Adapt API tests to use JSON payload

See galaxyproject#12152 for details.

lib/galaxy/tool_util/verify/interactor.py

@@ -480,11 +480,11 @@ def run_tool(self, testdef, history_id, resource_parameters=None):
     def _create_collection(self, history_id, collection_def):
         create_payload = dict(
             name=collection_def.name,
-            element_identifiers=dumps(self._element_identifiers(collection_def)),
+            element_identifiers=self._element_identifiers(collection_def),
             collection_type=collection_def.collection_type,
             history_id=history_id,
         )
-        return self._post("dataset_collections", data=create_payload).json()["id"]
+        return self._post("dataset_collections", data=create_payload, json=True).json()["id"]
 
     def _element_identifiers(self, collection_def):
         element_identifiers = []

lib/galaxy_test/api/test_dataset_collections.py

@@ -22,7 +22,7 @@ def test_create_pair_from_history(self):
             self.history_id,
             instance_type="history",
         )
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = self._check_create_response(create_response)
         returned_datasets = dataset_collection["elements"]
         assert len(returned_datasets) == 2, dataset_collection
@@ -33,11 +33,11 @@ def test_create_list_from_history(self):
         payload = dict(
             instance_type="history",
             history_id=self.history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
 
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = self._check_create_response(create_response)
         returned_datasets = dataset_collection["elements"]
         assert len(returned_datasets) == 3, dataset_collection
@@ -47,7 +47,7 @@ def test_create_list_of_existing_pairs(self):
             self.history_id,
             instance_type="history",
         )
-        pair_create_response = self._post("dataset_collections", pair_payload)
+        pair_create_response = self._post("dataset_collections", pair_payload, json=True)
         dataset_collection = self._check_create_response(pair_create_response)
         hdca_id = dataset_collection["id"]
 
@@ -58,10 +58,10 @@ def test_create_list_of_existing_pairs(self):
         payload = dict(
             instance_type="history",
             history_id=self.history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = self._check_create_response(create_response)
         returned_collections = dataset_collection["elements"]
         assert len(returned_collections) == 1, dataset_collection
@@ -73,9 +73,9 @@ def test_create_list_of_new_pairs(self):
             instance_type="history",
             history_id=self.history_id,
             name="a nested collection",
-            element_identifiers=json.dumps(identifiers),
+            element_identifiers=identifiers,
         )
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = self._check_create_response(create_response)
         assert dataset_collection["collection_type"] == "list:paired"
         assert dataset_collection["name"] == "a nested collection"
@@ -169,10 +169,10 @@ def test_hda_security(self):
             payload = dict(
                 instance_type="history",
                 history_id=history_id,
-                element_identifiers=json.dumps(element_identifiers),
+                element_identifiers=element_identifiers,
                 collection_type="paired",
             )
-            create_response = self._post("dataset_collections", payload)
+            create_response = self._post("dataset_collections", payload, json=True)
             self._assert_status_code_is(create_response, 403)
 
     def test_enforces_unique_names(self):
@@ -181,11 +181,11 @@ def test_enforces_unique_names(self):
         payload = dict(
             instance_type="history",
             history_id=self.history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
 
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         self._assert_status_code_is(create_response, 400)
 
     def test_upload_collection(self):
@@ -488,7 +488,7 @@ def _compare_collection_contents_elements(self, contents_elements, hdca_elements
     def _create_collection_contents_pair(self):
         # Create a simple collection, return hdca and contents_url
         payload = self.dataset_collection_populator.create_pair_payload(self.history_id, instance_type="history")
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         hdca = self._check_create_response(create_response)
         root_contents_url = self._get_contents_url_for_hdca(hdca)
         return hdca, root_contents_url

lib/galaxy_test/api/test_history_contents.py

@@ -348,7 +348,7 @@ def _check_pair_creation(self, endpoint, payload):
         pre_dataset_count = self.__count_contents(type="dataset")
         pre_combined_count = self.__count_contents(type="dataset,dataset_collection")
 
-        dataset_collection_response = self._post(endpoint, payload)
+        dataset_collection_response = self._post(endpoint, payload, json=True)
 
         dataset_collection = self.__check_create_collection_response(dataset_collection_response)
 
@@ -418,7 +418,7 @@ def test_dataset_collection_hide_originals(self):
         )
 
         payload["hide_source_items"] = True
-        dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload)
+        dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload, json=True)
         self.__check_create_collection_response(dataset_collection_response)
 
         contents_response = self._get(f"histories/{self.history_id}/contents")
@@ -430,10 +430,10 @@ def test_dataset_collection_hide_originals(self):
 
     def test_update_dataset_collection(self):
         hdca = self._create_pair_collection()
-        update_url = self._api_url(f"histories/{self.history_id}/contents/dataset_collections/{hdca['id']}", use_key=True)
-        # Awkward json.dumps required here because of https://trello.com/c/CQwmCeG6
-        body = json.dumps(dict(name="newnameforpair"))
-        update_response = put(update_url, data=body)
+        body = dict(name="newnameforpair")
+        update_response = self._put(
+            f"histories/{self.history_id}/contents/dataset_collections/{hdca['id']}", data=body, json=True
+        )
         self._assert_status_code_is(update_response, 200)
         show_response = self.__show(hdca)
         assert str(show_response.json()["name"]) == "newnameforpair"
@@ -457,7 +457,7 @@ def _create_pair_collection(self):
             self.history_id,
             type="dataset_collection"
         )
-        dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload)
+        dataset_collection_response = self._post(f"histories/{self.history_id}/contents", payload, json=True)
         self._assert_status_code_is(dataset_collection_response, 200)
         hdca = dataset_collection_response.json()
         return hdca
@@ -531,10 +531,10 @@ def test_hdca_from_library_datasets(self):
             history_id=history_id,
             type="dataset_collection",
             name="Test From Library",
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
-        create_response = self._post(f"histories/{history_id}/contents/dataset_collections", create_data)
+        create_response = self._post(f"histories/{history_id}/contents/dataset_collections", create_data, json=True)
         hdca = self.__check_create_collection_response(create_response)
         elements = hdca["elements"]
         assert len(elements) == 1
@@ -552,12 +552,12 @@ def test_hdca_from_inaccessible_library_datasets(self):
             history_id=self.history_id,
             type="dataset_collection",
             name="Test From Library",
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
         with self._different_user():
             second_history_id = self.dataset_populator.new_history()
-            create_response = self._post(f"histories/{second_history_id}/contents/dataset_collections", create_data)
+            create_response = self._post(f"histories/{second_history_id}/contents/dataset_collections", create_data, json=True)
             self._assert_status_code_is(create_response, 403)
 
     def __check_create_collection_response(self, response):

lib/galaxy_test/api/test_tools.py

@@ -1941,11 +1941,11 @@ def test_identifier_with_data_collection(self, history_id):
         payload = dict(
             instance_type="history",
             history_id=history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
 
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = create_response.json()
 
         inputs = {
@@ -1972,11 +1972,11 @@ def test_identifier_in_actions(self, history_id):
         payload = dict(
             instance_type="history",
             history_id=history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type="list",
         )
 
-        create_response = self._post("dataset_collections", payload)
+        create_response = self._post("dataset_collections", payload, json=True)
         dataset_collection = create_response.json()
 
         inputs = {

lib/galaxy_test/base/populators.py

@@ -1460,7 +1460,7 @@ def create_nested_collection(self, history_id, collection_type, name=None, colle
         payload = dict(
             instance_type="history",
             history_id=history_id,
-            element_identifiers=json.dumps(element_identifiers),
+            element_identifiers=element_identifiers,
             collection_type=collection_type,
             name=name,
         )
@@ -1594,7 +1594,7 @@ def __create_payload_collection(self, history_id, identifiers_func, collection_t
             del kwds["contents"]
 
         if "element_identifiers" not in kwds:
-            kwds["element_identifiers"] = json.dumps(identifiers_func(history_id, contents=contents))
+            kwds["element_identifiers"] = identifiers_func(history_id, contents=contents)
 
         if "name" not in kwds:
             kwds["name"] = "Test Dataset Collection"
@@ -1672,7 +1672,7 @@ def __init__(self, galaxy_interactor: ApiTestInteractor):
         self.dataset_populator = DatasetPopulator(galaxy_interactor)
 
     def _create_collection(self, payload: dict) -> Response:
-        create_response = self.galaxy_interactor.post("dataset_collections", data=payload)
+        create_response = self.galaxy_interactor.post("dataset_collections", data=payload, json=True)
         return create_response
 
 
@@ -1861,7 +1861,7 @@ def __init__(self, gi):
         self.dataset_collection_populator = GiDatasetCollectionPopulator(gi)
 
     def _create_collection(self, payload):
-        create_response = self._post("dataset_collections", data=payload)
+        create_response = self._post("dataset_collections", data=payload, json=True)
         return create_response
 
 

lib/galaxy_test/selenium/framework.py

@@ -644,7 +644,7 @@ def __init__(self, selenium_context: GalaxySeleniumContext):
         self.dataset_populator = SeleniumSessionDatasetPopulator(selenium_context)
 
     def _create_collection(self, payload: dict) -> Response:
-        create_response = self._post("dataset_collections", data=payload)
+        create_response = self._post("dataset_collections", data=payload, json=True)
         return create_response