diff --git a/README.md b/README.md index 7964db4cf..274df6e7a 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,21 @@ Katsu Metadata Service is a service to store epigenomic metadata. 6. Rest api service handles all generic functionality shared among other services +## Schemas +### Clinical Data + +Katsu implements the [Phenopacket V1.0.0](https://phenopacket-schema.readthedocs.io/en/1.0.0/) schema for clinical data. + +The schema definition for the phenopacket object is located in [chord_metadata_service/phenopackets/schemas.py](https://github.com/bento-platform/katsu/blob/4ab3c55d6052994ef69b188fb872261c47de24e0/chord_metadata_service/phenopackets/schemas.py#L336). + +### Experiments + +Katsu's experiments schemas are based on the IHEC [schema](https://github.com/IHEC/ihec-ecosystems/blob/master/docs/metadata/2.0/Ihec_metadata_specification.md#experiments), which is based on EBI/SRA schemas. + +The value options for `library_strategy` and `library_selection` are read from [chord_metadata_service/ontologies/xsd/SRA.experiment.xsd.xml](./chord_metadata_service/ontologies/xsd/SRA.experiment.xsd.xml), downloaded from the EBI's [SRA v1.5 database](http://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/). + +The `SRA.experiment.xsd.xml` file is licensed under Apache License V2.0, the full copyright text is included in the file's header. + ## REST API highlights * Swagger schema docs can be found diff --git a/chord_metadata_service/chord/ingest/exceptions.py b/chord_metadata_service/chord/ingest/exceptions.py index bea8da514..7f362a715 100644 --- a/chord_metadata_service/chord/ingest/exceptions.py +++ b/chord_metadata_service/chord/ingest/exceptions.py @@ -1,7 +1,113 @@ +from typing import List, Optional +from jsonschema.exceptions import ValidationError +from chord_metadata_service import __version__ +from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA_CHANGES +from chord_metadata_service.chord.data_types import DATA_TYPE_EXPERIMENT, DATA_TYPE_PHENOPACKET + __all__ = [ "IngestError", ] +DATA_TYPE_SCHEMA_CHANGES = { + DATA_TYPE_EXPERIMENT: EXPERIMENT_SCHEMA_CHANGES, + DATA_TYPE_PHENOPACKET: None +} + + +def parse_validation_errors(errors: List[ValidationError]) -> Optional[List[dict]]: + """ + Accepts a list of jsonschema ValidationError and converts them to a client error format. + + Parameters: + errors (List[ValidationError]): errors raised by jsonschema during validation + Returns: + List[dict]: + dict: + schema_path (str): Schema path string (e.g "properties.library_strategy") + faulty_value (str | obj): The value at the schema_path causing the error + property_schema (dict): JSON schema of the property (includes valid options) + message (str): The ValidationError.message + """ + error_descriptions = [] + for error in errors: + schema_path = ".".join(error.schema_path) + error_descriptions.append({ + "schema_path": schema_path, + "faulty_value": error.instance, + "message": error.message, + "property_schema": error.schema, + }) + return error_descriptions if len(error_descriptions) else None + + +def parse_property_warnings(data: dict, prop_name: str, property_changes: List[tuple]) -> Optional[dict]: + for (old_value, new_value) in property_changes: + value = data[prop_name] + property_warning = { + "property_name": prop_name, + "property_value": value, + "deprecated_value": old_value, + "suggested_replacement": new_value, + } + + if value == old_value: + # Naive comparison for dicts + return property_warning + + if isinstance(value, str) and isinstance(old_value, str): + # Lower case comparison for string values (JSON schema enum) + if value.lower() == old_value.lower(): + return property_warning + + # Only warn when necessary + return None + + +def parse_schema_warnings(data: dict, schema: dict) -> Optional[List[dict]]: + """ + Schema warnings are issued on Katsu releases that include schema changes. + Warnings are returned to highlight schema changes that may be the root cause of an IngestionError. + + Parameters: + data (dict): the data submitted for ingestion + + Returns: + List[dict]: + dict: + property_name (str): The name of the property + property_value (str | dict) + deprecated_value (str | dict): The deprecated property option + suggested_replacement (str | dict): The new suggested property option + version (str): The Katsu release version associated with the schema change + """ + if not data or not schema: + return None + + data_type = schema.get("$id", "").split("/")[-1] + applicable_changes = DATA_TYPE_SCHEMA_CHANGES.get(data_type, None) + + if not applicable_changes or __version__ not in applicable_changes: + # Skip if data type's schema is not affected in current Katsu version + return None + + warnings = [] + for (version, version_changes) in applicable_changes.items(): + for (prop_name, changes) in version_changes.get("properties", {}).items(): + if property_warning := parse_property_warnings(data, prop_name, changes): + property_warning["version"] = version + warnings.append(property_warning) + return warnings if len(warnings) else None + + class IngestError(Exception): - pass + + def __init__(self, + data: dict = None, + schema: dict = None, + schema_validation_errors: List[ValidationError] = [], + message="An error occured during ingestion."): + + self.validation_errors = parse_validation_errors(schema_validation_errors) + self.schema_warnings = parse_schema_warnings(data=data, schema=schema) + self.message = message diff --git a/chord_metadata_service/chord/ingest/experiments.py b/chord_metadata_service/chord/ingest/experiments.py index 4fbcd60a9..c852840ee 100644 --- a/chord_metadata_service/chord/ingest/experiments.py +++ b/chord_metadata_service/chord/ingest/experiments.py @@ -4,7 +4,8 @@ from chord_metadata_service.chord.models import Dataset from chord_metadata_service.experiments import models as em -from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA, EXPERIMENT_RESULT_SCHEMA +from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA, \ + EXPERIMENT_RESULT_SCHEMA, EXPERIMENT_WORKFLOW_SCHEMA from chord_metadata_service.phenopackets import models as pm from typing import Optional @@ -56,12 +57,24 @@ def create_experiment_result(er: dict) -> em.ExperimentResult: def validate_experiment(experiment_data, idx: Optional[int] = None) -> None: # Validate experiment data against experiments schema. - validation = schema_validation(experiment_data, EXPERIMENT_SCHEMA) - if not validation: - # TODO: Report more precise errors + if val_errors := schema_validation(experiment_data, EXPERIMENT_SCHEMA): raise IngestError( - f"Failed schema validation for experiment{(' ' + str(idx)) if idx is not None else ''} " - f"(check Katsu logs for more information)") + data=experiment_data, + schema=EXPERIMENT_SCHEMA, + schema_validation_errors=val_errors, + message=f"Failed schema validation for experiment{(' ' + str(idx)) if idx is not None else ''} " + f"(check Katsu logs for more information)" + ) + + +def validate_experiment_workflow(json_data: dict) -> None: + if val_errors := schema_validation(json_data, EXPERIMENT_WORKFLOW_SCHEMA): + raise IngestError( + data=json_data, + schema=EXPERIMENT_WORKFLOW_SCHEMA, + schema_validation_errors=val_errors, + message="Failed schema validation for experiments ingestion workflow payload.", + ) def ingest_experiment( @@ -139,6 +152,9 @@ def ingest_experiment( def ingest_experiments_workflow(json_data, dataset_id: str) -> list[em.Experiment]: + # First, validate the workflow's json_data + validate_experiment_workflow(json_data) + dataset = Dataset.objects.get(identifier=dataset_id) for rs in json_data.get("resources", []): @@ -146,7 +162,7 @@ def ingest_experiments_workflow(json_data, dataset_id: str) -> list[em.Experimen exps = json_data.get("experiments", []) - # First, validate all experiments with the schema before creating anything in the database. + # Second, validate all experiments with the schema before creating anything in the database. for idx, exp in enumerate(exps): validate_experiment(exp, idx) @@ -164,12 +180,16 @@ def ingest_derived_experiment_results(json_data: list[dict]) -> list[em.Experime # First, validate all experiment results with the schema before creating anything in the database. for idx, exp_result in enumerate(json_data): - validation = schema_validation(exp_result, EXPERIMENT_RESULT_SCHEMA) - if not validation: + val_errors = schema_validation(exp_result, EXPERIMENT_RESULT_SCHEMA) + if val_errors: # TODO: Report more precise errors raise IngestError( - f"Failed schema validation for experiment result {idx} " - f"(check Katsu logs for more information)") + data=exp_result, + schema=EXPERIMENT_RESULT_SCHEMA, + schema_validation_errors=val_errors, + message=f"Failed schema validation for experiment result {idx} " + f"(check Katsu logs for more information)" + ) # If everything passes, perform the actual ingestion next. diff --git a/chord_metadata_service/chord/ingest/phenopackets.py b/chord_metadata_service/chord/ingest/phenopackets.py index 03353dcd8..a978ae31a 100644 --- a/chord_metadata_service/chord/ingest/phenopackets.py +++ b/chord_metadata_service/chord/ingest/phenopackets.py @@ -85,12 +85,16 @@ def validate_phenopacket(phenopacket_data: dict[str, Any], idx: Optional[int] = None) -> None: # Validate phenopacket data against phenopackets schema. # validation = schema_validation(phenopacket_data, PHENOPACKET_SCHEMA) - validation = schema_validation(phenopacket_data, schema, registry=VRS_REF_REGISTRY) - if not validation: + val_errors = schema_validation(phenopacket_data, schema, registry=VRS_REF_REGISTRY) + if val_errors: # TODO: Report more precise errors raise IngestError( - f"Failed schema validation for phenopacket{(' ' + str(idx)) if idx is not None else ''} " - f"(check Katsu logs for more information)") + data=phenopacket_data, + schema=PHENOPACKET_SCHEMA, + schema_validation_errors=val_errors, + message=f"Failed schema validation for phenopacket{(' ' + str(idx)) if idx is not None else ''} " + f"(check Katsu logs for more information)" + ) def update_or_create_subject(subject: dict) -> pm.Individual: diff --git a/chord_metadata_service/chord/ingest/schema.py b/chord_metadata_service/chord/ingest/schema.py index 1a6af33dd..577ad1e5a 100644 --- a/chord_metadata_service/chord/ingest/schema.py +++ b/chord_metadata_service/chord/ingest/schema.py @@ -24,10 +24,10 @@ def schema_validation(obj, schema, registry=None): try: validator.validate(obj, schema) logger.info("JSON schema validation passed.") - return True + return None except ValidationError: errors = [e for e in validator.iter_errors(obj)] logger.info("JSON schema validation failed.") for i, error in enumerate(errors, 1): logger.error(f"{i} Validation error in {'.'.join(str(v) for v in error.path)}: {error.message}") - return False + return errors diff --git a/chord_metadata_service/chord/ingest/views.py b/chord_metadata_service/chord/ingest/views.py index af06f0379..3e9f5f76d 100644 --- a/chord_metadata_service/chord/ingest/views.py +++ b/chord_metadata_service/chord/ingest/views.py @@ -6,11 +6,11 @@ from django.core.exceptions import ValidationError from django.db import transaction +from rest_framework import status from rest_framework.decorators import api_view, permission_classes from rest_framework.permissions import AllowAny from rest_framework.response import Response - -from bento_lib.responses import errors +from typing import List from . import WORKFLOW_INGEST_FUNCTION_MAP from .exceptions import IngestError @@ -23,18 +23,55 @@ logger = logging.getLogger(__name__) +class IngestResponseBuilder: + + def __init__(self, workflow_id: str, dataset_id: str): + self.workflow_id = workflow_id + self.dataset_id = dataset_id + self.errors = [] + self.warnings = [] + + def add_error(self, error): + self.errors.append(error) + + def add_errors(self, errors: List): + self.errors.extend(errors) + + def add_ingest_error(self, error: IngestError): + if error.validation_errors: + self.add_errors(error.validation_errors) + else: + self.add_error(error.message) + + if error.schema_warnings: + self.warnings.extend(error.schema_warnings) + + def as_response(self, status_code: int) -> Response: + body = { + "success": status_code < status.HTTP_400_BAD_REQUEST, + "warnings": self.warnings, + "errors": self.errors, + } + logger.info(f"Finished {self.workflow_id} ingest request for dataset {self.dataset_id}", body) + return Response(body, status=status_code) + + @api_view(["POST"]) @permission_classes([AllowAny]) def ingest_into_dataset(request, dataset_id: str, workflow_id: str): logger.info(f"Received a {workflow_id} ingest request for dataset {dataset_id}.") + response_builder = IngestResponseBuilder(workflow_id=workflow_id, dataset_id=dataset_id) + # Check that the workflow exists if workflow_id not in WORKFLOW_INGEST_FUNCTION_MAP: - return Response(errors.bad_request_error(f"Ingestion workflow ID {workflow_id} does not exist"), status=400) + response_builder.add_error(f"Ingestion workflow ID {workflow_id} does not exist") + return response_builder.as_response(status.HTTP_400_BAD_REQUEST) if dataset_id not in DATASET_ID_OVERRIDES: if not Dataset.objects.filter(identifier=dataset_id).exists(): - return Response(errors.bad_request_error(f"Dataset with ID {dataset_id} does not exist"), status=400) + response_builder.add_error(f"Dataset with ID {dataset_id} does not exist") + return response_builder.as_response(status.HTTP_400_BAD_REQUEST) dataset_id = str(uuid.UUID(dataset_id)) # Normalize dataset ID to UUID's str format. try: @@ -43,17 +80,17 @@ def ingest_into_dataset(request, dataset_id: str, workflow_id: str): WORKFLOW_INGEST_FUNCTION_MAP[workflow_id](request.data, dataset_id) except IngestError as e: - return Response(errors.bad_request_error(f"Encountered ingest error: {e}"), status=400) + response_builder.add_ingest_error(e) + return response_builder.as_response(status.HTTP_400_BAD_REQUEST) except ValidationError as e: - return Response(errors.bad_request_error( - "Encountered validation errors during ingestion", - *(e.error_list if hasattr(e, "error_list") else e.error_dict.items()), - )) + response_builder.add_errors(e.error_list if hasattr(e, "error_list") else e.error_dict.items()) + return response_builder.as_response(status.HTTP_400_BAD_REQUEST) except Exception as e: # Encountered some other error from the ingestion attempt, return a somewhat detailed message logger.error(f"Encountered an exception while processing an ingest attempt:\n{traceback.format_exc()}") - return Response(errors.internal_server_error(f"Encountered an exception while processing an ingest attempt " - f"(error: {repr(e)}"), status=500) - return Response(status=204) + response_builder.add_error(f"Encountered an exception while processing an ingest attempt (error: {repr(e)})") + return response_builder.as_response(status.HTTP_500_INTERNAL_SERVER_ERROR) + + return response_builder.as_response(status.HTTP_201_CREATED) diff --git a/chord_metadata_service/chord/tests/example_experiment.json b/chord_metadata_service/chord/tests/example_experiment.json index 8f6868db4..e263eeca1 100644 --- a/chord_metadata_service/chord/tests/example_experiment.json +++ b/chord_metadata_service/chord/tests/example_experiment.json @@ -13,7 +13,7 @@ ], "library_strategy": "ChIP-Seq", "library_source": "Genomic", - "library_selection": "Random", + "library_selection": "RANDOM", "library_layout": "Single", "extraction_protocol": "NGS", "molecule": "genomic DNA", @@ -75,4 +75,4 @@ "url": "http://purl.obolibrary.org/obo/so.owl" } ] -} \ No newline at end of file +} diff --git a/chord_metadata_service/chord/tests/example_experiment_bad_biosample.json b/chord_metadata_service/chord/tests/example_experiment_bad_biosample.json index b1f051378..931f15521 100644 --- a/chord_metadata_service/chord/tests/example_experiment_bad_biosample.json +++ b/chord_metadata_service/chord/tests/example_experiment_bad_biosample.json @@ -13,7 +13,7 @@ ], "library_strategy": "ChIP-Seq", "library_source": "Genomic", - "library_selection": "Random", + "library_selection": "RANDOM", "library_layout": "Single", "extraction_protocol": "NGS", "molecule": "genomic DNA", @@ -75,4 +75,4 @@ "url": "http://purl.obolibrary.org/obo/so.owl" } ] -} \ No newline at end of file +} diff --git a/chord_metadata_service/chord/tests/example_invalid_experiment.json b/chord_metadata_service/chord/tests/example_invalid_experiment.json index 437d238cf..0e47f9b72 100644 --- a/chord_metadata_service/chord/tests/example_invalid_experiment.json +++ b/chord_metadata_service/chord/tests/example_invalid_experiment.json @@ -11,9 +11,9 @@ "label": "ChIP-seq" } ], - "library_strategy": "ChIP-Seq", + "library_strategy": "WES", "library_source": "Genomic", - "library_selection": "Random", + "library_selection": "random", "library_layout": "Single", "extraction_protocol": "NGS", "molecule": "genomic DNA", @@ -75,4 +75,4 @@ "url": "http://purl.obolibrary.org/obo/so.owl" } ] -} \ No newline at end of file +} diff --git a/chord_metadata_service/chord/tests/test_api_ingest.py b/chord_metadata_service/chord/tests/test_api_ingest.py index 0dc865de3..e90bc4196 100644 --- a/chord_metadata_service/chord/tests/test_api_ingest.py +++ b/chord_metadata_service/chord/tests/test_api_ingest.py @@ -1,10 +1,11 @@ import json +import uuid from django.urls import reverse from rest_framework import status from rest_framework.test import APITestCase - -from chord_metadata_service.restapi.tests.utils import load_local_json +from chord_metadata_service.chord.tests.example_ingest import EXAMPLE_INGEST_EXPERIMENT, \ + EXAMPLE_INGEST_INVALID_EXPERIMENT, EXAMPLE_INGEST_INVALID_PHENOPACKET, EXAMPLE_INGEST_PHENOPACKET from .constants import VALID_PROJECT_1, valid_dataset_1 from ..workflows.metadata import workflow_set, WORKFLOW_PHENOPACKETS_JSON @@ -60,14 +61,20 @@ def test_phenopackets_ingest(self): reverse("ingest-into-dataset", args=(self.dataset["identifier"], "phenopackets_json_invalid")), content_type="application/json", ) + c = r.json() self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) # No ingestion body r = self.client.post( reverse("ingest-into-dataset", args=(self.dataset["identifier"], "phenopackets_json")), content_type="application/json", ) + c = r.json() self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 2) # 2 required properties missing: 'id' and 'meta_data' # Bad ingestion body JSON r = self.client.post( @@ -75,22 +82,133 @@ def test_phenopackets_ingest(self): content_type="application/json", data="\{\}\}", # noqa: W605 ) + c = r.json() self.assertEqual(r.status_code, status.HTTP_500_INTERNAL_SERVER_ERROR) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) # 1 required property # Invalid phenopacket JSON validation - invalid_phenopacket = load_local_json("example_invalid_phenopacket.json") r = self.client.post( reverse("ingest-into-dataset", args=(self.dataset["identifier"], "phenopackets_json")), content_type="application/json", - data=json.dumps(invalid_phenopacket), + data=json.dumps(EXAMPLE_INGEST_INVALID_PHENOPACKET), ) + c = r.json() self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) # missing required phenopacket ID # Success - valid_phenopacket = load_local_json("example_phenopacket_v2.json") r = self.client.post( reverse("ingest-into-dataset", args=(self.dataset["identifier"], "phenopackets_json")), content_type="application/json", - data=json.dumps(valid_phenopacket), + data=json.dumps(EXAMPLE_INGEST_PHENOPACKET), + ) + c = r.json() + self.assertEqual(c["success"], True) + self.assertEqual(len(c["errors"]), 0) + self.assertEqual(len(c["warnings"]), 0) + self.assertEqual(r.status_code, status.HTTP_201_CREATED) + + def test_experiments_ingest_failures(self): + # Invalid workflow ID + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json_invalid")), + content_type="application/json", + ) + c = r.json() + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + + # No ingestion body + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + ) + c = r.json() + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + + # Bad ingestion body JSON + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + data="\{\}\}", # noqa: W605 + ) + c = r.json() + self.assertEqual(r.status_code, status.HTTP_500_INTERNAL_SERVER_ERROR) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + + # Invalid experiments JSON validation + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_INVALID_EXPERIMENT), + ) + c = r.json() + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 4) + + # Two of the errors concern experiment schema changes + warnings = c["warnings"] + self.assertEqual(len(warnings), 2) + warned_properties = [schema_warning["property_name"] for schema_warning in warnings] + self.assertTrue("library_selection" in warned_properties) + self.assertTrue("library_strategy" in warned_properties) + + # Biosample not present + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_EXPERIMENT), + ) + c = r.json() + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + self.assertEqual(r.status_code, status.HTTP_500_INTERNAL_SERVER_ERROR) + + # Wrong dataset id + r = self.client.post( + reverse("ingest-into-dataset", args=(uuid.uuid4(), "experiments_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_EXPERIMENT), + ) + c = r.json() + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST) + + # Missing biosample + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_EXPERIMENT), + ) + c = r.json() + self.assertEqual(c["success"], False) + self.assertEqual(len(c["errors"]), 1) + self.assertEqual(r.status_code, status.HTTP_500_INTERNAL_SERVER_ERROR) + + def test_experiment_ingest_success(self): + # Create the required phenopacket with a biosample first + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "phenopackets_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_PHENOPACKET), + ) + + # Ingest experiment + r = self.client.post( + reverse("ingest-into-dataset", args=(self.dataset["identifier"], "experiments_json")), + content_type="application/json", + data=json.dumps(EXAMPLE_INGEST_EXPERIMENT), ) - self.assertEqual(r.status_code, status.HTTP_204_NO_CONTENT) + c = r.json() + self.assertEqual(c["success"], True) + self.assertEqual(len(c["errors"]), 0) + self.assertEqual(len(c["warnings"]), 0) + self.assertEqual(r.status_code, status.HTTP_201_CREATED) diff --git a/chord_metadata_service/chord/tests/test_ingest.py b/chord_metadata_service/chord/tests/test_ingest.py index 468505475..59f19ed17 100644 --- a/chord_metadata_service/chord/tests/test_ingest.py +++ b/chord_metadata_service/chord/tests/test_ingest.py @@ -170,22 +170,22 @@ def test_reingesting_updating_phenopackets_json(self): def test_phenopackets_validation(self): # check invalid phenopacket, must fail validation & validate_phenopacket must raise - validation = schema_validation(EXAMPLE_INGEST_INVALID_PHENOPACKET, PHENOPACKET_SCHEMA) - self.assertEqual(validation, False) + val_errs = schema_validation(EXAMPLE_INGEST_INVALID_PHENOPACKET, PHENOPACKET_SCHEMA) + self.assertTrue(len(val_errs) > 0) with self.assertRaises(IngestError): validate_phenopacket(EXAMPLE_INGEST_INVALID_PHENOPACKET) with self.assertRaises(IngestError): ingest_phenopacket(EXAMPLE_INGEST_INVALID_PHENOPACKET, "dummy", validate=True) # valid phenopacket passes validation & doesn't raise - validation_2 = schema_validation(EXAMPLE_INGEST_PHENOPACKET, PHENOPACKET_SCHEMA) - self.assertEqual(validation_2, True) + val_errors_2 = schema_validation(EXAMPLE_INGEST_PHENOPACKET, PHENOPACKET_SCHEMA) + self.assertEqual(val_errors_2, None) validate_phenopacket(EXAMPLE_INGEST_PHENOPACKET) # valid experiments pass validation for exp in EXAMPLE_INGEST_EXPERIMENT["experiments"]: - validation_3 = schema_validation(exp, EXPERIMENT_SCHEMA) - self.assertEqual(validation_3, True) + val_errors_3 = schema_validation(exp, EXPERIMENT_SCHEMA) + self.assertEqual(val_errors_3, None) def test_ingesting_experiments_json(self): # ingest phenopackets data in order to match to biosample ids @@ -222,8 +222,8 @@ def test_ingesting_experiments_json(self): def test_ingesting_invalid_experiment_json(self): # check invalid experiment, must fail validation for exp in EXAMPLE_INGEST_INVALID_EXPERIMENT["experiments"]: - validation = schema_validation(exp, EXPERIMENT_SCHEMA) - self.assertEqual(validation, False) + val_errs = schema_validation(exp, EXPERIMENT_SCHEMA) + self.assertTrue(len(val_errs) > 0) with self.assertRaises(IngestError): validate_experiment(exp) with self.assertRaises(IngestError): @@ -231,8 +231,8 @@ def test_ingesting_invalid_experiment_json(self): # check valid experiment, must pass validation for exp in EXAMPLE_INGEST_EXPERIMENT["experiments"]: - validation_2 = schema_validation(exp, EXPERIMENT_SCHEMA) - self.assertEqual(validation_2, True) + val_errs_2 = schema_validation(exp, EXPERIMENT_SCHEMA) + self.assertEqual(val_errs_2, None) def test_ingesting_experiment_results_json(self): # ingest list of experiments diff --git a/chord_metadata_service/chord/workflows/wdls/experiments_json.wdl b/chord_metadata_service/chord/workflows/wdls/experiments_json.wdl index a6c7aaf47..1d77ef2fe 100644 --- a/chord_metadata_service/chord/workflows/wdls/experiments_json.wdl +++ b/chord_metadata_service/chord/workflows/wdls/experiments_json.wdl @@ -15,12 +15,14 @@ workflow experiments_json { katsu_url = katsu_url, project_dataset = project_dataset, token = access_token, - validate_ssl = validate_ssl + validate_ssl = validate_ssl, + # ingest_report = "~{run_dir}/ingest_report.json" } output { File stdout = ingest_task.txt_output File stderr = ingest_task.err_output + File ingest_report = ingest_task.ingest_report } } @@ -30,8 +32,12 @@ task ingest_task { String katsu_url String project_dataset String token + # String ingest_report Boolean validate_ssl } + + # TODO: add ingest report to outputs + # -o "~{ingest_report}" \ command <<< dataset_id=$(python3 -c 'print("~{project_dataset}".split(":")[1])') RESPONSE=$(curl -X POST ~{true="" false="-k" validate_ssl} -s -w "%{http_code}" \ @@ -39,7 +45,7 @@ task ingest_task { -H "Authorization: Bearer ~{token}" \ --data "@~{json_document}" \ "~{katsu_url}/ingest/${dataset_id}/experiments_json") - if [[ "${RESPONSE}" != "204" ]] + if [[ "${RESPONSE}" != "201" ]] then echo "Error: Metadata service replied with ${RESPONSE}" 1>&2 # to stderr exit 1 @@ -50,5 +56,6 @@ task ingest_task { output { File txt_output = stdout() File err_output = stderr() + # File ingest_report = "~{ingest_report}" } } diff --git a/chord_metadata_service/chord/workflows/wdls/phenopackets_json.wdl b/chord_metadata_service/chord/workflows/wdls/phenopackets_json.wdl index f281868ec..6d2a3e18f 100644 --- a/chord_metadata_service/chord/workflows/wdls/phenopackets_json.wdl +++ b/chord_metadata_service/chord/workflows/wdls/phenopackets_json.wdl @@ -15,6 +15,7 @@ workflow phenopackets_json { katsu_url = katsu_url, project_dataset = project_dataset, token = access_token, + # ingest_report = "~{run_dir}/ingest_report.json", validate_ssl = validate_ssl } @@ -30,8 +31,12 @@ task ingest_task { String katsu_url String project_dataset String token + # String ingest_report Boolean validate_ssl } + + # TODO: add ingest report to outputs + # -o "~{ingest_report}" \ command <<< dataset_id=$(python3 -c 'print("~{project_dataset}".split(":")[1])') RESPONSE=$(curl -X POST ~{true="" false="-k" validate_ssl} -s -w "%{http_code}" \ @@ -39,7 +44,7 @@ task ingest_task { -H "Authorization: Bearer ~{token}" \ --data "@~{json_document}" \ "~{katsu_url}/ingest/${dataset_id}/phenopackets_json") - if [[ "${RESPONSE}" != "204" ]] + if [[ "${RESPONSE}" != "201" ]] then echo "Error: Metadata service replied with ${RESPONSE}" 1>&2 # to stderr exit 1 @@ -50,5 +55,6 @@ task ingest_task { output { File txt_output = stdout() File err_output = stderr() + # File ingest_report = "~{ingest_report}" } } diff --git a/chord_metadata_service/experiments/migrations/0010_v6_2_0.py b/chord_metadata_service/experiments/migrations/0010_v6_2_0.py new file mode 100644 index 000000000..c8754cc66 --- /dev/null +++ b/chord_metadata_service/experiments/migrations/0010_v6_2_0.py @@ -0,0 +1,32 @@ +from typing import List, Tuple +from django.db import migrations +from chord_metadata_service.experiments.schemas import EXPERIMENT_SCHEMA_CHANGES + +V6_2_0_PROPERTIES = EXPERIMENT_SCHEMA_CHANGES["6.2.0"]["properties"] +LIB_STRATEGY_CONVERSIONS = V6_2_0_PROPERTIES["library_strategy"] +LIB_SELECTION_CONVERIONS = V6_2_0_PROPERTIES["library_selection"] + + +def set_experiment_library(apps, _schema_editor): + Experiment = apps.get_model("experiments", "Experiment") + for (old_val, new_val) in LIB_STRATEGY_CONVERSIONS: + # Modify library_strategy if necessary + for exp in Experiment.objects.filter(library_strategy=old_val): + exp.library_strategy = new_val + exp.save() + + for (old_val, new_val) in LIB_SELECTION_CONVERIONS: + # Modify library_selection if necessary + for exp in Experiment.objects.filter(library_selection=old_val): + exp.library_selection = new_val + exp.save() + + +class Migration(migrations.Migration): + dependencies = [ + ('experiments', '0009_v6_0_0'), + ] + + operations = [ + migrations.RunPython(set_experiment_library) + ] diff --git a/chord_metadata_service/experiments/schemas.py b/chord_metadata_service/experiments/schemas.py index cefd88049..92b780ea0 100644 --- a/chord_metadata_service/experiments/schemas.py +++ b/chord_metadata_service/experiments/schemas.py @@ -2,11 +2,27 @@ from .descriptions import EXPERIMENT, EXPERIMENT_RESULT, INSTRUMENT from chord_metadata_service.restapi.schemas import ONTOLOGY_CLASS_LIST, KEY_VALUE_OBJECT from chord_metadata_service.restapi.schema_utils import tag_ids_and_describe, get_schema_app_id, sub_schema_uri +from chord_metadata_service.ontologies import read_xsd_simple_type_values, SRA_EXPERIMENT_FILE_NAME __all__ = ["EXPERIMENT_SCHEMA", "EXPERIMENT_RESULT_SCHEMA", "INSTRUMENT_SCHEMA"] + base_uri = get_schema_app_id(Path(__file__).parent.name) +# Experiment library strategy options are read from the EBI xsd file +LIBRARY_STRATEGIES = read_xsd_simple_type_values( + SRA_EXPERIMENT_FILE_NAME, + "typeLibraryStrategy", +) + + +# Experiment library selection options are read from the EBI xsd file +LIBRARY_SELECTION = read_xsd_simple_type_values( + SRA_EXPERIMENT_FILE_NAME, + "typeLibrarySelection", +) + + EXPERIMENT_RESULT_SCHEMA = tag_ids_and_describe({ "$schema": "http://json-schema.org/draft-07/schema#", "$id": sub_schema_uri(base_uri, "experiment_result"), @@ -105,7 +121,7 @@ "molecule_ontology": ONTOLOGY_CLASS_LIST, "library_strategy": { "type": "string", - "enum": ["Bisulfite-Seq", "RNA-Seq", "ChIP-Seq", "WES", "WGS", "RAD-Seq", "AMPLICON", "Other"] + "enum": LIBRARY_STRATEGIES }, "library_source": { "type": "string", @@ -114,7 +130,7 @@ }, "library_selection": { "type": "string", - "enum": ["Random", "PCR", "Random PCR", "RT-PCR", "MF", "Exome capture", "Other"] + "enum": LIBRARY_SELECTION }, "library_layout": { "type": "string", @@ -144,3 +160,45 @@ }, "required": ["id", "experiment_type"] }, EXPERIMENT) + + +EXPERIMENT_WORKFLOW_SCHEMA = { + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "katsu:experiments:experiment_workflow_schema", + "title": "Experiment workflow schema", + "description": "Schema that describes the shape \ + of an experiment workflow ingestion", + "type": "object", + "properties": { + "experiments": { + "type": "array", + "items": {"type": "object"}, + "minItems": 1, + }, + "resources": { + "type": "array", + "items": {"type": "object"}, + } + }, + "required": ["experiments"] +} + +""" +Dictionary of schema changes for warnings. +""" +EXPERIMENT_SCHEMA_CHANGES = { + "6.2.0": { + "properties": { + "library_strategy": [ + ("WES", "WXS"), + ("Other", "OTHER"), + ], + "library_selection": [ + ("Random", "RANDOM"), + ("Random PCR", "RANDOM PCR"), + ("Exome capture", "Hybrid Selection"), + ("Other", "other"), + ] + } + } +} diff --git a/chord_metadata_service/experiments/tests/example_experiments.json b/chord_metadata_service/experiments/tests/example_experiments.json index e888df91b..a36023f59 100644 --- a/chord_metadata_service/experiments/tests/example_experiments.json +++ b/chord_metadata_service/experiments/tests/example_experiments.json @@ -13,7 +13,7 @@ ], "library_strategy": "ChIP-Seq", "library_source": "Genomic", - "library_selection": "Random", + "library_selection": "RANDOM", "library_layout": "Single", "extraction_protocol": "NGS", "molecule": "genomic DNA", @@ -77,7 +77,7 @@ ], "library_strategy": "ChIP-Seq", "library_source": "Genomic", - "library_selection": "Random", + "library_selection": "RANDOM", "library_layout": "Single", "extraction_protocol": "NGS", "molecule": "genomic DNA", @@ -139,4 +139,4 @@ "url": "http://purl.obolibrary.org/obo/so.owl" } ] -} \ No newline at end of file +} diff --git a/chord_metadata_service/ontologies/__init__.py b/chord_metadata_service/ontologies/__init__.py new file mode 100644 index 000000000..b05e2bc07 --- /dev/null +++ b/chord_metadata_service/ontologies/__init__.py @@ -0,0 +1,6 @@ +from .utils import read_xsd_simple_type_values, SRA_EXPERIMENT_FILE_NAME + +__all__ = [ + "read_xsd_simple_type_values", + "SRA_EXPERIMENT_FILE_NAME", +] diff --git a/chord_metadata_service/ontologies/utils.py b/chord_metadata_service/ontologies/utils.py new file mode 100644 index 000000000..36a28e9f8 --- /dev/null +++ b/chord_metadata_service/ontologies/utils.py @@ -0,0 +1,23 @@ +import os +from typing import List +import xmltodict +from pathlib import Path + +XSD_ONTOLOGIES_PATH = Path("chord_metadata_service/ontologies/xsd/") +SRA_EXPERIMENT_FILE_NAME = "SRA.experiment.xsd.xml" + + +def read_xsd_simple_type_values(xsd_file_name: str, type_name: str) -> List[str]: + """Reads an XML Schema Definition (XSD) file and returns a type's values. + The XSD file is parsed using xmltodict following this spec: + https://www.xml.com/pub/a/2006/05/31/converting-between-xml-and-json.html + """ + xsd_file_path = os.path.join(XSD_ONTOLOGIES_PATH, xsd_file_name) + with open(xsd_file_path, "r") as file: + xsd_file = file.read() + + xsd_data = xmltodict.parse(xsd_file, namespaces={"xs": None}) + simple_types = {sp["@name"]: sp for sp in xsd_data["schema"]["simpleType"]} + target_type = simple_types[type_name] + values = [val["@value"] for val in target_type["restriction"]["enumeration"]] + return values diff --git a/chord_metadata_service/ontologies/xsd/SRA.experiment.xsd.xml b/chord_metadata_service/ontologies/xsd/SRA.experiment.xsd.xml new file mode 100644 index 000000000..64d4931fa --- /dev/null +++ b/chord_metadata_service/ontologies/xsd/SRA.experiment.xsd.xml @@ -0,0 +1,799 @@ + + + + + + + + + Sequencing technique intended for this library. + + + + + Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details) + + + + + + Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details) + + + + + + Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details) + + + + + + Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see + pubmed 18611170 for details) + + + + + Strand-specific RNA sequencing. + + + + + + Single nucleus RNA sequencing is a method for profiling gene expression in cells which are difficult to isolate. + + + + + Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding + functional elements. (see pubmed 21787409 for details) + + + + + Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small + nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or + piRNA/piwi/RNA (piwi-interacting RNA). + + + + + Full-length sequencing of cDNA templates + + + + + Single pass sequencing of cDNA templates + + + + + Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. + + + + + Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA. + + + + + Random sequencing of a whole chromosome or other replicon isolated from a genome. + + + + + + Genomic clone based (hierarchical) sequencing. + + + + + Shotgun of pooled clones (usually BACs and Fosmids). + + + + + Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling + using SSU rRNA . + + + + + Clone end (5', 3', or both) sequencing. + + + + + Sequencing intended to finish (close) gaps in existing coverage. + + + + + ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein. + + + + + Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached. + + + + + Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. + + + + + + MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil + depending on methylation status. + + + + + Concatenated Tag Sequencing + + + + + Methylation-Sensitive Restriction Enzyme Sequencing. + + + + + Methylated DNA Immunoprecipitation Sequencing. + + + + + Methyl CpG Binding Domain Sequencing. + + + + + Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets + inserted into each gene of a colony after some time. + + + + + CGHub special request: Independent experiment to re-evaluate putative variants. + + + + + Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin. + + + + + Systematic Evolution of Ligands by Exponential enrichment + + + + + Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP). + + + + + Direct sequencing of proximity-ligated chromatin immunoprecipitates. + + + + + binning and barcoding of large DNA fragments to facilitate assembly of the fragment + + + + + Enrichment of a targeted subset of loci. + + + + + + Nucleosome Occupancy and Methylome sequencing. + + + + + ChIPmentation combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase (see pubmed 26280331 for details) + + + + + Genotyping by sequencing is a method to discover single nucleotide polymorphisms for genotyping studies. + + + + + Ribosome profiling (also named ribosome footprinting) that uses specialized messenger RNA (mRNA) sequencing to determine which mRNAs are being actively translated. It produces a "global snapshot" of all the ribosomes active in a cell at a particular moment, known as a translatome. + + + + + Library strategy not listed. + + + + + + + + The LIBRARY_SOURCE specifies the type of source material that is being sequenced. + + + + + Genomic DNA (includes PCR products from genomic DNA). + + + + + + Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). + + + + + + Mixed material from metagenome. + + + + + Transcription products from community targets + + + + + Synthetic DNA. + + + + + Viral RNA. + + + + + Other, unspecified, or unknown library source material. + + + + + + + + Method used to enrich the target in the sequence library preparation + + + + + No Selection or Random selection + + + + + target enrichment via PCR + + + + + Source material was selected by randomly generated primers. + + + + + target enrichment via + + + + + Hypo-methylated partial restriction digest + + + + + Methyl Filtrated + + + + + Selection for less repetitive (and more gene rich) sequence through Cot filtration (CF) or other fractionation + techniques based on DNA kinetics. + + + + + Physical selection of size appropriate targets. + + + + + Methylation Spanning Linking Library + + + + + PolyA selection or enrichment for messenger RNA (mRNA); synonymize with PolyA + + + + + + + PolyA selection or enrichment for messenger RNA (mRNA); should replace cDNA enumeration. + + + + + enrichment of messenger RNA (mRNA) by hybridization to Oligo-dT. + + + + + depletion of ribosomal RNA by oligo hybridization. + + + + + depletion of ribosomal RNA by inverse oligo hybridization. + + + + + Chromatin immunoprecipitation + + + + + Chromatin immunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein. + + + + + Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached. + + + + + DNase I endonuclease digestion and size selection reveals regions of chromatin where the DNA is highly sensitive to DNase I. + + + + + Selection by hybridization in array or solution. + + + + + Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable + number of loci to facilitate re-sampling. + + + + + DNA fractionation using restriction enzymes. + + + + + Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine + (m5C). + + + + + Enrichment by methyl-CpG binding domain. + + + + + Cap-analysis gene expression. + + + + + Rapid Amplification of cDNA Ends. + + + + + Multiple Displacement Amplification, a non-PCR based DNA amplification technique that amplifies a minute + quantifies of DNA to levels suitable for genomic analysis. + + + + + Targeted sequence capture protocol covering an arbitrary set of nonrepetitive genomics targets. An example is + capture bisulfite sequencing using padlock probes (BSPP). + + + + + Other library enrichment, screening, or selection process. + + + + + Library enrichment, screening, or selection is not specified. + + + + + + + + + + + + + + + + + + Assignment of read_group_tag to decoded read + + + + + + + + + + Label a sample within a scope of the pool + + + + + Proportion of this sample (in percent) that was included in sample pool. + + + + + + + + + + + + + Identifies a list of group/pool/multiplex sample members. This implies that + this sample record is a group, pool, or multiplex, but it continues to receive + its own accession and can be referenced by an experiment. By default if + no match to any of the listed members can be determined, then the default + sample reference is used. + + + + + + + Reference to the sample that is used when read membership cannot be determined. A default member should + be provided if there exists a possibility that some reads will be left over from barcode/MID resolution. A default member + is not needed when defining a true pool (where individual samples are not distinguished in the reads), or the reads have + been partitioned among the pool members (no leftovers). + + + + + Reference to the sample as determined from barcode/MID resolution or read partition. + + + + + + + + + + + + The LIBRARY_DESCRIPTOR specifies the origin of the material being + sequenced and any treatments that the material might have undergone that affect the + sequencing result. This specification is needed even if the platform does not + require a library construction step per se. + + + + + + The submitter's name for this library. + + + + + + + + + + LIBRARY_LAYOUT specifies whether to expect single, paired, or other configuration of reads. + In the case of paired reads, information about the relative distance and orientation is specified. + + + + + + + + + Reads are unpaired (usual case). + + + + + + + + + + + + + + + + + + Names the gene(s) or locus(loci) or other genomic feature(s) targeted by the sequence. + + + + + + + + + Reference to an archived primer or + probe set. Example: dbProbe + + + + + + + + + Bacterial small subunit ribosomal RNA, a locus used for + phylogenetic studies of bacteria and as a target for random target PCR in + environmental biodiversity screening. + + + + + Eukaryotic small subunit ribosomal RNA, a locus used for + phylogenetic studies of eukaryotes and as a target for random target PCR in + environmental biodiversity screening. + + + + + Structural ribosomal RNA for the large component, or large + subunit (LSU) of eukaryotic cytoplasmic ribosomes.. + + + + + RuBisCO large subunit : ribulose-1,5-bisphosphate + carboxylase/oxygenase large subunit, a locus used for phylogenetic studies + of plants. + + + + + Maturase K gene, a locus used for phylogenetic studies of + plants. + + + + + Mitochondrial cytochrome c oxidase 1 gene, a locus used for + phylogenetic studies of animals + + + + + Internal transcribed spacers 1 and 2 plus 5.8S rRNA region, + a locus used for phylogenetic studies of fungi. + + + + + All exonic regions of the genome. + + + + + Other locus, please describe. + + + + + + + + + Submitter supplied description of alternate locus and auxiliary + information. + + + + + + + + + + + + + + The optional pooling strategy indicates how the library or libraries are organized if multiple samples are involved. + + + + + + + + + + Free form text describing the protocol by which the sequencing library was constructed. + + + + + + + + + + Goal and setup of the individual library including library was constructed. + + + + + + Pick a sample to associate this experiment with. The sample may be an individual or a pool, + depending on how it is specified. + + + + + + The LIBRARY_DESCRIPTOR specifies the origin of the material being sequenced and any + treatments that the material might have undergone that affect the sequencing result. This specification is + needed even if the platform does not require a library construction step per se. + + + + + + The SPOT_DESCRIPTOR specifies how to decode the individual reads of interest from the + monolithic spot sequence. The spot descriptor contains aspects of the experimental design, platform, and + processing information. There will be two methods of specification: one will be an index into a table of + typical decodings, the other being an exact specification. This construct is needed for loading data and for + interpreting the loaded runs. It can be omitted if the loader can infer read layout (from multiple input + files or from one input files). + + + + + + + + + + + An Experiment specifies of what will be sequenced and how the sequencing will be performed. + It does not contain results. + An Experiment is composed of a design, a platform selection, and processing parameters. + + + + + + + + + + Short text that can be used to call out experiment records in searches or in displays. + This element is technically optional but should be used for all new records. + + + + + + + Identifies the parent study. + + + + + + + + + + + The library design including library properties, layout, protocol, targeting information, and spot and gap + descriptors. + + + + + + The PLATFORM record selects which sequencing platform and platform-specific runtime parameters. + This will be determined by the Center. + + + + + + + + + + Links to resources related to this experiment or experiment set (publication, datasets, online databases). + + + + + + + + + + + + + Properties and attributes of the experiment. These can be entered as free-form + tag-value pairs. + + + + + + + + + + + + + + + + + + + + + + + An EXPERMENT_SET is a container for a set of experiments and a common namespace. + + + + + + + \ No newline at end of file diff --git a/chord_metadata_service/phenopackets/schemas.py b/chord_metadata_service/phenopackets/schemas.py index 51be759b9..a5dc4d042 100644 --- a/chord_metadata_service/phenopackets/schemas.py +++ b/chord_metadata_service/phenopackets/schemas.py @@ -658,7 +658,7 @@ "required": ["id", "meta_data"], }, descriptions.PHENOPACKET) -VRS_REF_RESOURCE = Resource.from_contents(contents=vrs_schema_definitions, default_specification=DRAFT_07) +VRS_REF_RESOURCE = Resource.from_contents(contents=vrs_schema_definitions) VRS_REF_REGISTRY = VRS_REF_RESOURCE @ Registry() resolver = VRS_REF_REGISTRY.resolver() diff --git a/poetry.lock b/poetry.lock index 23903b429..5e787f45c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,19 +2,20 @@ [[package]] name = "adrf" -version = "0.1.2" 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module directory is renamed too -version = "6.0.0" +version = "6.2.0" description = "An implementation of a clin/pheno metadata store for the Bento platform." authors = [ "Ksenia Zaytseva", @@ -20,6 +20,7 @@ include = [ "chord_metadata_service/chord/workflows/wdls/*.wdl", "chord_metadata_service/chord/tests/*.json", "chord_metadata_service/dats/*", + "chord_metadata_service/ontologies/xsd/*.xml", "chord_metadata_service/restapi/tests/*.json", ] repository = "https://github.com/bento-platform/katsu" @@ -54,6 +55,7 @@ tabulate = "^0.9.0" uritemplate = "^4.1.1" pyhumps = "^3.8.0" adrf = "^0.1.1" +xmltodict="0.13.0" [tool.poetry.group.dev.dependencies] coverage = "^6.5.0"