Merge pull request #8910 from jmchilton/no_recompute_input_ext

Do not re-compute job input_ext/dbkey in job finish.

lib/galaxy/jobs/__init__.py

@@ -1695,14 +1695,25 @@ class JobWrapper(HasResourceParameters):
         self.cleanup(delete_files=delete_files)
 
     def discover_outputs(self, job, inp_data, out_data, out_collections):
-        input_ext = 'data'
-        input_dbkey = '?'
-        for _, data in inp_data.items():
-            # For loop odd, but sort simulating behavior in galaxy.tools.actions
-            if not data:
-                continue
-            input_ext = data.ext
-            input_dbkey = data.dbkey or '?'
+        # Try to just recover input_ext and dbkey from job parameters (used and set in
+        # galaxy.tools.actions). Old jobs may have not set these in the job parameters
+        # before persisting them.
+        input_params = job.raw_param_dict()
+        input_ext = input_params.get("__input_ext")
+        input_dbkey = input_params.get("dbkey")
+        if input_ext is not None:
+            input_ext = loads(input_ext)
+            input_dbkey = loads(input_dbkey)
+        else:
+            # Legacy jobs without __input_ext.
+            input_ext = 'data'
+            input_dbkey = '?'
+            for _, data in inp_data.items():
+                # For loop odd, but sort simulating behavior in galaxy.tools.actions
+                if not data:
+                    continue
+                input_ext = data.ext
+                input_dbkey = data.dbkey or '?'
 
         # Create generated output children and primary datasets.
         tool_working_directory = self.tool_working_directory

lib/galaxy/managers/jobs.py

@@ -283,7 +283,9 @@ class JobSearch(object):
             # parameter as these are not passed along when expanding tool parameters
             # and they can differ without affecting the resulting dataset.
             for parameter in job.parameters:
-                if parameter.name in {'__workflow_invocation_uuid__', 'chromInfo', 'dbkey'} or parameter.name.endswith('|__identifier__'):
+                if parameter.name.startswith("__"):
+                    continue
+                if parameter.name in {'chromInfo', 'dbkey'} or parameter.name.endswith('|__identifier__'):
                     continue
                 n_parameters += 1
             if not n_parameters == len(param_dump):

lib/galaxy/tools/actions/__init__.py

@@ -334,6 +334,7 @@ class DefaultToolAction(object):
 
         # Add the dbkey to the incoming parameters
         incoming["dbkey"] = input_dbkey
+        incoming["__input_ext"] = input_ext
         # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
         wrapped_params = self._wrapped_params(trans, tool, incoming, inp_data)