This might actually generate soft file with raw & supplemental data.

[htsworkflow.git] / htsworkflow / submission / geo.py

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
index 413d2c3ae5e99daa7025a6be3101edb50d96da85..097bea1083af8c1ffc39b3edea9a6e94e0a63fcd 100644 (file)
--- a/htsworkflow/submission/geo.py
+++ b/htsworkflow/submission/geo.py
@@ -17,8 +17,8 @@ from django.template import Context, loader
 LOGGER = logging.getLogger(__name__)
 
 class GEOSubmission(Submission):
-    def __init__(self, name, model):
-        super(GEOSubmission, self).__init__(name, model)
+    def __init__(self, name, model, host):
+        super(GEOSubmission, self).__init__(name, model, host)
 
     def make_soft(self, result_map):
         samples = []
@@ -36,7 +36,7 @@ class GEOSubmission(Submission):
                 LOGGER.error(errmsg.format(str(an_analysis),))
                 continue
             elif len(metadata) > 1:
-                errmsg = 'Confused there are more than one samples for %s'
+                errmsg = 'Confused there are more than one sample for %s'
                 LOGGER.debug(errmsg % (str(an_analysis),))
             metadata = metadata[0]
             metadata['raw'] = self.get_raw_files(an_analysis)
@@ -111,7 +111,7 @@ class GEOSubmission(Submission):
 
         context = Context({
             'submission': str(analysis_node.uri),
-            'file_class': str(geoSoftNS['supplemental'])
+            'file_class': str(geoSoftNS['supplemental'].uri)
             })
 
         return self.execute_query(query_template, context)
@@ -123,7 +123,7 @@ class GEOSubmission(Submission):
 
         context = Context({
             'submission': str(analysis_node.uri),
-            'file_class': str(geoSoftNS['raw']),
+            'file_class': str(geoSoftNS['raw'].uri),
             })
 
         lanes = {}