Merge pull request #125 from sennetconsortium/libpitt/116-board-eps

Libpitt/116 board eps

src/app.py

@@ -22,6 +22,7 @@
 
 # Local Modules
 from lib.file_upload_helper import UploadFileHelper
+from lib.neo4j_helper import Neo4jHelper
 
 # Set logging format and level (default is warning)
 # All the API logging is forwarded to the uWSGI server and gets written into the log file `uwsgi-ingest-api.log`
@@ -95,7 +96,7 @@
                                                   app.config['NEO4J_USERNAME'],
                                                   app.config['NEO4J_PASSWORD'])
 
-    app.neo4j_driver_instance = neo4j_driver_instance
+    Neo4jHelper.set_instance(neo4j_driver_instance)
 
     logger.info("Initialized neo4j_driver module successfully :)")
 except Exception:

src/instance/app.cfg.example

@@ -20,6 +20,8 @@ GLOBUS_CLIENT_APP_NAME = 'SenNet Data Portal'
 
 # Point to remote URL for testing and production deployment
 GLOBUS_CLIENT_APP_URI = 'https://data.dev.sennetconsortium.org/'
+DATA_INGEST_BOARD_APP_URI = 'http://localhost:3001/'
+DATA_INGEST_BOARD_NAME = ‘Data Ingest Board - DEV’
 
 GLOBUS_BASE_FILE_USER_NAME = 'hive'
 GLOBUS_ADMIN_FILE_USER_NAME = 'shirey'
@@ -35,6 +37,14 @@ UUID_WEBSERVICE_URL = 'http://uuid-api:8080/uuid'
 #Search-api
 SEARCH_WEBSERVICE_URL = 'https://search-api.dev.sennetconsortium.org'
 
+# The base url for the HuBMAP portal website
+PORTAL_URL = 'https://data.dev.sennetconsortium.org/'
+
+# The base url for the HuBMAP ingest website
+INGEST_URL = 'https://ingest-api.dev.sennetconsortium.org/'
+
+GLOBUS_APP_BASE_URL = 'https://app.globus.org'
+
 # Directory where file uploads will be placed temporarily
 # until they are committed
 # Remember to set the proper file system user and group permission
@@ -86,4 +96,3 @@ 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"}}'
-

src/lib/__init__.py

@@ -0,0 +1,36 @@
+from flask import Blueprint, jsonify, request, Response, current_app, abort, json
+import urllib.request
+from hubmap_commons import file_helper as commons_file_helper
+
+def get_globus_url(data_access_level, group_name, uuid):
+    globus_server_uuid = None
+    dir_path = " "
+    # public access
+    if data_access_level == "public":
+        globus_server_uuid = current_app.config['GLOBUS_PUBLIC_ENDPOINT_UUID']
+        access_dir = commons_file_helper.ensureTrailingSlashURL(current_app.config['ACCESS_LEVEL_PUBLIC'])
+        dir_path = dir_path + access_dir + "/"
+    # consortium access
+    elif data_access_level == 'consortium':
+        globus_server_uuid = current_app.config['GLOBUS_CONSORTIUM_ENDPOINT_UUID']
+        access_dir = commons_file_helper.ensureTrailingSlashURL(current_app.config['ACCESS_LEVEL_CONSORTIUM'])
+        dir_path = dir_path + access_dir + group_name + "/"
+    # protected access
+    elif data_access_level == 'protected':
+        globus_server_uuid = current_app.config['GLOBUS_PROTECTED_ENDPOINT_UUID']
+        access_dir = commons_file_helper.ensureTrailingSlashURL(current_app.config['ACCESS_LEVEL_PROTECTED'])
+        dir_path = dir_path + access_dir + group_name + "/"
+
+    if globus_server_uuid is not None:
+        dir_path = dir_path + uuid + "/"
+        dir_path = urllib.parse.quote(dir_path, safe='')
+
+        # https://current_app.globus.org/file-manager?origin_id=28bb03c-a87d-4dd7-a661-7ea2fb6ea631&origin_path=2%FIEC%20Testing%20Group%20F03584b3d0f8b46de1b29f04be1568779%2F
+        globus_url = commons_file_helper.ensureTrailingSlash(current_app.config[
+                                                                 'GLOBUS_APP_BASE_URL']) + "file-manager?origin_id=" + globus_server_uuid + "&origin_path=" + dir_path
+
+    else:
+        globus_url = ""
+    if uuid is None:
+        globus_url = ""
+    return globus_url

src/lib/file.py

@@ -1,11 +1,11 @@
 import csv
+import os
 import logging
 from hubmap_commons import file_helper as commons_file_helper
 from flask import current_app, request
 from atlas_consortia_commons.rest import *
 from werkzeug import utils
 from collections import OrderedDict
-
 from lib.file_upload_helper import UploadFileHelper
 
 logger = logging.getLogger(__name__)
@@ -80,4 +80,23 @@ def ln_err(error: str, row: int = None, column: str = None):
         'column': column,
         'error': error,
         'row': row
-    }
+    }
+
+
+def files_exist(uuid, data_access_level):
+    if not uuid or not data_access_level:
+        return False
+    if data_access_level == "public":
+        absolute_path = commons_file_helper.ensureTrailingSlashURL(current_app.config['GLOBUS_PUBLIC_ENDPOINT_FILEPATH'])
+    # consortium access
+    elif data_access_level == 'consortium':
+        absolute_path = commons_file_helper.ensureTrailingSlashURL(current_app.config['GLOBUS_CONSORTIUM_ENDPOINT_FILEPATH'])
+    # protected access
+    elif data_access_level == 'protected':
+        absolute_path = commons_file_helper.ensureTrailingSlashURL(current_app.config['GLOBUS_PROTECTED_ENDPOINT_FILEPATH'])
+
+    file_path = absolute_path + uuid
+    if os.path.exists(file_path) and os.path.isdir(file_path) and os.listdir(file_path):
+        return True
+    else:
+        return False

src/lib/neo4j_helper.py

@@ -0,0 +1,26 @@
+from neo4j import Driver
+
+neo4j_driver_instance = None
+
+
+class Neo4jHelper:
+    @staticmethod
+    def set_instance(neo4j):
+        global neo4j_driver_instance
+        neo4j_driver_instance = neo4j
+
+    @staticmethod
+    def get_instance():
+        global neo4j_driver_instance
+        return neo4j_driver_instance
+
+    @staticmethod
+    def close():
+        # Specify as module-scope variable
+        global neo4j_driver_instance
+
+        if isinstance(neo4j_driver_instance, Driver):
+            neo4j_driver_instance.close()
+            neo4j_driver_instance = None
+        else:
+            raise TypeError("The private module variable '_driver' is not a neo4j.Driver object")

src/lib/ontology.py

@@ -1,7 +1,6 @@
 from atlas_consortia_commons.ubkg.ubkg_sdk import UbkgSDK
 from flask import current_app
 
-
 def get_organ_types_ep():
     return UbkgSDK.get_endpoint(current_app.ubkg.organ_types)
 
@@ -15,4 +14,5 @@ class Ontology(UbkgSDK):
     def assay_types_ext():
         Ontology.Ops.key = 'data_type'
         Ontology.Ops.url_params = '&dataset_provider=external'
-        return Ontology.transform_ontology(current_app.ubkg.assay_types, 'AssayTypesExt')
+        return Ontology.transform_ontology(current_app.ubkg.assay_types, 'AssayTypesExt')
+

src/routes/auth/__init__.py

@@ -10,17 +10,48 @@
 
 # Endpoints for UI Login and Logout
 
-
 # Redirect users from react app login page to Globus auth login widget then redirect back
 @auth_blueprint.route('/login')
 def login():
+    return _login(current_app.config['GLOBUS_CLIENT_APP_URI'])
+
+@auth_blueprint.route('/data-ingest-board-login')
+def data_ingest_login():
+    return _login(redirect_uri=current_app.config['DATA_INGEST_BOARD_APP_URI'], key='ingest_board_tokens')
+
+
+@auth_blueprint.route('/logout')
+def logout():
+    return _logout(redirect_uri=current_app.config['GLOBUS_CLIENT_APP_URI'], app_name=current_app.config['GLOBUS_CLIENT_APP_NAME'])
+
+
+@auth_blueprint.route('/data-ingest-board-logout')
+def data_ingest_logout():
+    return _logout(redirect_uri=current_app.config['DATA_INGEST_BOARD_APP_URI'], app_name=current_app.config['DATA_INGEST_BOARD_NAME'],  key='ingest_board_tokens')
+
+
+def get_user_info(token):
+    auth_client = AuthClient(authorizer=AccessTokenAuthorizer(token))
+    return auth_client.oauth2_userinfo()
+
+
+def get_auth_header_dict(token) -> dict:
+    return {'Authorization': 'Bearer ' + token,  'X-SenNet-Application': 'ingest-api'}
+
+
+def get_auth_header() -> dict:
+    auth_helper_instance = AuthHelper.instance()
+    token = auth_helper_instance.getAuthorizationTokens(request.headers)
+    return get_auth_header_dict(token)
+
+def _login(redirect_uri, key = 'tokens'):
     #redirect_uri = url_for('login', _external=True)
-    redirect_uri = current_app.config['FLASK_APP_BASE_URI'] + 'login'
+    _redirect_uri = current_app.config['FLASK_APP_BASE_URI'] + request.path.replace('/', '')
 
-    confidential_app_auth_client =\
+    confidential_app_auth_client = \
         ConfidentialAppAuthClient(current_app.config['APP_CLIENT_ID'],
                                   current_app.config['APP_CLIENT_SECRET'])
-    confidential_app_auth_client.oauth2_start_flow(redirect_uri, refresh_tokens=True)
+    confidential_app_auth_client.oauth2_start_flow(_redirect_uri, refresh_tokens=True)
 
     # If there's no "code" query string parameter, we're in this route
     # starting a Globus Auth login flow.
@@ -57,57 +88,42 @@ def login():
         json_str = json.dumps(info)
 
         # Store the resulting tokens in server session
-        session.update(
-            tokens=token_response.by_resource_server
-        )
+        # session.update(
+        #     tokens=token_response.by_resource_server
+        # )
+        session[key] = token_response.by_resource_server
 
         logger.info(f"Logged in User: {user_info['name']}")
         # Finally redirect back to the client
-        return redirect(current_app.config['GLOBUS_CLIENT_APP_URI'] + '?info=' + str(json_str))
+        return redirect(redirect_uri + '?info=' + str(json_str))
 
 
-@auth_blueprint.route('/logout')
-def logout():
+def _logout(redirect_uri, app_name, key='tokens'):
     """
     - Revoke the tokens with Globus Auth.
     - Destroy the session state.
     - Redirect the user to the Globus Auth logout page.
     """
-    confidential_app_auth_client =\
+    confidential_app_auth_client = \
         ConfidentialAppAuthClient(current_app.config['APP_CLIENT_ID'],
                                   current_app.config['APP_CLIENT_SECRET'])
 
     # Revoke the tokens with Globus Auth
-    if 'tokens' in session:
+    if key in session:
         for token in (token_info['access_token']
-            for token_info in session['tokens'].values()):
-                confidential_app_auth_client.oauth2_revoke_token(token)
+                      for token_info in session[key].values()):
+            confidential_app_auth_client.oauth2_revoke_token(token)
 
     # Destroy the session state
     session.clear()
 
     # build the logout URI with query params
     # there is no tool to help build this (yet!)
     globus_logout_url = (
-        'https://auth.globus.org/v2/web/logout' +
-        '?client={}'.format(current_app.config['APP_CLIENT_ID']) +
-        '&redirect_uri={}'.format(current_app.config['GLOBUS_CLIENT_APP_URI']) +
-        '&redirect_name={}'.format(current_app.config['GLOBUS_CLIENT_APP_NAME']))
+            'https://auth.globus.org/v2/web/logout' +
+            '?client={}'.format(current_app.config['APP_CLIENT_ID']) +
+            '&redirect_uri={}'.format(redirect_uri) +
+            '&redirect_name={}'.format(app_name))
 
     # Redirect the user to the Globus Auth logout page
-    return redirect(globus_logout_url)
-
-
-def get_user_info(token):
-    auth_client = AuthClient(authorizer=AccessTokenAuthorizer(token))
-    return auth_client.oauth2_userinfo()
-
-
-def get_auth_header_dict(token) -> dict:
-    return {'Authorization': 'Bearer ' + token,  'X-SenNet-Application': 'ingest-api'}
-
-
-def get_auth_header() -> dict:
-    auth_helper_instance = AuthHelper.instance()
-    token = auth_helper_instance.getAuthorizationTokens(request.headers)
-    return get_auth_header_dict(token)
+    return redirect(globus_logout_url)