Merge remote-tracking branch 'origin/issue2191' #2191

RTXteam · Nov 16, 2023 · eb4bac7 · eb4bac7
2 parents ba57c30 + 6046411
commit eb4bac7
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diff --git a/code/ARAX/ARAXQuery/ARAX_database_manager.py b/code/ARAX/ARAXQuery/ARAX_database_manager.py
@@ -78,11 +78,8 @@ def __init__(self, allow_downloads=False):
 
         self.local_paths = {
             'cohd_database': f"{cohd_filepath}{os.path.sep}{self.RTXConfig.cohd_database_path.split('/')[-1]}",
-            'graph_database': f"{pred_filepath}{os.path.sep}{self.RTXConfig.graph_database_path.split('/')[-1]}",
-            'log_model': f"{pred_filepath}{os.path.sep}{self.RTXConfig.log_model_path.split('/')[-1]}",
             'curie_to_pmids': f"{ngd_filepath}{os.path.sep}{self.RTXConfig.curie_to_pmids_path.split('/')[-1]}",
             'node_synonymizer': f"{synonymizer_filepath}{os.path.sep}{self.RTXConfig.node_synonymizer_path.split('/')[-1]}",
-            'dtd_prob': f"{pred_filepath}{os.path.sep}{self.RTXConfig.dtd_prob_path.split('/')[-1]}",
             'kg2c_sqlite': f"{kg2c_filepath}{os.path.sep}{self.RTXConfig.kg2c_sqlite_path.split('/')[-1]}",
             'kg2c_meta_kg': f"{kg2c_meta_kg_filepath}{os.path.sep}{self.RTXConfig.kg2c_meta_kg_path.split('/')[-1]}",
             'fda_approved_drugs': f"{fda_approved_drugs_filepath}{os.path.sep}{self.RTXConfig.fda_approved_drugs_path.split('/')[-1]}",
@@ -97,11 +94,8 @@ def __init__(self, allow_downloads=False):
         # This portion of the db path is the same on arax-databases.rtx.ai as it is on the ARAX docker instance
         self.database_subpaths = {
             'cohd_database': self.get_database_subpath(self.RTXConfig.cohd_database_path),
-            'graph_database': self.get_database_subpath(self.RTXConfig.graph_database_path),
-            'log_model': self.get_database_subpath(self.RTXConfig.log_model_path),
             'curie_to_pmids': self.get_database_subpath(self.RTXConfig.curie_to_pmids_path),
             'node_synonymizer': self.get_database_subpath(self.RTXConfig.node_synonymizer_path),
-            'dtd_prob': self.get_database_subpath(self.RTXConfig.dtd_prob_path),
             'kg2c_sqlite': self.get_database_subpath(self.RTXConfig.kg2c_sqlite_path),
             'kg2c_meta_kg': self.get_database_subpath(self.RTXConfig.kg2c_meta_kg_path),
             'fda_approved_drugs': self.get_database_subpath(self.RTXConfig.fda_approved_drugs_path),
@@ -115,11 +109,8 @@ def __init__(self, allow_downloads=False):
         self.databases_server_dir_path = '/home/rtxconfig'
         self.remote_locations = {
             'cohd_database': self.get_remote_location('cohd_database'),
-            'graph_database': self.get_remote_location('graph_database'),
-            'log_model': self.get_remote_location('log_model'),
             'curie_to_pmids': self.get_remote_location('curie_to_pmids'),
             'node_synonymizer': self.get_remote_location('node_synonymizer'),
-            'dtd_prob': self.get_remote_location('dtd_prob'),
             'kg2c_sqlite': self.get_remote_location('kg2c_sqlite'),
             'kg2c_meta_kg': self.get_remote_location('kg2c_meta_kg'),
             'fda_approved_drugs': self.get_remote_location('fda_approved_drugs'),
@@ -133,11 +124,8 @@ def __init__(self, allow_downloads=False):
         self.docker_databases_dir_path = '/mnt/data/orangeboard/databases'
         self.docker_central_paths = {
             'cohd_database': self.get_docker_path('cohd_database'),
-            'graph_database': self.get_docker_path('graph_database'),
-            'log_model': self.get_docker_path('log_model'),
             'curie_to_pmids': self.get_docker_path('curie_to_pmids'),
             'node_synonymizer': self.get_docker_path('node_synonymizer'),
-            'dtd_prob': self.get_docker_path('dtd_prob'),
             'kg2c_sqlite': self.get_docker_path('kg2c_sqlite'),
             'kg2c_meta_kg': self.get_docker_path('kg2c_meta_kg'),
             'fda_approved_drugs': self.get_docker_path('fda_approved_drugs'),
@@ -154,14 +142,6 @@ def __init__(self, allow_downloads=False):
                 'path': self.local_paths['cohd_database'],
                 'version': self.RTXConfig.cohd_database_version
             },
-            'graph_database': {
-                'path': self.local_paths['graph_database'],
-                'version': self.RTXConfig.graph_database_version
-            },
-            'log_model': {
-                'path': self.local_paths['log_model'],
-                'version': self.RTXConfig.log_model_version
-            },
             'curie_to_pmids': {
                 'path': self.local_paths['curie_to_pmids'],
                 'version': self.RTXConfig.curie_to_pmids_version
@@ -170,10 +150,6 @@ def __init__(self, allow_downloads=False):
                 'path': self.local_paths['node_synonymizer'],
                 'version': self.RTXConfig.node_synonymizer_version
             },
-            'dtd_prob': {
-                'path': self.local_paths['dtd_prob'],
-                'version': self.RTXConfig.dtd_prob_version
-            },
             'kg2c_sqlite': {
                 'path': self.local_paths['kg2c_sqlite'],
                 'version': self.RTXConfig.kg2c_sqlite_version

diff --git a/code/RTXConfiguration.py b/code/RTXConfiguration.py
@@ -169,16 +169,10 @@ def _private_init(self):
         database_downloads = self.config_dbs["database_downloads"]
         self.cohd_database_path = database_downloads["cohd_database"]
         self.cohd_database_version = self.cohd_database_path.split('/')[-1].split('_v')[-1].replace('.db', '')
-        self.graph_database_path = database_downloads["graph_database"]
-        self.graph_database_version = self.graph_database_path.split('/')[-1].split('_v')[-1].replace('.sqlite', '')
-        self.log_model_path = database_downloads["log_model"]
-        self.log_model_version = self.log_model_path.split('/')[-1].split('_v')[-1].replace('.pkl', '')
         self.curie_to_pmids_path = database_downloads["curie_to_pmids"]
         self.curie_to_pmids_version = self.curie_to_pmids_path.split('/')[-1].split('_v')[-1].replace('.sqlite', '')
         self.node_synonymizer_path = database_downloads["node_synonymizer"]
         self.node_synonymizer_version = self.node_synonymizer_path.split('/')[-1].split('_v')[-1].replace('.sqlite', '')
-        self.dtd_prob_path = database_downloads["dtd_prob"]
-        self.dtd_prob_version = self.dtd_prob_path.split('/')[-1].split('_v')[-1].replace('.db', '')
         self.kg2c_sqlite_path = database_downloads["kg2c_sqlite"]
         self.kg2c_sqlite_version = self.kg2c_sqlite_path.split('/')[-1].split('_v')[-1].replace('.sqlite', '')
         self.kg2c_meta_kg_path = database_downloads["kg2c_meta_kg"]
@@ -195,8 +189,6 @@ def _private_init(self):
         self.xcrg_increase_model_version = self.xcrg_embeddings_path.split('/')[-1].split('_v')[-1].replace('.pt', '')
         self.xcrg_decrease_model_path = database_downloads["xcrg_decrease_model"]
         self.xcrg_decrease_model_version = self.xcrg_embeddings_path.split('/')[-1].split('_v')[-1].replace('.pt', '')
-        self.rel_max_path = database_downloads["rel_max"]
-        self.map_txt_path = database_downloads["map_txt"]
 
         # Set up mysql feedback
         self.mysql_feedback_host = self.config_secrets["mysql_feedback"]["host"]
@@ -275,7 +267,6 @@ def main():
     print("mysql feedback username: %s" % rtxConfig.mysql_feedback_username)
     print("mysql feedback password: %s" % rtxConfig.mysql_feedback_password)
     print(f"maturity: {rtxConfig.maturity}")
-    print(f"log_model_path: {rtxConfig.log_model_path}")
     print(f"current branch: {rtxConfig.current_branch_name}")
     print(f"is_itrb_instance: {rtxConfig.is_itrb_instance}")
     print(f"Total elapsed time: {(t1-t0)*1000:.2f} ms")

diff --git a/code/config_dbs.json b/code/config_dbs.json
@@ -8,11 +8,6 @@
       "curie_to_pmids": "/translator/data/orangeboard/databases/KG2.8.4/curie_to_pmids_v1.0_KG2.8.4.sqlite",
       "explainable_dtd_db": "/translator/data/orangeboard/databases/KG2.8.4/ExplainableDTD_v1.0_KG2.8.3_refreshedTo_KG2.8.4.db",
       "cohd_database": "/translator/data/orangeboard/databases/KG2.8.0/COHDdatabase_v1.0_KG2.8.0.db",
-      "graph_database": "/translator/data/orangeboard/databases/KG2.8.0.1/GRAPH_v1.0_KG2.8.0.1_refreshed.sqlite",
-      "dtd_prob": "/translator/data/orangeboard/databases/KG2.8.0.1/DTD_probability_database_v1.0_KG2.8.0.1_refreshed.db",
-      "log_model": "/translator/data/orangeboard/databases/KG2.7.6/LogModel_v1.0_KG2.7.6.pkl",
-      "rel_max": "/translator/data/orangeboard/databases/KG2.7.6/rel_max_v1.0_KG2.7.6.emb.gz",
-      "map_txt": "/translator/data/orangeboard/databases/KG2.7.6/map_v1.0_KG2.7.6.txt",
       "xcrg_embeddings": "/translator/data/orangeboard/databases/KG2.8.0.1/chemical_gene_embeddings_v1.0.KG2.8.0.1.npz",
       "xcrg_increase_model": "/translator/data/orangeboard/databases/KG2.8.0.1/xcrg_increase_model_v1.0.KG2.8.0.1.pt",
       "xcrg_decrease_model": "/translator/data/orangeboard/databases/KG2.8.0.1/xcrg_decrease_model_v1.0.KG2.8.0.1.pt"