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added submit_def.py with example to run batch of 50

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Tanushree Tunstall 2021-02-11 14:36:32 +00:00
parent 91f214f014
commit e67a716d82
2 changed files with 144 additions and 3 deletions
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31
dynamut/submit.py
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@ -44,7 +44,7 @@ out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) +
#%% request calculation (no def)
with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb_file, open ("/home/tanu/git/LSHTM_analysis/dynamut/snp_test2.csv") as mutation_list:
with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb_file, open ("/home/tanu/git/LSHTM_analysis/dynamut/snp_test2.csv", "rb") as mutation_list:
files = {"wild": pdb_file
, "mutation_list": mutation_list}
body = {"chain": 'A'
@ -57,6 +57,7 @@ with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb
url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
url = host + url_match.group()
print(url)
#===============
# writing file: result urls
#===============
@ -90,7 +91,31 @@ def request_calculation(pdb_file, mutation_list
@param prediction_url: dynamut url for prediction
@type string
@return response object
@type object
@return txt file containing batch no. of snps processed
@type string
"""
with open(pdb_file, "rb") as pdb_file, open (mutation_list) as mutation_list:
files = {"wild": pdb_file
, "mutation_list": mutation_list}
body = {"chain": 'A'
, "email": 'tanushree.tunstall@lshtm.ac.uk'}
response = requests.post(prediction_url, files = files, data = body)
print(response.status_code)
if response.history:
print('PASS: valid mutation submitted. Fetching result url')
url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
url = host + url_match.group()
print(url)
#===============
# writing file: result urls
#===============
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
print('Writing output url file:', out_url_file)
myfile = open(out_url_file, 'a')
myfile.write(url)
myfile.close()
#====================
# Submit first batch