Novelty Score Calculation Update

Updated novelty score calcualtions including integrations of: 1. Clinical Trials/ Clinical Approvals - MVP1 2. TDLs - MVP2 3. Gene Distinctiveness - MVP2
TranslatorSRI · Sep 26, 2024 · 79254fa · 79254fa
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diff --git a/app/novelty/chk_gene_nmf.py b/app/novelty/chk_gene_nmf.py
@@ -0,0 +1,147 @@
+"""Test Clinical Evidence function."""
+
+# imports
+import pytest
+import logging
+
+# add path of file
+import sys
+import os
+
+# Determine the path to startup_utils.py
+grandparent_dir = os.path.dirname(os.path.dirname(os.getcwd()))
+# print(grandparent_dir)
+sys.path.append(grandparent_dir)
+startup_utils_path = os.path.abspath("app/novelty/gene_nmf/gene_nmf_adapter.py")
+startup_utils_dir = os.path.dirname(startup_utils_path)
+sys.path.insert(0, startup_utils_dir)
+print("added to python path the following directory: {}".format(startup_utils_dir))
+
+# import file top test
+import app.novelty.gene_nmf.gene_nmf_adapter as adapter
+import app.novelty.gene_nmf.dcc.dcc_utils as dutils
+
+# logger
+logger = dutils.get_logger(name=__name__)
+logger.info("added to pyton path the following directory: {}".format(startup_utils_dir))
+
+# vars
+list_gene_test = [
+        "NCBIGene:5142",
+        "NCBIGene:4853",
+        "NCBIGene:4000",
+        "NCBIGene:5664",
+        "NCBIGene:9804",
+        "NCBIGene:22891",
+        "NCBIGene:5728",
+        "NCBIGene:3087",
+        "NCBIGene:5950",
+        "NCBIGene:6319",
+        "NCBIGene:114815",
+        "NCBIGene:6934",
+        "NCBIGene:3630",
+        "NCBIGene:3784",
+        "NCBIGene:3767",
+        "NCBIGene:3992",
+        "NCBIGene:9415",
+        "NCBIGene:7351",
+        "NCBIGene:7352",
+        "NCBIGene:4544",
+        "NCBIGene:10599",
+        "NCBIGene:6660",
+        "NCBIGene:7480",
+        "NCBIGene:8091",
+        "NCBIGene:7103",
+        "NCBIGene:6927",
+        "NCBIGene:2308",
+        "NCBIGene:5663",
+        "NCBIGene:9369",
+        "NCBIGene:4088",
+        "NCBIGene:10239",
+        "NCBIGene:9055",
+        "NCBIGene:79068",
+        "NCBIGene:6137",
+        "NCBIGene:7157",
+        "NCBIGene:6720",
+        "NCBIGene:6928",
+        "NCBIGene:8877",
+        "NCBIGene:9021",
+        "NCBIGene:6925",
+        "NCBIGene:4160",
+        "NCBIGene:3643",
+        "NCBIGene:7137",
+        "NCBIGene:129787",
+        "NCBIGene:338",
+        "NCBIGene:2646",
+        "NCBIGene:63892",
+        "NCBIGene:53335",
+        "NCBIGene:5966",
+        "NCBIGene:2888",
+        "NCBIGene:4760",
+        "NCBIGene:3667",
+        "NCBIGene:57761",
+        "NCBIGene:5335",
+        "NCBIGene:3172",
+        "NCBIGene:5770",
+        "NCBIGene:7022",
+        "NCBIGene:7332",
+        "NCBIGene:5468",
+        "NCBIGene:7325",
+        "NCBIGene:7384",
+        "NCBIGene:56999",
+        "NCBIGene:7018",
+        "NCBIGene:285195",
+        "NCBIGene:6514",
+        "NCBIGene:10644",
+        "NCBIGene:9370",
+        "NCBIGene:10296",
+        "NCBIGene:7466",
+        "NCBIGene:4214",
+        "NCBIGene:85480",
+        "NCBIGene:6239",
+        "NCBIGene:54901",
+        "NCBIGene:1432",
+        "NCBIGene:7422",
+        "NCBIGene:7021",
+        "NCBIGene:5314",
+        "NCBIGene:222546",
+        "NCBIGene:5167",
+        "NCBIGene:7128",
+        "NCBIGene:387082",
+        "NCBIGene:221895",
+        "NCBIGene:2645",
+        "NCBIGene:5506",
+        "NCBIGene:5078",
+        "NCBIGene:136259",
+        "NCBIGene:79660",
+        "NCBIGene:94241",
+        "NCBIGene:169026",
+        "NCBIGene:7436",
+        "NCBIGene:169792",
+        "NCBIGene:6194",
+        "NCBIGene:140803",
+        "NCBIGene:29979",
+        "NCBIGene:6812"
+    ]
+map_result = adapter.get_gene_nmf_novelty_for_gene_list(list_input_genes=list_gene_test, log=True)
+print(map_result)
+# def test_get_gene_nmf_novelty_for_gene_list():
+#     """
+#     Test that the gene nmf adaptare novelty function works.
+#     """
+#     # initialize
+#     map_result = {}
+#
+#     # call method
+#     map_result = adapter.get_gene_nmf_novelty_for_gene_list(list_input_genes=list_gene_test, log=True)
+#
+#     # logger
+#     logger.info("got map result of size: {}".format(len(map_result.get('gene_results'))))
+
+    # test
+    # assert map_result is not None
+    # assert map_result.get('gene_results') is not None
+    # assert len(map_result.get('gene_results')) > 0
+    # assert len(map_result.get('gene_results')) == len(list_gene_test)
+
+