Merge pull request #250 from OpenTreeOfLife/collection-saving

Collection saving

phylesystem_api/phylesystem_api/api_utils.py

@@ -331,6 +331,12 @@ def read_logging_config(request):
         logging_filepath = None
     return level, logging_format_name, logging_filepath
 
+def _raise_missing_auth_token():
+    raise HTTPBadRequest(json.dumps({
+            "error": 1,
+            "description":"You must provide an auth_token to authenticate to the OpenTree API"
+        }))
+
 def authenticate(request):
     """Verify that we received a valid Github authentication token
 
@@ -345,13 +351,10 @@ def authenticate(request):
 
     """
     # this is the GitHub API auth-token for a logged-in curator
-    auth_token   = find_in_request(request, 'auth_token', '')
+    auth_token = find_in_request(request, 'auth_token', '')
 
     if not auth_token:
-        raise HTTPBadRequest(json.dumps({
-            "error": 1,
-            "description":"You must provide an auth_token to authenticate to the OpenTree API"
-        }))
+        _raise_missing_auth_token()
     gh           = Github(auth_token)
     gh_user      = gh.get_user()
     auth_info = {}
@@ -367,6 +370,7 @@ def authenticate(request):
     # generate API calls regardless of author_name/author_email being specifed
     auth_info['name'] = find_in_request(request, 'author_name', gh_user.name)
     auth_info['email'] = find_in_request(request, 'author_email', gh_user.email)
+    auth_info['auth_token'] = auth_token
     return auth_info
 
 ''' ## using logging module directly
@@ -613,7 +617,7 @@ def call_http_json(url,
     return resp.status_code, resp.json()
 
 
-def deferred_push_to_gh_call(request, resource_id, doc_type='nexson', **kwargs):
+def deferred_push_to_gh_call(request, resource_id, doc_type='nexson', auth_token=None):
     ##TODO Thius needs to create a bare URL for collections, and pass in the resource id etc as data
     #_LOG.debug("deferred_push_to_gh_call")
     if READ_ONLY_MODE:
@@ -626,10 +630,9 @@ def deferred_push_to_gh_call(request, resource_id, doc_type='nexson', **kwargs):
     else:
         data = {}
     url = compose_push_to_github_url(request, resource_id, doc_type)
-    auth_token = copy.copy(kwargs.get('auth_token'))
-    if auth_token is not None:
-        data['auth_token'] = auth_token
-    assert data.get('auth_token')
+    if not auth_token:
+        _raise_missing_auth_token()
+    data['auth_token'] = auth_token
     #call_http_json(url=url, verb='PUT', data=data)
     threading.Thread(target=call_http_json, args=(url, 'PUT', data,)).start()
 
@@ -712,3 +715,25 @@ def remove_tags(markup):
     markup = markup.decode('utf-8')
     return markup
 
+def extract_json_from_http_call(request, data_field_name='data', request_params=None):
+    """Returns the json blob (as a deserialized object) from `request_params` or the request.body.
+
+    request_params can be the Pyramids request.params multidict or just a dict.
+    """
+    json_obj = None
+    try:
+        # check for kwarg data_field_name, or load the full request body
+        if data_field_name in request_params:
+            json_obj = request_params.get(data_field_name, {})
+        else:
+            json_obj = request.json_body
+
+        if not isinstance(json_obj, dict):
+            json_obj = json.loads(json_obj)
+        if data_field_name in json_obj:
+            json_obj = json_obj[data_field_name]
+    except:
+        # _LOG = api_utils.get_logger(request, 'ot_api.default.v1')
+        # _LOG.exception('Exception getting JSON content in extract_json_from_http_call')
+        raise HTTPBadRequest(body=json.dumps({"error": 1, "description": 'no collection JSON found in request'}))
+    return json_obj

phylesystem_api/phylesystem_api/views/amendment.py

@@ -13,7 +13,7 @@
 from peyotl.api import OTI
 from peyotl.phylesystem.git_workflows import GitWorkflowError
 import phylesystem_api.api_utils as api_utils
-from phylesystem_api.api_utils import find_in_request
+from phylesystem_api.api_utils import find_in_request, extract_json_from_http_call
 import json
 import logging
 
@@ -25,30 +25,10 @@
 _LOG = logging.getLogger('phylesystem_api')
 
 
-def __extract_json_from_http_call(request, data_field_name='data', **kwargs):
-    """Returns the json blob (as a deserialized object) from `kwargs` or the request.body"""
-    json_obj = None
-    try:
-        # check for kwarg data_field_name, or load the full request body
-        if data_field_name in kwargs:
-            json_obj = kwargs.get(data_field_name, {})
-        else:
-            json_obj = request.json_body
-
-        if not isinstance(json_obj, dict):
-            json_obj = json.loads(json_obj)
-        if data_field_name in json_obj:
-            json_obj = json_obj[data_field_name]
-    except:
-        # _LOG = api_utils.get_logger(request, 'ot_api.default.v1')
-        # _LOG.exception('Exception getting JSON content in __extract_json_from_http_call')
-        raise HTTPBadRequest(body=json.dumps({"error": 1, "description": 'no collection JSON found in request'}))
-    return json_obj
-
-def __extract_and_validate_amendment(request, **kwargs):
+def __extract_and_validate_amendment(request, kwargs):
     from pprint import pprint
     try:
-        amendment_obj = __extract_json_from_http_call(request, data_field_name='json', **kwargs)
+        amendment_obj = extract_json_from_http_call(request, data_field_name='json', request_params=kwargs)
     except HTTPException as err:
         # payload not found
         return None, None, None
@@ -98,7 +78,7 @@ def create_amendment(request, **kwargs):
     phylesystem = api_utils.get_phylesystem(request)   # set READONLY flag before testing!
     api_utils.raise_if_read_only()
     # fetch and parse the JSON payload, if any
-    amendment_obj, amendment_errors, amendment_adapter = __extract_and_validate_amendment(request, **kwargs)
+    amendment_obj, amendment_errors, amendment_adapter = __extract_and_validate_amendment(request, kwargs)
     if (amendment_obj is None):
         raise HTTPBadRequest(body=json.dumps({"error": 1, "description": "amendment JSON expected for HTTP method {}".format(request.method) }))
 
@@ -122,7 +102,7 @@ def create_amendment(request, **kwargs):
         # _LOG.debug('add_new_amendment failed with error code')
         raise HTTPBadRequest(body=json.dumps(commit_return))
     _LOG.debug("create ammendemt deferred_push_to_gh_call")
-    api_utils.deferred_push_to_gh_call(request, new_amendment_id, doc_type='amendment', **request.params)
+    api_utils.deferred_push_to_gh_call(request, new_amendment_id, doc_type='amendment', auth_token=auth_info['auth_token'])
     return commit_return
 
 
@@ -206,7 +186,7 @@ def update_amendment(request):
         commit_msg = None
 
     # fetch and parse the JSON payload, if any
-    amendment_obj, amendment_errors, amendment_adapter = __extract_and_validate_amendment(request, **kwargs)
+    amendment_obj, amendment_errors, amendment_adapter = __extract_and_validate_amendment(request, kwargs)
     if (amendment_obj is None):
         raise HTTPBadRequest(body=json.dumps({"error": 1, "description": "amendment JSON expected for HTTP method {}".format(request.method) }))
 
@@ -234,7 +214,7 @@ def update_amendment(request):
     # check for 'merge needed'?
     mn = commit_return.get('merge_needed')
     if (mn is not None) and (not mn):
-        api_utils.deferred_push_to_gh_call(request, amendment_id, doc_type='amendment', **request.json_body)
+        api_utils.deferred_push_to_gh_call(request, amendment_id, doc_type='amendment', auth_token=auth_info['auth_token'])
     return commit_return
 
 
@@ -275,7 +255,7 @@ def delete_amendment(request):
                                       parent_sha,
                                       commit_msg=commit_msg)
         if x.get('error') == 0:
-            api_utils.deferred_push_to_gh_call(request, None, doc_type='amendment', **request.json_body)
+            api_utils.deferred_push_to_gh_call(request, None, doc_type='amendment', auth_token=auth_info['auth_token'])
         return x
     except GitWorkflowError as err:
         raise HTTPBadRequest(body=err.msg)

phylesystem_api/phylesystem_api/views/collection.py

@@ -14,7 +14,7 @@
 from peyotl.api import OTI
 from peyotl.phylesystem.git_workflows import GitWorkflowError
 import phylesystem_api.api_utils as api_utils
-from phylesystem_api.api_utils import find_in_request
+from phylesystem_api.api_utils import find_in_request, extract_json_from_http_call
 import json
 from peyotl.collections_store import OWNER_ID_PATTERN, \
                                      COLLECTION_ID_PATTERN
@@ -23,31 +23,10 @@
 
 _LOG = logging.getLogger('phylesystem_api')
 
-
-def __extract_json_from_http_call(request, data_field_name='data', **kwargs):
-    """Returns the json blob (as a deserialized object) from `kwargs` or the request.body"""
-    json_obj = None
-    try:
-        # check for kwarg data_field_name, or load the full request body
-        if data_field_name in kwargs:
-            json_obj = kwargs.get(data_field_name, {})
-        else:
-            json_obj = request.json_body
-
-        if not isinstance(json_obj, dict):
-            json_obj = json.loads(json_obj)
-        if data_field_name in json_obj:
-            json_obj = json_obj[data_field_name]
-    except:
-        # _LOG = api_utils.get_logger(request, 'ot_api.default.v1')
-        # _LOG.exception('Exception getting JSON content in __extract_json_from_http_call')
-        raise HTTPBadRequest(body=json.dumps({"error": 1, "description": 'no collection JSON found in request'}))
-    return json_obj
-
-def __extract_and_validate_collection(request, **kwargs):
+def __extract_and_validate_collection(request, request_params):
     from pprint import pprint
     try:
-        collection_obj = __extract_json_from_http_call(request, data_field_name='json', **kwargs)
+        collection_obj = extract_json_from_http_call(request, data_field_name='json', request_params=request_params)
     except HTTPException as err:
         # payload not found
         return None, None, None
@@ -137,7 +116,7 @@ def create_collection(request):
     if commit_return['error'] != 0:
         # _LOG.debug('add_new_collection failed with error code')
         raise HTTPBadRequest(json.dumps(commit_return))
-    api_utils.deferred_push_to_gh_call(request, new_collection_id, doc_type='collection', **request.params)
+    api_utils.deferred_push_to_gh_call(request, new_collection_id, doc_type='collection', auth_token=auth_info['auth_token'])
     return commit_return
 
 @view_config(route_name='fetch_collection', renderer='json')
@@ -259,7 +238,7 @@ def update_collection(request):
     # check for 'merge needed'?
     mn = commit_return.get('merge_needed')
     if (mn is not None) and (not mn):
-        api_utils.deferred_push_to_gh_call(request, collection_id, doc_type='collection', **request.json_body)
+        api_utils.deferred_push_to_gh_call(request, collection_id, doc_type='collection', auth_token=auth_info['auth_token'])
     # Add updated commit history to the blob
     commit_return['versionHistory'] = docstore.get_version_history_for_doc_id(collection_id)
     return commit_return
@@ -287,7 +266,6 @@ def delete_collection(request):
     api_utils.raise_if_read_only()
 
     # remove this collection from the docstore
-    auth_info = api_utils.authenticate(request)
     owner_id = auth_info.get('login', None)
     docstore = api_utils.get_tree_collection_store(request)
     parent_sha = find_in_request(request, 'starting_commit_SHA', None)
@@ -299,7 +277,7 @@ def delete_collection(request):
                                        parent_sha,
                                        commit_msg=commit_msg)
         if x.get('error') == 0:
-            api_utils.deferred_push_to_gh_call(request, None, doc_type='collection', **request.params)
+            api_utils.deferred_push_to_gh_call(request, None, doc_type='collection', auth_token=auth_info['auth_token'])
         return x
     except GitWorkflowError as err:
         raise HTTPBadRequest(err.msg)

phylesystem_api/phylesystem_api/views/default.py

@@ -307,7 +307,7 @@ def include_tree_in_synth(request):
         # check for 'merge needed'?
         mn = commit_return.get('merge_needed')
         if (mn is not None) and (not mn):
-            api_utils.deferred_push_to_gh_call(request, default_collection_id, doc_type='collection', **kwargs)
+            api_utils.deferred_push_to_gh_call(request, default_collection_id, doc_type='collection', auth_token=auth_info['auth_token'])
 
     # fetch and return the updated list of synth-input trees
     return trees_in_synth(kwargs)
@@ -359,7 +359,7 @@ def exclude_tree_from_synth(request):
             # check for 'merge needed'?
             mn = commit_return.get('merge_needed')
             if (mn is not None) and (not mn):
-                api_utils.deferred_push_to_gh_call(request, coll_id, doc_type='collection', **kwargs)
+                api_utils.deferred_push_to_gh_call(request, coll_id, doc_type='collection', auth_token=auth_info['auth_token'])
 
     # fetch and return the updated list of synth-input trees
     return trees_in_synth(kwargs)

phylesystem_api/phylesystem_api/views/study.py

@@ -498,7 +498,7 @@ def create_study(request):
     if commit_return['error'] != 0:
         # _LOG.debug('ingest_new_study failed with error code')
         raise HTTPBadRequest(json.dumps(commit_return))
-    api_utils.deferred_push_to_gh_call(request, new_resource_id, doc_type='nexson', **request.params)
+    api_utils.deferred_push_to_gh_call(request, new_resource_id, doc_type='nexson', auth_token=auth_info['auth_token'])
     return commit_return
 
 
@@ -557,7 +557,7 @@ def update_study(request):
     #TIMING = api_utils.log_time_diff(_LOG, 'blob creation', TIMING)
     mn = blob.get('merge_needed')
     if (mn is not None) and (not mn):
-        api_utils.deferred_push_to_gh_call(request, study_id, doc_type='nexson', **request.params)
+        api_utils.deferred_push_to_gh_call(request, study_id, doc_type='nexson', auth_token=auth_info['auth_token'])
     # Add updated commit history to the blob
     blob['versionHistory'] = phylesystem.get_version_history_for_study_id(study_id)
     return blob
@@ -601,7 +601,7 @@ def delete_study(request):
         _LOG.warn(x)
         if x.get('error') == 0:
             _LOG.warn('calling deferred push...')
-            api_utils.deferred_push_to_gh_call(request, None, doc_type='nexson', **request.params)
+            api_utils.deferred_push_to_gh_call(request, None, doc_type='nexson', auth_token=auth_info['auth_token'])
             _LOG.warn('back from deferred push')
         return x
     except GitWorkflowError as err: