Abstract out exception handling for tool shed API exceptions.

planemo/commands/cmd_shed_upload.py

@@ -1,6 +1,5 @@
 """
 """
-import json
 import sys
 
 import click
@@ -96,20 +95,9 @@ def __handle_upload(ctx, realized_repository, **kwds):
     try:
         tsi.repositories.update_repository(repo_id, tar_path, **update_kwds)
     except Exception as e:
-        if hasattr(e, "read"):
-            exception_content = e.read()
-            try:
-                # Galaxy passes nice JSON messages as their errors, which bioblend
-                # blindly returns. Attempt to parse those.
-                upstream_error = json.loads(exception_content)
-                error(upstream_error['err_msg'])
-            except Exception as e2:
-                error("Could not update %s" % realized_repository.name)
-                error(exception_content)
-                error(e2.read())
-        else:
-            error("Could not update %s" % realized_repository.name)
-            error(str(e))
+        message = shed.api_exception_to_message(e)
+        error("Could not update %s" % realized_repository.name)
+        error(message)
         return -1
     info("Repository %s updated successfully." % realized_repository.name)
     return 0

planemo/shed.py

@@ -788,13 +788,9 @@ def find_repository_id(self, ctx, tsi):
             )
             return repo_id
         except Exception as e:
+            message = api_exception_to_message(e)
             error("Could not update %s" % self.name)
-            try:
-                error(e.read())
-            except AttributeError:
-                # I've seen a case where the error couldn't be read, so now
-                # wrapped in try/except
-                error("Could not query for repository in toolshed")
+            error(message)
         return None
 
     def create(self, ctx, tsi):
@@ -819,6 +815,20 @@ def create(self, ctx, tsi):
             return None
 
 
+def api_exception_to_message(e):
+    message = str(e)
+    if hasattr(e, "read"):
+        message = e.read()
+        try:
+            # Galaxy passes nice JSON messages as their errors, which bioblend
+            # blindly returns. Attempt to parse those.
+            upstream_error = json.loads(message)
+            message = upstream_error['err_msg']
+        except Exception:
+            pass
+    return message
+
+
 def _glob(path, pattern):
     pattern = os.path.join(path, pattern)
     if os.path.isdir(pattern):