""" CCP4DemoData.py: CCP4 GUI Project Copyright (C) 2015STFC 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.sstac 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 Sept 2015 - Create, download demo data """ import os import glob import time import shutil from PyQt4 import QtGui,QtCore from core.CCP4ErrorHandling import * from core import CCP4Utils from core import CCP4Modules class CDemoData: insts = None def __init__(self): self.builtInfo = False self.testDatasets = None self.restoreTestDatasets() def getOverviewPage(self): if not self.builtInfo: self.makeDemoDataInfo() return os.path.join(CCP4Utils.getDotDirectory(),'demo_data','README.html') def getTestDatasets(self): return self.testDatasets def loadTestDatasets(self): if self.testDatasets is None: #print 'CDemoData.loadTestDatasets' dirList = glob.glob(os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data','*')) dirList.extend(glob.glob(os.path.join(CCP4Utils.getDotDirectory(),'demo_data','*'))) self.testDatasets = [] for dr in dirList: #print 'loadTestDatasets',dr,'*',os.path.split(dr)[1] if os.path.isdir(dr) and os.path.split(dr)[1] != 'resources': try: infoText = CCP4Utils.readFile(os.path.join(dr,'INFO.txt')) label = infoText.split('\n')[0] except: label = os.path.split(dr)[1] self.testDatasets.append([os.path.split(dr)[1],label]) return self.testDatasets def saveTestDatasets(self): from lxml import etree if self.testDatasets is None: self.loadTestDatasets() fileName = os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data','datasets_list.xml') #print 'saveTestDatasets',len(self.testDatasets) root = etree.Element('datasetList') for name,label in self.testDatasets: ele = etree.SubElement(root,'dataset') e = etree.SubElement(ele,'name') e.text = name e = etree.SubElement(ele,'label') e.text = label CCP4Utils.saveEtreeToFile(root,fileName) def restoreTestDatasets(self): fileName = os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data','datasets_list.xml') #print 'restoreTestDatasets',os.path.exists(fileName) if not os.path.exists(fileName): self.saveTestDatasets() return root = CCP4Utils.openFileToEtree(fileName) self.testDatasets = [] for ele in root: self.testDatasets.append([ele.find('name').text,ele.find('label').text]) #print 'restoreTestDatasets',self.testDatasets def copyDemoDataToProject(self,parentWidget=None,projectId=None,dataset=None): source = os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data',dataset) if not os.path.exists(source): source = os.path.join(CCP4Utils.getDotDirectory(),'demo_data',dataset) dest = os.path.join(CCP4Modules.PROJECTSMANAGER().db().getProjectInfo(projectId=projectId,mode='projectdirectory'),dataset) if os.path.exists(dest): QtGui.QMessageBox.information(parentWidget,'Download demo data','Test data was already copied to the project directory '+dest) return try: shutil.copytree(source,dest) except: QtGui.QMessageBox.warning(parentWidget,'Download demo data','Failed to copy test data to the project directory '+dest) else: QtGui.QMessageBox.information(parentWidget,'Download demo data','Test data copied to the project directory '+dest) def makeDemoDataInfo(self): sectionList = ['Introduction','Molecular replacement','Ligands'] infoFileList = glob.glob(os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data','*','INFO.txt')) infoFileList.extend(glob.glob(os.path.join(CCP4Utils.getDotDirectory(),'demo_data','*','INFO.txt'))) for ii in range(len(infoFileList)-1,-1,-1): if infoFileList[ii].count('resources'): del infoFileList[ii] info = [] for fl in infoFileList: try: lines = CCP4Utils.readFile(fl).split('\n') if len(lines) < 3: lines.append('Others') relPath = os.path.relpath(os.path.split(fl)[0],os.path.join(CCP4Utils.getDotDirectory(),'demo_data')) info.append([relPath, lines[0], lines[1], lines[2]]) if not lines[2] in sectionList: sectionList.append(lines[2]) except: pass text = ''' Demo data overview

CCP4i2 demo data

The demo data sets provide a set of examples that you can copy to your project directory and that can be solved quickly as an introduction to CCP4i2.

''' for section in sectionList: text = text + '

' + section + '

\n\n' text = text + '''
Automatically created by CCP4i2: ''' + time.strftime("%a, %d %b %Y %H:%M:%S") + ''' ''' CCP4Utils.saveFile(os.path.join(CCP4Utils.getDotDirectory(),'demo_data','README.html'),text,overwrite=True) self.builtInfo=True def makeDemoData(self,parentWidget): dirPath = QtGui.QFileDialog.getExistingDirectory(parentWidget,'Select directory containing demo data').__str__() if not os.path.isdir(dirPath): return warningText = '' if not os.path.exists(os.path.join(dirPath,'README.html')): CCP4Utils.saveFile(os.path.join(dirPath,'README.html'),''' Demo data: ***dataset name****

CCP4i2 demo data: ***Short title***

***Short description***

Data files

Data files for this tutorial are located in the ccp4i2/test/data/***dataset name**** directory. When browsing to find files, the browser widget has a pull-down labelled "look in" which is populated by the projects known to your instance of ccp4i2 and (at the bottom) by CCP4I2_TOP: a shortcut to the ccp4i2 code base containing the demo data.
Last modified: Thu Feb 26 14:37:05 GMT 2015 ''') warningText = warningText + '''There was no README.html file in the directory. A template README.html file has been added - please edit in details of the demo.\n\n''' if not os.path.exists(os.path.join(dirPath,'INFO.txt')): CCP4Utils.saveFile(os.path.join(dirPath,'INFO.txt'),'''First line is name of dataset Second line is brief description for the overview page $CCP4I2/demo_data/README.html\n''') warningText = warningText + '''There was no INFO.txt file in the directory. A template INFO.txt file has been added - please edit in details of the demo.\n\n''' if len(warningText) > 0: QtGui.QMessageBox.warning(parentWidget,'Compress demo data','Data not saved - some files missing:\n\n'+warningText) return try: import zipfile zip = zipfile.ZipFile(dirPath+'.ccp4i2_demo.zip',mode='w') CCP4Utils.zipDirectory(zip,dirPath,rootRelPath=os.path.split(dirPath)[0]) zip.close() except: QtGui.QMessageBox.warning(parentWidget,'Compress demo data','Failed writing file:'+dirPath+'.ccp4i2_demo.zip') else: QtGui.QMessageBox.information(parentWidget,'Compress demo data','Compressed demo data saved to'+dirPath+'.ccp4i2_demo.zip') def downloadDemoData(self,parentWidget=None,projectId=None): if getattr(self,'downloadDialog',None) is None: self.downloadDialog = CDownloadDemoDataDialog(parentWidget) self.downloadDialog.show() self.downloadDialog.raise_() class CDownloadDemoDataDialog(QtGui.QDialog): ERROR_CODES = { 101 : {'description' : 'Failed to open compressed demo data file'}, 102 : {'description' : 'Failed to extract data from compressed demo data file'}, 103 : {'description' : 'Unknown error extracting data from compressed demo data file'}, 104 : {'description' : 'Error downloading compressed demo data file'}, 110 : {'description' : 'Failed reading URL'}} def __init__(self,parent): import functools from qtgui import CCP4Widgets self.path = '' self.makeTargetList() self.zipList = [] QtGui.QDialog.__init__(self,parent) self.setWindowTitle('Download demo data') self.setModal(True) self.setLayout(QtGui.QVBoxLayout()) self.layout().setContentsMargins(4,4,4,4) self.layout().setSpacing(4) line = QtGui.QHBoxLayout() self.layout().addLayout(line) line.addWidget(QtGui.QLabel('Enter URL for web page that has links to CCP4i2 demo data',self)) line.itemAt(0).widget().setObjectName('italic') line = QtGui.QHBoxLayout() self.layout().addLayout(line) line.addWidget(QtGui.QLabel('Web page',self)) self.source = QtGui.QComboBox(self) self.source.setMinimumWidth(400) self.source.setEditable(True) #for source in [ 'http://www.ysbl.york.ac.uk/~eap5/downloadPage.html' ]: for source in [ ]: self.source.addItem(source) line.addWidget(self.source) self.connect(self.source,QtCore.SIGNAL('editTextChanged(const QString &)'),self.handleSourceChanged) self.search = QtGui.QPushButton('Search page',self) self.search.setToolTip('Search the page for downloadable compressed demo data files') self.connect(self.search,QtCore.SIGNAL('released()'),self.handleHtmlSearch) line.addWidget(self.search) line = QtGui.QHBoxLayout() line.addWidget(QtGui.QLabel('Download to:',self)) self.targetButGroup = QtGui.QButtonGroup(self) id = -1 for label,path,useable in self.targetList: id = id + 1 if useable: rb = QtGui.QRadioButton(label,self) rb.setToolTip(path) self.targetButGroup.addButton(rb,id) line.addWidget(rb) self.targetButGroup.button(0).setChecked(True) self.layout().addLayout(line) line = QtGui.QHBoxLayout() line.addWidget(QtGui.QLabel('Downloadable demos..',self)) line.itemAt(0).widget().setObjectName('italic') self.layout().addLayout(line) frame = QtGui.QFrame(self) frame.setFrameShape(QtGui.QFrame.Box) frame.setLineWidth(2) frame.setLayout(QtGui.QVBoxLayout()) self.frame = QtGui.QFrame() self.frame.setLayout(QtGui.QVBoxLayout()) frame.layout().addWidget(self.frame) self.seleLine = QtGui.QFrame() self.seleLine.setLayout(QtGui.QHBoxLayout()) for butText,mode in [['Select all',True],['Unselect all',False]]: pb = QtGui.QPushButton(butText,self) self.connect(pb,QtCore.SIGNAL('released()'),functools.partial(self.selectAll,mode)) self.seleLine.layout().addWidget(pb) frame.layout().addWidget(self.seleLine) self.layout().addWidget(frame) self.setSelectVis() butBox = QtGui.QDialogButtonBox(self) but = butBox.addButton('Download',QtGui.QDialogButtonBox.ApplyRole) but.setDefault(False) self.connect(but,QtCore.SIGNAL('released()'),self.handleDownload) but = butBox.addButton(QtGui.QDialogButtonBox.Cancel) self.connect(but,QtCore.SIGNAL('released()'),self.close) line = QtGui.QHBoxLayout() line.addWidget(butBox) self.layout().addLayout(line) def makeTargetList(self): # Do we have write access to the ccp4i2 source - otherwise use dot dir self.targetList = [] fi = QtCore.QFileInfo(os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data')) self.targetList.append(['CCP4i2 installation',os.path.join(CCP4Utils.getCCP4I2Dir(),'demo_data'),fi.isDir() and fi.isWritable()]) target = os.path.join(CCP4Utils.getDotDirectory(),'demo_data') if not os.path.exists(target): os.mkdir(target) self.targetList.append(['My CCP4i2 area',target,True]) def handleFtpSearch(self): from ftplib import FTP self.host = str(self.source.currentText()) self.path = '' if self.host.count('/'): self.host,self.path = self.host.split('/',1) if len(self.path)>0 and not self.path.endswith('/'): self.path = self.path + '/' self.path = self.path + '*.ccp4i2_demo.zip' #print 'CDownloadDemoData.handleSearch',self.host,self.path self.ftp = FTP(self.host) # connect to host, default port self.ftp.login() # user anonymous, passwd anonymous@ self.retrlines = [] self.ftp.retrlines('NLST '+self.path,self.handleRetrlines) #print 'CDownloadDemoData handleSearch retrlines',self.retrlines def handleRetrlines(self,line): self.retrlines.append(line) def handleHtmlSearch(self): import urllib2 from lxml import etree self.path = str(self.source.currentText()) try: urlpath =urllib2.urlopen(self.path) except Exception as e0: if not self.path.startswith('http'): self.path = 'http://'+self.path try: urlpath =urllib2.urlopen(self.path) except Exception as e1: raise CException(self.__class__,110,str(e0)) else: self.source.setEditText(self.path) pageText = urlpath.read().decode('utf-8') urlpath.close() pageNode = etree.fromstring(pageText) self.zipList = [] for node in pageNode.iterfind('.//a'): if node.get('href') is not None and 'ccp4i2_demo.zip' in node.get('href'): self.zipList.append([node.get('href'),str(node.text)]) #print 'handleHtmlSearch',self.zipList self.loadFrame() def loadFrame(self): for w in self.frame.findChildren(QtGui.QCheckBox): w.hide() w.deleteLater() for link, desc in self.zipList: cb = QtGui.QCheckBox(desc,self) self.frame.layout().addWidget(cb) self.setSelectVis() def setSelectVis(self): vis = len(self.zipList)>0 for w in self.seleLine.findChildren(QtGui.QPushButton): w.setVisible(vis) def selectAll(self,mode): for w in self.frame.findChildren(QtGui.QCheckBox): w.setChecked(mode) def handleDownload(self): import urlparse downloadList = [] err = CErrorReport() ii = -1 for w in self.frame.findChildren(QtGui.QCheckBox): ii = ii + 1 if w.isChecked() and not 'DOWNLOADED' in str(w.text()): downloadList.append([w,urlparse.urljoin(os.path.split(self.path)[0]+'/',self.zipList[ii][0])]) #print 'handleDownload',self.path,downloadList if len(downloadList)==0: QtGui.QMessageBox.information(self,'Download demo data','No demo sets selected for download') return target = self.targetList[self.targetButGroup.checkedId()][1] for w,url in downloadList: try: self.downloadFile(url,target) except CException as e: err.extend(e) except Exception as e: err.append(self.__class__,103,'Extracting from '+url+' to '+target+'\n'+str(e)) else: w.setText(str(w.text())+' DOWNLOADED') w.repaint() CCP4Modules.DEMODATAMANAGER().makeDemoDataInfo() self.testDatasets = None self.saveTestDatasets() if len(err) > 0: err.warningMessage('Download demo data','Error downloaing demo data',parent=self) else: self.close() def downloadFile(self,url,target=None,replace=False): import urllib2 import tempfile import zipfile tmpFile =tempfile.mktemp(suffix='ccp4i2_demo.zip') demoDir = os.path.normpath(os.path.join(target,os.path.splitext(url.split('/')[-1])[0])) print 'Downloading demo data from',url,'to',tmpFile,'unpack to',demoDir if os.path.exists(demoDir): if replace: try: shutil.move(demoDir,fileName+'.bak') except: pass else: return #url = 'http://www.ysbl.york.ac.uk/~eap5/foo.ccp4i2_demo.zip' try: req = urllib2.urlopen(url) fp = open(tmpFile,'wb') shutil.copyfileobj(req, fp) req.close() fp.close() except: raise CException(self.__class__,104,tmpFile) try: czip = zipfile.ZipFile(tmpFile,mode='r') except: raise CException(self.__class__,101,tmpFile) #for zinfo in czip.infolist(): # print 'zinfo',zinfo.filename,zinfo.date_time try: czip.extractall(path=target) except: czip.close() raise CException(self.__class__,102,'Extracting from '+tmpFile+' to '+target) czip.close() def handleSourceChanged(self,source): if str(self.source.currentText()) != self.path: self.path = '' for w in self.frame.findChildren(QtGui.QCheckBox): w.hide() w.deleteLater() self.setSelectVis()