def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices, galaxyFn)
with stdout_redirector(open(galaxyFn, "w", 0)):
core = HtmlCore()
core.append(GalaxyInterface.getHtmlBeginForRuns(galaxyFn))
core.append(
GalaxyInterface.getHtmlForToggles(withRunDescription=False))
core.styleInfoBegin(styleClass='debug')
core.paragraph(
'GalaxyInterface.startPreProcessing({}, {}, {})'.format(
choices.genome, choices.track, username))
print core
if choices.parsingError == cls.MOVE_TO_PARSING_ERROR_CHOICE:
finished = False
while not finished:
DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS = True
try:
GalaxyInterface.startPreProcessing(
choices.genome, choices.track, username)
finished = True
except (PreprocessWarning, PreprocessError) as e:
print e
match = re.search("trackName=\"([^\"]+)\"", str(e))
if match:
trackName = match.group(1).split(':')
PlainMover().parseFiles(choices.genome,
trackName,
direction='std_to_error')
else: # cls.DO_NOTHING_CHOICE
GalaxyInterface.startPreProcessing(choices.genome,
choices.track, username)
core = HtmlCore()
core.styleInfoEnd()
core.script('done = true;')
core.end()
print core
class GtrackSpecParser(object):
def __init__(self, filPath, outFilePath):
self.core = HtmlCore()
self.specStr = open(filPath, 'r').read()
self.outFilePath = outFilePath
self.htmlMal = '<html><body>%s</body></html>'
self.htmlStr = ''
self.divCounter = 0
self.fullContentTab = []
def getContentList(self):
return self.specStr.split('\n----------------')[2].strip().split('\n')
def getContentlineSearcStr(self, line):
anchorIndex = 0
if line.strip().startswith('*'):
anchorIndex = 2
searchStr = line[2:].strip() + '\n----'
elif len(line.strip()) and line.strip().startswith('-'):
anchorIndex = line.find('-') + 4
searchStr = line.strip()[2:].strip() + '\n ----'
elif line.strip() != '':
anchorIndex = 8
searchStr = line.strip().replace(' ', ' ') + '\n ----'
else:
searchStr = None
return searchStr, anchorIndex
#x. Comments
def findAll(self, substring, string):
starts = [
match.start()
for match in re.finditer(re.escape(substring), string)
]
return [
x for i, x in enumerate(starts)
if i == 0 or i > 0 and x - starts[i - 1] != len(substring)
]
def checkHeader(self, header, contentStr, devNotes=True):
headerIndex = contentStr.find(header)
falseHeaderIndex = contentStr.find('"' + header)
if headerIndex != -1 and not (falseHeaderIndex != -1
and headerIndex == falseHeaderIndex + 1):
devChunckList = contentStr.split(header)
resultStr = devChunckList[0]
for value in devChunckList[1:]:
resultStr += '''<a onclick ="javascript:ShowHide('HiddenDiv%s')" href="javascript:;" >%s</a>''' % (
str(self.divCounter), header)
dashLine = '-' * len(header)
if devNotes:
dotList = value.split(dashLine)
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >%s%s%s%s</div>' % (
str(self.divCounter), dotList[0], dashLine, dotList[1],
dashLine) + dashLine.join(dotList[2:])
else:
lastDashLine = self.findAll('----', value)[-1]
if value[lastDashLine - 2:lastDashLine] == ' ':
lastDashLine -= 2
mainContent = ''.join(value[1:lastDashLine])
newHeader = ''.join(value[lastDashLine:])
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >%s</div>\n ' % (
str(self.divCounter),
mainContent) + dashLine + '\n\n' + newHeader
self.divCounter += 1
return resultStr
else:
return contentStr
def checkRestrictions(self, contentStr):
if contentStr.find('- Restrictions') > 0:
devChunckList = contentStr.split('- Restrictions')
resultStr = devChunckList[0]
for value in devChunckList[1:]:
resultStr += '''- <a onclick ="javascript:ShowHide('HiddenDiv%s')" href="javascript:;" >Restrictions</a>\n''' % str(
self.divCounter)
restrictTab, extraTab = [], []
valueTab = value.split('\n')
for index, resVal in enumerate(valueTab):
if resVal.strip() == '' or (len(resVal) > 2
and resVal[2].isspace()):
restrictTab.append(resVal)
else:
extraTab = valueTab[index:]
break
for val in restrictTab:
if val.strip() == '':
restrictTab = restrictTab[1:]
else:
break
for val in reversed(restrictTab):
if val.strip() == '':
restrictTab = restrictTab[:-1]
else:
break
resultStr += '<div class="mid" id="HiddenDiv%s" style="DISPLAY: none" >\n%s</div>' % (
str(self.divCounter),
'\n'.join(restrictTab)) + '\n\n' + '\n'.join(extraTab)
self.divCounter += 1
return resultStr
else:
return contentStr
def parseSpecFile(self):
contentList = self.getContentList()
self.core.begin()
self.core.script(
"function ShowHide(divId)\n{\nif(document.getElementById(divId).style.display == 'none')\n{\ndocument.getElementById(divId).style.display='block';\n}\nelse\n{\ndocument.getElementById(divId).style.display = 'none';\n}\n}\n"
)
self.core.append('<pre class="largefont">' +
self.specStr.split(contentList[0])[0])
for i in contentList:
searchStr, entry = self.getContentlineSearcStr(i)
self.core.append(i[:entry])
self.core.link(i[entry:], '#' + searchStr.split('\n')[0])
self.core.append('\n')
self.core.append('\n\n\n')
for index, value in enumerate(contentList):
print value
startPoint, entry = self.getContentlineSearcStr(value)
endPoint, entry = self.getContentlineSearcStr(
contentList[index +
1]) if index + 1 < len(contentList) else (None, 0)
self.core.anchor('', startPoint.split('\n')[0])
content = self.specStr[self.specStr.find(
startPoint):] if not endPoint else self.specStr[
self.specStr.find(startPoint):self.specStr.find(endPoint)]
# content = self.checkHeader('Parser notes:', content, True)
content = self.checkRestrictions(content)
self.core.append(content)
self.core.append('</pre>')
self.core.end()
utfil = open(self.outFilePath, 'w')
utfil.write(str(self.core))