options, args = parser.parse_args() if len(args) > 0: parser.error("Unknown commandline options: " + str(args)) if len(sys.argv) < 2: parser.print_help() parser.error("no options defined") params = {} for i in parser.option_list: if isinstance(i.dest, str): params[i.dest] = getattr(options, i.dest) return params if __name__ == "__main__": params = parseOptions() apProject.setDBfromProjectId(params["projectid"]) stackdata = apStack.getOnlyStackData(params["stackid"]) stackpath = stackdata["path"]["path"] # generate stack if it doesn't exist. if not os.path.isdir(stackpath): os.makedirs(stackpath) fname = os.path.join(stackpath, stackdata["name"]) # check if stack file already exists if os.path.isfile(fname): apDisplay.printError("file: '%s' already exists" % fname) vstackdata = apStack.getVirtualStackParticlesFromId(params["stackid"]) plist = [int(p["particleNumber"]) - 1 for p in vstackdata["particles"]]
def setAppiondb(sessionname): projectid = apProject.getProjectIdFromSessionName(sessionname) apProject.setDBfromProjectId(projectid, die=True)
selectq = " SELECT * FROM `install` WHERE `key`='version'" values = projectdb.returnCustomSQL(selectq) if values: projectdb.updateColumn("install", "value", "'2.0'", "install.key = 'version'",timestamp=False) else: insertq = "INSERT INTO `install` (`key`, `value`) VALUES ('version', '2.0')" projectdb.executeCustomSQL(insertq) if __name__ == "__main__": projectids = getProjectIds() projectdb = dbupgrade.DBUpgradeTools('projectdata', drop=True) for projectid in projectids: appiondbname = apProject.getAppionDBFromProjectId(projectid, die=False) if appiondbname is None: continue elif not projectdb.databaseExists(appiondbname): print "\033[31merror database %s does not exist\033[0m"%(appiondbname) time.sleep(1) continue if apProject.setDBfromProjectId(projectid, die=False): reconrunids = getReconRunsIds() for reconrunid in reconrunids: apRecon.setGoodBadParticlesFromReconId(reconrunid) # Tomography upgrades createExcludedColumnByFakeInsert() allalignrundata = getTomoAlignmentRuns() for alignrun in allalignrundata: insertTiltsInAlign(alignrun) upgradeProjectDB(projectdb,backup=False)
options, args = parser.parse_args() if len(args) > 0: parser.error("Unknown commandline options: " + str(args)) if len(sys.argv) < 2: parser.print_help() parser.error("no options defined") params = {} for i in parser.option_list: if isinstance(i.dest, str): params[i.dest] = getattr(options, i.dest) return params if __name__ == "__main__": params = parseOptions() apProject.setDBfromProjectId(params['projectid']) stackdata = apStack.getOnlyStackData(params['stackid']) stackpath = stackdata['path']['path'] # generate stack if it doesn't exist. if not os.path.isdir(stackpath): os.makedirs(stackpath) fname = os.path.join(stackpath, stackdata['name']) # check if stack file already exists if os.path.isfile(fname): apDisplay.printError("file: '%s' already exists" % fname) vstackdata = apStack.getVirtualStackParticlesFromId(params['stackid']) plist = [int(p['particleNumber']) - 1 for p in vstackdata['particles']]
"'2.0'", "install.key = 'version'", timestamp=False) else: insertq = "INSERT INTO `install` (`key`, `value`) VALUES ('version', '2.0')" projectdb.executeCustomSQL(insertq) if __name__ == "__main__": projectids = getProjectIds() projectdb = dbupgrade.DBUpgradeTools('projectdata', drop=True) for projectid in projectids: appiondbname = apProject.getAppionDBFromProjectId(projectid, die=False) if appiondbname is None: continue elif not projectdb.databaseExists(appiondbname): print "\033[31merror database %s does not exist\033[0m" % ( appiondbname) time.sleep(1) continue if apProject.setDBfromProjectId(projectid, die=False): reconrunids = getReconRunsIds() for reconrunid in reconrunids: apRecon.setGoodBadParticlesFromReconId(reconrunid) # Tomography upgrades createExcludedColumnByFakeInsert() allalignrundata = getTomoAlignmentRuns() for alignrun in allalignrundata: insertTiltsInAlign(alignrun) upgradeProjectDB(projectdb, backup=False)
options,args = parser.parse_args() if len(args) > 0: parser.error("Unknown commandline options: " +str(args)) if len(sys.argv) < 2: parser.print_help() parser.error("no options defined") params = {} for i in parser.option_list: if isinstance(i.dest, str): params[i.dest] = getattr(options, i.dest) return params if __name__=="__main__": params = parseOptions() apProject.setDBfromProjectId(params['projectid']) stackdata = apStack.getOnlyStackData(params['stackid']) stackpath = stackdata['path']['path'] # generate stack if it doesn't exist. if not os.path.isdir(stackpath): os.makedirs(stackpath) fname = os.path.join(stackpath, stackdata['name']) # check if stack file already exists if os.path.isfile(fname): apDisplay.printError("file: '%s' already exists"%fname) vstackdata = apStack.getVirtualStackParticlesFromId(params['stackid']) plist = [int(p['particleNumber'])-1 for p in vstackdata['particles']]