cli.py index abb0f03..97430f5 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -104,7 +104,7 @@ def deploy( "Please provide files to upload when using WebDAV/Nextcloud mode." ) - # Check that all given paths exist and are files or directories.# + # Check that all given paths exist and are files or directories. invalid = [f for f in distributions if not os.path.exists(f)] if invalid: raise click.UsageError( diff --git a/poetry.lock b/poetry.lock index f772e40..e3759ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -27,8 +27,6 @@ click = ">=8.0.0" mypy-extensions = ">=0.4.3" pathspec = ">=0.9.0" platformdirs = ">=2" -tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""} -typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""} [package.extras] colorama = ["colorama (>=0.4.3)"] @@ -199,25 +197,6 @@ files = [ ] markers = {main = "platform_system == \"Windows\"", dev = "platform_system == \"Windows\" or sys_platform == \"win32\""} -[[package]] -name = "exceptiongroup" -version = "1.3.1" -description = "Backport of PEP 654 (exception groups)" -optional = false -python-versions = ">=3.7" -groups = ["dev"] -markers = "python_version < \"3.11\"" -files = [ - 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{file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"}, - {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"}, -] - [[package]] name = "urllib3" version = "2.6.0" @@ -568,5 +465,5 @@ zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""] [metadata] lock-version = "2.1" -python-versions = "^3.9" -content-hash = "5961c30b6d27c388e50a2a08a598b37160f14e38719937c86faeb7d56ed770ec" +python-versions = "^3.11" +content-hash = "f625db7ea6714ebf87336efecaef03ec2dc4f6f7838c3239432828cd6649ff96" diff --git a/pyproject.toml b/pyproject.toml index 27bfca2..5593c74 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ license = "Apache-2.0 License" readme = "README.md" [tool.poetry.dependencies] -python = "^3.9" +python = "^3.11" click = "^8.0.4" requests = "^2.28.1" tqdm = "^4.42.1" @@ -23,7 +23,7 @@ ruff = "^0.5.5" databusclient = "databusclient.cli:app" [tool.ruff] -target-version = "py39" +target-version = "py311" src = ["databusclient", "tests"] [build-system] diff --git a/tests/test_databusclient.py b/tests/test_deploy.py similarity index 81% rename from tests/test_databusclient.py rename to tests/test_deploy.py index 2a559d4..aada04c 100644 --- a/tests/test_databusclient.py +++ b/tests/test_deploy.py @@ -4,11 +4,41 @@ import pytest -from databusclient.api.deploy import create_dataset, create_distribution, get_file_info +from databusclient.api.deploy import ( + create_dataset, + create_distribution, + get_file_info, + _get_content_variants, + BadArgumentException, +) EXAMPLE_URL = "https://raw.githubusercontent.com/dbpedia/databus/608482875276ef5df00f2360a2f81005e62b58bd/server/app/api/swagger.yml" +def test_get_content_variants(): + # With content variants + cvs = _get_content_variants( + "https://example.com/file.ttl|lang=en_type=parsed|ttl|none|sha256hash|12345" + ) + assert cvs == { + "lang": "en", + "type": "parsed", + } + + # Without content variants + cvs = _get_content_variants( + "https://example.com/file.ttl||ttl|none|sha256hash|12345" + ) + assert cvs == {} + + csv = _get_content_variants("https://example.com/file.ttl") + assert csv == {} + + # Wrong format + with pytest.raises(BadArgumentException): + _ = _get_content_variants("https://example.com/file.ttl|invalidformat") + + @pytest.mark.skip(reason="temporarily disabled since code needs fixing") def test_distribution_cases(): metadata_args_with_filler = OrderedDict() diff --git a/tests/test_download.py b/tests/test_download.py index 56dc6b6..76fe19b 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -2,6 +2,8 @@ from databusclient.api.download import download as api_download +# TODO: overall test structure not great, needs refactoring + DEFAULT_ENDPOINT = "https://databus.dbpedia.org/sparql" TEST_QUERY = """ PREFIX dcat: From a945b27b48f1f6125d82f43c8c81734cfae3b7a0 Mon Sep 17 00:00:00 2001 From: Fabian Hofer <57919013+Integer-Ctrl@users.noreply.github.com> Date: Tue, 9 Dec 2025 14:39:34 +0100 Subject: [PATCH 12/23] init: issue templates --- .../bug---context-of-the-bug--.md | 27 +++++++++++++++++++ .../feature---feature-request-.md | 17 ++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md create mode 100644 .github/ISSUE_TEMPLATE/feature---feature-request-.md diff --git a/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md b/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md new file mode 100644 index 0000000..8a6b062 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md @@ -0,0 +1,27 @@ +--- +name: 'bug: ' +about: Create a report to help us improve +title: '' +labels: bug +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature---feature-request-.md b/.github/ISSUE_TEMPLATE/feature---feature-request-.md new file mode 100644 index 0000000..25fe9a6 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature---feature-request-.md @@ -0,0 +1,17 @@ +--- +name: 'feature: ' +about: Create a report to help us improve +title: '' +labels: enhancement +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Additional context** +Add any other context or screenshots about the feature request here. From 2fc99d14c16f959dcfb3d574e5b9cedbb26b02a6 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Tue, 9 Dec 2025 14:55:51 +0100 Subject: [PATCH 13/23] init: pr template --- .../bug---context-of-the-bug--.md | 27 ----------------- .github/ISSUE_TEMPLATE/bug_issue_template.md | 29 +++++++++++++++++++ .../feature---feature-request-.md | 17 ----------- .../ISSUE_TEMPLATE/feature_issue_template.md | 22 ++++++++++++++ .github/pull_request_template.md | 25 ++++++++++++++++ 5 files changed, 76 insertions(+), 44 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md create mode 100644 .github/ISSUE_TEMPLATE/bug_issue_template.md delete mode 100644 .github/ISSUE_TEMPLATE/feature---feature-request-.md create mode 100644 .github/ISSUE_TEMPLATE/feature_issue_template.md create mode 100644 .github/pull_request_template.md diff --git a/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md b/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md deleted file mode 100644 index 8a6b062..0000000 --- a/.github/ISSUE_TEMPLATE/bug---context-of-the-bug--.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -name: 'bug: ' -about: Create a report to help us improve -title: '' -labels: bug -assignees: '' - ---- - -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error - -**Expected behavior** -A clear and concise description of what you expected to happen. - -**Screenshots** -If applicable, add screenshots to help explain your problem. - -**Additional context** -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/bug_issue_template.md b/.github/ISSUE_TEMPLATE/bug_issue_template.md new file mode 100644 index 0000000..234943c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_issue_template.md @@ -0,0 +1,29 @@ +--- +name: 'Bug Report Template' +about: Report a bug to help us improve +title: 'bug: ' +labels: bug +assignees: '' + +--- + +# Bug Report + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +What you expected to happen. + +**Screenshots (optional)** +Add screenshots if helpful. + +**Additional context (optional)** +Anything else relevant. diff --git a/.github/ISSUE_TEMPLATE/feature---feature-request-.md b/.github/ISSUE_TEMPLATE/feature---feature-request-.md deleted file mode 100644 index 25fe9a6..0000000 --- a/.github/ISSUE_TEMPLATE/feature---feature-request-.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -name: 'feature: ' -about: Create a report to help us improve -title: '' -labels: enhancement -assignees: '' - ---- - -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/ISSUE_TEMPLATE/feature_issue_template.md b/.github/ISSUE_TEMPLATE/feature_issue_template.md new file mode 100644 index 0000000..b1c66f4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_issue_template.md @@ -0,0 +1,22 @@ +--- +name: 'Feature Request' +about: Suggest an idea or enhancement +title: 'feature: ' +labels: enhancement +assignees: '' + +--- + +# Feature Request + +**Describe the feature you'd like** +A short description of the desired feature. + +**Why is this feature important?** +Explain the benefit or use case. Is your feature request related to a problem? + +**Describe alternatives you've considered** +List any alternative solutions or workarounds considered. + +**Additional context** +Add any other details or mockups here. \ No newline at end of file diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..ca76a4a --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,25 @@ +# Pull Request + +## Description + +Briefly describe the changes introduced in this PR. + +**Related Issues** +Link any related issues (e.g., `Issue #12`). + +## Type of change +- [ ] Bug fix (non-breaking change which fixes an issue) +- [ ] New feature (non-breaking change which adds functionality) +- [ ] Breaking change (fix or feature that would cause existing functionality to change) +- [ ] This change requires a documentation update +- [ ] Housekeeping + +## Checklist: +- [ ] My code follows the [ruff code style](http://stellarium.org/doc/head/codingStyle.html) of this project. +- [ ] I have performed a self-review of my own code +- [ ] I have commented my code, particularly in hard-to-understand areas +- [ ] I have made corresponding changes to the documentation (if applicable) +- [ ] I have added tests that prove my fix is effective or that my feature works +- [ ] New and existing unit tests pass locally with my changes + - [ ] `poetry run pytest` - all tests passed + - [ ] `poetry run ruff check` - no linting errors From 8c4cfeb5b3e2397361041621553a03c09b609d0a Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Thu, 11 Dec 2025 12:12:30 +0100 Subject: [PATCH 14/23] fix: wrong encoding caused wrong content lenght --- databusclient/api/download.py | 51 +++++++++++++++++------------------ 1 file changed, 25 insertions(+), 26 deletions(-) diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 190fada..22664ce 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -27,12 +27,9 @@ def _download_file( - url: the URL of the file to download - localDir: Local directory to download file to. If None, the databus folder structure is created in the current working directory. - vault_token_file: Path to Vault refresh token file + - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange - - Steps: - 1. Try direct GET without Authorization header. - 2. If server responds with WWW-Authenticate: Bearer, 401 Unauthorized), then fetch Vault access token and retry with Authorization header. """ if localDir is None: _host, account, group, artifact, version, file = ( @@ -54,7 +51,18 @@ def _download_file( if dirpath: os.makedirs(dirpath, exist_ok=True) # Create the necessary directories # --- 1. Get redirect URL by requesting HEAD --- - response = requests.head(url, stream=True, timeout=30) + headers = {} + # --- 1a. public databus --- + response = requests.head(url, timeout=30) + # --- 1b. Databus API key required --- + if response.status_code == 401: + # print(f"API key required for {url}") + if not databus_key: + raise ValueError("Databus API key not given for protected download") + + headers = {"X-API-KEY": databus_key} + response = requests.head(url, headers=headers, timeout=30) + # Check for redirect and update URL if necessary if response.headers.get("Location") and response.status_code in [ 301, @@ -66,33 +74,26 @@ def _download_file( url = response.headers.get("Location") print("Redirects url: ", url) - # --- 2. Try direct GET --- - response = requests.get(url, stream=True, allow_redirects=True, timeout=30) + # --- 2. Try direct GET to redirected URL --- + headers["Accept-Encoding"] = "identity" # disable gzip to get correct content-length + response = requests.get(url, headers=headers, stream=True, allow_redirects=True, timeout=30) www = response.headers.get( "WWW-Authenticate", "" - ) # get WWW-Authenticate header if present to check for Bearer auth + ) # Check if authentication is required - # Vault token required if 401 Unauthorized with Bearer challenge + # --- 3. If redirected to authentication 401 Unauthorized, get Vault token and retry --- if response.status_code == 401 and "bearer" in www.lower(): print(f"Authentication required for {url}") if not (vault_token_file): raise ValueError("Vault token file not given for protected download") - # --- 3. Fetch Vault token --- + # --- 3a. Fetch Vault token --- # TODO: cache token vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) - headers = {"Authorization": f"Bearer {vault_token}"} + headers["Authorization"] = f"Bearer {vault_token}" + headers.pop("Accept-Encoding") - # --- 4. Retry with token --- - response = requests.get(url, headers=headers, stream=True, timeout=30) - - # Databus API key required if only 401 Unauthorized - elif response.status_code == 401: - print(f"API key required for {url}") - if not databus_key: - raise ValueError("Databus API key not given for protected download") - - headers = {"X-API-KEY": databus_key} + # --- 3b. Retry with token --- response = requests.get(url, headers=headers, stream=True, timeout=30) try: @@ -104,6 +105,7 @@ def _download_file( else: raise e + # --- 4. Download with progress bar --- total_size_in_bytes = int(response.headers.get("content-length", 0)) block_size = 1024 # 1 KiB @@ -114,12 +116,9 @@ def _download_file( file.write(data) progress_bar.close() - # TODO: keep check or remove? + # --- 5. Verify download size --- if total_size_in_bytes != 0 and progress_bar.n != total_size_in_bytes: - localsize = os.path.getsize(filename) - print(f"\nHeaders: {response.headers}") - print(f"\n[WARNING]: Downloaded size {progress_bar.n} does not match Content-Length header {total_size_in_bytes} ( local file size: {localsize})") - # raise IOError("Downloaded size does not match Content-Length header") + raise IOError("Downloaded size does not match Content-Length header") def _download_files( From 8ff62c3555c1ec5c5333a208cdc3f2039bdfeb2c Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Tue, 16 Dec 2025 15:50:05 +0100 Subject: [PATCH 15/23] feat: batch deletions to allow cancellation before execution --- databusclient/api/delete.py | 112 +++++++++++++++++++++++++++++----- databusclient/api/download.py | 16 ++--- 2 files changed, 105 insertions(+), 23 deletions(-) diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index 41bb119..2ea8fb4 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -9,6 +9,39 @@ ) +class DeleteQueue: + """ + A queue to manage multiple Databus resource deletions. + Allows adding multiple databus URIs to a queue and executing their deletion in batch. + """ + + def __init__(self, databus_key: str): + self.databus_key = databus_key + self.queue: set[str] = set() + + def add_uri(self, databusURI: str): + self.queue.add(databusURI) + + def add_uris(self, databusURIs: List[str]): + for uri in databusURIs: + self.queue.add(uri) + + def is_empty(self) -> bool: + return len(self.queue) == 0 + + def is_not_empty(self) -> bool: + return len(self.queue) > 0 + + def execute(self): + for uri in self.queue: + print(f"[DELETE] {uri}") + _delete_resource( + uri, + self.databus_key, + force=True, + ) + + def _confirm_delete(databusURI: str) -> str: """ Confirm deletion of a Databus resource with the user. @@ -44,7 +77,11 @@ def _confirm_delete(databusURI: str) -> str: def _delete_resource( - databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False + databusURI: str, + databus_key: str, + dry_run: bool = False, + force: bool = False, + queue: DeleteQueue = None, ): """ Delete a single Databus resource (version, artifact, group). @@ -57,6 +94,7 @@ def _delete_resource( - databus_key: Databus API key to authenticate the deletion request - dry_run: If True, do not perform the deletion but only print what would be deleted - force: If True, skip confirmation prompt and proceed with deletion + - queue: If queue is provided, add the URI to the queue instead of deleting immediately """ # Confirm the deletion request, skip the request or cancel deletion process @@ -71,12 +109,15 @@ def _delete_resource( if databus_key is None: raise ValueError("Databus API key must be provided for deletion") - headers = {"accept": "*/*", "X-API-KEY": databus_key} - if dry_run: print(f"[DRY RUN] Would delete: {databusURI}") return + if queue is not None: + queue.add_uri(databusURI) + return + + headers = {"accept": "*/*", "X-API-KEY": databus_key} response = requests.delete(databusURI, headers=headers, timeout=30) if response.status_code in (200, 204): @@ -88,7 +129,11 @@ def _delete_resource( def _delete_list( - databusURIs: List[str], databus_key: str, dry_run: bool = False, force: bool = False + databusURIs: List[str], + databus_key: str, + dry_run: bool = False, + force: bool = False, + queue: DeleteQueue = None, ): """ Delete a list of Databus resources. @@ -96,13 +141,22 @@ def _delete_list( Parameters: - databusURIs: List of full databus URIs of the resources to delete - databus_key: Databus API key to authenticate the deletion requests + - dry_run: If True, do not perform the deletion but only print what would be deleted + - force: If True, skip confirmation prompt and proceed with deletion + - queue: If queue is provided, add the URIs to the queue instead of deleting immediately """ for databusURI in databusURIs: - _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_resource( + databusURI, databus_key, dry_run=dry_run, force=force, queue=queue + ) def _delete_artifact( - databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False + databusURI: str, + databus_key: str, + dry_run: bool = False, + force: bool = False, + queue: DeleteQueue = None, ): """ Delete an artifact and all its versions. @@ -114,6 +168,8 @@ def _delete_artifact( - databusURI: The full databus URI of the artifact to delete - databus_key: Databus API key to authenticate the deletion requests - dry_run: If True, do not perform the deletion but only print what would be deleted + - force: If True, skip confirmation prompt and proceed with deletion + - queue: If queue is provided, add the URI to the queue instead of deleting immediately """ artifact_body = fetch_databus_jsonld(databusURI, databus_key) @@ -134,14 +190,20 @@ def _delete_artifact( print(f"No version URIs found in artifact JSON-LD for: {databusURI}") else: # Delete all versions - _delete_list(version_uris, databus_key, dry_run=dry_run, force=force) + _delete_list( + version_uris, databus_key, dry_run=dry_run, force=force, queue=queue + ) # Finally, delete the artifact itself - _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force, queue=queue) def _delete_group( - databusURI: str, databus_key: str, dry_run: bool = False, force: bool = False + databusURI: str, + databus_key: str, + dry_run: bool = False, + force: bool = False, + queue: DeleteQueue = None, ): """ Delete a group and all its artifacts and versions. @@ -153,6 +215,8 @@ def _delete_group( - databusURI: The full databus URI of the group to delete - databus_key: Databus API key to authenticate the deletion requests - dry_run: If True, do not perform the deletion but only print what would be deleted + - force: If True, skip confirmation prompt and proceed with deletion + - queue: If queue is provided, add the URI to the queue instead of deleting immediately """ group_body = fetch_databus_jsonld(databusURI, databus_key) @@ -170,10 +234,12 @@ def _delete_group( # Delete all artifacts (which deletes their versions) for artifact_uri in artifact_uris: - _delete_artifact(artifact_uri, databus_key, dry_run=dry_run, force=force) + _delete_artifact( + artifact_uri, databus_key, dry_run=dry_run, force=force, queue=queue + ) # Finally, delete the group itself - _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force, queue=queue) def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool): @@ -190,6 +256,8 @@ def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool) - force: If True, skip confirmation prompt and proceed with deletion """ + queue = DeleteQueue(databus_key) + for databusURI in databusURIs: _host, _account, group, artifact, version, file = ( get_databus_id_parts_from_file_url(databusURI) @@ -197,18 +265,30 @@ def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool) if group == "collections" and artifact is not None: print(f"Deleting collection: {databusURI}") - _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_resource( + databusURI, databus_key, dry_run=dry_run, force=force, queue=queue + ) elif file is not None: print(f"Deleting file is not supported via API: {databusURI}") - continue # skip file deletions elif version is not None: print(f"Deleting version: {databusURI}") - _delete_resource(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_resource( + databusURI, databus_key, dry_run=dry_run, force=force, queue=queue + ) elif artifact is not None: print(f"Deleting artifact and all its versions: {databusURI}") - _delete_artifact(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_artifact( + databusURI, databus_key, dry_run=dry_run, force=force, queue=queue + ) elif group is not None and group != "collections": print(f"Deleting group and all its artifacts and versions: {databusURI}") - _delete_group(databusURI, databus_key, dry_run=dry_run, force=force) + _delete_group( + databusURI, databus_key, dry_run=dry_run, force=force, queue=queue + ) else: print(f"Deleting {databusURI} is not supported.") + + # Execute queued deletions + if queue.is_not_empty(): + print("\nExecuting queued deletions...") + queue.execute() diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 22664ce..df7c53c 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -75,11 +75,15 @@ def _download_file( print("Redirects url: ", url) # --- 2. Try direct GET to redirected URL --- - headers["Accept-Encoding"] = "identity" # disable gzip to get correct content-length - response = requests.get(url, headers=headers, stream=True, allow_redirects=True, timeout=30) + headers["Accept-Encoding"] = ( + "identity" # disable gzip to get correct content-length + ) + response = requests.get( + url, headers=headers, stream=True, allow_redirects=True, timeout=30 + ) www = response.headers.get( "WWW-Authenticate", "" - ) # Check if authentication is required + ) # Check if authentication is required # --- 3. If redirected to authentication 401 Unauthorized, get Vault token and retry --- if response.status_code == 401 and "bearer" in www.lower(): @@ -419,9 +423,7 @@ def _get_databus_versions_of_artifact( f"Unexpected type for 'databus:hasVersion': {type(versions).__name__}" ) - version_urls = [ - v["@id"] for v in versions if isinstance(v, dict) and "@id" in v - ] + version_urls = [v["@id"] for v in versions if isinstance(v, dict) and "@id" in v] if not version_urls: raise ValueError("No versions found in artifact JSON-LD") @@ -446,7 +448,7 @@ def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: """ databusIdUrl: List[str] = [] - + json_dict = json.loads(json_str) graph = json_dict.get("@graph", []) for node in graph: From 03964ae89ad0ab2c813b379ce174366e8c30863c Mon Sep 17 00:00:00 2001 From: Dhanashree Petare Date: Sun, 21 Dec 2025 21:38:28 +0530 Subject: [PATCH 16/23] Restrict Vault token exchange to specific hosts; improve auth errors; (Issue #19) (#40) * Restrict Vault token exchange to specific hosts; improve auth errors; add tests (fixes #19) * Restrict Vault token exchange to specific hosts; improve auth errors; add tests and docs note (fixes #19) * Fix vault redirect check (#19) --------- Co-authored-by: DhanashreePetare --- .gitignore | 1 + README.md | 2 + databusclient/api/download.py | 99 +++++++++++++++++++++++++------- databusclient/cli.py | 25 ++++---- tests/conftest.py | 30 ++++++++++ tests/test_download.py | 3 + tests/test_download_auth.py | 104 ++++++++++++++++++++++++++++++++++ 7 files changed, 233 insertions(+), 31 deletions(-) create mode 100644 tests/conftest.py create mode 100644 tests/test_download_auth.py diff --git a/.gitignore b/.gitignore index d22cb37..f5362e2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ # project-specific tmp/ +vault-token.dat # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/README.md b/README.md index dc9991f..b485008 100644 --- a/README.md +++ b/README.md @@ -164,6 +164,8 @@ docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOAD - If no `--localdir` is provided, the current working directory is used as base directory. The downloaded files will be stored in the working directory in a folder structure according to the Databus layout, i.e. `./$ACCOUNT/$GROUP/$ARTIFACT/$VERSION/`. - `--vault-token` - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. + + Note: Vault tokens are only required for certain protected Databus hosts (for example: `data.dbpedia.io`, `data.dev.dbpedia.link`). The client now detects those hosts and will fail early with a clear message if a token is required but not provided. Do not pass `--vault-token` for public downloads. - `--databus-key` - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. diff --git a/databusclient/api/download.py b/databusclient/api/download.py index df7c53c..ac55faa 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -1,6 +1,7 @@ import json import os from typing import List +from urllib.parse import urlparse import requests from SPARQLWrapper import JSON, SPARQLWrapper @@ -12,6 +13,18 @@ ) +# Hosts that require Vault token based authentication. Central source of truth. +VAULT_REQUIRED_HOSTS = { + "data.dbpedia.io", + "data.dev.dbpedia.link", +} + + +class DownloadAuthError(Exception): + """Raised when an authorization problem occurs during download.""" + + + def _download_file( url, localDir, @@ -52,16 +65,9 @@ def _download_file( os.makedirs(dirpath, exist_ok=True) # Create the necessary directories # --- 1. Get redirect URL by requesting HEAD --- headers = {} - # --- 1a. public databus --- - response = requests.head(url, timeout=30) - # --- 1b. Databus API key required --- - if response.status_code == 401: - # print(f"API key required for {url}") - if not databus_key: - raise ValueError("Databus API key not given for protected download") - headers = {"X-API-KEY": databus_key} - response = requests.head(url, headers=headers, timeout=30) + # --- 1a. public databus --- + response = requests.head(url, timeout=30, allow_redirects=False) # Check for redirect and update URL if necessary if response.headers.get("Location") and response.status_code in [ @@ -73,6 +79,30 @@ def _download_file( ]: url = response.headers.get("Location") print("Redirects url: ", url) + # Re-do HEAD request on redirect URL + response = requests.head(url, timeout=30) + + # Extract hostname from final URL (after redirect) to check if vault token needed. + # This is the actual download location that may require authentication. + parsed = urlparse(url) + host = parsed.hostname + + # --- 1b. Handle 401 on HEAD request --- + if response.status_code == 401: + # Check if this is a vault-required host + if host in VAULT_REQUIRED_HOSTS: + # Vault-required host: need vault token + if not vault_token_file: + raise DownloadAuthError( + f"Vault token required for host '{host}', but no token was provided. Please use --vault-token." + ) + # Token provided; will handle in GET request below + else: + # Not a vault host; might need databus API key + if not databus_key: + raise DownloadAuthError("Databus API key not given for protected download") + headers = {"X-API-KEY": databus_key} + response = requests.head(url, headers=headers, timeout=30) # --- 2. Try direct GET to redirected URL --- headers["Accept-Encoding"] = ( @@ -81,25 +111,54 @@ def _download_file( response = requests.get( url, headers=headers, stream=True, allow_redirects=True, timeout=30 ) - www = response.headers.get( - "WWW-Authenticate", "" - ) # Check if authentication is required + www = response.headers.get("WWW-Authenticate", "") # Check if authentication is required - # --- 3. If redirected to authentication 401 Unauthorized, get Vault token and retry --- + # --- 3. Handle authentication responses --- + # 3a. Server requests Bearer auth. Only attempt token exchange for hosts + # we explicitly consider Vault-protected (VAULT_REQUIRED_HOSTS). This avoids + # sending tokens to unrelated hosts and makes auth behavior predictable. if response.status_code == 401 and "bearer" in www.lower(): - print(f"Authentication required for {url}") - if not (vault_token_file): - raise ValueError("Vault token file not given for protected download") + # If host is not configured for Vault, do not attempt token exchange. + if host not in VAULT_REQUIRED_HOSTS: + raise DownloadAuthError( + "Server requests Bearer authentication but this host is not configured for Vault token exchange." + " Try providing a databus API key with --databus-key or contact your administrator." + ) + + # Host requires Vault; ensure token file provided. + if not vault_token_file: + raise DownloadAuthError( + f"Vault token required for host '{host}', but no token was provided. Please use --vault-token." + ) - # --- 3a. Fetch Vault token --- - # TODO: cache token + # --- 3b. Fetch Vault token and retry --- + # Token exchange is potentially sensitive and should only be performed + # for known hosts. __get_vault_access__ handles reading the refresh + # token and exchanging it; errors are translated to DownloadAuthError + # for user-friendly CLI output. vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) headers["Authorization"] = f"Bearer {vault_token}" - headers.pop("Accept-Encoding") + headers.pop("Accept-Encoding", None) - # --- 3b. Retry with token --- + # Retry with token response = requests.get(url, headers=headers, stream=True, timeout=30) + # Map common auth failures to friendly messages + if response.status_code == 401: + raise DownloadAuthError("Vault token is invalid or expired. Please generate a new token.") + if response.status_code == 403: + raise DownloadAuthError("Vault token is valid but has insufficient permissions to access this file.") + + # 3c. Generic forbidden without Bearer challenge + if response.status_code == 403: + raise DownloadAuthError("Access forbidden: your token or API key does not have permission to download this file.") + + # 3d. Generic unauthorized without Bearer + if response.status_code == 401: + raise DownloadAuthError( + "Unauthorized: access denied. Check your --databus-key or --vault-token settings." + ) + try: response.raise_for_status() # Raise if still failing except requests.exceptions.HTTPError as e: diff --git a/databusclient/cli.py b/databusclient/cli.py index 97430f5..069408e 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -7,7 +7,7 @@ import databusclient.api.deploy as api_deploy from databusclient.api.delete import delete as api_delete -from databusclient.api.download import download as api_download +from databusclient.api.download import download as api_download, DownloadAuthError from databusclient.extensions import webdav @@ -171,16 +171,19 @@ def download( """ Download datasets from databus, optionally using vault access if vault options are provided. """ - api_download( - localDir=localdir, - endpoint=databus, - databusURIs=databusuris, - token=vault_token, - databus_key=databus_key, - all_versions=all_versions, - auth_url=authurl, - client_id=clientid, - ) + try: + api_download( + localDir=localdir, + endpoint=databus, + databusURIs=databusuris, + token=vault_token, + databus_key=databus_key, + all_versions=all_versions, + auth_url=authurl, + client_id=clientid, + ) + except DownloadAuthError as e: + raise click.ClickException(str(e)) @app.command() diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..5f4c0a2 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,30 @@ +import sys +import types + +# Provide a lightweight fake SPARQLWrapper module for tests when not installed. +if "SPARQLWrapper" not in sys.modules: + mod = types.ModuleType("SPARQLWrapper") + mod.JSON = None + + class DummySPARQL: + def __init__(self, *args, **kwargs): + pass + + def setQuery(self, q): + self._q = q + + def setReturnFormat(self, f): + self._fmt = f + + def setCustomHttpHeaders(self, h): + self._headers = h + + def query(self): + class R: + def convert(self): + return {"results": {"bindings": []}} + + return R() + + mod.SPARQLWrapper = DummySPARQL + sys.modules["SPARQLWrapper"] = mod diff --git a/tests/test_download.py b/tests/test_download.py index 76fe19b..87d49dc 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -1,5 +1,7 @@ """Download Tests""" +import pytest + from databusclient.api.download import download as api_download # TODO: overall test structure not great, needs refactoring @@ -25,5 +27,6 @@ def test_with_query(): api_download("tmp", DEFAULT_ENDPOINT, [TEST_QUERY]) +@pytest.mark.skip(reason="Integration test: requires live databus.dbpedia.org connection") def test_with_collection(): api_download("tmp", DEFAULT_ENDPOINT, [TEST_COLLECTION]) diff --git a/tests/test_download_auth.py b/tests/test_download_auth.py new file mode 100644 index 0000000..7225e08 --- /dev/null +++ b/tests/test_download_auth.py @@ -0,0 +1,104 @@ +from unittest.mock import Mock, patch + +import pytest + +import requests + +import databusclient.api.download as dl + +from databusclient.api.download import VAULT_REQUIRED_HOSTS, DownloadAuthError + + +def make_response(status=200, headers=None, content=b""): + headers = headers or {} + mock = Mock() + mock.status_code = status + mock.headers = headers + mock.content = content + + def iter_content(chunk_size): + if content: + yield content + else: + return + + mock.iter_content = lambda chunk: iter(iter_content(chunk)) + + def raise_for_status(): + if mock.status_code >= 400: + raise requests.exceptions.HTTPError() + + mock.raise_for_status = raise_for_status + return mock + + +def test_vault_host_no_token_raises(): + vault_host = next(iter(VAULT_REQUIRED_HOSTS)) + url = f"https://{vault_host}/some/protected/file.ttl" + + with pytest.raises(DownloadAuthError) as exc: + dl._download_file(url, localDir='.', vault_token_file=None) + + assert "Vault token required" in str(exc.value) + + +def test_non_vault_host_no_token_allows_download(monkeypatch): + url = "https://example.com/public/file.txt" + + resp_head = make_response(status=200, headers={}) + resp_get = make_response(status=200, headers={"content-length": "0"}, content=b"") + + with patch("requests.head", return_value=resp_head), patch( + "requests.get", return_value=resp_get + ): + # should not raise + dl._download_file(url, localDir='.', vault_token_file=None) + + +def test_401_after_token_exchange_reports_invalid_token(monkeypatch): + vault_host = next(iter(VAULT_REQUIRED_HOSTS)) + url = f"https://{vault_host}/protected/file.ttl" + + # initial head and get -> 401 with Bearer + resp_head = make_response(status=200, headers={}) + resp_401 = make_response(status=401, headers={"WWW-Authenticate": "Bearer realm=\"auth\""}) + + # after retry with token -> still 401 + resp_401_retry = make_response(status=401, headers={}) + + # Mock requests.get side effects: first 401 (challenge), then 401 after token + get_side_effects = [resp_401, resp_401_retry] + + # Mock token exchange responses + post_resp_1 = Mock() + post_resp_1.json.return_value = {"access_token": "ACCESS"} + post_resp_2 = Mock() + post_resp_2.json.return_value = {"access_token": "VAULT"} + + with patch("requests.head", return_value=resp_head), patch( + "requests.get", side_effect=get_side_effects + ), patch("requests.post", side_effect=[post_resp_1, post_resp_2]): + # set REFRESH_TOKEN so __get_vault_access__ doesn't try to open a file + monkeypatch.setenv("REFRESH_TOKEN", "x" * 90) + + with pytest.raises(DownloadAuthError) as exc: + dl._download_file(url, localDir='.', vault_token_file="/does/not/matter") + + assert "invalid or expired" in str(exc.value) + + +def test_403_reports_insufficient_permissions(): + vault_host = next(iter(VAULT_REQUIRED_HOSTS)) + url = f"https://{vault_host}/protected/file.ttl" + + resp_head = make_response(status=200, headers={}) + resp_403 = make_response(status=403, headers={}) + + with patch("requests.head", return_value=resp_head), patch( + "requests.get", return_value=resp_403 + ): + # provide a token path so early check does not block + with pytest.raises(DownloadAuthError) as exc: + dl._download_file(url, localDir='.', vault_token_file="/some/token/file") + + assert "permission" in str(exc.value) or "forbidden" in str(exc.value) From b4bbfaaa2f6758d946323087ca759bb53277f1a9 Mon Sep 17 00:00:00 2001 From: Integer-Ctrl Date: Sun, 21 Dec 2025 17:16:22 +0100 Subject: [PATCH 17/23] chore: README download links --- README.md | 28 ++++++++++++++-------------- databusclient/api/delete.py | 13 ++++++------- 2 files changed, 20 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index b485008..e329578 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Command-line and Python client for downloading and deploying datasets on DBpedia - [DBpedia](#dbpedia) - [Registration (Access Token)](#registration-access-token) - [DBpedia Knowledge Graphs](#dbpedia-knowledge-graphs) - - [Download Live Fusion KG Snapshot (BUSL 1.1, registration needed)](#download-live-fusion-kg-snapshot-busl-11-registration-needed) + - [Download Live Fusion KG Dump (BUSL 1.1, registration needed)](#download-live-fusion-kg-dump-busl-11-registration-needed) - [Download Enriched Knowledge Graphs (BUSL 1.1, registration needed)](#download-enriched-knowledge-graphs-busl-11-registration-needed) - [Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikipedia-knowledge-graphs-cc-by-sa-no-registration-needed) - [Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed)](#download-dbpedia-wikidata-knowledge-graphs-cc-by-sa-no-registration-needed) @@ -77,48 +77,48 @@ To download BUSL 1.1 licensed datasets, you need to register and get an access t ### DBpedia Knowledge Graphs -#### Download Live Fusion KG Snapshot (BUSL 1.1, registration needed) -High-frequency, conflict-resolved knowledge graph that merges Live Wikipedia and Wikidata signals into a single, queryable snapshot for enterprise consumption. [More information](https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump) +#### Download Live Fusion KG Dump (BUSL 1.1, registration needed) +High-frequency, conflict-resolved knowledge graph that merges Live Wikipedia and Wikidata signals into a single, queryable dump for enterprise consumption. [More information](https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump) ```bash # Python -databusclient download https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump --vault-token vault-token.dat +databusclient download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/live-fusion-kg-dump --vault-token vault-token.dat +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/live-fusion-kg-dump --vault-token vault-token.dat ``` #### Download Enriched Knowledge Graphs (BUSL 1.1, registration needed) **DBpedia Wikipedia Extraction Enriched** -DBpedia-based enrichment of structured Wikipedia extractions (currently EN DBpedia only). [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump) +DBpedia-based enrichment of structured Wikipedia extractions (currently EN DBpedia only). [More information](https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump) ```bash # Python -databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +databusclient download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia-enterprise/dbpedia-wikipedia-kg-enriched-dump --vault-token vault-token.dat ``` #### Download DBpedia Wikipedia Knowledge Graphs (CC-BY-SA, no registration needed) -Original extraction of structured Wikipedia data before enrichment. [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump) +Original extraction of structured Wikipedia data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump) ```bash # Python -databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump +databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikipedia-kg-dump +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikipedia-kg-dump ``` #### Download DBpedia Wikidata Knowledge Graphs (CC-BY-SA, no registration needed) -Original extraction of structured Wikidata data before enrichment. [More information](https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump) +Original extraction of structured Wikidata data before enrichment. [More information](https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump) ```bash # Python -databusclient download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump +databusclient download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump # Docker -docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dev.dbpedia.link/fhofer/dbpedia-wikidata-kg-dump +docker run --rm -v $(pwd):/data dbpedia/databus-python-client download https://databus.dbpedia.org/dbpedia/dbpedia-wikidata-kg-dump ``` ## CLI Usage diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index 2ea8fb4..7107983 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -33,13 +33,11 @@ def is_not_empty(self) -> bool: return len(self.queue) > 0 def execute(self): - for uri in self.queue: - print(f"[DELETE] {uri}") - _delete_resource( - uri, - self.databus_key, - force=True, - ) + _delete_list( + list(self.queue), + self.databus_key, + force=True, + ) def _confirm_delete(databusURI: str) -> str: @@ -117,6 +115,7 @@ def _delete_resource( queue.add_uri(databusURI) return + print(f"[DELETE] {databusURI}") headers = {"accept": "*/*", "X-API-KEY": databus_key} response = requests.delete(databusURI, headers=headers, timeout=30) From f8aa6638b66c8d1e798b9864dc3b43cf171bd477 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Fri, 26 Dec 2025 20:26:00 +0530 Subject: [PATCH 18/23] Use api_deploy.create_distribution to avoid circular import --- databusclient/cli.py | 47 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/databusclient/cli.py b/databusclient/cli.py index 069408e..b5145bf 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -4,6 +4,7 @@ from typing import List import click +import re import databusclient.api.deploy as api_deploy from databusclient.api.delete import delete as api_delete @@ -213,5 +214,51 @@ def delete(databusuris: List[str], databus_key: str, dry_run: bool, force: bool) ) +@app.command() +@click.argument("url") +@click.option("--cv", "cvs", multiple=True, help="Content variant like key=value (repeatable). Keys must not contain '|' or '_'") +@click.option("--format", "file_format", help="Format extension (e.g. ttl)") +@click.option("--compression", help="Compression (e.g. gzip)") +@click.option("--sha-length", help="sha256:length (64 hex chars followed by ':' and integer length)") +@click.option("--json-output", is_flag=True, help="Output JSON distribution object instead of plain string") +def mkdist(url, cvs, file_format, compression, sha_length, json_output): + """Create a distribution string from components.""" + # Validate CVs + cvs_dict = {} + for cv in cvs: + if "=" not in cv: + raise click.BadParameter(f"Invalid content variant '{cv}': expected key=value") + key, val = cv.split("=", 1) + if any(ch in key for ch in ("|", "_")): + raise click.BadParameter("Invalid characters in content-variant key (forbidden: '|' and '_')") + if key in cvs_dict: + raise click.BadParameter(f"Duplicate content-variant key '{key}'") + cvs_dict[key] = val + + # Validate sha-length + sha_tuple = None + if sha_length: + if not re.match(r'^[A-Fa-f0-9]{64}:\d+$', sha_length): + raise click.BadParameter("Invalid --sha-length; expected SHA256HEX:length") + sha, length = sha_length.split(":", 1) + sha_tuple = (sha, int(length)) + + # Deterministic ordering + sorted_cvs = {k: cvs_dict[k] for k in sorted(cvs_dict)} + + dist = api_deploy.create_distribution(url=url, cvs=sorted_cvs, file_format=file_format, compression=compression, sha256_length_tuple=sha_tuple) + if json_output: + import json as _json + click.echo(_json.dumps({"distribution": dist})) + else: + click.echo(dist) + + +@app.command() +@click.argument("shell", type=click.Choice(["bash","zsh","fish","powershell"]), required=False) +def completion(shell="bash"): + click.echo(f"Run: eval \"$(_DATABUSCLIENT_COMPLETE=source_{shell} python -m databusclient)\"") + + if __name__ == "__main__": app() From 0437e1a9fb9988976d93b7a8d81213c9926831cf Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Sun, 4 Jan 2026 23:00:12 +0530 Subject: [PATCH 19/23] Add verbose CLI flag with redacted HTTP logging --- databusclient/api/download.py | 47 ++++++++++++++++++++++++++++++++--- databusclient/api/utils.py | 42 +++++++++++++++++++++++++++++++ databusclient/cli.py | 10 ++++++-- tests/test_download_auth.py | 30 ++++++++++++++++++++++ 4 files changed, 123 insertions(+), 6 deletions(-) diff --git a/databusclient/api/download.py b/databusclient/api/download.py index ac55faa..ca573b0 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -32,6 +32,7 @@ def _download_file( databus_key=None, auth_url=None, client_id=None, + verbose=False, ) -> None: """ Download a file from the internet with a progress bar using tqdm. @@ -43,6 +44,7 @@ def _download_file( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ if localDir is None: _host, account, group, artifact, version, file = ( @@ -67,7 +69,15 @@ def _download_file( headers = {} # --- 1a. public databus --- + if verbose: + from databusclient.api.utils import log_http + + log_http("HEAD", url, req_headers=headers) response = requests.head(url, timeout=30, allow_redirects=False) + if verbose: + from databusclient.api.utils import log_http + + log_http("HEAD", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) # Check for redirect and update URL if necessary if response.headers.get("Location") and response.status_code in [ @@ -108,9 +118,17 @@ def _download_file( headers["Accept-Encoding"] = ( "identity" # disable gzip to get correct content-length ) + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", url, req_headers=headers) response = requests.get( url, headers=headers, stream=True, allow_redirects=True, timeout=30 ) + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) www = response.headers.get("WWW-Authenticate", "") # Check if authentication is required # --- 3. Handle authentication responses --- @@ -136,12 +154,20 @@ def _download_file( # for known hosts. __get_vault_access__ handles reading the refresh # token and exchanging it; errors are translated to DownloadAuthError # for user-friendly CLI output. - vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) + vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id, verbose=verbose) headers["Authorization"] = f"Bearer {vault_token}" headers.pop("Accept-Encoding", None) # Retry with token + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", url, req_headers=headers) response = requests.get(url, headers=headers, stream=True, timeout=30) + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) # Map common auth failures to friendly messages if response.status_code == 401: @@ -191,6 +217,7 @@ def _download_files( databus_key: str = None, auth_url: str = None, client_id: str = None, + verbose: bool = False, ) -> None: """ Download multiple files from the databus. @@ -202,6 +229,7 @@ def _download_files( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ for url in urls: _download_file( @@ -211,6 +239,7 @@ def _download_files( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) @@ -294,7 +323,7 @@ def _get_file_download_urls_from_sparql_query( def __get_vault_access__( - download_url: str, token_file: str, auth_url: str, client_id: str + download_url: str, token_file: str, auth_url: str, client_id: str, verbose: bool = False ) -> str: """ Get Vault access token for a protected databus download. @@ -320,6 +349,10 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() + if verbose: + from databusclient.api.utils import log_http + + log_http("POST", auth_url, req_headers={"client_id": client_id}, status=resp.status_code, resp_headers=resp.headers) access_token = resp.json()["access_token"] # 3. Extract host as audience @@ -344,6 +377,10 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() + if verbose: + from databusclient.api.utils import log_http + + log_http("POST", auth_url, req_headers={"client_id": client_id, "audience": audience}, status=resp.status_code, resp_headers=resp.headers) vault_token = resp.json()["access_token"] print(f"Using Vault access token for {download_url}") @@ -598,6 +635,7 @@ def download( all_versions=None, auth_url="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", client_id="vault-token-exchange", + verbose: bool = False, ) -> None: """ Download datasets from databus. @@ -612,6 +650,7 @@ def download( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL. Default is "https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token". - client_id: Client ID for token exchange. Default is "vault-token-exchange". + - verbose: when True, print redacted HTTP request/response details """ for databusURI in databusURIs: host, account, group, artifact, version, file = ( @@ -647,8 +686,7 @@ def download( vault_token_file=token, databus_key=databus_key, auth_url=auth_url, - client_id=client_id, - ) + client_id=client_id, verbose=verbose, ) elif version is not None: print(f"Downloading version: {databusURI}") _download_version( @@ -709,4 +747,5 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index 7e27ff3..0a6ba74 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -48,3 +48,45 @@ def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: response.raise_for_status() return response.text + + +def _redact_headers(headers): + if not headers: + return headers + redacted = {} + for k, v in headers.items(): + key = k.lower() + if key == "authorization" or key.startswith("x-api-key"): + redacted[k] = "REDACTED" + else: + redacted[k] = v + return redacted + + +def log_http(method, url, req_headers=None, status=None, resp_headers=None, body_snippet=None): + print(f"[HTTP] {method} {url}") + if req_headers: + print(" Req headers:", _redact_headers(req_headers)) + if status is not None: + print(" Status:", status) + if resp_headers: + # try to convert to dict; handle Mock or response objects gracefully + try: + resp_dict = dict(resp_headers) + except Exception: + # resp_headers might be a Mock or requests.Response; try common attributes + if hasattr(resp_headers, "items"): + try: + resp_dict = dict(resp_headers.items()) + except Exception: + resp_dict = {"headers": str(resp_headers)} + elif hasattr(resp_headers, "headers"): + try: + resp_dict = dict(getattr(resp_headers, "headers") or {}) + except Exception: + resp_dict = {"headers": str(resp_headers)} + else: + resp_dict = {"headers": str(resp_headers)} + print(" Resp headers:", _redact_headers(resp_dict)) + if body_snippet: + print(" Body preview:", body_snippet[:500]) diff --git a/databusclient/cli.py b/databusclient/cli.py index b5145bf..7bdb366 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -13,9 +13,12 @@ @click.group() -def app(): +@click.option("-v", "--verbose", is_flag=True, help="Enable verbose HTTP request/response output") +@click.pass_context +def app(ctx, verbose): """Databus Client CLI""" - pass + ctx.ensure_object(dict) + ctx.obj["verbose"] = verbose @app.command() @@ -159,7 +162,9 @@ def deploy( show_default=True, help="Client ID for token exchange", ) +@click.pass_context def download( + ctx, databusuris: List[str], localdir, databus, @@ -182,6 +187,7 @@ def download( all_versions=all_versions, auth_url=authurl, client_id=clientid, + verbose=ctx.obj.get("verbose", False), ) except DownloadAuthError as e: raise click.ClickException(str(e)) diff --git a/tests/test_download_auth.py b/tests/test_download_auth.py index 7225e08..46bec79 100644 --- a/tests/test_download_auth.py +++ b/tests/test_download_auth.py @@ -102,3 +102,33 @@ def test_403_reports_insufficient_permissions(): dl._download_file(url, localDir='.', vault_token_file="/some/token/file") assert "permission" in str(exc.value) or "forbidden" in str(exc.value) + + +def test_verbose_redacts_authorization(monkeypatch, capsys): + vault_host = next(iter(VAULT_REQUIRED_HOSTS)) + url = f"https://{vault_host}/protected/file.ttl" + + resp_head = make_response(status=200, headers={}) + resp_401 = make_response(status=401, headers={"WWW-Authenticate": "Bearer realm=\"auth\""}) + resp_200 = make_response(status=200, headers={"content-length": "0"}, content=b"") + + get_side_effects = [resp_401, resp_200] + + post_resp_1 = Mock() + post_resp_1.json.return_value = {"access_token": "ACCESS"} + post_resp_2 = Mock() + post_resp_2.json.return_value = {"access_token": "VAULT"} + + with patch("requests.head", return_value=resp_head), patch( + "requests.get", side_effect=get_side_effects + ), patch("requests.post", side_effect=[post_resp_1, post_resp_2]): + monkeypatch.setenv("REFRESH_TOKEN", "x" * 90) + + # run download with verbose enabled + dl._download_file(url, localDir='.', vault_token_file="/does/not/matter", verbose=True) + captured = capsys.readouterr() + assert "[HTTP] HEAD" in captured.out or "[HTTP] GET" in captured.out + assert "REDACTED" in captured.out + # Ensure token values are not directly printed + assert "ACCESS" not in captured.out + assert "VAULT" not in captured.out From 5b4badd7f2999a606c8c49798371af756bc45637 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Tue, 6 Jan 2026 23:04:58 +0530 Subject: [PATCH 20/23] Add verbose (-v) flag using logging; redact Authorization and X-API-KEY headers; propagate verbose through download flows; add tests and docs --- CHANGELOG.md | 7 +++ PR_BODY.md | 19 ++++++++ README.md | 2 + databusclient/api/download.py | 90 ++++++++++++++++++++++++++--------- databusclient/api/utils.py | 23 ++++++--- databusclient/cli.py | 11 +++++ file.txt | 0 tests/test_cli_verbose.py | 38 +++++++++++++++ tests/test_download_auth.py | 13 ++--- tests/test_utils_verbose.py | 76 +++++++++++++++++++++++++++++ 10 files changed, 245 insertions(+), 34 deletions(-) create mode 100644 CHANGELOG.md create mode 100644 PR_BODY.md create mode 100644 file.txt create mode 100644 tests/test_cli_verbose.py create mode 100644 tests/test_utils_verbose.py diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..138ec26 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,7 @@ +# Changelog + +## 0.14.1 - 2026-01-01 + +- Add `-v/--verbose` global CLI option to enable redacted HTTP request/response logging for debugging. (CLI: `databusclient -v ...`) +- Ensure `Authorization` and `X-API-KEY` headers are redacted in verbose output. +- Add unit tests and README documentation for verbose mode. diff --git a/PR_BODY.md b/PR_BODY.md new file mode 100644 index 0000000..02b5221 --- /dev/null +++ b/PR_BODY.md @@ -0,0 +1,19 @@ +Title: Add verbose CLI flag (-v) with redacted HTTP logging + +Short description: +- Add a global `-v/--verbose` CLI flag to enable redacted HTTP request/response logging to help debug interactions with the Databus and Vault. + +What changed: +- Add global `-v/--verbose` option to `databusclient` CLI and propagate it to API calls. +- Implement redacted HTTP logging helper (redacts `Authorization` and `X-API-KEY` headers). +- Instrument `download` and Vault token exchange flows to print HTTP request/response details when `-v` is enabled. +- Add unit tests ensuring verbose logs are printed and sensitive tokens are redacted. +- Update `README.md` and add a `CHANGELOG.md` entry. + +Why: +- Provides safe, actionable debugging output for issues involving HTTP communication and auth problems without exposing secrets. + +Security note: +- Authorization and API-key headers are redacted in verbose output. Avoid enabling verbose output in public CI logs. + +Closes #27 diff --git a/README.md b/README.md index e329578..4493f70 100644 --- a/README.md +++ b/README.md @@ -166,6 +166,8 @@ docker run --rm -v $(pwd):/data dbpedia/databus-python-client download $DOWNLOAD - If the dataset/files to be downloaded require vault authentication, you need to provide a vault token with `--vault-token /path/to/vault-token.dat`. See [Registration (Access Token)](#registration-access-token) for details on how to get a vault token. Note: Vault tokens are only required for certain protected Databus hosts (for example: `data.dbpedia.io`, `data.dev.dbpedia.link`). The client now detects those hosts and will fail early with a clear message if a token is required but not provided. Do not pass `--vault-token` for public downloads. +- `-v, --verbose` + - Enable verbose HTTP request/response output for debugging. Headers that may contain secrets (for example `Authorization` and `X-API-KEY`) are redacted in the output. Use with caution and avoid enabling in public CI logs. - `--databus-key` - If the databus is protected and needs API key authentication, you can provide the API key with `--databus-key YOUR_API_KEY`. diff --git a/databusclient/api/download.py b/databusclient/api/download.py index ca573b0..373e5f9 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -6,6 +6,9 @@ import requests from SPARQLWrapper import JSON, SPARQLWrapper from tqdm import tqdm +import logging + +logger = logging.getLogger("databusclient") from databusclient.api.utils import ( fetch_databus_jsonld, @@ -69,12 +72,12 @@ def _download_file( headers = {} # --- 1a. public databus --- - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("HEAD", url, req_headers=headers) response = requests.head(url, timeout=30, allow_redirects=False) - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("HEAD", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) @@ -118,14 +121,14 @@ def _download_file( headers["Accept-Encoding"] = ( "identity" # disable gzip to get correct content-length ) - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("GET", url, req_headers=headers) response = requests.get( url, headers=headers, stream=True, allow_redirects=True, timeout=30 ) - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) @@ -159,12 +162,12 @@ def _download_file( headers.pop("Accept-Encoding", None) # Retry with token - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("GET", url, req_headers=headers) response = requests.get(url, headers=headers, stream=True, timeout=30) - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) @@ -243,13 +246,14 @@ def _download_files( ) -def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> str: +def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None, verbose: bool = False) -> str: """ Get SPARQL query of collection members from databus collection URI. Parameters: - uri: The full databus collection URI - databus_key: Optional Databus API key for authentication on protected resources + - verbose: when True, print redacted HTTP request/response details Returns: SPARQL query string to get download URLs of all files in the collection. @@ -257,13 +261,22 @@ def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> headers = {"Accept": "text/sparql"} if databus_key is not None: headers["X-API-KEY"] = databus_key + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", uri, req_headers=headers) response = requests.get(uri, headers=headers, timeout=30) + if verbose: + from databusclient.api.utils import log_http + + log_http("GET", uri, req_headers=headers, status=response.status_code, resp_headers=response.headers) + response.raise_for_status() return response.text -def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: +def _query_sparql_endpoint(endpoint_url, query, databus_key=None, verbose: bool = False) -> dict: """ Query a SPARQL endpoint and return results in JSON format. @@ -271,10 +284,17 @@ def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: - endpoint_url: the URL of the SPARQL endpoint - query: the SPARQL query string - databus_key: Optional API key for authentication + - verbose: when True, print redacted HTTP request/response details Returns: - Dictionary containing the query results """ + if verbose: + from databusclient.api.utils import log_http + + headers = {"X-API-KEY": databus_key} if databus_key is not None else None + log_http("POST", endpoint_url, req_headers=headers) + sparql = SPARQLWrapper(endpoint_url) sparql.method = "POST" sparql.setQuery(query) @@ -282,11 +302,17 @@ def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: if databus_key is not None: sparql.setCustomHttpHeaders({"X-API-KEY": databus_key}) results = sparql.query().convert() + + if verbose: + from databusclient.api.utils import log_http + + log_http("POST", endpoint_url, req_headers={"X-API-KEY": databus_key} if databus_key is not None else None, status=200) + return results def _get_file_download_urls_from_sparql_query( - endpoint_url, query, databus_key=None + endpoint_url, query, databus_key=None, verbose: bool = False ) -> List[str]: """ Execute a SPARQL query to get databus file download URLs. @@ -295,11 +321,12 @@ def _get_file_download_urls_from_sparql_query( - endpoint_url: the URL of the SPARQL endpoint - query: the SPARQL query string - databus_key: Optional API key for authentication + - verbose: when True, print redacted HTTP request/response details Returns: - List of file download URLs """ - result_dict = _query_sparql_endpoint(endpoint_url, query, databus_key=databus_key) + result_dict = _query_sparql_endpoint(endpoint_url, query, databus_key=databus_key, verbose=verbose) bindings = result_dict.get("results", {}).get("bindings") if not isinstance(bindings, list): @@ -336,7 +363,8 @@ def __get_vault_access__( with open(token_file, "r") as f: refresh_token = f.read().strip() if len(refresh_token) < 80: - print(f"Warning: token from {token_file} is short (<80 chars)") + logger.warning("Token from %s is short (<80 chars)", token_file) + # 2. Refresh token -> access token resp = requests.post( @@ -349,7 +377,7 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("POST", auth_url, req_headers={"client_id": client_id}, status=resp.status_code, resp_headers=resp.headers) @@ -377,13 +405,13 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() - if verbose: + if verbose or logger.isEnabledFor(logging.DEBUG): from databusclient.api.utils import log_http log_http("POST", auth_url, req_headers={"client_id": client_id, "audience": audience}, status=resp.status_code, resp_headers=resp.headers) vault_token = resp.json()["access_token"] - print(f"Using Vault access token for {download_url}") + logger.debug("Using Vault access token for %s", download_url) return vault_token @@ -395,6 +423,7 @@ def _download_collection( databus_key: str = None, auth_url: str = None, client_id: str = None, + verbose: bool = False, ) -> None: """ Download all files in a databus collection. @@ -407,10 +436,11 @@ def _download_collection( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ - query = _get_sparql_query_of_collection(uri, databus_key=databus_key) + query = _get_sparql_query_of_collection(uri, databus_key=databus_key, verbose=verbose) file_urls = _get_file_download_urls_from_sparql_query( - endpoint, query, databus_key=databus_key + endpoint, query, databus_key=databus_key, verbose=verbose ) _download_files( list(file_urls), @@ -419,6 +449,7 @@ def _download_collection( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) @@ -429,6 +460,7 @@ def _download_version( databus_key: str = None, auth_url: str = None, client_id: str = None, + verbose: bool = False, ) -> None: """ Download all files in a databus artifact version. @@ -440,8 +472,9 @@ def _download_version( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) _download_files( file_urls, @@ -450,6 +483,7 @@ def _download_version( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) @@ -461,6 +495,7 @@ def _download_artifact( databus_key: str = None, auth_url: str = None, client_id: str = None, + verbose: bool = False, ) -> None: """ Download files in a databus artifact. @@ -473,14 +508,15 @@ def _download_artifact( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) versions = _get_databus_versions_of_artifact(json_str, all_versions=all_versions) if isinstance(versions, str): versions = [versions] for version_uri in versions: print(f"Downloading version: {version_uri}") - json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key) + json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key, verbose=verbose) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) _download_files( file_urls, @@ -489,6 +525,7 @@ def _download_artifact( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) @@ -564,6 +601,7 @@ def _download_group( databus_key: str = None, auth_url: str = None, client_id: str = None, + verbose: bool = False, ) -> None: """ Download files in a databus group. @@ -576,8 +614,9 @@ def _download_group( - databus_key: Databus API key for protected downloads - auth_url: Keycloak token endpoint URL - client_id: Client ID for token exchange + - verbose: when True, print redacted HTTP request/response details """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) artifacts = _get_databus_artifacts_of_group(json_str) for artifact_uri in artifacts: print(f"Download artifact: {artifact_uri}") @@ -589,6 +628,7 @@ def _download_group( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) @@ -677,6 +717,7 @@ def download( databus_key, auth_url, client_id, + verbose=verbose, ) elif file is not None: print(f"Downloading file: {databusURI}") @@ -686,7 +727,9 @@ def download( vault_token_file=token, databus_key=databus_key, auth_url=auth_url, - client_id=client_id, verbose=verbose, ) + client_id=client_id, + verbose=verbose, + ) elif version is not None: print(f"Downloading version: {databusURI}") _download_version( @@ -696,6 +739,7 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) elif artifact is not None: print( @@ -709,6 +753,7 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) elif group is not None and group != "collections": print( @@ -722,6 +767,7 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, + verbose=verbose, ) elif account is not None: print("accountId not supported yet") # TODO @@ -738,7 +784,7 @@ def download( if uri_endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") res = _get_file_download_urls_from_sparql_query( - uri_endpoint, databusURI, databus_key=databus_key + uri_endpoint, databusURI, databus_key=databus_key, verbose=verbose ) _download_files( res, diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index 0a6ba74..e07f4c0 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -30,13 +30,14 @@ def get_databus_id_parts_from_file_url( return tuple(parts[:6]) # return only the first 6 parts -def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: +def fetch_databus_jsonld(uri: str, databus_key: str | None = None, verbose: bool = False) -> str: """ Retrieve JSON-LD representation of a databus resource. Parameters: - uri: The full databus URI - databus_key: Optional Databus API key for authentication on protected resources + - verbose: when True, print redacted HTTP request/response details Returns: JSON-LD string representation of the databus resource. @@ -44,7 +45,11 @@ def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: headers = {"Accept": "application/ld+json"} if databus_key is not None: headers["X-API-KEY"] = databus_key + if verbose: + log_http("GET", uri, req_headers=headers) response = requests.get(uri, headers=headers, timeout=30) + if verbose: + log_http("GET", uri, req_headers=headers, status=response.status_code, resp_headers=response.headers) response.raise_for_status() return response.text @@ -63,12 +68,17 @@ def _redact_headers(headers): return redacted +import logging + + def log_http(method, url, req_headers=None, status=None, resp_headers=None, body_snippet=None): - print(f"[HTTP] {method} {url}") + """Log HTTP request/response details at DEBUG level with sanitized headers.""" + logger = logging.getLogger("databusclient") + msg_lines = [f"[HTTP] {method} {url}"] if req_headers: - print(" Req headers:", _redact_headers(req_headers)) + msg_lines.append(f" Req headers: {_redact_headers(req_headers)}") if status is not None: - print(" Status:", status) + msg_lines.append(f" Status: {status}") if resp_headers: # try to convert to dict; handle Mock or response objects gracefully try: @@ -87,6 +97,7 @@ def log_http(method, url, req_headers=None, status=None, resp_headers=None, body resp_dict = {"headers": str(resp_headers)} else: resp_dict = {"headers": str(resp_headers)} - print(" Resp headers:", _redact_headers(resp_dict)) + msg_lines.append(f" Resp headers: {_redact_headers(resp_dict)}") if body_snippet: - print(" Body preview:", body_snippet[:500]) + msg_lines.append(" Body preview: " + body_snippet[:500]) + logger.debug("\n".join(msg_lines)) diff --git a/databusclient/cli.py b/databusclient/cli.py index 7bdb366..7beb59a 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -17,9 +17,20 @@ @click.pass_context def app(ctx, verbose): """Databus Client CLI""" + import logging + ctx.ensure_object(dict) ctx.obj["verbose"] = verbose + # Configure databusclient logger when verbose flag is used + logger = logging.getLogger("databusclient") + if verbose: + handler = logging.StreamHandler() + handler.setFormatter(logging.Formatter("%(message)s")) + if not logger.hasHandlers(): + logger.addHandler(handler) + logger.setLevel(logging.DEBUG) + @app.command() @click.option( diff --git a/file.txt b/file.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_cli_verbose.py b/tests/test_cli_verbose.py new file mode 100644 index 0000000..c5bba14 --- /dev/null +++ b/tests/test_cli_verbose.py @@ -0,0 +1,38 @@ +from click.testing import CliRunner +from unittest.mock import Mock, patch + +import databusclient.cli as cli + + +# CLI-level integration test for -v flag +def test_cli_download_verbose_logs_redacted(caplog): + caplog.set_level("DEBUG", logger="databusclient") + runner = CliRunner() + + # Prepare mocked HTTP responses + resp_head_401 = Mock() + resp_head_401.status_code = 401 + resp_head_401.headers = {} + + resp_head_200 = Mock() + resp_head_200.status_code = 200 + resp_head_200.headers = {} + + resp_get = Mock() + resp_get.status_code = 200 + resp_get.headers = {"content-length": "0"} + resp_get.iter_content = lambda chunk: iter([]) + + # Initial HEAD returns 401 so client uses --databus-key header on retry + with patch("requests.head", side_effect=[resp_head_401, resp_head_200]), patch( + "requests.get", return_value=resp_get + ): + # Run CLI with verbose flag and databus key (so X-API-KEY will be redacted in logs) + target = "https://example.com/account/group/artifact/1/file.txt" + res = runner.invoke(cli.app, ["-v", "download", target, "--localdir", ".", "--databus-key", "SECRET"]) + + assert res.exit_code == 0, res.output + # Should log HTTP activity and redact secret (captured by caplog) + assert "[HTTP]" in caplog.text + assert "REDACTED" in caplog.text + assert "SECRET" not in caplog.text diff --git a/tests/test_download_auth.py b/tests/test_download_auth.py index 46bec79..d2c2475 100644 --- a/tests/test_download_auth.py +++ b/tests/test_download_auth.py @@ -3,6 +3,7 @@ import pytest import requests +import logging import databusclient.api.download as dl @@ -104,7 +105,8 @@ def test_403_reports_insufficient_permissions(): assert "permission" in str(exc.value) or "forbidden" in str(exc.value) -def test_verbose_redacts_authorization(monkeypatch, capsys): +def test_verbose_redacts_authorization(monkeypatch, caplog): + caplog.set_level(logging.DEBUG, logger='databusclient') vault_host = next(iter(VAULT_REQUIRED_HOSTS)) url = f"https://{vault_host}/protected/file.ttl" @@ -126,9 +128,8 @@ def test_verbose_redacts_authorization(monkeypatch, capsys): # run download with verbose enabled dl._download_file(url, localDir='.', vault_token_file="/does/not/matter", verbose=True) - captured = capsys.readouterr() - assert "[HTTP] HEAD" in captured.out or "[HTTP] GET" in captured.out - assert "REDACTED" in captured.out + assert "[HTTP] HEAD" in caplog.text or "[HTTP] GET" in caplog.text + assert "REDACTED" in caplog.text # Ensure token values are not directly printed - assert "ACCESS" not in captured.out - assert "VAULT" not in captured.out + assert "ACCESS" not in caplog.text + assert "VAULT" not in caplog.text diff --git a/tests/test_utils_verbose.py b/tests/test_utils_verbose.py new file mode 100644 index 0000000..aa1b344 --- /dev/null +++ b/tests/test_utils_verbose.py @@ -0,0 +1,76 @@ +from unittest.mock import Mock, patch + +import databusclient.api.utils as utils +import databusclient.api.download as dl + +import requests +import logging + + + + +def make_response(status=200, headers=None, text=''): + headers = headers or {} + mock = Mock() + mock.status_code = status + mock.headers = headers + mock.text = text + def raise_for_status(): + if mock.status_code >= 400: + raise requests.exceptions.HTTPError() + mock.raise_for_status = raise_for_status + return mock + + +def test_fetch_databus_jsonld_verbose_redacts_api_key(caplog): + caplog.set_level(logging.DEBUG, logger='databusclient') + url = "https://databus.example/resource" + resp = make_response(status=200, headers={"content-type": "application/ld+json"}, text='{}') + with patch("databusclient.api.utils.requests.get", return_value=resp): + txt = utils.fetch_databus_jsonld(url, databus_key="SECRET", verbose=True) + assert "[HTTP] GET" in caplog.text + assert "REDACTED" in caplog.text + assert "SECRET" not in caplog.text + assert txt == '{}' + + + +def test_get_sparql_query_of_collection_verbose(caplog): + caplog.set_level(logging.DEBUG, logger='databusclient') + url = "https://databus.example/collections/col" + resp = make_response(status=200, headers={"content-type": "text/sparql"}, text='SELECT *') + with patch("databusclient.api.download.requests.get", return_value=resp): + txt = dl._get_sparql_query_of_collection(url, databus_key="SECRET", verbose=True) + assert "[HTTP] GET" in caplog.text + assert "REDACTED" in caplog.text + assert "SECRET" not in caplog.text + assert txt == 'SELECT *' + + + +def test_query_sparql_endpoint_verbose(caplog): + caplog.set_level(logging.DEBUG, logger='databusclient') + endpoint = "https://dbpedia.org/sparql" + sample = {"results": {"bindings": []}} + class MockSPARQL: + def __init__(self, url): + self.url = url + self.method = None + self._query = None + self._headers = None + def setQuery(self, q): + self._query = q + def setReturnFormat(self, fmt): + pass + def setCustomHttpHeaders(self, headers): + self._headers = headers + def query(self): + mock = Mock() + mock.convert.return_value = sample + return mock + with patch("databusclient.api.download.SPARQLWrapper", new=MockSPARQL): + res = dl._query_sparql_endpoint(endpoint, "SELECT ?s WHERE { ?s ?p ?o }", databus_key="SECRET", verbose=True) + assert "[HTTP] POST" in caplog.text + assert "REDACTED" in caplog.text + assert "SECRET" not in caplog.text + assert res == sample From 3cad31422a0167a6e6522791db4e9bab51d3bc16 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Wed, 7 Jan 2026 23:10:08 +0530 Subject: [PATCH 21/23] Add verbose logging support and stabilize auth tests --- tests/test_download_auth.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/test_download_auth.py b/tests/test_download_auth.py index d2c2475..d5fdf44 100644 --- a/tests/test_download_auth.py +++ b/tests/test_download_auth.py @@ -8,7 +8,9 @@ import databusclient.api.download as dl from databusclient.api.download import VAULT_REQUIRED_HOSTS, DownloadAuthError +from unittest.mock import patch +from databusclient.api.download import download, DownloadAuthError def make_response(status=200, headers=None, content=b""): headers = headers or {} From 3de6e16dd1cd19b7fce9df8e23de5530ffc9d582 Mon Sep 17 00:00:00 2001 From: Dhanashree Petare Date: Wed, 7 Jan 2026 18:52:17 +0530 Subject: [PATCH 22/23] * Restrict Vault token exchange to specific hosts; improve auth errors; add tests (fixes #19) * Restrict Vault token exchange to specific hosts; improve auth errors; add tests and docs note (fixes #19) * Release 0.15: bump version, add changelog, docstrings(issue #35) * Prepare PyPI release 0.15 with build artifacts and publishing guide (Issue #35) * Convert all docstrings to Google-style format --------- Co-authored-by: DhanashreePetare Co-authored-by: Fabian Hofer <57919013+Integer-Ctrl@users.noreply.github.com> --- CHANGELOG.md | 25 ++- README.md | 6 + RELEASE_NOTES.md | 97 +++++++++ databusclient/__init__.py | 14 ++ databusclient/__main__.py | 18 +- databusclient/api/delete.py | 115 ++++++----- databusclient/api/deploy.py | 42 ++++ databusclient/api/download.py | 314 ++++++++++------------------- databusclient/api/utils.py | 39 ++-- databusclient/cli.py | 22 +- databusclient/extensions/webdav.py | 32 +++ pyproject.toml | 2 +- 12 files changed, 437 insertions(+), 289 deletions(-) create mode 100644 RELEASE_NOTES.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 138ec26..c86fc78 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,24 @@ # Changelog -## 0.14.1 - 2026-01-01 +All notable changes to this project will be documented in this file. -- Add `-v/--verbose` global CLI option to enable redacted HTTP request/response logging for debugging. (CLI: `databusclient -v ...`) -- Ensure `Authorization` and `X-API-KEY` headers are redacted in verbose output. -- Add unit tests and README documentation for verbose mode. +## [0.15] - 2025-12-31 + +### Added +- Vault authentication improvements with host-restricted token exchange +- Comprehensive tests for Vault authentication behavior +- Enhanced docstrings across all modules for better documentation coverage +- Support for download redirect handling + +### Fixed +- Vault token exchange now restricted to known hosts for improved security +- Clearer authentication error messages +- README instructions now consistent with PyPI release + +### Changed +- Updated CLI usage documentation to reflect current command structure +- Improved error handling in download operations + +### Notes +- Version 0.15 skips 0.13 and 0.14 as requested in issue #35 +- This release updates the PyPI package to align with current repository features diff --git a/README.md b/README.md index 4493f70..ab93cc5 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,12 @@ Before using the client, install it via pip: python3 -m pip install databusclient ``` +Note: the PyPI release was updated and this repository prepares version `0.15`. If you previously installed `databusclient` via `pip` and observe different CLI behavior, upgrade to the latest release: + +```bash +python3 -m pip install --upgrade databusclient==0.15 +``` + You can then use the client in the command line: ```bash diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md new file mode 100644 index 0000000..b776ab2 --- /dev/null +++ b/RELEASE_NOTES.md @@ -0,0 +1,97 @@ +# Release Notes for databusclient 0.15 + +## Overview +This release addresses issue #35 by providing a new PyPI package (version 0.15) to ensure `pip install databusclient` provides the latest CLI features and bug fixes. + +## Version +**0.15** (skipping 0.13 and 0.14 as requested) + +## What's New + +### Features & Improvements +- **Vault Authentication Enhancement**: Host-restricted token exchange for improved security +- **Better Error Messages**: Clearer authentication error messages for easier debugging +- **Download Redirect Handling**: Improved handling of redirects during file downloads +- **Comprehensive Documentation**: Enhanced docstrings across all modules + +### Bug Fixes +- Fixed Vault token exchange to only work with known hosts +- Improved error handling in download operations +- Aligned README with current CLI behavior + +### Testing +- Added comprehensive tests for Vault authentication +- Improved test coverage overall + +## Installation + +After this release is published to PyPI, users can install or upgrade with: + +```bash +pip install databusclient==0.15 +# or to upgrade +pip install --upgrade databusclient +``` + +## Build Artifacts + +The following distribution files have been created and validated: +- `databusclient-0.15-py3-none-any.whl` (wheel format) +- `databusclient-0.15.tar.gz` (source distribution) + +Both files have passed `twine check` validation. + +## Publishing Instructions + +### Prerequisites +1. PyPI account with maintainer access to the `databusclient` package +2. PyPI API token configured + +### Steps to Publish + +1. **Verify the build artifacts** (already done): + ```bash + poetry build + twine check dist/* + ``` + +2. **Upload to TestPyPI** (recommended first): + ```bash + twine upload --repository testpypi dist/* + ``` + Then test installation: + ```bash + pip install --index-url https://test.pypi.org/simple/ databusclient==0.15 + ``` + +3. **Upload to PyPI**: + ```bash + twine upload dist/* + ``` + +4. **Create a Git tag**: + ```bash + git tag -a v0.15 -m "Release version 0.15" + git push origin v0.15 + ``` + +5. **Create a GitHub Release**: + - Go to GitHub repository → Releases → Draft a new release + - Choose tag `v0.15` + - Release title: `databusclient 0.15` + - Copy content from CHANGELOG.md + - Attach the dist files as release assets + +## Verification + +After publishing, verify the release: +```bash +pip install --upgrade databusclient==0.15 +databusclient --version +databusclient --help +``` + +## Notes +- This release resolves issue #35 +- The PyPI package will now be consistent with the repository's CLI documentation +- Version numbers 0.13 and 0.14 were intentionally skipped as requested diff --git a/databusclient/__init__.py b/databusclient/__init__.py index d15edb6..7b2c625 100644 --- a/databusclient/__init__.py +++ b/databusclient/__init__.py @@ -1,8 +1,22 @@ +"""Top-level package for the databus Python client. + +This module exposes a small set of convenience functions and the CLI +entrypoint so the package can be used as a library or via +``python -m databusclient``. +""" + from databusclient import cli from databusclient.api.deploy import create_dataset, create_distribution, deploy +__version__ = "0.15" __all__ = ["create_dataset", "deploy", "create_distribution"] def run(): + """Start the Click CLI application. + + This function is used by the ``__main__`` module and the package + entrypoint to invoke the command line interface. + """ + cli.app() diff --git a/databusclient/__main__.py b/databusclient/__main__.py index 8fe6fda..3a50f9a 100644 --- a/databusclient/__main__.py +++ b/databusclient/__main__.py @@ -1,3 +1,19 @@ +"""Module used for ``python -m databusclient`` execution. + +Runs the package's CLI application. +""" + from databusclient import cli -cli.app() + +def main(): + """Invoke the CLI application. + + Kept as a named function for easier testing and clarity. + """ + + cli.app() + + +if __name__ == "__main__": + main() diff --git a/databusclient/api/delete.py b/databusclient/api/delete.py index 7107983..edfb95c 100644 --- a/databusclient/api/delete.py +++ b/databusclient/api/delete.py @@ -1,3 +1,10 @@ +"""Helpers for deleting Databus resources via the Databus HTTP API. + +This module provides utilities to delete groups, artifacts and versions on a +Databus instance using authenticated HTTP requests. The class `DeleteQueue` +also allows batching of deletions. +""" + import json from typing import List @@ -16,23 +23,43 @@ class DeleteQueue: """ def __init__(self, databus_key: str): + """Create a DeleteQueue bound to a given Databus API key. + + Args: + databus_key: API key used to authenticate deletion requests. + """ self.databus_key = databus_key self.queue: set[str] = set() def add_uri(self, databusURI: str): + """Add a single Databus URI to the deletion queue. + + The URI will be deleted when `execute()` is called. + """ self.queue.add(databusURI) def add_uris(self, databusURIs: List[str]): + """Add multiple Databus URIs to the deletion queue. + + Args: + databusURIs: Iterable of full Databus URIs. + """ for uri in databusURIs: self.queue.add(uri) def is_empty(self) -> bool: + """Return True if the queue is empty.""" return len(self.queue) == 0 def is_not_empty(self) -> bool: + """Return True if the queue contains any URIs.""" return len(self.queue) > 0 def execute(self): + """Execute all queued deletions. + + Each queued URI will be deleted using `_delete_resource`. + """ _delete_list( list(self.queue), self.databus_key, @@ -41,16 +68,15 @@ def execute(self): def _confirm_delete(databusURI: str) -> str: - """ - Confirm deletion of a Databus resource with the user. + """Confirm deletion of a Databus resource with the user. - Parameters: - - databusURI: The full databus URI of the resource to delete + Args: + databusURI: The full databus URI of the resource to delete. Returns: - - "confirm" if the user confirms deletion - - "skip" if the user chooses to skip deletion - - "cancel" if the user chooses to cancel the entire deletion process + "confirm" if the user confirms deletion. + "skip" if the user chooses to skip deletion. + "cancel" if the user chooses to cancel the entire deletion process. """ print(f"Are you sure you want to delete: {databusURI}?") print( @@ -81,18 +107,17 @@ def _delete_resource( force: bool = False, queue: DeleteQueue = None, ): - """ - Delete a single Databus resource (version, artifact, group). + """Delete a single Databus resource (version, artifact, group). Equivalent to: curl -X DELETE "" -H "accept: */*" -H "X-API-KEY: " - Parameters: - - databusURI: The full databus URI of the resource to delete - - databus_key: Databus API key to authenticate the deletion request - - dry_run: If True, do not perform the deletion but only print what would be deleted - - force: If True, skip confirmation prompt and proceed with deletion - - queue: If queue is provided, add the URI to the queue instead of deleting immediately + Args: + databusURI: The full databus URI of the resource to delete. + databus_key: Databus API key to authenticate the deletion request. + dry_run: If True, do not perform the deletion but only print what would be deleted. + force: If True, skip confirmation prompt and proceed with deletion. + queue: If queue is provided, add the URI to the queue instead of deleting immediately. """ # Confirm the deletion request, skip the request or cancel deletion process @@ -134,15 +159,14 @@ def _delete_list( force: bool = False, queue: DeleteQueue = None, ): - """ - Delete a list of Databus resources. - - Parameters: - - databusURIs: List of full databus URIs of the resources to delete - - databus_key: Databus API key to authenticate the deletion requests - - dry_run: If True, do not perform the deletion but only print what would be deleted - - force: If True, skip confirmation prompt and proceed with deletion - - queue: If queue is provided, add the URIs to the queue instead of deleting immediately + """Delete a list of Databus resources. + + Args: + databusURIs: List of full databus URIs of the resources to delete. + databus_key: Databus API key to authenticate the deletion requests. + dry_run: If True, do not perform the deletion but only print what would be deleted. + force: If True, skip confirmation prompt and proceed with deletion. + queue: If queue is provided, add the URIs to the queue instead of deleting immediately. """ for databusURI in databusURIs: _delete_resource( @@ -157,18 +181,17 @@ def _delete_artifact( force: bool = False, queue: DeleteQueue = None, ): - """ - Delete an artifact and all its versions. + """Delete an artifact and all its versions. This function first retrieves all versions of the artifact and then deletes them one by one. Finally, it deletes the artifact itself. - Parameters: - - databusURI: The full databus URI of the artifact to delete - - databus_key: Databus API key to authenticate the deletion requests - - dry_run: If True, do not perform the deletion but only print what would be deleted - - force: If True, skip confirmation prompt and proceed with deletion - - queue: If queue is provided, add the URI to the queue instead of deleting immediately + Args: + databusURI: The full databus URI of the artifact to delete. + databus_key: Databus API key to authenticate the deletion requests. + dry_run: If True, do not perform the deletion but only print what would be deleted. + force: If True, skip confirmation prompt and proceed with deletion. + queue: If queue is provided, add the URI to the queue instead of deleting immediately. """ artifact_body = fetch_databus_jsonld(databusURI, databus_key) @@ -204,18 +227,17 @@ def _delete_group( force: bool = False, queue: DeleteQueue = None, ): - """ - Delete a group and all its artifacts and versions. + """Delete a group and all its artifacts and versions. This function first retrieves all artifacts of the group, then deletes each artifact (which in turn deletes its versions). Finally, it deletes the group itself. - Parameters: - - databusURI: The full databus URI of the group to delete - - databus_key: Databus API key to authenticate the deletion requests - - dry_run: If True, do not perform the deletion but only print what would be deleted - - force: If True, skip confirmation prompt and proceed with deletion - - queue: If queue is provided, add the URI to the queue instead of deleting immediately + Args: + databusURI: The full databus URI of the group to delete. + databus_key: Databus API key to authenticate the deletion requests. + dry_run: If True, do not perform the deletion but only print what would be deleted. + force: If True, skip confirmation prompt and proceed with deletion. + queue: If queue is provided, add the URI to the queue instead of deleting immediately. """ group_body = fetch_databus_jsonld(databusURI, databus_key) @@ -242,17 +264,16 @@ def _delete_group( def delete(databusURIs: List[str], databus_key: str, dry_run: bool, force: bool): - """ - Delete a dataset from the databus. + """Delete a dataset from the databus. Delete a group, artifact, or version identified by the given databus URI. Will recursively delete all data associated with the dataset. - Parameters: - - databusURIs: List of full databus URIs of the resources to delete - - databus_key: Databus API key to authenticate the deletion requests - - dry_run: If True, will only print what would be deleted without performing actual deletions - - force: If True, skip confirmation prompt and proceed with deletion + Args: + databusURIs: List of full databus URIs of the resources to delete. + databus_key: Databus API key to authenticate the deletion requests. + dry_run: If True, will only print what would be deleted without performing actual deletions. + force: If True, skip confirmation prompt and proceed with deletion. """ queue = DeleteQueue(databus_key) diff --git a/databusclient/api/deploy.py b/databusclient/api/deploy.py index ef8ebf5..23c77ea 100644 --- a/databusclient/api/deploy.py +++ b/databusclient/api/deploy.py @@ -1,3 +1,10 @@ +"""Build and publish Databus datasets (JSON-LD) from provided metadata. + +This module exposes helpers to create distribution strings, compute file +information (sha256 and size), construct dataset JSON-LD payloads and +publish them to a Databus instance using the Databus publish API. +""" + import hashlib import json from enum import Enum @@ -25,6 +32,13 @@ class DeployLogLevel(Enum): def _get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: + """Parse content-variant key/value pairs from a distribution string. + + The CLI supports passing a distribution as ``url|lang=en_type=parsed|...``. + This helper extracts the ``lang``/``type`` style key/value pairs as a + dictionary. + """ + args = distribution_str.split("|") # cv string is ALWAYS at position 1 after the URL @@ -50,6 +64,12 @@ def _get_content_variants(distribution_str: str) -> Optional[Dict[str, str]]: def _get_filetype_definition( distribution_str: str, ) -> Tuple[Optional[str], Optional[str]]: + """Extract an explicit file format and compression from a distribution string. + + Returns (file_extension, compression) where each may be ``None`` if the + format should be inferred from the URL path. + """ + file_ext = None compression = None @@ -87,6 +107,12 @@ def _get_filetype_definition( def _get_extensions(distribution_str: str) -> Tuple[str, str, str]: + """Return tuple `(extension_part, format_extension, compression)`. + + ``extension_part`` is the textual extension appended to generated + filenames (e.g. ".ttl.gz"). + """ + extension_part = "" format_extension, compression = _get_filetype_definition(distribution_str) @@ -126,6 +152,11 @@ def _get_extensions(distribution_str: str) -> Tuple[str, str, str]: def _get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int]]: + """Parse an optional ``sha256sum:length`` tuple from a distribution string. + + Returns (sha256sum, content_length) or (None, None) when not provided. + """ + metadata_list = distribution_str.split("|")[1:] # check whether there is the shasum:length tuple separated by : if len(metadata_list) == 0 or ":" not in metadata_list[-1]: @@ -146,6 +177,12 @@ def _get_file_stats(distribution_str: str) -> Tuple[Optional[str], Optional[int] def _load_file_stats(url: str) -> Tuple[str, int]: + """Download the file at ``url`` and compute its SHA-256 and length. + + This is used as a fallback when the caller did not supply checksum/size + information in the CLI or metadata file. + """ + resp = requests.get(url, timeout=30) if resp.status_code >= 400: raise requests.exceptions.RequestException(response=resp) @@ -156,6 +193,11 @@ def _load_file_stats(url: str) -> Tuple[str, int]: def get_file_info(distribution_str: str) -> Tuple[Dict[str, str], str, str, str, int]: + """Return parsed file information for a distribution string. + + Returns a tuple `(cvs, format_extension, compression, sha256sum, size)`. + """ + cvs = _get_content_variants(distribution_str) extension_part, format_extension, compression = _get_extensions(distribution_str) diff --git a/databusclient/api/download.py b/databusclient/api/download.py index 373e5f9..f045ce2 100644 --- a/databusclient/api/download.py +++ b/databusclient/api/download.py @@ -6,9 +6,6 @@ import requests from SPARQLWrapper import JSON, SPARQLWrapper from tqdm import tqdm -import logging - -logger = logging.getLogger("databusclient") from databusclient.api.utils import ( fetch_databus_jsonld, @@ -35,19 +32,16 @@ def _download_file( databus_key=None, auth_url=None, client_id=None, - verbose=False, ) -> None: - """ - Download a file from the internet with a progress bar using tqdm. - - Parameters: - - url: the URL of the file to download - - localDir: Local directory to download file to. If None, the databus folder structure is created in the current working directory. - - vault_token_file: Path to Vault refresh token file - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details + """Download a file from the internet with a progress bar using tqdm. + + Args: + url: The URL of the file to download. + localDir: Local directory to download file to. If None, the databus folder structure is created in the current working directory. + vault_token_file: Path to Vault refresh token file. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ if localDir is None: _host, account, group, artifact, version, file = ( @@ -72,15 +66,7 @@ def _download_file( headers = {} # --- 1a. public databus --- - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("HEAD", url, req_headers=headers) response = requests.head(url, timeout=30, allow_redirects=False) - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("HEAD", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) # Check for redirect and update URL if necessary if response.headers.get("Location") and response.status_code in [ @@ -121,17 +107,9 @@ def _download_file( headers["Accept-Encoding"] = ( "identity" # disable gzip to get correct content-length ) - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("GET", url, req_headers=headers) response = requests.get( url, headers=headers, stream=True, allow_redirects=True, timeout=30 ) - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) www = response.headers.get("WWW-Authenticate", "") # Check if authentication is required # --- 3. Handle authentication responses --- @@ -157,20 +135,12 @@ def _download_file( # for known hosts. __get_vault_access__ handles reading the refresh # token and exchanging it; errors are translated to DownloadAuthError # for user-friendly CLI output. - vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id, verbose=verbose) + vault_token = __get_vault_access__(url, vault_token_file, auth_url, client_id) headers["Authorization"] = f"Bearer {vault_token}" headers.pop("Accept-Encoding", None) # Retry with token - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("GET", url, req_headers=headers) response = requests.get(url, headers=headers, stream=True, timeout=30) - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("GET", url, req_headers=headers, status=response.status_code, resp_headers=response.headers) # Map common auth failures to friendly messages if response.status_code == 401: @@ -220,19 +190,16 @@ def _download_files( databus_key: str = None, auth_url: str = None, client_id: str = None, - verbose: bool = False, ) -> None: - """ - Download multiple files from the databus. - - Parameters: - - urls: List of file download URLs - - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. - - vault_token_file: Path to Vault refresh token file - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details + """Download multiple files from the databus. + + Args: + urls: List of file download URLs. + localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + vault_token_file: Path to Vault refresh token file. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ for url in urls: _download_file( @@ -242,59 +209,39 @@ def _download_files( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) -def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None, verbose: bool = False) -> str: - """ - Get SPARQL query of collection members from databus collection URI. +def _get_sparql_query_of_collection(uri: str, databus_key: str | None = None) -> str: + """Get SPARQL query of collection members from databus collection URI. - Parameters: - - uri: The full databus collection URI - - databus_key: Optional Databus API key for authentication on protected resources - - verbose: when True, print redacted HTTP request/response details + Args: + uri: The full databus collection URI. + databus_key: Optional Databus API key for authentication on protected resources. Returns: - SPARQL query string to get download URLs of all files in the collection. + SPARQL query string to get download URLs of all files in the collection. """ headers = {"Accept": "text/sparql"} if databus_key is not None: headers["X-API-KEY"] = databus_key - if verbose: - from databusclient.api.utils import log_http - - log_http("GET", uri, req_headers=headers) response = requests.get(uri, headers=headers, timeout=30) - if verbose: - from databusclient.api.utils import log_http - - log_http("GET", uri, req_headers=headers, status=response.status_code, resp_headers=response.headers) - response.raise_for_status() return response.text -def _query_sparql_endpoint(endpoint_url, query, databus_key=None, verbose: bool = False) -> dict: - """ - Query a SPARQL endpoint and return results in JSON format. +def _query_sparql_endpoint(endpoint_url, query, databus_key=None) -> dict: + """Query a SPARQL endpoint and return results in JSON format. - Parameters: - - endpoint_url: the URL of the SPARQL endpoint - - query: the SPARQL query string - - databus_key: Optional API key for authentication - - verbose: when True, print redacted HTTP request/response details + Args: + endpoint_url: The URL of the SPARQL endpoint. + query: The SPARQL query string. + databus_key: Optional API key for authentication. Returns: - - Dictionary containing the query results + Dictionary containing the query results. """ - if verbose: - from databusclient.api.utils import log_http - - headers = {"X-API-KEY": databus_key} if databus_key is not None else None - log_http("POST", endpoint_url, req_headers=headers) - sparql = SPARQLWrapper(endpoint_url) sparql.method = "POST" sparql.setQuery(query) @@ -302,31 +249,23 @@ def _query_sparql_endpoint(endpoint_url, query, databus_key=None, verbose: bool if databus_key is not None: sparql.setCustomHttpHeaders({"X-API-KEY": databus_key}) results = sparql.query().convert() - - if verbose: - from databusclient.api.utils import log_http - - log_http("POST", endpoint_url, req_headers={"X-API-KEY": databus_key} if databus_key is not None else None, status=200) - return results def _get_file_download_urls_from_sparql_query( - endpoint_url, query, databus_key=None, verbose: bool = False + endpoint_url, query, databus_key=None ) -> List[str]: - """ - Execute a SPARQL query to get databus file download URLs. + """Execute a SPARQL query to get databus file download URLs. - Parameters: - - endpoint_url: the URL of the SPARQL endpoint - - query: the SPARQL query string - - databus_key: Optional API key for authentication - - verbose: when True, print redacted HTTP request/response details + Args: + endpoint_url: The URL of the SPARQL endpoint. + query: The SPARQL query string. + databus_key: Optional API key for authentication. Returns: - - List of file download URLs + List of file download URLs. """ - result_dict = _query_sparql_endpoint(endpoint_url, query, databus_key=databus_key, verbose=verbose) + result_dict = _query_sparql_endpoint(endpoint_url, query, databus_key=databus_key) bindings = result_dict.get("results", {}).get("bindings") if not isinstance(bindings, list): @@ -350,7 +289,7 @@ def _get_file_download_urls_from_sparql_query( def __get_vault_access__( - download_url: str, token_file: str, auth_url: str, client_id: str, verbose: bool = False + download_url: str, token_file: str, auth_url: str, client_id: str ) -> str: """ Get Vault access token for a protected databus download. @@ -363,8 +302,7 @@ def __get_vault_access__( with open(token_file, "r") as f: refresh_token = f.read().strip() if len(refresh_token) < 80: - logger.warning("Token from %s is short (<80 chars)", token_file) - + print(f"Warning: token from {token_file} is short (<80 chars)") # 2. Refresh token -> access token resp = requests.post( @@ -377,10 +315,6 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("POST", auth_url, req_headers={"client_id": client_id}, status=resp.status_code, resp_headers=resp.headers) access_token = resp.json()["access_token"] # 3. Extract host as audience @@ -405,13 +339,9 @@ def __get_vault_access__( timeout=30, ) resp.raise_for_status() - if verbose or logger.isEnabledFor(logging.DEBUG): - from databusclient.api.utils import log_http - - log_http("POST", auth_url, req_headers={"client_id": client_id, "audience": audience}, status=resp.status_code, resp_headers=resp.headers) vault_token = resp.json()["access_token"] - logger.debug("Using Vault access token for %s", download_url) + print(f"Using Vault access token for {download_url}") return vault_token @@ -423,24 +353,21 @@ def _download_collection( databus_key: str = None, auth_url: str = None, client_id: str = None, - verbose: bool = False, ) -> None: + """Download all files in a databus collection. + + Args: + uri: The full databus collection URI. + endpoint: The databus SPARQL endpoint URL. + localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + vault_token: Path to Vault refresh token file for protected downloads. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ - Download all files in a databus collection. - - Parameters: - - uri: The full databus collection URI - - endpoint: the databus SPARQL endpoint URL - - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. - - vault_token: Path to Vault refresh token file for protected downloads - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details - """ - query = _get_sparql_query_of_collection(uri, databus_key=databus_key, verbose=verbose) + query = _get_sparql_query_of_collection(uri, databus_key=databus_key) file_urls = _get_file_download_urls_from_sparql_query( - endpoint, query, databus_key=databus_key, verbose=verbose + endpoint, query, databus_key=databus_key ) _download_files( list(file_urls), @@ -449,7 +376,6 @@ def _download_collection( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) @@ -460,21 +386,18 @@ def _download_version( databus_key: str = None, auth_url: str = None, client_id: str = None, - verbose: bool = False, ) -> None: + """Download all files in a databus artifact version. + + Args: + uri: The full databus artifact version URI. + localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + vault_token_file: Path to Vault refresh token file for protected downloads. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ - Download all files in a databus artifact version. - - Parameters: - - uri: The full databus artifact version URI - - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. - - vault_token_file: Path to Vault refresh token file for protected downloads - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details - """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) _download_files( file_urls, @@ -483,7 +406,6 @@ def _download_version( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) @@ -495,28 +417,25 @@ def _download_artifact( databus_key: str = None, auth_url: str = None, client_id: str = None, - verbose: bool = False, ) -> None: + """Download files in a databus artifact. + + Args: + uri: The full databus artifact URI. + localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + all_versions: If True, download all versions of the artifact; otherwise, only download the latest version. + vault_token_file: Path to Vault refresh token file for protected downloads. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ - Download files in a databus artifact. - - Parameters: - - uri: The full databus artifact URI - - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. - - all_versions: If True, download all versions of the artifact; otherwise, only download the latest version - - vault_token_file: Path to Vault refresh token file for protected downloads - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details - """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) versions = _get_databus_versions_of_artifact(json_str, all_versions=all_versions) if isinstance(versions, str): versions = [versions] for version_uri in versions: print(f"Downloading version: {version_uri}") - json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key, verbose=verbose) + json_str = fetch_databus_jsonld(version_uri, databus_key=databus_key) file_urls = _get_file_download_urls_from_artifact_jsonld(json_str) _download_files( file_urls, @@ -525,23 +444,21 @@ def _download_artifact( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) def _get_databus_versions_of_artifact( json_str: str, all_versions: bool ) -> str | List[str]: - """ - Parse the JSON-LD of a databus artifact to extract URLs of its versions. + """Parse the JSON-LD of a databus artifact to extract URLs of its versions. - Parameters: - - json_str: JSON-LD string of the databus artifact - - all_versions: If True, return all version URLs; otherwise, return only the latest version URL + Args: + json_str: JSON-LD string of the databus artifact. + all_versions: If True, return all version URLs; otherwise, return only the latest version URL. Returns: - - If all_versions is True: List of all version URLs - - If all_versions is False: URL of the latest version + If all_versions is True: List of all version URLs. + If all_versions is False: URL of the latest version. """ json_dict = json.loads(json_str) versions = json_dict.get("databus:hasVersion") @@ -569,15 +486,15 @@ def _get_databus_versions_of_artifact( def _get_file_download_urls_from_artifact_jsonld(json_str: str) -> List[str]: - """ - Parse the JSON-LD of a databus artifact version to extract download URLs. + """Parse the JSON-LD of a databus artifact version to extract download URLs. + Don't get downloadURLs directly from the JSON-LD, but follow the "file" links to count access to databus accurately. - Parameters: - - json_str: JSON-LD string of the databus artifact version + Args: + json_str: JSON-LD string of the databus artifact version. Returns: - List of all file download URLs in the artifact version. + List of all file download URLs in the artifact version. """ databusIdUrl: List[str] = [] @@ -601,22 +518,19 @@ def _download_group( databus_key: str = None, auth_url: str = None, client_id: str = None, - verbose: bool = False, ) -> None: + """Download files in a databus group. + + Args: + uri: The full databus group URI. + localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. + all_versions: If True, download all versions of each artifact in the group; otherwise, only download the latest version. + vault_token_file: Path to Vault refresh token file for protected downloads. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. + client_id: Client ID for token exchange. """ - Download files in a databus group. - - Parameters: - - uri: The full databus group URI - - localDir: Local directory to download files to. If None, the databus folder structure is created in the current working directory. - - all_versions: If True, download all versions of each artifact in the group; otherwise, only download the latest version - - vault_token_file: Path to Vault refresh token file for protected downloads - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL - - client_id: Client ID for token exchange - - verbose: when True, print redacted HTTP request/response details - """ - json_str = fetch_databus_jsonld(uri, databus_key=databus_key, verbose=verbose) + json_str = fetch_databus_jsonld(uri, databus_key=databus_key) artifacts = _get_databus_artifacts_of_group(json_str) for artifact_uri in artifacts: print(f"Download artifact: {artifact_uri}") @@ -628,7 +542,6 @@ def _download_group( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) @@ -675,22 +588,19 @@ def download( all_versions=None, auth_url="https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token", client_id="vault-token-exchange", - verbose: bool = False, ) -> None: - """ - Download datasets from databus. + """Download datasets from databus. Download of files, versions, artifacts, groups or databus collections via their databus URIs or user-defined SPARQL queries that return file download URLs. - Parameters: - - localDir: Local directory to download datasets to. If None, the databus folder structure is created in the current working directory. - - endpoint: the databus endpoint URL. If None, inferred from databusURI. Required for user-defined SPARQL queries. - - databusURIs: databus identifiers to specify datasets to download. - - token: Path to Vault refresh token file for protected downloads - - databus_key: Databus API key for protected downloads - - auth_url: Keycloak token endpoint URL. Default is "https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token". - - client_id: Client ID for token exchange. Default is "vault-token-exchange". - - verbose: when True, print redacted HTTP request/response details + Args: + localDir: Local directory to download datasets to. If None, the databus folder structure is created in the current working directory. + endpoint: The databus endpoint URL. If None, inferred from databusURI. Required for user-defined SPARQL queries. + databusURIs: Databus identifiers to specify datasets to download. + token: Path to Vault refresh token file for protected downloads. + databus_key: Databus API key for protected downloads. + auth_url: Keycloak token endpoint URL. Default is "https://auth.dbpedia.org/realms/dbpedia/protocol/openid-connect/token". + client_id: Client ID for token exchange. Default is "vault-token-exchange". """ for databusURI in databusURIs: host, account, group, artifact, version, file = ( @@ -717,7 +627,6 @@ def download( databus_key, auth_url, client_id, - verbose=verbose, ) elif file is not None: print(f"Downloading file: {databusURI}") @@ -728,7 +637,6 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) elif version is not None: print(f"Downloading version: {databusURI}") @@ -739,7 +647,6 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) elif artifact is not None: print( @@ -753,7 +660,6 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) elif group is not None and group != "collections": print( @@ -767,7 +673,6 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) elif account is not None: print("accountId not supported yet") # TODO @@ -784,7 +689,7 @@ def download( if uri_endpoint is None: # endpoint is required for queries (--databus) raise ValueError("No endpoint given for query") res = _get_file_download_urls_from_sparql_query( - uri_endpoint, databusURI, databus_key=databus_key, verbose=verbose + uri_endpoint, databusURI, databus_key=databus_key ) _download_files( res, @@ -793,5 +698,4 @@ def download( databus_key=databus_key, auth_url=auth_url, client_id=client_id, - verbose=verbose, ) diff --git a/databusclient/api/utils.py b/databusclient/api/utils.py index e07f4c0..8bd463a 100644 --- a/databusclient/api/utils.py +++ b/databusclient/api/utils.py @@ -1,3 +1,9 @@ +"""Utility helpers used by the API submodules. + +Contains small parsing helpers and HTTP helpers that are shared by +`download`, `deploy` and `delete` modules. +""" + from typing import Optional, Tuple import requests @@ -13,35 +19,38 @@ def get_databus_id_parts_from_file_url( Optional[str], Optional[str], ]: - """ - Extract databus ID parts from a given databus URI. + """Extract databus ID parts from a given databus URI. - Parameters: - - uri: The full databus URI of the form - "http(s)://host/accountId/groupId/artifactId/versionId/fileId" + Args: + uri: The full databus URI of the form "http(s)://host/accountId/groupId/artifactId/versionId/fileId". Returns: - A tuple containing (host, accountId, groupId, artifactId, versionId, fileId). - Each element is a string or None if not present. + A tuple containing (host, accountId, groupId, artifactId, versionId, fileId). + Each element is a string or None if not present. + """ + """Split a Databus URI into its six parts. + + The returned tuple is (host, accountId, groupId, artifactId, versionId, fileId). + Missing parts are returned as ``None``. """ + uri = uri.removeprefix("https://").removeprefix("http://") parts = uri.strip("/").split("/") parts += [None] * (6 - len(parts)) # pad with None if less than 6 parts return tuple(parts[:6]) # return only the first 6 parts -def fetch_databus_jsonld(uri: str, databus_key: str | None = None, verbose: bool = False) -> str: - """ - Retrieve JSON-LD representation of a databus resource. +def fetch_databus_jsonld(uri: str, databus_key: str | None = None) -> str: + """Fetch the JSON-LD representation of a Databus resource. - Parameters: - - uri: The full databus URI - - databus_key: Optional Databus API key for authentication on protected resources - - verbose: when True, print redacted HTTP request/response details + Args: + uri: Full Databus resource URI. + databus_key: Optional API key for protected resources. Returns: - JSON-LD string representation of the databus resource. + The response body as a string containing JSON-LD. """ + headers = {"Accept": "application/ld+json"} if databus_key is not None: headers["X-API-KEY"] = databus_key diff --git a/databusclient/cli.py b/databusclient/cli.py index 7beb59a..06ccba7 100644 --- a/databusclient/cli.py +++ b/databusclient/cli.py @@ -13,23 +13,13 @@ @click.group() -@click.option("-v", "--verbose", is_flag=True, help="Enable verbose HTTP request/response output") -@click.pass_context -def app(ctx, verbose): - """Databus Client CLI""" - import logging - - ctx.ensure_object(dict) - ctx.obj["verbose"] = verbose +def app(): + """Databus Client CLI. - # Configure databusclient logger when verbose flag is used - logger = logging.getLogger("databusclient") - if verbose: - handler = logging.StreamHandler() - handler.setFormatter(logging.Formatter("%(message)s")) - if not logger.hasHandlers(): - logger.addHandler(handler) - logger.setLevel(logging.DEBUG) + Provides `deploy`, `download`, and `delete` commands for interacting + with the DBpedia Databus. + """ + pass @app.command() diff --git a/databusclient/extensions/webdav.py b/databusclient/extensions/webdav.py index c0747f6..7981a49 100644 --- a/databusclient/extensions/webdav.py +++ b/databusclient/extensions/webdav.py @@ -1,3 +1,11 @@ +"""WebDAV/Nextcloud upload helper used by the deploy CLI. + +This module computes SHA-256 checksums and sizes for local files and uses +``rclone`` to copy files to a remote WebDAV/Nextcloud instance. The +`upload_to_webdav` function returns a list of metadata dictionaries suitable +for passing to ``deploy_from_metadata``. +""" + import hashlib import os import posixpath @@ -6,6 +14,14 @@ def compute_sha256_and_length(filepath): + """Compute the SHA-256 hex digest and total byte length of a file. + + Args: + filepath: Path to the file to hash. + + Returns: + Tuple of (sha256_hex, size_in_bytes). + """ sha256 = hashlib.sha256() total_length = 0 with open(filepath, "rb") as f: @@ -19,6 +35,11 @@ def compute_sha256_and_length(filepath): def get_all_files(path): + """Return a list of all files for a path. + + If `path` is a file, returns a single-element list. If it is a directory, + walks the directory recursively and returns absolute file paths. + """ if os.path.isfile(path): return [path] files = [] @@ -31,6 +52,17 @@ def get_all_files(path): def upload_to_webdav( source_paths: list[str], remote_name: str, remote_path: str, webdav_url: str ): + """Upload local files or folders to a configured rclone remote. + + Args: + source_paths: List of files or directories to upload. + remote_name: Name of the rclone remote (e.g., "nextcloud"). + remote_path: Destination path on the remote. + webdav_url: Public WebDAV URL used to construct download URLs. + + Returns: + A list of dicts with keys: ``filename``, ``checksum``, ``size``, ``url``. + """ result = [] for path in source_paths: if not os.path.exists(path): diff --git a/pyproject.toml b/pyproject.toml index 5593c74..92f479b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "databusclient" -version = "0.14" +version = "0.15" description = "A simple client for submitting, downloading, and deleting data on the DBpedia Databus" authors = ["DBpedia Association"] license = "Apache-2.0 License" From cef1580846ed6ee1daeb1f23f6691651043668f1 Mon Sep 17 00:00:00 2001 From: Tahoora Tabassum Date: Mon, 9 Feb 2026 23:01:26 +0530 Subject: [PATCH 23/23] test: skip live download integration tests --- tests/test_download.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/test_download.py b/tests/test_download.py index a8131b0..73a048c 100644 --- a/tests/test_download.py +++ b/tests/test_download.py @@ -23,6 +23,7 @@ ) +@pytest.mark.skip(reason="Integration test: requires live databus.dbpedia.org connection") def test_with_query(): api_download("tmp", DEFAULT_ENDPOINT, [TEST_QUERY])