infilename = sys.argv[1]
try:
# connect to the database
db = MySQLdb.connect(host="mysql.msi.umn.edu",
user="******",
passwd="uvNaui5sg",
db="packerc_snapshot_serengeti")
# use the database
with db:
snapshotDB.cur = db.cursor()
snapshotDB.addLinks(infilename)
# make a note in the log
snapshotDB.log(
"Margaret Kosmala",
"Loaded links from captures to Zooniverse IDs in " +
str(infilename))
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
line = line.rstrip()
tokens = line.split(',')
capture1 = int(tokens[0])
capture2 = int(tokens[1])
try:
snapshotDB.combineCaptures(capture1, capture2)
except TypeError as e:
print(
"Error: Error combining captures corresponding to line: " +
line)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Combined captures from file " + str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# remove header line
filereader.next()
# go through each line in the file
for line in filereader:
uname = line[0]
uhash = line[1]
userID = snapshotDB.getUser(uname)
if userID == None:
snapshotDB.addUser(uname,uhash)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Added users from file " +
str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0],e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
infile.readline()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
tokens = line.split(',')
person = tokens[0]
initials = tokens[1]
# add the person's name
snapshotDB.addPerson(person, initials)
# make an annotation in the log
snapshotDB.log("Margaret Kosmala", "Initialized Person table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
tokens = line.split(',')
season = tokens[0]
startdate = tokens[1]
enddate = tokens[2]
comments = tokens[3]
# put in the data
snapshotDB.addSeason(season, startdate, enddate, comments)
# make a note in the log
snapshotDB.log("Margaret Kosmala", "Initialized Seasons table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
exit(1)
infilename = sys.argv[1]
try:
# connect to the database
db = MySQLdb.connect(host="mysql.msi.umn.edu",
user="******",
passwd="uvNaui5sg",
db="packerc_snapshot_serengeti")
# use the database
with db:
snapshotDB.cur = db.cursor()
snapshotDB.addConsensusBlanks(infilename)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Loaded blank captures from " + str(infilename))
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
with db:
snapshotDB.cur = db.cursor()
# get rid of the header line in the file
infile.readline()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
# put in the data
snapshotDB.addSpecies(line)
# make a note in the log
snapshotDB.log("Margaret Kosmala", "Initialized Species table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
rollID = snapshotDB.addRoll(seasonnum,site,rollnum)
# create the capture if it's a new capture
if capture != lastcapture:
captureID = snapshotDB.addCapture(rollID,capture)
# create the image
snapshotDB.addImage(captureID,imagenum,path,timestampjpg)
# update for speed
lastroll = thisroll
lastcapture = capture
# make a note in the log
snapshotDB.log("Margaret Kosmala",
("Filled in Rolls, CaptureEvents, and Images " +
"tables for Season " + str(seasonnum)))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0],e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# in either case, update the capture timestamp
snapshotDB.setCaptureTimestamp(captureID, newtimestamp,
invalid)
# update for speed
lastseason = seasonnum
lastsite = site
lastroll = rollnum
except TypeError as e:
print("Error: Couldn't find image corresponding to line: " +
line)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Corrected timestamps for Seasons 1-3")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
comments = siteComments
elif moreComments != "":
comments = moreComments
actionNum = ""
uploadNum = ""
if action != "": actionNum = int(action)
if upload != "": uploadNum = int(upload)
# put in the data
snapshotDB.addSiteCheck(accessID, season, site, initials,
dateCheck, dateUpload, actionNum,
uploadNum, timeChange, timeFrom, timeTo,
comments)
# make a note in the log
snapshotDB.log("Margaret Kosmala", "Initialized SiteChecks table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
snapshotDB.cur = db.cursor()
# get rid of the header line in the file
infile.readline()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
tokens = line.split(',')
site = tokens[0]
gridx = tokens[1]
gridy = tokens[2]
snapshotDB.addGridCell(site, gridx, gridy)
snapshotDB.log("Margaret Kosmala", "Initialized GridCells table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
infilename = sys.argv[1]
try:
# connect to the database
db = MySQLdb.connect(host="mysql.msi.umn.edu",
user="******",
passwd="uvNaui5sg",
db="packerc_snapshot_serengeti")
# use the database
with db:
snapshotDB.cur = db.cursor()
snapshotDB.addManyUnlinkedZooniverseClassifications(infilename)
# make a note in the log
snapshotDB.log(
"Cory Teshera",
"Loaded zooniverse classifications from file " + str(infilename))
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
if int(imagenum) == 1:
snapshotDB.setCaptureTimestamp(captureID, newtimestamp,
invalid)
# update for speed
lastseason = seasonnum
lastsite = site
lastroll = rollnum
lastcapture = capturenum
except TypeError as e:
print("Error: Couldn't find image corresponding to line: " +
line)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Corrected timestamps for Season " + str(seasonnum))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
tokens = line.split(',')
index = tokens[0]
meaning = tokens[1]
# put in the data
snapshotDB.addZooniverseStatus(index,meaning)
# make a note in the log
snapshotDB.log("Margaret Kosmala","Initialized ZooniverseStatus table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0],e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
sreader = csv.reader(sfile,delimiter=',',quotechar='"')
# usually just 1 file for 1 season, but could handle more
for row in sreader:
season = row[0]
startdate = row[1]
enddate = row[2]
comments = row[3]
# see if this season is already in the DB
if not snapshotDB.seasonExists(season):
snapshotDB.addSeason(season,startdate,enddate,comments)
# make a note in the log
snapshotDB.log(fullname,"Added new season " + season)
# now the metadata
lastseason = "0"
lastsite = "0"
print "Validating the season and site values in the metadata file\n"
# Go through the file once to check seasons and sites
# We will not calculate roll start and stop times, as this is easy
# to do once the data are loaded, and makes this script cleaner.
with open(infilename,'rb') as infile:
# use CSV reader
freader = csv.reader(infile,delimiter=',',quotechar='"')
snapshotDB.setZooniverseStatus(captureID, 2)
# update for speed
lastseason = seasonnum
lastsite = site
lastroll = rollnum
lastcapture = capturenum
except TypeError as e:
print("Error: Couldn't find capture corresponding to line: " +
line)
# make a note in the log
snapshotDB.log(
"Margaret Kosmala",
"Updated Zooniverse status from file " + str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
snapshotDB.addCaptureEventAndZooniverseID(captureID, zoonid)
# update for speed
lastseason = seasonnum
lastsite = site
lastroll = rollnum
lastcapture = capturenum
except TypeError as e:
print("Error: Couldn't find capture corresponding to line: " +
line)
# make a note in the log
snapshotDB.log(
"Margaret Kosmala",
"Linked capture events and zooniverse IDs from file " +
str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
speciesID = getSpecies(species)
# create the vote
snapshotDB.addVote(consensusID, vote_index, speciesID,
species_votes, species_count_min,
species_count_median, species_count_max,
standing, resting, moving, eating,
interacting, babies)
except TypeError as e:
print("Error: Couldn't find image corresponding to line: " +
line)
# make a note in the log
snapshotDB.log(
"Margaret Kosmala",
"Added consensus classifications from file " + str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
infilename = sys.argv[1]
try:
# connect to the database
db = MySQLdb.connect(host="mysql.msi.umn.edu",
user="******",
passwd="uvNaui5sg",
db="packerc_snapshot_serengeti")
# use the database
with db:
snapshotDB.cur = db.cursor()
snapshotDB.addConsensusClassifications(infilename)
# make a note in the log
snapshotDB.log(
"Cory Teshera",
"Loaded consensus classifications in " + str(infilename))
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# userID,createdat,
# speciesID,countID,
# stand, rest, move,
# eat, interact, baby)
#else:
snapshotDB.addUnlinkedZooniverseClassification(zoonid,classid,
userID,createdat,
speciesID,countID,
stand, rest, move,
eat, interact, baby)
# print ("Warning: could not link to capture event for " +
# "Zooniverse ID " + zoonid)
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Added zooniverse classifications from file " +
str(infilename))
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0],e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
infile.readline()
# go through each line in the file
for line in infile:
#chomp and parse
line = line.rstrip()
tokens = line.split(',')
index = tokens[0]
meaning = tokens[1]
# put in the data
snapshotDB.addTimestampStatus(index, meaning)
# make a note in the log
snapshotDB.log("Margaret Kosmala", "Initialized TimestampStatus table")
# close the file
infile.close()
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
# exit(1)
#infilename = sys.argv[1]
try:
# connect to the database
db = MySQLdb.connect(host="mysql.msi.umn.edu",
user="******",
passwd="uvNaui5sg",
db="packerc_snapshot_serengeti")
# use the database
with db:
snapshotDB.cur = db.cursor()
snapshotDB.setUptimeForAllRollsNeedingIt()
# make a note in the log
snapshotDB.log("Margaret Kosmala",
"Set StartDate and StopDate in the Rolls table")
# catch errors
except MySQLdb.Error, e:
print "Error %d: %s" % (e.args[0], e.args[1])
sys.exit(1)
# close connection to the database
finally:
if db:
db.close()
