Test with tmpdir

zavolanlab · Sep 13, 2023 · 73ed136 · 73ed136
1 parent 77acd75
commit 73ed136
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Showing 3 changed files with 4,571 additions and 4 deletions.
diff --git a/htsinfer/mapping.py b/htsinfer/mapping.py
@@ -1,5 +1,6 @@
 """Mapping FASTQ's and managing the outputs of STAR."""
 
+import os
 import logging
 import math
 from pathlib import Path

diff --git a/tests/test_get_library_type.py b/tests/test_get_library_type.py
@@ -111,14 +111,14 @@ def test_evaluate_mate_relationship_split_mates(self):
             StatesTypeRelationship.split_mates
         )
 
-    def test_evaluate_mate_relationship_not_mates(self):
+    def test_evaluate_mate_relationship_not_mates(self, tmpdir):
         """Test mate relationship evaluation logic with input files that are
         not mates from a paired-end library.
         """
         CONFIG.args.path_1_processed = FILE_IDS_NOT_MATCH_1
         CONFIG.args.path_2_processed = FILE_MATE_2
         CONFIG.args.t_file_processed = FILE_TRANSCRIPTS
-        CONFIG.results.library_source.file_1.short_name = "hsapiens"
+        CONFIG.args.tmp_dir = tmpdir
         MAPPING.paths = (FILE_IDS_NOT_MATCH_1, FILE_MATE_2)
         MAPPING.transcripts_file = FILE_TRANSCRIPTS
         test_instance = GetLibType(config=CONFIG,
@@ -131,13 +131,13 @@ def test_evaluate_mate_relationship_not_mates(self):
             StatesTypeRelationship.not_mates
         )
 
-    def test_evaluate_split_mates_not_matching_ids(self):
+    def test_evaluate_split_mates_not_matching_ids(self, tmpdir):
         """Test mate relationship evaluation logic with input files that are
         not mates from a paired-end library.
         """
         CONFIG.args.path_1_processed = FILE_IDS_NOT_MATCH_1
         CONFIG.args.path_2_processed = FILE_IDS_NOT_MATCH_2
-        CONFIG.results.library_source.file_1.short_name = None
+        CONFIG.args.tmp_dir = tmpdir
         MAPPING.paths = (FILE_IDS_NOT_MATCH_1, FILE_IDS_NOT_MATCH_2)
         test_instance = GetLibType(config=CONFIG,
                                    mapping=MAPPING)