data freeze

cidc_api/resources/permissions.py

@@ -78,35 +78,37 @@ def get_permission(permission: Permissions) -> Permissions:
 @permissions_bp.route("/", methods=["POST"])
 @requires_auth("permissions_item", allowed_roles=[CIDCRole.ADMIN.value])
 @unmarshal_request(permission_schema, "permission")
-@marshal_response(permission_schema, 201)
+# @marshal_response(permission_schema, 201)
 def create_permission(permission: Permissions) -> Permissions:
     """Create a new permission record."""
-    if permission.granted_by_user is None:
-        granter = get_current_user()
-        permission.granted_by_user = granter.id
-    try:
-        permission.insert()
-    except IntegrityError as e:
-        raise BadRequest(str(e.orig))
-    except IAMException as e:
-        # We return info on this internal error, since this is an admin-only endpoint
-        raise InternalServerError(str(e))
+    return "Data Freeze", 503
+    # if permission.granted_by_user is None:
+    #     granter = get_current_user()
+    #     permission.granted_by_user = granter.id
+    # try:
+    #     permission.insert()
+    # except IntegrityError as e:
+    #     raise BadRequest(str(e.orig))
+    # except IAMException as e:
+    #     # We return info on this internal error, since this is an admin-only endpoint
+    #     raise InternalServerError(str(e))
 
-    return permission
+    # return permission
 
 
 @permissions_bp.route("/<int:permission>", methods=["DELETE"])
 @requires_auth("permissions_item", allowed_roles=[CIDCRole.ADMIN.value])
 @with_lookup(Permissions, "permission", check_etag=True)
 def delete_permission(permission: Permissions):
     """Delete a permission record."""
-    try:
-        deleter = get_current_user()
-        permission.delete(deleted_by=deleter)
-    except NoResultFound as e:
-        raise NotFound(str(e.orig))
-    except IAMException as e:
-        # We return info on this internal error, since this is an admin-only endpoint
-        raise InternalServerError(str(e))
-
-    return delete_response()
+    return "Data Freeze", 503
+    # try:
+    #     deleter = get_current_user()
+    #     permission.delete(deleted_by=deleter)
+    # except NoResultFound as e:
+    #     raise NotFound(str(e.orig))
+    # except IAMException as e:
+    #     # We return info on this internal error, since this is an admin-only endpoint
+    #     raise InternalServerError(str(e))
+
+    # return delete_response()

cidc_api/resources/trial_metadata.py

@@ -57,16 +57,17 @@ def list_trial_metadata(args, pagination_args):
 @trial_metadata_bp.route("/", methods=["POST"])
 @requires_auth("trial_metadata_item", trial_modifier_roles)
 @unmarshal_request(trial_metadata_schema, "trial")
-@marshal_response(trial_metadata_schema, 201)
+# @marshal_response(trial_metadata_schema, 201)
 def create_trial_metadata(trial):
     """Create a new trial metadata record."""
-    try:
-        # metadata was already validated by unmarshal_request
-        trial.insert(validate_metadata=False)
-    except IntegrityError as e:
-        raise BadRequest(str(e.orig))
+    return "Data Freeze", 503
+    # try:
+    #     # metadata was already validated by unmarshal_request
+    #     trial.insert(validate_metadata=False)
+    # except IntegrityError as e:
+    #     raise BadRequest(str(e.orig))
 
-    return trial
+    # return trial
 
 
 @trial_metadata_bp.route("/summaries", methods=["GET"])
@@ -92,35 +93,37 @@ def get_trial_metadata_by_trial_id(trial):
     TrialMetadata, "trial", check_etag=True, find_func=TrialMetadata.find_by_trial_id
 )
 @unmarshal_request(partial_trial_metadata_schema, "trial_updates", load_sqla=False)
-@marshal_response(trial_metadata_schema, 200)
+# @marshal_response(trial_metadata_schema, 200)
 def update_trial_metadata_by_trial_id(trial, trial_updates):
     """Update an existing trial metadata record by trial_id."""
     # Block updates to protected metadata JSON fields
-    metadata_updates = trial_updates.get("metadata_json")
-    if trial.metadata_json or metadata_updates:
-        for field in TrialMetadata.PROTECTED_FIELDS:
-            if trial.metadata_json.get(field) != metadata_updates.get(field):
-                raise BadRequest(
-                    f"updating metadata_json['{field}'] via the API is prohibited"
-                )
+    return "Data Freeze", 503
+    # metadata_updates = trial_updates.get("metadata_json")
+    # if trial.metadata_json or metadata_updates:
+    #     for field in TrialMetadata.PROTECTED_FIELDS:
+    #         if trial.metadata_json.get(field) != metadata_updates.get(field):
+    #             raise BadRequest(
+    #                 f"updating metadata_json['{field}'] via the API is prohibited"
+    #             )
 
-    trial.update(changes=trial_updates)
+    # trial.update(changes=trial_updates)
 
-    return trial
+    # return trial
 
 
 @trial_metadata_bp.route("/new_manifest", methods=["POST"])
 @requires_auth("new_manifest", [CIDCRole.ADMIN.value])
 def add_new_manifest_from_json():
-    try:
-        # schemas JSON blob hook
-        insert_manifest_into_blob(request.json, uploader_email=get_current_user().email)
-
-    except Exception as e:
-        res = jsonify(error=str(e))
-        res.status_code = 500
-    else:
-        res = jsonify(status="success")
-        res.status_code = 200
-    finally:
-        return res
+    return "Data Freeze", 503
+    # try:
+    #     # schemas JSON blob hook
+    #     insert_manifest_into_blob(request.json, uploader_email=get_current_user().email)
+
+    # except Exception as e:
+    #     res = jsonify(error=str(e))
+    #     res.status_code = 500
+    # else:
+    #     res = jsonify(status="success")
+    #     res.status_code = 200
+    # finally:
+    #     return res

cidc_api/resources/upload_jobs.py

@@ -155,34 +155,35 @@ def wrapped(args, *pos_args, **kwargs):
     "upload_job_updates",
     load_sqla=False,
 )
-@marshal_response(upload_job_schema, 200)
+# @marshal_response(upload_job_schema, 200)
 def update_upload_job(upload_job: UploadJobs, upload_job_updates: dict):
     """Update an upload_job."""
-    try:
-        if "gcs_file_map" in upload_job_updates and upload_job.gcs_file_map is not None:
-            upload_job_updates["metadata_patch"] = upload_job.metadata_patch.copy()
-            for uri, uuid in upload_job.gcs_file_map.items():
-                if uri not in upload_job_updates["gcs_file_map"]:
-                    upload_job_updates[
-                        "metadata_patch"
-                    ] = _remove_optional_uuid_recursive(
-                        upload_job_updates["metadata_patch"], uuid
-                    )
-
-        upload_job.update(changes=upload_job_updates)
-    except ValueError as e:
-        raise BadRequest(str(e))
-
-    # If this is a successful upload job, publish this info to Pub/Sub
-    if upload_job.status == UploadJobStatus.UPLOAD_COMPLETED.value:
-        gcloud_client.publish_upload_success(upload_job.id)
-
-    # Revoke the uploading user's bucket access, since their querying
-    # this endpoint indicates a completed / failed upload attempt.
-    gcloud_client.revoke_upload_access(upload_job.uploader_email)
-
-    # this is not user-input due to @with_lookup, so safe to return
-    return upload_job
+    return "Data Freeze", 503
+    # try:
+    #     if "gcs_file_map" in upload_job_updates and upload_job.gcs_file_map is not None:
+    #         upload_job_updates["metadata_patch"] = upload_job.metadata_patch.copy()
+    #         for uri, uuid in upload_job.gcs_file_map.items():
+    #             if uri not in upload_job_updates["gcs_file_map"]:
+    #                 upload_job_updates[
+    #                     "metadata_patch"
+    #                 ] = _remove_optional_uuid_recursive(
+    #                     upload_job_updates["metadata_patch"], uuid
+    #                 )
+
+    #     upload_job.update(changes=upload_job_updates)
+    # except ValueError as e:
+    #     raise BadRequest(str(e))
+
+    # # If this is a successful upload job, publish this info to Pub/Sub
+    # if upload_job.status == UploadJobStatus.UPLOAD_COMPLETED.value:
+    #     gcloud_client.publish_upload_success(upload_job.id)
+
+    # # Revoke the uploading user's bucket access, since their querying
+    # # this endpoint indicates a completed / failed upload attempt.
+    # gcloud_client.revoke_upload_access(upload_job.uploader_email)
+
+    # # this is not user-input due to @with_lookup, so safe to return
+    # return upload_job
 
 
 def _remove_optional_uuid_recursive(target: dict, uuid: str):
@@ -471,31 +472,32 @@ def upload_manifest(
     Response:
         201 if the upload succeeds. Otherwise, some error status code and message.
     """
-    try:
-        trial = TrialMetadata.patch_manifest(trial.trial_id, md_patch, commit=False)
-    except ValidationError as e:
-        raise BadRequest(json_validation.format_validation_error(e))
-    except ValidationMultiError as e:
-        raise BadRequest({"errors": e.args[0]})
-
-    # TODO maybe rely on default session
-    session = Session.object_session(trial)
-
-    manifest_upload = UploadJobs.create(
-        upload_type=template_type,
-        uploader_email=user.email,
-        metadata=md_patch,
-        gcs_xlsx_uri="",  # not saving xlsx so we won't have phi-ish stuff in it
-        gcs_file_map=None,
-        session=session,
-        send_email=True,
-        status=UploadJobStatus.MERGE_COMPLETED.value,
-    )
-
-    # Publish that a manifest upload has been received
-    gcloud_client.publish_patient_sample_update(manifest_upload.id)
-
-    return jsonify({"metadata_json_patch": md_patch})
+    return "Data Freeze", 503
+    # try:
+    #     trial = TrialMetadata.patch_manifest(trial.trial_id, md_patch, commit=False)
+    # except ValidationError as e:
+    #     raise BadRequest(json_validation.format_validation_error(e))
+    # except ValidationMultiError as e:
+    #     raise BadRequest({"errors": e.args[0]})
+
+    # # TODO maybe rely on default session
+    # session = Session.object_session(trial)
+
+    # manifest_upload = UploadJobs.create(
+    #     upload_type=template_type,
+    #     uploader_email=user.email,
+    #     metadata=md_patch,
+    #     gcs_xlsx_uri="",  # not saving xlsx so we won't have phi-ish stuff in it
+    #     gcs_file_map=None,
+    #     session=session,
+    #     send_email=True,
+    #     status=UploadJobStatus.MERGE_COMPLETED.value,
+    # )
+
+    # # Publish that a manifest upload has been received
+    # gcloud_client.publish_patient_sample_update(manifest_upload.id)
+
+    # return jsonify({"metadata_json_patch": md_patch})
 
 
 @ingestion_bp.route("/upload_assay", methods=["POST"])
@@ -505,7 +507,8 @@ def upload_manifest(
 @upload_handler(prism.SUPPORTED_ASSAYS)
 def upload_assay(*args, **kwargs):
     """Handle assay metadata / file uploads."""
-    return upload_data_files(*args, **kwargs)
+    # return upload_data_files(*args, **kwargs)
+    return "Data Freeze", 503
 
 
 @ingestion_bp.route("/upload_analysis", methods=["POST"])
@@ -515,7 +518,8 @@ def upload_assay(*args, **kwargs):
 @upload_handler(prism.SUPPORTED_ANALYSES)
 def upload_analysis(*args, **kwargs):
     """Handle analysis metadata / file uploads."""
-    return upload_data_files(*args, **kwargs)
+    # return upload_data_files(*args, **kwargs)
+    return "Data Freeze", 503
 
 
 def upload_data_files(
@@ -643,38 +647,38 @@ def extra_assay_metadata():
         [artifact_uuid_2]: [open extra metadata file 2]
     }
     """
+    return "Data Freeze", 503
+    # if not request.form:
+    #     raise BadRequest(
+    #         "Expected form content in request body, or failed to parse form content"
+    #     )
 
-    if not request.form:
-        raise BadRequest(
-            "Expected form content in request body, or failed to parse form content"
-        )
-
-    if "job_id" not in request.form:
-        raise BadRequest("Expected job_id in form")
+    # if "job_id" not in request.form:
+    #     raise BadRequest("Expected job_id in form")
 
-    if not request.files:
-        raise BadRequest(
-            "Expected files in request (mapping from artifact uuids to open files)"
-        )
+    # if not request.files:
+    #     raise BadRequest(
+    #         "Expected files in request (mapping from artifact uuids to open files)"
+    #     )
 
-    job_id = request.form["job_id"]
+    # job_id = request.form["job_id"]
 
-    files = request.files.to_dict()
+    # files = request.files.to_dict()
 
-    try:
-        UploadJobs.merge_extra_metadata(job_id, files)
-    except ValueError as e:
-        # thrown by parser itself if file cannot be parsed, e.g. wrong file uploaded
-        # wrapped by merger to include uuid / assay_hint information, just use that message
-        # thrown by UploadJobs.merge_extra_metadata if job_id doesn't exist or is already merged
-        # thrown by getting artifact if uuid doesn't exist in the trial
-        raise BadRequest(f"{e!s}")
+    # try:
+    #     UploadJobs.merge_extra_metadata(job_id, files)
+    # except ValueError as e:
+    #     # thrown by parser itself if file cannot be parsed, e.g. wrong file uploaded
+    #     # wrapped by merger to include uuid / assay_hint information, just use that message
+    #     # thrown by UploadJobs.merge_extra_metadata if job_id doesn't exist or is already merged
+    #     # thrown by getting artifact if uuid doesn't exist in the trial
+    #     raise BadRequest(f"{e!s}")
 
-    # Uncaught i.e. internal errors
-    # TypeError thrown by parser itself if file is not the right type
+    # # Uncaught i.e. internal errors
+    # # TypeError thrown by parser itself if file is not the right type
 
-    # TODO: return something here?
-    return jsonify({})
+    # # TODO: return something here?
+    # return jsonify({})
 
 
 INTAKE_ROLES = [
@@ -697,11 +701,17 @@ def create_intake_bucket(args):
     """
     user = get_current_user()
     intake_bucket = gcloud_client.create_intake_bucket(user.email)
-    bucket_subdir = f'{intake_bucket.name}/{args["trial_id"]}/{args["upload_type"]}'
-    gs_url = f"gs://{bucket_subdir}"
-    console_url = f"https://console.cloud.google.com/storage/browser/{bucket_subdir}"
+    # For Data Freeze, only return bucket if it exists
+    if intake_bucket:
+        bucket_subdir = f'{intake_bucket.name}/{args["trial_id"]}/{args["upload_type"]}'
+        gs_url = f"gs://{bucket_subdir}"
+        console_url = (
+            f"https://console.cloud.google.com/storage/browser/{bucket_subdir}"
+        )
 
-    return jsonify({"gs_url": gs_url, "console_url": console_url})
+        return jsonify({"gs_url": gs_url, "console_url": console_url})
+    else:
+        return "Data Freeze", 503
 
 
 @ingestion_bp.route("/intake_metadata", methods=["POST"])
@@ -730,11 +740,12 @@ def send_intake_metadata(form_args, file_args):
     """
     Send an email to the CIDC Admin mailing list with the provided metadata attached.
     """
-    user = get_current_user()
-    xlsx_gcp_url = gcloud_client.upload_xlsx_to_intake_bucket(
-        user.email, form_args["trial_id"], form_args["assay_type"], file_args["xlsx"]
-    )
-    emails.intake_metadata(
-        user, **form_args, xlsx_gcp_url=xlsx_gcp_url, send_email=True
-    )
-    return jsonify("ok")
+    return "Data Freeze", 503
+    # user = get_current_user()
+    # xlsx_gcp_url = gcloud_client.upload_xlsx_to_intake_bucket(
+    #     user.email, form_args["trial_id"], form_args["assay_type"], file_args["xlsx"]
+    # )
+    # emails.intake_metadata(
+    #     user, **form_args, xlsx_gcp_url=xlsx_gcp_url, send_email=True
+    # )
+    # return jsonify("ok")