Code cleanup for flake8 and mypy

src/pathme/reactome/rdf_sparql.py

@@ -5,17 +5,17 @@
 import logging
 import os
 from collections import defaultdict
-from typing import Set, Dict, Union, Tuple, List, Any
+from typing import Any, Dict, List, Set, Tuple, Union
 
 import rdflib
 import tqdm
 from pybel import to_pickle
 from rdflib import URIRef
-from rdflib.namespace import Namespace, RDFS, RDF, DCTERMS, DC, OWL, XSD, SKOS
+from rdflib.namespace import DC, DCTERMS, Namespace, OWL, RDF, RDFS, SKOS, XSD
 
 from pathme.constants import REACTOME_BEL
 from pathme.reactome.convert_to_bel import convert_to_bel
-from pathme.utils import query_result_to_dict, parse_rdf, get_pathway_statitics
+from pathme.utils import get_pathway_statitics, parse_rdf, query_result_to_dict
 
 log = logging.getLogger(__name__)
 
@@ -36,82 +36,73 @@
     'biopax3': Namespace('http://www.biopax.org/release/biopax-level3.owl#'),
 }
 
-#: SPARQL query string to get all the  primary types of entries (Pathway,  BiochemicalReaction) in a pathway network.
+#: SPARQL query string to get all the  primary types of entries (Pathway, BiochemicalReaction) in a pathway network.
 GET_ALL_TYPES = """
 SELECT DISTINCT (STRAFTER(STR(?rdf_type), str(biopax3:)) AS ?entry_type)
-WHERE
-    {
-        ?uri_id rdf:type ?rdf_type .
+WHERE {
+    ?uri_id rdf:type ?rdf_type .
 }
 """
 
 #: SPARQL query string to get pathway URIs and names in the RDF file.
 GET_ALL_PATHWAYS = """
 SELECT DISTINCT ?uri_id ?name
-WHERE
-    {
-        ?uri_id rdf:type biopax3:Pathway .
-        ?uri_id biopax3:displayName ?name .
-    }
+WHERE {
+    ?uri_id rdf:type biopax3:Pathway .
+    ?uri_id biopax3:displayName ?name .
+}
 """
 
 #: SPARQL query string to get all components of a pathway (predicate biopax3:pathwayComponent).
 GET_ALL_PATHWAY_COMPONENTS = """
 SELECT DISTINCT ?uri_id ?name ?comment (STRAFTER(STR(?uri_type), str(biopax3:)) AS ?component_type)
-WHERE
-    {
-        ?pathway biopax3:pathwayComponent ?uri_id .
-        ?uri_id rdf:type ?uri_type .
-        optional {?uri_id biopax3:displayName ?name .}
-        optional {?uri_id biopax3:comment ?comment .}
-    }
+WHERE {
+    ?pathway biopax3:pathwayComponent ?uri_id .
+    ?uri_id rdf:type ?uri_type .
+    optional {?uri_id biopax3:displayName ?name .}
+    optional {?uri_id biopax3:comment ?comment .}
+}
 """
 
 #: 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 (STR(?control_type) AS ?interaction_type)
-WHERE
-    {
-        ?component biopax3:left ?reactant .
-        ?component biopax3:right ?product .
-        optional {?control biopax3:controlled ?component .}
-        optional {?control biopax3:controlType ?control_type }
-    }
+SELECT DISTINCT 
+    (STRAFTER(STR(?component), '#') AS ?identifier) 
+    ?reactant 
+    ?product 
+    (STR(?control_type) AS ?interaction_type)
+WHERE {
+    ?component biopax3:left ?reactant .
+    ?component biopax3:right ?product .
+    optional {?control biopax3:controlled ?component .}
+    optional {?control biopax3:controlType ?control_type }
+}
 """
 
 #: SPARQL query to get all the possible metadate (optional statements) of an entity (Protein, Dna, Pathway...).
 GET_ENTITY_METADATA = """
-SELECT DISTINCT 
-(STRAFTER (STR(?uri_type), str(biopax3:)) AS ?entity_type) 
-
-(STRAFTER(STR(?entity), '#') AS ?identifier)
-(STR(?entity) AS ?uri_id) 
-
-(STRAFTER(STR(?entity), '#') AS ?reactome_id)
-(STR(?entity) AS ?uri_reactome_id) 
-
-(STR(?entity_reference) AS ?uri_id) 
-
-?name 
-?cell_locat 
-?display_name 
-?complex_components 
-?comment 
-
-WHERE
-    {        
-        ?entity rdf:type ?uri_type .
-        optional {?entity biopax3:comment ?comment .}
-        
-        optional {?entity biopax3:entityReference ?entity_reference .}
-   
-        optional {?entity biopax3:name ?name .}
-        optional {?entity biopax3:displayName ?display_name .}
-        
-        optional {?entity biopax3:cellularLocation ?cell_locat .}
-        optional {?entity biopax3:organism ?organism .}
-        optional {?entity biopax3:component ?complex_components .}
-    }
+SELECT DISTINCT
+    (STRAFTER (STR(?uri_type), str(biopax3:)) AS ?entity_type)
+    (STRAFTER(STR(?entity), '#') AS ?identifier)
+    (STR(?entity) AS ?uri_id)
+    (STRAFTER(STR(?entity), '#') AS ?reactome_id)
+    (STR(?entity) AS ?uri_reactome_id)
+    (STR(?entity_reference) AS ?uri_id)
+    ?name
+    ?cell_locat
+    ?display_name
+    ?complex_components
+    ?comment
+WHERE {        
+    ?entity rdf:type ?uri_type .
+    optional {?entity biopax3:comment ?comment .}
+    optional {?entity biopax3:entityReference ?entity_reference .}
+    optional {?entity biopax3:name ?name .}
+    optional {?entity biopax3:displayName ?display_name .}
+    optional {?entity biopax3:cellularLocation ?cell_locat .}
+    optional {?entity biopax3:organism ?organism .}
+    optional {?entity biopax3:component ?complex_components .}
+}
 """
 
 """Queries managers"""

src/pathme/reactome/utils.py

@@ -1,31 +1,37 @@
 # -*- coding: utf-8 -*-
 
-"""This module has utilities method for parsing, handling wikipathways RDF and data."""
+"""This module has utilities method for parsing, handling WikiPathways RDF and data."""
 
 import logging
 import tarfile
-from typing import List
+from typing import List, Tuple
 
+from bio2bel_chebi import Manager as ChebiManager
+from bio2bel_hgnc import Manager as HgncManager
+from bio2bel_hgnc.models import HumanGene
 from pybel.dsl import protein
 
 from pathme.utils import parse_id_uri
-from ..constants import HGNC, UNKNOWN, UNIPROT, ENSEMBL
+from ..constants import ENSEMBL, HGNC, UNIPROT, UNKNOWN
 
 log = logging.getLogger(__name__)
 
 """Download utilities"""
 
 
-def get_hgnc_node_info(gene):
+def get_hgnc_node_info(gene: HumanGene) -> Tuple[str, str, str]:
     """Return HGNC identifier, symbol and namespace from HGNC entry.
 
     :param bio2bel_hgnc.manager.models.HGNC gene:
-    :rtype: tuple[str,str,str]
     """
-    return gene.identifier, gene.symbol, HGNC
+    return str(gene.identifier), gene.symbol, HGNC
 
 
-def get_valid_node_parameters(node, hgnc_manager, chebi_manager):
+def get_valid_node_parameters(
+        node,
+        hgnc_manager: HgncManager,
+        chebi_manager: ChebiManager,
+) -> Tuple[str, str, str]:
     namespace = None
 
     if 'uri_id' in node:
@@ -106,22 +112,17 @@ def process_multiple_proteins(hgnc_entries: List) -> List:
     :param hgnc_entries: Results from query
     :return: List of Protein BEL nodes
     """
-    protein_group = list()
+    return [
+        protein(namespace='HGNC', name=hgnc_entry.symbol, identifier=hgnc_entry.id)
+        for hgnc_entry in hgnc_entries
+    ]
 
-    for hgnc_entry in hgnc_entries:
-        protein_group.append(
-            protein(namespace='HGNC', name=hgnc_entry.symbol, identifier=hgnc_entry.id)
-        )
 
-    return protein_group
-
-
-def untar_file(file_path, export_folder):
+def untar_file(file_path: str, export_folder: str) -> None:
     """Unzip file into a destination folder.
 
-    :param str file_path: name of the file
-    :param str export_folder: name of the file
-
+    :param file_path: name of the file
+    :param export_folder: name of the file
     """
     tar_ref = tarfile.open(file_path, 'r:bz2')
     tar_ref.extractall(export_folder)

src/pathme/utils.py

@@ -36,7 +36,7 @@ def __call__(self, *args, **kwargs):
         return self.method(*args, **kwargs)
 
 
-def parse_id_uri(uri):
+def parse_id_uri(uri: str) -> Tuple[str, str, str, str]:
     """Get the components of a given uri (with identifier at the last position).
 
     :param uri: URI