Multiple configs

config/biopathnet.yaml

@@ -9,9 +9,11 @@ biocypher:
         root_node: entity
 
 biopathnet:
-  file_format: txt
+  file_format: txt:bn 
   entity_types_file_stem: entity_types
   entity_names_file_stem: entity_names
   background_graph_file_stem: brg
   skg_file_stem: skg
+  targeted_relation: "(alteration, variant biomarker for treatment, drug)"
+  include_properties: False
 

config/owl.yaml

@@ -0,0 +1,16 @@
+biocypher:
+    debug: false
+    offline: true
+    dbms: owl
+
+    # Ontology configuration
+    head_ontology:
+        url: https://github.com/biolink/biolink-model/raw/v3.2.1/biolink-model.owl.ttl
+        root_node: entity
+
+owl:
+    edge_model: ObjectProperty
+    file_format: turtle
+    labels_order: "Ascending" # Default: From more specific to more generic.
+    node_labels_order: "Ascending" # Default: use labels_order.
+    edge_labels_order: "Leaves"

make.sh

@@ -78,19 +78,21 @@ fi
 
 echo "Weave data..." >&2
 
+echo "CONFIG = $CONFIG" >&2
+
 cmd="uv run python3 ${py_args} $script_dir/weave.py \
-    --omnipath-networks                     $data_dir/omnipath_networks/subset_omnipath_networks_different_type_entity_type_source_and_entity_type_target_shorter.tsv \
+    --copy-number-amplifications-external   $decider_dir/cnas_external.csv  \
+    --short-mutations-local                 $decider_dir/short_mutations_local.csv  \
+    --short-mutations-external              $decider_dir/short_mutations_external.csv  \
+    --copy-number-amplifications-local      $decider_dir/cnas_local.csv \
+    --open-targets-drug-molecule            $data_dir/OT/drug_molecule/
+    --open-targets-drug_mechanism_of_action $data_dir/OT/drug_mechanism_of_action/
+    --open-targets-target                   $data_dir/OT/target/
+    --cgi                                   $decider_dir/treatments_cgi.csv \
     --config $CONFIG \
     ${weave_args}" # \
-    # --copy-number-amplifications-external   $decider_dir/cnas_external.csv  \
-    # --short-mutations-local                 $decider_dir/short_mutations_local.csv  \
-    # --short-mutations-external              $decider_dir/short_mutations_external.csv  \
-    # --copy-number-amplifications-local      $decider_dir/cnas_local.csv \
+    # --omnipath-networks                     $data_dir/omnipath_networks/omnipath_networks_different_type_entity_type_source_and_entity_type_target_shorter.tsv \
     # --structural-variants                   $decider_dir/structural_variants.xlsx  \
-    # --open-targets-drug-molecule            $data_dir/OT/drug_molecule/
-    # --open-targets-drug_mechanism_of_action $data_dir/OT/drug_mechanism_of_action/
-    # --open-targets-target                   $data_dir/OT/target/
-    # --cgi                                   $decider_dir/treatments_cgi.csv \
     # --clinical                              $data_dir/DECIDER/clinical/clinical_export.xlsx \
     # --oncokb                     $data_dir/DECIDER/$data_version/treatments.csv \
 

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
   "seaborn>=0.13.2,<0.14",
   "ontoweaver>=1.4.0,<1.5.0",
   "openpyxl>=3.1.5",
-  "pyarrow<21.0.0",
+  "pyarrow>20.0.0",
   "fastparquet<2026.3.0",
 ]
 

weave.py

@@ -136,7 +136,8 @@ def process_OT(directory, name):
     parser = argparse.ArgumentParser(
         description=usage)
 
-    parser.add_argument("-C", "--config", metavar="FILE", default="config/neo4j.yaml",
+    parser.add_argument("-C", "--config", metavar="FILE", default=["config/neo4j.yaml"],
+                        action="append",
                         help="The BioCypher configuration to load [default: config/neo4j.yaml].")
 
     parser.add_argument("-i", "--clinical", metavar="CSV", nargs="+",
@@ -197,10 +198,6 @@ def process_OT(directory, name):
                         help="Set the verbose level (default: %(default)s).")
 
     asked = parser.parse_args()
-    bc = biocypher.BioCypher(
-        biocypher_config_path = asked.config,
-        schema_config_path = "config/schema.yaml"
-    )
 
     logging.basicConfig()
     logging.getLogger().setLevel(asked.verbose)
@@ -670,17 +667,26 @@ def process_OT(directory, name):
     # Export the final SKG.
     ###################################################
 
-    logging.info(f"Write the final SKG into files...")
-    if fnodes:
-        bc.write_nodes(n.as_tuple() for n in fnodes)
-    if fedges:
-        bc.write_edges(e.as_tuple() for e in fedges)
-    #bc.summary()
-    import_file = bc.write_import_call()
-    logging.info(f"OK, wrote files.")
-
-    # Print on stdout for other scripts to get.
-    print(import_file)
+    configs = asked.config
+
+    for config in configs:
+        logging.info(f"Write the final SKG into {config} files...")
+
+        bc = biocypher.BioCypher(
+            biocypher_config_path = config,
+            schema_config_path = "config/schema.yaml"
+        )
+
+        if fnodes:
+            bc.write_nodes(n.as_tuple() for n in fnodes)
+        if fedges:
+            bc.write_edges(e.as_tuple() for e in fedges)
+        #bc.summary()
+        import_file = bc.write_import_call()
+        logging.info(f"OK, wrote files.")
+
+        # Print on stdout for other scripts to get.
+        print(import_file)
 
     if asked.import_script_run:
         shell = os.environ["SHELL"]