add flake8 fixes

src/pathme/__init__.py

@@ -2,6 +2,7 @@
 
 """
 The goal of this package is to facilitate the evaluation of pathway knowledge across three of the major pathway databases by harmozing and consolidating different formats.
+
 PathMe does that by converting KEGG, Reactome, and WikiPathways to Biological Expression Language (BEL).
 Once the three databases are harmonized into BEL, we can evaluate the consensus and gaps in pathway knowledge.
 For that, PathMe is complemented with a web application (`PathMe Viewer <https://github.com/ComPath/PathMe-Viewer>`_)
@@ -59,4 +60,4 @@
 .. code-block:: python
 
     python3 -m pathme kegg download
-"""
+"""

src/pathme/mappings_parser.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""This module contains the methods that handle the mappings stored in ComPath resources"""
+"""This module contains the methods that handle the mappings stored in ComPath resources."""
 
 import pandas as pd
 

src/pathme/normalize_names.py

@@ -7,9 +7,11 @@
 from typing import List
 
 from networkx import relabel_nodes
+
 from pathme.constants import REACTOME, WIKIPATHWAYS
 from pathme.pybel_utils import multi_relabel
 from pybel import BELGraph
+
 from pybel.dsl import Abundance, BiologicalProcess, CentralDogma, ListAbundance, Reaction, MicroRna, Protein
 
 logger = logging.getLogger(__name__)
@@ -121,7 +123,6 @@ def munge_reactome_gene(gene):
 
 def normalize_graph_names(graph: BELGraph, database: str) -> None:
     """Normalize graph names."""
-
     # Victim to Survivor (one to one node) mapping
     one_to_one_mapping = {}
     # Victim to Survivors (one to many nodes) mapping

src/pathme/pybel_utils.py

@@ -5,16 +5,16 @@
 import logging
 from typing import Mapping, Iterable
 
-from pybel.dsl import BaseEntity
-
-logger = logging.getLogger(__name__)
-
 from pybel import BELGraph
+from pybel.dsl import BaseEntity
 
 from pybel_tools.node_utils import list_abundance_cartesian_expansion, reaction_cartesian_expansion
 
+logger = logging.getLogger(__name__)
+
 
 def flatten_complex_nodes(graph: BELGraph) -> None:
+    """Flatten complex nodes"""
     logger.info("Flat complexes and composites")
     list_abundance_cartesian_expansion(graph)
     reaction_cartesian_expansion(graph)

src/pathme/reactome/rdf_sparql.py

@@ -8,12 +8,14 @@
 from typing import Any, Dict, List, Set, Tuple, Union
 
 import rdflib
+
 from pathme.constants import REACTOME_BEL
 from pathme.reactome.convert_to_bel import convert_to_bel
 from pathme.utils import get_pathway_statitics, parse_rdf, query_result_to_dict
 from pybel import to_pickle
 from rdflib import URIRef
 from rdflib.namespace import DC, DCTERMS, Namespace, OWL, RDF, RDFS, SKOS, XSD
+
 from tqdm import tqdm
 
 log = logging.getLogger(__name__)
@@ -65,10 +67,10 @@
 
 #: SPARQL query string to get all participants in an interaction and its controlType (ACTIVATION or INHIBITION).
 GET_INTERACTION_PARTICIPANTS_AND_TYPE = """
-SELECT DISTINCT 
-    (STRAFTER(STR(?component), '#') AS ?identifier) 
-    ?reactant 
-    ?product 
+SELECT DISTINCT
+    (STRAFTER(STR(?component), '#') AS ?identifier)
+    ?reactant
+    ?product
     (STR(?control_type) AS ?interaction_type)
 WHERE {
     ?component biopax3:left ?reactant .
@@ -92,7 +94,7 @@
     ?display_name
     ?complex_components
     ?comment
-WHERE {        
+WHERE {
     ?entity rdf:type ?uri_type .
     optional {?entity biopax3:comment ?comment .}
     optional {?entity biopax3:entityReference ?entity_reference .}
@@ -176,7 +178,7 @@ def _get_entity_metadata(entity: rdflib.URIRef, rdf_graph: rdflib.Graph) -> Dict
 
 
 def _get_reaction_participants(component_uri: str, component, rdf_graph: rdflib.Graph) -> Tuple[
-    Dict[Union[str, Set[str]], Dict[str, Union[str, Set[str]]]], Dict[Any, Dict[str, Any]]]:
+        Dict[Union[str, Set[str]], Dict[str, Union[str, Set[str]]]], Dict[Any, Dict[str, Any]]]:
     """Get reaction participants (nodes and interactions) for a given reaction.
 
     :param component_uri: URI reference of the queried reaction component
@@ -227,13 +229,13 @@ def _get_reaction_participants(component_uri: str, component, rdf_graph: rdflib.
 
 
 def _get_pathway_components(pathway_uri: rdflib.URIRef, rdf_graph: rdflib.Graph) -> Tuple[
-    Dict[str, Dict[str, Union[str, Set[str]]]], List[Dict[str, Union[str, Set[str]]]]]:
+        Dict[str, Dict[str, Union[str, Set[str]]]], List[Dict[str, Union[str, Set[str]]]]]:
     """Get components (nodes and interactions) for a given pathway.
 
      :param pathway_uri: URI reference of the queried pathway
      :param rdf_graph: RDF Reactome Universe graph object
      :return: returns the pathway components as entities (Proteins, Complex, SmallMolecule...) and proteins (their links)
-     """
+    """
     interactions = {}
     nodes = {}
 

src/pathme/reactome/utils.py

@@ -32,6 +32,7 @@ def get_valid_node_parameters(
         hgnc_manager: HgncManager,
         chebi_manager: ChebiManager,
 ) -> Tuple[str, str, str]:
+    """Get valid node parameters."""
     namespace = None
 
     if 'uri_id' in node:

src/pathme/wikipathways/convert_to_bel.py

@@ -9,7 +9,6 @@
 from bio2bel_hgnc import Manager
 from pybel import BELGraph
 from pybel.dsl import BaseEntity, abundance, activity, bioprocess, complex_abundance, gene, protein, rna
-from typing import Collection
 from .utils import check_multiple, evaluate_wikipathways_metadata, get_valid_gene_identifier
 from ..constants import ACTIVITY_ALLOWED_MODIFIERS, HGNC
 from ..utils import add_bel_metadata, parse_id_uri

src/pathme/wikipathways/json_rdf_parser.py

@@ -343,6 +343,7 @@ def parse_entries(entries):
 
     return graph
 
+
 def convert_json(graph: rdflib.Graph):
     """Convert from rdflib importated graph object to python data structure (list of dicts of each entry).
 
@@ -354,6 +355,7 @@ def convert_json(graph: rdflib.Graph):
 
     return json_wp_pathway
 
+
 def parse_pathway(pathway_path):
     """After importing the indicated pathway from text file resources into a graph rdflib object(import_pathway), calls the diferent data types transformations (convert_json function) and the first statement of the parser that will return a graph data structure (parse_entries function). This retrieved graph will be converted to a networX graph (convert_to_nx function).
 

src/pathme/wikipathways/rdf_sparql.py

@@ -10,9 +10,11 @@
 import bio2bel_hgnc
 import rdflib
 import tqdm
+
 from pathme.utils import get_pathway_statitics, parse_rdf, query_result_to_dict
 from pathme.wikipathways.convert_to_bel import convert_to_bel
 from pathme.wikipathways.utils import debug_pathway_info
+
 from pybel import BELGraph, to_pickle
 from rdflib.namespace import DC, DCTERMS, Namespace, RDF, RDFS
 
@@ -49,7 +51,7 @@
 
 #: SPARQL query to get all data nodes in a pathway network with some arguments.
 GET_ALL_DATA_NODES_SPARQL = """
-SELECT DISTINCT 
+SELECT DISTINCT
     ?uri_id
     ?name
     (STRAFTER(STR(?uri_type), str(wp:)) AS ?node_types)
@@ -92,8 +94,8 @@
 
 #: SPARQL query to get all data nodes in a pathway network with some arguments.
 GET_ALL_COMPLEXES_SPARQL = """
-SELECT DISTINCT 
-    ?uri_id 
+SELECT DISTINCT
+    ?uri_id
     (STRAFTER(STR(?uri_type), str(wp:)) AS ?node_types)
     (?participants_entry AS ?participants)
     (?participants_id AS ?participants)
@@ -113,15 +115,15 @@
 # TODO: Check interaction complexes.
 #: SPARQL query to get all directed interactions in a pathway network with source and target.
 GET_ALL_DIRECTED_INTERACTIONS_SPARQL = """
-SELECT DISTINCT 
-    (?source_entry AS ?source) 
-    (?dc_source AS ?source) 
-    (?target_entry AS ?target) 
-    (?dc_target AS ?target) 
+SELECT DISTINCT
+    (?source_entry AS ?source)
+    (?dc_source AS ?source)
+    (?target_entry AS ?target)
+    (?dc_target AS ?target)
     ?uri_id
-    (STRAFTER(STR(?uri_id), "/Interaction/") AS ?identifier) 
-    (STRAFTER(STR(?uri_type), str(wp:)) AS ?interaction_types) 
-    (STRAFTER(STR(?ncbigene_source), str(ncbigene:)) AS ?source ) 
+    (STRAFTER(STR(?uri_id), "/Interaction/") AS ?identifier)
+    (STRAFTER(STR(?uri_type), str(wp:)) AS ?interaction_types)
+    (STRAFTER(STR(?ncbigene_source), str(ncbigene:)) AS ?source )
     (STRAFTER(STR(?ncbigene_target), str(ncbigene:)) AS ?target )
 WHERE {
    ?pathway a wp:Pathway .
@@ -214,7 +216,7 @@ def _get_pathway_components(graph) -> Tuple[
 
 def get_wp_statistics(resource_files, resource_folder, hgnc_manager) -> Tuple[
     Dict[str, Dict[str, int]], Dict[str, Dict[str, Dict[str, int]]]]:
-    """Load WikiPathways RDF to BELGraph
+    """Load WikiPathways RDF to BELGraph.
 
     :param iter[str] resource_files: RDF file path
     :param str resource_folder: RDF file path

src/pathme/wikipathways/utils.py

@@ -38,7 +38,7 @@
 
 
 def evaluate_wikipathways_metadata(metadata: Union[str, Set[str]]) -> str:
-    """Evaluates metadata in wikipathways and returns the string representation."""
+    """Evaluate metadata in wikipathways and return the string representation."""
     if isinstance(metadata, set):
         return ','.join(metadata)
 

tests/constants.py

@@ -45,8 +45,7 @@ class KeggTest(TemporaryConnectionMixin):
 
     @classmethod
     def setUpClass(cls):
-        """Create temporary file"""
-
+        """Create temporary file."""
         logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(name)s - %(message)s")
         log.setLevel(logging.INFO)