""" CCP4Container.py: CCP4 GUI Project Copyright (C) 2010 University of York 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 Aug 2010 - Generic container for CCP4Data objects """ import CCP4Data from CCP4ErrorHandling import * from CCP4DataManager import DATAMANAGER from CCP4Config import DEVELOPER,XMLPARSER class CContainer(CCP4Data.CData): ERROR_CODES = { 101 : { 'description' : 'Error parsing XML' }, 102 : { 'description' : 'Missing information' }, 103 : { 'description' : 'Unknown data class' }, 104 : { 'description' : 'Error creating data object' }, 105 : { 'description' : 'Error setting data object qualifiers' }, 106 : { 'description' : 'Error loading container definition' }, 107 : { 'description' : 'XML file does not have correct function defined in the header' }, 108 : { 'description' : 'XML undefined error interpreting sub-container' }, 109 : { 'description' : 'Error attempting to access unknown attribute', 'severity' : SEVERITY_WARNING }, 110 : { 'description' : 'Error creating sub-container' }, 111 : { 'description' : 'XML file does not have expected pluginName defined in the header' }, 113 : { 'description' : 'Attempting to add object that is not a CData' }, 114 : { 'description' : 'Attempting to add object without valid name' }, 115 : { 'description' : 'Attempting to add object with name that is already in container' }, 116 : { 'description' : 'Error while attempting to add object' }, 117 : { 'description' : 'Attempting to delete object with unrecognised name' }, 118 : { 'description' : 'Error while attempting to delete object' }, 119 : { 'description' : 'Error while attempting to set this container as object parent' }, 120 : { 'description' : 'Attempting to add object of unrecognised class to container contents' }, 121 : { 'description' : 'Error while attempting to add to container contents' }, 122 : { 'description' : 'Error while attempting to make object from new content in container' }, 123 : { 'description' : 'Unknown error while reading container header' }, 124 : { 'description' : 'Definition of sub-content for data of class that does not require sub-content' }, 125 : { 'description' : 'Unknown error while reading container content' }, 126 : { 'description' : 'No id for sub-container in XML file' }, 127 : { 'description' : 'Attempting to load container data from file that does not exist'}, 128 : { 'description' : 'Unknown error creating XML for sub-container'}, 129 : { 'description' : 'Error retieving data object for XML'}, 130 : { 'description' : 'Error saving data object to XML'}, 131 : { 'description' : 'Unknown error writing container contents to XML file'}, 132 : { 'description' : 'Error changing object name - no name given'}, 133 : { 'description' : 'Error changing object name - object with new name already exists'}, 134 : { 'description' : 'Error changing object name - no object with old name'}, 135 : { 'description' : 'Unknown error changing object name'}, 136 : { 'description' : 'Error inserting object in container data order'}, 137 : { 'description' : 'Unknown error restoring data from database'}, 138 : { 'description' : 'Attempting to copy from otherContainer which is not a CContainer'}, 139 : { 'severity' : SEVERITY_WARNING, 'description' : 'Attempting to copy data which is not in this container' }, 140 : { 'severity' : SEVERITY_WARNING, 'description' : 'Attempting to copy data which is not in the other container' }, 141 : { 'severity' : SEVERITY_WARNING, 'description' : 'Unknown error copying data' }, 142 : { 'description' : 'Unrecognised class name in file' }, 143 : { 'description' : 'Item in file does not have an id' }, 144 : { 'description' : 'Item id in file is not unique' }, 145 : { 'description' : 'Failed setting command line argument' }, 146 : { 'description' : 'Insufficient arguments at end of command line' }, 147 : { 'description' : 'Error handling XmlDataFile for file element in def xml' }, 148 : { 'description' : 'XmlDataFile for file element in def xml: file not found' }, 149 : { 'description' : 'XmlDataFile for file element in def xml: can not read xml' }, 150 : { 'description' : 'loadDataFromXml could not find plugin def file' }, 160 : { 'description' : 'Error in adding guiAdmin to CContainer' }, 161 : { 'description' : 'Error adding object to guiAdmin' }, 162 : { 'description' : 'Error adding guiAdmin to CContainer' }, 310 : { 'description' : 'Different number of file objects to compare' }, 311 : { 'description' : 'Different number of XData objects to compare' }, 312 : { 'description' : 'Different number of key-value pairs to compare' }, 313 : { 'description' : 'Different values of key-value pair' }, 314 : { 'description' : 'Error running comparison of object' } } def __init__(self,name=None,etreeElement=None,contents={},definitionFile='',parent=None,guiAdmin=False,**kw): self.__dict__['CONTENTS'] = { } CCP4Data.CData.__init__(self,parent=parent,name=name) self.__dict__['_dataOrder'] = [] # Retain order of data from XML to use in auto-generated GUI report = CException() if etreeElement is not None: report = self.loadContentsFromEtree(etreeElement) if guiAdmin: try: report.extend(self.addGuiAdminContents()) except: report.append(self.__class__,160,str(name),name=self.objectPath()) elif len(contents)>0: report.extend(self.setContents(contents)) elif len(definitionFile)>0: report.extend(self.loadContentsFromXml(definitionFile,guiAdmin=guiAdmin)) # Throw exception if any of these data loading methods # return error if report.maxSeverity()>= SEVERITY_ERROR: myException = CException() myException.extend(report) raise myException def __getattr__(self,name,default=NotImplemented): #print 'in CData.__getattr__',name if self.CONTENTS.has_key(name): return self._value[name] elif name == 'header': return getattr(self.__dict__,'header',None) elif name == 'paramsHeader': return getattr(self.__dict__,'paramsHeader',None) elif name == 'version': return self.getVersion() if default is NotImplemented: raise CException(self.__class__,109,name,name=self.objectPath()) else: return default def contents(self,name=None): if name is None: return self.CONTENTS elif self.CONTENTS.has_key(name): return self.CONTENTS[name] else: return None def setContents(self,contents={}): #myException = CException() myException = CErrorReport() for name,defn in contents.items(): obj = None cls = None if defn.has_key('class'): cls = defn['class'] elif defn.has_key('className'): cls = DATAMANAGER().getClass(defn['className']) if cls is None: myException.append(self.__class__,103,'Class: '+defn['className']+' specified for: '+name,name=self.objectPath()) else: myException.append(self.__class__,102,'For: '+name,name=self.objectPath()) if cls is not None: try: obj = cls(parent=self) obj.setObjectName(name) except CException as e: obj = None myException.extend(e) #except: # obj = None # myException.append(self.__class__,104,'For: '+name,name=self.objectPath()) if obj is not None and defn.has_key('qualifiers'): # Set the qualifiers - note that if this fails the obj is deleted try: obj.setQualifiers(qualifiers=defn['qualifiers']) except CException as e: myException.extend(e) obj = None except: myException.append(self.__class__,105,'Tag: '+name,name=self.objectPath()) obj = None if obj is not None: self.__dict__['_value'][name] = obj self.__dict__['CONTENTS'][name] = { 'class' : cls, 'qualifiers' : obj.qualifiers() } self.__dict__['_dataOrder'].append(name) # Not sure if we treat this as exception or return #if len(myException)>0: raise myException return myException def update(self,container=None): ''' Update from another container ''' for key in container.dataOrder(): try: obj = self.__getattr__(key) except: pass else: try: obj.set(container.__getattr__(key)) except: print 'ERROR in CContaner.update for key',key def loadContentsFromXml(self,fileName=None,guiAdmin=False): import CCP4File f = CCP4File.CI2XmlDataFile(fullPath=fileName) f.loadFile() #print 'CContainer.loadContentsFromXml',f.header.function if f.header.function != 'DEF': raise CException(self.__class__,107,'Filename: '+fileName,name=self.objectPath()) self.__dict__['header'] = f.header self.__dict__['header'].setParent(self) #print 'loadContentsFromXml', f.header.pluginName, f.header.pluginTitle,guiAdmin if f.header.pluginTitle is not None: self.setObjectName(str(f.header.pluginTitle)) if f.header.pluginName is not None: self.setObjectName(str(f.header.pluginName)) errorReport = self.loadContentsFromEtree(element=f.getBodyEtree()) #print 'CContainer.loadContentsFromXml after loadContentsFromEtree',self.objectName() if guiAdmin: self.addGuiAdminContents() return errorReport def addParamsSubContainers(self): for name in ['inputData','controlParameters','outputData']: self.addObject(CContainer(parent=self,name=name),name=name) def addGuiAdminContents(self): err = CErrorReport() if self.__dict__['_dataOrder'].count('guiAdmin'): return err import CCP4TaskManager,CCP4DataManager container = CContainer(name='guiAdmin') for id,className,qualifiers in [ ['followFrom','CFollowFromJob',{'guiLabel' : 'Follow from'}], ['jobTitle','CJobTitle',{'default': '', 'guiLabel' : 'Job title' }], ['jobStatus','CJobStatus',{}], ['patchSelection','CPatchSelection' ,{}] ]: cls = CCP4DataManager.DATAMANAGER().getClass(className) if cls is not None: try: obj = cls(parent=container,name=id,qualifiers=qualifiers) #print 'CContainer.addGuiAdminContents',id,obj container.addObject(obj) except: err.append(self.__class__,161,id,name=self.objectPath()) try: self.addObject(object=container,name='guiAdmin') except: err.append(self.__class__,162,name=self.objectPath()) return err def loadDataFromXml(self,fileName=None,guiAdmin=False,check=True,function='PARAMS',loadHeader=False): import CCP4File,CCP4TaskManager f = CCP4File.CI2XmlDataFile(fullPath=fileName) #f.loadFile() #print 'CContainer.loadDataFromXml',fileName,f.header.function,self.pluginName() if f.header.function != function: raise CException(self.__class__,107,'Filename: '+str(fileName),name=self.objectPath()) if self.pluginName() is None or len(self.pluginName())==0: # Try loading for the appropriate plugin def file pluginName = str(f.header.pluginName) pluginVersion = str(f.header.pluginVersion) try: defFile = CCP4TaskManager.TASKMANAGER().lookupDefFile(pluginName,pluginVersion) except: raise CException(self.__class__,150,pluginName,name=self.objectPath()) #print 'CContainer.loadDataFromXml loading contents from defFile',defFile self.loadContentsFromXml(defFile,guiAdmin=guiAdmin) else: if check and f.header.pluginName != self.pluginName(): #print 'loadDataFromXml',f.header.pluginName,self.pluginName() raise CException(self.__class__,111,'Filename: '+fileName,name=self.objectPath()) if loadHeader: self.__dict__['header'] = CCP4File.CI2XmlHeader() self.__dict__['header'].set(f.header) else: self.__dict__['paramsHeader'] = CCP4File.CI2XmlHeader() self.__dict__['paramsHeader'].set(f.header) errorReport = self.setEtree(f.getBodyEtree()) return errorReport def saveContentsToXml(self,fileName=None,header=None): import CCP4File f = CCP4File.CI2XmlDataFile(fullPath=fileName) if header is not None: f.header.set(header) elif self.header is not None: f.header.set(self.header) f.header.setCurrent() bodyEtree,errorReport = self.saveContentsToEtree() #print 'CContainer.saveContentsToXml',fileName,errorReport.report() try: f.saveFile(bodyEtree=bodyEtree) except CException as e: errorReport.append(e) except: errorReport.append(self.__class__,130,fileName,name=self.objectPath()) return errorReport def getEtree(self,excludeUnset=True): name = self.objectName() if name.count(' ')>0: import re name = re.sub(' ','_',name) return CCP4Data.CData.getEtree(self,excludeUnset=excludeUnset,name=name) def saveDataToXml(self,fileName=None,subContainer=None,function='PARAMS'): ''' Save the data to xml PARAMS file with option to save just one specified subContainer (used for interruptStatus) ''' errorReport = CErrorReport() import CCP4File f = CCP4File.CI2XmlDataFile(fullPath=fileName) if self.header is not None: f.header.set(self.header) f.header.function = function f.header.setCurrent() bodyEtree = self.getEtree(excludeUnset=True) if subContainer is not None: subConList = bodyEtree.xpath('./'+subContainer) if len(subConList)>0: #from lxml import etree #bodyEtree = etree.Element('dummy') #bodyEtree.append(subConList[0]) bodyEtree = subConList[0] try: f.saveFile(bodyEtree=bodyEtree) except CException as e: errorReport.append(e) except: errorReport.append(self.__class__,130,fileName,name=self.objectPath()) return errorReport def loadFromEtree(self,element): myException = CErrorReport() self.__dict__['_dataOrder'] = [] name = element.get('id',None) if name is not None: self.setObjectName(name) for ele in element.iterchildren(): className = ele.tag cls = DATAMANAGER().getClass(className) if cls is None: myException.append(self.__class__,142,className,name=self.objectPath()) else: name = ele.get('id',None) if name is None: myException.append(self.__class__,143,className,name=self.objectPath()) elif self._dataOrder.count(name): myException.append(self.__class__,144,name,name=self.objectPath()) else: try: obj = cls(parent=self,name=name) except CException as e: myException.extend(e) except Exception as e: myException.append(self.__class__,104,name,name=self.objectPath()) if obj is not None: try: self.addObject(object=obj) except CException as e: myException.extend(e) except Exception as e: myException.append(self.__class__,116,name,name=self.objectPath()) rv = self._value[name].setEtree(ele) if len(rv)>0: myException.extend(rv) return myException def loadContentsFromEtree(self,element,readHeader=True,overwrite=False): myException = CErrorReport() myOverwrite = overwrite if not myOverwrite: self.__dict__['_dataOrder'] = [] name = element.get('id',None) if name is not None and readHeader: # Beware reading the ccp4i2_body id from a 'base' def file # readHeader will be False in this case self.setObjectName(name) for ele in element.iterchildren(): obj = None if ele.tag == 'content': #try: e,obj = self.makeDataObjectFromEtree(ele) #except: # myException.append(self.__class__,125,'Content:'+str(ele.get('id')),name=self.objectPath()) myException.extend(e) elif ele.tag == 'container': name = ele.get('id',None) if name is None: CErrorReport.append(self.__class__,126,name=self.objectPath()) name = 'noName' # Allow that container may already exist and just load to it if self.__dict__['_value'].has_key(name): obj = self.__dict__['_value'][name] else: try: obj = CContainer(parent=self,name=name) except: myException.append(self.__class__,110,name=self.objectPath()) if obj is not None: if DEVELOPER(): obj.loadContentsFromEtree(ele,overwrite=myOverwrite) else: try: obj.loadContentsFromEtree(ele,overwrite=myOverwrite) except CException as e: myException.extend(e) obj = None except: myException.append(self.__class__,108,'Tag: '+name,name=self.objectPath()) obj = None elif ele.tag == 'header': if readHeader: try: if not hasattr(self.__dict__,'header'): import CCP4File self.__dict__['header']=CCP4File.CI2XmlHeader(parent=self,name='header') self.__dict__['header'].setEtree(ele) #print 'CContainer.loadContentsFromEtree header',self.__dict__['header'],self.__dict__['header'].pluginName if self.__dict__['header'].pluginName is not None: self.setObjectName(str(self.__dict__['header'].pluginName)) except CException as e: myException.extend(e) except: myException.append(self.__class__,123,name=self.objectPath()) elif ele.tag == 'qualifiers': self.setQualifiersEtree(ele) elif ele.tag == 'file': fileNameEle = ele.find('CI2XmlDataFile') if fileNameEle is None: myException.append(self.__class__,147,name=self.objectPath()) else: import CCP4File fileObj = CCP4File.CI2XmlDataFile() err = fileObj.setEtree(fileNameEle) if len(err)>0: myException.append(self.__class__,147,name=self.objectPath()) else: if not fileObj.exists(): myException.append(self.__class__,148,str(fileObj),name=self.objectPath()) else: try: fileContentEle = fileObj.getBodyEtree() except: myException.append(self.__class__,149,str(fileObj),name=self.objectPath()) else: err = self.loadContentsFromEtree(fileContentEle,readHeader=False) if len(err)>0: myException.extend(err) # We have read in a 'base' definition from another file and may now modify it by overwriting # with definitions from this file myOverwrite=True if obj is not None: if self.__dict__['CONTENTS'].has_key(obj.objectName()) and myOverwrite: self.replaceObject(object=obj,name=obj.objectName()) else: self.addObject(object=obj) # Not sure if we treat this as exception or return #if len(myException)>0: raise myException #print 'CContainer.loadContentsFromEtree myException',len(myException),myException.report() return myException def saveContentsToEtree(self): if XMLPARSER() == 'lxml': from lxml import etree errors = CErrorReport() # Create element element = etree.Element('container') name = self.objectName() if name is not None and len(name)>0: element.set('id',name) # Loop over contents for name in self._dataOrder: if self.CONTENTS.has_key(name): cls = self.CONTENTS[name].get('class',None) obj = self.__dict__['_value'].get(name,None) #print 'saveContentsToEtree',name,cls,obj if cls is None or obj is None: errors.append(self.__class__,129,name,name=self.objectPath()) elif cls == CContainer: #try: ele,errs = self.__dict__['_value'][name].saveContentsToEtree() errors.extend(errs) # also keep qualifiers qualiEle,errs = obj.qualifiersEtree(customOnly=True,tag='qualifiers',recurse=False) #print 'saveContentsToEtree qualiEle' #print etree.tostring(qualiEle, pretty_print=True) errors.extend(errs) ele.append(qualiEle) element.append(ele) #except: # errors.append(self.__class__,128,name) else: #try: ele = etree.Element('content') ele.set('id',name) classEle = etree.Element('className') cls = self.CONTENTS[name].get('class',None) if cls is not None: classEle.text = cls.__name__ else: classEle.text = 'UNKNOWN' ele.append(classEle) qualiEle,errs = obj.qualifiersEtree(customOnly=True,tag='qualifiers',recurse=False) errors.extend(errs) ele.append(qualiEle) if CCP4Data.isCollectionClass(cls): listEle,errs = obj.subItemEtree(customOnly=True) ele.append(listEle) errors.extend(errs) element.append(ele) #except: # errors.append(self.__class__,130,name) return element,errors def makeDataObjectFromEtree(self,element): rv = CErrorReport() if element.get('id') is not None: name = str(element.get('id')) else: name = None className = None qEle = None cEleList = [] for subEle in element.iterchildren(): if subEle.tag == 'className': className = str(subEle.text) elif subEle.tag == 'qualifiers': # Don't try to parse the qualifiers just # hand them over to the data class object qEle = subEle elif ['content','subItem','rowHeader','columnHeader'].count(str(subEle.tag)): # There is definition of some item of content cEleList.append(subEle) #print 'makeDataObjectFromEtree',name if len(cEleList)>0: e,subContents = self.subContentsFromEtree(cEleList) CErrorReport.extend(e) else: subContents = {} #if len(cEleList)>0: print 'makeDataObjectFromEtree',name,subContents if className is None: rv.append(self.__class__,102,'No className for tag: '+str(name),name=self.objectPath()) return rv,None else: cls = DATAMANAGER().getClass(className) if cls == None: rv.append(self.__class__,103,'Class: '+className+' specified for: '+str(name),name=self.objectPath()) return rv,None else: buildInInit = True if DEVELOPER(): if len(subContents)==0: obj = cls(parent=self,name=name) elif CCP4Data.isCollectionClass(cls): buildInInit = False obj = cls(parent=self,name=name,subItem=subContents.get('subItem',{}) ,build=False) else: obj = cls(parent=self,name=name,contents=subContents) else: try: if len(subContents)==0: obj = cls(parent=self,name=name,build=False) elif CCP4Data.isCollectionClass(cls): buildInInit = False obj = cls(parent=self,name=name,subItem=subContents.get('subItem',{}),build=False) else: obj = cls(parent=self,name=name,contents=subContents) except CException as e: rv.extend(e) except: rv.append(self.__class__,104,'Class: '+className+' specified for: '+name,name=self.objectPath()) #print 'makeDataObjectFromEtree',name,type(obj),qEle if obj is not None: if qEle is not None: rv.extend(obj.setQualifiersEtree(qEle)) if not buildInInit: obj.build(qualifiers=obj.__dict__['_qualifiers']) #print 'CContainer.makeDataObjectFromEtree',name,obj.__dict__['_value'],qEle.find('default') if qEle.find('default') is not None: obj.setDefault() return rv,obj def subContentsFromEtree(self,elementList=[]): rv = CErrorReport() tmpContainer = CContainer(name='temporary',parent=self) contents = {} for ele in elementList: e,subObj = tmpContainer.makeDataObjectFromEtree(ele) if subObj is not None: name = subObj.objectName() if name is None or len(name)==0: name = str(ele.tag) contents[name] = { 'class' : subObj.__class__, 'qualifiers' : subObj.qualifiers(default=False) } tmpContainer.deleteLater() rv.extend(e) #print 'subContentsFromEtree',contents return rv,contents def addContent(self,name=None,cls=None,qualifiers={},subItem={},value=None): # Add an item of content that is defined in Python code import types if name is None: raise CException(self.__class__,114,'Content name: '+name,name=self.objectPath()) elif self.__dict__['_value'].has_key(name): raise CException(self.__class__,115,'Content name: '+name,name=self.objectPath()) if cls is None: raise CException(self.__class__,120,name=self.objectPath()) if isinstance(cls,types.StringType): cls = DATAMANAGER().getClass(cls) if cls is None or not issubclass(cls,CCP4Data.CData): raise CException(self.__class__,120,'Content name: '+name,name=self.objectPath()) try: self.__dict__['CONTENTS'][name] = { 'class' : cls , 'qualifiers' : qualifiers } except: raise CException(self.__class__,121,'Content name: '+name,name=self.objectPath()) if cls == CContainer: self.__dict__['_value'][name] = CContainer(name=name) else: try: self.buildItem(key=name,cls=cls,qualifiers=qualifiers,subItem=subItem) self.__dict__['_dataOrder'].append(name) except CException as e: del self.__dict__['CONTENTS'][name] e.append(self.__class__,122,'Content name: '+name,name=self.objectPath()) raise e except: del self.__dict__['CONTENTS'][name] raise CException(self.__class__,122,'Content name: '+name,name=self.objectPath()) if value is not None: self.__dict__['_value'][name].set(value) return self.__dict__['_value'][name] def addObject(self,object=None,name=None,reparent=True,afterObject=None): #print 'CContainer.addObject',name, object.__class__,object.objectName() if object is None or not isinstance(object,CCP4Data.CData): raise CException(self.__class__,113,name=self.objectPath()) if name is None: name = object.objectName() if len(name)<=0: raise CException(self.__class__,114,name=self.objectPath()) if self.__dict__['_value'].has_key(name): raise CException(self.__class__,115,'Object name: '+name,name=self.objectPath()) if reparent: try: object.setParent(self) except: raise CException(self.__class__,119,'Object name: '+str(name),name=self.objectPath()) try: self.__dict__['CONTENTS'][name] = { 'class' : object.__class__, 'qualifiers' : object.qualifiers(default=False) } self.__dict__['_value'][name] = object except Exception as e: import sys raise CException(self.__class__,116,'Object name: '+name+' '+str(e),name=self.objectPath(),exc_info=sys.exc_info()) try: if afterObject is not None and self.__dict__['_dataOrder'].count(afterObject): ipos = self.__dict__['_dataOrder'].index(afterObject) else: ipos = -1 if ipos <0: self.__dict__['_dataOrder'].append(name) else: self.__dict__['_dataOrder'].insert(ipos+1,name) except Exception as e: import sys raise CException(self.__class__,116,'Object name: '+name+' '+str(e),name=self.objectPath(),exc_info=sys.exc_info()) def replaceObject(self,object=None,name=None,reparent=True): if name is None or not self.__dict__['CONTENTS'].has_key(name): raise CException(self.__class__,117,'Object name: '+str(name),name=self.objectPath()) if object is None or not isinstance(object,CCP4Data.CData): raise CException(self.__class__,113,name=self.objectPath()) if reparent: try: object.setParent(self) except: raise CException(self.__class__,119,'Object name: '+str(name),name=self.objectPath()) try: self.__dict__['CONTENTS'][name] = { 'class' : object.__class__, 'qualifiers' : object.qualifiers(default=False) } self.__dict__['_value'][name] = object except: raise CException(self.__class__,116,'Object name: '+name,name=self.objectPath()) def deleteObject(self,name=None): if name is None or not self.__dict__['CONTENTS'].has_key(name): raise CException(self.__class__,117,'Object name: '+str(name),name=self.objectPath()) try: del self.__dict__['CONTENTS'][name] del self.__dict__['_value'][name] except: raise CException(self.__class__,118,'Object name: '+str(name),name=self.objectPath()) if self.__dict__['_dataOrder'].count(name): self.__dict__['_dataOrder'].remove(name) def renameObject(self,oldName=None,newName=None): if oldName is None or newName is None or len(newName) is 0: raise CException(self.__class__,132,'Old name: '+str(oldName)+' new name:'+str(newName),name=self.objectPath()) elif self.__dict__['_value'].has_key(newName): raise CException(self.__class__,133,'Old name: '+str(oldName)+' new name:'+str(newName),name=self.objectPath()) if not self.__dict__['_value'].has_key(oldName): raise CException(self.__class__,134,'Old name: '+str(oldName)+' new name:'+str(newName),name=self.objectPath()) try: self.__dict__['CONTENTS'][newName] = self.__dict__['CONTENTS'].pop(oldName) self.__dict__['_value'][newName] = self.__dict__['_value'].pop(oldName) ii = self.__dict__['_dataOrder'].index(oldName) if ii>=0: self.__dict__['_dataOrder'][ii] = newName self.__dict__['_value'][newName].setObjectName(newName) except: raise CException(self.__class__,135,'Old name: '+str(oldName)+' new name:'+str(newName),name=self.objectPath()) def clear(self): self.__dict__['CONTENTS'] = {} self.__dict__['_value'] = {} self.__dict__['_dataOrder'] = [] def addHeader(self): #print 'CContainer.addHeader',repr(self), self.__dict__.has_key('header'), if not self.__dict__.has_key('header'): import CCP4File self.__dict__['header'] = CCP4File.CI2XmlHeader(parent=self) #print repr(self.__dict__['header']),self.__dict__['header'] return self.__dict__['header'] def getHeader(self): if self.__dict__.has_key('header'): return self.__dict__['header'] else: return None def getHeaderEtree(self,jobId=None,project=None,function='PARAMS'): # Return an eTree for a data file header # This method could be member of CTaskViewer import CCP4File import CCP4Config header = CCP4File.CI2XmlHeader(parent=self,name='header') if self.__dict__.has_key('header'): header.set(self.__dict__['header']) else: header.pluginName = self.objectName() header.function = function header.userId.setCurrentUser() header.creationTime.setCurrentTime() header.ccp4iVersion.set(CCP4Config.VERSION().ccp4iVersion) if jobId is not None: header.jobId = jobId if project is not None: header.project = project return header.getEtree() def nonexistantFiles(self): #Return a list of files that mustExist but do not! import CCP4File nonexistantList = [] for key,obj0 in self.__dict__['_value'].items(): objList,xmlText,keyValues = obj0.saveToDb() for obj in objList: if isinstance(obj,CCP4File.CDataFile): #print 'CContainer.nonexistantFiles',key,obj.qualifiers('mustExist'),obj.exists(), obj.isSet(), obj.qualifiers('allowUndefined') if not obj.isSet(): if not obj.qualifiers('allowUndefined'): nonexistantList.append(key) else: if obj.qualifiers('mustExist') and not obj.exists(): nonexistantList.append(key) return nonexistantList def inputFilesFileIds(self): import CCP4File ret= {} for key,obj0 in self.__dict__['_value'].items(): objList,xmlText,keyValues = obj0.saveToDb() for obj in objList: if isinstance(obj,CCP4File.CDataFile) and obj.dbFileId.isSet(): ret[str(obj.dbFileId)] = key return ret def dataOrder(self): return self.__dict__['_dataOrder'] def validity(self): err = CErrorReport() for key in self.dataOrder(): if isinstance(self.__dict__['CONTENTS'][key],CContainer): err.extend(self.__dict__['CONTENTS'][key].validity()) else: err.extend(self.__dict__['CONTENTS'][key].validity(self.__dict__['CONTENTS'][key].get())) return err def firstDataObject(self): #Return the first data (not container) object - # useful for initialising guis ii = -1 while ii+1 < len(self.__dict__['_dataOrder']): ii = ii + 1 name = self.__dict__['_dataOrder'][ii] #print 'firstDataItem',repr(self),ii,name if self.__dict__['CONTENTS'][name]['class'] == CContainer: firstItem = self.__dict__['_value'][name].firstDataObject() if firstItem is not None: return firstItem else: return self.__dict__['_value'][name] return None def pluginName(self): if self.__dict__.has_key('header') and self.__dict__['header'].pluginName is not None: return self.__dict__['header'].pluginName else: return self.objectName() def find(self,name=None): # Find an item in this or any child container if self.__dict__['_value'].has_key(name): return self.__dict__['_value'].get(name) else: splitName = name.split('.') if len(splitName)>1: if self.__dict__['_value'].has_key(splitName[0]) and isinstance(self.__dict__['_value'][splitName[0]],CContainer): newName = splitName[1] for item in splitName[2:]: newName = newName + '.' + item return self.__dict__['_value'][splitName[0]].find(newName) return None else: for key,obj in self.__dict__['_value'].items(): if isinstance(obj,CContainer): rv = obj.find(name) if rv is not None: return rv return None def copyData(self,otherContainer=None,dataList=None): import types report = CErrorReport() if otherContainer is None or not isinstance(otherContainer,CContainer): report.append(self.__class__,138,name=self.objectPath()) return report if dataList is None: dataList = self.dataOrder() for name in dataList: if isinstance(name,(types.ListType,types.TupleType)): if len(name)>=2: otherName = name[0] name = name[1] else: name = name[0] otherName = name[0] else: otherName = name myData = self.find(name) otherData = otherContainer.find(otherName) #print 'CContainer.copyData',name,myData,myData if myData is None: report.append(self.__class__,139,details=name,name=self.objectPath()) elif otherData is None: report.append(self.__class__,140,details=otherName,name=self.objectPath()) else: try: myData.set(otherData) except CException as e: report.extend(e) except Exception as e: report.append(self.__class__,141,details=name) return report def parseCommandLine(self,commandLine=[],template=[]): import types errorReport = CErrorReport() indx = -1 while indx+1 < len(commandLine): indx = indx + 1 # Try if cammand line keyword matches name of data object # If so then assume it is followed by one data value # This should work for the usual CCP4 com line dataObj = self.find(commandLine[indx]) if dataObj is not None: if isinstance(dataObj,CCP4Data.CBoolean): dataObj.set(True) else: if indx+1 < len(commandLine): indx = indx + 1 try: dataObj.set(commandLine[indx]) except CException as e: errorReport.extend(e) else: errorReport.append(self.__class__,146,commandLine[indx],name=self.objectPath()) # Alternatively try looking for keyword in the commandLineLookup else: for defn in template: found = 0 if isinstance(defn[0],types.ListType): found = defn[0].count(commandLine[indx]) elif commandLine[indx] == defn[0]: found = 1 if found: dataObj = self.find(defn[1]) if dataObj is not None: if len(defn)==2: if indx + 1 < len(commandLine): indx = indx + 1 #print 'parseCommandLine found dataObj',dataObj.objectName(),commandLine[indx] try: dataObj.set(commandLine[indx]) except CException as e: errorReport.extend(e) except Exception as e: errorReport.append(self.__class__,145,dataObj.objectName(),name=self.objectPath()) else: errorReport.append(self.__class__,146,commandLine[indx],name=self.objectPath()) else: dataDict = {} if indx + len(defn[2])