Recent IPAR xml config blocks include the runfolder name

I was previously extracting it in the gerald step, but since we
have a number of runfolders with no aligned directory that wasn't working.

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index f818b3495fbf2fd2d8f2fba13d698188e7680d3f..8203f5e0f29fda173728e3f504522f6cd579520f 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -75,6 +75,14 @@ class IPAR(object):
         if xml is not None:
             self.set_elements(xml)
 
         if xml is not None:
             self.set_elements(xml)
 

+    def _get_runfolder_name(self):
+        """Return runfolder name"""
+        if self.tree is None:
+            raise ValueError("Can't query an empty run")
+        runfolder = self.tree.xpath('RunParameters/Runfolder')
+        return runfolder
+    runfolder_name = property(_get_runfolder)
+    

     def _get_software(self):
         """Return software name"""
         if self.tree is None:
     def _get_software(self):
         """Return software name"""
         if self.tree is None:

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e217de63d5733e524ae551f06eea40528e11..26c592ce5f7eb6d65175031f9c9010dc400d9410 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -129,10 +129,12 @@ class PipelineRun(object):
             return path_fields[-1]
 
     def _get_runfolder_name(self):
             return path_fields[-1]
 
     def _get_runfolder_name(self):

-        if self.gerald is None:
-            return None
-        else:
+        if self.gerald:

             return self.gerald.runfolder_name
             return self.gerald.runfolder_name

+        elif hasattr(self.image_analysis, 'runfolder_name'):
+            return self.image_analysis.runfolder_name
+        else:
+            return None

     runfolder_name = property(_get_runfolder_name)
 
     def _get_run_dirname(self):
     runfolder_name = property(_get_runfolder_name)
 
     def _get_run_dirname(self):

diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py
index 63b4a8df0c7176b8ced6aa1a022a8b22f7c6a7bb..0db7857399cd8f9c391a8b8c58fb0b5023fef0f5 100644 (file)
--- a/htsworkflow/pipelines/test/test_runfolder_rta180.py
+++ b/htsworkflow/pipelines/test/test_runfolder_rta180.py
@@ -25,9 +25,8 @@ def make_runfolder(obj=None):
     temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
 
     flowcell_id = '4286GAAXX'
     temp_dir = tempfile.mkdtemp(prefix='tmp_runfolder_')
 
     flowcell_id = '4286GAAXX'

-    runfolder_dir = os.path.join(
-        temp_dir,
-        '090608_HWI-EAS229_0117_{0}'.format(flowcell_id))
+    runfolder = '090608_HWI-EAS229_0117_{0}'.format(flowcell_id)
+    runfolder_dir = os.path.join(temp_dir, runfolder)

     os.mkdir(runfolder_dir)
 
     data_dir = os.path.join(runfolder_dir, 'Data')
     os.mkdir(runfolder_dir)
 
     data_dir = os.path.join(runfolder_dir, 'Data')


@@ -50,6 +49,7 @@ def make_runfolder(obj=None):
     if obj is not None:
         obj.flowcell_id = flowcell_id
         obj.temp_dir = temp_dir
     if obj is not None:
         obj.flowcell_id = flowcell_id
         obj.temp_dir = temp_dir

+        obj.runfolder = runfolder

         obj.runfolder_dir = runfolder_dir
         obj.data_dir = data_dir
         obj.image_analysis_dir = intensities_dir
         obj.runfolder_dir = runfolder_dir
         obj.data_dir = data_dir
         obj.image_analysis_dir = intensities_dir


@@ -262,8 +262,9 @@ class RunfolderTests(TestCase):
 
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)
 
         # do we get the flowcell id from the filename?
         self.failUnlessEqual(len(runs), 1)

-        name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
+        name = 'run_4286GAAXX_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)        

         self.failUnlessEqual(runs[0].serialization_filename, name)
         self.failUnlessEqual(runs[0].serialization_filename, name)

+        self.assertEqual(runs[0].runfolder_name, '090220_HWI-EAS229_0093_30VR0AAXX')

 
         # do we get the flowcell id from the FlowcellId.xml file
         make_flowcell_id(self.runfolder_dir, '207BTAAXY')
 
         # do we get the flowcell id from the FlowcellId.xml file
         make_flowcell_id(self.runfolder_dir, '207BTAAXY')


@@ -272,6 +273,7 @@ class RunfolderTests(TestCase):
         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
         self.failUnlessEqual(runs[0].serialization_filename, name)
 
         name = 'run_207BTAAXY_%s.xml' % ( date.today().strftime('%Y-%m-%d'),)
         self.failUnlessEqual(runs[0].serialization_filename, name)
 

+

         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)
         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)