def fix():
# initialize databases
module_dir = os.path.dirname(os.path.abspath(__file__))
snl_f = os.path.join(module_dir, 'snl.yaml')
snldb = SNLMongoAdapter.from_file(snl_f)
snl = snldb.snl
snlgroups = snldb.snlgroups
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
tasks_f = os.path.join(module_dir, 'tasks.yaml')
with open(tasks_f) as f2:
task_creds = yaml.load(f2)
mc = MongoClient(task_creds['host'], task_creds['port'])
db = mc[task_creds['database']]
db.authenticate(task_creds['admin_user'], task_creds['admin_password'])
tasks = db['tasks']
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
fws = lpdb.fireworks
launches = lpdb.launches
sb_f = os.path.join(module_dir, 'submission.yaml')
sbdb = SubmissionMongoAdapter.from_file(sb_f)
submissions = sbdb.jobs
bad_crystal_ids = []
crystals_file = os.path.join(module_dir, 'bad_crystals.txt')
with open(crystals_file) as f:
for line in f:
bad_crystal_ids.append(int(line.strip()))
for c_id in bad_crystal_ids:
if c_id == 100892 or c_id == 100202:
print 'SKIP'
else:
# FIX SNL
for s in snl.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snl_id': 1}):
snl.update({'snl_id': s['snl_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SNLGROUPS
for s in snlgroups.find({'canonical_snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'snlgroup_id': 1}):
snlgroups.update({'snlgroup_id': s['snlgroup_id']}, {'$pushAll': {"canonical_snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 1
for s in fws.find({'spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX FWs pt 2
for s in fws.find({'spec.force_mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'fw_id': 1}):
fws.update({'fw_id': s['fw_id']}, {'$pushAll': {"spec.force_mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX Launches
for s in launches.find({'action.update_spec.mpsnl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'launch_id': 1}):
launches.update({'launch_id': s['launch_id']}, {'$pushAll': {"action.update_spec.mpsnl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX TASKS
for s in tasks.find({'snl.about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'task_id': 1}):
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
tasks.update({'task_id': s['task_id']}, {'$pushAll': {"snl_final.about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
# FIX SUBMISSIONS
for s in submissions.find({'about._materialsproject.deprecated.crystal_id_deprecated': c_id}, {'submission_id': 1}):
submissions.update({'submission_id': s['submission_id']}, {'$pushAll': {"about.remarks": ['DEPRECATED', 'SEVERE BUG IN ICSD CONVERSION']}})
print 'FIXED', c_id
import json
import os
from fireworks.core.launchpad import LaunchPad
from mpworks.submission.submission_mongo import SubmissionMongoAdapter
from pymatgen.matproj.snl import StructureNL
__author__ = 'Anubhav Jain'
__copyright__ = 'Copyright 2014, The Materials Project'
__version__ = '0.1'
__maintainer__ = 'Anubhav Jain'
__email__ = '*****@*****.**'
__date__ = 'Jan 24, 2014'
if __name__ == "__main__":
sma = SubmissionMongoAdapter.from_file('submission.yaml')
module_dir = os.path.dirname(os.path.abspath(__file__))
lp_f = os.path.join(module_dir, 'my_launchpad.yaml')
lpdb = LaunchPad.from_file(lp_f)
for s in os.listdir(os.path.join(module_dir, "snls")):
if '.json' in s:
print 'submitting', s
with open(os.path.join(module_dir, "snls",s)) as f:
snl = StructureNL.from_dict(json.load(f))
sma.submit_snl(snl, '*****@*****.**', {"priority": 10})
print 'DONE submitting', s
print 'DONE!'
