SQUASH: basic unit tests

q2_types/per_sample_sequences/_transformer.py

@@ -73,6 +73,14 @@
     yaml_fmt=YamlFormat,
 )
 
+_dirfmt_to_casava_partial = functools.partial(
+    _dirfmt_to_casava,
+    manifest_fmt=FastqManifestFormat,
+    abs_manifest_fmt=FastqAbsolutePathManifestFormat,
+    fastq_fmt=FastqGzFormat,
+    casava_fmt=CasavaOneEightSingleLanePerSampleDirFmt,
+)
+
 
 @plugin.register_transformer
 def _3(dirfmt: CasavaOneEightSingleLanePerSampleDirFmt) \
@@ -84,7 +92,7 @@ def _3(dirfmt: CasavaOneEightSingleLanePerSampleDirFmt) \
 @plugin.register_transformer
 def _3_and_a_half(dirfmt_in: SingleLanePerSampleSingleEndFastqDirFmt) \
         -> CasavaOneEightSingleLanePerSampleDirFmt:
-    return _dirfmt_to_casava(dirfmt_in)
+    return _dirfmt_to_casava_partial(dirfmt_in)
 
 
 @plugin.register_transformer
@@ -97,7 +105,7 @@ def _4(dirfmt: CasavaOneEightSingleLanePerSampleDirFmt) \
 @plugin.register_transformer
 def _4_and_a_half(dirfmt_in: SingleLanePerSamplePairedEndFastqDirFmt) \
         -> CasavaOneEightSingleLanePerSampleDirFmt:
-    return _dirfmt_to_casava(dirfmt_in)
+    return _dirfmt_to_casava_partial(dirfmt_in)
 
 
 @plugin.register_transformer

q2_types/per_sample_sequences/tests/test_transformer.py

@@ -1065,6 +1065,32 @@ def test_paired_end_fastq_manifest_phred64_to_slpspefdf(self):
         with obs.manifest.view(FastqManifestFormat).open() as obs_manifest:
             self.assertEqual(obs_manifest.read(), self.exp_pe_manifest)
 
+    def test_slpssefdf_to_casava_one_eight_single_lane_per_sample_dirfmt(self):
+        filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',)
+        _, obs = self.transform_format(
+            SingleLanePerSampleSingleEndFastqDirFmt,
+            CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames
+        )
+
+        exp_fp = ['Human-Kneecap_S1_L001_R1_001.fastq.gz']
+        obs_fp = [str(fp) for fp, _ in obs.sequences.iter_views(FastqGzFormat)]
+
+        self.assertEqual(obs_fp, exp_fp)
+
+    def test_slpspefdf_to_casava_one_eight_single_lane_per_sample_dirfmt(self):
+        filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',
+                     'paired_end_data/Human-Kneecap_S1_L001_R2_001.fastq.gz')
+        _, obs = self.transform_format(
+            SingleLanePerSamplePairedEndFastqDirFmt,
+            CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames
+        )
+
+        exp_fp = ['Human-Kneecap_S1_L001_R1_001.fastq.gz',
+                  'Human-Kneecap_S1_L001_R2_001.fastq.gz']
+        obs_fp = [str(fp) for fp, _ in obs.sequences.iter_views(FastqGzFormat)]
+
+        self.assertEqual(obs_fp, exp_fp)
+
 
 if __name__ == '__main__':
     unittest.main()