From 5644e2bfe7c1f7e5af99289cd918f783b61c441a Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 5 Dec 2013 14:45:59 -0800
Subject: [PATCH] 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.
---
 htsworkflow/pipelines/ipar.py                       |  8 ++++++++
 htsworkflow/pipelines/runfolder.py                  |  8 +++++---
 htsworkflow/pipelines/test/test_runfolder_rta180.py | 10 ++++++----
 3 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index f818b34..8203f5e 100644
--- 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)
 
+    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:
diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 7c06e21..26c592c 100644
--- 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):
-        if self.gerald is None:
-            return None
-        else:
+        if self.gerald:
             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):
diff --git a/htsworkflow/pipelines/test/test_runfolder_rta180.py b/htsworkflow/pipelines/test/test_runfolder_rta180.py
index 63b4a8d..0db7857 100644
--- 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'
-    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')
@@ -50,6 +49,7 @@ def make_runfolder(obj=None):
     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
@@ -262,8 +262,9 @@ class RunfolderTests(TestCase):
 
         # 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.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')
@@ -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)
 
+
         r1 = runs[0]
         xml = r1.get_elements()
         xml_str = ElementTree.tostring(xml)
-- 
2.30.2