def main():
reference = Reference(argv[1])
reference.get_regions_index()
print("Reference %s processed" % argv[1])
with gzip.open(argv[2], 'rt') as sam_file:
alignment = AlignmentInformation(reference)
print("Processing alignment information in SAM file...")
for line in sam_file.readlines(
)[2:]: # Information of reads alignment starts in 2nd line
read = Read(line)
if read.flag != 4 and read.quality == 255:
'''
Reads with flag value 4 (i.e. not aligned) and quality value different than 255 (optimal)
are not processed
'''
read.parse_cigar()
read.get_aligned_sequence()
for exon_range in reference.exons_index_list:
in_exons = read.is_aligned_to(exon_range)
if in_exons is True: # Only exon information is accounted
alignment.update_count_dictionary(read)
break
alignment.create_proportion_dictionary()
print("Progressive analysis in progress...")
progressive_analysis = ProgressiveAnalysis(
alignment) # Proportion_threshold value customizable, default=5
print("%i genes/s detected" %
len(list(progressive_analysis.result_alleles_dictionary.keys())))
print("Combined analysis in progress...")
combined_analysis = CombinedAnalysis(progressive_analysis, alignment)
write_output_file(progressive_analysis, combined_analysis, argv[2],
argv[3])
print("Analysis done, results written into output file: %s" % argv[3])
sam_file.close()
sam_file.close()
def reference(self, text='none', flags=None, isCurrent=True):
if (self.refWin == None or not self.refWin.isVisible()):
self.refWin = Reference(self, self.libMgr)
result = self.refWin.addSearch(text, flags, isCurrent)
if (isinstance(result, str) and result == 'noselection'):
QtGui.QMessageBox.about(self, "Selection Status",
"There is no text selected.")
elif (result):
self.refWin.show()
else:
QtGui.QMessageBox.about(self, "Match Status",
"There are no more matches.")
elif (self.refWin.isVisible()): #the window is open, reset
if (not self.refWin.addSearch(text, flags, isCurrent)):
QtGui.QMessageBox.about(self, "Match Status",
"There are no more matches.")
def reference(self, text='none', flags=None, isCurrent=True):
if(self.refWin == None or not self.refWin.isVisible()):
self.refWin = Reference(self, self.libMgr)
result = self.refWin.addSearch(text, flags, isCurrent)
if(isinstance(result, str) and result == 'noselection'):
QtGui.QMessageBox.about(self, "Selection Status", "There is no text selected.")
elif(result):
self.refWin.show()
else:
QtGui.QMessageBox.about(self, "Match Status", "There are no more matches.")
elif(self.refWin.isVisible()): #the window is open, reset
if(not self.refWin.addSearch(text, flags, isCurrent)):
QtGui.QMessageBox.about(self, "Match Status", "There are no more matches.")
def __init__(self, parent):
wx.Notebook.__init__(self, parent, id=wx.ID_ANY, style=wx.BK_DEFAULT)
self.AddPage(CourtCase.CourtCase(self), "Court Case")
self.AddPage(Reference.NestedReferencePanel(self), "Reference")
self.AddPage(Official.OfficialPanel(self), "Official")
self.AddPage(Defendant.NestedDefendantPanel(self), "Defendant")
self.AddPage(Plaintiff.NestedPlaintiffPanel(self), "Plaintiff")
self.AddPage(Prosecutor.NestedProsecutorPanel(self), "Prosecutor")
self.AddPage(Witness.NestedWitnessPanel(self), "Witness")
self.AddPage(Charges.ChargesPanel(self), "Charges")
self.AddPage(Summary.SummaryPanel(self), "Summary")
self.AddPage(CaseNotes.CaseNotesPanel(self), "Case Notes")
self.AddPage(HealingNotes.HealingNotesPanel(self), "Healing Notes")
self.AddPage(FurtherNotes.FurtherNotesPanel(self),
"Further Research Notes")
def main():
logger.debug('version %s starting' % VERSION)
opt, args = getParms()
# Reading a pickled file and repickling it doesn't make sense. But one day it will...
if opt.format == 'pickle':
refObj = ref.Reference.fromPickle(opt.ref)
else:
refObj = ref.Reference(opt.ref)
refObj.toPickle(opt.output)
logger.debug('finished')
return
mnist = input_data.read_data_sets(r'F:\tensorflow_basic_usage_oop\input_data',
one_hot=True)
#定义两个占位符，分别是原始输入&labels
placeholder_raw_input = tf.placeholder(tf.float32,
shape=[None, TIME_STEPS, ELEMENT_SIZE],
name='inputs')
placeholder_labels = tf.placeholder(tf.float32,
shape=[None, 10],
name='Labels')
processed_input = tf.transpose(placeholder_raw_input, perm=[1, 0, 2])
Simple_RNN = Reference.reference(processed_input, placeholder_labels,
BATCH_SIZE, TIME_STEPS,
ELEMENT_SIZE) #定义了一个新的网络对象
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
for i in range(10000): #10000--1000
batch_x, batch_y = mnist.train.next_batch(BATCH_SIZE) #读取下一个batch的值b
batch_x = batch_x.reshape([BATCH_SIZE, TIME_STEPS, ELEMENT_SIZE])
sess.run(Simple_RNN.train,
feed_dict={
placeholder_raw_input: batch_x,
placeholder_labels: batch_y
})
if i % 1000 == 0: #1000---100
class SiftFlow(QtGui.QMainWindow):
def __init__(self, parent=None):
#If we were opened from the base sift (not the gui) setup the app internaly
if (parent == None):
self.app = QtGui.QApplication(sys.argv)
self.app.setOrganizationName("Hewlett-Packard")
self.app.setOrganizationDomain("hp.com")
self.app.setApplicationName("SiftFlow")
if (sys.platform.startswith("darwin")):
self.app.setStyle("Cleanlooks")
#Setup the window
QtGui.QMainWindow.__init__(self)
self.parent = parent
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
#Declare interface object with backend
self.libMgr = SFLibManager(self, self.ui)
#Do additional Window setup
self.__initMainWindow()
#Only want one reference window at a time
self.refWin = None
self.aboutWin = None
self.findWin = None
self.repWin = None
#Set up actions and signals
QtCore.QObject.connect(self.ui.actionAbout,
QtCore.SIGNAL("triggered()"), self.__about)
QtCore.QObject.connect(self.ui.actionFind,
QtCore.SIGNAL("triggered()"), self.__find)
QtCore.QObject.connect(self.ui.actionFindInFiles,
QtCore.SIGNAL("triggered()"),
self.__findInFiles)
QtCore.QObject.connect(self.ui.actionReference,
QtCore.SIGNAL("triggered()"), self.reference)
QtCore.QObject.connect(self.ui.actionReferenceInFiles,
QtCore.SIGNAL("triggered()"),
self.referenceInFiles)
QtCore.QObject.connect(self.ui.actionCut, QtCore.SIGNAL("triggered()"),
self.__cut)
QtCore.QObject.connect(self.ui.actionCopy,
QtCore.SIGNAL("triggered()"), self.__copy)
QtCore.QObject.connect(self.ui.actionUndo,
QtCore.SIGNAL("triggered()"), self.__undo)
QtCore.QObject.connect(self.ui.actionRedo,
QtCore.SIGNAL("triggered()"), self.__redo)
QtCore.QObject.connect(self.ui.actionGoto,
QtCore.SIGNAL("triggered()"), self.__goto)
QtCore.QObject.connect(self.ui.actionIndent,
QtCore.SIGNAL("triggered()"), self.__indent)
QtCore.QObject.connect(self.ui.actionUnindent,
QtCore.SIGNAL("triggered()"), self.__unindent)
QtCore.QObject.connect(self.ui.actionComment,
QtCore.SIGNAL("triggered()"), self.__comment)
QtCore.QObject.connect(self.ui.actionUncomment,
QtCore.SIGNAL("triggered()"), self.__uncomment)
QtCore.QObject.connect(self.ui.actionPaste,
QtCore.SIGNAL("triggered()"), self.__paste)
QtCore.QObject.connect(self.ui.actionDownload,
QtCore.SIGNAL("triggered()"), self.__download)
QtCore.QObject.connect(self.ui.treeWidget_proj,
QtCore.SIGNAL("itemSelectionChanged()"),
self.__projSelectionChanged)
QtCore.QObject.connect(self.ui.treeWidget_nonProj,
QtCore.SIGNAL("itemSelectionChanged()"),
self.__nonProjSelectionChanged)
QtCore.QObject.connect(self.ui.splitter_leftright,
QtCore.SIGNAL("splitterMoved(int, int)"),
self.__resizeAll)
#QtCore.QObject.connect(self.ui.actionNewFlow, QtCore.SIGNAL("triggered()"), self.__newFlow)
QtCore.QObject.connect(self.ui.actionOpen,
QtCore.SIGNAL("triggered()"), self.__open)
QtCore.QObject.connect(self.ui.actionSave,
QtCore.SIGNAL("triggered()"), self.__save)
#QtCore.QObject.connect(self.ui.actionSave_All, QtCore.SIGNAL("triggered()"), self.__saveAll)
QtCore.QObject.connect(self.ui.menuRecent,
QtCore.SIGNAL("aboutToShow()"),
self.__fillMenuRecent)
QtCore.QObject.connect(self.ui.menuBuild,
QtCore.SIGNAL("aboutToShow()"),
self.__fillMenuBuild)
#SiftFlow, show thyself!!
if (parent == None): self.show()
def run(self):
"""Run the main QT event loop"""
self.app.exec_()
#--- Child Windows ---#
def __about(self):
if (self.aboutWin == None or self.aboutWin.isHidden()):
self.aboutWin = About(self, self.libMgr)
self.aboutWin.exec_()
def __find(self):
if (self.findWin == None or self.findWin.isHidden()):
self.findWin = Find(self, self.libMgr)
self.findWin.show()
def reference(self, text='none', flags=None, isCurrent=True):
if (self.refWin == None or not self.refWin.isVisible()):
self.refWin = Reference(self, self.libMgr)
result = self.refWin.addSearch(text, flags, isCurrent)
if (isinstance(result, str) and result == 'noselection'):
QtGui.QMessageBox.about(self, "Selection Status",
"There is no text selected.")
elif (result):
self.refWin.show()
else:
QtGui.QMessageBox.about(self, "Match Status",
"There are no more matches.")
elif (self.refWin.isVisible()): #the window is open, reset
if (not self.refWin.addSearch(text, flags, isCurrent)):
QtGui.QMessageBox.about(self, "Match Status",
"There are no more matches.")
def referenceInFiles(self):
self.reference(isCurrent='all')
#--- Signal Handlers ---#
def __projSelectionChanged(self):
self.libMgr.tvProjUpdate()
def __nonProjSelectionChanged(self):
self.libMgr.tvNonProjUpdate()
def __cut(self):
self.libMgr.cut()
def __copy(self):
self.libMgr.copy()
def __paste(self):
self.libMgr.paste()
def __findInFiles(self):
findWin = Find(self, self.libMgr)
findWin.findInFiles()
findWin.exec_()
def __undo(self):
self.libMgr.undo()
def __redo(self):
self.libMgr.redo()
def __goto(self):
lineNum, ok = QtGui.QInputDialog.getText(self, 'Go to..',
'Go To Line: ')
if ok:
self.libMgr.setCursorToReference(int(lineNum) - 1, 0)
def __indent(self):
self.libMgr.indent()
def __unindent(self):
self.libMgr.unindent()
def __comment(self):
self.libMgr.comment()
def __uncomment(self):
self.libMgr.uncomment()
def __newFlow(self):
print 'new flow'
def __save(self):
result = self.libMgr.saveCurrentTab()
#Reset the reference window if it is open, to reflect any changes in the files after saving
if (self.refWin and self.refWin.isVisible()): #the window is open
self.refWin.resetTabs()
#def __saveAll(self):
#For now I am removing save all from the ui, but will leave the functionality in.
#Save All would rarely be used and caused a few hard to solve cunundrums with file conflicts
#when a user had unsaved changes in both fmls and flows from those fmls. If in the future, this
#feature is demanded, then all that needs to be done is to reattach the action to the toolbar and
#uncomment this function, the signal and file menu entry near the bottom of this file
#result = self.libMgr.saveAllTabs()
#Reset the reference window if it is open, to reflect any changes in the files after saving
#if(self.refWin and self.refWin.isVisible()): #the window is open
#self.refWin.resetTabs()
def __download(self):
#Cannot download if there is no project loaded
if (not self.libMgr.isProjLoaded()):
self.libMgr.printError("Download failed!", 10)
QtGui.QMessageBox.about(self, "Download Failed",
"No Project Loaded.")
return
#Get a list of all files changed since .all was build
dList = self.libMgr.getDownloadFileList()
#If files have changed since the .all was built, download them to printer
if (len(dList) > 0):
#Turn that list into the command string
cmd = "download " + " ".join(dList)
#Send command to sift
self.parent.parse(cmd)
#If no files have changed, tell user and do nothing
else:
self.libMgr.out("No changed files to download", 6)
#--- Event Handlers ---#
def showEvent(self, se):
self.__resizeAll(0, 0)
def __resizeAll(self, index, pos):
self.libMgr.resizeTreeview()
def closeEvent(self, e):
#If there are any unsaved changes, ask user what they want to do
if (self.libMgr.anyUnsavedChanges()):
msg = "There are unsaved changes. Quitting will discharges these changes."
reply = QtGui.QMessageBox.question(self, "Warning", msg,
QtGui.QMessageBox.Save,
QtGui.QMessageBox.Discard,
QtGui.QMessageBox.Cancel)
if reply == QtGui.QMessageBox.Save:
self.libMgr.saveAnyUnsavedChanges()
elif reply == QtGui.QMessageBox.Cancel:
e.ignore()
return
#Save window size, treeview width, output box height
self.libMgr.saveWindowState(
self.width(), self.height(),
self.ui.splitter_leftright.widget(0).width())
#Close any open dialogs
if (self.aboutWin != None and not self.aboutWin.isHidden()):
self.aboutWin.close()
if (self.findWin != None and not self.findWin.isHidden()):
self.findWin.close()
if (self.repWin != None and not self.repWin.isHidden()):
self.repWin.close()
if (self.refWin != None and not self.refWin.isHidden()):
self.refWin.close()
if (self.parent != None):
self.parent.ui.edit.setEnabled(True)
#--- Opening Files ---#
# Signal handler for open file action
def __open(self):
#Get the last dir opened by the user (from config file)
lastDir = self.libMgr.getLastOpenDir()
#Use file dialog to allow user to select one or more .fmls
ofDialog = QtGui.QFileDialog(self)
files = ofDialog.getOpenFileNames(caption='Open file(s)',
directory=lastDir,
filter='Files (*.fml *.lua)')
#Only load files if the user select any
if not files.isEmpty():
#Place the chosen directory in the config file
self.libMgr.setLastOpenDir(os.path.split(str(files[0]))[0])
#Load the files
self.loadFiles(files)
#Loads a project file provided by sift
def loadProject(self, fileDirs, projPath, projName, projType):
#If not in linux or project_dir is not pointed to a build directory (ie bound to repo) or file_dirs is empty
#Use the project_dir as the file_dirs since the project files will be with the .hlg
if (not sys.platform.startswith('linux')
or not re.search("obj_\w+_\w+", projPath)
or len(fileDirs) == 0):
fileDirs = projPath
try:
self.libMgr.loadProject(fileDirs, projPath, projName, projType)
except:
print "SiftFlow Load Error: "
print "file_dirs: " + str(fileDirs)
print "project_dir: " + str(projPath)
print "project_name: " + str(projName)
print "project_type: " + str(projType)
print "".join(
traceback.format_exception(sys.exc_info()[0],
sys.exc_info()[1],
sys.exc_info()[2]))
return
#Add the .all name and the repo name (None if not in repo) to the window title
self.setWindowTitle('SiftFlow (' + (projName or "None") + ') (Repo: ' +
self.libMgr.getRepo() + ')')
#Loads files not associated with a project file
def loadFiles(self, args):
#If no loaded project, set window title
if (self.libMgr.getLoadedProjName() == ''):
self.setWindowTitle('SiftFlow (No Project)')
fileList = []
#Load files the user has specified from command line args rather than a project from sift
if (len(args) == 0):
#If no args were given, check cwd for any .fmls and open them
cwd = os.getcwd()
for infile in glob.glob(os.path.join(cwd, '*.fml')):
fileList.append(infile)
elif (len(args) > 0):
#Loop through the args and open files if they exist
for x in range(len(args)):
arg = str(args[x])
if ((arg.endswith('.fml') or arg.endswith('.lua'))
and os.path.exists(arg)):
fileList.append(arg)
else:
print arg + ' is not an fml or does not exist'
#If there are files, open them
if (len(fileList) > 0):
try:
self.libMgr.loadFiles(fileList)
except:
print "SiftFlow Load Error: "
print "file list: " + str(fileList)
print "".join(
traceback.format_exception(sys.exc_info()[0],
sys.exc_info()[1],
sys.exc_info()[2]))
return
def displayFlowFromSift(self, funcName, projName):
#Use project name to get the correct filename for the function
fileName = self.libMgr.getFileNameFromFuncName(projName, funcName)
if not fileName:
print "There was an error displaying the flow."
return
self.libMgr.displayFlow(fileName, projName, funcName)
def __displayFromRecent(self, todisplay):
fileName = todisplay[0]
path = todisplay[1]
proj = todisplay[2]
funcName = todisplay[3]
dIndex = todisplay[4]
#If file is not in the loaded file list, add it
if (not self.libMgr.isFileLoaded(fileName, path)):
self.libMgr.loadFiles([os.path.join(path, fileName)])
#Set up pathOrProj
if (self.libMgr.isProjLoaded(proj)):
pathOrProj = proj
else:
pathOrProj = path
#Display the thing
if (not funcName):
self.libMgr.displayFml(fileName, pathOrProj)
else:
self.libMgr.displayFlow(fileName,
pathOrProj,
funcName,
dIndex=dIndex)
#--- Setup Functions ---#
def __initMainWindow(self):
#Set Main Window starting size
self.resize(self.libMgr.getWindowSize())
#Treeview (navigation) Tab Control Init
self.ui.tabWidget_treeview.setCurrentIndex(0)
#Set all layout margins to zero
self.ui.gridLayout.setMargin(0)
self.ui.gridLayout_2.setMargin(0)
self.ui.gridLayout_3.setMargin(0)
self.ui.gridLayout_4.setMargin(0)
self.ui.gridLayout_5.setMargin(0)
#Set stretch factors so the resize widgets know what ratio each side can be
self.ui.splitter_leftright.setStretchFactor(1, 2)
#Set Left frame contents sizes
self.ui.splitter_leftright.widget(0).setMinimumWidth(125)
self.ui.splitter_leftright.setSizes([
self.libMgr.getTreeviewWidth(),
self.ui.splitter_leftright.widget(1).width()
])
#setup main icon
icon = QtGui.QIcon()
icon.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(), "SiftTeal.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.setWindowIcon(icon)
#setup find icon
iconF = QtGui.QIcon()
iconF.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "find.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionFind.setIcon(iconF)
#setup reference icon
iconRef = QtGui.QIcon()
iconRef.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(), "findreference.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionReference.setIcon(iconRef)
#setup reference icon
iconRefInFiles = QtGui.QIcon()
iconRefInFiles.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(),
"findreferenceinfiles.png")), QtGui.QIcon.Normal,
QtGui.QIcon.Off)
self.ui.actionReferenceInFiles.setIcon(iconRefInFiles)
#setup undo icon
iconU = QtGui.QIcon()
iconU.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "undo.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUndo.setIcon(iconU)
#setup redo icon
iconRed = QtGui.QIcon()
iconRed.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "redo.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionRedo.setIcon(iconRed)
#setup comment icon
iconCom = QtGui.QIcon()
iconCom.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(),
"comment.png")), QtGui.QIcon.Normal,
QtGui.QIcon.Off)
self.ui.actionComment.setIcon(iconCom)
#setup uncomment icon
iconUncom = QtGui.QIcon()
iconUncom.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(), "uncomment.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUncomment.setIcon(iconUncom)
#setup indent icon
iconIn = QtGui.QIcon()
iconIn.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(),
"indent.png")), QtGui.QIcon.Normal,
QtGui.QIcon.Off)
self.ui.actionIndent.setIcon(iconIn)
#setup unindent icon
iconUnin = QtGui.QIcon()
iconUnin.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(), "unindent.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUnindent.setIcon(iconUnin)
#setup goto icon
iconGoto = QtGui.QIcon()
iconGoto.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "goto.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionGoto.setIcon(iconGoto)
#setup open icon
iconO = QtGui.QIcon()
iconO.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "open.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionOpen.setIcon(iconO)
#setup save icon
iconSave = QtGui.QIcon()
iconSave.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "save.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionSave.setIcon(iconSave)
#setup saveall icon
iconSaveAll = QtGui.QIcon()
iconSaveAll.addPixmap(
QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(),
"saveall.png")), QtGui.QIcon.Normal,
QtGui.QIcon.Off)
self.ui.actionSave_All.setIcon(iconSaveAll)
#setup download icon
iconDownload = QtGui.QIcon()
iconDownload.addPixmap(
QtGui.QPixmap(
os.path.join(self.libMgr.getIconDir(), "download.png")),
QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionDownload.setIcon(iconDownload)
#Create File menu
#self.ui.menuNew = QtGui.QMenu('New')
#self.ui.actionNewFlow = QtGui.QAction(self.ui.menuNew)
#self.ui.actionNewFlow.setObjectName('actionNewFlow')
#self.ui.actionNewFlow.setText('Flow')
#self.ui.menuNew.addAction(self.ui.actionNewFlow)
#self.ui.menuFile.addMenu(self.ui.menuNew)
#self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionOpen)
self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionSave)
#self.ui.menuFile.addAction(self.ui.actionSave_All)
self.ui.menuFile.addSeparator()
#build recent menu
self.ui.menuRecent = QtGui.QMenu(self.ui.menuFile)
self.ui.menuRecent.setTitle('Recent')
self.ui.menuFile.addMenu(self.ui.menuRecent)
self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionExit)
#build...build menu
self.ui.menuBuild.addAction(self.ui.actionDownload)
def __fillMenuRecent(self):
list = self.libMgr.getRecentList()
self.ui.menuRecent.clear()
for item in reversed(list):
action = QtGui.QAction(self.ui.menuRecent)
#Display the flow name, or .fml if that all there is, tack on dIndex if there
dIndex = ''
if item[4]:
dIndex = '(' + str(item[4]) + ')'
action.setText((item[3] or item[0]) + dIndex)
#Pass in path:flow to the display function when the action is clicked for easy displaying
receiver = lambda todisplay=item: self.__displayFromRecent(
todisplay)
action.connect(action, QtCore.SIGNAL("triggered()"), receiver)
self.ui.menuRecent.addAction(action)
def __fillMenuBuild(self):
#build...build menu
self.ui.menuBuild.addAction(self.ui.actionDownload)
def main ():
logger.debug('version %s starting' % VERSION)
opt, args = getParms()
if opt.format == 'pickle':
reads = ref.Reference.fromPickle (opt.input)
else:
reads = ref.Reference (opt.input)
primers = ref.Reference (opt.primers)
aln = SWAligner.Aligner()
report = None
if opt.report is not None:
report = open (opt.report, 'w')
numReads = 0 # counter
for chr in reads.chromosomes(): # process all the reads
readIn = reads.sequence(chr)
aln.setRef (readIn)
numReads += 1
if numReads % TICK == 0:
logger.debug('tick %6d %s' % (numReads, chr))
if report is not None:
report.write ('>%s %d\n' % (chr, len(readIn)))
for pri in primers.chromosomes(): # for each read, look at all the primers
forPri = primers.sequence(pri)
revPri = forPri[::-1].translate(COMPLTAB)
if pri[0] == 'F':
trim = tryPrimer ('-', forPri, pri, aln, report)
if trim > 0:
readIn = readIn[ trim : ] # trim the read
aln.setRef (readIn) # update the aligner's target read if changed
trim = tryPrimer ('+', revPri, pri, aln, report)
if trim > 0:
readIn = readIn[ : trim ]
aln.setRef (readIn)
elif pri[0] == 'R':
trim = tryPrimer ('+', forPri, pri, aln, report)
if trim > 0:
readIn = readIn[ : trim ]
aln.setRef (readIn)
trim = tryPrimer ('-', revPri, pri, aln, report)
if trim > 0:
readIn = readIn[ trim : ]
aln.setRef (readIn)
else:
raise RuntimeError ('primer name %s does not begin with F or R' % pri)
writeFasta (chr, readIn)
if report is not None:
report.close()
logger.debug('finished')
return
class SiftFlow(QtGui.QMainWindow):
def __init__(self, parent=None):
#If we were opened from the base sift (not the gui) setup the app internaly
if (parent == None):
self.app = QtGui.QApplication(sys.argv)
self.app.setOrganizationName("Hewlett-Packard")
self.app.setOrganizationDomain("hp.com")
self.app.setApplicationName("SiftFlow")
if (sys.platform.startswith("darwin")):
self.app.setStyle("Cleanlooks")
#Setup the window
QtGui.QMainWindow.__init__(self)
self.parent = parent
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
#Declare interface object with backend
self.libMgr = SFLibManager(self, self.ui)
#Do additional Window setup
self.__initMainWindow()
#Only want one reference window at a time
self.refWin = None
self.aboutWin = None
self.findWin = None
self.repWin = None
#Set up actions and signals
QtCore.QObject.connect(self.ui.actionAbout, QtCore.SIGNAL("triggered()"), self.__about)
QtCore.QObject.connect(self.ui.actionFind, QtCore.SIGNAL("triggered()"), self.__find)
QtCore.QObject.connect(self.ui.actionFindInFiles, QtCore.SIGNAL("triggered()"), self.__findInFiles)
QtCore.QObject.connect(self.ui.actionReference, QtCore.SIGNAL("triggered()"), self.reference)
QtCore.QObject.connect(self.ui.actionReferenceInFiles, QtCore.SIGNAL("triggered()"), self.referenceInFiles)
QtCore.QObject.connect(self.ui.actionCut, QtCore.SIGNAL("triggered()"), self.__cut)
QtCore.QObject.connect(self.ui.actionCopy, QtCore.SIGNAL("triggered()"), self.__copy)
QtCore.QObject.connect(self.ui.actionUndo, QtCore.SIGNAL("triggered()"), self.__undo)
QtCore.QObject.connect(self.ui.actionRedo, QtCore.SIGNAL("triggered()"), self.__redo)
QtCore.QObject.connect(self.ui.actionGoto, QtCore.SIGNAL("triggered()"), self.__goto)
QtCore.QObject.connect(self.ui.actionIndent, QtCore.SIGNAL("triggered()"), self.__indent)
QtCore.QObject.connect(self.ui.actionUnindent, QtCore.SIGNAL("triggered()"), self.__unindent)
QtCore.QObject.connect(self.ui.actionComment, QtCore.SIGNAL("triggered()"), self.__comment)
QtCore.QObject.connect(self.ui.actionUncomment, QtCore.SIGNAL("triggered()"), self.__uncomment)
QtCore.QObject.connect(self.ui.actionPaste, QtCore.SIGNAL("triggered()"), self.__paste)
QtCore.QObject.connect(self.ui.actionDownload, QtCore.SIGNAL("triggered()"), self.__download)
QtCore.QObject.connect(self.ui.treeWidget_proj, QtCore.SIGNAL("itemSelectionChanged()"), self.__projSelectionChanged)
QtCore.QObject.connect(self.ui.treeWidget_nonProj, QtCore.SIGNAL("itemSelectionChanged()"), self.__nonProjSelectionChanged)
QtCore.QObject.connect(self.ui.splitter_leftright, QtCore.SIGNAL("splitterMoved(int, int)"), self.__resizeAll)
#QtCore.QObject.connect(self.ui.actionNewFlow, QtCore.SIGNAL("triggered()"), self.__newFlow)
QtCore.QObject.connect(self.ui.actionOpen, QtCore.SIGNAL("triggered()"), self.__open)
QtCore.QObject.connect(self.ui.actionSave, QtCore.SIGNAL("triggered()"), self.__save)
#QtCore.QObject.connect(self.ui.actionSave_All, QtCore.SIGNAL("triggered()"), self.__saveAll)
QtCore.QObject.connect(self.ui.menuRecent, QtCore.SIGNAL("aboutToShow()"), self.__fillMenuRecent)
QtCore.QObject.connect(self.ui.menuBuild, QtCore.SIGNAL("aboutToShow()"), self.__fillMenuBuild)
#SiftFlow, show thyself!!
if(parent == None): self.show()
def run(self):
"""Run the main QT event loop"""
self.app.exec_()
#--- Child Windows ---#
def __about(self):
if(self.aboutWin == None or self.aboutWin.isHidden()):
self.aboutWin = About(self, self.libMgr)
self.aboutWin.exec_()
def __find(self):
if(self.findWin == None or self.findWin.isHidden()):
self.findWin = Find(self, self.libMgr)
self.findWin.show()
def reference(self, text='none', flags=None, isCurrent=True):
if(self.refWin == None or not self.refWin.isVisible()):
self.refWin = Reference(self, self.libMgr)
result = self.refWin.addSearch(text, flags, isCurrent)
if(isinstance(result, str) and result == 'noselection'):
QtGui.QMessageBox.about(self, "Selection Status", "There is no text selected.")
elif(result):
self.refWin.show()
else:
QtGui.QMessageBox.about(self, "Match Status", "There are no more matches.")
elif(self.refWin.isVisible()): #the window is open, reset
if(not self.refWin.addSearch(text, flags, isCurrent)):
QtGui.QMessageBox.about(self, "Match Status", "There are no more matches.")
def referenceInFiles(self):
self.reference(isCurrent='all')
#--- Signal Handlers ---#
def __projSelectionChanged(self):
self.libMgr.tvProjUpdate()
def __nonProjSelectionChanged(self):
self.libMgr.tvNonProjUpdate()
def __cut(self):
self.libMgr.cut()
def __copy(self):
self.libMgr.copy()
def __paste(self):
self.libMgr.paste()
def __findInFiles(self):
findWin = Find(self, self.libMgr)
findWin.findInFiles()
findWin.exec_()
def __undo(self):
self.libMgr.undo()
def __redo(self):
self.libMgr.redo()
def __goto(self):
lineNum, ok = QtGui.QInputDialog.getText(self, 'Go to..', 'Go To Line: ')
if ok:
self.libMgr.setCursorToReference(int(lineNum) - 1, 0)
def __indent(self):
self.libMgr.indent()
def __unindent(self):
self.libMgr.unindent()
def __comment(self):
self.libMgr.comment()
def __uncomment(self):
self.libMgr.uncomment()
def __newFlow(self):
print 'new flow'
def __save(self):
result = self.libMgr.saveCurrentTab()
#Reset the reference window if it is open, to reflect any changes in the files after saving
if(self.refWin and self.refWin.isVisible()): #the window is open
self.refWin.resetTabs()
#def __saveAll(self):
#For now I am removing save all from the ui, but will leave the functionality in.
#Save All would rarely be used and caused a few hard to solve cunundrums with file conflicts
#when a user had unsaved changes in both fmls and flows from those fmls. If in the future, this
#feature is demanded, then all that needs to be done is to reattach the action to the toolbar and
#uncomment this function, the signal and file menu entry near the bottom of this file
#result = self.libMgr.saveAllTabs()
#Reset the reference window if it is open, to reflect any changes in the files after saving
#if(self.refWin and self.refWin.isVisible()): #the window is open
#self.refWin.resetTabs()
def __download(self):
#Cannot download if there is no project loaded
if(not self.libMgr.isProjLoaded()):
self.libMgr.printError("Download failed!", 10)
QtGui.QMessageBox.about(self, "Download Failed", "No Project Loaded.")
return
#Get a list of all files changed since .all was build
dList = self.libMgr.getDownloadFileList()
#If files have changed since the .all was built, download them to printer
if(len(dList) > 0):
#Turn that list into the command string
cmd = "download " + " ".join(dList)
#Send command to sift
self.parent.parse(cmd)
#If no files have changed, tell user and do nothing
else:
self.libMgr.out("No changed files to download", 6)
#--- Event Handlers ---#
def showEvent(self, se):
self.__resizeAll(0, 0)
def __resizeAll(self, index, pos):
self.libMgr.resizeTreeview()
def closeEvent(self, e):
#If there are any unsaved changes, ask user what they want to do
if(self.libMgr.anyUnsavedChanges()):
msg = "There are unsaved changes. Quitting will discharges these changes."
reply = QtGui.QMessageBox.question(self, "Warning", msg, QtGui.QMessageBox.Save,
QtGui.QMessageBox.Discard, QtGui.QMessageBox.Cancel)
if reply == QtGui.QMessageBox.Save:
self.libMgr.saveAnyUnsavedChanges()
elif reply == QtGui.QMessageBox.Cancel:
e.ignore()
return
#Save window size, treeview width, output box height
self.libMgr.saveWindowState(self.width(), self.height(),
self.ui.splitter_leftright.widget(0).width())
#Close any open dialogs
if(self.aboutWin != None and not self.aboutWin.isHidden()):
self.aboutWin.close()
if(self.findWin != None and not self.findWin.isHidden()):
self.findWin.close()
if(self.repWin != None and not self.repWin.isHidden()):
self.repWin.close()
if(self.refWin != None and not self.refWin.isHidden()):
self.refWin.close()
if (self.parent != None):
self.parent.ui.edit.setEnabled(True)
#--- Opening Files ---#
# Signal handler for open file action
def __open(self):
#Get the last dir opened by the user (from config file)
lastDir = self.libMgr.getLastOpenDir()
#Use file dialog to allow user to select one or more .fmls
ofDialog = QtGui.QFileDialog(self)
files = ofDialog.getOpenFileNames(caption='Open file(s)',
directory=lastDir,
filter='Files (*.fml *.lua)')
#Only load files if the user select any
if not files.isEmpty():
#Place the chosen directory in the config file
self.libMgr.setLastOpenDir(os.path.split(str(files[0]))[0])
#Load the files
self.loadFiles(files)
#Loads a project file provided by sift
def loadProject(self, fileDirs, projPath, projName, projType):
#If not in linux or project_dir is not pointed to a build directory (ie bound to repo) or file_dirs is empty
#Use the project_dir as the file_dirs since the project files will be with the .hlg
if(not sys.platform.startswith('linux') or
not re.search("obj_\w+_\w+", projPath) or
len(fileDirs) == 0):
fileDirs = projPath
try:
self.libMgr.loadProject(fileDirs, projPath, projName, projType)
except:
print "SiftFlow Load Error: "
print "file_dirs: " + str(fileDirs)
print "project_dir: " + str(projPath)
print "project_name: " + str(projName)
print "project_type: " + str(projType)
print "".join(traceback.format_exception(sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2]))
return
#Add the .all name and the repo name (None if not in repo) to the window title
self.setWindowTitle('SiftFlow (' + (projName or "None") + ') (Repo: ' + self.libMgr.getRepo() + ')')
#Loads files not associated with a project file
def loadFiles(self, args):
#If no loaded project, set window title
if(self.libMgr.getLoadedProjName() == ''):
self.setWindowTitle('SiftFlow (No Project)')
fileList = []
#Load files the user has specified from command line args rather than a project from sift
if(len(args) == 0):
#If no args were given, check cwd for any .fmls and open them
cwd = os.getcwd()
for infile in glob.glob(os.path.join(cwd, '*.fml')):
fileList.append(infile)
elif(len(args) > 0):
#Loop through the args and open files if they exist
for x in range(len(args)):
arg = str(args[x])
if ((arg.endswith('.fml') or arg.endswith('.lua')) and
os.path.exists(arg)):
fileList.append(arg)
else:
print arg + ' is not an fml or does not exist'
#If there are files, open them
if(len(fileList) > 0):
try:
self.libMgr.loadFiles(fileList)
except:
print "SiftFlow Load Error: "
print "file list: " + str(fileList)
print "".join(traceback.format_exception(sys.exc_info()[0], sys.exc_info()[1], sys.exc_info()[2]))
return
def displayFlowFromSift(self, funcName, projName):
#Use project name to get the correct filename for the function
fileName = self.libMgr.getFileNameFromFuncName(projName, funcName)
if not fileName:
print "There was an error displaying the flow."
return
self.libMgr.displayFlow(fileName, projName, funcName)
def __displayFromRecent(self, todisplay):
fileName = todisplay[0]
path = todisplay[1]
proj = todisplay[2]
funcName = todisplay[3]
dIndex = todisplay[4]
#If file is not in the loaded file list, add it
if(not self.libMgr.isFileLoaded(fileName, path)):
self.libMgr.loadFiles([os.path.join(path,fileName)])
#Set up pathOrProj
if(self.libMgr.isProjLoaded(proj)):
pathOrProj = proj
else:
pathOrProj = path
#Display the thing
if(not funcName):
self.libMgr.displayFml(fileName, pathOrProj)
else:
self.libMgr.displayFlow(fileName, pathOrProj, funcName, dIndex=dIndex)
#--- Setup Functions ---#
def __initMainWindow(self):
#Set Main Window starting size
self.resize(self.libMgr.getWindowSize())
#Treeview (navigation) Tab Control Init
self.ui.tabWidget_treeview.setCurrentIndex(0)
#Set all layout margins to zero
self.ui.gridLayout.setMargin(0)
self.ui.gridLayout_2.setMargin(0)
self.ui.gridLayout_3.setMargin(0)
self.ui.gridLayout_4.setMargin(0)
self.ui.gridLayout_5.setMargin(0)
#Set stretch factors so the resize widgets know what ratio each side can be
self.ui.splitter_leftright.setStretchFactor(1, 2)
#Set Left frame contents sizes
self.ui.splitter_leftright.widget(0).setMinimumWidth(125)
self.ui.splitter_leftright.setSizes([self.libMgr.getTreeviewWidth(), self.ui.splitter_leftright.widget(1).width()])
#setup main icon
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "SiftTeal.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.setWindowIcon(icon)
#setup find icon
iconF = QtGui.QIcon()
iconF.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "find.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionFind.setIcon(iconF)
#setup reference icon
iconRef = QtGui.QIcon()
iconRef.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "findreference.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionReference.setIcon(iconRef)
#setup reference icon
iconRefInFiles = QtGui.QIcon()
iconRefInFiles.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "findreferenceinfiles.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionReferenceInFiles.setIcon(iconRefInFiles)
#setup undo icon
iconU = QtGui.QIcon()
iconU.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "undo.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUndo.setIcon(iconU)
#setup redo icon
iconRed = QtGui.QIcon()
iconRed.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "redo.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionRedo.setIcon(iconRed)
#setup comment icon
iconCom = QtGui.QIcon()
iconCom.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "comment.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionComment.setIcon(iconCom)
#setup uncomment icon
iconUncom = QtGui.QIcon()
iconUncom.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "uncomment.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUncomment.setIcon(iconUncom)
#setup indent icon
iconIn = QtGui.QIcon()
iconIn.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "indent.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionIndent.setIcon(iconIn)
#setup unindent icon
iconUnin = QtGui.QIcon()
iconUnin.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "unindent.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionUnindent.setIcon(iconUnin)
#setup goto icon
iconGoto = QtGui.QIcon()
iconGoto.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "goto.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionGoto.setIcon(iconGoto)
#setup open icon
iconO = QtGui.QIcon()
iconO.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "open.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionOpen.setIcon(iconO)
#setup save icon
iconSave = QtGui.QIcon()
iconSave.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "save.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionSave.setIcon(iconSave)
#setup saveall icon
iconSaveAll = QtGui.QIcon()
iconSaveAll.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "saveall.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionSave_All.setIcon(iconSaveAll)
#setup download icon
iconDownload = QtGui.QIcon()
iconDownload.addPixmap(QtGui.QPixmap(os.path.join(self.libMgr.getIconDir(), "download.png")), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.ui.actionDownload.setIcon(iconDownload)
#Create File menu
#self.ui.menuNew = QtGui.QMenu('New')
#self.ui.actionNewFlow = QtGui.QAction(self.ui.menuNew)
#self.ui.actionNewFlow.setObjectName('actionNewFlow')
#self.ui.actionNewFlow.setText('Flow')
#self.ui.menuNew.addAction(self.ui.actionNewFlow)
#self.ui.menuFile.addMenu(self.ui.menuNew)
#self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionOpen)
self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionSave)
#self.ui.menuFile.addAction(self.ui.actionSave_All)
self.ui.menuFile.addSeparator()
#build recent menu
self.ui.menuRecent = QtGui.QMenu(self.ui.menuFile)
self.ui.menuRecent.setTitle('Recent')
self.ui.menuFile.addMenu(self.ui.menuRecent)
self.ui.menuFile.addSeparator()
self.ui.menuFile.addAction(self.ui.actionExit)
#build...build menu
self.ui.menuBuild.addAction(self.ui.actionDownload)
def __fillMenuRecent(self):
list = self.libMgr.getRecentList()
self.ui.menuRecent.clear()
for item in reversed(list):
action = QtGui.QAction(self.ui.menuRecent)
#Display the flow name, or .fml if that all there is, tack on dIndex if there
dIndex = ''
if item[4]:
dIndex = '(' + str(item[4]) + ')'
action.setText((item[3] or item[0]) + dIndex)
#Pass in path:flow to the display function when the action is clicked for easy displaying
receiver = lambda todisplay=item: self.__displayFromRecent(todisplay)
action.connect(action, QtCore.SIGNAL("triggered()"), receiver)
self.ui.menuRecent.addAction(action)
def __fillMenuBuild(self):
#build...build menu
self.ui.menuBuild.addAction(self.ui.actionDownload)
def process_comment(comment, is_edit=False):
""" process dat comment """
# Anime/Manga requests that are found go into separate arrays
animeArray = []
mangaArray = []
lnArray = []
vnArray = []
# ignores all "code" markup (i.e. anything between backticks)
comment.body = re.sub(r"\`[{<\[]+(.*?)[}>\]]+\`", "", comment.body)
num_so_far = 0
numOfRequest = 0
numOfExpandedRequest = 0
# Ignore any blacklisted users
if (comment.author.name.lower() in user_blacklist):
print('User in blacklist: ' + comment.author.name)
commentReply = ''
# This checks for requests. First up we check all known tags for the !stats request
elif re.search('({!stats.*?}|{{!stats.*?}}|<!stats.*?>|<<!stats.*?>>)', comment.body, re.S) is not None:
username = USERNAME_PATTERN.search(comment.body)
subreddit = SUBREDDIT_PATTERN.search(comment.body)
if username:
commentReply = CommentBuilder.buildStatsComment(
username=username.group(1)
)
elif subreddit:
commentReply = CommentBuilder.buildStatsComment(
subreddit=subreddit.group(1)
)
else:
commentReply = CommentBuilder.buildStatsComment()
else:
# The basic algorithm here is:
# If it's an expanded request, build a reply using the data in the
# braces, clear the arrays, add the reply to the relevant array and
# ignore everything else. If it's a normal request, build a reply using
# the data in the braces, add the reply to the relevant array.
# Counts the number of expanded results vs total results. If it's not
# just a single expanded result, they all get turned into normal
# requests.
forceNormal = False
for match in find_requests('all', comment.body, expanded=True):
numOfRequest += 1
numOfExpandedRequest += 1
for match in find_requests('all', comment.body):
numOfRequest += 1
if (numOfExpandedRequest >= 1) and (numOfRequest > 1):
forceNormal = True
# Determine whether we'll build an expanded reply just once.
subredditName = str(comment.subreddit).lower()
isExpanded = False if (forceNormal or (subredditName in disableexpanded)) else True
# The final comment reply. We add stuff to this progressively.
commentReply = ''
# Expanded Anime
for match in find_requests('anime', comment.body, expanded=True):
if num_so_far < 30:
reply = Search.buildAnimeReply(match, isExpanded, comment)
if (reply is not None):
num_so_far = num_so_far + 1
animeArray.append(reply)
# Normal Anime
for match in find_requests('anime', comment.body):
if num_so_far < 30:
reply = Search.buildAnimeReply(match, False, comment)
if (reply is not None):
num_so_far = num_so_far + 1
animeArray.append(reply)
# Expanded Manga
# NORMAL EXPANDED
for match in find_requests('manga', comment.body, expanded=True):
if num_so_far < 30:
reply = Search.buildMangaReply(match, isExpanded, comment)
if (reply is not None):
num_so_far = num_so_far + 1
mangaArray.append(reply)
# Normal Manga
# NORMAL
for match in find_requests('manga', comment.body):
if num_so_far < 30:
reply = Search.buildMangaReply(match, False, comment)
if (reply is not None):
num_so_far = num_so_far + 1
mangaArray.append(reply)
# Expanded LN
for match in find_requests('light_novel', comment.body, expanded=True):
if num_so_far < 30:
reply = Search.buildLightNovelReply(match, isExpanded, comment)
if (reply is not None):
num_so_far = num_so_far + 1
lnArray.append(reply)
# Normal LN
for match in find_requests('light_novel', comment.body):
if num_so_far < 30:
reply = Search.buildLightNovelReply(match, False, comment)
if (reply is not None):
num_so_far = num_so_far + 1
lnArray.append(reply)
# Expanded VN
for match in find_requests('visual_novel', comment.body, expanded=True):
if num_so_far < 30:
reply = Search.buildVisualNovelReply(match, isExpanded, comment)
if (reply is not None):
num_so_far = num_so_far + 1
vnArray.append(reply)
# Normal VN
for match in find_requests('visual_novel', comment.body):
if num_so_far < 30:
reply = Search.buildVisualNovelReply(match, False, comment)
if (reply is not None):
num_so_far = num_so_far + 1
vnArray.append(reply)
# Here is where we create the final reply to be posted
# Basically just to keep track of people posting the same title
# multiple times (e.g. {Nisekoi}{Nisekoi}{Nisekoi})
postedAnimeTitles = []
postedMangaTitles = []
postedLNTitles = []
postedVNTitles = []
# Adding all the anime to the final comment. If there's manga too we
# split up all the paragraphs and indent them in Reddit markup by
# adding a '>', then recombine them
for i, animeReply in enumerate(animeArray):
if not (i is 0):
commentReply += '\n\n'
if not (animeReply['title'] in postedAnimeTitles):
postedAnimeTitles.append(animeReply['title'])
commentReply += animeReply['comment']
if mangaArray:
commentReply += '\n\n'
# Adding all the manga to the final comment
for i, mangaReply in enumerate(mangaArray):
if not (i is 0):
commentReply += '\n\n'
if not (mangaReply['title'] in postedMangaTitles):
postedMangaTitles.append(mangaReply['title'])
commentReply += mangaReply['comment']
if lnArray:
commentReply += '\n\n'
# Adding all the light novels to the final comment
for i, lnReply in enumerate(lnArray):
if not (i is 0):
commentReply += '\n\n'
if not (lnReply['title'] in postedLNTitles):
postedLNTitles.append(lnReply['title'])
commentReply += lnReply['comment']
if vnArray:
commentReply += '\n\n'
# Adding all the visual novels to the final comment
for i, vnReply in enumerate(vnArray):
if not (i is 0):
commentReply += '\n\n'
if not (vnReply['title'] in postedVNTitles):
postedVNTitles.append(vnReply['title'])
commentReply += vnReply['comment']
# If there are more than 10 requests, shorten them all
lenRequests = sum(map(len, (animeArray, mangaArray, lnArray, vnArray)))
if not (commentReply is '') and (lenRequests >= 10):
commentReply = re.sub(r"\^\((.*?)\)", "", commentReply, flags=re.M)
# If there was actually something found, add the signature and post the
# comment to Reddit. Then, add the comment to the "already seen" database.
if commentReply is not '':
if num_so_far >= 30:
commentReply += ("\n\nI'm limited to 30 requests at once and have "
"had to cut off some, sorry for the "
"inconvenience!\n\n")
commentReply += Config.getSignature(comment.permalink)
commentReply += Reference.get_bling(comment.author.name)
total_expected = int(numOfRequest)
total_found = sum(map(len, (animeArray, mangaArray, lnArray, vnArray)))
if total_found != total_expected:
commentReply += ' | ({0}/{1})'.format(total_found,
total_expected)
if is_edit:
return commentReply
else:
try:
comment.reply(commentReply)
print("Comment made.\n")
except praw.errors.Forbidden:
print('Request from banned '
'subreddit: {0}\n'.format(comment.subreddit))
except Exception as e:
logger.debug(traceback.print_exc())
logger.warn(e)
comment_author = comment.author.name if comment.author else '!UNKNOWN!'
try:
DatabaseHandler.addComment(
comment.id,
comment_author,
comment.subreddit,
True
)
except Exception as e:
logger.debug(traceback.print_exc())
logger.warn(e)
else:
try:
if is_edit:
return None
else:
comment_author = comment.author.name if comment.author else '!UNKNOWN!'
DatabaseHandler.addComment(
comment.id,
comment_author,
comment.subreddit,
False
)
except Exception as e:
logger.debug(traceback.print_exc())
logger.warn(e)
def process_comment(comment, is_edit=False):
#Anime/Manga requests that are found go into separate arrays
animeArray = []
mangaArray = []
lnArray = []
#ignores all "code" markup (i.e. anything between backticks)
comment.body = re.sub(r"\`(?s)(.*?)\`", "", comment.body)
#This checks for requests. First up we check all known tags for the !stats request
if re.search('({!stats.*?}|{{!stats.*?}}|<!stats.*?>|<<!stats.*?>>)', comment.body, re.S) is not None:
username = re.search('[uU]\/([A-Za-z0-9_-]+?)(>|}|$)', comment.body, re.S)
subreddit = re.search('[rR]\/([A-Za-z0-9_]+?)(>|}|$)', comment.body, re.S)
if username:
commentReply = CommentBuilder.buildStatsComment(username=username.group(1))
elif subreddit:
commentReply = CommentBuilder.buildStatsComment(subreddit=subreddit.group(1))
else:
commentReply = CommentBuilder.buildStatsComment()
else:
#The basic algorithm here is:
#If it's an expanded request, build a reply using the data in the braces, clear the arrays, add the reply to the relevant array and ignore everything else.
#If it's a normal request, build a reply using the data in the braces, add the reply to the relevant array.
#Counts the number of expanded results vs total results. If it's not just a single expanded result, they all get turned into normal requests.
numOfRequest = 0
numOfExpandedRequest = 0
forceNormal = False
for match in re.finditer("\{{2}([^}]*)\}{2}|\<{2}([^>]*)\>{2}", comment.body, re.S):
numOfRequest += 1
numOfExpandedRequest += 1
for match in re.finditer("(?<=(?<!\{)\{)([^\{\}]*)(?=\}(?!\}))|(?<=(?<!\<)\<)([^\<\>]*)(?=\>(?!\>))", comment.body, re.S):
numOfRequest += 1
if (numOfExpandedRequest >= 1) and (numOfRequest > 1):
forceNormal = True
#Expanded Anime
for match in re.finditer("\{{2}([^}]*)\}{2}", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower() in disableexpanded):
reply = Search.buildAnimeReply(match.group(1), False, comment)
else:
reply = Search.buildAnimeReply(match.group(1), True, comment)
if (reply is not None):
animeArray.append(reply)
#Normal Anime
for match in re.finditer("(?<=(?<!\{)\{)([^\{\}]*)(?=\}(?!\}))", comment.body, re.S):
reply = Search.buildAnimeReply(match.group(1), False, comment)
if (reply is not None):
animeArray.append(reply)
#Expanded Manga
#NORMAL EXPANDED
for match in re.finditer("\<{2}([^>]*)\>{2}(?!(:|\>))", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower() in disableexpanded):
reply = Search.buildMangaReply(match.group(1), False, comment)
else:
reply = Search.buildMangaReply(match.group(1), True, comment)
if (reply is not None):
mangaArray.append(reply)
#AUTHOR SEARCH EXPANDED
for match in re.finditer("\<{2}([^>]*)\>{2}:\(([^)]+)\)", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower() in disableexpanded):
reply = Search.buildMangaReplyWithAuthor(match.group(1), match.group(2), False, comment)
else:
reply = Search.buildMangaReplyWithAuthor(match.group(1), match.group(2), True, comment)
if (reply is not None):
mangaArray.append(reply)
#Normal Manga
#NORMAL
for match in re.finditer("(?<=(?<!\<)\<)([^\<\>]+)\>(?!(:|\>))", comment.body, re.S):
reply = Search.buildMangaReply(match.group(1), False, comment)
if (reply is not None):
mangaArray.append(reply)
#AUTHOR SEARCH
for match in re.finditer("(?<=(?<!\<)\<)([^\<\>]*)\>:\(([^)]+)\)", comment.body, re.S):
reply = Search.buildMangaReplyWithAuthor(match.group(1), match.group(2), False, comment)
if (reply is not None):
mangaArray.append(reply)
#Expanded LN
for match in re.finditer("\]{2}([^]]*)\[{2}", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower() in disableexpanded):
reply = Search.buildLightNovelReply(match.group(1), False, comment)
else:
reply = Search.buildLightNovelReply(match.group(1), True, comment)
if (reply is not None):
lnArray.append(reply)
#Normal LN
for match in re.finditer("(?<=(?<!\])\])([^\]\[]*)(?=\[(?!\[))", comment.body, re.S):
reply = Search.buildLightNovelReply(match.group(1), False, comment)
if (reply is not None):
lnArray.append(reply)
#Here is where we create the final reply to be posted
#The final comment reply. We add stuff to this progressively.
commentReply = ''
#Basically just to keep track of people posting the same title multiple times (e.g. {Nisekoi}{Nisekoi}{Nisekoi})
postedAnimeTitles = []
postedMangaTitles = []
postedLNTitles = []
#Adding all the anime to the final comment. If there's manga too we split up all the paragraphs and indent them in Reddit markup by adding a '>', then recombine them
for i, animeReply in enumerate(animeArray):
if not (i is 0):
commentReply += '\n\n'
if not (animeReply['title'] in postedAnimeTitles):
postedAnimeTitles.append(animeReply['title'])
commentReply += animeReply['comment']
if mangaArray:
commentReply += '\n\n'
#Adding all the manga to the final comment
for i, mangaReply in enumerate(mangaArray):
if not (i is 0):
commentReply += '\n\n'
if not (mangaReply['title'] in postedMangaTitles):
postedMangaTitles.append(mangaReply['title'])
commentReply += mangaReply['comment']
if lnArray:
commentReply += '\n\n'
#Adding all the manga to the final comment
for i, lnReply in enumerate(lnArray):
if not (i is 0):
commentReply += '\n\n'
if not (lnReply['title'] in postedLNTitles):
postedLNTitles.append(lnReply['title'])
commentReply += lnReply['comment']
#If there are more than 10 requests, shorten them all
if not (commentReply is '') and (len(animeArray) + len(mangaArray)+ len(lnArray) >= 10):
commentReply = re.sub(r"\^\((.*?)\)", "", commentReply, flags=re.M)
#If there was actually something found, add the signature and post the comment to Reddit. Then, add the comment to the "already seen" database.
if commentReply is not '':
'''if (comment.author.name == 'treborabc'):
commentReply = '[No.](https://www.reddit.com/r/anime_irl/comments/4sba1n/anime_irl/d58xkha)'''
commentReply += Config.getSignature(comment.permalink)
commentReply += Reference.get_bling(comment.author.name)
if is_edit:
return commentReply
else:
try:
comment.reply(commentReply)
print("Comment made.\n")
except praw.errors.Forbidden:
print('Request from banned subreddit: ' + str(comment.subreddit) + '\n')
except Exception:
traceback.print_exc()
try:
DatabaseHandler.addComment(comment.id, comment.author.name, comment.subreddit, True)
except:
traceback.print_exc()
else:
try:
if is_edit:
return None
else:
DatabaseHandler.addComment(comment.id, comment.author.name, comment.subreddit, False)
except:
traceback.print_exc()
def process_comment(comment, is_edit=False):
#Anime/Manga requests that are found go into separate arrays
animeArray = []
mangaArray = []
lnArray = []
#ignores all "code" markup (i.e. anything between backticks)
comment.body = re.sub(r"\`(?s)(.*?)\`", "", comment.body)
#This checks for requests. First up we check all known tags for the !stats request
if re.search('({!stats.*?}|{{!stats.*?}}|<!stats.*?>|<<!stats.*?>>)',
comment.body, re.S) is not None:
username = re.search('[uU]\/([A-Za-z0-9_-]+?)(>|}|$)', comment.body,
re.S)
subreddit = re.search('[rR]\/([A-Za-z0-9_]+?)(>|}|$)', comment.body,
re.S)
if username:
commentReply = CommentBuilder.buildStatsComment(
username=username.group(1))
elif subreddit:
commentReply = CommentBuilder.buildStatsComment(
subreddit=subreddit.group(1))
else:
commentReply = CommentBuilder.buildStatsComment()
else:
#The basic algorithm here is:
#If it's an expanded request, build a reply using the data in the braces, clear the arrays, add the reply to the relevant array and ignore everything else.
#If it's a normal request, build a reply using the data in the braces, add the reply to the relevant array.
#Counts the number of expanded results vs total results. If it's not just a single expanded result, they all get turned into normal requests.
numOfRequest = 0
numOfExpandedRequest = 0
forceNormal = False
for match in re.finditer("\{{2}([^}]*)\}{2}|\<{2}([^>]*)\>{2}",
comment.body, re.S):
numOfRequest += 1
numOfExpandedRequest += 1
for match in re.finditer(
"(?<=(?<!\{)\{)([^\{\}]*)(?=\}(?!\}))|(?<=(?<!\<)\<)([^\<\>]*)(?=\>(?!\>))",
comment.body, re.S):
numOfRequest += 1
if (numOfExpandedRequest >= 1) and (numOfRequest > 1):
forceNormal = True
#Expanded Anime
for match in re.finditer("\{{2}([^}]*)\}{2}", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower()
in disableexpanded):
reply = Search.buildAnimeReply(match.group(1), False, comment)
else:
reply = Search.buildAnimeReply(match.group(1), True, comment)
if (reply is not None):
animeArray.append(reply)
#Normal Anime
for match in re.finditer("(?<=(?<!\{)\{)([^\{\}]*)(?=\}(?!\}))",
comment.body, re.S):
reply = Search.buildAnimeReply(match.group(1), False, comment)
if (reply is not None):
animeArray.append(reply)
#Expanded Manga
#NORMAL EXPANDED
for match in re.finditer("\<{2}([^>]*)\>{2}(?!(:|\>))", comment.body,
re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower()
in disableexpanded):
reply = Search.buildMangaReply(match.group(1), False, comment)
else:
reply = Search.buildMangaReply(match.group(1), True, comment)
if (reply is not None):
mangaArray.append(reply)
#AUTHOR SEARCH EXPANDED
for match in re.finditer("\<{2}([^>]*)\>{2}:\(([^)]+)\)", comment.body,
re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower()
in disableexpanded):
reply = Search.buildMangaReplyWithAuthor(
match.group(1), match.group(2), False, comment)
else:
reply = Search.buildMangaReplyWithAuthor(
match.group(1), match.group(2), True, comment)
if (reply is not None):
mangaArray.append(reply)
#Normal Manga
#NORMAL
for match in re.finditer("(?<=(?<!\<)\<)([^\<\>]+)\>(?!(:|\>))",
comment.body, re.S):
reply = Search.buildMangaReply(match.group(1), False, comment)
if (reply is not None):
mangaArray.append(reply)
#AUTHOR SEARCH
for match in re.finditer("(?<=(?<!\<)\<)([^\<\>]*)\>:\(([^)]+)\)",
comment.body, re.S):
reply = Search.buildMangaReplyWithAuthor(match.group(1),
match.group(2), False,
comment)
if (reply is not None):
mangaArray.append(reply)
#Expanded LN
for match in re.finditer("\]{2}([^]]*)\[{2}", comment.body, re.S):
reply = ''
if (forceNormal) or (str(comment.subreddit).lower()
in disableexpanded):
reply = Search.buildLightNovelReply(match.group(1), False,
comment)
else:
reply = Search.buildLightNovelReply(match.group(1), True,
comment)
if (reply is not None):
lnArray.append(reply)
#Normal LN
for match in re.finditer("(?<=(?<!\])\])([^\]\[]*)(?=\[(?!\[))",
comment.body, re.S):
reply = Search.buildLightNovelReply(match.group(1), False, comment)
if (reply is not None):
lnArray.append(reply)
#Here is where we create the final reply to be posted
#The final comment reply. We add stuff to this progressively.
commentReply = ''
#Basically just to keep track of people posting the same title multiple times (e.g. {Nisekoi}{Nisekoi}{Nisekoi})
postedAnimeTitles = []
postedMangaTitles = []
postedLNTitles = []
#Adding all the anime to the final comment. If there's manga too we split up all the paragraphs and indent them in Reddit markup by adding a '>', then recombine them
for i, animeReply in enumerate(animeArray):
if not (i is 0):
commentReply += '\n\n'
if not (animeReply['title'] in postedAnimeTitles):
postedAnimeTitles.append(animeReply['title'])
commentReply += animeReply['comment']
if mangaArray:
commentReply += '\n\n'
#Adding all the manga to the final comment
for i, mangaReply in enumerate(mangaArray):
if not (i is 0):
commentReply += '\n\n'
if not (mangaReply['title'] in postedMangaTitles):
postedMangaTitles.append(mangaReply['title'])
commentReply += mangaReply['comment']
if lnArray:
commentReply += '\n\n'
#Adding all the manga to the final comment
for i, lnReply in enumerate(lnArray):
if not (i is 0):
commentReply += '\n\n'
if not (lnReply['title'] in postedLNTitles):
postedLNTitles.append(lnReply['title'])
commentReply += lnReply['comment']
#If there are more than 10 requests, shorten them all
if not (commentReply is '') and (
len(animeArray) + len(mangaArray) + len(lnArray) >= 10):
commentReply = re.sub(r"\^\((.*?)\)", "", commentReply, flags=re.M)
#If there was actually something found, add the signature and post the comment to Reddit. Then, add the comment to the "already seen" database.
if commentReply is not '':
'''if (comment.author.name == 'treborabc'):
commentReply = '[No.](https://www.reddit.com/r/anime_irl/comments/4sba1n/anime_irl/d58xkha)'''
commentReply += Config.getSignature(comment.permalink)
commentReply += Reference.get_bling(comment.author.name)
if is_edit:
return commentReply
else:
try:
comment.reply(commentReply)
print("Comment made.\n")
except praw.errors.Forbidden:
print('Request from banned subreddit: ' +
str(comment.subreddit) + '\n')
except Exception:
traceback.print_exc()
try:
DatabaseHandler.addComment(comment.id, comment.author.name,
comment.subreddit, True)
except:
traceback.print_exc()
else:
try:
if is_edit:
return None
else:
DatabaseHandler.addComment(comment.id, comment.author.name,
comment.subreddit, False)
except:
traceback.print_exc()
# coding: utf-8
import Reference
Reference = Reference.Reference()
result = Reference.scraping()
# 確認
for i, num in enumerate(result):
for num2, key in enumerate(result[i]):
print(key, result[i][key])