def newExperiment(explog_path, plan_json=''):
'''Create Experiment record'''
folder = os.path.dirname(explog_path)
# Test if Experiment object already exists
try:
newExp = models.Experiment.objects.get(unique=folder)
except:
newExp = None
if newExp is None:
# Parse the explog.txt file
text = load_log_path(explog_path)
explog = parse_log(text)
explog["planned_run_short_id"] = '' # don't allow getting plan by shortId - other plans may exist with that id
try:
planObj, expObj, easObj = get_planned_exp_objects(explog,folder)
newExp = update_exp_objects_from_log(explog,folder, planObj, expObj, easObj)
if plan_json:
update_plan_info(plan_json, planObj, easObj)
except:
newExp = None
print traceback.format_exc()
return newExp
def newExperiment(explog_path):
'''Create Experiment record'''
# Parse the explog.txt file
text = load_log_path(explog_path)
dict = parse_log(text)
# Create the Experiment Record
folder = os.path.dirname(explog_path)
# Test if Experiment object already exists
try:
newExp = models.Experiment.objects.get(unique=folder)
except:
newExp = None
if newExp is None:
try:
expArgs,st = exp_kwargs(dict,folder)
newExp = models.Experiment(**expArgs)
newExp.save()
except:
newExp = None
print traceback.format_exc()
return newExp
def newExperiment(explog_path):
'''Create Experiment record'''
# Parse the explog.txt file
text = load_log_path(explog_path)
dict = parse_log(text)
# Create the Experiment Record
folder = os.path.dirname(explog_path)
# Test if Experiment object already exists
try:
newExp = models.Experiment.objects.get(unique=folder)
except:
newExp = None
if newExp is None:
try:
expArgs, st = exp_kwargs(dict, folder)
newExp = models.Experiment(**expArgs)
newExp.save()
except:
newExp = None
print traceback.format_exc()
return newExp
def newExperiment(_explog_path, _plan_json=''):
'''Create Experiment record'''
folder = os.path.dirname(_explog_path)
# Test if Experiment object already exists
try:
_newExp = models.Experiment.objects.get(unique=folder)
print("DEBUG: Experiment exists in database: %s" % folder)
except:
print("DEBUG: Experiment does not exist in database")
_newExp = None
if _newExp is None:
# Parse the explog.txt file
text = load_log_path(_explog_path)
explog = parse_log(text)
explog[
"planned_run_short_id"] = '' # don't allow getting plan by shortId - other plans may exist with that id
try:
ret_val = generate_updateruninfo_post(folder, logger)
if ret_val == "Generated POST":
# Get experiment object
exp_set = models.Experiment.objects.filter(unique=folder)
if exp_set:
# Experiment object exists in database
_newExp = exp_set[0]
else:
print(
"ERROR: Could not update/generate new Experiment record in database"
)
print(ret_val)
return None
# Append to expName to indicate imported dataset.
_newExp.expName += "_foreign"
chefLog_parsed = isChefInfoAvailable(folder)
if chefLog_parsed:
update_chefSummary(_newExp, chefLog_parsed)
_newExp.save()
if _plan_json:
planObj = _newExp.plan
easObj = _newExp.get_EAS()
update_plan_info(_plan_json, planObj, easObj)
except:
print("DEBUG: There was an error adding the experiment")
_newExp = None
print(traceback.format_exc())
return _newExp
def newExperiment(_explog_path, _plan_json=''):
'''Create Experiment record'''
folder = os.path.dirname(_explog_path)
# Test if Experiment object already exists
try:
_newExp = models.Experiment.objects.get(unique=folder)
print("DEBUG: Experiment exists in database: %s" % folder)
except:
print("DEBUG: Experiment does not exist in database")
_newExp = None
if _newExp is None:
# Parse the explog.txt file
text = load_log_path(_explog_path)
explog = parse_log(text)
explog[
"planned_run_short_id"] = '' # don't allow getting plan by shortId - other plans may exist with that id
try:
ret_val = generate_updateruninfo_post(folder, logger)
if ret_val == "Generated POST":
# Get experiment object
exp_set = models.Experiment.objects.filter(unique=folder)
if exp_set:
# Experiment object exists in database
_newExp = exp_set[0]
else:
print("ERROR: Could not update/generate new Experiment record in database")
print(ret_val)
return None
# Append to expName to indicate imported dataset.
_newExp.expName += "_foreign"
chefLog_parsed = isChefInfoAvailable(folder)
if chefLog_parsed:
update_chefSummary(_newExp, chefLog_parsed)
_newExp.save()
except:
print("DEBUG: There was an error adding the experiment")
_newExp = None
print(traceback.format_exc())
if _plan_json:
update_plan_info(_plan_json, _newExp.plan, _newExp.get_EAS())
return _newExp
def newExperiment(_explog_path, _plan_json=""):
"""Create Experiment record"""
folder = os.path.dirname(_explog_path)
# Test if Experiment object already exists
try:
_newExp = models.Experiment.objects.get(unique=folder)
print "DEBUG: Experiment exists in database: %s" % (folder)
except:
print "DEBUG: Experiment does not exist in database"
_newExp = None
if _newExp is None:
# Parse the explog.txt file
text = load_log_path(_explog_path)
explog = parse_log(text)
explog["planned_run_short_id"] = "" # don't allow getting plan by shortId - other plans may exist with that id
try:
ret_val = generate_updateruninfo_post(folder, logger)
if ret_val == "Generated POST":
# Get experiment object
exp_set = models.Experiment.objects.filter(unique=folder)
if exp_set:
# Experiment object exists in database
_newExp = exp_set[0]
else:
print "ERROR: Could not update/generate new Experiment record in database"
print ret_val
return None
# Append to expName to indicate imported dataset.
_newExp.expName += "_foreign"
_newExp.save()
if _plan_json:
planObj = _newExp.plan
easObj = _newExp.get_EAS()
update_plan_info(_plan_json, planObj, easObj)
except:
print "DEBUG: There was an error adding the experiment"
_newExp = None
print traceback.format_exc()
return _newExp
#!/usr/bin/env python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved
'''Parses explog.txt and explog_final.txt'''
from ion.utils.explogparser import load_log_path
from ion.utils.explogparser import parse_log
explog_path = "./explog.txt"
# Parse the explog.txt file
text = load_log_path(explog_path)
dict = parse_log(text)
#NOTE: keywords will have spaces replaced with underscores and all letters lowercased.
keywords = [
"experimenterrorlog",
"experimentinfolog",
"explog_done",
"experiment_name",
"f",
]
for key,value in dict.items():
if any(key.startswith(item) for item in keywords):
print "(%s) ==> %s" % (key, value)
#!/usr/bin/env python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved
'''Parses explog.txt and explog_final.txt'''
from ion.utils.explogparser import load_log_path
from ion.utils.explogparser import parse_log
explog_path = "./explog.txt"
# Parse the explog.txt file
text = load_log_path(explog_path)
dict = parse_log(text)
#NOTE: keywords will have spaces replaced with underscores and all letters lowercased.
keywords = [
"experimenterrorlog",
"experimentinfolog",
"explog_done",
"experiment_name",
"f",
]
for key, value in dict.items():
if any(key.startswith(item) for item in keywords):
print "(%s) ==> %s" % (key, value)
