def DB_addURL(session, isisSerial, inputfile, tid):
newisisSerial = isisSerial.split(':')[0]
likestr = '%' + newisisSerial + '%'
Qobj = session.query(DataFiles).filter(
DataFiles.isisid.like(likestr)).first()
if str(Qobj.isisid) == str(isisSerial):
outputfile = inputfile.replace(derived_base, '$thumbnail_server/')
print(Qobj.upcid)
DBinput = MetaString(upcid=Qobj.upcid, typeid=tid, value=outputfile)
try:
session.merge(DBinput)
session.commit()
return 'SUCCESS'
except:
return 'ERROR'
def DB_addURL(session, isisSerial, inputfile, tid):
# pdb.set_trace()
newisisSerial = isisSerial.split(':')[0]
likestr = '%' + newisisSerial + '%'
Qobj = session.query(DataFiles).filter(
DataFiles.isisid.like(likestr)).first()
if str(Qobj.isisid) == str(isisSerial):
outputfile = inputfile.replace('/pds_san/PDS_Derived/UPC/images/',
'$browse_server/')
print(Qobj.upcid)
DBinput = MetaString(upcid=Qobj.upcid, typeid=tid, value=outputfile)
try:
session.merge(DBinput)
session.commit()
return 'SUCCESS'
except:
return 'ERROR'
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")