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updates to artifact class registration #283

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merged 5 commits into from
Oct 28, 2022
Merged

updates to artifact class registration #283

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6e72183
initial artifact class annotations
gregcaporaso Oct 6, 2022
8d93cea
updates for new api
gregcaporaso Oct 17, 2022
2b5d043
add first import usage example
gregcaporaso Oct 17, 2022
5729940
address comment from @ebolyen
gregcaporaso Oct 25, 2022
cc840e6
lint
gregcaporaso Oct 25, 2022
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2 changes: 1 addition & 1 deletion q2_types/distance_matrix/_type.py
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Expand Up @@ -17,5 +17,5 @@
plugin.register_semantic_types(DistanceMatrix)
plugin.register_semantic_type_to_format(
DistanceMatrix,
artifact_format=DistanceMatrixDirectoryFormat
directory_format=DistanceMatrixDirectoryFormat
)
20 changes: 10 additions & 10 deletions q2_types/feature_data/_type.py
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Expand Up @@ -59,33 +59,33 @@

plugin.register_semantic_type_to_format(
FeatureData[Taxonomy],
artifact_format=TSVTaxonomyDirectoryFormat)
directory_format=TSVTaxonomyDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[Sequence],
artifact_format=DNASequencesDirectoryFormat)
directory_format=DNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[RNASequence],
artifact_format=RNASequencesDirectoryFormat)
directory_format=RNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[PairedEndSequence],
artifact_format=PairedDNASequencesDirectoryFormat)
directory_format=PairedDNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[PairedEndRNASequence],
artifact_format=PairedRNASequencesDirectoryFormat)
directory_format=PairedRNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[AlignedSequence],
artifact_format=AlignedDNASequencesDirectoryFormat)
directory_format=AlignedDNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[AlignedRNASequence],
artifact_format=AlignedRNASequencesDirectoryFormat)
directory_format=AlignedRNASequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[Differential], DifferentialDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[ProteinSequence],
artifact_format=ProteinSequencesDirectoryFormat)
directory_format=ProteinSequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[AlignedProteinSequence],
artifact_format=AlignedProteinSequencesDirectoryFormat)
directory_format=AlignedProteinSequencesDirectoryFormat)
plugin.register_semantic_type_to_format(
FeatureData[BLAST6],
artifact_format=BLAST6DirectoryFormat)
directory_format=BLAST6DirectoryFormat)
2 changes: 1 addition & 1 deletion q2_types/feature_table/_type.py
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Expand Up @@ -43,5 +43,5 @@
FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence | Balance | Composition |
PercentileNormalized | Design],
artifact_format=BIOMV210DirFmt
directory_format=BIOMV210DirFmt
)
22 changes: 19 additions & 3 deletions q2_types/feature_table/tests/test_type.py
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Expand Up @@ -38,9 +38,25 @@ def test_balance_semantic_type_registration(self):

def test_feature_table_semantic_type_to_v210_format_registration(self):
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Frequency | RelativeFrequency | PresenceAbsence |
Composition | Balance | PercentileNormalized |
Design],
FeatureTable[Frequency],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[RelativeFrequency],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[PresenceAbsence],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Composition],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Balance],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[PercentileNormalized],
BIOMV210DirFmt)
self.assertSemanticTypeRegisteredToFormat(
FeatureTable[Design],
BIOMV210DirFmt)


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4 changes: 2 additions & 2 deletions q2_types/multiplexed_sequences/_type.py
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Expand Up @@ -23,9 +23,9 @@

plugin.register_semantic_type_to_format(
MultiplexedSingleEndBarcodeInSequence,
artifact_format=MultiplexedSingleEndBarcodeInSequenceDirFmt
directory_format=MultiplexedSingleEndBarcodeInSequenceDirFmt
)
plugin.register_semantic_type_to_format(
MultiplexedPairedEndBarcodeInSequence,
artifact_format=MultiplexedPairedEndBarcodeInSequenceDirFmt,
directory_format=MultiplexedPairedEndBarcodeInSequenceDirFmt,
)
4 changes: 2 additions & 2 deletions q2_types/ordination/_type.py
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Expand Up @@ -19,11 +19,11 @@
plugin.register_semantic_types(PCoAResults, ProcrustesStatistics)
plugin.register_semantic_type_to_format(
PCoAResults,
artifact_format=OrdinationDirectoryFormat
directory_format=OrdinationDirectoryFormat
)

plugin.register_semantic_type_to_format(
ProcrustesStatistics,

artifact_format=ProcrustesStatisticsDirFmt
directory_format=ProcrustesStatisticsDirFmt
)
26 changes: 18 additions & 8 deletions q2_types/per_sample_sequences/_type.py
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Expand Up @@ -26,19 +26,29 @@
PairedEndSequencesWithQuality,
JoinedSequencesWithQuality)

plugin.register_semantic_type_to_format(
plugin.register_artifact_class(
SampleData[Sequences],
artifact_format=QIIME1DemuxDirFmt
directory_format=QIIME1DemuxDirFmt,
description=("Collections of sequences associated with specified samples "
"(i.e., demultiplexed sequences).")
)
plugin.register_semantic_type_to_format(
plugin.register_artifact_class(
SampleData[SequencesWithQuality],
artifact_format=SingleLanePerSampleSingleEndFastqDirFmt
directory_format=SingleLanePerSampleSingleEndFastqDirFmt,
description=("Collections of sequences with quality scores associated "
"with specified samples (i.e., demultiplexed sequences).")
)
plugin.register_semantic_type_to_format(
plugin.register_artifact_class(
SampleData[JoinedSequencesWithQuality],
artifact_format=SingleLanePerSampleSingleEndFastqDirFmt
directory_format=SingleLanePerSampleSingleEndFastqDirFmt,
description=("Collections of joined paired-end sequences with quality "
"scores associated with specified samples (i.e., "
"demultiplexed sequences).")
)
plugin.register_semantic_type_to_format(
plugin.register_artifact_class(
SampleData[PairedEndSequencesWithQuality],
artifact_format=SingleLanePerSamplePairedEndFastqDirFmt
directory_format=SingleLanePerSamplePairedEndFastqDirFmt,
description=("Collections of unjoined paired-end sequences with quality "
"scores associated with specified samples (i.e., "
"demultiplexed sequences).")
)
2 changes: 1 addition & 1 deletion q2_types/sample_data/_type.py
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Expand Up @@ -21,5 +21,5 @@

plugin.register_semantic_type_to_format(
SampleData[AlphaDiversity],
artifact_format=AlphaDiversityDirectoryFormat
directory_format=AlphaDiversityDirectoryFormat
)
38 changes: 34 additions & 4 deletions q2_types/tree/_type.py
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Expand Up @@ -6,12 +6,16 @@
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

from io import StringIO

from skbio import TreeNode

from qiime2.plugin import SemanticType
from qiime2.plugin.util import transform

from ..plugin_setup import plugin
from . import NewickDirectoryFormat


Phylogeny = SemanticType('Phylogeny', field_names=['type'])

Rooted = SemanticType('Rooted', variant_of=Phylogeny.field['type'])
Expand All @@ -22,8 +26,34 @@

plugin.register_semantic_types(Phylogeny, Rooted, Unrooted, Hierarchy)

plugin.register_semantic_type_to_format(Phylogeny[Rooted | Unrooted],
artifact_format=NewickDirectoryFormat)
plugin.register_artifact_class(
Phylogeny[Unrooted], NewickDirectoryFormat,
"A phylogenetic tree not containing a defined root.")


# Phylogeny[Rooted] import usage example
def phylogeny_rooted_usage(use):
def factory():
from q2_types.tree import NewickFormat

tree = TreeNode.read(StringIO(
'(SEQUENCE1:0.000000003,SEQUENCE2:0.000000003);'))
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Should the root be trifurcating in this particular example, since that's the common-ish convention?

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(Or we can switch it to Phylogeny[Rooted])

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Thanks for catching that! I updated to Phylogeny[Rooted] and set this as ready for review.

ff = transform(tree, to_type=NewickFormat)
ff.validate()
return ff

to_import = use.init_format('my-tree', factory, ext='.tre')

use.import_from_format('tree',
semantic_type='Phylogeny[Rooted]',
variable=to_import,
view_type='NewickFormat')


plugin.register_artifact_class(
Phylogeny[Rooted], NewickDirectoryFormat,
"A phylogenetic tree containing a defined root.",
examples={'Import rooted phylogenetic tree': phylogeny_rooted_usage})

plugin.register_semantic_type_to_format(Hierarchy,
artifact_format=NewickDirectoryFormat)
directory_format=NewickDirectoryFormat)
4 changes: 3 additions & 1 deletion q2_types/tree/tests/test_type.py
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Expand Up @@ -30,7 +30,9 @@ def test_hierarchy_semantic_type_registration(self):

def test_phylogeny_rooted_unrooted_to_newick_dir_fmt_registration(self):
self.assertSemanticTypeRegisteredToFormat(
Phylogeny[Rooted | Unrooted], NewickDirectoryFormat)
Phylogeny[Rooted], NewickDirectoryFormat)
self.assertSemanticTypeRegisteredToFormat(
Phylogeny[Unrooted], NewickDirectoryFormat)

def test_hierarchy_to_newick_dir_fmt_registration(self):
self.assertSemanticTypeRegisteredToFormat(
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