mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Nicola Soranzo
142 lines
4.0 KiB
Python
Executable File
142 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Submit a DRMAA job given a user id and a job template file (in JSON format)
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defining any or all of the following: args, remoteCommand, outputPath,
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errorPath, nativeSpecification, name, email, project
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"""
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import errno
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import json
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import os
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import pwd
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import sys
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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from galaxy import eggs
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eggs.require("drmaa")
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import drmaa
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DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification',
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'workingDirectory', 'jobName', 'email', 'project' ]
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def load_job_template_from_file(jt, filename):
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f = open(filename, 'r')
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data = json.load(f)
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for attr in DRMAA_jobTemplate_attributes:
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if attr in data:
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setattr(jt, attr, data[attr])
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def valid_numeric_userid(userid):
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try:
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uid = int(userid)
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except:
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return False
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try:
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pwd.getpwuid(uid)
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except KeyError:
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sys.stderr.write("error: User-ID (%d) is not valid.\n" % uid)
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exit(1)
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return True
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def get_user_id_by_name(username):
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try:
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pw = pwd.getpwnam(username)
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except KeyError:
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sys.stderr.write("error: User name (%s) is not valid.\n" % username)
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exit(1)
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return pw.pw_uid
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def json_file_exists(json_filename):
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if not os.path.exists(json_filename):
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sys.stderr.write("error: JobTemplate file (%s) doesn't exist\n" % ( json_filename ) )
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exit(1)
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return True
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def validate_paramters():
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assign_all_groups = False
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if "--assign_all_groups" in sys.argv:
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assign_all_groups = True
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sys.argv.remove("--assign_all_groups")
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if len(sys.argv) < 3:
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sys.stderr.write("usage: %s [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n" % sys.argv[0])
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exit(1)
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userid = sys.argv[1]
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json_filename = sys.argv[2]
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if valid_numeric_userid(userid):
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uid = int(userid)
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else:
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uid = get_user_id_by_name(userid)
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if uid == 0:
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sys.stderr.write("error: userid must not be 0 (root)\n")
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exit(1)
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return uid, json_filename, assign_all_groups
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def set_user(uid, assign_all_groups):
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try:
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# Get user's default group and set it to current process to make sure file permissions are inherited correctly
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# Solves issue with permission denied for JSON files
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gid = pwd.getpwuid(uid).pw_gid
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import grp
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os.setgid(gid)
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if assign_all_groups:
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# Added lines to assure read/write permission for groups
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user = pwd.getpwuid(uid).pw_name
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groups = [g.gr_gid for g in grp.getgrall() if user in g.gr_mem]
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os.setgroups(groups)
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os.setuid(uid)
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except OSError, e:
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if e.errno == errno.EPERM:
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sys.stderr.write( "error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid )
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exit(1)
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else:
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pass
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if os.getuid() == 0:
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sys.stderr.write( "error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n" )
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exit(1)
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if os.geteuid() == 0:
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sys.stderr.write( "error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n" )
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exit(1)
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def main():
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userid, json_filename, assign_all_groups = validate_paramters()
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set_user(userid, assign_all_groups)
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json_file_exists(json_filename)
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# Added to disable LSF generated messages that would interfer with this
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# script. Fix thank to Chong Chen at IBM.
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os.environ['BSUB_QUIET'] = 'Y'
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s = drmaa.Session()
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s.initialize()
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jt = s.createJobTemplate()
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load_job_template_from_file(jt, json_filename)
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# runJob will raise if there's a submittion error
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jobId = s.runJob(jt)
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s.deleteJobTemplate(jt)
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s.exit()
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# Print the Job-ID and exit. Galaxy will pick it up from there.
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print jobId
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if __name__ == "__main__":
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main()
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