From: Diane Trout <diane@ghic.org>
Date: Thu, 2 Jun 2016 00:08:07 +0000 (-0700)
Subject: Match what generate_sample_results_tree creates
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=73347c9c6c9a1370fe00034b5a713dc2235c7cd2

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 3f43576..47b6ed3 100644
--- 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 8daee44..ed2519a 100644
--- 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" .