def runTest():
print('Running testcases...')
# Import HelloLexer
if not DIST in sys.path:
sys.path.append(DIST)
from Fragment import Fragment
# Read all test files
testfiles = sorted(os.listdir(TESTS))
for filename in testfiles:
printBreak()
print('Running test : ' + filename)
printBreak()
filepath = os.path.join(DIR, './tests', filename)
# file = open(filepath, 'r')
# code = file.read()
# print(code)
# file.close()
lexer = Fragment(FileStream(filepath))
tokens = []
token = lexer.nextToken()
while token.type != Token.EOF:
tokens.append(token.text)
token = lexer.nextToken()
tokens.append('<EOF>')
print(','.join(tokens))
printBreak()
print('Run tests completely')
def partition(frame):
""" Partition Frame into processed fragments
Args:
frame (np.ndarry): Frame to partition.
Returns:
A list of Fragments derived from Frame.
"""
height, width = frame.shape[:2]
partitionSize = height // 4
fragments = []
for i in range(4):
startPartition = i * partitionSize
# Extract and color-process fragment
fragment = Fragment(frame[startPartition:(startPartition +
partitionSize), 0:width])
# Set center points to be relative to full Frame
fragment.setRelativeContourCtrX(0)
fragment.setRelativeImageCtrX(0)
fragment.setRelativeContourCtrY(startPartition)
fragment.setRelativeImageCtrY(startPartition)
fragments.append(fragment)
return fragments
class Matchset:
fragment_1 = Fragment() # Contour Fragment 1
fragment_2 = Fragment() # Contour Fragment 2
match_1_start = 0
match_1_end = 0
match_2_end = 0
match_2_start = 0
match_1 = Fragment()
match_2 = Fragment()
i = 0
j = 0
score = 0 # Matching Score
def retrieve(self,filepath,order):
#initial configs
logger = Logger.getInstance()
order = int(order)
tokens = filepath.split('/');
filetitle = tokens[len(tokens)-1]
logger.logInfo('retrieving from file: ' + filetitle)
reader = ParserProvider.getParser(filetitle)
filepointer = reader.openFile(filepath)
fr = reader.readFile(filepointer)
#recover fragment
fragment = Fragment('',filepath,order,'')
text = reader.readCertSegment(filepointer,order)
if(text!=''):
fragment.set_text(text)
return fragment
def consume_packet(self, header_bstr, packet_time):
"""
Accept new packet and associate it with appropriate trace
Keyword arguments:
header_bstr -- binary string of the packet header
packet_time -- time tuple (sec, ms) since epoch of header
"""
# Check if packet isn't complete
new_fragment = Fragment(header_bstr, packet_time)
if new_fragment.id in self.incomplete_packets:
packet = self.incomplete_packets[new_fragment.id]
packet.add_frag(new_fragment)
else:
packet = Packet(new_fragment)
self.incomplete_packets[packet.id] = packet
# Set start time if very first packet
if self.ref_time is None:
self.ref_time = packet.time
if packet.is_complete():
del self.incomplete_packets[packet.id]
if (packet.protocol == Protocol.UDP
or (packet.protocol == Protocol.ICMP
and packet.type == Type.ECHO)):
self.traces[packet.get_trace_sig()] = Trace(
packet, self.ref_time)
self.trace_order.append(packet.get_trace_sig())
elif packet.protocol == Protocol.ICMP and packet.type == Type.TIME_EXCEEDED:
if packet.get_trace_sig() in [
trace.get_sig() for trace in self.traces.values()
]:
self.traces[packet.get_trace_sig()].add_resp(packet)
else:
if DEV_ENV:
print("Error: ICMP receieved for nonexistant probe")
print(packet.get_trace_sig())
else:
if DEV_ENV:
print("Protocol not savable in traces")
def __init__(self, filename, admin):
# initialize class variables to default state
self.id = 0
self.name = filename
self.fileSize = os.path.getsize('upload/' + filename)
self.admin = admin
self.startDate = datetime.datetime.now()
self.endDate = datetime.datetime.now()
self.volunteers = []
self.fragments = []
self.state = 'started'
self.files = 'upload/' + filename
#initialize project id
number = 0
for project in db.projects.find():
number = number + 1
self.id = number + 1
# Create project fragments using Fragments class
Fragment.fragments(filename)
# Create Fragment class instances and save in Project class fragments list variable
#for index, file in enumerate(os.listdir('fragments/')):
# if file[-3:] == 'zip':
# fragment = Fragment()
# fragment.id = index
# fragment.size = os.path.getsize('fragments/' + file)
# self.fragments.append(fragment)
#create fragments list to store in project class
for index, file in enumerate(os.listdir('fragments/')):
if file[-3:] == 'zip':
fragment = dict()
fragment['id'] = index
fragment['size'] = os.path.getsize('fragments/' + file)
fragment['time'] =datetime.datetime.now()
self.fragments.append(fragment)
#fragment.append(index)
#fragment.append(os.path.getsize('fragments/' + file))
#fragment.append(datetime.datetime.now())
#fragment.append()
#Save the project and files in the mongodb
project = db.projects()
project['id'] = self.id
project['name'] = self.name
project['fileSize'] = self.fileSize
project['admin'] = self.admin
project['startDate'] = self.startDate
project['endDate'] = self.endDate
project['volunteers'] = self.volunteers
project['fragments'] = self.fragments
#for fragment in
project['state'] = self.state
project.save()
#self.project = project
# get _id of the saved project
for project in db.projects.find({ 'id' : self.id }):
docid = str(project['_id'])
#Save project files in mongodb in Project Document
file = open('upload/' + filename)
project.fs.put(file)
#project.files = self.files = 'upload/' + filename
#Save fragments in mongodb
for file in os.listdir('fragments/'):
fragment = db.files()
fragment['projectid'] = self.id
fragment['name'] = file
fragment['docid'] = docid
fragment['type'] = 'fragment'
fragment.save()
open_file = open('fragments/' + file, 'rb')
fragment.fs.file.put(open_file)
alignment_bucket = [None, None]
current_read = alignment.read_name
# Skip non-primary and supplemental alignments
if alignment.flag & (256 + 2048):
continue
if alignment.strand == '+':
alignment_bucket[0] = alignment
elif alignment.strand == '-':
alignment_bucket[1] = alignment
# process if the bucket is full
if alignment_bucket[0] and alignment_bucket[1]:
fragment = Fragment(alignment_bucket[0], alignment_bucket[1])
# Check if fragment ends are conteined in a primer region
# Return range if True, None otherwise.
range_left = primer_range.is_contained(fragment.ref_start, 'left')
range_right = primer_range.is_contained(fragment.ref_end, 'right')
# Chop ends of the fragment overlapping to primer
fragment.slice(range_left)
fragment.slice(range_right)
if args.verbose:
sys.stderr.write(current_read + ':')
sys.stderr.write(' Fragment interval: {}-{}\n'.format(
fragment.ref_start, fragment.ref_end))
sys.stderr.write(
def test(self):
f = Fragment("test", "/home/mgazzola/test.txt", 1, "test")
self.assertEqual("test", f.get_text(), "OK")