Take into account HDA name, metadata, element_identifier and datatype

lib/galaxy/managers/jobs.py

@@ -49,7 +49,7 @@ class JobSearch(object):
         self.ldda_manager = LDDAManager(app)
         self.decode_id = self.app.security.decode_id
 
-    def by_tool_input(self, trans, tool_id, tool_version, param_dump=None, job_state='ok'):
+    def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state='ok'):
         """Search for jobs producing same results using the 'inputs' part of a tool POST."""
         user = trans.user
         input_data = defaultdict(list)
@@ -63,7 +63,19 @@ class JobSearch(object):
                 for p in path:
                     current_case = current_case[p]
                 src = current_case['src']
-                input_data[path_key].append({'src': src, 'id': value})
+                current_case = param
+                for i, p in enumerate(path):
+                    if p == 'values' and i == len(path) - 2:
+                        continue
+                    if isinstance(current_case, (list, dict)):
+                        current_case = current_case[p]
+                identifier = getattr(current_case, "element_identifier", None)
+                name = current_case.name
+                input_data[path_key].append({'src': src,
+                                             'id': value,
+                                             'identifier': identifier,
+                                             'name': name,
+                                             })
                 input_ids[src][value] = "__id_wildcard__"
                 return key, value
             return key, value
@@ -111,18 +123,32 @@ class JobSearch(object):
             for type_values in input_list:
                 t = type_values['src']
                 v = type_values['id']
+                identifier = type_values['identifier']
                 if t == 'hda':
                     a = aliased(model.JobToInputDatasetAssociation)
                     b = aliased(model.HistoryDatasetAssociation)
                     c = aliased(model.HistoryDatasetAssociation)
+                    d = aliased(model.JobParameter)
                     query = query.filter(and_(
                         model.Job.id == a.job_id,
                         a.name == k,
                         a.dataset_id == b.id,
                         c.dataset_id == b.dataset_id,
-                        c.id == v,
+                        c.id == v,  # c is the requested job input HDA
+                        # We can only compare input dataset names and metadata for a job
+                        # if we know that the input dataset hasn't changed since the job was run.
+                        # This is relatively strict, we may be able to lift this requirement if we record the jobs'
+                        # relevant parameters as JobParameters in the database
+                        b.update_time < model.Job.create_time,
+                        b.name == c.name,
+                        b.extension == c.extension,
+                        b._metadata == c._metadata,
                         or_(b.deleted == false(), c.deleted == false())
                     ))
+                    if identifier:
+                        query = query.filter(model.Job.id == d.job_id,
+                                             d.name == "%s|__identifier__" % k,
+                                             d.value == json.dumps(identifier))
                 elif t == 'ldda':
                         a = aliased(model.JobToInputLibraryDatasetAssociation)
                         query = query.filter(and_(
@@ -134,15 +160,17 @@ class JobSearch(object):
                     a = aliased(model.JobToInputDatasetCollectionAssociation)
                     b = aliased(model.HistoryDatasetCollectionAssociation)
                     c = aliased(model.HistoryDatasetCollectionAssociation)
+                    name = type_values['name']
                     query = query.filter(and_(
                         model.Job.id == a.job_id,
                         a.name == k,
                         b.id == a.dataset_collection_id,
                         c.id == v,
-                        or_(and_(b.deleted == false(), b.id == v),
+                        or_(and_(b.deleted == false(), b.id == v, b.name == name),
                             and_(or_(c.copied_from_history_dataset_collection_association_id == b.id,
                                      b.copied_from_history_dataset_collection_association_id == c.id),
-                                 c.deleted == false()
+                                 c.deleted == false(),
+                                 c.name == name,
                                  )
                             )
                     ))

lib/galaxy/tools/__init__.py

@@ -1302,6 +1302,7 @@ class Tool(object, Dictifiable):
                     trans=trans,
                     tool_id=self.id,
                     tool_version=self.version,
+                    param=param,
                     param_dump=self.params_to_strings(param, self.app, nested=True),
                 )
             execution_tracker = execute_job(trans, self, mapping_params, history=request_context.history, rerun_remap_job_id=rerun_remap_job_id, collection_info=collection_info, completed_jobs=completed_jobs)

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -302,10 +302,11 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
             return []
         params_dump = [tool.params_to_strings(param, self.app, nested=True) for param in all_params]
         jobs = []
-        for param_dump in params_dump:
+        for param_dump, param in zip(params_dump, all_params):
             job = self.job_search.by_tool_input(trans=trans,
                                                 tool_id=tool_id,
                                                 tool_version=tool.version,
+                                                param=param,
                                                 param_dump=param_dump,
                                                 job_state=payload.get('state'))
             if job:

lib/galaxy/workflow/modules.py

@@ -879,6 +879,7 @@ class ToolModule(WorkflowModule):
                 trans=trans,
                 tool_id=tool.id,
                 tool_version=tool.version,
+                param=param,
                 param_dump=tool.params_to_strings(param, trans.app, nested=True),
             )
         try:

test/api/test_jobs.py

@@ -298,6 +298,21 @@ class JobsApiTestCase(api.ApiTestCase):
         self._assert_status_code_is(delete_respone, 200)
         self._search(search_payload, expected_search_count=0)
 
+    def test_search_handle_identifiers(self):
+        # Test that input name and element identifier of a jobs' output must match for a job to be returned.
+        history_id, dataset_id = self.__history_with_ok_dataset()
+        inputs = json.dumps({
+            'input1': {'src': 'hda', 'id': dataset_id}
+        })
+        self._job_search(tool_id='identifier_single', history_id=history_id, inputs=inputs)
+        dataset_details = self._get("histories/%s/contents/%s" % (history_id, dataset_id)).json()
+        dataset_details['name'] = 'Renamed Test Dataset'
+        dataset_update_response = self._put("histories/%s/contents/%s" % (history_id, dataset_id), data=dict(name='Renamed Test Dataset'))
+        self._assert_status_code_is(dataset_update_response, 200)
+        assert dataset_update_response.json()['name'] == 'Renamed Test Dataset'
+        search_payload = self._search_payload(history_id=history_id, tool_id='identifier_single', inputs=inputs)
+        self._search(search_payload, expected_search_count=0)
+
     def test_search_delete_outputs(self):
         history_id, dataset_id = self.__history_with_ok_dataset()
         inputs = json.dumps({

test/base/api.py

@@ -76,6 +76,9 @@ class UsesApiTestCaseMixin:
     def _delete(self, *args, **kwds):
         return self.galaxy_interactor.delete(*args, **kwds)
 
+    def _put(self, *args, **kwds):
+        return self.galaxy_interactor.put(*args, **kwds)
+
     def _patch(self, *args, **kwds):
         return self.galaxy_interactor.patch(*args, **kwds)
 
@@ -129,3 +132,6 @@ class ApiTestInteractor(BaseInteractor):
 
     def patch(self, *args, **kwds):
         return self._patch(*args, **kwds)
+
+    def put(self, *args, **kwds):
+        return self._put(*args, **kwds)

test/base/interactor.py

@@ -6,7 +6,13 @@ import time
 from json import dumps
 from logging import getLogger
 
-from requests import delete, get, patch, post
+from requests import (
+    delete,
+    get,
+    patch,
+    post,
+    put,
+)
 from six import StringIO, text_type
 
 from galaxy import util
@@ -479,6 +485,17 @@ class GalaxyInteractorApi(object):
             params = {}
         return patch("%s/%s" % (self.api_url, path), params=params, data=data)
 
+    def _put(self, path, data={}, key=None, admin=False, anon=False):
+        if not anon:
+            if not key:
+                key = self.api_key if not admin else self.master_api_key
+            params = dict(key=key)
+            data = data.copy()
+            data['key'] = key
+        else:
+            params = {}
+        return put("%s/%s" % (self.api_url, path), params=params, data=data)
+
     def _get(self, path, data={}, key=None, admin=False, anon=False):
         if not anon:
             if not key: