Initial port to python3

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

diff --git a/htsworkflow/submission/geo.py b/htsworkflow/submission/geo.py
index 85947158390f699afa8a76cd719a0b1fadf26ebf..20a56a06ff7fad01a36cd9f9325ad342acf0ca4f 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 = []
@@ -28,7 +28,7 @@ class GEOSubmission(Submission):
         series = self.get_series_metadata()
         series_attribs = dict(series)
         series_id = series_attribs['^series']
-        for lib_id, result_dir in result_map.items():
+        for lib_id, result_dir in list(result_map.items()):
             an_analysis = self.get_submission_node(result_dir)
             metadata = self.get_sample_metadata(an_analysis)
             if len(metadata) == 0:
@@ -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)
@@ -52,7 +52,7 @@ class GEOSubmission(Submission):
             'platform_id': platform_id,
             'series_id': series_id,
         })
-        print str(soft_template.render(context))
+        print(str(soft_template.render(context)))
 
     def check_for_name(self, analysis_node):
         name = fromTypedNode(
@@ -129,12 +129,12 @@ class GEOSubmission(Submission):
         lanes = {}
         for row in self.execute_query(query_template, context):
             data = {}
-            for k, v in row.items():
+            for k, v in list(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 list(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)