From 8d7855fc67d6ad000e9c87a410f7f55248b0c5a0 Mon Sep 17 00:00:00 2001 From: Matthew Dillon Date: Tue, 30 Jul 2019 06:28:15 -0700 Subject: [PATCH] MAINT: Bring back BIOMV100, drop downcast trnsfrmr --- q2_types/feature_table/_transformer.py | 23 ----------------- .../feature_table/tests/test_transformer.py | 25 ------------------- 2 files changed, 48 deletions(-) diff --git a/q2_types/feature_table/_transformer.py b/q2_types/feature_table/_transformer.py index 67c0ec46..ededf819 100644 --- a/q2_types/feature_table/_transformer.py +++ b/q2_types/feature_table/_transformer.py @@ -73,13 +73,6 @@ def _table_to_v210(data): return ff -def _table_to_v100(data): - ff = BIOMV100Format() - with ff.open() as fh: - data.to_json(generated_by=_get_generated_by(), direct_io=fh) - return ff - - def _dataframe_to_table(df): if df.index.inferred_type != 'string': raise TypeError("Please provide a DataFrame with a string-based Index") @@ -87,16 +80,6 @@ def _dataframe_to_table(df): sample_ids=df.index) -@plugin.register_transformer -def _1(data: biom.Table) -> BIOMV100Format: - data = _drop_axis_metadata(data) - - ff = BIOMV100Format() - with ff.open() as fh: - fh.write(data.to_json(generated_by=_get_generated_by())) - return ff - - @plugin.register_transformer def _2(ff: BIOMV100Format) -> biom.Table: return _parse_biom_table_v100(ff) @@ -152,12 +135,6 @@ def _10(df: pd.DataFrame) -> BIOMV210Format: return _table_to_v210(_dataframe_to_table(df)) -@plugin.register_transformer -def _11(ff: BIOMV210Format) -> BIOMV100Format: - data = _parse_biom_table_v210(ff) - return _table_to_v100(data) - - @plugin.register_transformer def _12(data: biom.Table) -> qiime2.Metadata: return _table_to_metadata(data) diff --git a/q2_types/feature_table/tests/test_transformer.py b/q2_types/feature_table/tests/test_transformer.py index e2e749d7..a1805689 100644 --- a/q2_types/feature_table/tests/test_transformer.py +++ b/q2_types/feature_table/tests/test_transformer.py @@ -24,20 +24,6 @@ class TestTransformers(TestPluginBase): package = 'q2_types.feature_table.tests' - def test_biom_table_to_biom_v100_format(self): - filepath = self.get_data_path('feature-table_v100.biom') - transformer = self.get_transformer(biom.Table, BIOMV100Format) - input = biom.load_table(filepath) - - obs = transformer(input) - obs = biom.load_table(str(obs)) - - exp = input - self.assertEqual(obs.ids(axis='observation').all(), - exp.ids(axis='observation').all()) - self.assertEqual(obs.ids(axis='sample').all(), - exp.ids(axis='sample').all()) - def test_biom_v100_format_to_biom_table(self): input, obs = self.transform_format(BIOMV100Format, biom.Table, filename='feature-table_v100.biom') @@ -111,17 +97,6 @@ def test_biom_v100_format_to_biom_v210_format(self): self.assertEqual(obs.ids(axis='sample').all(), exp.ids(axis='sample').all()) - def test_biom_v210_format_to_biom_v100_format(self): - input, obs = self.transform_format(BIOMV210Format, BIOMV100Format, - filename='feature-table_v210.biom') - exp = biom.load_table(str(input)) - obs = biom.load_table(str(obs)) - - self.assertEqual(obs.ids(axis='observation').all(), - exp.ids(axis='observation').all()) - self.assertEqual(obs.ids(axis='sample').all(), - exp.ids(axis='sample').all()) - def test_to_pandas_data_frame_to_biom_v210_format(self): filepath = self.get_data_path('feature-table_v100.biom') transformer1 = self.get_transformer(BIOMV100Format, pd.DataFrame)