def run_test(server_base_url, delayed_jobs_server_base_path):
"""
Tests that getting the data of a context
:param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
:param delayed_jobs_server_base_path: base path for the delayed_jobs
"""
print('-------------------------------------------')
print('Testing getting the data of a context')
print('-------------------------------------------')
job_id = utils.submit_similarity_search_job(delayed_jobs_server_base_path)
utils.wait_until_job_finished(delayed_jobs_server_base_path, job_id)
print('Now going to load this context')
context_params = {
'delayed_jobs_base_url': delayed_jobs_server_base_path,
'context_type': 'SIMILARITY',
'context_id': f'{job_id}'
}
url = f'{server_base_url}/contexts/get_context_data'
request = requests.post(url, data=context_params)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
def run_test(server_base_url, delayed_jobs_server_base_path):
"""
Tests that parsing a search term works
:param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
:param delayed_jobs_server_base_path: base path for the delayed_jobs
"""
print('-------------------------------------------')
print('Testing parsing s search')
print('-------------------------------------------')
term_params = {
'search_term':
'MDCK',
'es_indexes':
'chembl_molecule,chembl_target,chembl_assay,chembl_document,chembl_cell_line,chembl_tissue',
}
url = f'{server_base_url}/search_parsing/parse_free_text_search'
request = requests.post(url, data=term_params)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
def run_test(server_base_url, delayed_jobs_server_base_path):
"""
Tests that a simple query to elasticsearch
:param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
:param delayed_jobs_server_base_path: base path for the delayed_jobs
"""
print('-------------------------------------------')
print('Testing a simple query')
print('-------------------------------------------')
print('delayed_jobs_server_base_path: ', delayed_jobs_server_base_path)
url = utils.get_url_for_get_es_data(server_base_url)
print('url: ', url)
index_name = 'chembl_molecule'
print('index_name: ', index_name)
es_query = {
"size": 24,
"from": 0,
"query": {
"bool": {
"must": [
{"query_string": {"analyze_wildcard": True, "query": "*"}}
],
"filter": []
}
},
"sort": []
}
print('es_query: ', es_query)
payload = {
'index_name': index_name,
'es_query': json.dumps(es_query)
}
request = requests.post(url, data=payload)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
response_json = request.json()
hits = response_json['es_response']['hits']['hits']
assert len(hits) > 0, 'I should have gotten hits!'
def run_test(server_base_url, delayed_jobs_server_base_path):
"""
Tests that a url can be shortened
:param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
:param delayed_jobs_server_base_path: base path for the delayed_jobs
"""
print('-------------------------------------------')
print('Testing the url shortening')
print('-------------------------------------------')
print('delayed_jobs_server_base_path: ', delayed_jobs_server_base_path)
url = f'{server_base_url}/url_shortening/shorten_url'
print('url: ', url)
long_url = '#substructure_search_results/C[C@H](CCc1ccccc1)NC[C@H](O)c1ccc(O)c(C(N)=O)c1'
payload = {
"long_url": long_url
}
request = requests.post(url, data=payload)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
response_json = request.json()
url_hash = response_json.get('hash')
assert url_hash is not None, 'The url hash was not returned!'
expansion_url = f'{server_base_url}/url_shortening/expand_url/{url_hash}'
request = requests.get(expansion_url)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
time.sleep(5) # make it sleep to make sure the url is saved in ES
response_json = request.json()
long_url_got = response_json.get('long_url')
assert long_url == long_url_got, 'The long url was not obtained!'
def run_test(server_base_url, delayed_jobs_server_base_path):
"""
Tests that a simple query to elasticsearch
:param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
:param delayed_jobs_server_base_path: base path for the delayed_jobs
"""
print('-------------------------------------------')
print('Testing a es_query with context')
print('-------------------------------------------')
job_id = utils.submit_similarity_search_job(delayed_jobs_server_base_path)
utils.wait_until_job_finished(delayed_jobs_server_base_path, job_id)
print('Now going to make a request with this context')
url = utils.get_url_for_get_es_data(server_base_url)
print('url: ', url)
es_query = {
"size": 24,
"from": 0,
"query": {
"bool": {
"must": [{
"query_string": {
"analyze_wildcard": 'true',
"query": "*"
}
}],
"filter": []
}
},
"sort": []
}
context_obj = {
"delayed_jobs_base_url":
delayed_jobs_server_base_path,
"context_type":
"SIMILARITY",
"context_id":
"STRUCTURE_SEARCH-V4s_piFIe9FL7sOuJ0jl6U0APMEsoV-b4HfFE_dtojc=",
}
payload = {
'index_name': 'chembl_molecule',
'es_query': json.dumps(es_query),
'context_obj': json.dumps(context_obj),
'contextual_sort_data': {},
}
print('payload: ', payload)
request = requests.post(url, data=payload)
status_code = request.status_code
print(f'status_code: {status_code}')
response_text = request.text
utils.print_es_response(response_text)
assert status_code == 200, 'The request failed!'
response_json = request.json()
hits = response_json['es_response']['hits']['hits']
assert len(hits) > 0, 'I should have gotten hits!'
metadata = response_json['metadata']
print('metadata: ', metadata)
assert metadata['total_results'] > 0, 'There should be more than 0 results!'