def createDefaultRequest(sample_id):
"""
Doesn't really create a request, just returns a dictionary
with the default parameters that can be passed to addRequesttoSample().
But note that these then get overwritten anyway, and I no longer expose them in screen params dialog
"""
sample = db_lib.getSampleByID(sample_id)
try:
propNum = sample["proposalID"]
except KeyError:
propNum = 999999
if (propNum == None):
propNum = 999999
if (propNum != getProposalID()):
setProposalID(propNum)
screenPhist = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_phist"))
screenPhiend = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_phi_end"))
screenWidth = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_width"))
screenDist = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_dist"))
screenExptime = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_time"))
screenReso = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_reso"))
screenWave = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_wave"))
screenEnergy = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_energy"))
screenbeamWidth = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_beamWidth"))
screenbeamHeight = float(db_lib.getBeamlineConfigParam(beamline,"screen_default_beamHeight"))
screenTransmissionPercent = float(db_lib.getBeamlineConfigParam(beamline,"screen_transmission_percent"))
sampleName = str(db_lib.getSampleNamebyID(sample_id))
basePath = os.getcwd()
runNum = db_lib.getSampleRequestCount(sample_id)
(puckPosition,samplePositionInContainer,containerID) = db_lib.getCoordsfromSampleID(beamline,sample_id)
request = {"sample": sample_id}
request["beamline"] = beamline
requestObj = {
"sample": sample_id,
"sweep_start": screenPhist, "sweep_end": screenPhiend,
"img_width": screenWidth,
"exposure_time": screenExptime,
"protocol": "standard",
"detDist": screenDist,
"parentReqID": -1,
"basePath": basePath,
"file_prefix": sampleName,
"directory": basePath+"/" + str(getVisitName()) + "/"+sampleName+"/" + str(runNum) + "/" +db_lib.getContainerNameByID(containerID)+"_"+str(samplePositionInContainer+1)+"/",
# "directory": basePath+"/" + str(getProposalID()) + "/"+sampleName+"/" + str(runNum) + "/" +db_lib.getContainerNameByID(containerID)+"_"+str(samplePositionInContainer+1)+"/",
"file_number_start": 1,
"energy":screenEnergy,
"wavelength": energy2wave(screenEnergy),
"resolution": screenReso,
"slit_height": screenbeamHeight, "slit_width": screenbeamWidth,
"attenuation": screenTransmissionPercent,
"pos_x": -999, "pos_y": 0, "pos_z": 0, "pos_type": 'A', "gridStep": 30}
request["request_obj"] = requestObj
return request
def mountRobotSample(puckPos, pinPos, sampID, init=0, warmup=0):
global retryMountCount
global sampXadjust, sampYadjust, sampZadjust
absPos = (pinsPerPuck * (puckPos % 3)) + pinPos + 1
logger.info(f'init: {init} warmup: {warmup}')
if (getBlConfig('robot_online')):
if (not daq_lib.waitGovRobotSE()):
daq_lib.setGovRobot('SE')
if (getBlConfig(TOP_VIEW_CHECK) == 1):
try:
sample = db_lib.getSampleByID(sampID)
sampName = sample['name']
reqCount = sample['request_count']
prefix1 = sampName + "_" + str(puckPos) + "_" + str(
pinPos) + "_" + str(reqCount) + "_PA_0"
prefix90 = sampName + "_" + str(puckPos) + "_" + str(
pinPos) + "_" + str(reqCount) + "_PA_90"
daq_macros.topViewSnap(prefix1,
os.getcwd() + "/pinAlign",
1,
acquire=0)
except Exception as e:
e_s = str(e)
message = "TopView check ERROR, will continue: " + e_s
daq_lib.gui_message(message)
logger.error(message)
logger.info("mounting " + str(puckPos) + " " + str(pinPos) + " " +
str(sampID))
logger.info("absPos = " + str(absPos))
platePos = int(puckPos / 3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
logger.info("dewar target,CP")
logger.info("%s %s" % (rotMotTarget, rotCP))
if (abs(rotMotTarget - rotCP) > 1):
logger.info("rot dewar")
try:
if (init == 0):
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
message = "ROBOT Park ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
beamline_lib.mvaDescriptor("dewarRot", rotMotTarget)
try:
if (init):
logger.debug('main loading part')
setPvDesc("boostSelect", 0)
if (getPvDesc("sampleDetected") == 0
): #reverse logic, 0 = true
setPvDesc("boostSelect", 1)
else:
robotStatus = beamline_support.get_any_epics_pv(
"SW:RobotState", "VAL")
if (robotStatus != "Ready"):
if (daq_utils.beamline == "fmx"):
daq_macros.homePins()
time.sleep(3.0)
if (not daq_lib.setGovRobot('SE')):
return
if (getBlConfig(TOP_VIEW_CHECK) == 1):
omegaCP = beamline_lib.motorPosFromDescriptor("omega")
if (omegaCP > 89.5 and omegaCP < 90.5):
beamline_lib.mvrDescriptor("omega", 85.0)
logger.info("calling thread")
_thread.start_new_thread(wait90TopviewThread,
(prefix1, prefix90))
logger.info("called thread")
setPvDesc("boostSelect", 0)
if (getPvDesc("gripTemp") > -170):
try:
logger.debug('mounting')
RobotControlLib.mount(absPos)
except Exception as e:
e_s = str(e)
message = "ROBOT mount ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
else:
time.sleep(0.5)
if (getPvDesc("sampleDetected") == 0):
logger.info("full mount")
RobotControlLib.mount(absPos)
else:
logger.debug('quick mount')
RobotControlLib.initialize()
RobotControlLib._mount(absPos)
setPvDesc("boostSelect", 1)
else:
if (getBlConfig(TOP_VIEW_CHECK) == 1):
omegaCP = beamline_lib.motorPosFromDescriptor("omega")
if (omegaCP > 89.5 and omegaCP < 90.5):
beamline_lib.mvrDescriptor("omega", 85.0)
logger.info("calling thread")
_thread.start_new_thread(wait90TopviewThread,
(prefix1, prefix90))
logger.info("called thread")
if (warmup):
RobotControlLib._mount(absPos, warmup=True)
else:
RobotControlLib._mount(absPos)
logger.info(f'{getBlConfig(TOP_VIEW_CHECK)} {daq_utils.beamline}')
if (getBlConfig(TOP_VIEW_CHECK) == 1):
if (sampYadjust == 0):
logger.info("Cannot align pin - Mount next sample.")
daq_lib.setGovRobot('SA')
return 1
except Exception as e:
logger.error(e)
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(
e_s +
". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
if (e_s.find("tilted") != -1
or e_s.find("Load Sample Failed") != -1):
if (getBlConfig("queueCollect") == 0):
daq_lib.gui_message(e_s + ". Try mounting again")
return 0
else:
if (retryMountCount == 0):
retryMountCount += 1
mountStat = mountRobotSample(puckPos, pinPos, sampID,
init)
if (mountStat == 1):
retryMountCount = 0
return mountStat
else:
retryMountCount = 0
daq_lib.gui_message("ROBOT: Could not recover from " +
e_s)
return 2
daq_lib.gui_message("ROBOT mount ERROR: " + e_s)
return 0
return 1
else:
return 1
def createDefaultRequest(sample_id, createVisit=True):
"""
Doesn't really create a request, just returns a dictionary
with the default parameters that can be passed to addRequesttoSample().
But note that these then get overwritten anyway, and I no longer expose them in screen params dialog
"""
sample = db_lib.getSampleByID(sample_id)
try:
propNum = sample["proposalID"]
except KeyError:
propNum = 999999
if (propNum == None):
propNum = 999999
if (propNum != getProposalID()):
setProposalID(propNum, createVisit)
screenDist, screenEnergy, screenExptime, screenPhiend, screenPhist, screenReso, screenTransmissionPercent, screenWidth, screenbeamHeight, screenbeamWidth = getScreenDefaultParams(
)
sampleName = str(db_lib.getSampleNamebyID(sample_id))
basePath = os.getcwd()
runNum = db_lib.getSampleRequestCount(sample_id)
(puckPosition, samplePositionInContainer,
containerID) = db_lib.getCoordsfromSampleID(beamline, sample_id)
request = {"sample": sample_id}
request["beamline"] = beamline
requestObj = {
"sample":
sample_id,
"sweep_start":
screenPhist,
"sweep_end":
screenPhiend,
"img_width":
screenWidth,
"exposure_time":
screenExptime,
"protocol":
"standard",
"detDist":
screenDist,
"parentReqID":
-1,
"basePath":
basePath,
"file_prefix":
sampleName,
"directory":
basePath + "/" + str(getVisitName()) + "/" + sampleName + "/" +
str(runNum) + "/" + db_lib.getContainerNameByID(containerID) + "_" +
str(samplePositionInContainer + 1) + "/",
"file_number_start":
1,
"energy":
screenEnergy,
"wavelength":
energy2wave(screenEnergy),
"resolution":
screenReso,
"slit_height":
screenbeamHeight,
"slit_width":
screenbeamWidth,
"attenuation":
screenTransmissionPercent,
"pos_x":
-999,
"pos_y":
0,
"pos_z":
0,
"pos_type":
'A',
"gridStep":
20
}
request["request_obj"] = requestObj
return request
owner,
resultObj,
beamline=os.environ["BEAMLINE_ID"])
newResult = db_lib.getResult(resultID)
visitName = getBlConfig("visitName")
try:
ispybLib.insertResult(newResult, "fastDP", request, visitName, ispybDCID,
fastDPResultFile)
except Exception as e:
logger.error("runfastdph5 insert result ispyb error: %s" % e)
if (runFastEP):
os.system("fast_ep") #looks very bad! running on ca1!
if (runDimple):
logger.info('run dimple selected')
sampleID = request["sample"]
sample = db_lib.getSampleByID(sampleID)
try:
modelFilename = sample["model"]
if (modelFilename == 'nan'):
modelPDBname = "model.pdb"
else:
modelPDBname = modelFilename + ".pdb"
except KeyError:
modelPDBname = "model.pdb"
dimpleRunningDir = directory + "/dimpleOutput"
comm_s = "mkdir -p " + dimpleRunningDir
os.system(comm_s)
os.chdir(dimpleRunningDir)
comm_s = "ssh -q " + dimpleNode + " \"cd " + dimpleRunningDir + ";" + dimpleComm + " " + runningDir + "/fast_dp.mtz " + baseDirectory + "/" + modelPDBname + " " + dimpleRunningDir + "\""
logger.info(comm_s)
logger.info("running dimple")
fd = open(fastDPResultFile)
resultObj = xmltodict.parse(fd.read())
print("finished fast_dp")
print(resultObj)
resultID = db_lib.addResultforRequest("fastDP",request_id,owner,resultObj,beamline=os.environ["BEAMLINE_ID"])
newResult = db_lib.getResult(resultID)
visitName = db_lib.getBeamlineConfigParam(os.environ["BEAMLINE_ID"],"visitName")
try:
ispybLib.insertResult(newResult,"fastDP",request,visitName,ispybDCID,fastDPResultFile)
except:
print("ispyb error")
if (runFastEP):
os.system("fast_ep") #looks very bad! running on ca1!
if (runDimple):
sampleID = request["sample"]
sample = db_lib.getSampleByID(sampleID)
try:
modelFilename = sample["model"]
if (modelFilename == 'nan'):
modelPDBname = "model.pdb"
else:
modelPDBname = modelFilename + ".pdb"
except KeyError:
modelPDBname = "model.pdb"
dimpleRunningDir = directory+"/dimpleOutput"
comm_s = "mkdir -p " + dimpleRunningDir
os.system(comm_s)
os.chdir(dimpleRunningDir)
# comm_s = "ssh -q " + node + " \"cd " + runningDir +";source /nfs/skinner/wrappers/fastDPWrap;fast_ep"
# comm_s = "ssh -q " + dimpleNode + " \"cd " + dimpleRunningDir +";dimple " + runningDir + "/fast_dp.mtz /GPFS/CENTRAL/xf17id2/jjakoncic/model.pdb " + dimpleRunningDir + "\""
comm_s = "ssh -q " + dimpleNode + " \"cd " + dimpleRunningDir +";" + dimpleComm + " " + runningDir + "/fast_dp.mtz " + baseDirectory + "/" + modelPDBname + " " + dimpleRunningDir + "\""
