Merge pull request #180 from sennetconsortium/libpitt/cedar-support

Libpitt/cedar support

src/instance/app.cfg.example

@@ -99,3 +99,6 @@ DATACITE_SENNET_PREFIX = ''
 UBKG_SERVER = 'https://ontology.api.hubmapconsortium.org/'
 UBKG_ENDPOINT_VALUESET = 'valueset?parent_sab=SENNET&parent_code={code}&child_sabs=SENNET'
 UBKG_CODES = '{"specimen_categories":"C020076", "organ_types":{"code": "C000008", "key": "organs", "endpoint": "organs?application_context=SENNET"}, "entities": "C000012", "source_types":"C050020", "assay_types":{"code": "C004000", "key": "datasets", "endpoint": "datasets?application_context=SENNET"}}'
+
+# CEDAR API KEY, get one at: https://cedar.metadatacenter.org/
+CEDAR_API_KEY = ''

src/routes/validation/validation.py

@@ -17,6 +17,8 @@
 import time
 import csv
 
+from ..privs import get_groups_token
+
 validation_blueprint = Blueprint('validation', __name__)
 logger = logging.getLogger(__name__)
 
@@ -105,7 +107,12 @@ def validate_tsv(schema='metadata', path=None):
         result = {'Preflight': str(e)}
     else:
         try:
-            result = iv_utils.get_tsv_errors(path, schema_name=schema_name, report_type=table_validator.ReportType.JSON)
+            app_context = {
+                'request_header': {'X-SenNet-Application': 'ingest-api'},
+                'entities_url': f"{commons_file_helper.ensureTrailingSlashURL(current_app.config['ENTITY_WEBSERVICE_URL'])}entities/"
+            }
+            result = iv_utils.get_tsv_errors(path, schema_name=schema_name, report_type=table_validator.ReportType.JSON,
+                                             cedar_api_key=current_app.config['CEDAR_API_KEY'], globus_token=get_groups_token(), app_context=app_context)
         except Exception as e:
             result = rest_server_err(e, True)
     return json.dumps(result)