mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Marek Vavrusa
43cd2083f6
this fixes an issue with when the Galaxy lib (and therefore working directory) is not shared with the compute nodes
144 lines
4.0 KiB
Python
Executable File
144 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 os
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import sys
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import errno
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import pwd
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import json
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#import drmaa
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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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import pkg_resources
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pkg_resources.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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