Changes to the qiime plugin and qiime tests to handle changes in the …

…tempdir creation methods.
USDA-ARS-GBRU · Sep 23, 2024 · a313cbe · a313cbe
1 parent dc27066
commit a313cbe
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/itsxpress/q2_itsxpress.py b/itsxpress/q2_itsxpress.py
@@ -31,15 +31,11 @@
 
 #default_cluster_id=0.995
 default_cluster_id=1.0
-try:
-    tempdir = tempfile.mkdtemp(prefix='itsxpress_')
-    print("tempdir location {}".format(tempdir))
 
-except Exception as e:
-    raise ValueError("Could not create temporary directory")
 
 def _set_fastqs_and_check(fastq: str,
                           fastq2: str,
+                          tempdir: str,
                           sample_id: str,
                           single_end: bool,
                           reversed_primers: bool,
@@ -196,6 +192,11 @@ def main(per_sample_sequences,
     # Setting the taxa
     taxa = _taxa_prefix_to_taxa(taxa)
     samples = per_sample_sequences.manifest.view(pd.DataFrame)
+    try:
+        tempdir = tempfile.mkdtemp(prefix='itsxpress_')
+        # print("tempdir location {}".format(tempdir))
+    except Exception as e:
+        raise ValueError("Could not create temporary directory")
     # Creating result dir
     results = CasavaOneEightSingleLanePerSampleDirFmt()
     # Running the for loop for each sample
@@ -204,6 +205,7 @@ def main(per_sample_sequences,
         sobj = _set_fastqs_and_check(
             fastq=sample.forward,
             fastq2=sample.reverse if paired_in else None,
+            tempdir=tempdir,
             sample_id=sample.Index,
             single_end=False if paired_in else True,
             reversed_primers=reversed_primers,

diff --git a/tests/test_main_pytest.py b/tests/test_main_pytest.py
@@ -278,6 +278,8 @@ def test_create_paired_trimmed_seqs():
 	import pandas as pd
 	import itsxpress.q2_itsxpress as q2_itsxpress
 	import itsxpress.plugin_setup
+
+	tempdir = tempfile.mkdtemp()
 	# The test data dir
 	TEST_DIR = os.path.join(os.path.dirname(os.path.abspath(__name__)),"tests")
 	# Test info 1
@@ -341,6 +343,7 @@ def test_single(self):
 			for sample in samples.itertuples():
 				obs = q2_itsxpress._set_fastqs_and_check(fastq=sample.forward,
 													fastq2=None,
+													tempdir=tempdir,
 													sample_id=sample.Index,
 													single_end=True,
 													reversed_primers=False,
@@ -352,6 +355,7 @@ def test_paired(self):
 			for sample in samples.itertuples():
 				obs = q2_itsxpress._set_fastqs_and_check(fastq=sample.forward,
 													fastq2=sample.reverse,
+													tempdir=tempdir,
 													sample_id=sample.Index,
 													single_end=True,
 													reversed_primers=False,
@@ -366,6 +370,7 @@ def test_trim_single_no_cluster():
 				# Fix for missing argument
 				obs = q2_itsxpress._set_fastqs_and_check(fastq=sample.forward,
 														 fastq2=None,
+														 tempdir=tempdir,
 														 sample_id=sample.Index,
 														 single_end=True,
 														 reversed_primers=False,