DEV-1483: add black and reformat (#389)

reformat all using black

.pre-commit-config.yaml

@@ -20,6 +20,11 @@ repos:
         args: [--autofix]
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+  - repo: https://github.com/psf/black
+    rev: 20.8b1  # for pre-commit 1.21.0 in jenkins
+    hooks:
+      - id: black
+        additional_dependencies: [click==8.0.4]
   - repo: https://github.com/pycqa/isort
     rev: 5.6.4    # last version to support pre-commit 1.21.0 in Jenkins
     hooks:

.secrets.baseline

@@ -3,7 +3,7 @@
     "files": "^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2022-10-11T18:55:31Z",
+  "generated_at": "2022-10-14T21:28:31Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -69,7 +69,7 @@
         "hashed_secret": "5d0fa74acf95d1d6bebd0d37f76a94e77d604fd9",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 33,
+        "line_number": 36,
         "type": "Basic Auth Credentials"
       }
     ]

bin/update_related_case_caches.py

@@ -25,19 +25,22 @@ def recursive_update_related_case_caches(node, case, visited_ids=set()):
 
     """
 
-    logger.info("{}: | case: {} | project: {}".format(
-        node, case, node._props.get('project_id', '?')))
+    logger.info(
+        "{}: | case: {} | project: {}".format(
+            node, case, node._props.get("project_id", "?")
+        )
+    )
 
     visited_ids.add(node.node_id)
 
     for edge in node.edges_in:
         if edge.src is None:
             continue
 
-        if edge.__class__.__name__.endswith('RelatesToCase'):
+        if edge.__class__.__name__.endswith("RelatesToCase"):
             continue
 
-        if not hasattr(edge.src, '_related_cases'):
+        if not hasattr(edge.src, "_related_cases"):
             continue
 
         original = set(edge.src._related_cases)
@@ -61,27 +64,36 @@ def update_project_related_case_cache(project):
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("-H", "--host", type=str, action="store",
-                        required=True, help="psql-server host")
-    parser.add_argument("-U", "--user", type=str, action="store",
-                        required=True, help="psql test user")
-    parser.add_argument("-D", "--database", type=str, action="store",
-                        required=True, help="psql test database")
-    parser.add_argument("-P", "--password", type=str, action="store",
-                        help="psql test password")
+    parser.add_argument(
+        "-H", "--host", type=str, action="store", required=True, help="psql-server host"
+    )
+    parser.add_argument(
+        "-U", "--user", type=str, action="store", required=True, help="psql test user"
+    )
+    parser.add_argument(
+        "-D",
+        "--database",
+        type=str,
+        action="store",
+        required=True,
+        help="psql test database",
+    )
+    parser.add_argument(
+        "-P", "--password", type=str, action="store", help="psql test password"
+    )
 
     args = parser.parse_args()
     prompt = "Password for {}:".format(args.user)
     password = args.password or getpass.getpass(prompt)
     g = PsqlGraphDriver(args.host, args.user, password, args.database)
 
     with g.session_scope():
-        projects = g.nodes(md.Project).not_props(state='legacy').all()
+        projects = g.nodes(md.Project).not_props(state="legacy").all()
         for p in projects:
             update_project_related_case_cache(p)
 
     print("Done.")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

docs/bin/schemata_to_graphviz.py

@@ -6,19 +6,21 @@
 
 
 def build_visualization():
-    print('Building schema documentation...')
+    print ("Building schema documentation...")
 
     # Load directory tree info
     bin_dir = os.path.dirname(os.path.realpath(__file__))
-    root_dir = os.path.join(os.path.abspath(
-        os.path.join(bin_dir, os.pardir, os.pardir)))
+    root_dir = os.path.join(
+        os.path.abspath(os.path.join(bin_dir, os.pardir, os.pardir))
+    )
 
     # Create graph
     dot = Digraph(
-        comment="High level graph representation of GDC data model", format='pdf')
-    dot.graph_attr['rankdir'] = 'RL'
-    dot.node_attr['fillcolor'] = 'lightblue'
-    dot.node_attr['style'] = 'filled'
+        comment="High level graph representation of GDC data model", format="pdf"
+    )
+    dot.graph_attr["rankdir"] = "RL"
+    dot.node_attr["fillcolor"] = "lightblue"
+    dot.node_attr["style"] = "filled"
 
     # Add nodes
     for node in m.Node.get_subclasses():
@@ -28,18 +30,18 @@ def build_visualization():
 
     # Add edges
     for edge in m.Edge.get_subclasses():
-        if edge.__dst_class__ == 'Case' and edge.label == 'relates_to':
+        if edge.__dst_class__ == "Case" and edge.label == "relates_to":
             # Skip case cache edges
             continue
 
         src = m.Node.get_subclass_named(edge.__src_class__)
         dst = m.Node.get_subclass_named(edge.__dst_class__)
         dot.edge(src.get_label(), dst.get_label(), edge.get_label())
 
-    gv_path = os.path.join(root_dir, 'docs', 'viz', 'gdc_data_model.gv')
+    gv_path = os.path.join(root_dir, "docs", "viz", "gdc_data_model.gv")
     dot.render(gv_path)
-    print('graphviz output to {}'.format(gv_path))
+    print ("graphviz output to {}".format(gv_path))
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     build_visualization()

gdcdatamodel/__main__.py

@@ -1,20 +1,25 @@
 import argparse
 import getpass
 
-import psqlgraph
 from models import *  # noqa
 from models.versioned_nodes import VersionedNode  # noqa
 from psqlgraph import *  # noqa
 from sqlalchemy import *  # noqa
 
 try:
     import IPython
+
     ipython = True
 except Exception as e:
-    print(('{}, using standard interactive console. '
-           'If you install IPython, then it will automatically '
-           'be used for this repl.').format(e))
+    print(
+        (
+            "{}, using standard interactive console. "
+            "If you install IPython, then it will automatically "
+            "be used for this repl."
+        ).format(e)
+    )
     import code
+
     ipython = False
 
 
@@ -31,26 +36,40 @@
 """
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument('-d', '--database', default='test', type=str,
-                        help='name of the database to connect to')
-    parser.add_argument('-i', '--host', default='localhost', type=str,
-                        help='host of the postgres server')
-    parser.add_argument('-u', '--user', default='test', type=str,
-                        help='user to connect to postgres as')
-    parser.add_argument('-p', '--password', default=None, type=str,
-                        help='password for given user. If no '
-                        'password given, one will be prompted.')
+    parser.add_argument(
+        "-d",
+        "--database",
+        default="test",
+        type=str,
+        help="name of the database to connect to",
+    )
+    parser.add_argument(
+        "-i",
+        "--host",
+        default="localhost",
+        type=str,
+        help="host of the postgres server",
+    )
+    parser.add_argument(
+        "-u", "--user", default="test", type=str, help="user to connect to postgres as"
+    )
+    parser.add_argument(
+        "-p",
+        "--password",
+        default=None,
+        type=str,
+        help="password for given user. If no " "password given, one will be prompted.",
+    )
 
     args = parser.parse_args()
 
     print(message.format(args.database, args.host, args.user))
     if args.password is None:
         args.password = getpass.getpass()
 
-    g = psqlgraph.PsqlGraphDriver(
-        args.host, args.user, args.password, args.database)
+    g = psqlgraph.PsqlGraphDriver(args.host, args.user, args.password, args.database)
 
     with g.session_scope() as s:
         rb = s.rollback