import sys, os import urllib import urllib2 import traceback class ccp4i2CootInterface(): FileTypes = [('chemical/x-pdb',None,'Import coordinates from project'), ('application/CCP4-mtz-map', 1, 'Import 2Fo-Fc maps from project'), ('application/CCP4-mtz-map', 2, 'Import Fo-Fc maps from project'), ('application/refmac-dictionary', None, 'Import CIF dictionary'), ] def __init__(self, dropDir=None): self.dropDir = dropDir print '** Drop directory for output files is ', self.dropDir #Cache relevant environment variables self.ccp4i2HTTPPort = os.environ.get('CCP4I2_HTTP_PORT',None) print '** CCP4I2_HTTP_PORT is ', self.ccp4i2HTTPPort if self.ccp4i2HTTPPort is not None: self.serverRoot = "http://127.0.0.1:%s/database"%self.ccp4i2HTTPPort else: self.serverRoot = None self.ccp4i2ProjectName = os.environ.get('CCP4I2_PROJECT_NAME',None) print '** CCP4I2_PROJECT_NAME is ' print self.ccp4i2ProjectName self.ccp4i2ProjectID = os.environ.get('CCP4I2_PROJECT_ID',None) print '** CCP4I2_PROJECT_ID is ' print self.ccp4i2ProjectID def addSeparator(self, menu): import gtk sep = gtk.MenuItem() menu.add(sep) sep.show() def installMenus(self): import gtk menu = coot_menubar_menu("CCP4i2 extensions") self.ccp4i2ExtensionsMenuItem = menu.get_attach_widget() self.ccp4i2ExtensionsMenuItem.connect('activate', self.populateMenus) if self.serverRoot is not None: #Add menu button to import coordinates #First coordinates self.projectDirectory = self.performDatabaseLookup("getProjectDirectory",projectId=self.ccp4i2ProjectID) for fileType, subType, menuText in self.FileTypes: menuitem = gtk.MenuItem(menuText) menu.append(menuitem) menuitem.show() self.addSeparator(menu) # Add broader project interrogating item self.otherProjectsMenuItem = gtk.MenuItem('Other projects') menu.append(self.otherProjectsMenuItem) self.otherProjectsMenuItem.show() self.addSeparator(menu) # Add simple save options add_simple_coot_menu_menuitem(menu, "Save mol to CCP4i2...", lambda func : self.selectAndSave() ) add_simple_coot_menu_menuitem(menu, "Save to CCP4i2", lambda func : self.saveToDatabase(0) ) fileMenu = coot_menubar_menu("File") self.addSeparator(fileMenu) add_simple_coot_menu_menuitem(fileMenu, "Save mol to CCP4i2...", lambda func : self.selectAndSave() ) add_simple_coot_menu_menuitem(fileMenu, "Save to CCP4i2", lambda func : self.saveToDatabase(0) ) def populateMenus(self, menuitem): import gtk self.files = [] self.populateSubmenus(menuitem, [self.ccp4i2ProjectID]) projectList = self.performDatabaseLookup('listProjects') #print projectList #sys.stdout.flush() projectSubMenu = gtk.Menu() projectSubMenu.show() for projectInfo in projectList: projectMenuItem = gtk.MenuItem(projectInfo[1]) projectMenuItem.connect('activate', self.populateSubmenus, projectInfo) projectMenuItem.show() fileTypesMenu = gtk.Menu() fileTypesMenu.show() projectMenuItem.set_submenu(fileTypesMenu) for fileType, subType, menuText in self.FileTypes: fileTypeMenuItem = gtk.MenuItem(menuText) fileTypeMenuItem.show() fileTypesMenu.append(fileTypeMenuItem) projectSubMenu.append(projectMenuItem) projectMenuItem.show() self.otherProjectsMenuItem.set_submenu(projectSubMenu) self.otherProjectsMenuItem.show() def addFilesOfProject_ofType_subType_toMenu(self, projectId, fileType, subType, menu): import gtk self.projectDirectory = self.performDatabaseLookup("getProjectDirectory",projectId=projectId) fileTypeAndSubType = fileType if subType is not None: fileTypeAndSubType+= ('_'+str(subType)) getFilesArgs = {'projectId':projectId, 'fileType':fileType, 'topLevelOnly':True} if subType is not None: getFilesArgs['subType'] = subType newFiles2 = self.getProjectFiles(**getFilesArgs) newFiles1 = sorted(newFiles2, key=lambda fileJob: int(str(fileJob[6]).split('.')[0])) newFiles = [] for newFile1 in newFiles1: file = {'fileid':newFile1[1], 'jobnumber':newFile1[6], 'filename':newFile1[4],'annotation':newFile1[5]} file['fullpath'] = os.path.join(self.projectDirectory,'CCP4_JOBS', 'job_'+str(file['jobnumber']),file['filename']) textToUse = 'Default label' try: textToUse = file['jobnumber'] except: pass try: textToUse += file['annotation'] except: pass menuItem = gtk.MenuItem(textToUse) menuItem.connect('activate',self.loadFileClicked, file['fileid'], fileTypeAndSubType) menuItem.show() menu.append(menuItem) newFiles.append(file) self.files += newFiles def loadFileClicked(self, menuitem, fileId, type): self.retrieveAndLoadFileByID(fileId=fileId, type=type) def populateSubmenus(self, menuitem, projectInfo): import gtk sys.stdout.flush() for child in menuitem.get_submenu().get_children(): for fileType, subType, menuText in self.FileTypes: if child.get_label().__str__() == menuText: subMenu = gtk.Menu() subMenu.show() self.addFilesOfProject_ofType_subType_toMenu(projectInfo[0], fileType, subType, subMenu) child.set_submenu(subMenu) continue sys.stdout.flush() def retrieveAndLoadFileByID(self, fileId=None, type='PDB'): if fileId is None: return outputFilename = 'ProjectFile_'+fileId if type == 'chemical/x-pdb': outputFilename += '.pdb' elif type == 'application/CCP4-mtz-map_1': outputFilename += '_2FoFc.mtz' elif type == 'application/CCP4-mtz-map_2': outputFilename += '_FoFc.mtz' destination = os.path.normpath(os.path.join(self.dropDir, outputFilename)) downloadedFilePath = self.retrieveFileByID(fileId=fileId, destination=outputFilename) if downloadedFilePath is not None: fileInfo = self.getFileInfo(fileId=fileId,mode='all') annotation = fileInfo['annotation'].replace('/','_') jobnumber = self.getFileInfo(fileId=fileId,mode='jobnumber')['jobnumber'] projectname = self.getFileInfo(fileId=fileId,mode='projectname')['projectname'] annotationRoot = "" if projectname != self.ccp4i2ProjectName: annotationRoot = projectname+":" if type == 'chemical/x-pdb': newMol = read_pdb(downloadedFilePath) set_molecule_name(newMol,annotationRoot + 'Job '+str(jobnumber)+': '+annotation) elif type == 'application/CCP4-mtz-map_1': newMap=make_and_draw_map(downloadedFilePath, 'F', 'PHI', 'PHI', 0, 0) set_molecule_name(newMap,annotationRoot + 'Job '+str(jobnumber)+': '+annotation) elif type == 'application/CCP4-mtz-map_2': newMap=make_and_draw_map(downloadedFilePath, 'F', 'PHI', 'PHI', 0, 1) set_molecule_name(newMap,annotationRoot + 'Job '+str(jobnumber)+': '+annotation) elif type == 'application/refmac-dictionary': read_cif_dictionary(downloadedFilePath) def retrieveFileByID(self, fileId=None, destination=None): if fileId is None: return if destination is None: return url = self.serverRoot + "?File?fileId="+fileId try: with open(destination,"w") as f: #proxy = urllib2.ProxyHandler({}) #opener = urllib2.build_opener(proxy) #urllib2.install_opener(opener) f.write(urllib.urlopen(url,proxies={}).read()) except IOError: print 'Unable to retrieve '+url return None print 'Ostensibly recovered url '+url+' to '+destination if os.path.isfile(destination): return destination else: print 'But not found it at '+destination+':-(' return None def getJobsWithOutputFiles(self, **kwargs): #Premissible arguments: projectId=None, fileTypeId=None,projectName=None,fileType=None,fileTypeClass=None, #subType=None,contentFlag=None,topLevelOnly=True,importFiles=False): return self.performDatabaseLookup("getJobsWithOutputFiles",**kwargs) def getProjectFiles(self, **kwargs): #Premissible arguments: projectId=None, fileTypeId=None,projectName=None,fileType=None,fileTypeClass=None, #subType=None,contentFlag=None,topLevelOnly=True,importFiles=False): return self.performDatabaseLookup("getProjectFiles",**kwargs) def getFullPath(self, **kwargs): return self.performDatabaseLookup("getFullPath",**kwargs) def getFileInfo(self, **kwargs): print type(kwargs) return self.performDatabaseLookup("getFileInfo",**kwargs) def performDatabaseLookup(self, command, **kwargs): url = self.serverRoot + "?" + command for key in kwargs: url+="?"+str(key)+"="+str(kwargs[key]) # fetch the url json = urllib.urlopen(url,proxies={}).read() # convert to a native python object (true,false,null) = (True,False,None) fileInfo = eval(json) return fileInfo def saveToDatabase(self, molNo): import os,glob outList = glob.glob(os.path.normpath(os.path.join(self.dropDir,'output*.pdb'))) #print 'saveToDatabase outList:' maxIndx = 0 for f in outList: fpath,fname = os.path.split(f) maxIndx = max(maxIndx,int(fname[6:-4])) #print 'saveToDatabase',dropDir,maxIndx save_coordinates(molNo,os.path.normpath(os.path.join (self.dropDir,'output'+str(maxIndx+1)+'.pdb') )) save_state_file(os.path.normpath(os.path.join (self.dropDir,'state'+str(maxIndx+1)+'.py') ) ) return def selectAndSave(self): molecule_chooser_gui ("Molecule to capture: ", lambda imol : self.saveToDatabase(imol)) return def addInterestingBitsMenu(self, title='Interesting bits', interestingBits = []): import gtk menu = coot_menubar_menu("CCP4i2 extensions") self.addSeparator(menu) import gtk #Create submenu for the "interesting bts" menuitem = gtk.MenuItem(title) menu.append(menuitem) submenu = gtk.Menu() menuitem.set_submenu(submenu) menuitem.show() for interestingBit in interestingBits: textToUse = 'Chain %s %s-%s'%( interestingBit['chain'], interestingBit['firstResidue'], interestingBit['lastResidue'] ) menuItem = gtk.MenuItem ( textToUse ) submenu.append ( menuItem ) menuItem.connect ( 'activate', self.interestingBitItemClicked, interestingBit['chain'], interestingBit['firstResidue'] ) menuItem.show ( ) def interestingBitItemClicked(self, menuitem, chain, residue): self.centreOn(chain=chain, residue=residue, iMol = 0) def centreOn(self, chain='A', residue='1', iMol=0): import re literals = re.findall ( '\D' , str(residue) ) number = int ( re.findall ( '\d+', str(residue) )[0] ) if len ( literals ) > 0 : literal = literals[0] else : literal = "" centreList = residue_centre_py(int(iMol),str(chain),int(number),str(literal)) set_rotation_centre(centreList[0],centreList[1],centreList[2]) def patchMoleculeName(self, molNo, fileName): if not hasattr(self,'files'): self.populateMenus(self.ccp4i2ExtensionsMenuItem) label = 'Molecule '+str(molNo) for file in self.files: if 'fullpath' in file and file['fullpath'] == fileName: label = 'Job '+str(file['jobnumber'])+': '+file['annotation'].replace('/','_') set_molecule_name(molNo, label)