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# Download ENA records so that we can discover newly uploaded data
# 2025-04-12
# Hui
import os
import sys
import time
import shutil
from configure import TEMP_DIR, UPDATE_NETWORK_LOG_FILE
from log import write_log_file
from configure import INFO_DIR
accession = 3702 # arabidopsis
types = ['read_run', 'read_experiment', 'sample', 'study']
for t in types:
url = f'https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession={accession}&result={t}'
print(url)
if not os.path.exists(TEMP_DIR):
sys.exit()
cmd = 'wget "%s" -O %s' % (url, os.path.join(TEMP_DIR, 'ena_'+t+'.xml')) # save XML data to file
os.system(cmd)
time.sleep(5)
for t in types:
fname = os.path.join(TEMP_DIR, 'ena_'+t+'.xml')
if os.path.exists(fname):
print(f'Move {fname} to {INFO_DIR}')
shutil.move(fname, INFO_DIR)
time.sleep(5)
write_log_file('[download_ena_records.py] ENA records updated. Check folder %s' % (INFO_DIR), UPDATE_NETWORK_LOG_FILE)
#https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=read_run
#https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=read_experiment
#https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=sample
#https://www.ebi.ac.uk/ena/browser/api/xml/links/taxon?accession=3702&result=study
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