qsip data subtypes

q2_qsip2/plugin_setup.py

@@ -13,7 +13,7 @@
 
 from q2_qsip2 import __version__
 from q2_qsip2.workflow import standard_workflow, create_qsip_data
-from q2_qsip2.types import QSIP2Data
+from q2_qsip2.types import QSIP2Data, Unfiltered, Filtered, EAF
 from q2_qsip2.visualizers._visualizers import (
     plot_weighted_average_densities, plot_sample_curves, plot_density_outliers,
     show_comparison_groups
@@ -40,7 +40,7 @@
     function=standard_workflow,
     inputs={
         'table': FeatureTable[Frequency],
-        'qsip_metadata': QSIP2Data,
+        'qsip_metadata': QSIP2Data[Unfiltered],
     },
     parameters={},
     outputs=[
@@ -76,7 +76,7 @@
         'gradient_pos_amt_column': Str,
     },
     outputs=[
-        ('qsip_data', QSIP2Data)
+        ('qsip_data', QSIP2Data[Unfiltered])
     ],
     input_descriptions={},
     parameter_descriptions={
@@ -101,7 +101,7 @@
 plugin.visualizers.register_function(
     function=plot_weighted_average_densities,
     inputs={
-        'qsip_data': QSIP2Data
+        'qsip_data': QSIP2Data[Unfiltered]
     },
     parameters={
         'group': Str
@@ -124,7 +124,7 @@
 plugin.visualizers.register_function(
     function=plot_sample_curves,
     inputs={
-        'qsip_data': QSIP2Data
+        'qsip_data': QSIP2Data[Unfiltered]
     },
     parameters={},
     input_descriptions={
@@ -141,7 +141,7 @@
 plugin.visualizers.register_function(
     function=plot_density_outliers,
     inputs={
-        'qsip_data': QSIP2Data
+        'qsip_data': QSIP2Data[Unfiltered]
     },
     parameters={},
     input_descriptions={
@@ -159,7 +159,7 @@
 plugin.visualizers.register_function(
     function=show_comparison_groups,
     inputs={
-        'qsip_data': QSIP2Data
+        'qsip_data': QSIP2Data[Unfiltered]
     },
     parameters={
         'groups': List[Str]

q2_qsip2/types/__init__.py

@@ -1,8 +1,13 @@
 from q2_qsip2.types._formats import (
-    QSIP2DataFormat, QSIP2DataDirectoryFormat
+    QSIP2DataUnfilteredFormat, QSIP2DataUnfilteredDirectoryFormat,
+    QSIP2DataFilteredFormat, QSIP2DataFilteredDirectoryFormat,
+    QSIP2DataEAFFormat, QSIP2DataEAFDirectoryFormat
 )
-from q2_qsip2.types._types import QSIP2Data
+from q2_qsip2.types._types import QSIP2Data, Unfiltered, Filtered, EAF
 
 __all__ = [
-    'QSIP2DataFormat', 'QSIP2DataDirectoryFormat', 'QSIP2Data'
+    'QSIP2Data', 'Unfiltered', 'Filtered', 'EAF',
+    'QSIP2DataUnfilteredFormat', 'QSIP2DataUnfilteredDirectoryFormat',
+    'QSIP2DataFilteredFormat', 'QSIP2DataFilteredDirectoryFormat',
+    'QSIP2DataEAFFormat', 'QSIP2DataEAFDirectoryFormat'
 ]

q2_qsip2/types/_deferred_setup/__init__.py

@@ -9,21 +9,49 @@
 import importlib
 
 from q2_qsip2.plugin_setup import plugin
-from q2_qsip2.types import (
-    QSIP2Data, QSIP2DataFormat, QSIP2DataDirectoryFormat
+from q2_qsip2.types._types import (
+    QSIP2Data, Unfiltered, Filtered, EAF
+)
+from q2_qsip2.types._formats import (
+    QSIP2DataUnfilteredFormat, QSIP2DataUnfilteredDirectoryFormat,
+    QSIP2DataFilteredFormat, QSIP2DataFilteredDirectoryFormat,
+    QSIP2DataEAFFormat, QSIP2DataEAFDirectoryFormat
 )
 
 
-plugin.register_semantic_types(QSIP2Data)
+plugin.register_semantic_types(QSIP2Data, Unfiltered, Filtered, EAF)
 
 plugin.register_formats(
-    QSIP2DataFormat, QSIP2DataDirectoryFormat
+    QSIP2DataUnfilteredFormat, QSIP2DataUnfilteredDirectoryFormat,
+    QSIP2DataFilteredFormat, QSIP2DataFilteredDirectoryFormat,
+    QSIP2DataEAFFormat, QSIP2DataEAFDirectoryFormat
+)
+
+plugin.register_artifact_class(
+    QSIP2Data[Unfiltered],
+    directory_format=QSIP2DataUnfilteredDirectoryFormat,
+    description=(
+        'Represents initial imported qSIP2 data, containing source- and '
+        'sample-level metadata and a feature table.'
+    )
+)
+
+plugin.register_artifact_class(
+    QSIP2Data[Filtered],
+    directory_format=QSIP2DataFilteredDirectoryFormat,
+    description=(
+        'Represents filtered qSIP2 data, containg labeled and unlabeled '
+        'sources that constitute a desired comparison.'
+    )
 )
 
 plugin.register_artifact_class(
-    QSIP2Data,
-    directory_format=QSIP2DataDirectoryFormat,
-    description="A serialized qSIP2 data object."
+    QSIP2Data[EAF],
+    directory_format=QSIP2DataEAFDirectoryFormat,
+    description=(
+        'Represents fully process qSIP2 data that has been resampled and '
+        'had excess atom fractions (EAF) calculated.'
+    )
 )
 
 importlib.import_module('._transformers', __name__)

q2_qsip2/types/_deferred_setup/_transformers.py

@@ -11,21 +11,53 @@
 import pickle
 
 from q2_qsip2.plugin_setup import plugin
-from q2_qsip2.types import QSIP2DataFormat
+from q2_qsip2.types import (
+    QSIP2DataUnfilteredFormat, QSIP2DataFilteredFormat, QSIP2DataEAFFormat
+)
 
 
-@plugin.register_transformer
-def _1(qsip_object: RS4) -> QSIP2DataFormat:
-    ff = QSIP2DataFormat()
+def _format_to_qsip_object(ff):
+    with ff.open() as fh:
+        qsip_object = pickle.load(fh)
+
+    return qsip_object
+
+
+def _qsip_object_to_format(qsip_object, ff):
     with ff.open() as fh:
         pickle.dump(qsip_object, fh)
 
     return ff
 
 
 @plugin.register_transformer
-def _2(ff: QSIP2DataFormat) -> RS4:
-    with ff.open() as fh:
-        qsip_object = pickle.load(fh)
+def _1(qsip_object: RS4) -> QSIP2DataUnfilteredFormat:
+    ff = QSIP2DataUnfilteredFormat()
+    return _qsip_object_to_format(qsip_object, ff)
 
-    return qsip_object
+
+@plugin.register_transformer
+def _2(ff: QSIP2DataUnfilteredFormat) -> RS4:
+    return _format_to_qsip_object(ff)
+
+
+@plugin.register_transformer
+def _3(qsip_object: RS4) -> QSIP2DataFilteredFormat:
+    ff = QSIP2DataFilteredFormat()
+    return _qsip_object_to_format(qsip_object, ff)
+
+
+@plugin.register_transformer
+def _4(ff: QSIP2DataFilteredFormat) -> RS4:
+    return _format_to_qsip_object(ff)
+
+
+@plugin.register_transformer
+def _5(qsip_object: RS4) -> QSIP2DataEAFFormat:
+    ff = QSIP2DataFilteredFormat()
+    return _qsip_object_to_format(qsip_object, ff)
+
+
+@plugin.register_transformer
+def _6(ff: QSIP2DataEAFFormat) -> RS4:
+    return _format_to_qsip_object(ff)

q2_qsip2/types/_formats.py

@@ -15,16 +15,19 @@
 
 
 # TODO: communicate warning about using pickled data
-class QSIP2DataFormat(model.BinaryFileFormat):
+class QSIP2DataFormatBase(model.BinaryFileFormat):
     package = 'q2_qsip2.types.tests'
 
+    def stage_specific_validation_method(self, qsip_data_obj):
+        pass
+
     def _validate_(self, level):
         with self.open() as fh:
             qsip_data_obj = pickle.load(fh)
 
         try:
-            # TODO: why not implemented in R package?
             ro.r['validate'](qsip_data_obj)
+            self.stage_specific_validation_method(qsip_data_obj)
         except Exception as e:
             msg = (
                 'There was a problem loading your qSIP2 data. See the below '
@@ -33,6 +36,40 @@ def _validate_(self, level):
             raise ValidationError(msg)
 
 
-QSIP2DataDirectoryFormat = model.SingleFileDirectoryFormat(
-    'QSIP2DataDirectoryFormat', 'qsip-data.pickle', QSIP2DataFormat
+class QSIP2DataUnfilteredFormat(QSIP2DataFormatBase):
+    def stage_specific_validation_method(self, qsip_data_obj):
+        # TODO: update once implemented in R
+        pass
+
+
+QSIP2DataUnfilteredDirectoryFormat = model.SingleFileDirectoryFormat(
+    'QSIP2DataUnfilteredDirectoryFormat',
+    'qsip-data.pickle',
+    QSIP2DataUnfilteredFormat
+)
+
+
+class QSIP2DataFilteredFormat(QSIP2DataFormatBase):
+    def stage_speicif_validation_method(self, qsip_data_obj):
+        # TODO: update once implemented in R
+        pass
+
+
+QSIP2DataFilteredDirectoryFormat = model.SingleFileDirectoryFormat(
+    'QSIP2DataFilteredDirectoryFormat',
+    'qsip-data.pickle',
+    QSIP2DataFilteredFormat
+)
+
+
+class QSIP2DataEAFFormat(QSIP2DataFormatBase):
+    def stage_specific_validation_method(self, qsip_data_obj):
+        # TODO: update once implemented in R
+        pass
+
+
+QSIP2DataEAFDirectoryFormat = model.SingleFileDirectoryFormat(
+    'QSIP2DataEAFDirectoryFormat',
+    'qsip-data.pickle',
+    QSIP2DataEAFFormat
 )

q2_qsip2/types/_types.py

@@ -9,4 +9,10 @@
 from qiime2.plugin import SemanticType
 
 
-QSIP2Data = SemanticType('QSIP2Data')
+QSIP2Data = SemanticType('QSIP2Data', field_names='stage')
+
+Unfiltered = SemanticType('Unfiltered', variant_of=QSIP2Data.field['stage'])
+
+Filtered = SemanticType('Filtered', variant_of=QSIP2Data.field['stage'])
+
+EAF = SemanticType('EAF', variant_of=QSIP2Data.field['stage'])

q2_qsip2/types/tests/test_formats.py

@@ -20,7 +20,7 @@
 from qiime2.plugin import ValidationError
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_qsip2.types import QSIP2DataFormat
+from q2_qsip2.types import QSIP2DataUnfilteredFormat
 from q2_qsip2.workflow import create_qsip_data
 
 
@@ -47,31 +47,31 @@ def get_feature_table(self):
             df.values, observation_ids=df.index, sample_ids=df.columns
         )
 
-    def test_valid_QSIP2DataFormat_from_files(self):
+    def test_valid_QSIP2DataUnfilteredFormat_from_files(self):
         source_md = self.get_source_metadata()
         sample_md = self.get_sample_metadata()
         table = self.get_feature_table()
 
         qsip_object = create_qsip_data(table, sample_md, source_md)
 
         transformer = self.get_transformer(
-            RS4, QSIP2DataFormat
+            RS4, QSIP2DataUnfilteredFormat
         )
         format = transformer(qsip_object)
 
         format.validate()
 
-    def test_valid_QSIP2DataFormat_from_pickle(self):
+    def test_valid_QSIP2DataUnfilteredFormat_from_pickle(self):
         pickle_fp = (
             importlib.resources.files(__package__) /
             'data' / 'qsip-data.pickle'
         )
 
-        format = QSIP2DataFormat(pickle_fp, mode='r')
+        format = QSIP2DataUnfilteredFormat(pickle_fp, mode='r')
 
         format.validate()
 
-    def test_invalid_QSIP2DataFormat(self):
+    def test_invalid_QSIP2DataUnfilteredFormat(self):
         # create useless rpy2 object to pickle
         vector = ro.r("c('Q', 'I', 'I', 'M', 'E', '2')")
 
@@ -81,7 +81,7 @@ def test_invalid_QSIP2DataFormat(self):
             with open(fp, 'wb') as fh:
                 pickle.dump(vector, fh)
 
-            format = QSIP2DataFormat(fp, mode='r')
+            format = QSIP2DataUnfilteredFormat(fp, mode='r')
 
             msg = 'There was a problem loading your qSIP2 data.*'
             with self.assertRaisesRegex(ValidationError, msg):

q2_qsip2/types/tests/test_transformers.py

@@ -14,7 +14,7 @@
 
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_qsip2.types import QSIP2DataFormat
+from q2_qsip2.types import QSIP2DataUnfilteredFormat
 
 
 class TestTransformers(TestPluginBase):
@@ -26,13 +26,17 @@ def get_qsip_object(self):
             'data' / 'qsip-data.pickle'
         )
 
-        transformer = self.get_transformer(QSIP2DataFormat, RS4)
+        transformer = self.get_transformer(QSIP2DataUnfilteredFormat, RS4)
 
-        return transformer(QSIP2DataFormat(pickle_fp, mode='r'))
+        return transformer(QSIP2DataUnfilteredFormat(pickle_fp, mode='r'))
 
     def test_object_to_pickle_file_and_back(self):
-        from_object_transformer = self.get_transformer(RS4, QSIP2DataFormat)
-        from_format_transformer = self.get_transformer(QSIP2DataFormat, RS4)
+        from_object_transformer = self.get_transformer(
+            RS4, QSIP2DataUnfilteredFormat
+        )
+        from_format_transformer = self.get_transformer(
+            QSIP2DataUnfilteredFormat, RS4
+        )
 
         qsip_object = self.get_qsip_object()
         ro.r['validate'](qsip_object)

q2_qsip2/types/tests/test_types.py

@@ -8,11 +8,14 @@
 
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_qsip2.types import QSIP2Data
+from q2_qsip2.types import QSIP2Data, Unfiltered, Filtered, EAF
 
 
 class TestTypes(TestPluginBase):
     package = 'q2_qsip2.types.tests'
 
-    def test_QSIP2Data_type_is_registered(self):
+    def test_QSIP2Data_types_registered(self):
         self.assertRegisteredSemanticType(QSIP2Data)
+        self.assertRegisteredSemanticType(Unfiltered)
+        self.assertRegisteredSemanticType(Filtered)
+        self.assertRegisteredSemanticType(EAF)