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gregcaporasogregcaporaso
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NEW: adds ImmutableMetadata semantic type and supporting formats (#293)
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‎q2_types/__init__.py‎

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importlib.import_module('q2_types.sample_data')
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importlib.import_module('q2_types.per_sample_sequences')
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importlib.import_module('q2_types.bowtie2')
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importlib.import_module('q2_types.metadata')

‎q2_types/metadata/__init__.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import importlib
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from ._format import ImmutableMetadataFormat, ImmutableMetadataDirectoryFormat
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from ._type import ImmutableMetadata
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__all__ = ['ImmutableMetadataFormat',
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'ImmutableMetadataDirectoryFormat',
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'ImmutableMetadata']
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importlib.import_module('q2_types.metadata._transformer')

‎q2_types/metadata/_format.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import qiime2.plugin.model as model
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from qiime2.plugin import ValidationError
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from qiime2 import Metadata
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from qiime2.metadata import MetadataFileError
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from ..plugin_setup import plugin
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class ImmutableMetadataFormat(model.TextFileFormat):
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def _validate_(self, level):
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try:
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Metadata.load(str(self))
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except (MetadataFileError,) as e:
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raise ValidationError(str(e))
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ImmutableMetadataDirectoryFormat = model.SingleFileDirectoryFormat(
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'ImmutableMetadataDirectoryFormat', 'metadata.tsv',
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ImmutableMetadataFormat)
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plugin.register_formats(ImmutableMetadataFormat,
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ImmutableMetadataDirectoryFormat)

‎q2_types/metadata/_transformer.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import qiime2
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from ..plugin_setup import plugin
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from . import ImmutableMetadataFormat
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@plugin.register_transformer
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def _1(ff: ImmutableMetadataFormat) -> qiime2.Metadata:
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return qiime2.Metadata.load(str(ff))

‎q2_types/metadata/_type.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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from qiime2.plugin import SemanticType
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from ..plugin_setup import plugin
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from . import ImmutableMetadataDirectoryFormat
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ImmutableMetadata = SemanticType('ImmutableMetadata')
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plugin.register_semantic_types(ImmutableMetadata)
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plugin.register_artifact_class(
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ImmutableMetadata,
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directory_format=ImmutableMetadataDirectoryFormat,
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description=("Immutable sample or feature metadata.")
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)

‎q2_types/metadata/tests/__init__.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------

‎q2_types/metadata/tests/data/invalid-metadata-1.tsv‎

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bad-id-label barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start
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#q2:types categorical categorical numeric numeric numeric categorical categorical numeric
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L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0
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L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84
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L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112
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L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140
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L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84
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L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112
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L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140
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L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168
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L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0
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L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84
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L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112
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L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140
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L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168
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L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0
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L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84
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L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112
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L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140
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L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168
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L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0
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L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84
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L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140
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L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168
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L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0
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L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84
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L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140
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L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168
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L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0
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L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84
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L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140
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L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168
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L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0
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L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84
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L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140
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L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168

‎q2_types/metadata/tests/data/metadata.tsv‎

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sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start
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#q2:types categorical categorical numeric numeric numeric categorical categorical numeric
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L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0
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L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84
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L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112
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L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140
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L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84
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L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112
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L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140
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L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168
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L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0
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L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84
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L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112
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L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140
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L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168
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L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0
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L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84
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L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112
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L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140
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L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168
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L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0
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L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84
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L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140
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L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168
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L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0
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L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84
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L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140
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L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168
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L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0
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L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84
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L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140
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L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168
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L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0
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L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84
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L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140
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L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168

‎q2_types/metadata/tests/test_format.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import shutil
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from q2_types.metadata import (ImmutableMetadataDirectoryFormat,
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ImmutableMetadataFormat)
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from qiime2.plugin.testing import TestPluginBase
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from qiime2.plugin import ValidationError
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class TestFormats(TestPluginBase):
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package = "q2_types.metadata.tests"
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def test_metadata_format_validate_positive(self):
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filepath = self.get_data_path('metadata.tsv')
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format = ImmutableMetadataFormat(filepath, mode='r')
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format.validate()
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def test_metadata_dir_format_validate_positive(self):
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filepath = self.get_data_path('metadata.tsv')
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shutil.copy(filepath, self.temp_dir.name)
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format = ImmutableMetadataDirectoryFormat(self.temp_dir.name, mode='r')
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format.validate()
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def test_metadata_format_validate_negative(self):
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filepath = self.get_data_path('invalid-metadata-1.tsv')
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format = ImmutableMetadataFormat(filepath, mode='r')
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with self.assertRaisesRegex(ValidationError,
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"column name 'bad-id-label'"):
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format.validate()

‎q2_types/metadata/tests/test_transformer.py‎

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# ----------------------------------------------------------------------------
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# Copyright (c) 2016-2023, QIIME 2 development team.
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#
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# Distributed under the terms of the Modified BSD License.
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#
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# The full license is in the file LICENSE, distributed with this software.
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# ----------------------------------------------------------------------------
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import qiime2
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from q2_types.metadata import ImmutableMetadataFormat
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from qiime2.plugin.testing import TestPluginBase
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from qiime2.metadata import MetadataFileError
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class TestTransformers(TestPluginBase):
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package = "q2_types.metadata.tests"
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def test_metadata_format_to_metadata(self):
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filename = 'metadata.tsv'
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_, obs = self.transform_format(ImmutableMetadataFormat,
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qiime2.Metadata,
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filename)
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exp_md = qiime2.Metadata.load(self.get_data_path(filename))
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self.assertEqual(obs, exp_md)
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def test_non_metadata(self):
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filename = 'invalid-metadata-1.tsv'
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with self.assertRaisesRegex(MetadataFileError,
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"column name 'bad-id-label'"):
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self.transform_format(ImmutableMetadataFormat, qiime2.Metadata,
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filename)

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