REQ-456 Retire python3.5 to support psqlgraph (#401)

* REQ-456 Retire python3.5 to support psqlgraph

.travis.yml

@@ -3,7 +3,6 @@ language: python
 dist: focal
 
 python:
-  - 3.5
   - 3.6.8
   - 3.7
   - 3.8

bin/update_related_case_caches.py

@@ -57,7 +57,7 @@ def update_project_related_case_cache(project):
 
     """
 
-    logger.info("Project: {}".format(project.code))
+    logger.info(f"Project: {project.code}")
     for case in project.cases:
         recursive_update_related_case_caches(case, case)
 
@@ -83,7 +83,7 @@ def main():
     )
 
     args = parser.parse_args()
-    prompt = "Password for {}:".format(args.user)
+    prompt = f"Password for {args.user}:"
     password = args.password or getpass.getpass(prompt)
     g = PsqlGraphDriver(args.host, args.user, password, args.database)
 

dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile
+# This file is autogenerated by pip-compile with python 3.6
 # To update, run:
 #
 #    pip-compile dev-requirements.in
@@ -55,6 +55,11 @@ ipykernel==5.5.6
     #   jupyter-console
     #   notebook
     #   qtconsole
+ipython==7.9.0
+    # via
+    #   ipykernel
+    #   ipywidgets
+    #   jupyter-console
 ipython-genutils==0.2.0
     # via
     #   ipykernel
@@ -63,11 +68,6 @@ ipython-genutils==0.2.0
     #   notebook
     #   qtconsole
     #   traitlets
-ipython==7.9.0
-    # via
-    #   ipykernel
-    #   ipywidgets
-    #   jupyter-console
 ipywidgets==7.7.2
     # via jupyter
 jedi==0.17.2
@@ -80,6 +80,8 @@ jsonschema==3.2.0
     # via
     #   -c requirements.txt
     #   nbformat
+jupyter==1.0.0
+    # via -r dev-requirements.in
 jupyter-client==4.4.0
     # via
     #   -r dev-requirements.in
@@ -99,8 +101,8 @@ jupyter-core==4.6.3
     #   nbformat
     #   notebook
     #   qtconsole
-jupyter==1.0.0
-    # via -r dev-requirements.in
+jupyterlab-widgets==1.1.4
+    # via ipywidgets
 markupsafe==1.1.1
     # via jinja2
 mistune==0.8.4
@@ -130,8 +132,6 @@ pandocfilters==1.5.0
     # via nbconvert
 parso==0.7.1
     # via jedi
-pathlib2==2.3.7.post1
-    # via pytest
 pexpect==4.8.0
     # via ipython
 pickleshare==0.7.5
@@ -161,12 +161,12 @@ pyrsistent==0.16.1
     # via
     #   -c requirements.txt
     #   jsonschema
-pytest-cov==2.8.1
-    # via -r dev-requirements.in
 pytest==4.6.10
     # via
     #   -r dev-requirements.in
     #   pytest-cov
+pytest-cov==2.8.1
+    # via -r dev-requirements.in
 pyyaml==5.3.1
     # via
     #   -c requirements.txt
@@ -186,7 +186,6 @@ six==1.15.0
     #   bleach
     #   cfgv
     #   jsonschema
-    #   pathlib2
     #   pre-commit
     #   prompt-toolkit
     #   pytest

gdcdatamodel/gdc_postgres_admin.py

@@ -24,7 +24,7 @@
 logger.setLevel(logging.INFO)
 
 name_root = "table_creator_"
-app_name = "{}{}".format(name_root, random.randint(1000, 9999))
+app_name = f"{name_root}{random.randint(1000, 9999)}"
 
 
 GRANT_READ_PRIVS_SQL = """
@@ -106,7 +106,7 @@ def create_graph_tables(engine, timeout, namespace=None):
     trans = connection.begin()
     logger.info("Setting lock_timeout to %d", timeout)
 
-    timeout_str = "{}s".format(int(timeout + 1))
+    timeout_str = f"{int(timeout + 1)}s"
     connection.execute("SET LOCAL lock_timeout = %s;", timeout_str)
 
     orm_base = ext.get_orm_base(namespace) if namespace else ORMBase
@@ -137,7 +137,7 @@ def create_tables(engine, delay, retries, namespace=None):
             raise RuntimeError("Max retries exceeded")
 
         logger.info(
-            "Trying again in {} seconds ({} retries remaining)".format(delay, retries)
+            f"Trying again in {delay} seconds ({retries} retries remaining)"
         )
         time.sleep(delay)
 

gdcdatamodel/models/__init__.py

@@ -69,7 +69,7 @@ def remove_spaces(s):
 def get_cls_package(package_namespace=None):
     cls_package = "gdcdatamodel.models"
     if package_namespace:
-        cls_package = "{}.{}".format(cls_package, package_namespace)
+        cls_package = f"{cls_package}.{package_namespace}"
     return cls_package
 
 
@@ -198,7 +198,7 @@ def _versions(self):
         session = self.get_session()
         if not session:
             raise RuntimeError(
-                "{} not bound to a session. Try .get_versions(session).".format(self)
+                f"{self} not bound to a session. Try .get_versions(session)."
             )
         return self.get_versions(session)
 
@@ -509,7 +509,7 @@ def generate_edge_tablename(src_label, label, dst_label):
     # truncate the each part of the name
     if len(tablename) > 40:
         oldname = tablename
-        logger.debug("Edge tablename {} too long, shortening".format(oldname))
+        logger.debug(f"Edge tablename {oldname} too long, shortening")
         tablename = "edge_{}_{}".format(
             hashlib.md5(py3_to_bytes(tablename)).hexdigest()[:8],
             "{}{}{}".format(
@@ -518,7 +518,7 @@ def generate_edge_tablename(src_label, label, dst_label):
                 "".join([a[:2] for a in dst_label.split("_")])[:10],
             ),
         )
-        logger.debug("Shortening {} -> {}".format(oldname, tablename))
+        logger.debug(f"Shortening {oldname} -> {tablename}")
 
     return tablename
 
@@ -648,7 +648,7 @@ def load_nodes(dictionary, node_cls=None, package_namespace=None):
                 cls = NodeFactory(_id, subschema, node_cls, package_namespace)
                 register_class(cls, package_namespace)
             except Exception:
-                print("Unable to load {}".format(name))
+                print(f"Unable to load {name}")
                 raise
 
 
@@ -684,7 +684,7 @@ def parse_edge(
     edge_name = "".join(map(get_class_name_from_id, [src_label, edge_label, dst_label]))
 
     if edge_cls.is_subclass_loaded(name):
-        return "_{}_out".format(edge_name)
+        return f"_{edge_name}_out"
 
     edge = EdgeFactory(
         edge_name,
@@ -698,7 +698,7 @@ def parse_edge(
         package_namespace=package_namespace,
     )
 
-    return "_{}_out".format(edge.__name__)
+    return f"_{edge.__name__}_out"
 
 
 def load_edges(dictionary, node_cls=Node, edge_cls=Edge, package_namespace=None):
@@ -712,7 +712,7 @@ def load_edges(dictionary, node_cls=Node, edge_cls=Edge, package_namespace=None)
 
         src_cls = node_cls.get_subclass(src_label)
         if not src_cls:
-            raise RuntimeError("No source class labeled {}".format(src_label))
+            raise RuntimeError(f"No source class labeled {src_label}")
 
         for name, link in get_links(subschema).items():
             edge_label = link["label"]
@@ -747,7 +747,7 @@ def load_edges(dictionary, node_cls=Node, edge_cls=Edge, package_namespace=None)
             "required": False,
             "target_type": "case",
             "label": "relates_to",
-            "backref": "_related_{}".format(src_cls.label),
+            "backref": f"_related_{src_cls.label}",
         }
 
         parse_edge(

gdcdatamodel/models/caching.py

@@ -53,7 +53,7 @@ def get_related_case_edge_cls_name(node):
 
     """
 
-    return "{}RelatesToCase".format(node.__class__.__name__)
+    return f"{node.__class__.__name__}RelatesToCase"
 
 
 def get_edge_src(edge):
@@ -219,7 +219,7 @@ def update_cache_edges(node, session, correct_cases):
 
     # Get information about the existing edges
     edge_name = get_related_case_edge_cls_name(node)
-    existing_edges = getattr(node, "_{}_out".format(edge_name))
+    existing_edges = getattr(node, f"_{edge_name}_out")
 
     # Remove edges that should no longer exist
     cases_disconnected = [

gdcdatamodel/models/indexes.py

@@ -32,20 +32,20 @@ def index_name(cls, description):
 
     """
 
-    name = "index_{}_{}".format(cls.__tablename__, description)
+    name = f"index_{cls.__tablename__}_{description}"
 
     # If the name is too long, prepend it with the first 8 hex of it's hash
     # truncate the each part of the name
     if len(name) > 40:
         oldname = index_name
-        logger.debug("Edge tablename {} too long, shortening".format(oldname))
+        logger.debug(f"Edge tablename {oldname} too long, shortening")
         name = "index_{}_{}_{}".format(
             hashlib.md5(py3_to_bytes(cls.__tablename__)).hexdigest()[:8],
             "".join([a[:4] for a in cls.get_label().split("_")])[:20],
             "_".join([a[:8] for a in description.split("_")])[:25],
         )
 
-        logger.debug("Shortening {} -> {}".format(oldname, index_name))
+        logger.debug(f"Shortening {oldname} -> {index_name}")
 
     return name
 

gdcdatamodel/models/versioning.py

@@ -7,7 +7,7 @@
 UUID_NAMESPACE_SEED = os.getenv(
     "UUID_NAMESPACE_SEED", "86bb916a-24c5-48e4-8a46-5ea73a379d47"
 )
-UUID_NAMESPACE = uuid.UUID("urn:uuid:{}".format(UUID_NAMESPACE_SEED), version=4)
+UUID_NAMESPACE = uuid.UUID(f"urn:uuid:{UUID_NAMESPACE_SEED}", version=4)
 
 
 class TagKeys:
@@ -106,7 +106,7 @@ def is_taggable(self, node):
 
 def __generate_hash(seed, label):
     namespace = UUID_NAMESPACE
-    name = "{}-{}".format(seed, label)
+    name = f"{seed}-{label}"
     return str(uuid.uuid5(namespace, name))
 
 

gdcdatamodel/validators/graph_validators.py

@@ -1,7 +1,7 @@
 from gdcdictionary import gdcdictionary
 
 
-class GDCGraphValidator(object):
+class GDCGraphValidator:
     """
     Validator that validates entities' relationship with existing nodes in
     database.
@@ -28,7 +28,7 @@ def record_errors(self, graph, entities):
                     self.optional_validators[validator_name].validate()
 
 
-class GDCLinksValidator(object):
+class GDCLinksValidator:
     def validate(self, entities, graph=None):
         for entity in entities:
             for link in gdcdictionary.schema[entity.node.label]["links"]:
@@ -57,7 +57,7 @@ def validate_edge_group(self, schema, entity):
         if schema.get("required") is True and len(submitted_links) == 0:
             names = ", ".join(schema_links[:-2] + [" or ".join(schema_links[-2:])])
             entity.record_error(
-                "Entity is missing a required link to {}".format(names),
+                f"Entity is missing a required link to {names}",
                 keys=schema_links,
             )
 
@@ -70,7 +70,7 @@ def validate_edge_group(self, schema, entity):
                 keys=schema_links,
             )
             for edge in entity.node.edges_out:
-                entity.record_error("{}".format(edge.dst.submitter_id))
+                entity.record_error(f"{edge.dst.submitter_id}")
 
         result = {"length": num_of_edges, "name": ", ".join(schema_links)}
 
@@ -86,7 +86,7 @@ def validate_edge(self, link_sub_schema, entity):
             if multi in ["many_to_one", "one_to_one"]:
                 if len(targets) > 1:
                     entity.record_error(
-                        "'{}' link has to be {}".format(association, multi),
+                        f"'{association}' link has to be {multi}",
                         keys=[association],
                     )
 
@@ -108,13 +108,13 @@ def validate_edge(self, link_sub_schema, entity):
         else:
             if link_sub_schema.get("required") is True:
                 entity.record_error(
-                    "Entity is missing required link to {}".format(association),
+                    f"Entity is missing required link to {association}",
                     keys=[association],
                 )
         return result
 
 
-class GDCUniqueKeysValidator(object):
+class GDCUniqueKeysValidator:
     def validate(self, entities, graph=None):
         for entity in entities:
             schema = gdcdictionary.schema[entity.node.label]

gdcdatamodel/validators/json_validators.py

@@ -22,7 +22,7 @@ def get_keys(error_msg):
         return []
 
 
-class GDCJSONValidator(object):
+class GDCJSONValidator:
     def __init__(self):
         self.schemas = gdcdictionary
 

migrations/update_case_cache_append_only.py

@@ -161,7 +161,7 @@ def seed_level_1(graph, cls):
             cls_to_case_edge_table=case_edge.__tablename__,
         )
 
-        print("Seeding {} through {}".format(cls.get_label(), case_edge.__name__))
+        print(f"Seeding {cls.get_label()} through {case_edge.__name__}")
         graph.current_session().execute(statement)
 
 

migrations/update_legacy_states.py

@@ -107,7 +107,7 @@ def print_cls_query_summary(graph):
         "%s: %d"
         % (
             "legacy_stateless_nodes".ljust(40),
-            sum([query.count() for query in cls_queries.itervalues()]),
+            sum(query.count() for query in cls_queries.itervalues()),
         )
     )