Merge pull request #54 from AMP-SCZ/revert-52-revert-43-kcho/pronet

Revert "Revert "UPENN Cognitive battery REDCap option (redcap + redcap OR rpms + redcap)""

lochness/__init__.py

@@ -83,24 +83,26 @@ def asdict(self):
                 'metadata_csv': self.metadata_csv}
 
 
-def initialize_metadata(Lochness, args, multiple_site_in_a_repo) -> None:
+def initialize_metadata(Lochness, args,
+                        multiple_site_in_a_repo, upenn_redcap) -> None:
     '''Create (overwrite) metadata.csv using either REDCap or RPMS database'''
     for study_name in args.studies:
         # if 'redcap' or 'rpms' is in the sources, create (overwrite)
-        if 'redcap' in args.input_sources:
-            id_fieldname = 'chric_subject_id'
-            consent_fieldname = 'chric_consent_date'
-            REDCap.initialize_metadata(
-                    Lochness, study_name, id_fieldname, consent_fieldname,
-                    multiple_site_in_a_repo)
-
-        elif 'rpms' in args.input_sources:
-            # metadata.csv
+        if 'rpms' in args.input_sources:
+            # when rpms is included in the sources, initiate metadata using
+            # rpms
             id_fieldname = Lochness['RPMS_id_colname']
             consent_fieldname = Lochness['RPMS_consent_colname']
             RPMS.initialize_metadata(
                     Lochness, study_name, id_fieldname, consent_fieldname,
-                    multiple_site_in_a_repo)
+                    multiple_site_in_a_repo, upenn_redcap)
+
+        elif 'redcap' in args.input_sources:
+            id_fieldname = 'chric_subject_id'
+            consent_fieldname = 'chric_consent_date'
+            REDCap.initialize_metadata(
+                    Lochness, study_name, id_fieldname, consent_fieldname,
+                    multiple_site_in_a_repo, upenn_redcap)
 
         else:
             pass
@@ -296,6 +298,7 @@ def _parse_beiwe(value, default_id=None):
 def _parse_redcap(value, default_id=None):
     '''helper function to parse a redcap metadata value'''
     default = 'redcap.*:{ID}'.format(ID=default_id)
+
     return _simple_parser(value, default=default)
 
 
@@ -376,9 +379,9 @@ def listdir(Lochness, d):
 def attempt(f, Lochness, *args, **kwargs):
     '''attempt a function call'''
     if len(attempt.warnings) >= 5:
-        lochness.email.attempts_error(Lochness, attempt)
+        # lochness.email.attempts_error(Lochness, attempt)
         attempt.warnings = []
-        #raise AttemptsError('too many attempt warnings')
+        raise AttemptsError('too many attempt warnings')
     try:
         f(Lochness, *args, **kwargs)
     except Exception as e:

lochness/box/__init__.py

@@ -15,9 +15,12 @@
 import lochness.net as net
 import lochness.tree as tree
 from os.path import join, basename
+logging.getLogger('boxsdk').setLevel(logging.CRITICAL)
 from boxsdk import Client, OAuth2
+from boxsdk.exception import BoxOAuthException
 import cryptease as enc
 import re
+import requests
 
 
 logger = logging.getLogger(__name__)
@@ -26,6 +29,7 @@
 
 CHUNK_SIZE = 65536
 
+
 def delete_on_success(Lochness, module_name):
     ''' get module-specific delete_on_success flag with a safe default '''
     value = Lochness.get('box', dict()) \
@@ -44,6 +48,35 @@ def base(Lochness, module_name):
                    .get('base', '')
 
 
+def get_access_token(client_id: str, client_secret: str, user_id: str) -> str:
+    '''Get new access token using Box API
+
+    Key Argument:
+        client_id: Client ID from the box app from box dev console, str
+        client_secret: Client secret from the box app from box dev console, str
+        user_id: user id from the box app from box dev console, str of digits.
+
+    Returns:
+        api_token: API TOKEN used to pull data, str.
+
+    Notes:
+        Current version of get_access_token function uses User ID rather
+        than Enterprise ID. (Both works in pulling data from BOX account)
+    '''
+    url = "https://api.box.com/oauth2/token"
+    headers = {"Content-Type": "application/x-www-form-urlencoded"}
+    data = {"client_id": client_id,
+            "client_secret": client_secret,
+            "grant_type": "client_credentials",
+            "box_subject_type": "user",
+            "box_subject_id": user_id}
+
+    response = requests.post(url, headers=headers, data=data)
+    api_token = response.json()['access_token']
+
+    return api_token
+
+
 def get_box_object_based_on_name(client: boxsdk.client,
                                  box_folder_name: str,
                                  box_path_id: str = '0') \
@@ -301,9 +334,11 @@ def sync_module(Lochness: 'lochness.config',
         _passphrase = keyring.passphrase(Lochness, subject.study)
         enc_key = enc.kdf(_passphrase)
 
-        client_id, client_secret, api_token = keyring.box_api_token(
+        client_id, client_secret, user_id = keyring.box_api_token(
                 Lochness, module_name)
 
+        api_token = get_access_token(client_id, client_secret, user_id)
+
         # box authentication
         auth = OAuth2(
             client_id=client_id,
@@ -312,6 +347,14 @@ def sync_module(Lochness: 'lochness.config',
         )
         client = Client(auth)
 
+        # check if the login details are correct
+        try:
+            _ = client.user().get()
+        except BoxOAuthException:
+            logger.debug('Failed to login to BOX. Please check Box keyrings.')
+            return
+
+
         bx_base = base(Lochness, module_basename)
 
         # get the id of the bx_base path in box

lochness/keyring/__init__.py

@@ -40,11 +40,11 @@ def box_api_token(Lochness, key):
     '''get box api token from keyring'''
     if key not in Lochness['keyring']:
         raise KeyringError('\'{0}\' not in keyring'.format(key))
-    if 'API_TOKEN' not in Lochness['keyring'][key]:
-        raise KeyringError('\'API_TOKEN\' not in {0}'.format(key))
+    if 'USER_ID' not in Lochness['keyring'][key]:
+        raise KeyringError('\'USER_ID\' not in {0}'.format(key))
     return (Lochness['keyring'][key]['CLIENT_ID'],
             Lochness['keyring'][key]['CLIENT_SECRET'],
-            Lochness['keyring'][key]['API_TOKEN'])
+            Lochness['keyring'][key]['USER_ID'])
 
 
 def rsync_token(Lochness, key):