Merge pull request #87 from icgc-dcc/log-file-bug

egasub/submission/submit.py

@@ -109,7 +109,7 @@ def submit_dataset(ctx, dry_run=True):
     for sub_folder in os.listdir(ctx.obj['CURRENT_DIR']):
         sub_folder_path = os.path.join(ctx.obj['CURRENT_DIR'],sub_folder)
         if ctx.obj['CURRENT_DIR_TYPE'] == "unaligned":
-            file_log = os.path.join(sub_folder_path,'.status','analysis.log')
+            file_log = os.path.join(sub_folder_path,'.status','run.log')
             yaml_file = os.path.join(sub_folder_path,'experiment.yaml')
             is_run = True
         else:
@@ -202,4 +202,3 @@ def submittable_status(_file):
         return last.strip().split('\t')
     except Exception:
         return None
-

requirements-test.txt

@@ -1,5 +1,5 @@
 pytest
 pytest-cov
 coverage
-coveralls
+coveralls==1.1
 httpretty

tests/conftest.py

@@ -136,11 +136,11 @@ def mock_server(ctx):
                     content_type="application/json")
 
     # for submitter DELETE
-    httpretty.register_uri(httpretty.DELETE, "https://ega.crg.eu/submitterportal/v1/samples/12345",
+    httpretty.register_uri(httpretty.DELETE, "https://ega.crg.eu:443/submitterportal/v1/samples/12345",
                            body='{"header" : {"code" : "200"}, "response" : {"result" : [{ "id":"12345", "alias": "fgfg", "status": "VALIDATED"}]}}',
                            content_type="application/json")
 
-    httpretty.register_uri(httpretty.PUT, "https://ega.crg.eu/submitterportal/v1/submissions/12345?action=SUBMIT",
+    httpretty.register_uri(httpretty.PUT, "https://ega.crg.eu:443/submitterportal/v1/submissions/12345?action=SUBMIT",
                     body='{"header" : {"code" : "200"}, "response" : {"result" : [{ "id":"12345", "alias": "fgfg", "status": "VALIDATED"}]}}',
                     content_type="application/json",
                     X_Token= "sdfsd")
@@ -161,4 +161,4 @@ def mock_server(ctx):
 
     httpretty.register_uri(httpretty.PUT, "%sanalysiss/555?action=SUBMIT" % (ctx.obj['SETTINGS']['apiUrl']),
                            body='{"header" : {"code" : "200"}, "response" : {"result" : [{ "id":"555", "alias": "fgfg", "status": "VALIDATED"}]}}',
-                           content_type="application/json")
+                           content_type="application/json")