Merge pull request #40 from UMCUGenetics/hotfix/3.3.1

HOTFIX 3.3.1 fixed issue where a warning after an error did not propagate the error

rsync_to_rdisc.py

@@ -276,13 +276,14 @@ def run_vcf_upload(vcf_file, vcf_type, run):
 
 
 def get_upload_state(upload_result):
+    return_value = 'ok'
     for msg in upload_result:
         if 'error' in msg.lower():
-            return 'error'
+            return_value = 'error'
+            break
         elif 'warning' in msg.lower():
-            return 'warning'
-    return 'ok'
-
+            return_value = 'warning'
+    return return_value
 
 def upload_gatk_vcf(run, run_folder):
     # Remove projects from run

test_rsync_to_rdisc.py

@@ -397,8 +397,18 @@ def test_run_vcf_upload(mocker, set_up_test):
     (["warning"], "warning"),
     (["Warning"], "warning"),
     (["vcf_upload_warning"], "warning"),
-    (["ok"], "ok")
-   ])
+    (["ok"], "ok"),
+    (["error", "error"], "error"),
+    (["warning", "warning"], "warning"),
+    (["error", "warning"], "error"),
+    (["warning", "error"], "error"),
+    (["warning", "ok"], "warning"),
+    (["ok", "warning"], "warning"),
+    (["warning", "error", "ok"], "error"),
+    (["ok", "warning", "ok", "error"], "error"),
+    (["ok", "warning", "error"], "error"),
+    (["ok", "error", "warning"], "error")
+])
 def test_get_upload_state(msg, expected):
     return_state = rsync_to_rdisc.get_upload_state(msg)
     assert return_state == expected