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)
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']]