https://github.com/galaxyproject/galaxy
Tip revision: 565e8b9c7b427af2347581e33732e5356cb3136c authored by Daniel Blankenberg on 22 April 2015, 18:36:36 UTC
Fix for abitrary code execution in the ToolShed when uploaded tools
Fix for abitrary code execution in the ToolShed when uploaded tools
Tip revision: 565e8b9
import.py
#!/usr/bin/env python
"""
Script that imports locally stored data as a new dataset for the user
Usage: import id outputfile
"""
import sys, os
assert sys.version_info[:2] >= ( 2, 4 )
BUFFER = 1048576
dataid = sys.argv[1]
out_name = sys.argv[2]
id2name = {
'eryth' : 'ErythPreCRMmm3_cusTrk.txt',
'cishg16' : 'ReglRegHBBhg16CusTrk.txt',
'cishg17' : 'ReglRegHBBhg17CusTrk.txt',
'exons' : 'ExonsKnownGenes_mm3.txt',
'krhg16' : 'known_regulatory_hg16.bed',
'krhg17' : 'known_regulatory_hg17.bed',
'tARhg16mmc' : 'hg16.mouse.t_AR.cold.bed',
'tARhg16mmm' : 'hg16.mouse.t_AR.medium.bed',
'tARhg16mmh' : 'hg16.mouse.t_AR.hot.bed',
'tARhg16rnc' : 'hg16.rat.t_AR.cold.bed',
'tARhg16rnm' : 'hg16.rat.t_AR.medium.bed',
'tARhg16rnh' : 'hg16.rat.t_AR.hot.bed',
'phastConsHg16' : 'phastConsMost_hg16.bed',
'omimhg16' : 'omimDisorders_hg16.tab',
'omimhg17' : 'omimDisorders_hg17.tab',
}
fname = id2name.get(dataid, '')
if not fname:
print 'Importing invalid data %s' % dataid
sys.exit()
else:
print 'Imported %s' % fname
# this path is hardcoded
inp_name = os.path.join('database', 'import', fname)
try:
inp = open(inp_name, 'rt')
except:
print 'Could not find file %s' % inp_name
sys.exit()
out = open(out_name, 'wt')
while 1:
data = inp.read(BUFFER)
if not data:
break
out.write(data)
inp.close()
out.close()