Add abundance with ACTIVITY_ALLOWED_MODIFIERS

src/pathme/constants.py

@@ -5,6 +5,7 @@
 import os
 
 from bio2bel.utils import get_connection
+from pybel.dsl.nodes import abundance, complex_abundance, protein, rna
 
 MODULE_NAME = 'pathme'
 DEFAULT_PATHME_DIR = os.path.join(os.path.expanduser('~'), '.pathme')
@@ -40,7 +41,7 @@ def get_data_dir() -> str:
 UNIVERSE_DIR = os.path.join(DATA_DIR, 'universe')
 
 
-def ensure_pathme_folders(): # TODO why is this a function?
+def ensure_pathme_folders():  # TODO why is this a function?
     """Ensure data folders are created."""
     os.makedirs(KEGG_DIR, exist_ok=True)
     os.makedirs(REACTOME_DIR, exist_ok=True)
@@ -89,6 +90,14 @@ def ensure_pathme_folders(): # TODO why is this a function?
     'ubiquitination': 'Ub',
     'methylation': 'Me',
 }
+
+ACTIVITY_ALLOWED_MODIFIERS = {
+    abundance,
+    protein,
+    complex_abundance,
+    rna
+}
+
 KEGG_CITATION = '10592173'
 REACTOME_CITATION = '29145629'
 

src/pathme/kegg/convert_to_bel.py

@@ -10,7 +10,7 @@
 from pybel import BELGraph, to_pickle
 from pybel.dsl.edges import activity
 from pybel.dsl.node_classes import CentralDogma
-from pybel.dsl.nodes import abundance, bioprocess, complex_abundance, composite_abundance, pmod, protein, reaction, rna
+from pybel.dsl.nodes import bioprocess, composite_abundance, pmod, reaction
 from pybel.struct.summary import count_functions, edge_summary
 
 from pathme.constants import *
@@ -512,7 +512,7 @@ def add_simple_edge(graph, u, v, relation_type):
                     graph.add_increases(
                         u, v_modified,
                         citation=KEGG_CITATION, evidence='Extracted from KEGG',
-                        subject_modifier=activity() if u in {protein, complex_abundance, rna} else None,
+                        subject_modifier=activity() if u in ACTIVITY_ALLOWED_MODIFIERS else None,
                         # Add the activity function if subject is one of the following nodes (BEL 2.0 specifications)
                         annotations={},
                     )
@@ -522,7 +522,7 @@ def add_simple_edge(graph, u, v, relation_type):
                     graph.add_decreases(
                         u, v_modified,
                         citation=KEGG_CITATION, evidence='Extracted from KEGG',
-                        subject_modifier=activity() if u in {protein, complex_abundance, rna} else None,
+                        subject_modifier=activity() if u in ACTIVITY_ALLOWED_MODIFIERS else None,
                         # Add the activity function if subject is one of the following nodes (BEL 2.0 specifications)
                         annotations={},
                     )
@@ -539,7 +539,7 @@ def add_simple_edge(graph, u, v, relation_type):
             graph.add_increases(
                 u, v_modified,
                 citation=KEGG_CITATION, evidence='Extracted from KEGG',
-                subject_modifier=activity() if u in {protein, complex_abundance, rna} else None,
+                subject_modifier=activity() if u in ACTIVITY_ALLOWED_MODIFIERS else None,
                 annotations={},
             )
 
@@ -552,7 +552,7 @@ def add_simple_edge(graph, u, v, relation_type):
         graph.add_decreases(
             u, v,
             citation=KEGG_CITATION, evidence='Extracted from KEGG',
-            subject_modifier=activity() if u in {protein, complex_abundance, rna} else None,
+            subject_modifier=activity() if u in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
@@ -561,7 +561,7 @@ def add_simple_edge(graph, u, v, relation_type):
         graph.add_increases(
             u, v,
             citation=KEGG_CITATION, evidence='Extracted from KEGG',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
@@ -570,7 +570,7 @@ def add_simple_edge(graph, u, v, relation_type):
         graph.add_increases(
             u, v,
             citation=KEGG_CITATION, evidence='Extracted from KEGG',
-            subject_modifier=activity('cat') if u in {protein, complex_abundance, rna} else None,
+            subject_modifier=activity('cat') if u in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
@@ -579,7 +579,7 @@ def add_simple_edge(graph, u, v, relation_type):
         graph.add_decreases(
             u, v,
             citation=KEGG_CITATION, evidence='Extracted from KEGG',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 

src/pathme/reactome/convert_to_bel.py

@@ -22,7 +22,7 @@
     NamedComplexAbundance
 )
 
-from pathme.constants import UNKNOWN, REACTOME_CITATION
+from pathme.constants import ACTIVITY_ALLOWED_MODIFIERS, UNKNOWN, REACTOME_CITATION
 from pathme.reactome.utils import get_valid_node_parameters, process_multiple_proteins
 from pathme.utils import add_bel_metadata, parse_id_uri
 
@@ -167,15 +167,15 @@ def add_simple_edge(graph: BELGraph, u, v, edge_types):
         graph.add_increases(
             u, v,
             citation=REACTOME_CITATION, evidence='Extracted from Reactome',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
     elif 'INHIBITION' in edge_types:
         graph.add_decreases(
             u, v,
             citation=REACTOME_CITATION, evidence='Extracted from Reactome',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
     else:

src/pathme/wikipathways/convert_to_bel.py

@@ -11,7 +11,7 @@
 from pybel.dsl import BaseEntity, abundance, activity, bioprocess, complex_abundance, gene, protein, reaction, rna
 
 from .utils import check_multiple, evaluate_wikipathways_metadata, get_valid_gene_identifier
-from ..constants import HGNC
+from ..constants import HGNC, ACTIVITY_ALLOWED_MODIFIERS
 from ..utils import add_bel_metadata, parse_id_uri
 
 log = logging.getLogger(__name__)
@@ -205,23 +205,23 @@ def add_simple_edge(graph: BELGraph, u, v, edge_types, uri_id):
         graph.add_increases(
             u, v,
             citation=uri_id, evidence='Extracted from WikiPathways',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
     elif 'Inhibition' in edge_types:
         graph.add_decreases(
             u, v,
             citation=uri_id, evidence='Extracted from WikiPathways',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )
 
     elif 'Catalysis' in edge_types:
         graph.add_increases(
             u, v,
             citation=uri_id, evidence='Extracted from WikiPathways',
-            object_modifier=activity() if v in {protein, complex_abundance, rna} else None,
+            object_modifier=activity() if v in ACTIVITY_ALLOWED_MODIFIERS else None,
             annotations={},
         )