mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +08:00
Nicola Soranzo
a353b2e88f
using: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 . ```
110 lines
5.7 KiB
Python
Executable File
110 lines
5.7 KiB
Python
Executable File
#!/usr/bin/env python
|
|
"""
|
|
Fetch jobs using gops_intersect, gops_merge, gops_subtract, gops_complement, gops_coverage
|
|
wherein the second dataset doesn't have chr, start and end in standard columns 1, 2 and 3.
|
|
"""
|
|
import ConfigParser
|
|
import os
|
|
import sys
|
|
import tempfile
|
|
|
|
import sqlalchemy as sa
|
|
|
|
import galaxy.app
|
|
import galaxy.model.mapping
|
|
|
|
assert sys.version_info[:2] >= (2, 4)
|
|
|
|
|
|
class TestApplication(object):
|
|
"""Encapsulates the state of a Universe application"""
|
|
def __init__(self, database_connection=None, file_path=None):
|
|
print >> sys.stderr, "python path is: " + ", ".join(sys.path)
|
|
if database_connection is None:
|
|
raise Exception("CleanupDatasetsApplication requires a database_connection value")
|
|
if file_path is None:
|
|
raise Exception("CleanupDatasetsApplication requires a file_path value")
|
|
self.database_connection = database_connection
|
|
self.file_path = file_path
|
|
# Setup the database engine and ORM
|
|
self.model = galaxy.model.mapping.init(self.file_path, self.database_connection, engine_options={}, create_tables=False)
|
|
|
|
|
|
def main():
|
|
ini_file = sys.argv[1]
|
|
conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
|
|
conf_parser.read(ini_file)
|
|
configuration = {}
|
|
for key, value in conf_parser.items("app:main"):
|
|
configuration[key] = value
|
|
database_connection = configuration['database_connection']
|
|
file_path = configuration['file_path']
|
|
app = TestApplication(database_connection=database_connection, file_path=file_path)
|
|
jobs = {}
|
|
try:
|
|
for job in app.model.Job.filter(sa.and_(app.model.Job.table.c.create_time.between('2008-05-23', '2008-11-29'),
|
|
app.model.Job.table.c.state == 'ok',
|
|
sa.or_(sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_intersect_1',
|
|
app.model.Job.table.c.tool_id == 'gops_subtract_1',
|
|
app.model.Job.table.c.tool_id == 'gops_coverage_1'),
|
|
sa.not_(app.model.Job.table.c.command_line.like('%-2 1,2,3%'))),
|
|
sa.and_(sa.or_(app.model.Job.table.c.tool_id == 'gops_complement_1',
|
|
app.model.Job.table.c.tool_id == 'gops_merge_1'),
|
|
sa.not_(app.model.Job.table.c.command_line.like('%-1 1,2,3%')))))).all():
|
|
print "# processing job id %s" % str(job.id)
|
|
for jtoda in job.output_datasets:
|
|
print "# --> processing JobToOutputDatasetAssociation id %s" % str(jtoda.id)
|
|
hda = app.model.HistoryDatasetAssociation.get(jtoda.dataset_id)
|
|
print "# ----> processing HistoryDatasetAssociation id %s" % str(hda.id)
|
|
if not hda.deleted:
|
|
# Probably don't need this check, since the job state should suffice, but...
|
|
if hda.dataset.state == 'ok':
|
|
history = app.model.History.get(hda.history_id)
|
|
print "# ------> processing history id %s" % str(history.id)
|
|
if history.user_id:
|
|
cmd_line = str(job.command_line)
|
|
new_output = tempfile.NamedTemporaryFile('w')
|
|
if job.tool_id in ['gops_intersect_1', 'gops_subtract_1', 'gops_coverage_1']:
|
|
new_cmd_line = " ".join(map(str, cmd_line.split()[:4])) + " " + new_output.name + " " + " ".join(map(str, cmd_line.split()[5:]))
|
|
job_output = cmd_line.split()[4]
|
|
else:
|
|
new_cmd_line = " ".join(map(str, cmd_line.split()[:3])) + " " + new_output.name + " " + " ".join(map(str, cmd_line.split()[4:]))
|
|
job_output = cmd_line.split()[3]
|
|
try:
|
|
os.system(new_cmd_line)
|
|
except:
|
|
pass
|
|
diff_status = os.system('diff %s %s >> /dev/null' % (new_output.name, job_output))
|
|
if diff_status == 0:
|
|
continue
|
|
print "# --------> Outputs differ"
|
|
user = app.model.User.get(history.user_id)
|
|
jobs[job.id] = {}
|
|
jobs[job.id]['hda_id'] = hda.id
|
|
jobs[job.id]['hda_name'] = hda.name
|
|
jobs[job.id]['hda_info'] = hda.info
|
|
jobs[job.id]['history_id'] = history.id
|
|
jobs[job.id]['history_name'] = history.name
|
|
jobs[job.id]['history_update_time'] = history.update_time
|
|
jobs[job.id]['user_email'] = user.email
|
|
except Exception as e:
|
|
print "# caught exception: %s" % str(e)
|
|
|
|
print "\n\n# Number of incorrect Jobs: %d\n\n" % (len(jobs))
|
|
print "#job_id\thda_id\thda_name\thda_info\thistory_id\thistory_name\thistory_update_time\tuser_email"
|
|
for jid in jobs:
|
|
print '%s\t%s\t"%s"\t"%s"\t%s\t"%s"\t"%s"\t%s' % \
|
|
(str(jid),
|
|
str(jobs[jid]['hda_id']),
|
|
jobs[jid]['hda_name'],
|
|
jobs[jid]['hda_info'],
|
|
str(jobs[jid]['history_id']),
|
|
jobs[jid]['history_name'],
|
|
jobs[jid]['history_update_time'],
|
|
jobs[jid]['user_email'])
|
|
sys.exit(0)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
main()
|