def __init__(self, urlGenome = None, text = None):
assert urlGenome or text
xmlDict = xmldict.XMLDict({
xmldict.XMLDict.toList : [ 'codonTable', 'acceptedMutations', 'rejectedMutations', 'attempt', 'genes', 'hanReferences', 'groups', 'strokes', 'overlaps', 'segments', 'segment' ],
xmldict.XMLDict.ignore : []
})
if urlGenome:
dictGenome = xmlDict.load(urlGenome)['genome']
else:
dictGenome = xmlDict.loads(text)['genome']
self.author = 'author' in dictGenome and dictGenome['author'] or None
self.creationDate = 'creationDate' in dictGenome and dictGenome['creationDate'] or None
self.creationTool = 'creationTool' in dictGenome and dictGenome['creationTool'] or None
self.creationParameters = 'creationParameters' in dictGenome and dictGenome['creationParameters'] or None
if 'seed' in dictGenome:
self.seed = dictGenome['seed'][xmldict.XMLDict.value]
self.seedID = dictGenome['seed']['processorID']
else:
self.seed = None
self.seedID = None
self.codonTable = CodonTableElement(dictGenome=dictGenome)
self.bases = dictGenome['bases'][xmldict.XMLDict.value]
self.termination = Termination(dictGenome)
self.statistics = Statistics(dictGenome)
self.lineage = Lineage(dictGenome)
self.gene = Gene(dictGenome['genes'][xmldict.XMLDict.children][0][1])
return
def __init__(self, urlHan):
xmlDict = xmldict.XMLDict({
xmldict.XMLDict.toList:
['groups', 'strokes', 'forward', 'reverse', 'overlaps']
})
dictHan = xmlDict.load(urlHan)['hanDefinition']
self.uuid = dictHan['uuid']
self.unicode = dictHan['unicode']
self.creationDate = 'creationDate' in dictHan and dictHan[
'creationDate'] or None
self.creationTool = 'creationTool' in dictHan and dictHan[
'creationTool'] or None
self.creationParameters = 'creationParameters' in dictHan and dictHan[
'creationParameters'] or None
self.bounds = Rectangle(dictRect=dictHan['bounds'])
self.length = dictHan['length'][xmldict.XMLDict.value]
self.minimumStrokeLength = dictHan['minimumStrokeLength'][
xmldict.XMLDict.value]
self.aryGroups = [
HanGroup(dictGroup)
for tag, dictGroup in dictHan['groups'][xmldict.XMLDict.children]
]
self.aryStrokes = [
HanStroke(dictStroke)
for tag, dictStroke in dictHan['strokes'][xmldict.XMLDict.children]
]
self.aryOverlaps = 'overlaps' in dictHan and [
HanOverlap(dictOverlap) for tag, dictOverlap in dictHan['overlaps']
[xmldict.XMLDict.children]
] or []
return
def __init__(self, urlCodonTable=None):
dictCodonTable = None
if urlCodonTable:
xmlDict = xmldict.XMLDict({
xmldict.XMLDict.toList : [ 'codonTable' ],
xmldict.XMLDict.ignore : []
})
dictCodonTable = xmlDict.load(urlCodonTable)['codonTable']
super(CodonTable, self).__init__(dictCodonTable=dictCodonTable)
return
def validate(self, urls, grf):
if self.strNameType == 'asis' and not self.strName:
raise BiologicError('asis requires specifying a name')
if (grf & self.GENOME) or self.strNameType != 'dir':
if not self.strGenome:
raise BiologicError('Required genome was not supplied')
urls.validate(URLs.GENOME)
self.urlGenome = pathToURL(makeHanPath(resolvePath(self.strGenome)), urls.urlGenome)
if grf & (self.DATA | self.REPORT):
if self.strNameType == 'asis' or self.strNameType == 'file':
self.idGenome = os.path.splitext(os.path.basename(self.urlGenome))[0]
elif self.strNameType == 'uuid':
if not Constants.reUUID.match(self.strGenome):
xmlDict = XMLDict.XMLDict({ XMLDict.XMLDict.ignore : [ 'seed', 'bases', 'statistics', 'lineage', 'genes' ] })
try: self.idGenome = str(xmlDict.load(self.urlGenome)['genome']['uuid']).upper()
except LookupError, err: raise BiologicError('Genome (%s) is missing a UUID' % self.urlGenome)
elif self.strNameType == 'unicode':
aryParts = os.path.split(self.urlGenome)
mo = Constants.reBASENAMEUNICODE.match(aryParts[1])
if mo and mo.groups():
self.idGenome = mo.groups()[0]
else:
raise BiologicError('unicode name patterns required a genome file whose name begins with a unicode value')
if grf & self.PLAN or self.fAppendPlan:
if not self.strPlan:
raise BiologicError('Required plan was not supplied')
urls.validate(URLs.PLAN)
self.urlPlan = pathToURL(resolvePath(self.strPlan), urls.urlPlan)
self.idPlan = os.path.splitext(os.path.basename(self.urlPlan))[0]
if grf & self.DATA:
if not self.strDataPath:
raise BiologicError('Required datapath was not supplied')
self.pathData = resolvePath(self.strDataPath)
if self.strNameType == 'asis':
self.pathData = os.path.join(self.pathData, self.strName)
else:
idGenome = self.fAppendPlan and (self.idGenome + '--' + self.idPlan) or self.idGenome
self.pathData = os.path.join(self.pathData, self.strName, idGenome)
# Expand the data path unless expanding reports (since report expansion will set the data path as needed)
if self.strExpand and not grf & self.REPORT:
self.urlGenome, self.pathExpandData = self.__expandGenome__(self.pathData, Constants.extXML)
self.pathData = os.path.join(self.pathData, self.pathExpandData)
if not self.nFirstPlanTrial:
self.nFirstPlanTrial = 1
self.pathData = os.path.normpath(os.path.normcase(self.pathData))
if grf & self.REPORT:
if not self.strReportPath:
raise BiologicError('Required reportpath was not supplied')
self.pathReport = resolvePath(self.strReportPath)
if self.strNameType == 'asis':
self.pathReport = os.path.join(self.pathReport, self.strName)
elif self.strNameType == 'dir':
strHead, strTail = os.path.split(self.strDataPath)
if not strTail:
strHead, strTail = os.path.split(strHead)
strTail, strExt = os.path.splitext(strTail)
self.pathReport = os.path.join(self.pathReport, strTail)
else:
idGenome = self.fAppendPlan and (self.idGenome + '--' + self.idPlan) or self.idGenome
self.pathReport = os.path.join(self.pathReport, self.strName, idGenome)
if self.strNameType != 'dir' and self.strExpand:
strNotUsed, self.pathExpandReport = self.__expandGenome__(self.pathReport, Constants.extXML)
self.pathReport = os.path.join(self.pathReport, self.pathExpandReport)
# Map the report path to the data path (since the data may have already been expanded once or more)
self.pathData = os.path.normpath(os.path.normcase(os.path.join(self.pathData, self.pathExpandReport)))
self.pathReport = os.path.normpath(os.path.normcase(self.pathReport))