def insertMisc(self):
print "inserting into database"
miscq = appiondata.ApMiscData()
if self.params['reconid'] is not None:
miscq['refineRun'] = self.recondata
sessiondata = apRecon.getSessionDataFromReconId(self.params['reconid'])
miscq['session'] = sessiondata
projectid = apProject.getProjectIdFromSessionName(sessiondata['name'])
miscq['REF|projectdata|projects|project'] = projectid
elif self.params['fulltomoid'] is not None:
miscq['fulltomogram'] = self.tomodata
sessiondata = self.tomodata['session']
miscq['session'] = sessiondata
projectid = apProject.getProjectIdFromSessionName(sessiondata['name'])
miscq['REF|projectdata|projects|project'] = projectid
elif self.params['sessionname'] is not None:
miscq['session'] = self.sessiondata
projectid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
miscq['REF|projectdata|projects|project'] = projectid
miscq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
miscq['name'] = self.filename
miscq['description'] = self.params['description']
miscq['md5sum'] = apFile.md5sumfile(self.newfile)
miscq['hidden'] = False
if self.params['commit'] is True:
miscq.insert()
else:
apDisplay.printWarning("not committing to DB")
def checkGlobalConflicts(self):
"""
put in any conflicting parameters
"""
appionScript.AppionScript.checkGlobalConflicts(self)
if self.params['runname'] is None:
apDisplay.printError("please enter a runname, example: 'runname=run1'")
if self.params['runname'] == 'templates':
apDisplay.printError("templates is a reserved runname, please use another runname")
if self.params['runname'] == 'models':
apDisplay.printError("models is a reserved runname, please use another runname")
if self.params['rundir']is not None and self.params['runname'] != os.path.basename(self.params['rundir']):
apDisplay.printError("runname and rundir basename are different: "
+self.params['runname']+" vs. "+os.path.basename(self.params['rundir']))
if self.params['mrcnames'] and self.params['preset']:
apDisplay.printError("preset can not be specified if particular images have been specified")
if (self.params['sessionname'] is None and self.params['expid'] is None) and self.params['mrcnames'] is None:
apDisplay.printError("please specify an mrc name or session")
if self.params['sessionname'] is None and self.params['expid'] is not None:
self.params['sessionname'] = apDatabase.getSessionDataFromSessionId(self.params['expid'])['name']
if self.params['sessionname'] is not None and self.params['projectid'] is not None:
### Check that project and images are in sync
imgproject = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if imgproject and imgproject != self.params['projectid']:
apDisplay.printError("project id and session do not correlate")
def start(self):
if self.params['stackid'] is not None:
self.useStackForTemplate()
elif self.params['alignid'] is not None:
self.useAlignForTemplate()
elif self.params['clusterid'] is not None:
self.useClusterForTemplate()
else:
apDisplay.printMsg("Using local file: '"+str(self.params['template'])+"' to upload template")
#find the number of template files
apTemplate.findTemplates(self.params)
### check for templates
apDisplay.printColor("Template List:","green")
pprint.pprint(self.params['templatelist'])
if not self.params['templatelist']:
apDisplay.printError("Could not find templates")
time.sleep(2)
# copy templates to final location
apTemplate.copyTemplatesToOutdir(self.params, self.timestamp)
self.params['projectId'] = apProject.getProjectIdFromSessionName(self.params['sessionname'])
# insert templates to database
apTemplate.insertTemplateImage(self.params)
def start(self):
if self.params['stackid'] is not None:
self.useStackForTemplate()
elif self.params['alignid'] is not None:
self.useAlignForTemplate()
elif self.params['clusterid'] is not None:
self.useClusterForTemplate()
else:
apDisplay.printMsg("Using local file: '" +
str(self.params['template']) +
"' to upload template")
#find the number of template files
apTemplate.findTemplates(self.params)
### check for templates
apDisplay.printColor("Template List:", "green")
pprint.pprint(self.params['templatelist'])
if not self.params['templatelist']:
apDisplay.printError("Could not find templates")
time.sleep(2)
# copy templates to final location
apTemplate.copyTemplatesToOutdir(self.params, self.timestamp)
self.params['projectId'] = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
# insert templates to database
apTemplate.insertTemplateImage(self.params)
def onInit(self):
"""
standard appionScript
"""
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
if sessiondata:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError("You cannot assign an existing session (PID %d) to a different project (PID %d)"%
(oldprojectid, self.params['projectid']))
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
### die for now
apDisplay.printError("Uploading stack to a new session not allowed")
try:
directory = leginon.leginonconfig.mapPath(leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
userdata = None
sessiondata = self.createSession(userdata, self.params['sessionname'], self.params['description'], directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.sessiondata = sessiondata
return
def start(self):
if self.params['reconid'] is not None:
self.recondata = apRecon.getRefineRunDataFromID(
self.params['reconid'])
print "Associated with", self.recondata[
'name'], ":", self.recondata['path']
if self.params['fulltomoid'] is not None:
self.tomodata = apTomo.getFullTomoData(self.params['fulltomoid'])
print "Associated with", self.tomodata['name'], ":", self.tomodata[
'path']['path']
if self.params['sessionname'] is not None:
self.sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.params['projectId'] = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
self.filename = os.path.basename(self.params['file'])
self.newfile = os.path.join(self.params['rundir'], self.filename)
if os.path.isfile(self.newfile):
apDisplay.printError("File " + self.filename +
" already exists in dir " +
self.params['rundir'])
shutil.copy(self.oldfile, self.newfile)
# insert the info
self.insertMisc()
def checkGlobalConflicts(self):
"""
put in any conflicting parameters
"""
appionScript.AppionScript.checkGlobalConflicts(self)
if self.params['runname'] is None:
apDisplay.printError(
"please enter a runname, example: 'runname=run1'")
if self.params['runname'] == 'templates':
apDisplay.printError(
"templates is a reserved runname, please use another runname")
if self.params['runname'] == 'models':
apDisplay.printError(
"models is a reserved runname, please use another runname")
if self.params['rundir'] is not None and self.params[
'runname'] != os.path.basename(self.params['rundir']):
apDisplay.printError(
"runname and rundir basename are different: " +
self.params['runname'] + " vs. " +
os.path.basename(self.params['rundir']))
if self.params['mrcnames'] and self.params['preset']:
apDisplay.printError(
"preset can not be specified if particular images have been specified"
)
if self.params['sessionname'] is None and self.params[
'mrcnames'] is None:
apDisplay.printError("please specify an mrc name or session")
if self.params['sessionname'] is not None and self.params[
'projectid'] is not None:
### Check that project and tilt series are in sync
seriesproject = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
if seriesproject and seriesproject != self.params['projectid']:
apDisplay.printError("project id and session do not correlate")
def checkConflicts(self):
if self.params['sessionname'] is None:
apDisplay.printError("Enter a session name (e.g. --session=06jul12a)")
if self.params['projectid'] is not None:
projid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if projid != self.params['projectid']:
apDisplay.printError("Project ID and Session name do not match")
if self.params['description'] is None:
apDisplay.printError("Enter a description of the initial model")
if self.params['chimeraonly'] is True:
self.params['commit'] = False
if self.params['newbox'] is not None and self.params['newbox'] % 8 != 0:
apDisplay.printWarning("Box size is not a multiple of 8")
### program requires either a model id or density id or filename
checkvalue = int(self.params['file'] is not None)
checkvalue += int(self.params['oldmodelid'] is not None)
checkvalue += int(self.params['densityid'] is not None)
if checkvalue != 1:
apDisplay.printError("Either provide a modelid or densityid or file, but not more than one of them")
elif self.params['oldmodelid'] is not None and self.params['newbox'] is None:
apDisplay.printError("Please specify either a new boxsize or scale for your model")
elif self.params['densityid'] is not None:
self.getDensityParams()
elif self.params['oldmodelid'] is not None:
self.getModelParams()
elif self.params['file'] is not None:
if not os.path.isfile(self.params['file']):
apDisplay.printError("could not find file: "+self.params['file'])
if self.params['file'][-4:] != ".mrc":
apDisplay.printError("uploadModel.py only supports MRC files")
self.params['file'] = os.path.abspath(self.params['file'])
else:
apDisplay.printError("Please provide either a --modelid=112 or --file=initmodel.mrc")
### required only if now model id is provided
if self.params['newapix'] is None:
apDisplay.printError("Enter the pixel size of the model")
if self.params['symmetry'] is None:
apSymmetry.printSymmetries()
apDisplay.printError("Enter a symmetry ID, e.g. --symm=19")
self.params['symdata'] = apSymmetry.findSymmetry(self.params['symmetry'])
if self.params['res'] is None:
apDisplay.printError("Enter the resolution of the initial model")
self.params['oldbox'] = apVolume.getModelDimensions(self.params['file'])
if self.params['newbox'] is None:
self.params['newbox'] = self.params['oldbox']
if self.params['oldapix'] is None:
self.params['oldapix'] = self.params['newapix']
def start(self):
if self.params['reconid'] is not None:
self.recondata = apRecon.getRefineRunDataFromID(self.params['reconid'])
print "Associated with",self.recondata['name'],":",self.recondata['path']
if self.params['fulltomoid'] is not None:
self.tomodata = apTomo.getFullTomoData(self.params['fulltomoid'])
print "Associated with",self.tomodata['name'],":",self.tomodata['path']['path']
if self.params['sessionname'] is not None:
self.sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.params['projectId'] = apProject.getProjectIdFromSessionName(self.params['sessionname'])
self.filename = os.path.basename(self.params['file'])
self.newfile = os.path.join(self.params['rundir'], self.filename)
if os.path.isfile(self.newfile):
apDisplay.printError("File "+self.filename+" already exists in dir "+self.params['rundir'])
shutil.copy(self.oldfile, self.newfile)
# insert the info
self.insertMisc()
def onInit(self):
"""
standard appionScript
"""
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
if sessiondata:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError(
"You cannot assign an existing session (PID %d) to a different project (PID %d)"
% (oldprojectid, self.params['projectid']))
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
### die for now
apDisplay.printError(
"Uploading stack to a new session not allowed")
try:
directory = leginon.leginonconfig.mapPath(
leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
userdata = None
sessiondata = self.createSession(userdata,
self.params['sessionname'],
self.params['description'],
directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.sessiondata = sessiondata
return
def setAppiondb(sessionname):
projectid = apProject.getProjectIdFromSessionName(sessionname)
apProject.setDBfromProjectId(projectid, die=True)
def checkConflicts(self):
"""
standard appionScript
"""
if self.params['batchscript'] is None:
#mode 1: command line params
if self.params['apix'] is None:
apDisplay.printError(
"If not specifying a parameter file, supply apix")
if self.params['df'] is None:
apDisplay.printError(
"If not specifying a parameter file, supply defocus of the images"
)
if self.params['df'] > 0:
apDisplay.printWarning("defocus is being switched to negative")
self.params['df'] *= -1
if self.params['df'] > -0.1:
apDisplay.printError("defocus must be in microns")
if self.params['mag'] is None:
apDisplay.printError(
"If not specifying a parameter file, supply magnification")
if self.params['kv'] is None:
apDisplay.printError(
"If not specifying a parameter file, supply a high tension"
)
if self.params['kv'] > 1000:
apDisplay.printError(
"High tension must be in kilovolts (e.g., 120)")
if self.params['cs'] < 0.0:
apDisplay.printError("Cs value must be in mm (e.g., 2.0)")
if self.params['imgdir'] is None:
apDisplay.printError(
"If not specifying a parameter file, specify directory containing images"
)
if not os.path.exists(self.params['imgdir']):
apDisplay.printError("specified path '%s' does not exist\n" %
self.params['imgdir'])
elif not os.path.isfile(self.params["batchscript"]):
#mode 2: batch script
apDisplay.printError("Could not find Batch parameter file: %s" %
(self.params["batchscript"]))
if self.params['sessionname'] is None:
apDisplay.printError(
"Please provide a Session name, e.g., --session=09feb12b")
if self.params['projectid'] is None:
apDisplay.printError(
"Please provide a Project database ID, e.g., --projectid=42")
if self.params['description'] is None:
apDisplay.printError(
"Please provide a Description, e.g., --description='awesome data'"
)
if self.params['userid'] is None:
self.params['userid'] = self.getLeginonUserId()
#This really is not conflict checking but to set up new session.
#There is no place in Appion script for this special case
sessionq = leginon.leginondata.SessionData(
name=self.params['sessionname'])
sessiondatas = sessionq.query()
if len(sessiondatas) > 0:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
sessiondata = sessiondatas[0]
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError(
"You cannot assign an existing session (PID %d) to a different project (PID %d)"
% (oldprojectid, self.params['projectid']))
if self.params['rundir'] is not None and self.params[
'rundir'] != sessiondata['image path']:
apDisplay.printError(
"Specified Rundir is different from current session path\n%s\n%s"
% (self.params['rundir'], sessiondata['image path']))
### only allows uploading more images if all images are uploaded through appion host.
instrumentq = leginon.leginondata.InstrumentData(hostname='appion',
name='AppionTEM')
appiontems = instrumentq.query()
allappionscopeems = []
for appiontem in appiontems:
scopeemq = leginon.leginondata.ScopeEMData(
session=sessiondatas[0], tem=appiontem)
appionscopeems = scopeemq.query()
if appionscopeems:
allappionscopeems.extend(appionscopeems)
scopeemq = leginon.leginondata.ScopeEMData(session=sessiondatas[0])
allscopeems = scopeemq.query()
if len(allscopeems) > len(allappionscopeems):
apDisplay.printError(
"You can only add more images to an existing session that contains only appion uploads"
)
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
try:
directory = leginon.leginonconfig.mapPath(
leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
if self.params['userid'] is not None:
userdata = leginon.leginondata.UserData.direct_query(
self.params['userid'])
else:
userdata = None
sessiondata = self.createSession(userdata,
self.params['sessionname'],
self.params['description'],
directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.session = sessiondata
return
def checkConflicts(self):
"""
standard appionScript
"""
if self.params['batchscript'] is None:
#mode 1: command line params
if self.params['apix'] is None:
apDisplay.printError("If not specifying a parameter file, supply apix")
if self.params['df'] is None:
apDisplay.printError("If not specifying a parameter file, supply defocus of the images")
if self.params['df'] > 0:
apDisplay.printWarning("defocus is being switched to negative")
self.params['df']*=-1
if self.params['df'] > -0.1:
apDisplay.printError("defocus must be in microns")
if self.params['mag'] is None:
apDisplay.printError("If not specifying a parameter file, supply magnification")
if self.params['kv'] is None:
apDisplay.printError("If not specifying a parameter file, supply a high tension")
if self.params['kv'] > 1000:
apDisplay.printError("High tension must be in kilovolts (e.g., 120)")
if self.params['cs'] < 0.0:
apDisplay.printError("Cs value must be in mm (e.g., 2.0)")
if self.params['imgdir'] is None:
apDisplay.printError("If not specifying a parameter file, specify directory containing images")
if not os.path.exists(self.params['imgdir']):
apDisplay.printError("specified path '%s' does not exist\n"%self.params['imgdir'])
elif not os.path.isfile(self.params["batchscript"]):
#mode 2: batch script
apDisplay.printError("Could not find Batch parameter file: %s"%(self.params["batchscript"]))
if self.params['sessionname'] is None:
apDisplay.printError("Please provide a Session name, e.g., --session=09feb12b")
if self.params['projectid'] is None:
apDisplay.printError("Please provide a Project database ID, e.g., --projectid=42")
if self.params['description'] is None:
apDisplay.printError("Please provide a Description, e.g., --description='awesome data'")
if self.params['userid'] is None:
self.params['userid'] = self.getLeginonUserId()
#This really is not conflict checking but to set up new session.
#There is no place in Appion script for this special case
sessionq = leginon.leginondata.SessionData(name=self.params['sessionname'])
sessiondatas = sessionq.query()
if len(sessiondatas) > 0:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
sessiondata = sessiondatas[0]
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError("You cannot assign an existing session (PID %d) to a different project (PID %d)"%
(oldprojectid, self.params['projectid']))
if self.params['rundir'] is not None and self.params['rundir'] != sessiondata['image path']:
apDisplay.printError("Specified Rundir is different from current session path\n%s\n%s"
%( self.params['rundir'], sessiondata['image path']))
### only allows uploading more images if all images are uploaded through appion host.
instrumentq = leginon.leginondata.InstrumentData(hostname='appion',name='AppionTEM')
appiontems = instrumentq.query()
allappionscopeems = []
for appiontem in appiontems:
scopeemq = leginon.leginondata.ScopeEMData(session=sessiondatas[0],tem=appiontem)
appionscopeems = scopeemq.query()
if appionscopeems:
allappionscopeems.extend(appionscopeems)
scopeemq = leginon.leginondata.ScopeEMData(session=sessiondatas[0])
allscopeems = scopeemq.query()
if len(allscopeems) > len(allappionscopeems):
apDisplay.printError("You can only add more images to an existing session that contains only appion uploads")
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
try:
directory = leginon.leginonconfig.mapPath(leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
if self.params['userid'] is not None:
userdata = leginon.leginondata.UserData.direct_query(self.params['userid'])
else:
userdata = None
sessiondata = self.createSession(userdata, self.params['sessionname'], self.params['description'], directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.session = sessiondata
return
def setAppiondb(sessionname):
projectid = apProject.getProjectIdFromSessionName(sessionname)
apProject.setDBfromProjectId(projectid, die=True)
