Merge pull request #238 from informatics-isi-edu/Issue-229

Issue 229 - changes applied to production.

config-scripts/pdb/order_by.json

@@ -8,6 +8,7 @@
     "ihm_ordered_ensemble": ["process_id", "edge_id"],
     "ihm_related_datasets": ["dataset_list_id_derived", "dataset_list_id_primary"],
     "ihm_struct_assembly_class_link": ["assembly_id", "class_id"],
-    "pdbx_entity_poly_na_type": ["entity_id", "type"]
+    "pdbx_entity_poly_na_type": ["entity_id", "type"],
+    "ihm_ordered_model": ["process_id", "edge_id"]
 }
 

config-scripts/schema-updates/ciff_extension/2024_16_update_vocab.py

@@ -0,0 +1,78 @@
+import sys
+import json
+from deriva.core import get_credential, DerivaServer, BaseCLI
+from deriva.core.ermrest_model import Key, Column, builtin_types
+import utils
+
+ihm_cross_link_list_linker_type_rows = [
+        {'Name': 'PDH', 'Description': 'PDH'},
+        {'Name': 'DMTMM', 'Description': 'DMTMM'}
+    ]
+
+ihm_dataset_list_data_type_rows = [
+    {'Name': 'Crosslinking-MS data', 'Description': 'Crosslinking-MS data'}
+    ]
+
+ihm_dataset_group_application_rows = [
+    {'Name': 'modeling', 'Description': 'modeling'}
+    ]
+
+ihm_dataset_related_db_reference_db_name_rows = [
+    {'Name': 'ProteomeXchange', 'Description': 'ProteomeXchange'}
+    ]
+
+struct_pdbx_structure_determination_methodology_rows = [
+        {'Name': 'computational', 'Description': 'computational'},
+        {'Name': 'experimental', 'Description': 'experimental'},
+        {'Name': 'integrative', 'Description': 'integrative'}
+    ]
+
+ihm_relaxation_time_unit_rows = [
+        {'Name': 'seconds', 'Description': 'seconds'},
+        {'Name': 'milliseconds', 'Description': 'milliseconds'},
+        {'Name': 'microseconds', 'Description': 'microseconds'}
+    ]
+
+ihm_equilibrium_constant_determination_method_rows = [
+        {'Name': 'from population', 'Description': 'from population'},
+        {'Name': 'from kinetic rates', 'Description': 'from kinetic rates'},
+        {'Name': 'other', 'Description': 'other'}
+    ]
+
+ihm_ensemble_info_model_group_superimposed_flag_rows = [
+        {'Name': 'YES', 'Description': 'YES'},
+        {'Name': 'NO', 'Description': 'NO'}
+    ]
+
+def main(server_name, catalog_id, credentials):
+    server = DerivaServer('https', server_name, credentials)
+    catalog = server.connect_ermrest(catalog_id)
+    catalog.dcctx['cid'] = "oneoff/model"
+    model = catalog.getCatalogModel()
+
+    """
+    Create new Vocab tables
+    """
+    utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('struct_pdbx_structure_determination_methodology', 'Structure determination methodology'))
+    utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_relaxation_time_unit', 'Relaxation time unit'))
+    utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_equilibrium_constant_determination_method', 'Method used to determine the equilibrium constant'))
+    utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_ensemble_info_model_group_superimposed_flag', 'Model group superimposed flag'))
+
+    """
+    Load data into new and existing vocabulary tables
+    """
+    utils.add_rows_to_vocab_table(catalog, 'ihm_cross_link_list_linker_type', ihm_cross_link_list_linker_type_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_list_data_type', ihm_dataset_list_data_type_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_group_application', ihm_dataset_group_application_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_related_db_reference_db_name', ihm_dataset_related_db_reference_db_name_rows)
+    utils.add_rows_to_vocab_table(catalog, 'struct_pdbx_structure_determination_methodology', struct_pdbx_structure_determination_methodology_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_relaxation_time_unit', ihm_relaxation_time_unit_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_equilibrium_constant_determination_method', ihm_equilibrium_constant_determination_method_rows)
+    utils.add_rows_to_vocab_table(catalog, 'ihm_ensemble_info_model_group_superimposed_flag', ihm_ensemble_info_model_group_superimposed_flag_rows) 
+
+if __name__ == '__main__':
+    args = BaseCLI("ad-hoc table creation tool", None, 1).parse_cli()
+    credentials = get_credential(args.host, args.credential_file)
+
+    main(args.host, 1, credentials)
+