flake

Author: cmungall

src/semsql/builder/builder.py

@@ -76,7 +76,7 @@ def db_from_owl(input: str) -> str:
         make(db)
         return db
     else:
-        raise ValueError(f"Path must be an OWL file")
+        raise ValueError("Path must be an OWL file")
 
 
 def download_obo_sqlite(ontology: str, destination: str):
@@ -108,8 +108,7 @@ def connect(owl_file: str):
     """
     db = db_from_owl(owl_file)
     engine = create_engine(f"sqlite:///{db}")
-    Session = sessionmaker(bind=engine)
-    session = Session()
+    session = sessionmaker(bind=engine)()
     return session
 
 
@@ -133,16 +132,18 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st
         if ont == generic:
             command = "curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp"
         elif ont.zip_extract_file:
-            command = f"curl -L -s {ont.url} > $@.zip.tmp && unzip -p $@.zip.tmp {ont.zip_extract_file} > $@.tmp && rm $@.zip.tmp"
+            command = (f"curl -L -s {ont.url} > $@.zip.tmp && "
+                       "unzip -p $@.zip.tmp {ont.zip_extract_file} "
+                       "> $@.tmp && rm $@.zip.tmp")
         else:
             command = f"curl -L -s {ont.url} > $@.tmp"
         download_rule = MakefileRule(
             target=f"download/{ont.id}.owl",
             dependencies=["STAMP"],
             commands=[
                 command,
-                f"sha256sum -b $@.tmp > $@.sha256",
-                f"mv $@.tmp $@",
+                "sha256sum -b $@.tmp > $@.sha256",
+                "mv $@.tmp $@",
             ],
             precious=True,
         )
@@ -151,11 +152,11 @@ def compile_registry(registry_path: str, local_prefix_file: TextIO = None) -> st
         target = f"db/{ont.id}.owl"
         dependencies = [f"download/{ont.id}.owl"]
         if ont.has_imports or (ont.format and ont.format != "rdfxml"):
-            command = f"robot merge -i $< -o $@"
+            command = "robot merge -i $< -o $@"
         elif ont.build_command:
             command = ont.build_command.format(ont=ont)
         else:
-            command = f"cp $< $@"
+            command = "cp $< $@"
         rule = MakefileRule(
             target=target, dependencies=dependencies, commands=[command]
         )

src/semsql/ontlib/__init__.py

@@ -1 +1,3 @@
 from semsql.ontlib.subgraph import extract_subgraph
+
+__all__ = ["extract_subgraph"]

src/semsql/ontlib/subgraph.py

@@ -164,7 +164,7 @@ def to_obo_format(g: OboGraphDict) -> None:
     for n in g["nodes"]:
         id = n["id"]
         print()
-        print(f"[Term]")
+        print("[Term]")
         print(f"id: {id}")
         print(f'name: {n["lbl"]}')
         if "meta" in n:
@@ -189,14 +189,16 @@ def to_obo_format(g: OboGraphDict) -> None:
                     print(f"relationship: {p} {o}{cmt}")
 
 
-def to_markdown(g: OboGraphDict, prefixes: PREFIX_MAP = {}, definitions=True) -> None:
+def to_markdown(g: OboGraphDict, prefixes: PREFIX_MAP = None, definitions=True) -> None:
     """
     Serialization to markdown
 
     This should probably move elsewhere
     :param g:
     :return:
     """
+    if prefixes is None:
+        prefixes = {}
     eix = graph_to_subject_index(g)
     nix = {n["id"]: n for n in g["nodes"]}
     for n in g["nodes"]:
@@ -225,7 +227,7 @@ def to_markdown(g: OboGraphDict, prefixes: PREFIX_MAP = {}, definitions=True) ->
                 print(f"     * {plink} {olink} {cmt}")
 
 
-def _id_to_markdown_link(id: str, prefixes={}):
+def _id_to_markdown_link(id: str, prefixes=None):
     pfx, localid = id.split(":")
     if pfx in prefixes:
         url = f"{prefixes[pfx]}{localid}"
@@ -238,7 +240,7 @@ def render_edges(
     session,
     edges: List[Row],
     to_format: str = "text",
-    seeds: List[CURIE] = [],
+    seeds: List[CURIE] = None,
     stylemap: str = None,
     configure: str = None,
 ):
@@ -251,6 +253,8 @@ def render_edges(
     :param stylemap: used for graphviz rendering
     :return:
     """
+    if seeds is None:
+        seeds = []
     prefixes = get_prefixes(session)
     if to_format == "obojson":
         g = edges_to_obograph(session, edges, definitions=True)

tests/test_builder/test_builder.py

@@ -1,10 +1,7 @@
 import os
 import unittest
 
-from click.testing import CliRunner
-
 from semsql.builder import builder
-from semsql.builder.cli import main
 from semsql.builder.registry import path_to_ontology_registry
 
 cwd = os.path.abspath(os.path.dirname(__file__))

tests/test_ontlib/test_common_queries.py

@@ -20,8 +20,7 @@ class CommonQueriesTestCase(unittest.TestCase):
     def setUp(self):
         path = os.path.join(DB_DIR, "go-nucleus.db")
         engine = create_engine(f"sqlite:///{path}")
-        Session = sessionmaker(bind=engine)
-        self.session = Session()
+        self.session = sessionmaker(bind=engine)()
 
     def test_common_queries(self):
 

tests/test_ontlib/test_subgraph.py

@@ -23,21 +23,20 @@ class SubgraphTestCase(unittest.TestCase):
     def test_subgraph(self):
         path = os.path.join(DB_DIR, "go-nucleus.db")
         engine = create_engine(f"sqlite:///{path}")
-        Session = sessionmaker(bind=engine)
-        session = Session()
+        session = sessionmaker(bind=engine)()
         edges = extract_subgraph(
             session, terms=["CL:0000000"], view=SubgraphEdgeByAncestor
         )
         lines = []
-        print(f'graph for descendants of "cell"')
+        print('graph for descendants of "cell"')
         for e in edges:
             line = f"{e.subject} {e.predicate} {e.object}"
             print(line)
             lines.append(line)
         assert "GO:0031967 BFO:0000050 GO:0043229" in lines
         assert "GO:0031975 rdfs:subClassOf GO:0110165" in lines
 
-        print(f'graph for ancestors of "nuclear membrane"')
+        print('graph for ancestors of "nuclear membrane"')
         edges = extract_subgraph(
             session, terms=["GO:0031965"], view=SubgraphEdgeByDescendant
         )

tests/test_orm/test_basic_sqla.py

@@ -17,8 +17,7 @@ class SQLAlchemyTestCase(unittest.TestCase):
     def setUp(self) -> None:
         path = os.path.join(DB_DIR, "go-nucleus.db")
         engine = create_engine(f"sqlite:///{path}")
-        SessionClass = sessionmaker(bind=engine)
-        self.session = SessionClass()
+        self.session = sessionmaker(bind=engine)()
 
     def test_basic_sqla(self):
         """
@@ -87,8 +86,9 @@ def add_label(q, join_slot):
         q = add_label(q, RdfsSubclassOfStatement.subject)
         q = add_label(q, OwlSomeValuesFrom.filler)
         null = "NONE"
-        for ax, ex, sl, fl in q.all():
-            line = f'{ax.subject} "{sl.value if sl else null}" subClassOf {ex.on_property} SOME {ex.filler} "{fl.value if fl else null}"'
+        for ax, _ex, sl, _fl in q.all():
+            line = f'{ax.subject} "{sl.value if sl else null}"'
+            ' subClassOf {ex.on_property} SOME {ex.filler} "{fl.value if fl else null}"'
             logging.info(line)
             # print(line)
             lines.append(line)

tests/test_orm/test_crud.py

@@ -23,8 +23,7 @@ def test_crud(self):
         """
         copyfile(SRC_DB, TEST_DB)
         engine = create_engine(f"sqlite:///{TEST_DB}")
-        Session = sessionmaker(bind=engine)
-        session = Session()
+        session = sessionmaker(bind=engine)()
         q = (
             session.query(Statements)
             .filter(Statements.predicate == "rdfs:label")

tests/test_orm/test_problems.py

@@ -18,8 +18,7 @@ def test_problems(self):
         """
         path = os.path.join(DB_DIR, "go-nucleus.db")
         engine = create_engine(f"sqlite:///{path}")
-        Session = sessionmaker(bind=engine)
-        session = Session()
+        session = sessionmaker(bind=engine)()
         print("OWL query:")
         q = session.query(AllProblems)
         n = 0