def main():
redis_lock = RedisLock(lock_obj)
args = Args()
args.parse_args()
if args.status:
print_status(redis_lock)
return
# Inclusion of 'status' operator forces positional arguments to be optional even though they
# are conceptually required. Make sure that they are specified.
if args.action is None or args.target is None:
print("Usage:\t ./lock_queue.py <action> <target>")
return
action = args.action
target = args.target
if target == 'all':
action += '_all'
target = None
else:
target = {'key': target}
if target is not None:
t = target['key']
if redis_lock.get(t) is None:
print("Unable to locate '{}'\nAvailable queues:".format(t))
for key in redis_lock.get_all():
print("\t{}".format(key))
return
func = getattr(redis_lock, action)
# if kwargs exist pass kwargs else pass empty param set
# Allows for parameterization of foo(required_param) and bar().
func(**(target or {}))
print_status(redis_lock)
def main():
args = Args()
args.parse_args()
override = args.override
logger = logging.getLogger('Ingest_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + 'Ingest.log')
print("Log File: {}Ingest.log".format(pds_log))
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info("Starting Ingest Process")
PDSinfoDICT = json.load(open(pds_info, 'r'))
RQ_main = RedisQueue('Ingest_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ_main.id_name: '1'})
RQ_work = RedisQueue('Ingest_WorkQueue')
RQ_upc = RedisQueue('UPC_ReadyQueue')
RQ_thumb = RedisQueue('Thumbnail_ReadyQueue')
RQ_browse = RedisQueue('Browse_ReadyQueue')
logger.info("UPC Queue: %s", RQ_upc.id_name)
logger.info("Thumbnail Queue: %s", RQ_thumb.id_name)
logger.info("Browse Queue: %s", RQ_browse.id_name)
try:
session, engine = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
return 1
index = 1
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
RQ_work.QueueAdd(inputfile)
subfile = inputfile.replace(PDSinfoDICT[archive]['path'], '')
# Calculate checksum in chunks of 4096
f_hash = hashlib.md5()
with open(inputfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
filechecksum = f_hash.hexdigest()
QOBJ = session.query(Files).filter_by(filename=subfile).first()
runflag = False
if QOBJ is None or filechecksum != QOBJ.checksum:
runflag = True
if runflag or override:
date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
fileURL = inputfile.replace(archive_base, web_base)
# If all upc requirements are in 'inputfile,' flag for upc
upcflag = all(x in inputfile
for x in PDSinfoDICT[archive]['upc_reqs'])
filesize = os.path.getsize(inputfile)
try:
# If we found an existing file and want to overwrite the data
if QOBJ is not None and override:
ingest_entry = QOBJ
# If the file was not found, create a new entry
else:
ingest_entry = Files()
ingest_entry.archiveid = PDSinfoDICT[archive]['archiveid']
ingest_entry.filename = subfile
ingest_entry.entry_date = date
ingest_entry.checksum = filechecksum
ingest_entry.upc_required = upcflag
ingest_entry.validation_required = True
ingest_entry.header_only = False
ingest_entry.release_date = date
ingest_entry.file_url = fileURL
ingest_entry.file_size = filesize
ingest_entry.di_pass = True
ingest_entry.di_date = date
session.merge(ingest_entry)
session.flush()
if upcflag:
RQ_upc.QueueAdd((inputfile, ingest_entry.fileid, archive))
RQ_thumb.QueueAdd(
(inputfile, ingest_entry.fileid, archive))
RQ_browse.QueueAdd(
(inputfile, ingest_entry.fileid, archive))
#RQ_pilotB.QueueAdd((inputfile,ingest_entry.fileid, archive))
RQ_work.QueueRemove(inputfile)
index = index + 1
except Exception as e:
logger.error("Error During File Insert %s : %s", str(subfile),
str(e))
elif not runflag and not override:
RQ_work.QueueRemove(inputfile)
logger.warn(
"Not running ingest: file %s already present"
" in database and no override flag supplied", inputfile)
if index >= 250:
try:
session.commit()
logger.info("Commit 250 files to Database: Success")
index = 1
except Exception as e:
session.rollback()
logger.warn("Unable to commit to database: %s", str(e))
else:
logger.info("No Files Found in Ingest Queue")
try:
session.commit()
logger.info("Commit to Database: Success")
except Exception as e:
logger.error("Unable to commit to database: %s", str(e))
session.rollback()
# Close connection to database
session.close()
engine.dispose()
if RQ_main.QueueSize() == 0 and RQ_work.QueueSize() == 0:
logger.info("Process Complete All Queues Empty")
elif RQ_main.QueueSize() == 0 and RQ_work.QueueSize() != 0:
logger.warning("Process Done Work Queue NOT Empty Contains %s Files",
str(RQ_work.QueueSize()))
logger.info("Ingest Complete")
def main():
# Connect to database - ignore engine information
pds_session, pds_engine = db_connect(pds_db)
# Connect to database - ignore engine information
session, upc_engine = db_connect(upc_db)
# ***************** Set up logging *****************
logger = logging.getLogger('UPC_Process')
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
PDSinfoDICT = json.load(open(pds_info, 'r'))
# Redis Queue Objects
RQ_main = RedisQueue('UPC_ReadyQueue')
logger.info("UPC Processing Queue: %s", RQ_main.id_name)
RQ_lock = RedisLock(lock_obj)
# If the queue isn't registered, add it and set it to "running"
RQ_lock.add({RQ_main.id_name: '1'})
proc_date_tid = get_tid('processdate', session)
err_type_tid = get_tid('errortype', session)
err_msg_tid = get_tid('errormessage', session)
err_flag_tid = get_tid('error', session)
isis_footprint_tid = get_tid('isisfootprint', session)
isis_centroid_tid = get_tid('isiscentroid', session)
start_time_tid = get_tid('starttime', session)
stop_time_tid = get_tid('stoptime', session)
checksum_tid = get_tid('checksum', session)
# while there are items in the redis queue
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
# get a file from the queue
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
#inputfile = (RQ_main.QueueGet()).decode('utf-8')
if os.path.isfile(inputfile):
pass
else:
print("{} is not a file\n".format(inputfile))
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
# @TODO refactor this logic. We're using an object to find a path, returning it,
# then passing it back to the object so that the object can use it.
recipeOBJ = Recipe()
recipe_json = recipeOBJ.getRecipeJSON(archive)
#recipe_json = recipeOBJ.getRecipeJSON(getMission(str(inputfile)))
recipeOBJ.AddJsonFile(recipe_json, 'upc')
infile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCinput.cub'
outfile = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '.UPCoutput.cub'
caminfoOUT = workarea + os.path.splitext(
str(os.path.basename(inputfile)))[0] + '_caminfo.pvl'
EDRsource = inputfile.replace(
'/pds_san/PDS_Archive/',
'https://pdsimage.wr.ugs.gov/Missions/')
status = 'success'
# Iterate through each process listed in the recipe
for item in recipeOBJ.getProcesses():
# If any of the processes failed, discontinue processing
if status.lower() == 'error':
break
elif status.lower() == 'success':
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
# Handle processing based on string description.
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'thmproc':
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
thmproc_odd = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.odd.cub'
thmproc_even = str(workarea) + str(
os.path.splitext(os.path.basename(inputfile))
[0]) + '.UPCoutput.raw.even.cub'
elif item == 'handmos':
processOBJ.updateParameter('from_', thmproc_even)
processOBJ.updateParameter('mosaic', thmproc_odd)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'cubeatt':
band_infile = infile + '+' + str(1)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
elif item == 'footprintinit':
processOBJ.updateParameter('from_', infile)
elif item == 'caminfo':
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', caminfoOUT)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
pwd = os.getcwd()
# iterate through functions listed in process obj
for k, v in processOBJ.getProcess().items():
# load a function into func
func = getattr(isis, k)
try:
os.chdir(workarea)
# execute function
func(**v)
os.chdir(pwd)
if item == 'handmos':
if os.path.isfile(thmproc_odd):
os.rename(thmproc_odd, infile)
else:
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
if '2isis' in item:
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
elif item == 'thmproc':
pass
elif item == 'handmos':
label = pvl.load(infile)
infile_bandlist = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
infile_centerlist = label['IsisCube'][
'BandBin']['Center']
except ProcessError as e:
print(e)
status = 'error'
processError = item
# keyword definitions
keywordsOBJ = None
if status.lower() == 'success':
try:
keywordsOBJ = UPCkeywords(caminfoOUT)
except:
with open(caminfoOUT, 'r') as f:
filedata = f.read()
filedata = filedata.replace(';', '-').replace('&', '-')
filedata = re.sub(r'\-\s+', r'', filedata, flags=re.M)
with open(caminfoOUT, 'w') as f:
f.write(filedata)
keywordsOBJ = UPCkeywords(caminfoOUT)
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == keywordsOBJ.getKeyword(
'TargetName').upper()).first()
instrument_Qobj = session.query(upc_models.Instruments).filter(
upc_models.Instruments.instrument ==
keywordsOBJ.getKeyword('InstrumentId')).first()
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first() is None:
test_input = upc_models.DataFiles(
isisid=keywordsOBJ.getKeyword('IsisId'),
productid=keywordsOBJ.getKeyword('ProductId'),
edr_source=EDRsource,
edr_detached_label='',
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(test_input)
session.commit()
Qobj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == keywordsOBJ.getKeyword(
'IsisId')).first()
UPCid = Qobj.upcid
print(UPCid)
# block to add band information to meta_bands
if isinstance(infile_bandlist, list):
index = 0
while index < len(infile_bandlist):
B_DBinput = upc_models.MetaBands(
upcid=UPCid,
filter=str(infile_bandlist[index]),
centerwave=infile_centerlist[index])
session.merge(B_DBinput)
index = index + 1
else:
try:
# If infile_centerlist is in "Units" format, grab the value
f_centerlist = float(infile_centerlist[0])
except TypeError:
f_centerlist = float(infile_centerlist)
B_DBinput = upc_models.MetaBands(upcid=UPCid,
filter=infile_bandlist,
centerwave=f_centerlist)
session.merge(B_DBinput)
session.commit()
# Block to add common keywords
testjson = json.load(open(keyword_def, 'r'))
for element_1 in testjson['instrument']['COMMON']:
keyvalue = ""
keytype = testjson['instrument']['COMMON'][element_1][
'type']
keyword = testjson['instrument']['COMMON'][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid == 1)).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into table\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
for element_1 in testjson['instrument'][archive]:
keyvalue = ""
keytype = testjson['instrument'][archive][element_1][
'type']
keyword = testjson['instrument'][archive][element_1][
'keyword']
keyword_Qobj = session.query(upc_models.Keywords).filter(
and_(
upc_models.Keywords.typename == element_1,
upc_models.Keywords.instrumentid.in_(
(1, instrument_Qobj.instrumentid)))).first()
if keyword_Qobj is None:
continue
else:
keyvalue = keywordsOBJ.getKeyword(keyword)
if keyvalue is None:
logger.debug("Keyword %s not found", keyword)
continue
keyvalue = db2py(keytype, keyvalue)
try:
DBinput = upc_models.create_table(
keytype,
upcid=UPCid,
typeid=keyword_Qobj.typeid,
value=keyvalue)
except Exception as e:
logger.warn("Unable to enter %s into database\n\n%s",
keytype, e)
continue
session.merge(DBinput)
try:
session.flush()
except:
logger.warn("Unable to flush database connection")
session.commit()
# geometry stuff
G_centroid = 'point ({} {})'.format(
str(keywordsOBJ.getKeyword('CentroidLongitude')),
str(keywordsOBJ.getKeyword('CentroidLatitude')))
G_keyword_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isiscentroid').first()
G_footprint_Qobj = session.query(
upc_models.Keywords.typeid).filter(
upc_models.Keywords.typename ==
'isisfootprint').first()
G_footprint = keywordsOBJ.getKeyword('GisFootprint')
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_keyword_Qobj,
value=G_centroid)
session.merge(G_DBinput)
G_DBinput = upc_models.MetaGeometry(upcid=UPCid,
typeid=G_footprint_Qobj,
value=G_footprint)
session.merge(G_DBinput)
session.flush()
session.commit()
f_hash = hashlib.md5()
with open(inputfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
DBinput = upc_models.MetaString(upcid=UPCid,
typeid=checksum_tid,
value=checksum)
session.merge(DBinput)
DBinput = upc_models.MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=False)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, True)
os.remove(infile)
os.remove(caminfoOUT)
elif status.lower() == 'error':
try:
label = pvl.load(infile)
except Exception as e:
logger.info('%s', e)
continue
date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
if '2isis' in processError or processError == 'thmproc':
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source ==
EDRsource.decode("utf-8")).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
error1_input = upc_models.DataFiles(
isisid='1', edr_source=EDRsource)
session.merge(error1_input)
session.commit()
EQ1obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.edr_source == EDRsource).first()
UPCid = EQ1obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
session.commit()
else:
try:
label = pvl.load(infile)
except Exception as e:
logger.warn('%s', e)
continue
isisSerial = getISISid(infile)
if session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid ==
isisSerial).first() is None:
target_Qobj = session.query(upc_models.Targets).filter(
upc_models.Targets.targetname == str(
label['IsisCube']['Instrument']
['TargetName']).upper()).first()
instrument_Qobj = session.query(
upc_models.Instruments).filter(
upc_models.Instruments.instrument == str(
label['IsisCube']['Instrument']
['InstrumentId'])).first()
if target_Qobj is None or instrument_Qobj is None:
continue
error2_input = upc_models.DataFiles(
isisid=isisSerial,
productid=label['IsisCube']['Archive']
['ProductId'],
edr_source=EDRsource,
instrumentid=instrument_Qobj.instrumentid,
targetid=target_Qobj.targetid)
session.merge(error2_input)
session.commit()
try:
EQ2obj = session.query(upc_models.DataFiles).filter(
upc_models.DataFiles.isisid == isisSerial).first()
UPCid = EQ2obj.upcid
errorMSG = 'Error running {} on file {}'.format(
processError, inputfile)
DBinput = MetaTime(upcid=UPCid,
typeid=proc_date_tid,
value=date)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_type_tid,
value=processError)
session.merge(DBinput)
DBinput = MetaString(upcid=UPCid,
typeid=err_msg_tid,
value=errorMSG)
session.merge(DBinput)
DBinput = MetaBoolean(upcid=UPCid,
typeid=err_flag_tid,
value=True)
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_footprint_tid,
value='POINT(361 0)')
session.merge(DBinput)
DBinput = MetaGeometry(upcid=UPCid,
typeid=isis_centroid_tid,
value='POINT(361 0)')
session.merge(DBinput)
except:
pass
try:
v = label['IsisCube']['Instrument']['StartTime']
except KeyError:
v = None
except:
continue
try:
DBinput = MetaTime(upcid=UPCid,
typeid=start_time_tid,
value=v)
session.merge(DBinput)
except:
continue
try:
v = label['IsisCube']['Instrument']['StopTime']
except KeyError:
v = None
DBinput = MetaTime(upcid=UPCid,
typeid=stop_time_tid,
value=v)
session.merge(DBinput)
session.commit()
AddProcessDB(pds_session, fid, False)
os.remove(infile)
# Disconnect from db sessions
pds_session.close()
session.close()
# Disconnect from the engines
pds_engine.dispose()
upc_engine.dispose()
logger.info("UPC processing exited successfully")
def main():
args = Args()
args.parse_args()
key = args.key
namespace = args.namespace
if namespace is None:
namespace is default_namespace
workarea = scratch + args.key + '/'
RQ_file = RedisQueue(key + '_FileQueue', namespace)
RQ_work = RedisQueue(key + '_WorkQueue', namespace)
RQ_zip = RedisQueue(key + '_ZIP', namespace)
RQ_loggy = RedisQueue(key + '_loggy', namespace)
RQ_final = RedisQueue('FinalQueue', namespace)
RHash = RedisHash(key + '_info')
RHerror = RedisHash(key + '_error')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({'MAP':'1'})
if int(RQ_file.QueueSize()) == 0 and RQ_lock.available('MAP'):
print("No Files Found in Redis Queue")
else:
jobFile = RQ_file.Qfile2Qwork(
RQ_file.getQueueName(), RQ_work.getQueueName()).decode('utf-8')
# Setup system logging
basename = os.path.splitext(os.path.basename(jobFile))[0]
logger = logging.getLogger(key + '.' + basename)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + '/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting MAP Processing')
loggyOBJ = Loggy(basename)
# File Naming
infile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.input.cub'
outfile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.output.cub'
# Recipe Stuff
RQ_recipe = RedisQueue(key + '_recipe')
status = 'success'
for element in RQ_recipe.RecipeGet():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
process = processOBJ.JSON2Process(element)
if 'gdal_translate' not in processOBJ.getProcessName():
if 'cubeatt-band' in processOBJ.getProcessName():
if '+' in jobFile:
processOBJ.updateParameter('from_', jobFile)
processOBJ.updateParameter('to', outfile)
processOBJ.ChangeProcess('cubeatt')
else:
continue
elif 'map2map' in processOBJ.getProcessName():
if '+' in jobFile:
processOBJ.updateParameter('from_', infile)
else:
processOBJ.updateParameter('from_', jobFile)
processOBJ.updateParameter('to', outfile)
elif 'cubeatt-bit' in processOBJ.getProcessName():
if RHash.OutBit().decode('utf-8') == 'unsignedbyte':
temp_outfile = outfile + '+lsb+tile+attached+unsignedbyte+1:254'
elif RHash.OutBit().decode('utf-8') == 'signedword':
temp_outfile = outfile + '+lsb+tile+attached+signedword+-32765:32765'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', temp_outfile)
processOBJ.ChangeProcess('cubeatt')
elif 'isis2pds' in processOBJ.getProcessName():
# finalfile = infile.replace('.input.cub', '_final.img')
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.img'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', finalfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
print(processOBJ.getProcess())
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
subloggyOBJ = SubLoggy(k)
try:
func(**v)
logger.info('Process %s :: Success', k)
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
except ProcessError as e:
logger.error('Process %s :: Error', k)
logger.error(e)
status = 'error'
eSTR = 'Error Executing ' + k + \
' Standard Error: ' + str(e)
RHerror.addError(os.path.splitext(
os.path.basename(jobFile))[0], eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
else:
GDALcmd = ""
for process, v, in processOBJ.getProcess().items():
subloggyOBJ = SubLoggy(process)
GDALcmd += process
for key, value in v.items():
GDALcmd += ' ' + key + ' ' + value
img_format = RHash.Format().decode('utf-8')
if img_format == 'GeoTiff-BigTiff':
fileext = 'tif'
elif img_format == 'GeoJPEG-2000':
fileext = 'jp2'
elif img_format == 'JPEG':
fileext = 'jpg'
elif img_format == 'PNG':
fileext = 'png'
elif img_format == 'GIF':
fileext = 'gif'
logGDALcmd = GDALcmd + ' ' + basename + '.input.cub ' + RHash.getMAPname().decode('utf-8') + '.' + fileext
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.' + fileext
GDALcmd += ' ' + infile + ' ' + finalfile
print(GDALcmd)
try:
subprocess.call(GDALcmd, shell=True)
logger.info('Process GDAL translate :: Success')
status = 'success'
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'www.gdal.org/gdal_translate.html')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
os.remove(infile)
except OSError as e:
logger.error('Process GDAL translate :: Error')
logger.error(e)
status = 'error'
RHerror.addError(os.path.splitext(os.path.basename(jobFile))[0],
'Process GDAL translate :: Error')
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
subloggyOBJ.errorOut(e)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if status == 'success':
if RHash.Format().decode('utf-8') == 'ISIS3':
finalfile = workarea + RHash.getMAPname().decode('utf-8') + '.cub'
shutil.move(infile, finalfile)
if RHash.getStatus() != b'ERROR':
RHash.Status('SUCCESS')
try:
RQ_zip.QueueAdd(finalfile)
logger.info('File Added to ZIP Queue')
except:
logger.error('File NOT Added to ZIP Queue')
try:
RQ_loggy.QueueAdd(loggyOBJ.Loggy2json())
logger.info('JSON Added to Loggy Queue')
except:
logger.error('JSON NOT Added to Loggy Queue')
RQ_work.QueueRemove(jobFile)
elif status == 'error':
RHash.Status('ERROR')
if os.path.isfile(infile):
os.remove(infile)
if RQ_file.QueueSize() == 0 and RQ_work.QueueSize() == 0:
try:
RQ_final.QueueAdd(key)
logger.info('Key %s Added to Final Queue: Success', key)
logger.info('Job Complete')
except:
logger.error('Key NOT Added to Final Queue')
else:
logger.warning('Queues Not Empty: filequeue = %s work queue = %s', str(
RQ_file.QueueSize()), str(RQ_work.QueueSize()))
def main():
# pdb.set_trace()
PDSinfoDICT = json.load(open(pds_info, 'r'))
# ********* Set up logging *************
logger = logging.getLogger('DI_Process')
logger.setLevel(logging.INFO)
#logFileHandle = logging.FileHandler('/usgs/cdev/PDS/logs/DI.log')
logFileHandle = logging.FileHandler(pds_log + 'DI.log')
#logFileHandle = logging.FileHandler('/home/arsanders/PDS-Pipelines/logs/DI.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting DI Process')
try:
session, engine = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except:
logger.error('DataBase Connection: Error')
RQ = RedisQueue('DI_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ.id_name: '1'})
index = 0
while int(RQ.QueueSize()) > 0 and RQ_lock.available(RQ.id_name):
item = literal_eval(RQ.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
try:
Qelement = session.query(Files).filter(
Files.filename == inputfile).one()
except:
logger.error('Query for File: %s', inputfile)
archive_path = PDSinfoDICT[archive]['path']
cpfile = archive_path + Qelement.filename
if os.path.isfile(cpfile):
f_hash = hashlib.md5()
with open(cpfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
if checksum == Qelement.checksum:
Qelement.di_pass = True
else:
Qelement.di_pass = False
Qelement.di_date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
session.flush()
index = index + 1
if index > 50:
session.commit()
logger.info('Session Commit for 50 Records: Success')
index = 0
else:
logger.error('File %s Not Found', cpfile)
try:
session.commit()
logger.info("End Commit DI process to Database: Success")
index = 1
except:
session.rollback()
# Close connection to database
session.close()
engine.dispose()
def main():
PDSinfoDICT = json.load(open(pds_info, 'r'))
args = Args()
args.parse_args()
# Set up logging
logger = logging.getLogger('DI_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + 'DI.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting DI Process')
try:
session, engine = db_connect(pds_db)
logger.info('DataBase Connecton: Success')
except Exception as e:
logger.error('DataBase Connection Error: %s', str(e))
return 1
RQ = RedisQueue('DI_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ.id_name: '1'})
index = 0
logger.info("DI Queue: %s", RQ.id_name)
while int(RQ.QueueSize()) > 0 and RQ_lock.available(RQ.id_name):
item = literal_eval(RQ.QueueGet().decode("utf-8"))
inputfile = item[0]
archive = item[1]
try:
Qelement = session.query(Files).filter(
Files.filename == inputfile).one()
except Exception as e:
logger.warn('Filename query failed for inputfile %s: %s',
inputfile, str(e))
continue
archive_path = PDSinfoDICT[archive]['path']
cpfile = archive_path + Qelement.filename
if os.path.isfile(cpfile):
f_hash = hashlib.md5()
with open(cpfile, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
f_hash.update(chunk)
checksum = f_hash.hexdigest()
Qelement.di_pass = checksum == Qelement.checksum
Qelement.di_date = datetime.datetime.now(
pytz.utc).strftime("%Y-%m-%d %H:%M:%S")
session.flush()
index = index + 1
if index > 50:
session.commit()
logger.info('Session Commit for 50 Records: Success')
index = 0
else:
logger.warn('File %s Not Found', cpfile)
try:
session.commit()
logger.info("End Commit DI process to Database: Success")
index = 1
except Exception as e:
logger.warn("Unable to commit changes to database\n\n%s", e)
session.rollback()
# Close connection to database
session.close()
engine.dispose()
def main():
args = Args()
args.parse_args()
key = args.key
namespace = args.namespace
if namespace is None:
namespace is default_namespace
workarea = scratch + key + '/'
RQ_file = RedisQueue(key + '_FileQueue', namespace)
RQ_work = RedisQueue(key + '_WorkQueue', namespace)
RQ_zip = RedisQueue(key + '_ZIP', namespace)
RQ_loggy = RedisQueue(key + '_loggy', namespace)
RQ_final = RedisQueue('FinalQueue', namespace)
RHash = RedisHash(key + '_info')
RHerror = RedisHash(key + '_error')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({'POW': '1'})
if int(RQ_file.QueueSize()) == 0 and RQ_lock.available('POW'):
print("No Files Found in Redis Queue")
else:
print(RQ_file.getQueueName())
jobFile = RQ_file.Qfile2Qwork(RQ_file.getQueueName(),
RQ_work.getQueueName()).decode('utf-8')
# Setup system logging
basename = os.path.splitext(os.path.basename(jobFile))[0]
logger = logging.getLogger(key + '.' + basename)
logger.setLevel(logging.INFO)
logFileHandle = logging.FileHandler(pds_log + '/Service.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
logger.info('Starting POW Processing')
# set up loggy
loggyOBJ = Loggy(basename)
# File Naming
if '+' in jobFile:
bandSplit = jobFile.split('+')
inputFile = bandSplit[0]
else:
inputFile = jobFile
infile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.input.cub'
outfile = workarea + \
os.path.splitext(os.path.basename(jobFile))[0] + '.output.cub'
RQ_recipe = RedisQueue(key + '_recipe')
status = 'success'
for element in RQ_recipe.RecipeGet():
if status == 'error':
break
elif status == 'success':
processOBJ = Process()
process = processOBJ.JSON2Process(element)
if 'gdal_translate' not in processOBJ.getProcessName():
print(processOBJ.getProcessName())
if '2isis' in processOBJ.getProcessName():
processOBJ.updateParameter('from_', inputFile)
processOBJ.updateParameter('to', outfile)
elif 'cubeatt-band' in processOBJ.getProcessName():
if '+' in jobFile:
infileB = infile + '+' + bandSplit[1]
processOBJ.updateParameter('from_', infileB)
processOBJ.updateParameter('to', outfile)
processOBJ.ChangeProcess('cubeatt')
else:
continue
elif 'cubeatt-bit' in processOBJ.getProcessName():
if RHash.OutBit() == b'unsignedbyte':
temp_outfile = outfile + '+lsb+tile+attached+unsignedbyte+1:254'
elif RHash.OutBit() == b'signedword':
temp_outfile = outfile + '+lsb+tile+attached+signedword+-32765:32765'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', temp_outfile)
processOBJ.ChangeProcess('cubeatt')
elif 'spice' in processOBJ.getProcessName():
processOBJ.updateParameter('from_', infile)
elif 'ctxevenodd' in processOBJ.getProcessName():
label = pvl.load(infile)
SS = label['IsisCube']['Instrument']['SpatialSumming']
print(SS)
if SS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'mocevenodd' in processOBJ.getProcessName():
label = pvl.load(infile)
CTS = label['IsisCube']['Instrument'][
'CrosstrackSumming']
print(CTS)
if CTS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'mocnoise50' in processOBJ.getProcessName():
label = pvl.load(infile)
CTS = label['IsisCube']['Instrument'][
'CrosstrackSumming']
if CTS != 1:
continue
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif 'cam2map' in processOBJ.getProcessName():
processOBJ.updateParameter('from', infile)
processOBJ.updateParameter('to', outfile)
if RHash.getGRtype() == 'smart' or RHash.getGRtype(
) == 'fill':
subloggyOBJ = SubLoggy('cam2map')
camrangeOUT = workarea + basename + '_camrange.txt'
isis.camrange(from_=infile, to=camrangeOUT)
cam = pvl.load(camrangeOUT)
if cam['UniversalGroundRange']['MaximumLatitude'] < float(RHash.getMinLat()) or \
cam['UniversalGroundRange']['MinimumLatitude'] > float(RHash.getMaxLat()) or \
cam['UniversalGroundRange']['MaximumLongitude'] < float(RHash.getMinLon()) or \
cam['UniversalGroundRange']['MinimumLongitude'] > float(RHash.getMaxLon()):
status = 'error'
eSTR = "Error Ground Range Outside Extent Range"
RHerror.addError(
os.path.splitext(
os.path.basename(jobFile))[0], eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
break
elif RHash.getGRtype() == 'smart':
if cam['UniversalGroundRange'][
'MinimumLatitude'] > float(
RHash.getMinLat()):
minlat = cam['UniversalGroundRange'][
'MinimumLatitude']
else:
minlat = RHash.getMinLat()
if cam['UniversalGroundRange'][
'MaximumLatitude'] < float(
RHash.getMaxLat()):
maxlat = cam['UniversalGroundRange'][
'MaximumLatitude']
else:
maxlat = RHash.getMaxLat()
if cam['UniversalGroundRange'][
'MinimumLongitude'] > float(
RHash.getMinLon()):
minlon = cam['UniversalGroundRange'][
'MinimumLongitude']
else:
minlon = RHash.getMinLon()
if cam['UniversalGroundRange'][
'MaximumLongitude'] < float(
RHash.getMaxLon()):
maxlon = cam['UniversalGroundRange'][
'MaximumLongitude']
else:
maxlon = RHash.getMaxLon()
elif RHash.getGRtype() == 'fill':
minlat = RHash.getMinLat()
maxlat = RHash.getMaxLat()
minlon = RHash.getMinLon()
maxlon = RHash.getMaxLon()
processOBJ.AddParameter('minlat', minlat)
processOBJ.AddParameter('maxlat', maxlat)
processOBJ.AddParameter('minlon', minlon)
processOBJ.AddParameter('maxlon', maxlon)
#os.remove(camrangeOUT)
elif 'isis2pds' in processOBJ.getProcessName():
finalfile = infile.replace('.input.cub', '_final.img')
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', finalfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
print(processOBJ.getProcess())
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
subloggyOBJ = SubLoggy(k)
try:
func(**v)
logger.info('Process %s :: Success', k)
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if os.path.isfile(outfile):
os.rename(outfile, infile)
status = 'success'
except ProcessError as e:
logger.error('Process %s :: Error', k)
logger.error(e)
status = 'error'
eSTR = 'Error Executing ' + k + \
' Standard Error: ' + str(e)
RHerror.addError(
os.path.splitext(os.path.basename(jobFile))[0],
eSTR)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(processOBJ.LogCommandline())
subloggyOBJ.setHelpLink(processOBJ.LogHelpLink())
subloggyOBJ.errorOut(eSTR)
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
else:
GDALcmd = ""
for process, v, in processOBJ.getProcess().items():
subloggyOBJ = SubLoggy(process)
GDALcmd += process
for key, value in v.items():
GDALcmd += ' ' + key + ' ' + value
frmt = RHash.Format().decode('utf-8')
if frmt == 'GeoTiff-BigTiff':
fileext = 'tif'
elif frmt == 'GeoJPEG-2000':
fileext = 'jp2'
elif frmt == 'JPEG':
fileext = 'jpg'
elif frmt == 'PNG':
fileext = 'png'
elif frmt == 'GIF':
fileext = 'gif'
logGDALcmd = GDALcmd + ' ' + basename + \
'.input.cub ' + basename + '_final.' + fileext
finalfile = infile.replace('.input.cub',
'_final.' + fileext)
GDALcmd += ' ' + infile + ' ' + finalfile
print(GDALcmd)
result = subprocess.call(GDALcmd, shell=True)
if result == 0:
logger.info('Process GDAL translate :: Success')
status = 'success'
subloggyOBJ.setStatus('SUCCESS')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
#os.remove(infile)
else:
errmsg = 'Error Executing GDAL translate: Error'
logger.error(errmsg)
status = 'error'
RHerror.addError(
os.path.splitext(os.path.basename(jobFile))[0],
errmsg)
subloggyOBJ.setStatus('ERROR')
subloggyOBJ.setCommand(logGDALcmd)
subloggyOBJ.setHelpLink(
'http://www.gdal.org/gdal_translate.html')
subloggyOBJ.errorOut('Process GDAL translate :: Error')
loggyOBJ.AddProcess(subloggyOBJ.getSLprocess())
if status == 'success':
if RHash.Format() == 'ISIS3':
finalfile = infile.replace('.input.cub', '_final.cub')
shutil.move(infile, finalfile)
if RHash.getStatus() != 'ERROR':
RHash.Status('SUCCESS')
try:
RQ_zip.QueueAdd(finalfile)
logger.info('File Added to ZIP Queue')
except:
logger.error('File NOT Added to ZIP Queue')
elif status == 'error':
RHash.Status('ERROR')
if os.path.isfile(infile):
#os.remove(infile)
pass
try:
RQ_loggy.QueueAdd(loggyOBJ.Loggy2json())
RQ_work.QueueRemove(jobFile)
logger.info('JSON Added to Loggy Queue')
except:
logger.error('JSON NOT Added to Loggy Queue')
if RQ_file.QueueSize() == 0 and RQ_work.QueueSize() == 0:
try:
RQ_final.QueueAdd(key)
logger.info('Key %s Added to Final Queue: Success', key)
logger.info(
'Both Queues Empty: filequeue = %s work queue = %s',
str(RQ_file.QueueSize()), str(RQ_work.QueueSize()))
logger.info('JOB Complete')
except:
logger.error('Key NOT Added to Final Queue')
elif RQ_file.QueueSize() == 0 and RQ_work.QueueSize() != 0:
logger.warning(
'Work Queue Not Empty: filequeue = %s work queue = %s',
str(RQ_file.QueueSize()), str(RQ_work.QueueSize()))
def main():
# pdb.set_trace()
args = Args()
args.parse_args()
logger = logging.getLogger('Browse_Process')
level = logging.getLevelName(args.log_level)
logger.setLevel(level)
logFileHandle = logging.FileHandler(pds_log + 'Process.log')
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s, %(message)s')
logFileHandle.setFormatter(formatter)
logger.addHandler(logFileHandle)
RQ_main = RedisQueue('Browse_ReadyQueue')
RQ_lock = RedisLock(lock_obj)
RQ_lock.add({RQ_main.id_name: '1'})
PDSinfoDICT = json.load(open(pds_info, 'r'))
pds_session, pds_engine = db_connect(pds_db)
upc_session, upc_engine = db_connect(upc_db)
tid = get_tid('fullimageurl', upc_session)
while int(RQ_main.QueueSize()) > 0 and RQ_lock.available(RQ_main.id_name):
item = literal_eval(RQ_main.QueueGet().decode("utf-8"))
inputfile = item[0]
fid = item[1]
archive = item[2]
if os.path.isfile(inputfile):
logger.info('Starting Process: %s', inputfile)
finalpath = makedir(inputfile)
recipeOBJ = Recipe()
recip_json = recipeOBJ.getRecipeJSON(archive)
recipeOBJ.AddJsonFile(recip_json, 'reduced')
infile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Binput.cub'
outfile = workarea + os.path.splitext(
os.path.basename(inputfile))[0] + '.Boutput.cub'
status = 'success'
for item in recipeOBJ.getProcesses():
if status == 'error':
logger.error("Error processing %s", inputfile)
break
elif status == 'success':
processOBJ = Process()
processOBJ.ProcessFromRecipe(item, recipeOBJ.getRecipe())
if '2isis' in item:
processOBJ.updateParameter('from_', inputfile)
processOBJ.updateParameter('to', outfile)
elif item == 'spiceinit':
processOBJ.updateParameter('from_', infile)
elif item == 'cubeatt':
label = pvl.load(infile)
bands = PDSinfoDICT[archive]['bandorder']
query_bands = label['IsisCube']['BandBin'][
PDSinfoDICT[archive]['bandbinQuery']]
# Create a set from the list / single value
try:
query_band_set = set(query_bands)
except:
query_band_set = set([query_bands])
# Iterate through 'bands' and grab the first value that is present in the
# set defined by 'bandbinquery' -- if not present, default to 1
exband = next(
(band for band in bands if band in query_band_set),
1)
band_infile = infile + '+' + str(exband)
processOBJ.updateParameter('from_', band_infile)
processOBJ.updateParameter('to', outfile)
elif item == 'ctxevenodd':
label = pvl.load(infile)
SS = label['IsisCube']['Instrument']['SpatialSumming']
if SS != 1:
break
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'reduce':
label = pvl.load(infile)
Nline = label['IsisCube']['Core']['Dimensions'][
'Lines']
Nsample = label['IsisCube']['Core']['Dimensions'][
'Samples']
Nline = int(Nline)
Nsample = int(Nsample)
Sfactor = scaleFactor(Nline, Nsample, recip_json)
processOBJ.updateParameter('lscale', Sfactor)
processOBJ.updateParameter('sscale', Sfactor)
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
elif item == 'isis2std':
final_outfile = finalpath + '/' + os.path.splitext(
os.path.basename(inputfile))[0] + '.browse.jpg'
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', final_outfile)
else:
processOBJ.updateParameter('from_', infile)
processOBJ.updateParameter('to', outfile)
for k, v in processOBJ.getProcess().items():
func = getattr(isis, k)
try:
func(**v)
logger.info('Process %s :: Success', k)
if os.path.isfile(outfile):
if '.cub' in outfile:
os.rename(outfile, infile)
status = 'success'
if '2isis' in item:
isisSerial = getISISid(infile)
except ProcessError as e:
print(e)
logger.error('Process %s :: Error', k)
status = 'error'
if status == 'success':
DB_addURL(upc_session, isisSerial, final_outfile, tid)
os.remove(infile)
logger.info('Browse Process Success: %s', inputfile)
AddProcessDB(pds_session, fid, 't')
else:
logger.error('File %s Not Found', inputfile)
upc_session.close()
pds_session.close()
upc_engine.dispose()
pds_engine.dispose()