Get actual list of sequencers used for a library.

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

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
index 8ff349fe9ae7444c5cc82f20c15e8458d6cc0599..ad6642251931df7a49db3ec1c23a34d4c30ab4c0 100644 (file)
--- a/htsworkflow/submission/geo.py
+++ b/htsworkflow/submission/geo.py
@@ -40,6 +40,7 @@ class GEOSubmission(Submission):
             metadata['supplimental'] = self.get_sample_files(
                 an_analysis,
                 geoSoftNS['supplemental'])
+            metadata['run'] = self.get_run_details(an_analysis)
             samples.append(metadata)
 
         soft_template = loader.get_template('geo_submission.soft')
@@ -98,8 +99,8 @@ class GEOSubmission(Submission):
 
         results = self.execute_query(query_template, context)
         for r in results:
-
             r['dataProtocol'] = str(r['dataProtocol']).replace('\n', ' ')
+
         return results
 
     def get_sample_files(self, analysis_node, file_class):
@@ -114,6 +115,17 @@ class GEOSubmission(Submission):
 
         return self.execute_query(query_template, context)
 
+    def get_run_details(self, analysis_node):
+        """Get information about runs
+        """
+        query_template = loader.get_template('geo_run_details.sparql')
+
+        context = Context({
+            'submission': str(analysis_node.uri),
+            })
+
+        return self.execute_query(query_template, context)
+
     def query_to_soft_dictionary(self, results, heading):
         attributes = []
         for r in results: