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https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
John Chilton
ff6b9d61fb
Two sources for bio.tools data: - Configurable directory from Github (https://github.com/bio-tools/content/). - API requests to bio.tools web service (cachable). Code is structured into a stand-alone package decouple from Galaxy for dealing with bio.tools data and APIs and then an adapt to Galaxy's config.
50 lines
1.6 KiB
Python
50 lines
1.6 KiB
Python
from galaxy.tool_util.biotools.source import (
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ApiBiotoolsMetadataSource,
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BiotoolsMetadataSourceConfig,
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get_biotools_metadata_source,
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GitContentBiotoolsMetadataSource,
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)
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from ._util import content_dir
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def test_git_content():
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metadata_source = GitContentBiotoolsMetadataSource(content_dir)
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bwa_entry = metadata_source.get_biotools_metadata("bwa")
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assert bwa_entry is not None
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assert len(bwa_entry.function) == 6
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missing_entry = metadata_source.get_biotools_metadata("johnscoolbowtie")
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assert missing_entry is None
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def test_api_content():
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metadata_source = ApiBiotoolsMetadataSource()
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bwa_entry = metadata_source.get_biotools_metadata("bwa")
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assert bwa_entry is not None
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assert len(bwa_entry.function) >= 6
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missing_entry = metadata_source.get_biotools_metadata("johnscoolbowtie")
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assert missing_entry is None
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def test_cascade_content():
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config = BiotoolsMetadataSourceConfig()
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config.content_directory = content_dir
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metadata_source = get_biotools_metadata_source(config)
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bwa_entry = metadata_source.get_biotools_metadata("bwa")
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assert bwa_entry is not None
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assert len(bwa_entry.function) == 6
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# by default API isn't used so bowtie2 empty...
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bowtie2 = metadata_source.get_biotools_metadata("bowtie2")
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assert bowtie2 is None
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# but can be enabled with API
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config = BiotoolsMetadataSourceConfig()
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config.content_directory = content_dir
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config.use_api = True
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metadata_source = get_biotools_metadata_source(config)
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bowtie2 = metadata_source.get_biotools_metadata("bowtie2")
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assert bowtie2 is not None
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assert len(bowtie2.topic) == 3
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