a44e3254174152b2d4b3f241d1935654cd139181 vsmalladi Tue May 8 10:11:21 2012 -0700 Renamed library from ucscgenomics to ucscGb. Redmine #7029. diff --git python/lib/ucscgenomics/cv.py python/lib/ucscgenomics/cv.py deleted file mode 100644 index 014a733..0000000 --- python/lib/ucscgenomics/cv.py +++ /dev/null @@ -1,453 +0,0 @@ -import re -import os -from ucscgenomics import ra, encode - -def extractValue(val, prefix='', removeComments=1): - val2 = val.replace(prefix, '') - if removeComments and '#' in val2: - val2 = val2.split('#', 1)[0] - return val2.strip() - -def extractList(val, prefix='', removeComments=1): - val2 = val.replace(prefix, '') - if removeComments and '#' in val2: - val2 = val2.split('#', 1)[0] - return map(str.strip, val2.split(',')) - -class CvFile(ra.RaFile): - ''' - cv.ra representation. Mainly adds CV-specific validation to the RaFile - - To create a CvFile, the simplest way is just to call it with no params, - but you can specify a file path if you want to open up something other - than the alpha cv in your tree, specify this. The handler can almost - always be left blank, since that simply provides a function to handle - validation errors that would otherwise throw an exception. You also should - specify a protocolPath if you want to validate, since it will check the - protocol documents when you validate, to ensure that the cv matches them. - - Validation recurses over all stanzas, calling the overridden validation - function for the more developed stanzas. To start validation, you can - simply call validate() on the cv object. - - For more information about other things not specific to the cv, but for - all ra files, look at the RaFile documentation. - ''' - - def __init__(self, filePath=None, handler=None, protocolPath=None): - '''sets up exception handling method, and optionally reads from a file''' - ra.RaFile.__init__(self) - - self.handler = handler - if handler == None: - self.handler = self.raiseException - - if filePath == None: - filePath = encode.defaultCvPath() - - self.protocolPath = protocolPath - if protocolPath == None: - self.protocolPath == os.path.expanduser('~/htdocsExtras/ENCODE/') - - self.missingTypes = set() - - self.read(filePath) - - def raiseException(self, exception): - '''wrapper function for raising exception''' - raise exception - - def readStanza(self, stanza, key=None): - '''overriden method from RaFile which makes specialized stanzas based on type''' - entry = CvStanza() - - key, val = entry.readStanza(stanza) - return key, val, entry - - - def validate(self): - '''base validation method which calls all stanzas' validate''' - for stanza in self.itervalues(): - stanza.validate(self) - #print self.missingTypes - - def getTypeOfTermStanza(self, type): - - if type == 'mouseCellType': - mousestanza = CvStanza() - mousestanza['term'] = 'mouseCellType' - mousestanza['tag'] = 'MOUSECELLTYPE' - mousestanza['type'] = 'typeOfTerm' - mousestanza['label'] = 'Cell, tissue or DNA sample specific to mouse' - mousestanza['description'] = 'NOT FOR USE! ONLY FOR VALIDATION. Cell line or tissue used as the source of experimental material specific to mouse.' - mousestanza['searchable'] = 'multiSelect' - mousestanza['cvDefined'] = 'yes' - mousestanza['validate'] = 'cv or None' - mousestanza['requiredVars'] = 'term,tag,type,description,organism,vendorName,orderUrl,age,strain,sex #Provisional' - mousestanza['optionalVars'] = 'label,tissue,termId,termUrl,color,protocol,category,vendorId,lots,deprecated #Provisional' - return mousestanza - - types = self.filter(lambda s: s['term'] == type and s['type'] == 'typeOfTerm', lambda s: s) - if len(types) != 1: - return None - return types[0] - -class CvStanza(ra.RaStanza): - '''base class for a single stanza in the cv, which adds validation''' - - def __init__(self): - ra.RaStanza.__init__(self) - - def readStanza(self, stanza): - ''' - Populates this entry from a single stanza - ''' - - for line in stanza: - self.readLine(line) - - return self.readName(stanza[0]) - - def readName(self, line): - ''' - Extracts the Stanza's name from the value of the first line of the - stanza. - ''' - - if len(line.split(' ', 1)) != 2: - raise ValueError() - - names = map(str.strip, line.split(' ', 1)) - self._name = names[1] - return names - - def readLine(self, line): - ''' - Reads a single line from the stanza, extracting the key-value pair - ''' - - if line.startswith('#') or line == '': - self.append(line) - else: - raKey = line.split(' ', 1)[0] - raVal = '' - if (len(line.split(' ', 1)) == 2): - raVal = line.split(' ', 1)[1] - - if raKey in self: - count = 0 - while raKey + '__$$' + str(count) in self: - count = count + 1 - - self[raKey + '__$$' + str(count)] = raVal - - else: - self[raKey] = raVal - -# validate [cv/date/exists/float/integer/list:/none/regex:] outlines the expected values. ENFORCED by mdbPrint -validate -# cv: must be defined term in cv (e.g. cell=GM12878). "cv or None" indicates that "None is also acceptable. -# "cv or control" indicates that cv-defined terms of type "control" are also acceptable. -# date: must be date in YYYY-MM-DD format -# exists: not enforced. (e.g. fileName could be validated to exist in download directory) -# float: must be floating point number -# integer: must be integer -# "list:": must be one of several terms in comma delimeited list (e.g. "list: yes,no,maybe" ) # ("list:" includes colon) -# none: not validated in any way -# "regex:": must match regular expression (e.g. "regex: ^GS[M,E][0-9]$" ) # ("regex:" includes colon) -# # NOTE: that validate rules may end comment delimited by a '#' - - def validate(self, cvfile): - type = self['type'] - if self['type'] == 'Cell Line': # :( - if 'organism' in self and self['organism'] == 'human': - type = 'cellType' - elif 'organism' in self and self['organism'] == 'mouse': - type = 'mouseCellType' - else: - cvfile.handler(OrganismError(self)) - - typeStanza = cvfile.getTypeOfTermStanza(type) - if typeStanza == None: - cvfile.handler(InvalidTypeError(self, self['type'] + '(%s)' % type)) - return - required = list() - if 'requiredVars' in typeStanza: - required = extractList(typeStanza['requiredVars']) - optional = list() - if 'optionalVars' in typeStanza: - optional = extractList(typeStanza['optionalVars']) - - self.checkMandatory(cvfile, required) - required.extend(optional) - self.checkExtraneous(cvfile, required) - self.checkDuplicates(cvfile) - - for key in self.iterkeys(): - - itemType = cvfile.getTypeOfTermStanza(key) - if itemType == None: - cvfile.missingTypes.add(key) - #cvfile.handler(InvalidTypeError(self, key)) #RELEASE THE FLOODGATES - continue - validation = itemType['validate'] - val = self[key] - - if validation.startswith('cv'): - if validation == 'cv or None' and val == 'None': - pass - else: - self.checkRelational(cvfile, val, key) - elif validation == 'date': - try: - d = datetime.datetime.strptime(val, '%Y-%m-%d') - except: - cvfile.handler(InvalidDateError(self, val)) - elif validation == 'exists': - if not os.path.exists(val): - cvfile.handler(MissingFileError(self, val)) - elif validation == 'float': - try: - f = float(val) - except: - cvfile.handler(InvalidFloatError(self, val)) - elif validation == 'integer': - try: - i = int(val) - except: - cvfile.handler(InvalidIntError(self, val)) - elif validation.startswith('list:'): - validVals = extractList(validation, 'list:') - if val not in validVals: - cvfile.handler(InvalidListError(self, val, validVals)) - elif validation == 'none': - pass - elif validation.startswith('regex:'): - regex = extractValue(validation, 'regex:') - if not re.match(val, regex): - cvfile.handler(UnmatchedRegexError(self, val, regex)) - # else: - # cvfile.handler(TypeValidationError(itemType)) - - def checkDuplicates(self, cvfile): - '''ensure that all keys are present and not blank in the stanza''' - for key in self.iterkeys(): - if '__$$' in key: - newkey = key.split('__$$', 1)[0] - cvfile.handler(DuplicateKeyError(self, newkey)) - - def checkMandatory(self, cvfile, keys): - '''ensure that all keys are present and not blank in the stanza''' - for key in keys: - if not key in self.keys(): - cvfile.handler(MissingKeyError(self, key)) - elif self[key] == '': - cvfile.handler(BlankKeyError(self, key)) - - def checkExtraneous(self, cvfile, keys): - '''check for keys that are not in the list of keys''' - for key in self.iterkeys(): - if key not in keys and '__$$' not in key: - cvfile.handler(ExtraKeyError(self, key)) - - def checkFullRelational(self, cvfile, key, other, type): - '''check that the value at key matches the value of another - stanza's value at other, where the stanza type is specified by type''' - - p = 0 - if key not in self: - return - - for entry in cvfile.itervalues(): - if 'type' in entry and other in entry: - if entry['type'] == type and self[key] == entry[other]: - p = 1 - break - if p == 0: - cvfile.handler(NonmatchKeyError(self, key, other)) - - def checkRelational(self, cvfile, key, other): - '''check that the value at key matches the value at other''' - p = 0 - - if key not in self: - return - - for entry in cvfile.itervalues(): - if 'type' in entry and other in entry: - if entry['type'] == key and self[key] == entry[other]: - p = 1 - break - if p == 0: - cvfile.handler(NonmatchKeyError(self, key, other)) - - def checkListRelational(self, cvfile, key, other): - '''check that the value at key matches the value at other''' - - if key not in self: - return - - for val in self[key].split(','): - val = val.strip() - p = 0 - - for entry in cvfile.itervalues(): - if 'type' in entry and other in entry: - - if entry['type'] == key and val == entry[other]: - p = 1 - break - if p == 0: - cvfile.handler(NonmatchKeyError(self, key, other)) - - def checkProtocols(self, cvfile, path): - if 'protocol' in self: - protocols = self['protocol'].split() - for protocol in protocols: - if ':' not in protocol: - cvfile.handler(InvalidProtocolError(self, protocol)) - else: - p = protocol.split(':', 1)[1] - if cvfile.protocolPath != None and not os.path.isfile(cvfile.protocolPath + path + p): - cvfile.handler(InvalidProtocolError(self, protocol)) - -class CvError(Exception): - '''base error class for the cv.''' - def __init__(self, stanza): - Exception.__init__(self) - self.stanza = stanza - self.msg = '' - self.strict = 0 - - def __str__(self): - return str('%s[%s] %s: %s' % (self.stanza.name, self.stanza['type'], self.__class__.__name__, self.msg)) - -class MissingKeyError(CvError): - '''raised if a mandatory key is missing''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 1 - -class DuplicateKeyError(CvError): - '''raised if a key is duplicated''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 1 - -class BlankKeyError(CvError): - '''raised if a mandatory key is blank''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 0 - -class ExtraKeyError(CvError): - '''raised if an extra key not in the list of keys is found''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 0 - -class NonmatchKeyError(CvError): - '''raised if a relational key does not match any other value''' - - def __init__(self, stanza, key, val): - CvError.__init__(self, stanza) - self.msg = '%s does not match %s' % (key, val) - self.strict = 1 - -class DuplicateVendorIdError(CvError): - '''When there exists more than one connected component of stanzas (through derivedFrom) with the same vendorId''' - - def __init__(self, stanza): - CvError.__init__(self, stanza) - self.msg = '%s' % self.stanza['vendorId'] - self.strict = 0 - -class InvalidProtocolError(CvError): - '''raised if a protocol doesnt match anything in the directory''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 0 - -class InvalidTypeError(CvError): - '''raised if a relational key does not match any other value''' - - def __init__(self, stanza, key): - CvError.__init__(self, stanza) - self.msg = key - self.strict = 1 - -class TypeValidationError(CvError): - '''raised if the terms type of term has an invalid validation value''' - - def __init__(self, stanza): - CvError.__init__(self, stanza) - self.msg = 'validation ' + stanza['validation'] - self.strict = 1 - -class InvalidDateError(CvError): - '''raised if the value is an invalid date''' - - def __init__(self, stanza, val): - CvError.__init__(self, stanza) - self.msg = val + ' does not match a YYYY-MM-DD date' - self.strict = 1 - -class MissingFileError(CvError): - '''raised if the value is a filename that does not exist''' - - def __init__(self, stanza, val): - CvError.__init__(self, stanza) - self.msg = val + ' does not exist' - self.strict = 1 - -class InvalidFloatError(CvError): - '''raised if the value not a float''' - - def __init__(self, stanza, val): - CvError.__init__(self, stanza) - self.msg = val + ' is not a float' - self.strict = 1 - -class InvalidIntError(CvError): - '''raised if the value is not an int''' - - def __init__(self, stanza, val): - CvError.__init__(self, stanza) - self.msg = val + ' is not an int' - self.strict = 1 - -class InvalidListError(CvError): - '''raised if the value is not among the given list of values''' - - def __init__(self, stanza, val, list): - CvError.__init__(self, stanza) - self.msg = val + ' is not in ' + list.join(',') - self.strict = 1 - -class UnmatchedRegexError(CvError): - '''raised if the value is a filename that does not exist''' - - def __init__(self, stanza, val, regex): - CvError.__init__(self, stanza) - self.msg = val + ' does not match the regex ' + regex - self.strict = 1 - -class OrganismError(CvError): - '''raised if the value is a filename that does not exist''' - - def __init__(self, stanza): - CvError.__init__(self, stanza) - if 'organism' in stanza: - self.msg = 'organism ' + stanza['organism'] + ' does not match human or mouse' - else: - self.msg = 'organism does not exist in stanza' - self.strict = 1 \ No newline at end of file