Rename stripNamespace strip_namespace

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

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
index 413d2c3ae5e99daa7025a6be3101edb50d96da85..1d98bd5c9550e36408b3ba4faed02ee8d28cedee 100644 (file)
--- a/htsworkflow/submission/geo.py
+++ b/htsworkflow/submission/geo.py
@@ -8,7 +8,7 @@ from htsworkflow.submission.submission import Submission
 from htsworkflow.util.rdfhelp import \
      fromTypedNode, \
      geoSoftNS, \
-     stripNamespace, \
+     strip_namespace, \
      submissionOntology
 
 from django.conf import settings
@@ -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 = {}
@@ -131,10 +131,10 @@ class GEOSubmission(Submission):
             data = {}
             for k, v in row.items():
                 data[k] = v
-            lane = str(data['lane'])
-            lanes.setdefault(lane, []).append(data)
+            library = str(data['library'])
+            lanes.setdefault(library, []).append(data)
         result = []
-        for lane, files in lanes.items():
+        for library, files in lanes.items():
             if len(files) > 2:
                 errmsg = "Don't know what to do with more than 2 raw files"
                 raise ValueError(errmsg)
@@ -143,7 +143,7 @@ class GEOSubmission(Submission):
             elif len(files) == 1:
                 is_paired = False
             elif len(files) == 0:
-                raise RuntimeError("Empty lane list discovered")
+                raise RuntimeError("Empty library list discovered")
             files = self._format_filename(files, is_paired)
             files = self._format_flowcell_type(files, is_paired)
             files = self._format_read_length(files, is_paired)
@@ -207,7 +207,7 @@ class GEOSubmission(Submission):
     def query_to_soft_dictionary(self, results, heading):
         attributes = []
         for r in results:
-            name = stripNamespace(geoSoftNS, r['name'])
+            name = strip_namespace(geoSoftNS, r['name'])
             if name is not None:
                 if name.lower() == heading.lower():
                     name = '^' + name