def process(self, **kwargs):
output_dir = self.project_dir
if BLredis.get('SMX') =='0':
file_to_link = 'CORRECT.LP_hsymm'
elif BLredis.get('SMX') == '1':
return
src = os.path.join(output_dir, file_to_link)
dst = os.path.join(output_dir, 'CORRECT.LP')
try:
os.symlink(src, dst)
except:
print "warning, %s to %s symlink could not be made" % (src, dst)
def run_xdsme(self, extra):
hostname = socket.gethostname().split('.')[0]
args = get_xdsme_commandline(hostname)
if int(BLredis.get('SMX')) == 1:
args.extend(['--index_refine'])
args.extend(['-p', self.output.project])
if self.XDS_INPUT:
args.extend(['-i', ' '.join(self.XDS_INPUT)])
if self.p1:
sg, cell = self.__get_cell_and_sg()
args.extend(['-s', sg])
args.extend(['-c', cell])
args.extend(self.args)
args.extend(extra)
args.extend(self.output.images)
if args[0] in ['xdsme', 'nice']:
call(args, cwd=self.base_dir)
else:
labels=dict(
epn=mxvars.EPN,
project=self.output.project,
xds="master")
try:
jib_request = dict(labels=labels, working_dir=self.base_dir, hostname=hostname.lower())
call(args, stderr=STDOUT, env={"JIB_REQUEST":json.dumps(jib_request)})
except CalledProcessError as e:
print 'call error output and returncode', e.output, e.returncode
os.makedirs(newdir)
os.symlink(newdir, 'AR')
except EnvironmentError:
pass
else:
print "Something funny happened while trying to figure out the unique dir. Not parsing this file"
print runall()
sys.exit()
newkey = 'shelx:trigger'
correct_file = "CORRECT.LP_hsymm"
table_header = "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION"
table_offest = 4 #start of data
table_size = 14 #total table size
if redis.get(newkey):
print 'clear redis anom key'
print redis.get(newkey)
redis.set(newkey, json.dumps('off'))
else:
print "redis was empty"
redis.set(newkey, json.dumps('off'))
anon_cutoff = 15
anon_col = 11
res_col = 0
get_number = lambda x: int(re.sub(r'[^-\d.]+', '', x))
# get table from correct file
try:
from beamline import redis
import pickle
import pandas as pd
# for getting the COVID pdbs off redis and into a spreadsheet
redpickle = redis.get('eleanor:covid_pdb_getter:something')
cov_data = pickle.loads(redpickle)
# convert dataframe to csv
cov_data.to_csv(r"Rapid_access_PDBs_2020.csv", header=True, index=False)
Setup(suffix='retrigger', detector=blconfig.detector_type),
XDSme(base, base, '-a', subtype='r'), po,
Aimless(base),
AimlessPlot(base),
AimlessScalePlot(base),
CountOverloads(base),
XDSme('p1', 'p1', '-5', '-a', p1=True),
XDSme(base + '_NOANOM', base + '_NOANOM', '-5'),
Truncate(base),
LinkCorrect(base),
Autorickshaw(base),
RunSpreadsheetCalculator(base)
]
from beamline import redis as BLredis
if int(BLredis.get('SMX')) == 1:
if blconfig.detector_type == 'eiger': #TODO get this information from collection object
delphi = 'DELPHI=15'
else:
delphi = 'DELPHI=45'
p1n = 'p1_noscale'
hsn = 'hsymm_noscale'
po = Pointless(base, nonchiral=True)
default = [
Setup(suffix='process', detector=blconfig.detector_type),
CornerResolution(base),
XDSme(base, base, '-a', '-i', delphi, subtype='p'), po,
Aimless(base),