Merge pull request #277 from kkaris/update-tweeting

Update tweeting

emmaa/subscription/notifications.py

@@ -296,7 +296,8 @@ def get_model_deltas(model_name, date, model_stats, test_stats_by_corpus):
     model_name : str
         A name of the model to get the updates for.
     date : str
-        A date for which the updates should be generated.
+        A date for which the updates should be generated. The
+        format should be "YYYY-MM-DD".
     model_stats : dict
         A dictionary containing the stats for the given model.
     test_stats_by_corpus : dict
@@ -308,18 +309,24 @@ def get_model_deltas(model_name, date, model_stats, test_stats_by_corpus):
         A dictionary containing the deltas for the given model and test
         corpora.
     """
-    deltas = {}
-    deltas['model_name'] = model_name
-    deltas['date'] = date
     # Model deltas
     stmts_delta = model_stats['model_delta']['statements_hashes_delta']
     paper_delta = model_stats['paper_delta']['raw_paper_ids_delta']
     new_papers = len(paper_delta['added'])
-    deltas['stmts_delta'] = stmts_delta
-    deltas['new_papers'] = new_papers
+
     # Test deltas
-    deltas['tests'] = {}
+    deltas = {
+        'model_name': model_name,
+        'date': date,
+        'stmts_delta': stmts_delta,
+        'new_papers': new_papers,
+        'tests': {}
+    }
     for test_corpus, test_stats in test_stats_by_corpus.items():
+        if test_stats is None:
+            logger.info(f"No test stats for {test_corpus}")
+            continue
+
         test_deltas = {}
         test_name = None
         test_data = test_stats['test_round_summary'].get('test_data')
@@ -392,7 +399,7 @@ def get_all_update_messages(deltas, is_tweet=False):
     return msg_dicts
 
 
-def tweet_deltas(deltas, twitter_cred):
+def tweet_deltas(deltas, twitter_cred, verbose=False):
     """Tweet the model updates.
 
     Parameters
@@ -403,12 +410,19 @@ def tweet_deltas(deltas, twitter_cred):
     twitter_cred : dict
         A dictionary containing consumer_token, consumer_secret, access_token,
         and access_secret for a model Twitter account.
+    verbose : bool
+        If True, the return from `tweepy.Client.create_tweet` will be printed
     """
     msgs = get_all_update_messages(deltas, is_tweet=True)
     for msg in msgs:
-        update_status(msg['message'], twitter_cred)
+        res = update_status(msg['message'], twitter_cred)
+        if verbose:
+            print(res)
         time.sleep(1)
-    logger.info('Done tweeting')
+    if msgs:
+        logger.info(f'Done tweeting {len(msgs)} messages')
+    else:
+        logger.info('No tweets to send')
 
 
 def make_model_html_email(msg_dicts, email, domain='emmaa.indra.bio'):
@@ -428,7 +442,8 @@ def get_all_stats(model_name, test_corpora, date):
     test_corpora : list[str]
         A list of test corpora names to get the test updates for.
     date : str
-        A date for which the updates should be generated.
+        A date for which the updates should be generated. The
+        format should be "YYYY-MM-DD".
 
     Returns
     -------
@@ -443,7 +458,9 @@ def get_all_stats(model_name, test_corpora, date):
         test_stats, _ = get_model_stats(model_name, 'test', tests=test_corpus,
                                         date=date)
         if not test_stats:
-            logger.info(f'Could not find test stats for {test_corpus}')
+            logger.info(
+                f"Could not find test stats for {test_corpus} for date {date}"
+            )
         test_stats_by_corpus[test_corpus] = test_stats
     return model_stats, test_stats_by_corpus
 

emmaa/tests/test_reactome_prior.py

@@ -29,7 +29,7 @@ def test_get_pathways_containing_genes():
     # Check if function returns a reasonable number of pathways
     assert len(KRAS_pathways) > 3
     # Signaling Downstream of RAS mutants
-    assert 'R-HSA-9649948.1' in KRAS_pathways
+    assert 'R-HSA-9649948.2' in KRAS_pathways
 
 
 def test_get_genes_contained_in_pathway():

emmaa/util.py

@@ -348,36 +348,76 @@ class NotAClassName(Exception):
     pass
 
 
-def get_credentials(key):
-    client = boto3.client('ssm')
+def get_credentials(
+        key: str, profile_name: str = None, cred_type: str = "oauth1_0a"
+):
+    """Get twitter credentials from AWS SSM
+
+    Parameters
+    ----------
+    key : str
+        The initial key to the credentials in SSM. The full key will be
+        /twitter/{key}/{par} where par is determined by the type of
+        credentials.
+    profile_name : str
+        The name of the AWS profile to use. If None (default), the default
+        profile will be used.
+    cred_type : str
+        The type of credentials to get. Choices are "oauth1_0a" and "bearer".
+        Default: "oauth1_0a". Bearer uses OAuth 2.0.
+
+    Returns
+    -------
+    dict
+        A dictionary with the requested credentials.
+    """
+    if profile_name is not None:
+        client = boto3.session.Session(
+            profile_name=profile_name).client('ssm', region_name='us-east-1')
+    else:
+        client = boto3.client('ssm')
+    params = ['app_id']
+    if cred_type == 'oauth1_0a':
+        params += ['consumer_token', 'consumer_secret',
+                   'access_token', 'access_secret']
+    elif cred_type == 'bearer':
+        params += ['bearer_token']
+    else:
+        raise ValueError(f"Unknown credential type: {cred_type}. Must be one "
+                         f"of oath1_0a or bearer.")
     auth_dict = {}
-    for par in ['consumer_token', 'consumer_secret', 'access_token',
-                'access_secret']:
+    for par in params:
         name = f'/twitter/{key}/{par}'
         try:
             response = client.get_parameter(Name=name, WithDecryption=True)
             val = response['Parameter']['Value']
             auth_dict[par] = val
         except Exception as e:
-            print(e)
+            logger.exception(e)
             break
     return auth_dict
 
 
-def get_oauth_dict(auth_dict):
-    oauth = tweepy.OAuthHandler(auth_dict.get('consumer_token'),
-                                auth_dict.get('consumer_secret'))
-    oauth.set_access_token(auth_dict.get('access_token'),
-                           auth_dict.get('access_secret'))
-    return oauth
-
-
 def update_status(msg, twitter_cred):
-    twitter_auth = get_oauth_dict(twitter_cred)
-    if twitter_auth is None:
-        return
-    twitter_api = tweepy.API(twitter_auth)
-    twitter_api.update_status(msg)
+    if 'consumer_secret' in twitter_cred and 'access_secret' in twitter_cred:
+        twitter_client = tweepy.Client(
+            consumer_key=twitter_cred['consumer_token'],
+            consumer_secret=twitter_cred['consumer_secret'],
+            access_token=twitter_cred['access_token'],
+            access_token_secret=twitter_cred['access_secret']
+        )
+        user_auth = True
+    elif 'bearer_token' in twitter_cred:
+        twitter_client = tweepy.Client(
+            bearer_token=twitter_cred['bearer_token']
+        )
+        user_auth = False
+    else:
+        raise ValueError('Missing credentials')
+
+    # Set user_auth=True when authenticating with consumer key/secret pair
+    # and access token/secret pair, and False when using bearer token
+    return twitter_client.create_tweet(text=msg, user_auth=user_auth)
 
 
 def _make_delta_msg(model_name, msg_type, delta, date, mc_type=None,