diff --git a/EGA_curation/Import_BSD_API.py b/EGA_curation/Import_BSD_API.py new file mode 100644 index 0000000..f946b21 --- /dev/null +++ b/EGA_curation/Import_BSD_API.py @@ -0,0 +1,39 @@ +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]) + + +