mirror of
https://github.com/galaxyproject/galaxy.git
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Dannon Baker
c782772584
Support compact identifiers (e.g., drs://drs.anv0:object-id) by resolving prefixes via identifiers.org. Includes caching and tests.
99 lines
3.7 KiB
Python
99 lines
3.7 KiB
Python
import os
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import tempfile
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from unittest.mock import (
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Mock,
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patch,
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)
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import pytest
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from galaxy.files.sources.util import fetch_drs_to_file
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class TestDRSCompactIdentifiersIntegration:
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@patch("galaxy.files.sources.util.requests.get")
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@patch("galaxy.files.sources.util.stream_url_to_file")
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def test_fetch_compact_identifier_drs_file(self, mock_stream, mock_get):
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namespace_response = Mock()
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namespace_response.json.return_value = {
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"_links": {
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"self": {"href": "https://registry.api.identifiers.org/restApi/namespaces/123"},
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"resources": {"href": "https://registry.api.identifiers.org/restApi/namespaces/123/resources"},
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}
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}
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namespace_response.raise_for_status.return_value = None
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resources_response = Mock()
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resources_response.json.return_value = {
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"_embedded": {
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"resources": [{"urlPattern": "https://example-drs.com/ga4gh/drs/v1/objects/{$id}", "official": True}]
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}
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}
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resources_response.raise_for_status.return_value = None
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drs_response = Mock()
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drs_response.json.return_value = {
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"id": "test-object-id",
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"access_methods": [
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{
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"type": "https",
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"access_url": {
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"url": "https://download.example.com/test-file.txt",
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"headers": ["Authorization: Bearer test-token"],
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},
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}
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],
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}
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drs_response.raise_for_status.return_value = None
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drs_response.status_code = 200
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mock_get.side_effect = [namespace_response, resources_response, drs_response]
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with tempfile.NamedTemporaryFile(delete=False) as tmp:
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try:
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fetch_drs_to_file("drs://drs.test:test-object-id", tmp.name, None)
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assert mock_get.call_count == 3
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mock_get.assert_any_call(
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"https://registry.api.identifiers.org/restApi/namespaces/search/findByPrefix?prefix=drs.test",
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timeout=600,
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)
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mock_get.assert_any_call(
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"https://registry.api.identifiers.org/restApi/namespaces/123/resources",
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timeout=600,
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)
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mock_get.assert_any_call(
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"https://example-drs.com/ga4gh/drs/v1/objects/test-object-id", timeout=600, headers=None
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)
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mock_stream.assert_called_once()
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call_args = mock_stream.call_args
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assert call_args[0][0] == "https://download.example.com/test-file.txt"
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assert call_args[1]["target_path"] == tmp.name
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finally:
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if os.path.exists(tmp.name):
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os.unlink(tmp.name)
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def test_compact_identifier_error_handling(self):
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invalid_uris = [
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"drs://", # No identifier
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"drs://no-colon", # Missing colon
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"drs://:only-accession", # Missing prefix
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"drs://prefix:", # Missing accession
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"drs://UPPERCASE:accession", # Invalid prefix format
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"https://not-drs:accession", # Wrong scheme
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]
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for uri in invalid_uris:
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with pytest.raises(ValueError):
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fetch_drs_to_file(uri, "/tmp/output", None)
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@patch("galaxy.files.sources.util.CompactIdentifierResolver._query_identifiers_org")
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def test_meta_resolver_failure_handling(self, mock_identifiers):
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mock_identifiers.return_value = None
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with pytest.raises(ValueError, match="Failed to resolve compact identifier DRS URI"):
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fetch_drs_to_file("drs://unknown.prefix:accession", "/tmp/output", None)
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