Match what generate_sample_results_tree creates

The turtle rules I was using for scanning a submission directory
didn't match what I was creating, which was generating some
warning messages.

Fix this cut down on logger warning messages being generated
during test runs.

diff --git a/htsworkflow/submission/test/submission_test_common.py b/htsworkflow/submission/test/submission_test_common.py
index 3f435761b8d0ba7a8b0aae3a33da87219cdee32d..47b6ed390c2504bd88c5189d65a0a6523a28e7c8 100644 (file)
--- a/htsworkflow/submission/test/submission_test_common.py
+++ b/htsworkflow/submission/test/submission_test_common.py
@@ -34,7 +34,7 @@ S1_TURTLE = TURTLE_PREFIX + """
 <http://localhost/library/1000/>
   htswlib:cell_line "Cell1000" ;
   htswlib:library_id "1000" ;
-  htswlib:library_type "Single" ;
+  htswlib:library_type "Single End (non-multiplexed)" ;
   htswlib:replicate "1" ;
   htswlib:has_lane <http://localhost/lane/1> ;
   a htswlib:IlluminaLibrary .

diff --git a/htsworkflow/submission/test/test_submission.py b/htsworkflow/submission/test/test_submission.py
index 8daee447edb16c77890962d71c52e3d63711c175..ed2519a27d4506e5c15ab6b5004da206da8d1544 100644 (file)
--- a/htsworkflow/submission/test/test_submission.py
+++ b/htsworkflow/submission/test/test_submission.py
@@ -83,15 +83,15 @@ class TestSubmission(TestCase):
     def test_scan_submission_dirs(self):
         turtle = get_turtle_header() + """
 @prefix thisView: <http://jumpgate.caltech.edu/wiki/SubmissionsLog/test/view/> .
-thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq\\.bz2$" ;
+thisView:Fastq ucscDaf:filename_re ".*[^12]\\.fastq$" ;
                a geoSoft:raw ;
                geoSoft:fileTypeLabel "fastq" ;
                ucscDaf:output_type "read" .
-thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq\\.bz2$" ;
+thisView:FastqRead1 ucscDaf:filename_re ".*r1\\.fastq$" ;
                a geoSoft:raw ;
                geoSoft:fileTypeLabel "fastq" ;
                ucscDaf:output_type "read1" .
-thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq\\.bz2$" ;
+thisView:FastqRead2 ucscDaf:filename_re ".*r2\\.fastq$" ;
                a geoSoft:raw ;
                geoSoft:fileTypeLabel "fastq" ;
                ucscDaf:output_type "read2" .