J waldrip/ivt validation

.gitignore

@@ -55,4 +55,6 @@ venv-hm-ingest-api/*
 .vscode/settings.json
 src/venv-hm-ingest-api
 .vscode/launch.json
-src/test/file_upload/temp_dir
+src/test/file_upload/temp_dir
+.python-version
+.vscode/*

src/app.py

@@ -67,7 +67,8 @@
 from routes.validation import validation_blueprint
 from routes.datasets_bulk_submit import datasets_bulk_submit_blueprint, DatasetHelper as ds_helper
 from routes.privs import privs_blueprint
-from ingest_validation_tools import schema_loader, table_validator 
+from ingest_validation_tools import schema_loader
+from ingest_validation_tools.local_validation import table_validator
 from ingest_validation_tools import validation_utils as iv_utils
 
 # Set logging format and level (default is warning)

src/instance/app.cfg.example

@@ -164,7 +164,6 @@ APPLICATION_CONTEXT = 'HUBMAP'
 # CEDAR API KEY, get one at: https://cedar.metadatacenter.org/
 
 CEDAR_API_KEY = ''
-CEDAR_API_URL = 'https://resource.metadatacenter.org/templates/https%3A%2F%2Frepo.metadatacenter.org%2Ftemplates%2F'
 
 #URL of Data Portal
 PORTAL_URL = 'https://portal.hubmapconsortium.org'

src/routes/validation/__init__.py

@@ -15,8 +15,8 @@
 
 from hubmap_commons import file_helper as commons_file_helper
 from hubmap_commons.hm_auth import AuthHelper
+from hubmap_commons.file_helper import ensureTrailingSlashURL
 
-from version_helper import VersionHelper
 
 from utils.string import equals, to_title_case
 from utils.rest import (
@@ -40,7 +40,7 @@
 ingest_validation_tools_validation_utils = import_module('ingest_validation_tools.validation_utils')
 ingest_validation_tools_plugin_validator = import_module('ingest_validation_tools.plugin_validator')
 ingest_validation_tools_schema_loader = import_module('ingest_validation_tools.schema_loader')
-ingest_validation_tools_table_validator = import_module('ingest_validation_tools.table_validator')
+ingest_validation_tools_table_validator = import_module('ingest_validation_tools.local_validation.table_validator')
 
 __all__ = ["ingest_validation_tools_upload",
            "ingest_validation_tools_error_report",
@@ -379,16 +379,20 @@ def validate_metadata_upload():
                 # if ensure_latest_cedar_version is == None: #maybe check for true specifically?
                 # IE "isLatestVersion, "isLatestPublishedVersion or "isLatestDraftVersion" 
                 try:
-                    schema_id = VersionHelper.get_schema_id(upload.get('fullpath'), str)
-                    if type(schema_id) == tuple:
-                       return rest_response(StatusCodes.BAD_REQUEST,  "Error", "metadata_schema_id not found in header")
-                    # if schema_id is None:
-                    latestVersion = VersionHelper.get_latest_published_schema(schema_id)
-                    isLatest = (schema_id == latestVersion)
-                    if isLatest != True:
+                    # Obtain the schema object 
+                    schema_obj = ingest_validation_tools_validation_utils.get_schema_version(
+                        path=upload.get('fullpath'), encoding="ascii"
+                    )
+                    # extract version value if the returned object has one
+                    schemaVers = getattr(schema_obj, 'version', schema_obj)
+                    isLatest = ingest_validation_tools_validation_utils.is_schema_latest_version(
+                        schemaVers, current_app.config['CEDAR_API_KEY']
+                    )
+                    if not isLatest:
                         return rest_response(StatusCodes.BAD_REQUEST,  "This is not the latest version of the metadata specification as defined in CEDAR", "This is not the latest version of the metadata specification as defined in CEDAR")
+
                 except Exception as e:
-                    return rest_server_err(e, True)
+                    return rest_server_err(e, False)
 
             if check_cedar(entity_type, sub_type, upload) is False:
                 id_sub_type = get_cedar_schema_ids().get(sub_type)