Merge pull request #59 from chanzuckerberg/valenzuelaomar/fix-test-fi…

…le-mutations

Fix mutations test

docker-compose-dev.yml

@@ -22,6 +22,7 @@ services:
       - PLATFORMICS_DATABASE_NAME=platformics
       - DEFAULT_UPLOAD_BUCKET=local-bucket
       - DEFAULT_UPLOAD_PROTOCOL=s3
+      - OUTPUT_S3_PREFIX=platformics
       - BOTO_ENDPOINT_URL=http://motoserver.platformics:4000
       - AWS_REGION=us-west-2
       - AWS_ACCESS_KEY_ID=test

docker-compose.yml

@@ -30,6 +30,7 @@ services:
       - PLATFORMICS_DATABASE_NAME=platformics
       - DEFAULT_UPLOAD_BUCKET=local-bucket
       - DEFAULT_UPLOAD_PROTOCOL=s3
+      - OUTPUT_S3_PREFIX=platformics
       - BOTO_ENDPOINT_URL=http://motoserver.platformics:4000
       - AWS_REGION=us-west-2
       - AWS_ACCESS_KEY_ID=test

platformics/database/models/file.py

@@ -81,7 +81,7 @@ def before_delete(mapper: Mapper, connection: Connection, target: File) -> None:
     settings = File.get_settings()
     s3_client = File.get_s3_client()
 
-    # If this file is managed by NextGen, see if it needs to be deleted from S3
+    # If this file is managed by platformics, see if it needs to be deleted from S3
     if target.path.startswith(f"{settings.OUTPUT_S3_PREFIX}/") and target.protocol == FileAccessProtocol.s3:
         # Is this the last File object pointing to this path?
         files_pointing_to_same_path = connection.execute(

test_app/Makefile

@@ -60,7 +60,7 @@ clean: ## Remove all codegen'd artifacts.
 	rm -rf cerbos
 	rm -rf support
 	rm -rf database
-	rm -f .moto_recording
+	rm -rf .moto_recording
 	rm -rf test_infra
 	$(docker_compose) --profile '*' down
 

test_app/docker-compose.yml

@@ -62,6 +62,7 @@ services:
       - PLATFORMICS_DATABASE_NAME=platformics
       - DEFAULT_UPLOAD_BUCKET=local-bucket
       - DEFAULT_UPLOAD_PROTOCOL=s3
+      - OUTPUT_S3_PREFIX=platformics
       - BOTO_ENDPOINT_URL=http://motoserver.platformics:4000
       - AWS_REGION=us-west-2
       - AWS_ACCESS_KEY_ID=test

test_app/schema/schema.yaml

@@ -342,5 +342,4 @@ classes:
         range: string
         required: true
     annotations:
-      mutable: false
       plural: ImmutableTypes

test_app/tests/test_field_visibility.py

@@ -130,7 +130,9 @@ async def test_update_fields(
     ]
     fields = [field["name"] for field in create_type["inputFields"]]
     # We have a limited subset of mutable fields on SequencingRead
-    assert set(fields) == set(["nucleicAcid", "sampleId", "technology", "protocol", "deletedAt", "primerFileId", "collectionId"])
+    assert set(fields) == set(
+        ["nucleicAcid", "sampleId", "technology", "protocol", "deletedAt", "primerFileId", "collectionId"]
+    )
 
 
 # Make sure we only allow certain fields to be set at entity creation time.

test_app/tests/test_file_mutations.py

@@ -189,7 +189,7 @@ async def test_create_file(
     # Upload a fastq file to a mock bucket so we can create a file object from it
     file_namespace = "local-bucket"
     file_path = "test1.fastq"
-    file_path_local = "tests/fixtures/test1.fasta"
+    file_path_local = "tests/fixtures/test1.fastq"
     file_size = os.stat(file_path_local).st_size
     with open(file_path_local, "rb") as fp:
         moto_client.put_object(Bucket=file_namespace, Key=file_path, Body=fp)
@@ -211,7 +211,7 @@ async def test_create_file(
                 path
                 size
             }}
-
+        }}
     """
     output = await gql_client.query(mutation, member_projects=[123], service_identity="workflows")
     assert output["data"]["createFile"]["size"] == file_size
@@ -221,9 +221,9 @@ async def test_create_file(
 @pytest.mark.parametrize(
     "file_path,multiple_files_for_one_path,should_delete",
     [
-        ("nextgen/test1.fastq", False, True),
+        ("platformics/test1.fastq", False, True),
         ("bla/test1.fastq", False, False),
-        ("nextgen/test1.fastq", True, False),
+        ("platformics/test1.fastq", True, False),
         ("bla/test1.fastq", True, False),
     ],
 )