Support scanning HiSeq runs with multiple analyses.

[htsworkflow.git] / htsworkflow / pipelines / test / test_runfolder_casava_1_7.py

diff --git a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
index ae910553bd4fde1dea0b2d5f20e4793cb159120c..96a5bcf1102a1a558c00ac93876cfb870cc50677 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
+++ b/htsworkflow/pipelines/test/test_runfolder_casava_1_7.py
@@ -13,7 +13,7 @@ from htsworkflow.pipelines import gerald
 from htsworkflow.pipelines import ipar
 from htsworkflow.pipelines import runfolder
 from htsworkflow.pipelines import srf
-from htsworkflow.pipelines.runfolder import ElementTree
+from htsworkflow.pipelines import ElementTree
 
 from htsworkflow.pipelines.test.simulate_runfolder import *
 
@@ -197,7 +197,6 @@ class RunfolderTests(TestCase):
 
 
     def test_eland(self):
-        ls_tree(self.runfolder_dir)
         hg_map = {'Lambda.fa': 'Lambda.fa'}
         for i in range(1,22):
           short_name = 'chr%d.fa' % (i,)
@@ -269,21 +268,21 @@ class RunfolderTests(TestCase):
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         # do we get the flowcell id from the FlowcellId.xml file
         make_flowcell_id(self.runfolder_dir, FCID)
         runs = runfolder.get_runs(self.runfolder_dir)
         self.failUnlessEqual(len(runs), 1)
         name = 'run_%s_%s.xml' % ( FCID, date.today().strftime('%Y-%m-%d'),)
-        self.failUnlessEqual(runs[0].name, name)
+        self.failUnlessEqual(runs[0].serialization_filename, name)
 
         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)
 
         r2 = runfolder.PipelineRun(xml=xml)
-        self.failUnlessEqual(r1.name, r2.name)
+        self.failUnlessEqual(r1.serialization_filename, r2.serialization_filename)
         self.failIfEqual(r2.image_analysis, None)
         self.failIfEqual(r2.bustard, None)
         self.failIfEqual(r2.gerald, None)
@@ -299,8 +298,6 @@ class RunfolderTests(TestCase):
             glob.fnmatch.fnmatch("s_1_0001_qseq.txt", pattern),
             False)
 
-        print pattern
-
 
 def suite():
     from unittest2 import TestSuite, defaultTestLoader