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Import Json from accession ID #2

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39 changes: 39 additions & 0 deletions EGA_curation/Import_BSD_API.py
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import sys


"""
With file with samples accession BSD ID, get all json files.
WARNING: remove EOF of AccessionFile
"""

def main(AccessionFile, AAP_USERNAME, AAP_PASSWORD):
af = open(AccessionFile, 'r')
file1 = open('Import_json.sh', 'w')
file1.write('#!/bin/bash' + '\n' + '\n')
BSD_ID = af.read().split('\n')
j = 0
file1.write("curl -u " + AAP_USERNAME + ":" + AAP_PASSWORD + " https://api.aai.ebi.ac.uk/auth > aap.jwt" + '\n')
file1.write('TOKEN=`cat aap.jwt`' + '\n' + '\n')
for i in range (0,len(BSD_ID)):
j+=1
if j != 999:
accession = BSD_ID[i]
accession = accession.replace('\r','')
file1.write("curl 'https://www.ebi.ac.uk/biosamples/samples/"+ accession + "'"+ " -X GET -H " + '"Content-Type: application/json;charset=UTF-8"'
+ ' -H ' + '"Accept: application/hal+json"' +' -H '+ '"Authorization: Bearer $TOKEN" ' + '>> Json_EGA_samples.txt' + '\n' + '\n' + 'echo -e ' +"'\n'"+ '>> Json_EGA_samples.txt' + '\n' + '\n')
else:
j = 0
file1.write("curl -u " + AAP_USERNAME + ":" + AAP_PASSWORD + " https://api.aai.ebi.ac.uk/auth > aap.jwt" + '\n')
file1.write('TOKEN=`cat aap.jwt`' + '\n' + '\n')
accession = BSD_ID[i]
accession = accession.replace('\r','')
file1.write("curl 'https://www.ebi.ac.uk/biosamples/samples/"+ accession + "'"+ " -X GET -H " + '"Content-Type: application/json;charset=UTF-8"'
+ ' -H ' + '"Accept: application/hal+json"' +' -H '+ '"Authorization: Bearer $TOKEN" ' + '>> Json_EGA_samples.txt' + '\n' + '\n' + 'echo -e ' +"'\n'"+ '>> Json_EGA_samples.txt' + '\n' + '\n')



if __name__ == "__main__":
main(sys.argv[1], sys.argv[2], sys.argv[3])