def loadGFF_UTR(self,fields,line,transcriptBeginEnd,GFF,
transcripts,readOrder,genes):
exonBegin=int(fields[3])-1
exonEnd=int(fields[4])
exonScore=fields[5]
strand=fields[6]
frame=fields[7]
transcriptId=None
rex=Rex()
if(rex.find('transgrp[:=]\s*(\S+)',line)): transcriptId=rex[1]
elif(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):
transcriptId=rex[1]
elif(rex.find('Parent=([^;,\s]+)',line)): transcriptId=rex[1]
geneId=None
if(rex.find('genegrp=(\S+)',line)): geneId=rex[1]
elif(rex.find('gene_id[:=]?\s*"?([^\s\;"]+)"?',line)): geneId=rex[1]
if(transcriptId is None): transcriptId=geneId
if(geneId is None): geneId=transcriptId
if(transcriptId is None):
raise Exception(line+" : no transcript ID found")
if(rex.find("(\S+);$",transcriptId)): transcriptId=rex[1]
if(rex.find("(\S+);$",geneId)): geneId=rex[1]
extra=""
for i in range(8,len(fields)): extra+=fields[i]+" "
if(exonBegin>exonEnd): (exonBegin,exonEnd)=(exonEnd,exonBegin)
transcript=transcripts.get(transcriptId,None)
if(not transcript):
transcripts[transcriptId]=transcript= \
Transcript(transcriptId,strand)
transcript.setStopCodons(self.stopCodons)
transcript.readOrder=readOrder
readOrder+=1
transcript.substrate=fields[0]
transcript.source=fields[1]
if(transcriptBeginEnd.get(transcriptId,None) is not None):
(begin,end)=transcriptBeginEnd[transcriptId]
transcript.setBegin(begin)
transcript.setEnd(end)
else:
transcript.setBegin(exonBegin)
transcript.setEnd(exonEnd)
transcript.geneId=geneId
gene=genes.get(geneId,None)
if(gene is None):
genes[geneId]=gene=Gene(); gene.setId(geneId)
transcript.setGene(gene)
exon=Exon(exonBegin,exonEnd,transcript)
exon.extraFields=extra
if(transcript.rawExons is not None):
exon.frame=frame
exon.score=exonScore
exon.type=fields[2]
transcript.rawExons.append(exon)
elif(not transcript.exonOverlapsExon(exon)):
exon.frame=frame
exon.score=exonScore
exon.type=fields[2]
transcript.UTR.append(exon) # OK -- we sort later
gene.addTranscript(transcript)
def __init__(self,
model_arch,
model_weight,
model_priori_proba_file,
fst_folder,
acoustic_model_labels_file,
words_lexicon_file=Config.RECOGNITION_DIR +
"ForcedAlignmnet/words_lexicon.txt",
phones_lexicon_file=Config.RECOGNITION_DIR +
"ForcedAlignmnet/phones_lexicon.txt",
grammerFileName=""):
if fst_folder and fst_folder[-1] != '/': fst_folder += "/"
self.decoder = Decoder(fst_folder, acoustic_model_labels_file,
grammerFileName)
self.classifier = Classifier(model_arch, model_weight,
model_priori_proba_file)
self.trans = Transcript(words_lexicon_file, phones_lexicon_file)
class ASR:
def __init__(self,
model_arch,
model_weight,
model_priori_proba_file,
fst_folder,
acoustic_model_labels_file,
words_lexicon_file=Config.RECOGNITION_DIR +
"ForcedAlignmnet/words_lexicon.txt",
phones_lexicon_file=Config.RECOGNITION_DIR +
"ForcedAlignmnet/phones_lexicon.txt",
grammerFileName=""):
if fst_folder and fst_folder[-1] != '/': fst_folder += "/"
self.decoder = Decoder(fst_folder, acoustic_model_labels_file,
grammerFileName)
self.classifier = Classifier(model_arch, model_weight,
model_priori_proba_file)
self.trans = Transcript(words_lexicon_file, phones_lexicon_file)
def speech_to_text(self,
wav_file,
max_active_tokens,
beam_width,
acoustic_model_weigh,
latticeBeam=1,
include_alignment=False):
features = np.transpose(np.array(self._get_features(wav_file)))
states_seq = self._decode(features, max_active_tokens, beam_width,
acoustic_model_weigh, latticeBeam)
if (not include_alignment):
states_seq = self._remove_selfloops(states_seq)
return ' '.join(self._get_words_from_states_seq(states_seq))
else:
frames_count = len(features)
return self.trans.get_transcript(states_seq, frames_count)
def _decode(self, features, max_active_tokens, beam_width,
acoustic_model_weight, latticeBeam):
activations = self.classifier.eval(features)
return self.decoder.decode(activations, max_active_tokens, beam_width,
1 / acoustic_model_weight, latticeBeam)
def _remove_selfloops(self, states_seq):
return [
state for i, state in enumerate(states_seq)
if not i or states_seq[i][-1] != states_seq[i - 1][-1]
] # remove self loops
def _get_words_from_states_seq(self, states_seq):
return [
outlabel for _, outlabel, _ in states_seq
if not self.decoder.is_special_sym(outlabel)
]
def _get_features(self, wav_file):
return wav_to_feat(wav_file)
def post(self):
"""
This method handles a post request to audit a transcript
"""
args = parser.parse_args()
data = ast.literal_eval(args['transcript'])
transcript = Transcript(data['major'], data['courses'])
degree = degree_catalog.get_degree(data['major'])
result = {}
audit = transcript.audit_transcript(degree)
result['audit'] = audit
reccommendations = transcript.reccommend(degree_catalog)
result['reccommendations'] = reccommendations
return result, 201
def loadGFF_transcript(self,fields,line,transcriptBeginEnd,GFF,
transcripts,readOrder,genes):
begin=int(fields[3])-1
end=int(fields[4])
rex=Rex()
if(rex.find('transcript_id[:=]?\s*"?([^\s";]+)"?',line)):
transcriptId=rex[1]
transcriptBeginEnd[transcriptId]=[begin,end]
strand=fields[6]
score=fields[5]
transcriptExtraFields=""
for i in range(8,len(fields)):
transcriptExtraFields+=fields[i]+" "
transcript=transcripts.get(transcriptId,None)
if(transcript is None):
transcripts[transcriptId]=transcript= \
Transcript(transcriptId,strand)
transcript.setStopCodons(self.stopCodons)
transcript.readOrder=readOrder;
readOrder+=1
transcript.substrate=fields[0]
transcript.source=fields[1]
transcript.setBegin(begin)
transcript.setEnd(end)
if(transcript.score is None and
score!="."): transcript.score=float(score)
geneId=None
if(rex.find("genegrp=(\S+)",line)): geneId=rex[1]
elif(rex.find('gene_id[:=]?\s*\"?([^\s\;"]+)\"?',line)):
geneId=rex[1]
if(not geneId): raise Exception("can't parse GTF: "+line)
transcript.geneId=geneId
gene=genes.get(geneId,None)
if(not gene): genes[geneId]=gene=Gene(); gene.setId(geneId)
transcript.setGene(gene)
gene.addTranscript(transcript)
transcript.extraFields=transcriptExtraFields
return None
#============================= main() =================================
parser=EssexParser(infile)
while(True):
report=parser.nextElem()
if(not report): break
statusNode=report.findChild("status");
if(not statusNode): continue
siteType="donor"
brokenNode=statusNode.findChild("broken-donor")
if(not brokenNode):
siteType="acceptor"
brokenNode=statusNode.findChild("broken-acceptor")
if(not brokenNode): continue
sitePos=int(brokenNode.getIthElem(0))
geneID=report.getAttribute("gene-ID")
transID=report.getAttribute("transcript-ID")
mappedNode=report.findChild("mapped-transcript")
strand=mappedNode.getAttribute("strand")
mappedTranscript=Transcript(mappedNode)
mappedExons=mappedTranscript.getRawExons()
mappedExons.sort(key=lambda exon: exon.begin)
interval=getInterval(sitePos,mappedExons)
#if(interval is None): print(mappedTranscript.toGff())
if(interval is None): continue
print(indiv,hap,geneID,transID,strand,interval.exon,siteType,
interval.begin,sitePos,interval.end,sep="\t",flush=True)
def assembleTranscriptome(self):
"""
Loop over uniqueGeneSet, in which the ENSG-IDs are saved,
and assemble all the transcripts and exons for this gene and save it as a Gene object.
This gene obeject ist then added to the geneList of this Genome object
"""
# transcriptsByType = defaultdict(list)
# construct Genes
for uniqGene in self.uniqGeneSet:
geneId, chromosome, strand = uniqGene
geneNames = list(self.uniqGene_to_names[uniqGene])
geneType = self.uniqGene_to_source[uniqGene]
geneExons = set()
geneCds = set()
# get exons from all transcripts
for transcriptId in self.uniqGene_to_transcriptIds[uniqGene]:
geneExons |= self.transcriptId_to_exons[
transcriptId] # add new exon tuples to geneExons set
geneCds |= self.transcriptId_to_cds[transcriptId]
# usually gtf Files are sorted, but this can't be assumed
geneExons = sorted(geneExons, reverse=not strand)
geneCds = sorted(geneCds, reverse=not strand)
gene = Gene(geneId, chromosome, strand, geneType, geneNames,
geneExons, geneCds)
geneExons = dict(zip(geneExons, xrange(1000000)))
geneCds = dict(zip(geneCds, xrange(1000000)))
self.geneList.append(gene)
# construct transcripts
for transcriptId in self.uniqGene_to_transcriptIds[uniqGene]:
transcriptNames = self.transcriptId_to_names[transcriptId]
protId = self.transcriptId_to_protId[
transcriptId] if transcriptId in self.transcriptId_to_protId else None
exons = sorted(self.transcriptId_to_exons[transcriptId])
codingExons = sorted(self.transcriptId_to_cds[transcriptId])
exonIndices = array('H', [geneExons[e] for e in exons])
codingExonIndices = array('H',
[geneCds[e] for e in codingExons])
codingFrames = array('H', [
int(frame) for exonNumber, frame in sorted(
self.transcriptId_to_codingFrames[transcriptId])
])
startCodon = tuple([
interval for exonNumber, interval in sorted(
self.transcriptId_to_startCodons[transcriptId])
])
stopCodon = tuple([
interval for exonNumber, interval in sorted(
self.transcriptId_to_stopCodons[transcriptId])
])
if len(codingExons) != len(codingFrames):
raise Exception(
"Number of coding Exons and Frames differ for %s %s" %
geneId, transcriptId)
transcript = Transcript(gene, transcriptId,
list(transcriptNames), protId,
exonIndices, codingExonIndices,
codingFrames, startCodon, stopCodon)
gene.addTranscript(transcript)
class ByuSession:
def __init__(self, username, password):
# Check to make sure all information is present
if not username or not password:
raise ByuSessionError("Please enter a username and password to continue.")
self.username = username.lower().strip()
self.password = password
self.transcript = []
self.parsed_transcript = None
self.session = None
self.semesters = []
def signIn(self):
sys.stdout.write("Logging in... ")
session_requests = requests.session()
login_url = "https://cas.byu.edu/cas/login?service=https://my.byu.edu/uPortal/Login"
result = session_requests.get(login_url)
# Must return a HTTP 200 code
if str(result.status_code)[0] is not "2":
raise ByuSessionError("Could not gather CAS login page. HTTP error Code: " + str(result.status_code))
tree = html.fromstring(result.text)
execution = list(set(tree.xpath("//input[@name='execution']/@value")))[0]
lt = list(set(tree.xpath("//input[@name='lt']/@value")))[0]
# Prepare http post data
payload = {
"username": self.username,
"password": self.password,
"execution": execution,
"lt": lt,
"_eventId": "submit"
}
# Post the credentials
result = session_requests.post(
login_url,
data = payload,
headers = dict(referer=login_url)
)
# Must return a HTTP 200 code
if str(result.status_code)[0] is not "2":
raise ByuSessionError("Login failed. Please check your username and password. HTTP error Code: " + str(result.status_code))
if "Unable to sign in:" in result.text:
raise ByuSessionError("Login failed. Please check your username and password.")
self.session = session_requests
sys.stdout.flush()
sys.stdout.write("Done.\n")
def getTranscript(self):
sys.stdout.write("Retreiving transcript... ")
if self.session is None:
raise ByuSessionError("Please sign in first.")
return
url = 'https://y.byu.edu/ry/ae/prod/records/cgi/stdCourseWork.cgi'
result = self.session.get(
url,
headers = dict(referer = url)
)
# Must return a HTTP 200 code
if str(result.status_code)[0] is not "2":
raise ByuSessionError("The transcript page returned with errors. HTTP error Code: " + str(result.status_code))
tree = html.fromstring(result.content)
elem = tree.xpath("//pre/descendant-or-self::text()")
for x in elem:
self.transcript.append(x.replace("\\n", "\n"))
if not self.transcript:
raise ByuSessionError("The transcript could not be collected.\n***Please check your username and password.***")
sys.stdout.flush()
sys.stdout.write("Done.\n")
def getAndParseTranscript(self):
# If the transcript has not been collected yet, get it
if not self.transcript:
self.signIn()
self.getTranscript()
# Patterns to look for in the transcript
semester_start_pattern = re.compile("((?:Fall|Winter|Spring|Summer)\s(?:Semester|Term)\s[0-9]{4}).*")
current_semester_signifier = re.compile("(?:CURRENT ENROLLMENT).*")
transfer_credits_start = re.compile("(?:YRTRM).*")
end_pattern = re.compile("(?:SEM|TRN|--------------------------------------------------------------).*")
past_class_pattern = re.compile("[\s\S]{6}(?:[0-9]{3}|[0-9]{3}[A-Z])\s+[0-9]{3}[\s\S]{42}[0-9]\.[0-9]{2}.*[A-P|W][+-]?")
current_class_pattern = re.compile("[\s\S]{6}(?:[0-9]{3}|[0-9]{3}[A-Z])\s+[0-9]{3}[\s\S]{42}[0-9]\.[0-9]{2}")
start_semester = False
start_current_semester = False
transfer_semester = False
semesters = []
recording_semester = ""
# Otherwise, only get the current semester
for line in self.transcript:
# End of semester, current semester, and transfer credits
if end_pattern.match(line.strip()) and start_semester:
start_semester = False
semesters.append(recording_semester)
# Current semester sigifier
elif current_semester_signifier.match(line):
start_current_semester = True
# Start of any semester
elif semester_start_pattern.match(line):
start_semester = True
semester_name = line.split() # [name] Semester [year]
recording_semester = Semester(semester_name[0], semester_name[2], start_current_semester)
# Append class to semester
elif start_semester:
line = line.strip()
if not start_current_semester:
recording_semester.addClass(self.parsePastClass(line))
else:
if past_class_pattern.match(line):
recording_semester.addClass(self.parsePastClass(line))
else:
recording_semester.addClass(self.parseCurrentClass(line))
elif transfer_credits_start.match(line.strip()): # Transfer credits
print "Transfer Credits Started!: ", line
transfer_semester = True
recording_semester = Semester("Transfer", "N/A", False)
elif end_pattern.match(line.strip()) and transfer_semester: # Transfer credits ended
print "Transfer Credits Ended: ", line
transfer_semester = False
semesters.append(recording_semester)
elif transfer_semester: # Record transfer semester
print "Transfer Line: ", line
recording_semester.addClass(self.parseTransferClass(line))
if not semesters:
raise ByuSessionError("There are no classes listed for the selected semester.\nIf you are receiving this message in error, please try again.")
self.parsed_transcript = Transcript(semesters)
return self.parsed_transcript
def getTargetSemester(self, semester_name, year):
semester_name = semester_name.lower().capitalize()
if semester_name == "Semester" or (semester_name != "All" and not year):
raise ByuSessionError("Please enter a valid semester and year to continue.")
if not self.transcript:
self.getAndParseTranscript()
# If all semesters are selected, print entire thing
if semester_name == "All":
return self.parsed_transcript
else:
return self.parsed_transcript.getSemester(semester_name, year)
def parsePastClass(self, aClass):
aClass_list = self.parseClass(aClass, 2)
department = aClass_list[0]
number = aClass_list[1]
section = aClass_list[2]
name = aClass_list[3]
points_total = aClass_list[4]
grade = aClass_list[5]
# Combine classes
return Class(department, number, int(section), name, float(points_total), grade)
def parseCurrentClass(self, aClass):
aClass_list = self.parseClass(aClass, 1)
department = aClass_list[0]
number = aClass_list[1]
section = aClass_list[2]
name = aClass_list[3]
points_total = aClass_list[4]
# Combine classes
return Class(department, number, int(section), name, float(points_total))
def parseClass(self, aClass, parse_offset):
aClass_list = aClass.split()
# Check for department name in first indexes
if not aClass_list[1][0].isdigit():
aClass_list[0:2] = [" ".join(aClass_list[0:2])]
# Merge class description
aClass_list[3:(len(aClass_list) - parse_offset)] = [" ".join(aClass_list[3:(len(aClass_list) - parse_offset)])]
return aClass_list
def parseTransferClass(self, aClass):
credits_pattern = re.compile("[0-9][.][0-9]{2}")
grades_pattern = re.compile("\s[A-F][\-|\+]?\s")
aClass_list = aClass.split()
department = aClass_list[1]
number = aClass_list[2]
section = 000
name = ""
finished = False
for item in aClass_list[3:]:
if not finished:
for letter in item:
if letter.isdigit():
finished = True
break
if not finished:
name = name + " " + item
credit_hours = float(credits_pattern.search(aClass).group(0))
letter_grade = grades_pattern.search(aClass).group(0).strip()
print "Credit Hours: ", str(credit_hours), "\nLetter Grade: ", str(letter_grade)
return Class(department, number, section, name, credit_hours, letter_grade)
def getAndParseTranscript(self):
# If the transcript has not been collected yet, get it
if not self.transcript:
self.signIn()
self.getTranscript()
# Patterns to look for in the transcript
semester_start_pattern = re.compile("((?:Fall|Winter|Spring|Summer)\s(?:Semester|Term)\s[0-9]{4}).*")
current_semester_signifier = re.compile("(?:CURRENT ENROLLMENT).*")
transfer_credits_start = re.compile("(?:YRTRM).*")
end_pattern = re.compile("(?:SEM|TRN|--------------------------------------------------------------).*")
past_class_pattern = re.compile("[\s\S]{6}(?:[0-9]{3}|[0-9]{3}[A-Z])\s+[0-9]{3}[\s\S]{42}[0-9]\.[0-9]{2}.*[A-P|W][+-]?")
current_class_pattern = re.compile("[\s\S]{6}(?:[0-9]{3}|[0-9]{3}[A-Z])\s+[0-9]{3}[\s\S]{42}[0-9]\.[0-9]{2}")
start_semester = False
start_current_semester = False
transfer_semester = False
semesters = []
recording_semester = ""
# Otherwise, only get the current semester
for line in self.transcript:
# End of semester, current semester, and transfer credits
if end_pattern.match(line.strip()) and start_semester:
start_semester = False
semesters.append(recording_semester)
# Current semester sigifier
elif current_semester_signifier.match(line):
start_current_semester = True
# Start of any semester
elif semester_start_pattern.match(line):
start_semester = True
semester_name = line.split() # [name] Semester [year]
recording_semester = Semester(semester_name[0], semester_name[2], start_current_semester)
# Append class to semester
elif start_semester:
line = line.strip()
if not start_current_semester:
recording_semester.addClass(self.parsePastClass(line))
else:
if past_class_pattern.match(line):
recording_semester.addClass(self.parsePastClass(line))
else:
recording_semester.addClass(self.parseCurrentClass(line))
elif transfer_credits_start.match(line.strip()): # Transfer credits
print "Transfer Credits Started!: ", line
transfer_semester = True
recording_semester = Semester("Transfer", "N/A", False)
elif end_pattern.match(line.strip()) and transfer_semester: # Transfer credits ended
print "Transfer Credits Ended: ", line
transfer_semester = False
semesters.append(recording_semester)
elif transfer_semester: # Record transfer semester
print "Transfer Line: ", line
recording_semester.addClass(self.parseTransferClass(line))
if not semesters:
raise ByuSessionError("There are no classes listed for the selected semester.\nIf you are receiving this message in error, please try again.")
self.parsed_transcript = Transcript(semesters)
return self.parsed_transcript
def makeTranscript(self,root):
id=root["extra"]["ID"]
strand=root["strand"]
transcript=Transcript(id,strand)
root["object"]=transcript
transcript.substrate=root["substrate"]
transcript.source=root["source"]
transcript.begin=int(root["begin"])
transcript.end=int(root["end"])
children=root.get("children",None)
if(children is None): return transcript
for child in children:
obj=self.labelStructure(child)
if(obj is None): continue
if(type(obj)==Exon):
childType=child["type"]
if(childType=="CDS" or
re.search("-exon",childType)): transcript.addExon(obj)
elif(childType=="exon"): transcript.addRawExon(obj)
elif(re.search("UTR",childType)): transcript.addUTR(obj)
obj.transcript=transcript
transcript.parseRawExons()
transcript.setExonTypes()
transcript.setUTRtypes()
transcript.sortExons()
transcript.adjustOrders()
extra=root["extra"]
transcript.extraFields=""
for key in extra:
transcript.extraFields+=key+"="+extra[key]+";"
return transcript
def get_transcripts_list(paths):
# Get list of sorted Transcript files
transcripts = []
for path in sorted_paths(paths):
transcripts.append(Transcript(path))
return transcripts
import ast
app = Flask(__name__)
cors = CORS(app)
api = Api(app)
parser = reqparse.RequestParser()
parser.add_argument('transcript')
course_catalog = CourseCatalog()
course_catalog.load_courses('coursecatalog.csv')
degree_catalog = DegreeCatalog()
degree_catalog.load_degrees('degrees.json')
test_transcript = Transcript('ComputerScienceBA')
test_transcript.load_transcript('transcriptExample.json')
test_degree = degree_catalog.get_degree('ComputerScienceBA')
test_transcript.reccommend(degree_catalog)
#print(test_transcript.audit_transcript(degree_catalog.get_degree('Manangement Information System Major')))
#print(res)
class HelloWorld(Resource):
"""
Test REST Endpoint
"""
def get(self):
class MainWindow(QtWidgets.QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.transcript = Transcript()
self.student_info = StudentInfo()
self.selected_department = ""
self.selectable_courses = {}
self.current_season = ""
self.resize(510, 700)
self.setFixedWidth(510)
self.setWindowFlags(QtCore.Qt.WindowCloseButtonHint
| QtCore.Qt.WindowMinimizeButtonHint)
self.menu_bar = QtWidgets.QMenuBar()
self.file_menu = QtWidgets.QMenu("Dosya")
self.open = self.file_menu.addAction("Aç")
self.save = self.file_menu.addAction("Kaydet")
self.save_as = self.file_menu.addAction("Farklı Kaydet")
self.menu_bar.addMenu(self.file_menu)
self.setMenuBar(self.menu_bar)
user_name_label = QtWidgets.QLabel("Kullanıcı adı:")
self.user_name_show_label = QtWidgets.QLabel("")
self.user_select_button = QtWidgets.QPushButton("Transcript Yükle")
user_layout = QtWidgets.QHBoxLayout()
user_layout.addWidget(user_name_label, 0)
user_layout.addWidget(self.user_name_show_label, 1)
user_layout.addWidget(self.user_select_button, 2)
code_select_label = QtWidgets.QLabel("Bölüm Kodu Seç")
code_select_label.setMaximumSize(110, 25)
education_year_label = QtWidgets.QLabel("Eğitim Yılını Seç")
education_season_label = QtWidgets.QLabel("Eğitim Dönemini Seç")
education_season_label.setMaximumSize(150, 25)
self.code_select_cbox = QtWidgets.QComboBox()
self.code_select_cbox.addItem("Seç")
self.code_select_cbox.setFixedSize(100, 25)
self.education_season_cbox = QtWidgets.QComboBox()
self.education_year_cbox = QtWidgets.QComboBox()
self.season_select = QtWidgets.QPushButton("Seç")
hor_spacer = QtWidgets.QSpacerItem(40, 20,
QtWidgets.QSizePolicy.Expanding)
top_grid_layout = QtWidgets.QGridLayout()
top_grid_layout.addWidget(code_select_label, 0, 0)
top_grid_layout.addWidget(self.code_select_cbox, 0, 1)
top_grid_layout.addItem(hor_spacer, 0, 2)
top_grid_layout.addWidget(education_year_label, 0, 3)
top_grid_layout.addWidget(self.education_year_cbox, 0, 4)
top_grid_layout.addWidget(education_season_label, 1, 3)
top_grid_layout.addWidget(self.education_season_cbox, 1, 4)
top_grid_layout.addWidget(self.season_select, 2, 4)
self.course_table = QtWidgets.QTableWidget()
self.course_table.setColumnCount(8)
self.course_table.setFixedWidth(438)
self.course_table.setColumnHidden(4, True)
self.course_table.setColumnHidden(5, True)
self.course_table.setColumnHidden(6, True)
self.course_table.setColumnHidden(7, True)
course_code_label = QtWidgets.QLabel("Ders Kodu")
course_num_label = QtWidgets.QLabel("Ders Numarası")
not_label = QtWidgets.QLabel("Not")
gen_not_ort_label = QtWidgets.QLabel("Genel Not Ortalaması:")
self.gpa_show_label = QtWidgets.QLabel()
self.course_code_cbox = QtWidgets.QComboBox()
self.course_code_cbox.addItem("Seç")
self.course_num_cbox = QtWidgets.QComboBox()
self.course_num_cbox.addItem("Seç")
self.grade_cbox = QtWidgets.QComboBox()
self.grade_cbox.addItem("Seç")
self.gpa_show_label = QtWidgets.QLabel()
self.remove_course_button = QtWidgets.QPushButton(
"Seçilen Dersi Çıkar")
bottom_grid_layout = QtWidgets.QGridLayout()
bottom_grid_layout.addWidget(course_code_label, 0, 0)
bottom_grid_layout.addWidget(self.course_code_cbox, 0, 1)
bottom_grid_layout.addWidget(self.remove_course_button, 0, 3)
bottom_grid_layout.addWidget(course_num_label, 1, 0)
bottom_grid_layout.addWidget(self.course_num_cbox, 1, 1)
bottom_grid_layout.addWidget(gen_not_ort_label, 1, 2)
bottom_grid_layout.addWidget(self.gpa_show_label, 1, 3)
bottom_grid_layout.addWidget(not_label, 2, 0)
bottom_grid_layout.addWidget(self.grade_cbox, 2, 1)
self.add = QtWidgets.QPushButton("Ders Ekle")
bottom_hor_layout = QtWidgets.QHBoxLayout()
bottom_hor_layout.addWidget(self.add)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addLayout(user_layout, 0)
main_layout.addLayout(top_grid_layout, 1)
main_layout.addWidget(self.course_table, 2)
main_layout.addLayout(bottom_grid_layout, 3)
main_layout.addLayout(bottom_hor_layout, 4)
self.central_widget = QtWidgets.QWidget()
self.central_widget.setLayout(main_layout)
self.setCentralWidget(self.central_widget)
self.setWindowTitle("İTÜ Ortalama Hesaplayıcı")
QtCore.QObject.connect(self.code_select_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.read_selected_department)
QtCore.QObject.connect(self.course_code_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.set_course_num_cbox)
QtCore.QObject.connect(self.education_year_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.set_education_season_cbox)
QtCore.QObject.connect(self.season_select, QtCore.SIGNAL("clicked()"),
self.add_season)
QtCore.QObject.connect(self.add, QtCore.SIGNAL("clicked()"),
self.add_course)
QtCore.QObject.connect(self.remove_course_button,
QtCore.SIGNAL("clicked()"), self.remove_row)
if self.get_transcript_data():
self.write_transcript_table()
self.set_education_year_cbox()
self.set_gpa_show_label()
self.set_code_select_cbox(save_data.read_verify_departments_code())
self.set_grade_cbox()
self.set_user_name_label()
def set_code_select_cbox(self, departments: dict):
for code in sorted(list(departments.values())):
self.code_select_cbox.addItem(code)
def set_course_code_cbox(self):
self.course_code_cbox.clear()
self.course_code_cbox.addItem("Seç")
for code in sorted(self.selectable_courses.keys()):
self.course_code_cbox.addItem(code)
def set_course_num_cbox(self):
department_code = self.course_code_cbox.currentText()
self.course_num_cbox.clear()
self.course_num_cbox.addItem("Seç")
if department_code not in ["", "Seç"]:
for code in sorted(set(self.selectable_courses[department_code])):
self.course_num_cbox.addItem(code)
def set_grade_cbox(self):
for grades in ["AA", "BA", "BB", "CB", "CC", "DC", "DD", "FF", "VF"]:
self.grade_cbox.addItem(grades)
def set_education_year_cbox(self):
years = self.calculate_years()
for year in years:
self.education_year_cbox.addItem(year)
def set_education_season_cbox(self):
self.education_season_cbox.clear()
seasons = ["Güz", "Bahar", "Yaz Öğretimi"]
education_year = self.education_year_cbox.currentText()
last_season = self.transcript.get_last_season()
last_year = last_season[:9]
if education_year == last_year:
for i in range(seasons.index(last_season[12:]) + 1, 3):
self.education_season_cbox.addItem(seasons[i])
else:
for season in seasons:
self.education_season_cbox.addItem(season)
def set_gpa_show_label(self):
self.gpa_show_label.setText(str(round(self.transcript.get_gpa(), 2)))
def set_rows_header(self):
course_counter = 1
for i in range(self.course_table.rowCount()):
item = QtWidgets.QTableWidgetItem()
if self.course_table.item(i, 5).text() == "Course":
item.setText(str(course_counter))
course_counter += 1
else:
item.setBackgroundColor(QtGui.QColor(QtCore.Qt.gray))
item.setText("")
self.course_table.setVerticalHeaderItem(i, item)
def set_user_name_label(self):
self.user_name_show_label.setText(self.transcript.user_name)
def calculate_years(self):
last_season = self.transcript.get_last_season()
years = []
if last_season[12:] != "Yaz Öğretimi":
first_ind = 0
else:
first_ind = 1
for i in range(first_ind, 5):
years.append(
str(int(last_season[:4]) + i) + "-" +
str(int(last_season[5:9]) + i))
return years
def read_selected_department(self):
self.selected_department = self.code_select_cbox.currentText()
self.selectable_courses = curriculums.parse_courses_code(
self.selected_department)
self.set_course_code_cbox()
def read_course_code_cbox(self):
return self.course_code_cbox.currentText()
def read_course_num_cbox(self):
return self.course_num_cbox.currentText()
def read_grade_cbox(self):
return self.grade_cbox.currentText()
def add_row(self, row_data, row_number=None):
if not row_number:
row_number = self.course_table.rowCount()
if row_data[5] == "Course":
self.add_course_row(row_data, row_number)
elif row_data[5] == "Season":
self.add_season_row(row_data, row_number)
def add_season_row(self, row_data, row_number):
self.course_table.insertRow(row_number)
for i, data in enumerate(row_data):
item = QtWidgets.QTableWidgetItem(str(data))
item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
item.setBackgroundColor(QtGui.QColor(QtCore.Qt.gray))
self.course_table.setItem(row_number, i, item)
def add_course_row(self, row_data, row_number):
self.course_table.insertRow(row_number)
for i, data in enumerate(row_data):
if row_data[4] and i == 3:
grade_cbox = QtWidgets.QComboBox()
if row_data[7]:
grade_cbox.setEnabled(False)
grade_cbox.addItem(data)
else:
if int(row_data[2]):
for grades in [
"AA", "BA", "BB", "CB", "CC", "DC", "DD", "FF",
"VF"
]:
grade_cbox.addItem(grades)
else:
for grades in ["BZ", "BL"]:
grade_cbox.addItem(grades)
grade_cbox.setCurrentText(data.strip())
self.course_table.setCellWidget(row_number, i, grade_cbox)
QtCore.QObject.connect(
self.course_table.cellWidget(row_number, i),
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.update_course_data)
else:
item = QtWidgets.QTableWidgetItem(str(data))
item.setFlags(QtCore.Qt.ItemIsEnabled
| QtCore.Qt.ItemIsSelectable)
self.course_table.setItem(row_number, i, item)
def add_season(self):
education_year = self.education_year_cbox.currentText()
education_season = self.education_season_cbox.currentText()
season = education_year + " / " + education_season
self.current_season = season
try:
self.transcript.add_season(season)
self.write_transcript_table()
except IntegrityError:
pass
def add_course(self):
if not self.current_season:
QtWidgets.QMessageBox.information(self, "Hata",
"Önce Dönem Seçin!",
QtWidgets.QMessageBox.Ok)
else:
course_code = self.read_course_code_cbox()
if course_code == "Seç":
QtWidgets.QMessageBox.information(self, "Hata",
"Ders Kodu Seçin",
QtWidgets.QMessageBox.Ok)
return False
course_num = self.read_course_num_cbox()
if course_num == "Seç":
QtWidgets.QMessageBox.information(self, "Hata",
"Ders No Seçin",
QtWidgets.QMessageBox.Ok)
return False
course_grade = self.read_grade_cbox()
if course_grade == "Seç":
QtWidgets.QMessageBox.information(self, "Hata",
"Ders Notu Seçin",
QtWidgets.QMessageBox.Ok)
return False
course_data = self.find_course_data(course_code + " " + course_num)
data = [
course_data["Ders Kodu"], course_data["Ders Adı"],
course_data["Kredi"], course_grade, 0, self.current_season
]
try:
self.transcript.check_course_before_added(data[0])
self.transcript.add_course(data)
self.write_transcript_table()
self.set_gpa_show_label()
except IntegrityError:
QtWidgets.QMessageBox.information(
self, "Hata", "Bir Döneme Aynı Dersten İki Tane Eklenemez",
QtWidgets.QMessageBox.Ok)
def write_transcript_table(self):
self.course_table.clear()
self.course_table.setRowCount(0)
transcript_data = self.transcript.get_transcript_data()
for row in transcript_data:
self.add_row(row)
self.set_rows_header()
self.course_table.setHorizontalHeaderItem(
0, QtWidgets.QTableWidgetItem("Ders Kodu"))
self.course_table.setHorizontalHeaderItem(
1, QtWidgets.QTableWidgetItem("Ders İsmi"))
self.course_table.setHorizontalHeaderItem(
2, QtWidgets.QTableWidgetItem("Kredi"))
self.course_table.setHorizontalHeaderItem(
3, QtWidgets.QTableWidgetItem("Not"))
self.course_table.setHorizontalHeaderItem(
4, QtWidgets.QTableWidgetItem("Editable"))
self.course_table.setHorizontalHeaderItem(
5, QtWidgets.QTableWidgetItem("Tag"))
self.course_table.setHorizontalHeaderItem(
6, QtWidgets.QTableWidgetItem("Season Name"))
self.course_table.setHorizontalHeaderItem(
7, QtWidgets.QTableWidgetItem("Passive"))
def find_course_data(self, course_code):
department_code = self.code_select_cbox.currentText()
courses = save_data.read_elective_courses(
department_code) + save_data.read_departments_curriculum(
department_code)
for item in courses:
key = item["Ders Kodu"]
if course_code == key or course_code[:
-1] == key or course_code == key[:
-1]:
item["Ders Kodu"] = course_code
return item
return {}
def update_course_data(self):
table_data = []
for row in reversed(range(self.course_table.rowCount())):
if self.course_table.item(row, 4).text() == '0':
break
elif self.course_table.item(row, 5).text() == "Season":
continue
table_data.append([
self.course_table.cellWidget(row, 3).currentText(),
self.course_table.item(row, 6).text()
])
db_data = self.transcript.get_editable_data()
for i, course in enumerate(reversed(db_data)):
if table_data[i][0] != course[1].strip():
self.transcript.update_course(table_data[i][1], course[0],
table_data[i][0])
self.transcript.update_season_gpa(table_data[i][1])
self.update_season_gpa(table_data[i][1])
break
self.set_gpa_show_label()
def update_season_gpa(self, season_name):
gpa = self.transcript.get_season_gpa(season_name)
for row in reversed(range(self.course_table.rowCount())):
if self.course_table.item(row, 5).text() == "Season" \
and self.course_table.item(row, 0).text() == season_name[:9] \
and self.course_table.item(row, 1).text() == season_name[12:]:
item = self.course_table.takeItem(row, 3)
item.setText(str(gpa))
self.course_table.setItem(row, 3, item)
def remove_row(self):
current_row = self.course_table.currentRow()
if self.course_table.item(current_row, 4).text() == "0":
QtWidgets.QMessageBox.information(self, "Hata",
"Bu Satırı Silemezsiniz.",
QtWidgets.QMessageBox.Ok)
return
if self.course_table.item(current_row, 5).text() == "Course":
self.transcript.delete_course(
self.course_table.item(current_row, 6).text(),
self.course_table.item(current_row, 0).text())
self.transcript.update_season_gpa(
self.course_table.item(current_row, 6).text())
self.transcript.update_season_credit(
self.course_table.item(current_row, 6).text())
self.write_transcript_table()
self.set_gpa_show_label()
else:
self.transcript.delete_season(
self.course_table.item(current_row, 6).text())
self.write_transcript_table()
self.set_gpa_show_label()
def get_transcript_data(self):
self.student_info.reset_student_info()
self.student_info.show()
if self.student_info.exec_() == QtWidgets.QDialog.Accepted:
self.transcript.set_user_name(self.student_info.user_name)
self.transcript.set_path(self.student_info.path)
self.user_name_show_label.setText(self.transcript.user_name)
return 1
else:
return 0
def __init__(self):
super(MainWindow, self).__init__()
self.transcript = Transcript()
self.student_info = StudentInfo()
self.selected_department = ""
self.selectable_courses = {}
self.current_season = ""
self.resize(510, 700)
self.setFixedWidth(510)
self.setWindowFlags(QtCore.Qt.WindowCloseButtonHint
| QtCore.Qt.WindowMinimizeButtonHint)
self.menu_bar = QtWidgets.QMenuBar()
self.file_menu = QtWidgets.QMenu("Dosya")
self.open = self.file_menu.addAction("Aç")
self.save = self.file_menu.addAction("Kaydet")
self.save_as = self.file_menu.addAction("Farklı Kaydet")
self.menu_bar.addMenu(self.file_menu)
self.setMenuBar(self.menu_bar)
user_name_label = QtWidgets.QLabel("Kullanıcı adı:")
self.user_name_show_label = QtWidgets.QLabel("")
self.user_select_button = QtWidgets.QPushButton("Transcript Yükle")
user_layout = QtWidgets.QHBoxLayout()
user_layout.addWidget(user_name_label, 0)
user_layout.addWidget(self.user_name_show_label, 1)
user_layout.addWidget(self.user_select_button, 2)
code_select_label = QtWidgets.QLabel("Bölüm Kodu Seç")
code_select_label.setMaximumSize(110, 25)
education_year_label = QtWidgets.QLabel("Eğitim Yılını Seç")
education_season_label = QtWidgets.QLabel("Eğitim Dönemini Seç")
education_season_label.setMaximumSize(150, 25)
self.code_select_cbox = QtWidgets.QComboBox()
self.code_select_cbox.addItem("Seç")
self.code_select_cbox.setFixedSize(100, 25)
self.education_season_cbox = QtWidgets.QComboBox()
self.education_year_cbox = QtWidgets.QComboBox()
self.season_select = QtWidgets.QPushButton("Seç")
hor_spacer = QtWidgets.QSpacerItem(40, 20,
QtWidgets.QSizePolicy.Expanding)
top_grid_layout = QtWidgets.QGridLayout()
top_grid_layout.addWidget(code_select_label, 0, 0)
top_grid_layout.addWidget(self.code_select_cbox, 0, 1)
top_grid_layout.addItem(hor_spacer, 0, 2)
top_grid_layout.addWidget(education_year_label, 0, 3)
top_grid_layout.addWidget(self.education_year_cbox, 0, 4)
top_grid_layout.addWidget(education_season_label, 1, 3)
top_grid_layout.addWidget(self.education_season_cbox, 1, 4)
top_grid_layout.addWidget(self.season_select, 2, 4)
self.course_table = QtWidgets.QTableWidget()
self.course_table.setColumnCount(8)
self.course_table.setFixedWidth(438)
self.course_table.setColumnHidden(4, True)
self.course_table.setColumnHidden(5, True)
self.course_table.setColumnHidden(6, True)
self.course_table.setColumnHidden(7, True)
course_code_label = QtWidgets.QLabel("Ders Kodu")
course_num_label = QtWidgets.QLabel("Ders Numarası")
not_label = QtWidgets.QLabel("Not")
gen_not_ort_label = QtWidgets.QLabel("Genel Not Ortalaması:")
self.gpa_show_label = QtWidgets.QLabel()
self.course_code_cbox = QtWidgets.QComboBox()
self.course_code_cbox.addItem("Seç")
self.course_num_cbox = QtWidgets.QComboBox()
self.course_num_cbox.addItem("Seç")
self.grade_cbox = QtWidgets.QComboBox()
self.grade_cbox.addItem("Seç")
self.gpa_show_label = QtWidgets.QLabel()
self.remove_course_button = QtWidgets.QPushButton(
"Seçilen Dersi Çıkar")
bottom_grid_layout = QtWidgets.QGridLayout()
bottom_grid_layout.addWidget(course_code_label, 0, 0)
bottom_grid_layout.addWidget(self.course_code_cbox, 0, 1)
bottom_grid_layout.addWidget(self.remove_course_button, 0, 3)
bottom_grid_layout.addWidget(course_num_label, 1, 0)
bottom_grid_layout.addWidget(self.course_num_cbox, 1, 1)
bottom_grid_layout.addWidget(gen_not_ort_label, 1, 2)
bottom_grid_layout.addWidget(self.gpa_show_label, 1, 3)
bottom_grid_layout.addWidget(not_label, 2, 0)
bottom_grid_layout.addWidget(self.grade_cbox, 2, 1)
self.add = QtWidgets.QPushButton("Ders Ekle")
bottom_hor_layout = QtWidgets.QHBoxLayout()
bottom_hor_layout.addWidget(self.add)
main_layout = QtWidgets.QVBoxLayout()
main_layout.addLayout(user_layout, 0)
main_layout.addLayout(top_grid_layout, 1)
main_layout.addWidget(self.course_table, 2)
main_layout.addLayout(bottom_grid_layout, 3)
main_layout.addLayout(bottom_hor_layout, 4)
self.central_widget = QtWidgets.QWidget()
self.central_widget.setLayout(main_layout)
self.setCentralWidget(self.central_widget)
self.setWindowTitle("İTÜ Ortalama Hesaplayıcı")
QtCore.QObject.connect(self.code_select_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.read_selected_department)
QtCore.QObject.connect(self.course_code_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.set_course_num_cbox)
QtCore.QObject.connect(self.education_year_cbox,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.set_education_season_cbox)
QtCore.QObject.connect(self.season_select, QtCore.SIGNAL("clicked()"),
self.add_season)
QtCore.QObject.connect(self.add, QtCore.SIGNAL("clicked()"),
self.add_course)
QtCore.QObject.connect(self.remove_course_button,
QtCore.SIGNAL("clicked()"), self.remove_row)
if self.get_transcript_data():
self.write_transcript_table()
self.set_education_year_cbox()
self.set_gpa_show_label()
self.set_code_select_cbox(save_data.read_verify_departments_code())
self.set_grade_cbox()
self.set_user_name_label()
def makeTranscript(self, root):
id = root["extra"]["ID"]
strand = root["strand"]
transcript = Transcript(id, strand)
root["object"] = transcript
transcript.substrate = root["substrate"]
transcript.source = root["source"]
transcript.begin = int(root["begin"])
transcript.end = int(root["end"])
children = root.get("children", None)
if (children is None): return transcript
for child in children:
obj = self.labelStructure(child)
if (obj is None): continue
if (type(obj) == Exon):
childType = child["type"]
if (childType == "CDS" or re.search("-exon", childType)):
transcript.addExon(obj)
elif (childType == "exon"):
transcript.addRawExon(obj)
elif (re.search("UTR", childType)):
transcript.addUTR(obj)
obj.transcript = transcript
transcript.parseRawExons()
transcript.setExonTypes()
transcript.setUTRtypes()
transcript.sortExons()
transcript.adjustOrders()
extra = root["extra"]
transcript.extraFields = ""
for key in extra:
transcript.extraFields += key + "=" + extra[key] + ";"
return transcript
