Merge pull request #150 from sennetconsortium/maxsibilla/werkzeug-fix

Maxsibilla/werkzeug fix

src/requirements.txt

@@ -1,6 +1,7 @@
 Flask==2.1.3
 globus_sdk==2.0.1
 hubmap-sdk==1.0.4
+Werkzeug==2.1.0
 
 # The commons package requires requests>=2.22.0
 requests==2.25.1

src/routes/entity_CRUD/__init__.py

@@ -4,6 +4,7 @@
 import os
 import re
 import datetime
+import time
 from typing import List
 import urllib.request
 import yaml
@@ -988,39 +989,43 @@ def submit_upload(upload_uuid):
 #AirFlow interface
 @entity_CRUD_blueprint.route('/uploads/<upload_uuid>/validate', methods=['PUT'])
 def validate_upload(upload_uuid):
+    start_time = time.time()
     if not request.is_json:
         return Response("json request required", 400)
 
     upload_changes = request.json
 
-    #get auth info to use in other calls
-    #add the app specific header info
+    # get auth info to use in other calls
+    # add the app specific header info
     http_headers = {
         'Authorization': request.headers["AUTHORIZATION"],
         'Content-Type': 'application/json',
-        'X-SenNet-Application':'ingest-api'
+        'X-SenNet-Application': 'ingest-api'
     }
 
-    #update the Upload with any changes from the request
-    #and change the status to "Processing", the validate
-    #pipeline will update the status when finished
+    # update the Upload with any changes from the request
+    # and change the status to "Processing", the validate
+    # pipeline will update the status when finished
 
-    #run the pipeline validation
+    # run the pipeline validation
     upload_changes['status'] = 'Processing'
     update_url = commons_file_helper.ensureTrailingSlashURL(current_app.config['ENTITY_WEBSERVICE_URL']) + 'entities/' + upload_uuid
 
     # Disable ssl certificate verification
-    resp = requests.put(update_url, headers=http_headers, json=upload_changes, verify = False)
+    resp = requests.put(update_url, headers=http_headers, json=upload_changes, verify=False)
     if resp.status_code >= 300:
         return Response(resp.text, resp.status_code)
+    logger.debug("--- %s seconds to update Entity API ---" % (time.time() - start_time))
 
-    #disable validations stuff for now...
+    # disable validations stuff for now...
     ##call the AirFlow validation workflow
-    validate_url = commons_file_helper.ensureTrailingSlashURL(current_app.config['INGEST_PIPELINE_URL']) + 'uploads/' + upload_uuid + "/validate"
+    validate_url = commons_file_helper.ensureTrailingSlashURL(
+        current_app.config['INGEST_PIPELINE_URL']) + 'uploads/' + upload_uuid + "/validate"
     ## Disable ssl certificate verification
-    resp2 = requests.put(validate_url, headers=http_headers, json=upload_changes, verify = False)
+    resp2 = requests.put(validate_url, headers=http_headers, json=upload_changes, verify=False)
     if resp2.status_code >= 300:
         return Response(resp2.text, resp2.status_code)
+    logger.debug("--- %s seconds to send validate request to Airflow ---" % (time.time() - start_time))
 
     return Response(resp.text, resp.status_code)