def loadProps(path):
props = Properties()
try:
propReader = FileReader(path)
props.load(propReader)
propReader.close()
except:
type, value, traceback = sys.exc_info()
print "Error loading properties from file:" + path + ":" + ` value `
return props
def _parse_and_rewrite_svg_file(svg_input_path, svg_output_path):
write_str = ""
file_reader = FileReader(svg_input_path)
buffered_reader = BufferedReader(file_reader)
read_line = ""
check = False
while True:
read_line = buffered_reader.readLine()
if read_line is None:
break
if "viewBox" in read_line:
view_box_content = _get_viewbox_content(read_line)
view_box_values = _get_viewbox_values(view_box_content)
if view_box_values[0] != 0:
view_box_values[2] = abs(view_box_values[2]) + abs(
view_box_values[0])
view_box_values[0] = 0
if view_box_values[1] != 0:
view_box_values[3] = abs(view_box_values[3]) + abs(
view_box_values[1])
view_box_values[1] = 0
read_line = re.sub(r"viewBox=\"[\-|0-9| ]+\"", "", read_line, 1)
read_line = re.sub(r"width=\"[0-9]+\"",
"width=\"" + str(view_box_values[2]) + "\"",
read_line, 1)
read_line = re.sub(r"height=\"[0-9]+\"",
"height=\"" + str(view_box_values[3]) + "\"",
read_line, 1)
check = True
if "g id=\"ID" in read_line and not check:
if "transform=" in read_line:
_log.info(read_line)
read_line = read_line[0:read_line.find("transform")] + ">"
check = True
write_str += read_line + "\n"
buffered_reader.close()
file_reader.close()
file_writer = PrintWriter(svg_output_path)
file_writer.print(write_str)
file_writer.close()
def assign_ids_from_list(tax, filename):
count = 0
if True:
infile = FileReader(filename)
r = CSVReader(infile)
while True:
row = r.readNext()
if row == None: break
[qid, ids] = row
taxon = tax.lookupQid(QualifiedId(qid))
if taxon != None:
for id in ids.split(';'):
z = tax.lookupId(id)
if z == None:
taxon.taxonomy.addId(taxon, id)
count += 1
infile.close()
print '| Assigned %s ids from %s' % (count, filename)
def assign_ids_from_list(tax, filename):
count = 0
if True:
infile = FileReader(filename)
r = CSVReader(infile)
while True:
row = r.readNext()
if row == None: break
[qid, ids] = row
taxon = tax.lookupQid(QualifiedId(qid))
if taxon != None:
for id in ids.split(';'):
z = tax.lookupId(id)
if z == None:
taxon.taxonomy.addId(taxon, id)
count += 1
infile.close()
print '| Assigned %s ids from %s' % (count, filename)
def _parse_and_rewrite_svg_file(svg_input_path, svg_output_path):
write_str = ""
file_reader = FileReader(svg_input_path)
buffered_reader = BufferedReader(file_reader)
read_line = ""
check = False
while True:
read_line = buffered_reader.readLine()
if read_line is None:
break
if "viewBox" in read_line:
view_box_content = _get_viewbox_content(read_line)
view_box_values = _get_viewbox_values(view_box_content)
if view_box_values[0] != 0:
view_box_values[2] = abs(view_box_values[2]) + abs(view_box_values[0])
view_box_values[0] = 0
if view_box_values[1] != 0:
view_box_values[3] = abs(view_box_values[3]) + abs(view_box_values[1])
view_box_values[1] = 0
read_line = re.sub(r"viewBox=\"[\-|0-9| ]+\"", "", read_line, 1)
read_line = re.sub(r"width=\"[0-9]+\"", "width=\""+ str(view_box_values[2]) + "\"",
read_line, 1)
read_line = re.sub(r"height=\"[0-9]+\"", "height=\""+ str(view_box_values[3]) + "\"",
read_line, 1)
check = True
if "g id=\"ID" in read_line and not check:
if "transform=" in read_line:
_log.info(read_line)
read_line = read_line[0:read_line.find("transform")] + ">"
check = True
write_str += read_line + "\n"
buffered_reader.close()
file_reader.close()
file_writer = PrintWriter(svg_output_path)
file_writer.print(write_str)
file_writer.close()
def _parse_and_rewrite_svg_file(svg_input_path, svg_output_path):
write_str = ""
file_reader = FileReader(svg_input_path)
buffered_reader = BufferedReader(file_reader)
read_line = ""
while True:
read_line = buffered_reader.readLine()
if read_line is None:
break
if "viewBox" in read_line:
view_box_content = _get_viewbox_content(read_line)
view_box_values = _get_viewbox_values(view_box_content)
if view_box_values[0] != 0:
view_box_values[2] += view_box_values[0]
view_box_values[0] = 0
if view_box_values[1] != 0:
view_box_values[3] += view_box_values[1]
view_box_values[1] = 0
new_view_box = str(view_box_values[0]) + " " + str(view_box_values[1]) + " " + \
str(view_box_values[2]) + " " + str(view_box_values[3])
read_line = re.sub(r"viewBox=\"[\-|0-9| ]+\"", "viewBox=\""
+ new_view_box + "\"", read_line, 1)
read_line = re.sub(r"width=\"[0-9]+\"", "width=\""+ str(view_box_values[2]) + "\"",
read_line, 1)
read_line = re.sub(r"height=\"[0-9]+\"", "height=\""+ str(view_box_values[3]) + "\"",
read_line, 1)
write_str += read_line + "\n"
buffered_reader.close()
file_reader.close()
file_writer = PrintWriter(svg_output_path)
file_writer.print(write_str)
file_writer.close()
def retain_ids_from_list(tax, filename):
count = 0
change_count = 0
infile = FileReader(filename)
r = CSVReader(infile)
while True:
row = r.readNext()
if row == None: break
[qid_string, ids] = row
tracep = (qid_string == 'ncbi:33543' or qid_string == 'gbif:2433391'
or qid_string == 'gbif:2467506'
or qid_string == 'ncbi:28376')
if tracep:
print '# Tracing %s %s' % (qid_string, ids)
qid = QualifiedId(qid_string)
taxon = tax.lookupQid(qid)
if taxon != None:
id_list = ids.split(';')
qid_id = id_list[0]
if tracep == False:
tracep = (qid_id == '565578' or qid_id == '5541322')
if tracep:
print '# qid %s, id_list %s' % (qid, id_list)
# Look for collision
tenant = tax.lookupId(qid_id)
if tenant != None:
# qid_id is unavailable
# Happens 7700 or so times; most cases ought to be homonymized,
# but not all
if tracep:
print '# %s (for %s) is in use by %s' % (qid_id, taxon,
tenant)
False
# Qid from list is one of the taxon's qids.
# Use the proposed id if the qid's node has no id
elif taxon.id == None:
# Happens 87854 for OTT 3.0
if tracep: print '# Setting %s as id of %s' % (qid_id, taxon)
taxon.setId(qid_id)
# Deal with aliases
for id in id_list[1:]:
if tax.lookupId(id) == None:
if tracep:
print '# adding %s as id for %s' % (id, taxon)
tax.addId(taxon, id)
else:
if tracep:
print '# alias %s (for %s) is in use by %s' % (
id, taxon, tax.lookupId(id))
count += 1
# If it has an id, but qid is not the primary qid, skip it
elif taxon.sourceIds != None and taxon.sourceIds[0] != qid:
if tracep: print '# %s is minor for %s' % (qid_id, taxon)
False
# Use the id in the id_list if it's smaller than the one in taxon
elif int(qid_id) < int(taxon.id):
if tracep:
print '# %s is replacing %s as the id of %s' % (
qid_id, taxon.id, taxon)
taxon.setId(qid_id)
for id in id_list[1:]:
if tax.lookupId(id) == None:
tax.addId(taxon, id)
change_count += 1
else:
if tracep: print '# %s has id %s < %s' % (qid, qid_id, taxon)
else:
if tracep: print '# no taxon with qid %s; ids %s' % (qid, ids)
infile.close()
print '| Assigned %s ids, changed %s ids from %s' % (count, change_count,
filename)
from java.io import FileWriter
from java.io import File
from java.io import FileReader
f1 = File("file2.txt")
fr = FileReader(f1)
f2 = File("file3.txt")
fw = FileWriter(f2)
while True:
ch = fr.read()
if ch != -1:
fw.write(ch)
else:
break
fr.close()
fw.close()
if line[:eqPos] == 'passwd': passwd = line[eqPos+1:].strip()
if line[:eqPos] == 'fromQuery': fromQuery = line[eqPos+1:].strip()
if line[:eqPos] == 'toQuery': toQuery = re.sub(r'\/\w+?\/', r'%s', line[eqPos+1:]).strip()
file.close()
else:
inform('configuration file (config.ini) is missing')
sys.exit()
inform('getting database connection')
dbHandler = MySQLAccess(url, user, passwd, toQuery)
db = dbHandler.connect()
arffFile = FileReader(TrainData)
data = Instances(arffFile)
data.setClassIndex(data.numAttributes() - 1)
arffFile.close()
arffFileNum = FileReader(TrainDataNum)
dataNum = Instances(arffFileNum)
dataNum.setClassIndex(dataNum.numAttributes() - 1)
arffFileNum.close()
if not Path.isfile(model):
inform('training J48')
j48 = J48()
j48.setOptions('-R -N 3 -Q 1 -M 2'.split()) # reduced error pruning, use j48.setOptions('-C 0.1 -M 2'.split()) for confidence interval pruning
j48.buildClassifier(data)
serialize.write(model, j48)
inform('saved model to '+model)
else:
inform('import '+model)
