[CZID-8457] Create a file - part 2

entities/api/files.py

@@ -38,7 +38,7 @@ def download_link(
     ) -> typing.Optional[SignedURL]:
         if not self.path:  # type: ignore
             return None
-        key = self.path.lstrip("/")  # type: ignore
+        key = self.path  # type: ignore
         bucket_name = self.namespace  # type: ignore
         url = s3_client.generate_presigned_url(
             ClientMethod="get_object", Params={"Bucket": bucket_name, "Key": key}, ExpiresIn=expiration
@@ -62,7 +62,7 @@ async def mark_upload_complete(
 
     validator = get_validator(file.file_format)
     try:
-        file_size = validator.validate(s3_client, file.namespace, file.path.lstrip("/"))
+        file_size = validator.validate(s3_client, file.namespace, file.path)
     except:  # noqa
         file.status = db.FileStatus.FAILED
     else:
@@ -122,7 +122,7 @@ async def create_file(
     await session.commit()
 
     # Create a signed URL
-    response = s3_client.generate_presigned_post(Bucket=file.namespace, Key=file.path.lstrip("/"), ExpiresIn=expiration)
+    response = s3_client.generate_presigned_post(Bucket=file.namespace, Key=file.path, ExpiresIn=expiration)
     return SignedURL(
         url=response["url"], fields=response["fields"], protocol="https", method="POST", expiration=expiration
     )

entities/api/tests/test_file_writes.py

@@ -4,7 +4,7 @@
 from platformics.database.connect import SyncDB
 from test_infra import factories as fa
 from mypy_boto3_s3.client import S3Client
-from database.models import File
+from database.models import File, SequencingRead
 import sqlalchemy as sa
 
 
@@ -27,7 +27,7 @@ async def test_file_validation(
         file = session.execute(sa.select(File)).scalars().one()
 
     valid_fastq_file = "test_infra/fixtures/test1.fastq"
-    moto_client.put_object(Bucket=file.namespace, Key=file.path.lstrip("/"), Body=open(valid_fastq_file, "rb"))
+    moto_client.put_object(Bucket=file.namespace, Key=file.path, Body=open(valid_fastq_file, "rb"))
 
     # Mark upload complete
     query = f"""
@@ -64,7 +64,7 @@ async def test_invalid_fastq(
         session.commit()
         file = session.execute(sa.select(File)).scalars().one()
 
-    moto_client.put_object(Bucket=file.namespace, Key=file.path.lstrip("/"), Body="this is not a fastq file")
+    moto_client.put_object(Bucket=file.namespace, Key=file.path, Body="this is not a fastq file")
 
     # Mark upload complete
     query = f"""
@@ -80,3 +80,56 @@ async def test_invalid_fastq(
     res = await gql_client.query(query, member_projects=[project1_id])
     fileinfo = res["data"]["markUploadComplete"]
     assert fileinfo["status"] == "FAILED"
+
+
+# Test creating files
+@pytest.mark.asyncio
+@pytest.mark.parametrize(
+    "member_projects,project_id,entity_field",
+    [
+        ([456], 123, "sequence_file"),  # Can't create file for entity you don't have access to
+        ([123], 123, "does_not_exist"),  # Can't create file for entity that isn't connected to a valid file type
+        ([123], 123, "sequence_file"),  # Can create file for entity you have access to
+    ],
+)
+async def test_create_file(
+    member_projects: list[int],
+    project_id: int,
+    entity_field: str,
+    sync_db: SyncDB,
+    gql_client: GQLTestClient,
+) -> None:
+    user_id = 12345
+
+    # Create mock data
+    with sync_db.session() as session:
+        fa.SessionStorage.set_session(session)
+        fa.SequencingReadFactory.create(owner_user_id=user_id, collection_id=project_id)
+        fa.FileFactory.update_file_ids()
+        session.commit()
+
+        sequencing_read = session.execute(sa.select(SequencingRead)).scalars().one()
+        entity_id = sequencing_read.entity_id
+
+    # Try creating a file
+    mutation = f"""
+        mutation MyQuery {{
+          createFile(entityId: "{entity_id}", entityFieldName: "{entity_field}",
+            fileName: "test.fastq", fileSize: 123, fileFormat: "fastq") {{
+            url
+            expiration
+            method
+            protocol
+            fields
+          }}
+        }}
+    """
+    output = await gql_client.query(mutation, member_projects=member_projects)
+
+    # If don't have access to this entity, or trying to link an entity with a made up file type, should get an error
+    if project_id not in member_projects or entity_field == "does_not_exist":
+        assert output["data"] is None
+        assert output["errors"] is not None
+        return
+
+    assert output["data"]["createFile"]["url"] == "https://local-bucket.s3.amazonaws.com/"

entities/test_infra/factories.py

@@ -1,4 +1,5 @@
 import factory
+import faker
 import sqlalchemy as sa
 from database.models import File, FileStatus, Sample, SequencingRead
 from factory import Faker, fuzzy
@@ -11,6 +12,12 @@
 Faker.add_provider(EnumProvider)
 
 
+def generate_relative_file_path(obj) -> str:  # type: ignore
+    fake = faker.Faker()
+    # Can't use absolute=True param because that requires newer version of faker than faker-biology supports
+    return fake.file_path(depth=3, extension=obj.file_format).lstrip("/")
+
+
 # TODO, this is a lame singleton to prevent this library from
 # requiring an active SA session at import-time. We should try
 # to refactor it out when we know more about factoryboy
@@ -50,8 +57,7 @@ class Meta:
     status = factory.Faker("enum", enum_cls=FileStatus)
     protocol = fuzzy.FuzzyChoice(["S3", "GCP"])
     namespace = fuzzy.FuzzyChoice(["local-bucket", "remote-bucket"])
-    # path = factory.LazyAttribute(lambda o: {factory.Faker("file_path", depth=3, extension=o.file_format)})
-    path = factory.Faker("file_path", depth=3)
+    path = factory.LazyAttribute(lambda o: generate_relative_file_path(o))
     file_format = fuzzy.FuzzyChoice(["fasta", "fastq", "bam"])
     compression_type = fuzzy.FuzzyChoice(["gz", "bz2", "xz"])
     size = fuzzy.FuzzyInteger(1024, 1024 * 1024 * 1024)  # Between 1k and 1G