def main():
logging.basicConfig()
logging.root.setLevel(logging.INFO)
args = parse_args()
# connect to db
with open(args.config, 'rb') as f:
db.connect(json.load(f))
# load translations if present
translations = {}
if args.species_translations is not None:
translations = load_translations(args.species_translations)
_log.info('Loaded %d species name translations', len(translations))
# lookup taxons (species) in BLA and local db
taxons = load_taxons_by_spno(args.csv, translations)
set_db_id_for_taxons(taxons.itervalues())
# wipe existing vettings
db.vettings.delete().where(db.vettings.c.user_id == args.user_id).execute()
# create new vettings
for spno, taxon in taxons.iteritems():
insert_vettings_for_taxon(taxon, spno, args.user_id)
def main():
args = parse_args()
logging.basicConfig()
logging.root.setLevel(logging.INFO)
with open(args.config, 'rb') as f:
config = json.load(f)
db.connect(config)
if 'alaVettingSyncUrl' not in config or len(config['alaVettingSyncUrl']) == 0:
logging.critical('"alaVettingSyncUrl" must be present in the config')
return
if 'alaApiKey' not in config or len(config['alaApiKey']) == 0:
logging.critical('"alaApiKey" must be present in the config')
return
while True:
next_vetting = next_vetting_to_sync()
if next_vetting is None:
log_info('=========== No vettings to send. Sleeping for a while.')
time.sleep(60)
else:
send_vetting(next_vetting, config['alaVettingSyncUrl'], config['alaApiKey'])
db.engine.dispose()
time.sleep(5)
def main():
args = parse_args()
logging.basicConfig()
logging.root.setLevel(logging.INFO)
with open(args.config, 'rb') as f:
db.connect(json.load(f))
while True:
next_species = next_species_row_to_vet()
if next_species is None:
log_info('=========== No species need vetting. Sleeping for a while.')
time.sleep(60)
else:
vet_species(next_species)
db.engine.dispose()
def main():
args = parse_args()
with open(args.config, "rb") as f:
config = json.load(f)
db.connect(config)
if "alaApiKey" in config and config["alaApiKey"] is not None:
ala.set_api_key(config["alaApiKey"])
if "logLevel" in config:
logging.basicConfig()
logging.root.setLevel(logging.__dict__[config["logLevel"]])
if "maxRetrySeconds" in config:
ala.set_max_retry_secs(float(config["maxRetrySeconds"]))
logging.info("Started at %s", str(datetime.now()))
connection = db.engine.connect()
try:
syncer = sync.Syncer(ala, args.species_type, connection)
syncer.sync(sync_species=config["updateSpecies"], sync_occurrences=config["updateOccurrences"])
finally:
logging.info("Ended at %s", str(datetime.now()))
def test_suite():
test_config_path = os.path.abspath(__file__ + "/../../../config.unittests.json")
with open(test_config_path) as f:
db.connect(json.load(f))
return unittest.makeSuite(TestSync)
def main():
# make sure this isn't run accidentally
if '--go' not in sys.argv:
print
print "Wipes the database clean and inserts some debug data."
print "Don't use this in production!"
print
print "Usage:"
print "\t{0} --go [--big]".format(sys.argv[0])
print
sys.exit()
# connect
with open('config.json', 'rb') as f:
db.connect(json.load(f))
# wipe
db.sensitive_occurrences.delete().execute()
db.occurrences.delete().execute()
db.vettings.delete().execute()
db.species.delete().execute()
db.sources.delete().execute()
# insert ALA source
db.sources.insert().execute(
name='ALA',
last_import_time=None)
# insert species
db.species.insert().execute(
scientific_name='Motacilla flava',
common_name='Yellow Wagtail')
db.species.insert().execute(
scientific_name='Ninox (Rhabdoglaux) strenua',
common_name='Powerful Owl')
db.species.insert().execute(
scientific_name='Ninox (Hieracoglaux) connivens',
common_name='Barking Owl')
db.species.insert().execute(
scientific_name='Tyto alba',
common_name='Barn Owl')
db.species.insert().execute(
scientific_name='Falco (Hierofalco) hypoleucos',
common_name='Grey Falcon')
# 1000 records, of which 79 are sensitive
db.species.insert().execute(
scientific_name='Atrichornis (Atrichornis) rufescens',
common_name='Rufous Scrub-bird')
if '--big' in sys.argv:
# 400k records.
db.species.insert().execute(
scientific_name='Cracticus tibicen',
common_name='Australian Magpie')
db.species.insert().execute(
scientific_name='Dacelo (Dacelo) leachii',
common_name='Blue-winged Kookaburra')
db.species.insert().execute(
scientific_name='Tyto (Megastrix) novaehollandiae',
common_name='Masked Owl')
db.species.insert().execute(
scientific_name='Ninox (Ninox) novaeseelandiae',
common_name='Southern Boobook')
db.species.insert().execute(
scientific_name='Corvus tasmanicus',
common_name='Forest Raven')
def main():
# make sure this isn't run accidentally
if '--go' not in sys.argv:
print
print "Wipes the database clean and fills database with Costa Rica data."
print
print "Assumes input csv is called costa_rica_import.csv, and is in the"
print "same folder as config.json. The folder you're in now.."
print
print "Usage:"
print "\t{0} --go".format(sys.argv[0])
print
sys.exit()
import_file_path = 'costa_rica_import.csv'
import_threshold_file_path = 'costa_rica_import_threshold.csv'
log = logging.getLogger()
log.setLevel(logging.DEBUG)
log.addHandler(logging.StreamHandler())
species_count = 0
occurrences_count = 0
# take note of import start time
import_d = datetime.utcnow()
# connect
with open('config.json', 'rb') as f:
db.connect(json.load(f))
# wipe
db.species.delete().execute()
db.sources.delete().execute()
db.occurrences.delete().execute()
# insert COSTA_RICA_CSV with last_import_time.
result = db.sources.insert().execute(
name='COSTA_RICA_CSV',
last_import_time=import_d)
db_source_id = result.lastrowid
# open threshold csv..
with open(import_threshold_file_path, 'rb') as tf:
# open the costa_rica csv..
with open(import_file_path, 'rb') as f:
reader = csv.reader(f)
# skip the header
header = reader.next()
# iterate over the csv rows
for csv_row_array in reader:
in_collection_code = csv_row_array.pop(0)
in_catalog_number = csv_row_array.pop(0)
in_occurrence_remarks = csv_row_array.pop(0)
in_record_number = csv_row_array.pop(0)
in_event_date = csv_row_array.pop(0)
in_location_id = csv_row_array.pop(0)
in_state_province = csv_row_array.pop(0)
in_county = csv_row_array.pop(0)
in_municipality = csv_row_array.pop(0)
in_locality = csv_row_array.pop(0)
in_decimal_latitude = csv_row_array.pop(0)
in_decimal_longitude = csv_row_array.pop(0)
in_scientific_name = csv_row_array.pop(0)
in_kingdom = csv_row_array.pop(0)
in_phylum = csv_row_array.pop(0)
in_class = csv_row_array.pop(0)
in_order = csv_row_array.pop(0)
in_family = csv_row_array.pop(0)
in_genus = csv_row_array.pop(0)
in_specific_epithet = csv_row_array.pop(0)
in_infraspecific_epithet = csv_row_array.pop(0)
in_taxon_rank = csv_row_array.pop(0)
# Add species if necessary..
# Look up species by scientific_name
row = db.species.select('id')\
.where(db.species.c.scientific_name == in_scientific_name)\
.execute().fetchone()
db_species_id = None
if row is None:
# If we couldn't find it..
# so add the species
tf.seek(0)
threshold_reader = csv.reader(tf)
in_threshold = 1 # The max (will wipe out all values)
for threshold_csv_row_array in threshold_reader:
in_species_name = threshold_csv_row_array[0]
in_threshold = threshold_csv_row_array[1]
# compare species sci_names
conv_in_scientific_name = in_scientific_name.strip()
conv_in_scientific_name = conv_in_scientific_name.replace('.', '')
conv_in_scientific_name = conv_in_scientific_name.replace(' ', '_')
#print conv_in_scientific_name
#print in_species_name
#print '...........'
if conv_in_scientific_name == in_species_name:
print '************'
print in_species_name
if in_threshold == 'na':
in_threshold = '1'
print in_threshold
break
sys.stdout.flush()
result = db.species.insert().execute(
scientific_name=in_scientific_name,
distribution_threshold=in_threshold,
)
species_count = species_count + 1
db_species_id = result.lastrowid
else:
# We found it, grab the species id
db_species_id = row['id']
# insert the occurrence into the db.
# NOTE: Some records have empty in_record_numbers.
# The sql db validates source_id vs source_record_id
# data, so if we have an empty source_record_id, leave it as unspecified
#
occurrences_count = occurrences_count + 1
if in_record_number.strip() != '':
result = db.occurrences.insert().execute(
species_id=db_species_id,
latitude=in_decimal_latitude,
longitude=in_decimal_longitude,
source_id=db_source_id,
source_record_id=in_record_number,
classification='irruptive'
)
else:
result = db.occurrences.insert().execute(
species_id=db_species_id,
latitude=in_decimal_latitude,
longitude=in_decimal_longitude,
source_id=db_source_id,
# source_record_id=in_record_number,
classification='irruptive'
)
log.debug("Species: %i", species_count)
log.debug("Occurrences: %i", occurrences_count)