Reading fix

indra_db/cli/content.py

@@ -226,7 +226,7 @@ class ContentManager(object):
     tr_cols: Tuple = NotImplemented
     tc_cols: Tuple = NotImplemented
     primary_col: str = NotImplemented
-    err_patt = re.compile('.*?constraint "(.*?)".*?Key \((.*?)\)=\((.*?)\).*?',
+    err_patt = re.compile(r'.*?constraint "(.*?)".*?Key \((.*?)\)=\((.*?)\).*?',
                           re.DOTALL)
 
     def __init__(self):
@@ -1513,7 +1513,7 @@ def get_file_data(self):
 
     def get_tarname_from_filename(self, fname):
         "Get the name of the tar file based on the file name (or a pmcid)."
-        re_match = re.match('(PMC00\d).*?', fname)
+        re_match = re.match(r'(PMC00\d).*?', fname)
         if re_match is not None:
             tarname = re_match.group(0) + 6*'X' + '.xml.tar.gz'
         else:

indra_db/cli/reading.py

@@ -395,7 +395,7 @@ def run_local(task, buffer, num_procs):
     readers = ['SPARSER', 'REACH', 'EIDOS', 'TRIPS']
     bulk_manager = BulkLocalReadingManager(readers,
                                            buffer_days=buffer,
-                                           n_procs=num_procs)
+                                           n_proc=num_procs)
     if task == 'all':
         bulk_manager.read_all(db)
     elif task == 'new':

indra_db/reading/read_db.py

@@ -193,7 +193,7 @@ def __init__(self, result, reading_id=None, db_info_id=None,
 class DatabaseStatementData(DatabaseResultData):
     def __init__(self, *args, **kwargs):
         super(DatabaseStatementData, self).__init__(*args, **kwargs)
-        self.__text_patt = re.compile('[\W_]+')
+        self.__text_patt = re.compile(r'[\W_]+')
 
     @staticmethod
     def get_cols():

indra_db/util/aws.py

@@ -3,7 +3,7 @@
 
 
 def uncamel(word):
-    return re.sub(r'([a-z])([A-Z])', '\g<1>_\g<2>', word).lower()
+    return re.sub(r'([a-z])([A-Z])', r'\g<1>_\g<2>', word).lower()
 
 
 def get_role_kwargs(role):

indra_db/util/data_gatherer.py

@@ -183,7 +183,7 @@ def digest_s3_files():
     bucket = S3_DATA_LOC['bucket']
     prefix = S3_DATA_LOC['prefix']
 
-    patt = re.compile(prefix + '([0-9]+)/(\w*?)/?(\w+)_([0-9]+).json')
+    patt = re.compile(prefix + r'([0-9]+)/(\w*?)/?(\w+)_([0-9]+).json')
 
     # Get a list of the prefixes for each day.
     res = s3.list_objects_v2(Bucket=bucket, Prefix=prefix, Delimiter='/')

indra_db/util/s3_path.py

@@ -86,7 +86,7 @@ def from_key_parts(cls, bucket, *key_elements):
 
     @classmethod
     def from_string(cls, s3_key_str):
-        patt = re.compile('s3://([a-z0-9\-.]+)/(.*)')
+        patt = re.compile(r's3://([a-z0-9\-.]+)/(.*)')
         m = patt.match(s3_key_str)
         if m is None:
             raise ValueError("Invalid format for s3 path: %s" % s3_key_str)