""" CCP4CustomTaskManager.py: CCP4 GUI Project Copyright (C) 2013 STFC This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ """ Liz Potterton July 2013 - create and manage custom tasks """ import os import CCP4Modules,CCP4Data,CCP4Container,CCP4File,CCP4CustomManager,CCP4DataManager from CCP4ErrorHandling import * class CCustomTaskManager(CCP4CustomManager.CCustomManager): ERROR_CODES = { } ERROR_CODES.update(CCP4CustomManager.CCustomManager.ERROR_CODES ) ERROR_CODES.update( { 201 : { 'description' : 'Data class not recognised' }, 202 : { 'description' : 'Error creating data object' }, 203 : { 'description' : 'Can not find paramter to substitute into command' }, 204 : { 'description' : 'Paramter to substitute into command is unset' }, 205 : { 'description' : '' } } ) insts = None def __init__(self,parent=None): CCP4CustomManager.CCustomManager.__init__(self,parent,'task') def createCustomTask(self,name=None,title=None,container=None,overwrite=False): import CCP4XtalData err = CErrorReport() self.createDirectory(name = name, overwrite=overwrite) container.header.pluginName = name container.header.pluginTitle = title taskFile = self.getCustomFile(name=name,mustExist=False) #print 'CCustomTaskManager.createCustomTask',name,title,taskFile,container.paramList container.saveDataToXml(fileName=taskFile) if title is None: import copy title = copy.deepcopy(name) paramsContainer = CCP4Container.CContainer() header = paramsContainer.addHeader() header.setCurrent() header.function='DEF' header.pluginName.set(name) header.pluginTitle.set(title) paramsContainer.addParamsSubContainers() mergedMtzs = self.getMergedMtzs(container.paramList) for parDef in container.paramList: if parDef.function.__str__() in [ 'input','output','control parameter' ] and \ not (parDef.function.__str__()=='input' and mergedMtzs.has_key(parDef.name.__str__())): cls = CCP4DataManager.DATAMANAGER().getClass(parDef.dataType.__str__()) if cls is None: err.append(self.__class__,201,parDef.dataType.__str__()+' for '+parDef.name.__str__()) else: #try: if 1: qualifiers = { 'allowUndefined' : not(parDef.obligatory.__bool__()), 'saveToDb' : parDef.saveDataToDb.__bool__() } if issubclass(cls,CCP4File.CDataFile): qualifiers['fromPreviousJob'] = True if parDef.dataType.__str__() in ['CObsDataFile','CPhsDataFile'] and False in parDef.requiredContentType.get(): requiredContentType = parDef.requiredContentType.get() if parDef.dataType.__str__() == 'CObsDataFile': flagList = [CCP4XtalData.CObsDataFile.CONTENT_FLAG_IPAIR,CCP4XtalData.CObsDataFile.CONTENT_FLAG_FPAIR,CCP4XtalData.CObsDataFile.CONTENT_FLAG_IMEAN,CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN] else: flagList = [CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL,CCP4XtalData.CPhsDataFile.CONTENT_FLAG_PHIFOM] qualifiers['requiredContentFlag'] = [] for indx in range(len(flagList)): if requiredContentType[indx]: qualifiers['requiredContentFlag'].append(flagList[indx]) #print 'CCustomTaskManager.createCustomTask',parDef.name.__str__(),qualifiers obj = cls(name=parDef.name.__str__(),qualifiers = qualifiers ) #except Exception as e: # err.append(self.__class__,202,parDef.name.__str__()+' '+str(e)) #else: if parDef.function == 'input' : paramsContainer.inputData.addObject(obj,name=parDef.name.__str__()) elif parDef.function == 'output' : paramsContainer.outputData.addObject(obj,name=parDef.name.__str__()) elif parDef.function == 'control parameter' : paramsContainer.controlParameters.addObject(obj,name=parDef.name.__str__()) defFile = os.path.join(self.getDirectory(name=name),name+'.def.xml') #print 'CCustomTaskManager.createCustomTask defFile',defFile err.extend(paramsContainer.saveContentsToXml(fileName=self.getDefFile(name,False),header=header)) self.emitSignal('listChanged') return err def getMergedMtzs(self,paramList,function=None): mergedMtzs = {} for parDef in paramList: if parDef.mergeTo.isSet(): mergeToObj,indx = paramList.getItemByName(parDef.mergeTo.__str__()) if mergeToObj is not None and (function is None or mergeToObj.function == function): if not mergedMtzs.has_key(parDef.mergeTo.__str__()): mergedMtzs[parDef.mergeTo.__str__()] = [ ] if function == 'input': mergedMtzs[parDef.mergeTo.__str__()].append(parDef.name.__str__()) else: mergedMtzs[parDef.mergeTo.__str__()].append([parDef.name.__str__(),parDef.splitColumns.get()]) return mergedMtzs def getDefFile(self,name=None,mustExist=True): defFile = os.path.join(self.getDirectory(name=name),name+'.def.xml') if not mustExist or os.path.exists(defFile): return defFile else: return None def extractParams(self,tag,text): import re tagLen = len(tag) hits = re.findall(tag+'[0-9,a-z,A-Z,\-,_]*',text) ret = [] for item in hits: ret.append(item[tagLen:]) return ret def substituteParams(self,text='',tag='#',container=None,mergedMtzFileNames={}): err = CErrorReport() import re paramNameList = self.extractParams(tag,text) for paramName in paramNameList: obj = container.find(paramName) if obj is None: if mergedMtzFileNames.has_key(paramName): text = re.sub(tag+paramName,mergedMtzFileNames[paramName],text) else: err.append(self.__class__,203,paramName) elif not obj.isSet(): text = re.sub(tag+paramName,'',text) if not obj.qualifier('allowUndefined'): err.append(self.__class__,204,paramName) else: text = re.sub(tag+paramName,obj.__str__(),text) return text,err class CCustomComFile(CCP4Data.CData): CONTENTS = { 'text' : { 'class' : CCP4Data.CString}, 'name' : { 'class' : CCP4Data.CString, 'qualifiers' : { 'default' : './com.txt' } } } def getTableTextItems(self): try: text = self.__dict__['_value']['text'].__str__().split('\n')[0] except: text = '' return [ str(self.__dict__['_value']['name']) , text ] class CCustomComFileList(CCP4Data.CList): SUBITEM = { 'class' : CCustomComFile } class CCustomTaskDefinition(CCP4Container.CContainer): def __init__(self,parent=None,name=None,title=None): CCP4Container.CContainer.__init__(self,parent=parent,name=None,title=None) header = self.addHeader() header.setCurrent() header.function='CUSTOMTASK' header.pluginName.set(name) header.pluginTitle.set(title) # Duplicate name/title to simplify handling by gui self.addObject(CCP4Data.COneWord(parent=self,name='name')) self.addObject(CCP4Data.CString(parent=self,name='title')) self.addObject(CCP4Data.CString(parent=self,name='tagCharacter',qualifiers= { 'default' : '#' })) self.addObject(CCP4Data.CString(parent=self,name='comLine')) self.addObject(CCustomComFileList(parent=self,name='comFileList')) #print 'CCustomTaskDefinition.__init__',len(self.comFileList) self.comFileList.append({'comFileName' : './com.txt', 'comFileText' : ''}) self.addObject(CCustomTaskParamList(parent=self,name='paramList')) self.paramList.addItem() ''' def setEtree(self,element,checkValidity=True): CCP4Container.CContainer.setEtree(self,element,checkValidity=checkValidity) print 'CCustomTaskDefinition.setEtree', self.name.set(self.header.pluginName.__str__()) self.title.set(self.header.pluginTitle.__str__()) def getEtree(self,element): self.header.pluginName.set(self.name.__str__()) self.header.pluginTitle.set(self.title.__str__()) return CCP4Container.CContainer.getEtree(self) ''' class CCustomTaskFileFunction(CCP4Data.CString): QUALIFIERS = { 'enumerators' : ['unknown', 'input' , 'output', 'control parameter', 'log' ] } class CCustomTaskParam(CCP4Data.CData): CONTENTS = { 'name' : { 'class' : CCP4Data.COneWord}, 'dataType' : { 'class' : CCP4Data.CI2DataType , 'qualifiers' : {'default': 'CPdbDataFile' } }, 'label' : { 'class' : CCP4Data.CString}, 'obligatory' : { 'class' : CCP4Data.CBoolean, 'qualifiers' : {'default': True } }, 'saveDataToDb' : { 'class' : CCP4Data.CBoolean,'qualifiers' : {'default': False } }, 'function' : { 'class' : CCustomTaskFileFunction, 'qualifiers' : {'default': 'input' } } , 'mergeTo' : { 'class' : CCP4Data.CString }, 'splitColumns' : { 'class' : CCP4Data.CString }, 'requiredContentType' : { 'class' : CCP4Data.CList, 'subItem' : { 'class' : CCP4Data.CBoolean } }, # list length CObsDataFile=4, CPhsDataFile=2, others=0 'outputFilePath' : { 'class' : CCP4Data.CString } } def __init__(self,value=None,qualifiers={},parent=None,name=None,**kw): CCP4Data.CData.__init__(self,value=value,qualifiers=qualifiers,parent=parent,name=name,**kw) self.connectSignal(self.__dict__['_value']['dataType'],'dataChanged',self.handleDataTypeChange) self.handleDataTypeChange() def handleDataTypeChange(self): # Set requiredContentType list to appropriate length if self.__dict__['_value']['dataType'] == 'CObsDataFile': self.__dict__['_value']['requiredContentType'].set([True,True,True,True]) elif self.__dict__['_value']['dataType'] == 'CPhsDataFile': self.__dict__['_value']['requiredContentType'].set([True,True]) else: self.__dict__['_value']['requiredContentType'].unSet() #print 'CCustomTaskParam.handleDataTypeChange',self.__dict__['_value']['dataType'] ,self.__dict__['_value']['requiredContentType'] def getTableTextItems(self): if self.__dict__['_value']['dataType'].isCDataFile(): fileFunction = self.__dict__['_value']['function'].__str__() else: fileFunction = '_' if self.__dict__['_value']['obligatory']: oblig = 'yes' else: oblig = 'no' if self.__dict__['_value']['saveDataToDb']: save = 'yes' else: save = 'no' contentType = '' n = 0 if self.__dict__['_value']['dataType'] in ['CObsDataFile','CPhsDataFile']: if self.__dict__['_value']['dataType'] == 'CObsDataFile': dataTypeList = ['I+/-','F+/-','Imean','Fmean'] else: dataTypeList = ['HL coeffs','Phi/FOM'] for idx in range(len(dataTypeList)): if self.__dict__['_value']['requiredContentType'][idx]: contentType = contentType + dataTypeList[idx] + ' ' n = n + 1 if n == len(dataTypeList): contentType = '' return [ str(self.__dict__['_value']['name']), str(self.__dict__['_value']['label']), str(self.__dict__['_value']['dataType']), fileFunction, oblig, save, self.__dict__['_value']['mergeTo'].__str__(), self.__dict__['_value']['outputFilePath'].__str__(), contentType, self.__dict__['_value']['splitColumns'].__str__() ] class CCustomTaskParamList(CCP4Data.CList): SUBITEM = { 'class' : CCustomTaskParam } def getItemByName(self,name=None): if name is None: return None,None for ii in range(len(self.__dict__['_value'])): if self.__dict__['_value'][ii].name == name: return self.__dict__['_value'][ii],ii return None,None