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adding performance, sharing functions between them, better error hand…
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@@ -4,4 +4,5 @@ __pycache__ | |
| .log | ||
| kubernets | ||
| *coverage | ||
| .idea | ||
| .idea | ||
| /deploy/performance_results | ||
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| import os | ||
| import yaml | ||
| import json | ||
| import time | ||
| import random | ||
| import requests | ||
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| from validate import send_cypher_query, send_trapi_query | ||
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| def quick_jsonl_file_iterator(json_file): | ||
| with open(json_file, 'r', encoding='utf-8') as fp: | ||
| for line in fp: | ||
| try: | ||
| yield json.loads(line) | ||
| except json.decoder.JSONDecodeError as j: | ||
| yield {} | ||
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| def run_performance_analysis(deployments_to_validate=None, performance_spec=None, iterations=3): | ||
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| graph_deployment_spec_path = os.path.join(os.path.dirname(__file__), 'deployment_spec.yaml') | ||
| with open(graph_deployment_spec_path) as graph_deployment_spec_file: | ||
| deployment_spec = yaml.safe_load(graph_deployment_spec_file) | ||
| plater_performance_results = {} | ||
| for deployment in deployment_spec['deployments']: | ||
| deployment_env = deployment['deployment_environment'] | ||
| automat_url = deployment['automat_url'] | ||
| if not deployments_to_validate or deployment_env in deployments_to_validate: | ||
| print(f'Running performance analysis for environment: {deployment_env}') | ||
| for plater, query_details in performance_spec.items(): | ||
| if plater not in plater_performance_results: | ||
| plater_performance_results[plater] = {} | ||
| plater_performance_results[plater][deployment_env] = {} | ||
| url = automat_url + plater + "/" if "localhost" not in automat_url else automat_url | ||
| query_files = query_details["files"] | ||
| queries = query_details["queries"] if "queries" in query_details else None | ||
| for q_file in query_files: | ||
| for performance_query in quick_jsonl_file_iterator(f'./{q_file}'): | ||
| if not performance_query: | ||
| continue | ||
| query_name = performance_query.pop('name') | ||
| if queries and query_name not in queries: | ||
| continue | ||
| plater_performance_results[plater][deployment_env][query_name] = {'success_duration': [], | ||
| 'errors': []} | ||
| for i in range(iterations): | ||
| print(f'Sending query {query_name} to {deployment_env}: {plater}, iteration {i+1}') | ||
| start_time = time.time() | ||
| try: | ||
| trapi_response = send_trapi_query(url, | ||
| performance_query, | ||
| profile=False, | ||
| validate=False) | ||
| num_results = len(trapi_response['message']['results']) | ||
| # print(trapi_response) | ||
| duration = time.time() - start_time | ||
| print(f'Got back {num_results} in {duration}.') | ||
| plater_performance_results[plater][deployment_env][query_name]['success_duration'].append(duration) | ||
| except requests.exceptions.HTTPError as e: | ||
| duration = time.time() - start_time | ||
| print(f'Error occured after {duration} seconds: {e}.') | ||
| plater_performance_results[plater][deployment_env][query_name]['errors'].append(str(e)) | ||
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| average = sum(plater_performance_results[plater][deployment_env][query_name]['success_duration']) \ | ||
| / len(plater_performance_results[plater][deployment_env][query_name]['success_duration']) | ||
| print(f'Average time for {query_name} to {deployment_env}, {plater}: {average}') | ||
| with open(f'./performance_results/performance_analysis_results_{random.randrange(100000)}.json', 'w') as p_out: | ||
| p_out.write(json.dumps(plater_performance_results, indent=4)) | ||
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| if __name__ == '__main__': | ||
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| # environments = ['exp', 'dev', 'robokop'] | ||
| environments = ['robokop'] | ||
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| performance_spec = { | ||
| "robokopkg": {"files": ["./performance_queries/robokopkg_performance_queries.jsonl"], | ||
| "queries": ["gene_to_chemical_qualifier_40"]} | ||
| # "hmdb": {"files": ["./performance_queries/hmdb_performance_queries.jsonl"]} | ||
| } | ||
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| # to run for only certain environments | ||
| run_performance_analysis(environments, performance_spec, iterations=3) | ||
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| # or all of them | ||
| # run_performance_analysis() | ||
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| {"query_name":"hmdb_example_1", "message":{"query_graph":{"nodes":{"n0":{"categories":["biolink:Pathway"],"ids":["SMPDB:SMP0000044"]},"n1":{"categories":["biolink:SmallMolecule"]}},"edges":{"e01":{"subject":"n0","object":"n1","predicates":["biolink:has_participant"]}}}},"workflow":[{"id":"lookup"}]} |
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deploy/performance_queries/robokopkg_performance_queries.jsonl
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| {"name": "gene_to_chemical_1", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_5", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_10", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_20", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_30", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306", "NCBIGene:53637","NCBIGene:14396","NCBIGene:367","NCBIGene:1576","NCBIGene:3569","NCBIGene:2904","NCBIGene:338442","NCBIGene:2902","NCBIGene:59340","NCBIGene:5144"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_40", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306", "NCBIGene:53637","NCBIGene:14396","NCBIGene:367","NCBIGene:1576","NCBIGene:3569","NCBIGene:2904","NCBIGene:338442","NCBIGene:2902","NCBIGene:59340","NCBIGene:5144","NCBIGene:6531","NCBIGene:140","NCBIGene:2556","NCBIGene:3269","NCBIGene:3766","NCBIGene:774","NCBIGene:1813","NCBIGene:1903","NCBIGene:24947","NCBIGene:135"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_1", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_5", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_10", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_20", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_30", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306","NCBIGene:53637","NCBIGene:14396","NCBIGene:367","NCBIGene:1576","NCBIGene:3569","NCBIGene:2904","NCBIGene:338442","NCBIGene:2902","NCBIGene:59340","NCBIGene:5144"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
| {"name": "gene_to_chemical_qualifier_40", "message":{"query_graph":{"nodes":{"source":{"categories":["biolink:ChemicalEntity"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]},"i":{"ids":["NCBIGene:6868","NCBIGene:1557","NCBIGene:3738","NCBIGene:5141","NCBIGene:3754","NCBIGene:2908","NCBIGene:2350","NCBIGene:6573","NCBIGene:1723","NCBIGene:8698","NCBIGene:7099","NCBIGene:1565","NCBIGene:90134","NCBIGene:151","NCBIGene:148","NCBIGene:5150","NCBIGene:151306","NCBIGene:5142","NCBIGene:6532","NCBIGene:4306","NCBIGene:53637","NCBIGene:14396","NCBIGene:367","NCBIGene:1576","NCBIGene:3569","NCBIGene:2904","NCBIGene:338442","NCBIGene:2902","NCBIGene:59340","NCBIGene:5144","NCBIGene:6531","NCBIGene:140","NCBIGene:2556","NCBIGene:3269","NCBIGene:3766","NCBIGene:774","NCBIGene:1813","NCBIGene:1903","NCBIGene:24947","NCBIGene:135"],"categories":["biolink:Gene","biolink:Protein"],"set_interpretation":"BATCH","constraints":[],"member_ids":[]}},"edges":{"edge_1":{"subject":"source","object":"i","predicates":["biolink:affects"],"attribute_constraints":[],"qualifier_constraints":[{"qualifier_set":[{"qualifier_type_id":"biolink:object_aspect_qualifier","qualifier_value":"activity_or_abundance"},{"qualifier_type_id":"biolink:object_direction_qualifier","qualifier_value":"decreased"}]}]}}}},"bypass_cache":true,"submitter":"infores:aragorn"} | ||
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