update path and comment flake+pytest + linted code

kgcl_rdflib/apply/kgcl_2_sparql.py

@@ -1,19 +1,21 @@
 """KGCL SPARQL implementation."""
 import logging
 import re
-from typing import Optional, List
+from typing import List, Optional
 
-from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
-                                        NewSynonym, NodeAnnotationChange, NodeCreation,
+from kgcl_schema.datamodel.kgcl import (Change, ClassCreation, EdgeCreation,
+                                        EdgeDeletion, NewSynonym,
+                                        NodeAnnotationChange, NodeCreation,
                                         NodeDeepening, NodeDeletion, NodeMove,
-                                        NodeObsoletion, NodeRename, NodeShallowing,
-                                        NodeUnobsoletion, PlaceUnder, PredicateChange,
-                                        RemovedNodeFromSubset, RemoveUnder, Change)
-
+                                        NodeObsoletion, NodeRename,
+                                        NodeShallowing, NodeUnobsoletion,
+                                        PlaceUnder, PredicateChange,
+                                        RemovedNodeFromSubset, RemoveUnder)
 
 CURIE_PATTERN = re.compile(r"^(\w+):(\S+)$")
 SPARQL_COMMAND = str
 
+
 def get_prefix(curie):
     """Get prefix."""
     return curie.split(":")[0]
@@ -52,20 +54,22 @@ def get_prefix(curie):
 
 def get_sparql_prefix_header(prefixes: List[str]) -> str:
     if prefixes is None:
-        prefixes = ['rdfs', 'rdf']
-    return "\n".join([f"PREFIX {prefix}: {prefix_2_uri[prefix]}" for prefix in prefixes])
+        prefixes = ["rdfs", "rdf"]
+    return "\n".join(
+        [f"PREFIX {prefix}: {prefix_2_uri[prefix]}" for prefix in prefixes]
+    )
 
 
 def get_representation(node_term: str) -> Optional[str]:
     if node_term is None:
         logging.warning(f"None value for representation")
         return None
-    elif node_term.startswith('<http'):
-        return 'uri'
-    elif ':' in node_term and CURIE_PATTERN.match(node_term):
-        return 'curie'
+    elif node_term.startswith("<http"):
+        return "uri"
+    elif ":" in node_term and CURIE_PATTERN.match(node_term):
+        return "curie"
     else:
-        return 'label'
+        return "label"
 
 
 def is_label(input: str) -> bool:

kgcl_rdflib/diff/change_detection.py

@@ -1,12 +1,11 @@
 """Detect changes."""
 import rdflib
+from kgcl_schema.datamodel.kgcl import (NodeAnnotationChange, NodeMove,
+                                        NodeRename, PredicateChange)
+from kgcl_schema.datamodel.ontology_model import Edge
 from rdflib import Literal, URIRef
 from rdflib.namespace import RDFS
 
-from kgcl_schema.datamodel.kgcl import (NodeAnnotationChange, NodeMove, NodeRename,
-                                        PredicateChange)
-from kgcl_schema.datamodel.ontology_model import Edge
-
 
 def id_generator():
     """Return a new ID for KGCL change operations."""

kgcl_rdflib/diff/diff_2_kgcl_existential.py

@@ -1,11 +1,11 @@
 """Existential restriction change information."""
 
 import rdflib
+from kgcl_schema.datamodel.kgcl import EdgeCreation, EdgeDeletion
 
 from kgcl_rdflib.diff.graph_diff import (get_added_existentials,
                                          get_deleted_existentials)
 from kgcl_rdflib.diff.render_operations import render
-from kgcl_schema.datamodel.kgcl import EdgeCreation, EdgeDeletion
 
 
 def id_generator():

kgcl_rdflib/diff/diff_2_kgcl_single.py

@@ -1,5 +1,7 @@
 """Single triple change summary."""
 import rdflib
+from kgcl_schema.datamodel.kgcl import (ClassCreation, NewSynonym, PlaceUnder,
+                                        RemoveUnder)
 from rdflib import Graph, Literal, URIRef
 from rdflib.namespace import OWL, RDF, RDFS
 
@@ -10,7 +12,6 @@
 from kgcl_rdflib.diff.graph_diff import (get_added_thin_triples,
                                          get_deleted_thin_triples)
 from kgcl_rdflib.diff.render_operations import render
-from kgcl_schema.datamodel.kgcl import ClassCreation, NewSynonym, PlaceUnder, RemoveUnder
 
 
 def id_generator():

kgcl_rdflib/diff/diff_2_kgcl_triple_annotation.py

@@ -1,12 +1,12 @@
 """Triple annotation change summary."""
 import rdflib
+from kgcl_schema.datamodel.kgcl import EdgeCreation, EdgeDeletion
+from kgcl_schema.datamodel.ontology_model import Annotation
 from rdflib import Graph, Literal, URIRef
 
 from kgcl_rdflib.diff.graph_diff import (get_added_triple_annotations,
                                          get_deleted_triple_annotations)
 from kgcl_rdflib.diff.render_operations import render
-from kgcl_schema.datamodel.kgcl import EdgeCreation, EdgeDeletion
-from kgcl_schema.datamodel.ontology_model import Annotation
 
 
 def id_generator():

kgcl_rdflib/diff/pretty_print_kgcl.py

@@ -1,13 +1,14 @@
 """Print KGCL in user-friendly format."""
+from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation,
+                                        EdgeDeletion, NewSynonym,
+                                        NodeAnnotationChange, NodeCreation,
+                                        NodeDeletion, NodeMove, NodeObsoletion,
+                                        NodeRename, NodeUnobsoletion,
+                                        PlaceUnder, PredicateChange,
+                                        RemoveUnder)
 from kgcl_schema.grammar.parser import parse_statement
 from rdflib.namespace import RDFS
 
-from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
-                                        NewSynonym, NodeAnnotationChange, NodeCreation,
-                                        NodeDeletion, NodeMove, NodeObsoletion,
-                                        NodeRename, NodeUnobsoletion, PlaceUnder,
-                                        PredicateChange, RemoveUnder)
-
 # TODO: maintain this dictionary in a file
 prefix_2_uri = {
     "obo": "http://purl.obolibrary.org/obo/",

kgcl_rdflib/diff/render_operations.py

@@ -1,11 +1,13 @@
 """Render operations."""
 # TODO: move this to grammar package
 
-from kgcl_schema.datamodel.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
-                                        NewSynonym, NodeAnnotationChange, NodeCreation,
+from kgcl_schema.datamodel.kgcl import (Change, ClassCreation, EdgeCreation,
+                                        EdgeDeletion, NewSynonym,
+                                        NodeAnnotationChange, NodeCreation,
                                         NodeDeletion, NodeMove, NodeObsoletion,
-                                        NodeRename, NodeUnobsoletion, PlaceUnder,
-                                        PredicateChange, RemoveUnder, Change)
+                                        NodeRename, NodeUnobsoletion,
+                                        PlaceUnder, PredicateChange,
+                                        RemoveUnder)
 
 
 # TODO: replace this with rdflib methods

kgcl_rdflib/kgcl.py

@@ -4,10 +4,10 @@
 
 import click
 import rdflib
+from kgcl_schema.grammar import parser
 from rdflib.util import guess_format
 
 from kgcl_rdflib.apply import graph_transformer
-from kgcl_schema.grammar import parser
 
 # TODO: remove this
 sys.path.append("../")
@@ -16,12 +16,9 @@
 @click.command()
 @click.option("-i", "--graph", type=click.Path(), required=True)
 @click.option("--kgcl-file", type=click.File("r"))
-@click.option("--output",
-              "-o",
-              type=click.File(mode='wb'),
-              default=sys.stdout)
+@click.option("--output", "-o", type=click.File(mode="wb"), default=sys.stdout)
 @click.option("-v", "--verbose", count=True)
-@click.argument('patch')
+@click.argument("patch")
 def cli(patch, verbose: int, graph, kgcl_file, output):
     """
     Modify graph based on KGCL commands.

kgcl_rdflib/kgcl_diff.py

@@ -7,12 +7,12 @@
 from typing import List
 
 import click
-import kgcl_rdflib.diff.diff_2_kgcl_existential as existential
-import kgcl_rdflib.diff.diff_2_kgcl_single as single
-import kgcl_rdflib.diff.diff_2_kgcl_triple_annotation as annotation
 import rdflib
 from kgcl_schema.datamodel.kgcl import Change
 
+import kgcl_rdflib.diff.diff_2_kgcl_existential as existential
+import kgcl_rdflib.diff.diff_2_kgcl_single as single
+import kgcl_rdflib.diff.diff_2_kgcl_triple_annotation as annotation
 from kgcl_rdflib.diff.pretty_print_kgcl import render_instances
 
 
@@ -34,14 +34,14 @@ def diff(g1: rdflib.Graph, g2: rdflib.Graph) -> List[Change]:
 
 
 @click.command()
-@click.option("--output-directory",
-              "-d",
-              type=click.Path(), required=False)
-@click.option("--output",
-              "-o",
-              type=click.File(mode='w'),
-              default=sys.stdout,
-              help="Where to write derived diffs")
+@click.option("--output-directory", "-d", type=click.Path(), required=False)
+@click.option(
+    "--output",
+    "-o",
+    type=click.File(mode="w"),
+    default=sys.stdout,
+    help="Where to write derived diffs",
+)
 @click.option("-v", "--verbose", count=True)
 @click.argument("ingraph", type=click.Path(), required=True)
 @click.argument("outgraph", type=click.Path(), required=True)
@@ -73,6 +73,7 @@ def cli(ingraph, outgraph, verbose: int, output, output_directory):
     if output_directory:
         write_summaries(g1, g2, output_directory)
 
+
 def write_summaries(g1: rdflib.Graph, g2: rdflib.Graph, output_directory):
     Path(output_directory).mkdir(parents=True, exist_ok=True)
 
@@ -176,12 +177,12 @@ def write_summaries(g1: rdflib.Graph, g2: rdflib.Graph, output_directory):
             f.write(k)
             f.write("\n")
 
-    #with open(patch_folder + "/edge_creations.txt", "w") as f:
+    # with open(patch_folder + "/edge_creations.txt", "w") as f:
     #    for k in single_triple_summary.get_edge_creations():
     #        f.write(k)
     #        f.write("\n")
 
-    #with open(patch_folder + "/edge_deletions.txt", "w") as f:
+    # with open(patch_folder + "/edge_deletions.txt", "w") as f:
     #    for k in single_triple_summary.get_edge_deletions():
     #        f.write(k)
     #        f.write("\n")

kgcl_rdflib/render_kgcl.py

@@ -2,8 +2,9 @@
 from kgcl_schema.model.kgcl import (ClassCreation, EdgeCreation, EdgeDeletion,
                                     NewSynonym, NodeCreation, NodeDeepening,
                                     NodeDeletion, NodeMove, NodeObsoletion,
-                                    NodeRename, NodeShallowing, NodeUnobsoletion,
-                                    PredicateChange, RemovedNodeFromSubset)
+                                    NodeRename, NodeShallowing,
+                                    NodeUnobsoletion, PredicateChange,
+                                    RemovedNodeFromSubset)
 
 
 def render(kgcl_instance):

tests/__init__.py

@@ -11,9 +11,8 @@
 
 sys.path.append(join(dirname(dirname(__file__)), "src/"))
 
-INPUT = os.path.join(INPUT_DIR, 'go-nucleus.owl.ttl')
-TMP_OUTPUT = os.path.join(OUTPUT_DIR, 'go-nucleus-modified.owl.ttl')
-TMP_YAML = os.path.join(OUTPUT_DIR, 'tmp.yaml')
-DIFF_OUTPUT = os.path.join(OUTPUT_DIR, 'diff.kgcl')
-DIFF_OUTPUT_DIR = os.path.join(OUTPUT_DIR, 'diff-info')
-
+INPUT = os.path.join(INPUT_DIR, "go-nucleus.owl.ttl")
+TMP_OUTPUT = os.path.join(OUTPUT_DIR, "go-nucleus-modified.owl.ttl")
+TMP_YAML = os.path.join(OUTPUT_DIR, "tmp.yaml")
+DIFF_OUTPUT = os.path.join(OUTPUT_DIR, "diff.kgcl")
+DIFF_OUTPUT_DIR = os.path.join(OUTPUT_DIR, "diff-info")