def getAllCidsForAssayActivity(activity):
url = ("http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/activity/" +
activity + "/aids/txt?list_return=listkey")
readfile.getresult(url)
# url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/listkey/"+listkey+"/cids/xml"
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/25425,12345/cids/xml"
print(("url: " + url))
xml = readfile.getresult(url)
# init parser
handler = DictHandler()
parser = sax.make_parser()
parser.setContentHandler(handler)
tempfile = open("tempfile", "w")
# handle the last line, there is sometimes some random output
lastline_arr = xml.split("\n")
# print(lastline_arr)
print("l: ")
print((len(lastline_arr)))
lastline = lastline_arr[len(lastline_arr) - 1]
print(("lastline: " + lastline))
print(("lastline-2: " + lastline_arr[len(lastline_arr) - 2]))
cidlastline = getIDofLine(lastline)
# aidkey = "-1"
if cidlastline != "-1":
i = len(lastline_arr) - 2
# search for nex aid entry
while i >= 0 and "AID" not in lastline_arr[i]:
i -= 1
# if i >= 0:
# aid = getIDofLine(lastline_arr[i])
# if aid != "-1":
# aidkey = aid
# remove the last line and put the array back together
lastline_arr_list = list(lastline_arr)
# lastline_arr_list.remove(lastline)
xml2 = "\n".join(lastline_arr_list)
tempfile.write(xml2)
# add the last tags
# tempfile.write("</Information></InformationList>")
tempfile.close()
parser.parse(open("tempfile", "r"))
dic = handler.ergebnis
# add the last line
# if cidlastline != "-1":
# dic[aidkey].append(cidlastline)
return dic
def getAllCidsForAssayActivity(activity):
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/activity/" + activity + "/aids/txt?list_return=listkey"
listkey = readfile.getresult(url)
# url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/listkey/"+listkey+"/cids/xml"
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/25425,12345/cids/xml"
print ("url: " + url)
xml = readfile.getresult(url)
# init parser
handler = DictHandler()
parser = sax.make_parser()
parser.setContentHandler(handler)
tempfile = open("tempfile", "w")
# handle the last line, there is sometimes some random output
lastline_arr = xml.split("\n")
# print(lastline_arr)
print ("l: ")
print (len(lastline_arr))
lastline = lastline_arr[len(lastline_arr) - 1]
print ("lastline: " + lastline)
print ("lastline-2: " + lastline_arr[len(lastline_arr) - 2])
cidlastline = getIDofLine(lastline)
aidkey = "-1"
if cidlastline != "-1":
i = len(lastline_arr) - 2
# search for nex aid entry
while i >= 0 and "AID" not in lastline_arr[i]:
i -= 1
if i >= 0:
aid = getIDofLine(lastline_arr[i])
if aid != "-1":
aidkey = aid
# remove the last line and put the array back together
lastline_arr_list = list(lastline_arr)
# lastline_arr_list.remove(lastline)
xml2 = "\n".join(lastline_arr_list)
tempfile.write(xml2)
# add the last tags
# tempfile.write("</Information></InformationList>")
tempfile.close()
parser.parse(open("tempfile", "r"))
dic = handler.ergebnis
# add the last line
# if cidlastline != "-1":
# dic[aidkey].append(cidlastline)
return dic
def main(args):
url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
if args.type == "assay":
url+="aid/"
elif args.type == "compound":
url+="cid/"
elif args.type == "substance":
url+="sid/"
if args.id_file is None:
idstring=str(args.id)
else:
idlist=readfile.getListFromFile(args.id_file)
idstring=",".join(idlist)
url+=idstring+"/"+args.operation+"/"
if args.operation == "property":
url+=args.property_value+"/"
if args.operation in csv_output:
url+="csv"
elif args.operation in txt_output:
url+="txt"
else:
url+="xml"
if args.operation in check_for_id_type and not args.id_type is None:
url+="?"+args.operation+"_type="+args.id_type
print('The constructed REST URL is: %s' % url)
data=readfile.getresult(url)
outfile=args.outfile
outfile.write(data)
outfile.close()
def main(args):
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/" + args.type + "/"
if args.type == "assay":
url += "aid/"
elif args.type == "compound":
url += "cid/"
elif args.type == "substance":
url += "sid/"
if args.id_file is None:
idstring = str(args.id)
else:
idlist = readfile.getListFromFile(args.id_file)
idstring = ",".join(idlist)
url += idstring + "/" + args.operation + "/"
if args.operation == "property":
url += args.property_value + "/"
if args.operation in csv_output:
url += "csv"
elif args.operation in txt_output:
url += "txt"
else:
url += "xml"
if args.operation in check_for_id_type and not args.id_type is None:
url += "?" + args.operation + "_type=" + args.id_type
print(url)
data = readfile.getresult(url)
outfile = args.outfile
outfile.write(data)
outfile.close()
def get_dict_key_value(url, key, value):
xml = readfile.getresult(url)
tmp = tempfile.TemporaryFile()
tmp.write(xml)
tmp.seek(0)
dic = dict_from_xml(tmp, key, value)
tmp.close()
return dic
def get_dict_key_value(url, key, value):
xml=readfile.getresult(url)
tmp = tempfile.TemporaryFile()
tmp.write(xml)
tmp.seek(0)
dic=dict_from_xml(tmp, key, value)
tmp.close()
return dic
def main(args):
#search for acitivity or target
url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/"
if args.activity is None:
#target
url+= "target/%s/%s" % ( args.targettype, args.targetid )
else:
url+="activity/"+args.activity
url+="/aids/txt"
data=readfile.getresult(url)
args.outfile.write(data)
args.outfile.close()
def get_dict_key_value(url, key, value):
"""
Get all ids from a XML file, obtained from the given URL
and convert the information into a dictionary
"""
xml = readfile.getresult(url)
tmp = tempfile.TemporaryFile()
tmp.write(xml)
tmp.seek(0)
dic = dict_from_xml(tmp, key, value)
tmp.close()
return dic
def get_dict_key_value(url, key, value):
"""
Get all ids from a XML file, obtained from the given URL
and convert the information into a dictionary
"""
xml = readfile.getresult(url)
tmp = tempfile.TemporaryFile()
tmp.write(xml)
tmp.seek(0)
dic = dict_from_xml(tmp, key, value)
tmp.close()
return dic
def getAllAssayIDs():
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/all/aids/TXT"
data = readfile.getresult(url)
self.keywertlist = readfile.getListFromString(data)
return self.keywertlist
def getAllAssayIDs():
url = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/type/all/aids/TXT"
data = readfile.getresult(url)
aidlist = readfile.getListFromString(data)
return aidlist