__author__ = 'Artur Cieslewicz'
import json
import os
import xml.etree.ElementTree as ET
import initials
defs = initials.defaults()
def getJsonKeys(jsonArg, tabDelimiter):
result = ""
if isinstance(jsonArg, dict):
tabD = tabDelimiter + '\t'
for key, value in jsonArg.iteritems():
result += tabDelimiter + key + '\n'
if isinstance(value, dict):
result += getJsonKeys(value, tabD)
if isinstance(value, list):
for item in value:
result += getJsonKeys(item, tabD)
return result
def getShortJsonKeys(jsonArg, tabDelimiter):
result = ""
if isinstance(jsonArg, dict):
tabD = tabDelimiter + '\t'
for key, value in jsonArg.iteritems():
result += tabDelimiter + key + '\n'
if isinstance(value, dict):
__author__ = 'Jakub Dutkiewicz'
from os import listdir
from initials import defaults
import xml.etree.ElementTree as ET
import json
import urllib2
defs = defaults()
working_dir = defs.root + defs.xmldocs
for i, file in enumerate(listdir(working_dir)):
if i % 10 == 0:
print i
xmlTree = ET.parse(working_dir + '/' + file).getroot()
for c in xmlTree:
if c.tag == 'METADATA':
jsonTree = json.loads(c.text)
try:
geo_acc_link = 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=' + jsonTree[
'dataItem']['geo_accession']
geoaccess = 1
response = urllib2.urlopen(geo_acc_link)
html = response.read()
oFile = open(
defs.root + defs.geohtmls + '/' + file.split('.')[0] +
'_geo.html', 'w+')
oFile.write(html)
oFile.close()
except:
geoaccess = 0