def logMxRequestParams(currentRequest):
global currentIspybDCID
reqObj = currentRequest["request_obj"]
transmissionReadback = beamline_support.getPvValFromDescriptor("transmissionRBV")
flux = beamline_support.getPvValFromDescriptor("flux")
resultObj = {"requestObj":reqObj,"transmissionReadback":transmissionReadback,"flux":flux}
resultID = db_lib.addResultforRequest("mxExpParams",currentRequest["uid"],owner=daq_utils.owner,result_obj=resultObj,proposalID=daq_utils.getProposalID(),beamline=daq_utils.beamline)
newResult = db_lib.getResult(resultID)
db_lib.beamlineInfo(daq_utils.beamline, 'currentSampleID', info_dict={'sampleID':currentRequest["sample"]})
db_lib.beamlineInfo(daq_utils.beamline, 'currentRequestID', info_dict={'requestID':currentRequest["uid"]})
logfile = open("dataColLog.txt","a+")
try:
logfile.write("\n\ntimestamp: " + time.ctime(currentRequest["time"])+"\n")
except KeyError:
print("caught key error in logging")
print(currentRequest)
logfile.write("protocol: " + reqObj["protocol"] +"\n")
logfile.write("data prefix: " + reqObj["file_prefix"] +"\n")
logfile.write("flux: " + str(flux) +"\n")
logfile.write("transimission percent: " + str(transmissionReadback) +"\n")
logfile.write("total current (BCU): " + str(beamline_support.getPvValFromDescriptor("totalCurrentBCU")) +"\n")
logfile.write("omega start: " + str(reqObj["sweep_start"]) +"\n")
logfile.write("omega end: " + str(reqObj["sweep_end"]) +"\n")
logfile.write("image width: " + str(reqObj["img_width"]) +"\n")
logfile.write("exposure time per image (s): " + str(reqObj["exposure_time"]) +"\n")
logfile.write("detector distance: " + str(reqObj["detDist"]) +"\n")
logfile.write("wavelength: " + str(reqObj["wavelength"]) +"\n")
logfile.close()
visitName = daq_utils.getVisitName()
try: #I'm worried about unforseen ispyb db errors
currentIspybDCID = ispybLib.insertResult(newResult,"mxExpParams",currentRequest,visitName)
except:
currentIspybDCID = 999999
print("ispyb error")
def logMxRequestParams(currentRequest, wait=True):
global currentIspybDCID
reqObj = currentRequest["request_obj"]
transmissionReadback = getPvDesc("transmissionRBV")
flux = getPvDesc("flux")
resultObj = {
"requestObj": reqObj,
"transmissionReadback": transmissionReadback,
"flux": flux
}
resultID = db_lib.addResultforRequest("mxExpParams",
currentRequest["uid"],
owner=daq_utils.owner,
result_obj=resultObj,
proposalID=daq_utils.getProposalID(),
beamline=daq_utils.beamline)
newResult = db_lib.getResult(resultID)
newResult['result_obj']['requestObj']['xbeam'] = reqObj['xbeam']
newResult['result_obj']['requestObj']['ybeam'] = reqObj['ybeam']
db_lib.beamlineInfo(daq_utils.beamline,
'currentSampleID',
info_dict={'sampleID': currentRequest["sample"]})
db_lib.beamlineInfo(daq_utils.beamline,
'currentRequestID',
info_dict={'requestID': currentRequest["uid"]})
logfile = open("dataColLog.txt", "a+")
try:
logfile.write("\n\ntimestamp: " + time.ctime(currentRequest["time"]) +
"\n")
except KeyError:
logger.error("caught key error in logging")
logger.error(currentRequest)
logfile.write("protocol: " + reqObj["protocol"] + "\n")
logfile.write("data prefix: " + reqObj["file_prefix"] + "\n")
logfile.write("flux: " + str(flux) + "\n")
logfile.write("transimission percent: " + str(transmissionReadback) + "\n")
logfile.write("total current (BCU): " + str(getPvDesc("totalCurrentBCU")) +
"\n")
logfile.write("omega start: " + str(reqObj["sweep_start"]) + "\n")
logfile.write("omega end: " + str(reqObj["sweep_end"]) + "\n")
logfile.write("image width: " + str(reqObj["img_width"]) + "\n")
logfile.write("exposure time per image (s): " +
str(reqObj["exposure_time"]) + "\n")
logfile.write("detector distance: " + str(reqObj["detDist"]) + "\n")
logfile.write("wavelength: " + str(reqObj["wavelength"]) + "\n")
logfile.close()
visitName = daq_utils.getVisitName()
try: #I'm worried about unforseen ispyb db errors
#rasters results are entered in ispyb by the GUI, no need to wait
if wait:
time.sleep(getBlConfig(ISPYB_RESULT_ENTRY_DELAY))
currentIspybDCID = ispybLib.insertResult(newResult, "mxExpParams",
currentRequest, visitName)
except Exception as e:
currentIspybDCID = 999999
logger.error("logMxRequestParams - ispyb error: %s" % e)
dimpleNode = sys.argv[7]
ispybDCID = int(sys.argv[8])
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}fast_dp.sh {request_id} {numstart}\""
logger.info(comm_s)
os.system(comm_s)
fastDPResultFile = runningDir + "/fast_dp.xml"
fd = open(fastDPResultFile)
resultObj = xmltodict.parse(fd.read())
logger.info("finished fast_dp")
resultID = db_lib.addResultforRequest("fastDP",
request_id,
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):
dimpleComm = getBlConfig("dimpleComm")
comm_s = f"ssh -q {dimpleNode} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}dimple.sh {request_id} {numstart}\""
logger.info(f"running dimple: {comm_s}")
os.system(comm_s)
dimpleComm = db_lib.getBeamlineConfigParam(os.environ["BEAMLINE_ID"],"dimpleComm")
comm_s = "ssh -q " + node + " \"cd " + runningDir + fastdpComm + hdfFilepattern + "\""
#comm_s = "ssh -q " + node + " \"cd " + runningDir +";source /nfs/skinner/wrappers/fastDPWrap2;fast_dp -j 12 -J 12 -k 60 " + hdfFilepattern + "\""
#comm_s = "ssh -q " + node + " \"cd " + runningDir +";source /nfs/skinner/wrappers/fastDPWrap;/usr/local/crys-local/fast_dp/bin/fast_dp -J 16 -j 16 -k 70 " + hdfFilepattern + "\""
print(comm_s)
os.system(comm_s)
fastDPResultFile = runningDir+"/fast_dp.xml"
#fastDPResultFile = "/GPFS/CENTRAL/xf17id2/skinner/ispyb/fast_dp.xml"
#fd = open("fast_dp.xml")
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: