adding COHD

Common/data_sources.py

@@ -6,6 +6,7 @@
 CHEBI_PROPERTIES = 'CHEBIProps'
 CLINICAL_TRIALS_KP = 'ClinicalTrialsKP'
 CORD19 = 'Cord19'
+COHD = 'COHD'
 CTD = 'CTD'
 DRUG_CENTRAL = 'DrugCentral'
 DRUGMECHDB = 'DrugMechDB'
@@ -56,6 +57,7 @@
     CHEBI_PROPERTIES: ("parsers.chebi.src.loadChebiProperties", "ChebiPropertiesLoader"),
     CLINICAL_TRIALS_KP: ("parsers.clinicaltrials.src.loadCTKP", "CTKPLoader"),
     CORD19: ("parsers.cord19.src.loadCord19", "Cord19Loader"),
+    COHD: ("parsers.cohd.src.loadCOHD", "COHDLoader"),
     CTD: ("parsers.CTD.src.loadCTD", "CTDLoader"),
     DRUG_CENTRAL: ("parsers.drugcentral.src.loaddrugcentral", "DrugCentralLoader"),
     DRUGMECHDB: ("parsers.drugmechdb.src.loadDrugMechDB", "DrugMechDBLoader"),

graph_specs/default-graph-spec.yml

@@ -75,6 +75,15 @@ graphs:
     sources:
       - source_id: CAM-KP
 
+  - graph_id: COHD_Automat
+    graph_name: COHD
+    graph_description:
+    graph_url:
+    conflation: False
+    output_format: neo4j
+    sources:
+      - source_id: COHD
+
   - graph_id: CTD_Automat
     graph_name: CTD
     graph_description: 'The Comparative Toxicogenomics Database (CTD) is an open-source database that provides manually curated information about chemical-gene/protein, chemical-disease, and gene/protein-disease relationships, with additional support for the curated relationships provided by function and pathway data.'

parsers/cohd/src/loadCOHD.py

@@ -0,0 +1,76 @@
+
+import os
+import requests
+import yaml
+
+from Common.loader_interface import SourceDataLoader
+from Common.biolink_constants import PRIMARY_KNOWLEDGE_SOURCE
+from Common.utils import GetData, quick_jsonl_file_iterator
+
+
+##############
+# Class: COHD source loader
+#
+# Desc: Class that loads/parses the COHD data.
+##############
+class COHDLoader(SourceDataLoader):
+
+    source_id: str = 'COHD'
+    provenance_id: str = 'infores:cohd'
+    parsing_version: str = '1.0'
+
+    def __init__(self, test_mode: bool = False, source_data_dir: str = None):
+        """
+        :param test_mode - sets the run into test mode
+        :param source_data_dir - the specific storage directory to save files in
+        """
+        super().__init__(test_mode=test_mode, source_data_dir=source_data_dir)
+
+        self.data_url = 'https://stars.renci.org/var/data_services/cohd_2/'
+        self.version_file = 'cohd.yaml'
+        self.cohd_nodes = 'cohd_nodes.jsonl'
+        self.cohd_edges = 'cohd_edges.jsonl'
+        self.data_files = [self.cohd_nodes, self.cohd_edges]
+
+    def get_latest_source_version(self) -> str:
+        version_file_url = f"{self.data_url}{self.version_file}"
+        r = requests.get(version_file_url)
+        if not r.ok:
+            r.raise_for_status()
+        version_yaml = yaml.full_load(r.text)
+        build_version = str(version_yaml['build'])
+        return build_version
+
+    def get_data(self) -> bool:
+        for data_file in self.data_files:
+            source_data_url = f'{self.data_url}{data_file}'
+            data_puller = GetData()
+            data_puller.pull_via_http(source_data_url, self.data_path)
+        return True
+
+    def parse_data(self) -> dict:
+        """
+        Parses the data file for graph nodes/edges
+
+        :return: ret_val: load_metadata
+        """
+        record_counter = 0
+        skipped_record_counter = 0
+
+        nodes_file_path: str = os.path.join(self.data_path, self.cohd_nodes)
+        for node_json in quick_jsonl_file_iterator(nodes_file_path):
+            self.output_file_writer.write_normalized_node(node_json)
+
+        edges_file_path: str = os.path.join(self.data_path, self.cohd_edges)
+        for edge_json in quick_jsonl_file_iterator(edges_file_path):
+            sources = edge_json.pop("sources")
+            for source in sources:
+                edge_json[source["resource_role"]] = source["resource_id"]
+            self.output_file_writer.write_normalized_edge(edge_json)
+            record_counter += 1
+
+        # load up the metadata
+        load_metadata: dict = {
+            'num_source_lines': record_counter,
+            'unusable_source_lines': skipped_record_counter}
+        return load_metadata