SQUASH: Make the test actually work

qiime2 · Sep 2, 2019 · 3f357bc · 3f357bc
1 parent dbb860f
commit 3f357bc
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/q2_types/per_sample_sequences/_transformer.py b/q2_types/per_sample_sequences/_transformer.py
@@ -11,6 +11,7 @@
 import gzip
 import shutil
 import warnings
+import tempfile
 import collections
 
 import skbio
@@ -97,7 +98,11 @@ def _11(dirfmt: CasavaOneEightLanelessPerSampleDirFmt) \
 @plugin.register_transformer
 def _12(dirfmt: SingleLanePerSampleSingleEndFastqDirFmt) \
         -> CasavaOneEightSingleLanePerSampleDirFmt:
-    return CasavaOneEightSingleLanePerSampleDirFmt(str(dirfmt), mode='r')
+    casavaDir = tempfile.mkdtemp()
+    for file in os.listdir(str(dirfmt)):
+        if 'MANIFEST' not in file and 'metadata' not in file:
+            shutil.copy(os.path.join(str(dirfmt), file), casavaDir)
+    return CasavaOneEightSingleLanePerSampleDirFmt(casavaDir, mode='r')
 
 
 @plugin.register_transformer

diff --git a/q2_types/per_sample_sequences/tests/test_transformer.py b/q2_types/per_sample_sequences/tests/test_transformer.py
@@ -139,11 +139,12 @@ def test_casava_one_eight_single_lane_per_sample_dirfmt_to_slpssefdf(self):
             self.assertEqual(act, exp)
 
     def test_slpssefdf_to_casava_one_eight_single_lane_per_sample_dirfmt(self):
-        filenames = ('Human-Kneecap_S1_L001_R1_001.fastq.gz',)
+        filenames = ('single-end-two-sample-data2/MANIFEST',
+                     'metadata.yml',
+                     'Human-Kneecap_S1_L001_R1_001.fastq.gz')
         input, obs = self.transform_format(
             SingleLanePerSampleSingleEndFastqDirFmt,
-            CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames
-        )
+            CasavaOneEightSingleLanePerSampleDirFmt, filenames=filenames)
 
         input = skbio.io.read(
             '%s/Human-Kneecap_S1_L001_R1_001.fastq.gz' % str(input),