def create_structure(self):
"""
Creates the necessary model input data in the database to ingest against.
:return: An integer representing the replication created.
"""
myrun = DimRun()
myrun.name = "AUTO SCOTTY TEST RUN"
myrun.models_key_id = 1
myrun.save()
mychannel = DimChannel.objects.get(pk=228441)
myrun.dimchannel_set.add(mychannel)
myex = DimExecution()
myex.run_key_id = myrun.id
myex.save()
myrep = DimReplication()
myrep.execution_key_id = myex.id
myrep.seed_used = 99
myrep.series_id = 100
myrep.save()
self.model_input.append([myrun.id, myex.id, myrep.id, mychannel.id])
return myrep.id
def __init__(self, zip_file=None, execid=None, seriesid=None, chan_list=None, msg=None):
"""
This init method will take several arguments and use those to ingest data into the vecnet-CI datawarehouse
This takes a zip file (the path to the zip file), execid, seriesid, and chan_list. Given this information,
this ingester will create a replication, and then fill that replication with the data in the zip file. If
execid and/or seriesid are not specified, the filename is assumed to be of the type "REPID-XXXX.zip" where
the replication id will be parsed from the file name.
:param str zip_file: A path to a zip file on the file system.
:raises TypeError: When any file address is not of type str
:raises ObjectDoesNotExist: When the replication_id given does not exist in the data warehouse
"""
self.FileList = dict()
self.DataList = dict()
self.alreadyIngested = None
# the files needed by EMOD
self.FILES_OF_INTEREST = ('DemographicsSummary', 'VectorSpeciesReport', 'InsetChart', 'BinnedReport')
# create a unique temporary directory for the needed files
self.BASE_PATH = os.path.sep + 'tmp'
self.temporary_path = self.BASE_PATH + os.path.sep + str(uuid.uuid4())
# get the replication ID from the filename. filename is expected to be of the following format
# path/to/file/file_name-replication_number.zip
if not execid and not seriesid:
replication_id = int(os.path.basename(zip_file).strip(".zip").split("-")[1])
try:
self.replication = DimReplication.objects.get(pk=replication_id)
except:
raise ObjectDoesNotExist('No replication with id %s is available in the DB' % replication_id)
else:
execution = DimExecution.objects.filter(pk=execid)
if not execution.exists():
raise ObjectDoesNotExist("No execution with id %s is available in the DB" % execid)
replication = execution[0].dimreplication_set.filter(series_id=seriesid)
if not replication.exists():
replication = DimReplication(
execution_key=execution[0],
series_id=seriesid,
seed_used=-1
)
replication.save()
self.replication = replication
else:
self.replication = replication[0]
if zip_file is None:
if msg is None:
msg = "An error has occurred during the processing of this replication"
self.set_status(-1, msg)
return
input_files = self.unpack_files(zip_file)
VSRF = input_files['VectorSpeciesReport'] if 'VectorSpeciesReport' in input_files else ''
DSF = input_files['DemographicsSummary'] if 'DemographicsSummary' in input_files else ''
ICF = input_files['InsetChart'] if 'InsetChart' in input_files else ''
BRF = input_files['BinnedReport'] if 'BinnedReport' in input_files else ''
if not isinstance(VSRF, str):
raise TypeError('VSRF must be a string containing the file address to the VSRF')
elif VSRF is not '':
self.FileList['VectorSpeciesReport'] = VSRF
if not isinstance(DSF, str):
raise TypeError('DSF must be a string containing the file address to the DSF')
elif DSF is not '':
self.FileList['DemographicsSummary'] = DSF
if not isinstance(ICF, str):
raise TypeError('ICF must be a string containing the file address to the ICF')
elif ICF is not '':
self.FileList['InsetChart'] = ICF
if not isinstance(BRF, str):
raise TypeError('BRF must be a string containing the file address to the BRF')
elif BRF is not '':
self.FileList['BinnedReport'] = BRF
# -------------- Grab the channel listing and other objects needed for the ingester
# replication = DimReplication.objects.filter(pk=replication_id)
# if not replication.exists():
# raise ObjectDoesNotExist('Replication with id %s does not exist' % replication_id)
# replication = replication[0]
self.run = self.replication.execution_key.run_key
# Attach CSV output for non-sweep runs only
if self.run.numjobs() == 1:
convert_to_csv(self.temporary_path)
filename = os.path.join(self.temporary_path, "output.csv.zip")
csv_file = SimulationInputFile.objects.create_file(contents=open(filename, "rb").read(),
name="output.csv.zip",
created_by_id=1)
self.run.csv_output = csv_file
self.run.save()
if self.run.models_key.model != 'EMOD':
raise ValueError("Target Run is not EMOD during EMOD submission!")
if chan_list is not None and isinstance(chan_list, list):
chans = DimChannel.objects.filter(pk__in=chan_list)
if not chans.exists():
raise ObjectDoesNotExist('No channels were found with IDs %s' % chan_list)
new_chans = [self.run.dimchannel_set.add(channel) for channel in chans]
if len(new_chans) != len(chans):
print "WARNING: Not all channels in list were ingested"
self.run.save()
else:
chans = self.run.dimchannel_set.all()
self.Channel_dict = dict()
for channel in chans:
if channel.file_name not in self.Channel_dict:
self.Channel_dict[channel.file_name] = list()
self.Channel_dict[channel.file_name].append(channel)
self.Channel_dict['VectorSpeciesReport'] = list()
self.alreadyIngested = BaseFactData.objects.filter(
run_key=self.run,
replication_key=self.replication
).distinct('channel_key')
self.alreadyIngested = [data.channel_key for data in self.alreadyIngested]
# self.Channel_list = [x.file_name for x in chans]
# Setup class variables
self.fact_data_name = 'fact_data_run_%s' % self.run.id
self.cursor = connections['default'].cursor()
self.cursor.execute("select nextval('base_fact_data_id_seq');")
self.next_id = int(self.cursor.fetchone()[0])
def handle(self, *args, **options):
print "BEGIN TEST"
# Create execution, replication, and run
myrun = DimRun()
myrun.name = "AUTO SCOTTY TEST RUN"
myrun.models_key_id = 1
myrun.save()
mychannel = DimChannel.objects.get(pk=228441)
myrun.dimchannel_set.add(mychannel)
myex = DimExecution()
myex.run_key_id = myrun.id
myex.save()
myrep = DimReplication()
myrep.execution_key_id = myex.id
myrep.seed_used = 99
myrep.series_id = 100
myrep.save()
replication_number = myrep.id
print "REPLICATION NUMBER", replication_number
print "CHANNEL NUMBER", mychannel.id
print "RUN NUMBER", myrun.id
print "EXECUTION NUMBER", myex.id
# rename the test zip_file
oldfilename = options['filename']
oldlist = oldfilename.split(".")
newfilename = oldlist[0] + "-" + str(replication_number) + "." + oldlist[1]
shutil.copyfile(oldfilename, newfilename)
# make sure this replication output data doesn't already exist
results = [i for i in BaseFactData.objects.filter(replication_key_id=replication_number,
channel_key_id=mychannel.id, run_key_id=myrun.id)]
count = len(results)
if count != 0:
print "There currently exists data in BaseFactData for the chosen replication, channel, and run." \
"Please choose a replication, channel, and run which have not previously been ingested."
# Curl the files to AutoScotty
print "Beam us up, Scotty.\nAye, Sir."
print "File: ", newfilename
f = open(newfilename, 'rb')
files = {'zip_file': f}
urlname = options['urlname']
model_type = options['modeltype']
if options['hashname']:
r = requests.post(urlname, files=files, data={'model_type': model_type, 'sync': True,
'zip_file_hash': options['hashname']})
else:
myhash = hashlib.sha1()
myhash.update(f.read())
f.seek(0)
r = requests.post(urlname, files=files, data={'model_type': model_type, 'sync': True,
'zip_file_hash': myhash.hexdigest()})
# remove the temporary copy of the file
os.remove(newfilename)
if r.status_code != 200:
print "There was an ingestion error at the server. The HTTP Response code is: ", r.status_code
print "Please check the celery and apache logs on the server to determine the source of the error."
# fetch the ingested results
results = BaseFactData.objects.filter(replication_key_id=replication_number, channel_key_id=mychannel.id,
run_key_id=myrun.id).aggregate(Count("timestep"))
count = results['timestep__count']
if count == 10950:
print "The anticipated number of entries in BaseFactData were present. The data was successfully ingested."
else:
print "The count of " + str(count) + " is not the expected number of entries. Please make sure channel " \
"228441 exists, and that you used the 'autoscottytest.zip' file."
# remove the ingested data
BaseFactData.objects.filter(replication_key_id=replication_number, channel_key_id=mychannel.id,
run_key_id=myrun.id).delete()
myrun.dimchannel_set.remove(mychannel)
myrep.delete()
myex.delete()
myrun.delete()
# make sure data was deleted
results = BaseFactData.objects.filter(replication_key_id=replication_number, channel_key_id=mychannel.id,
run_key_id=myrun.id).aggregate(Count("timestep"))
count = results['timestep__count']
if count == 0:
print "The data was successfully purged."
else:
print "There was an error removing the ingested data. There are still entries in BaseFactData " \
"corresponding to your replication, channel, and run. Please see the server logs and the database " \
"administrator for assistance."
# return response
print "Live long and prosper."