Merge pull request #12136 from davelopez/update_fastapi_0.65.2

Update fastapi to 0.65.2 and dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -62,7 +62,7 @@ dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 fabric3==1.14.post1
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
-fastapi==0.63.0; python_version >= "3.6"
+fastapi==0.65.2; python_version >= "3.6"
 fluent-logger==0.10.0; python_version >= "3.5"
 funcsigs==1.0.2
 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
@@ -150,7 +150,7 @@ pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0"
 pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
 pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"
 pycryptodome==3.10.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
+pydantic==1.8.2; python_version >= "3.6" and python_version < "4.0"
 pydot==1.4.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
 pyeventsystem==0.1.0
 pyfaidx==0.5.9.5
@@ -228,7 +228,7 @@ sqlalchemy==1.4.18
 sqlitedict==1.7.0
 sqlparse==0.4.1; python_version >= "3.5"
 starlette-context==0.3.2; python_version >= "3.7"
-starlette==0.13.6; python_version >= "3.6"
+starlette==0.14.2; python_version >= "3.6"
 statsd==3.3.0
 stevedore==3.3.0; python_version >= "3.6"
 svgwrite==1.4.1; python_version >= "3.6"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -57,7 +57,7 @@ dogpile.cache==1.1.2; python_version >= "3.6"
 ecdsa==0.14.1; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 fabric3==1.14.post1
 fastapi-utils==0.2.1; python_version >= "3.6" and python_version < "4.0"
-fastapi==0.63.0; python_version >= "3.6"
+fastapi==0.65.2; python_version >= "3.6"
 funcsigs==1.0.2
 future==0.18.2; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.3.0")
 galaxy-sequence-utils==1.1.5
@@ -133,7 +133,7 @@ pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0"
 pyasn1==0.4.8; python_version >= "3.5" and python_version < "4"
 pycparser==2.20; python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0"
 pycryptodome==3.10.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
-pydantic==1.7.3; python_version >= "3.6" and python_version < "4.0"
+pydantic==1.8.2; python_version >= "3.6" and python_version < "4.0"
 pydot==1.4.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
 pyeventsystem==0.1.0
 pyfaidx==0.5.9.5
@@ -184,7 +184,7 @@ sqlalchemy==1.4.18
 sqlitedict==1.7.0
 sqlparse==0.4.1; python_version >= "3.5"
 starlette-context==0.3.2; python_version >= "3.7"
-starlette==0.13.6; python_version >= "3.6"
+starlette==0.14.2; python_version >= "3.6"
 stevedore==3.3.0; python_version >= "3.6"
 svgwrite==1.4.1; python_version >= "3.6"
 tempita==0.5.2

lib/galaxy_test/api/test_datasets.py

@@ -128,7 +128,10 @@ def test_tag_change(self):
             'item_class': 'HistoryDatasetAssociation',
             'item_tags': ['cool:tag_a', 'cool:tag_b', 'tag_c', 'name:tag_d', '#tag_e'],
         })
-        put_response = self._put("tags", payload)
+
+        # TODO remove the headers here and add json parameter to _put method
+        put_response = self._put("tags", data=payload, headers={'Content-Type': 'application/json'})
+
         self._assert_status_code_is_ok(put_response)
         updated_hda = self._get(
             f"histories/{self.history_id}/contents/{hda_id}").json()

pyproject.toml

@@ -35,7 +35,7 @@ cwltool = "==3.0.20201109103151"
 dictobj = "*"
 docutils = "!=0.17, !=0.17.1"
 Fabric3 = "*"
-fastapi = ">=0.63.0"
+fastapi = ">=0.65.2"
 fastapi-utils = "*"
 future = "*"
 galaxy_sequence_utils = "*"

test/integration/test_tool_data_delete.py

@@ -61,7 +61,10 @@ def test_admin_delete_data_table_entry(self):
         self.assertEquals(len(updated_fields), original_count + 1)
         new_field = updated_fields[-1]
         url = self._api_url(f"tool_data/testbeta?key={self.galaxy_interactor.api_key}")
-        delete_response = delete(url, data=json.dumps({"values": "\t".join(new_field)}))
+
+        # TODO remove the headers here, use the interactor _delete method and add json parameter to it
+        delete_response = delete(url, data=json.dumps({"values": "\t".join(new_field)}), headers={'Content-Type': 'application/json'})
+
         delete_response.raise_for_status()
         time.sleep(2)
         show_response = self._get("tool_data/testbeta")