illumina.py: fixed small bug where exception was not raised for missi…

…ng files (#926) * illumina.py: fixed small bug where exception was not raised for missing files
broadinstitute · Feb 14, 2019 · aeb76dd · aeb76dd
1 parent e922e7a
commit aeb76dd
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/illumina.py b/illumina.py
@@ -596,13 +596,17 @@ def close(self):
             self.tempDir = None
 
     def get_RunInfo(self):
-        if self.runinfo is None and os.path.isfile(os.path.join(self.path, 'RunInfo.xml')):
-            self.runinfo = RunInfo(os.path.join(self.path, 'RunInfo.xml'))
+        if self.runinfo is None:
+            runinfo_file = os.path.join(self.path, 'RunInfo.xml')
+            util.file.check_paths(runinfo_file)
+            self.runinfo = RunInfo(runinfo_file)
         return self.runinfo
 
     def get_SampleSheet(self, only_lane=None):
-        if self.samplesheet is None and os.path.isfile(os.path.join(self.path, 'SampleSheet.csv')):
-            self.samplesheet = SampleSheet(os.path.join(self.path, 'SampleSheet.csv'), only_lane=only_lane)
+        if self.samplesheet is None:
+            samplesheet_file = os.path.join(self.path, 'SampleSheet.csv')
+            util.file.check_paths(samplesheet_file)
+            self.samplesheet = SampleSheet(samplesheet_file, only_lane=only_lane)
         return self.samplesheet
 
     def get_intensities_dir(self):

diff --git a/test/unit/test_illumina.py b/test/unit/test_illumina.py
@@ -192,9 +192,9 @@ def test_tarball_run_info(self):
     def test_tarball_fail_missing_data(self):
         inDir = util.file.get_test_input_path(self)
         with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-runinfo.tar.gz')) as idir:
-            self.assertRaises(Exception, idir.get_SampleSheet())
+            self.assertRaises(Exception, idir.get_SampleSheet)
         with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-samplesheet.tar.gz')) as idir:
-            self.assertRaises(Exception, idir.get_RunInfo())
+            self.assertRaises(Exception, idir.get_RunInfo)
 
 
 class TestDifficultSampleNames(TestCaseWithTmp):