Fixing a few errors caught by eagle-eyed Bill

src/biokbase/narrative/contents/kbasewsmanager.py

@@ -16,18 +16,12 @@
 """
 import itertools
 import json
-
-# System
 import os
 import re
 
-# IPython
-# from IPython import nbformat
 import nbformat
 from nbformat import ValidationError, validate
 from notebook.services.contents.manager import ContentsManager
-
-# Third-party
 from tornado.web import HTTPError
 from traitlets.traitlets import List, Unicode
 
@@ -39,16 +33,9 @@
 from biokbase.narrative.services.user import UserService
 
 from .kbasecheckpoints import KBaseCheckpoints
-
-# Local
-# Local
 from .manager_util import base_model
 from .narrativeio import KBaseWSManagerMixin
 
-# -----------------------------------------------------------------------------
-# Classes
-# -----------------------------------------------------------------------------
-
 
 class KBaseWSManager(KBaseWSManagerMixin, ContentsManager):
     """
@@ -139,9 +126,9 @@ def get_userid(self):
         """Return the current user id (if logged in), or None"""
         return util.kbase_env.user
 
-    def _clean_id(self, id):
+    def _clean_id(self, dirty_id):
         """Clean any whitespace out of the given id"""
-        return self.wsid_regex.sub("", id.replace(" ", "_"))
+        return self.wsid_regex.sub("", dirty_id.replace(" ", "_"))
 
     #####
     # API part 1: methods that must be implemented in subclasses.
@@ -152,8 +139,7 @@ def dir_exists(self, path):
         that dir, so it's real."""
         if not path:
             return True
-        else:
-            return False
+        return False
 
     def is_hidden(self, path):
         """We can only see what gets returned from Workspace lookup,
@@ -179,13 +165,12 @@ def file_exists(self, path):
                         path
                     ),
                 )
-            else:
-                raise HTTPError(
-                    err.http_code,
-                    "An error occurred while trying to find the Narrative with id {}".format(
-                        path
-                    ),
-                )
+            raise HTTPError(
+                err.http_code,
+                "An error occurred while trying to find the Narrative with id {}".format(
+                    path
+                ),
+            )
 
     def exists(self, path):
         """Looks up whether a directory or file path (i.e. narrative)
@@ -217,7 +202,11 @@ def _parse_path(self, path):
             raise HTTPError(404, "Invalid Narrative path {}".format(path))
         try:
             return NarrativeRef(
-                dict(wsid=m.group("wsid"), objid=m.group("objid"), ver=m.group("ver"))
+                {
+                    "wsid": m.group("wsid"),
+                    "objid": m.group("objid"),
+                    "ver": m.group("ver"),
+                }
             )
         except RuntimeError as e:
             raise HTTPError(500, str(e))
@@ -300,7 +289,7 @@ def save(self, model, path):
 
             nb = result[0]
             self.validate_notebook_model(model)
-            validation_message = model.get("message", None)
+            validation_message = model.get("message")
 
             model = self.get(path, content=False)
             if validation_message:
@@ -409,7 +398,7 @@ def validate_notebook_model(self, model):
             )
         return model
 
-    def new_untitled(self, path="", type="", ext=""):
+    def new_untitled(self, path="", model_type="", ext=""):
         """Create a new untitled file or directory in path
 
         path must be a directory
@@ -423,8 +412,8 @@ def new_untitled(self, path="", type="", ext=""):
             raise HTTPError(404, "No such directory: %s" % path)
 
         model = {}
-        if type:
-            model["type"] = type
+        if model_type:
+            model["type"] = model_type
 
         if ext == ".ipynb":
             model.setdefault("type", "notebook")

src/biokbase/narrative/jobs/job.py

@@ -243,9 +243,6 @@ def __setattr__(self, name, value):
             raise AttributeError(
                 "Job attributes must be updated using the `update_state` method"
             )
-            raise AttributeError(
-                "Job attributes must be updated using the `update_state` method"
-            )
 
         object.__setattr__(self, name, value)
 

src/scripts/kb-log-tail

@@ -10,26 +10,25 @@ import sys
 
 import pymongo
 import yaml
-#
-from bson import json_util
-
-#
 from bson import json_util
 
 logging.basicConfig()
 _log = logging.getLogger("kb-log-tail")
 
+
 def error(msg):
     _log.error(msg)
-
+
+
 def print_rec(rec):
     print(json.dumps(rec, indent=2, default=json_util.default))
 
+
 def main(args):
     conf = args.conf
     try:
         info = yaml.load(open(conf))
-        for key in 'db_host', 'db_port', 'db', 'user', 'password':
+        for key in "db_host", "db_port", "db", "user", "password":
             if not key in info:
                 error("Configuration file is missing value for '{}'".format(key))
                 return -1
@@ -43,15 +42,21 @@ def main(args):
     try:
         db = pymongo.MongoClient(info["db_host"], info["db_port"])[info["db"]]
     except pymongo.errors.PyMongoError as err:
-        error("Cannot connect to MongoDB '{}' at {}:{}".format(
-            info["db"], info["db_host"], info["db_port"]))
+        error(
+            "Cannot connect to MongoDB '{}' at {}:{}".format(
+                info["db"], info["db_host"], info["db_port"]
+            )
+        )
     if not db.authenticate(info["user"], info["password"]):
-        error("Could not authenticate to MongoDB '{}' at {}:{}".format(
-            info["db"], info["db_host"], info["db_port"]))
+        error(
+            "Could not authenticate to MongoDB '{}' at {}:{}".format(
+                info["db"], info["db_host"], info["db_port"]
+            )
+        )
     c = db[info["collection"]]
     recs = c.find({}, sort=[("created", -1)], limit=args.num)
     first = True
-    separator = '-' * 40
+    separator = "-" * 40
     for rec in recs:
         if not first:
             print(separator)
@@ -61,14 +66,23 @@ def main(args):
         print("No records found")
     return 0
 
+
 def parse_args():
     conf = os.environ.get("KBASE_PROXY_CONFIG", "narrative-log-proxy.conf")
     p = argparse.ArgumentParser(description=__doc__.strip())
-    p.add_argument("-c", "--conf", dest='conf', default=conf,
-                   help="Configuration file (default=%(default)s)")
-    p.add_argument("num", nargs='?', default=1, type=int, help="Number of records (default=1)")
+    p.add_argument(
+        "-c",
+        "--conf",
+        dest="conf",
+        default=conf,
+        help="Configuration file (default=%(default)s)",
+    )
+    p.add_argument(
+        "num", nargs="?", default=1, type=int, help="Number of records (default=1)"
+    )
     args = p.parse_args()
     return args
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     sys.exit(main(parse_args()))