def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("*** EDPluginExecDIMPLEPDBSETv10.postProcess")
self.programTermination()
# Create some output data
# xsDataResult = CCP4DataResultPDBSET()
# self.setDataOutput( xsDataResult )
strLog = self.readProcessLogFile()
ccp4ReturnStatus = self.getPDBSETReturnStatus(strLog)
ccp4DataResultPDBSET = CCP4DataResultPDBSET()
# Set the output PDB file
ccp4DataResultPDBSET.setXYZOUT(XSDataString(self.getDataInput().getXYZOUT().getPath().getValue()))
# Set the output log file
ccp4DataResultPDBSET.setOutputLogFile(XSDataString(self.getScriptLogFileName()))
# Set the return status
ccp4DataResultPDBSET.setReturnStatus(ccp4ReturnStatus)
# Set the data output for the job
self.setDataOutput(ccp4DataResultPDBSET)
if not os.path.isfile(self.getDataOutput().getXYZOUT().getValue()):
raise RuntimeError, "File %s does not exist" % self.getDataOutput().getXYZOUT().getValue()
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecRsync.postProcess")
# Create some output data
xsDataResult = XSDataResultRsync(log=XSDataString(""))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDataverv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultDataver()
xsDataResult.outputCurve = XSDataFile(XSDataString(self.strOutFile))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.postProcess")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
xsData.filename = XSDataFile(XSDataString(words[-1]))
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataBoolean(bool(int(words[7])))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
listXSDOut.append(xsData)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecAutoPROCv1_0.postProcess")
strWorkingDir = self.getWorkingDirectory()
# Log file
self.dataOutput.logFile = XSDataFile(XSDataString(os.path.join(strWorkingDir, self.getScriptLogFileName())))
# ISPyB XML files
ispybXML = os.path.join(strWorkingDir, "autoPROC.xml")
if os.path.exists(ispybXML):
self.dataOutput.ispybXML = XSDataFile(XSDataString(ispybXML))
ispybXML_staraniso = os.path.join(strWorkingDir, "autoPROC_staraniso.xml")
if os.path.exists(ispybXML_staraniso):
self.dataOutput.ispybXML_staraniso = XSDataFile(XSDataString(ispybXML_staraniso))
# Report PDFs
reportPdf = os.path.join(strWorkingDir, "report.pdf")
if os.path.exists(reportPdf):
self.dataOutput.reportPdf = XSDataFile(XSDataString(reportPdf))
else:
self.dataOutput.reportPdf = None
reportPdf_staraniso = os.path.join(strWorkingDir, "report_staraniso.pdf")
if os.path.exists(reportPdf_staraniso):
self.dataOutput.reportPdf_staraniso = XSDataFile(XSDataString(reportPdf_staraniso))
# Working directory
self.dataOutput.workingDirectory = XSDataFile(XSDataString(strWorkingDir))
# processDirectory
if self.dataInput.masterH5:
processDirectory = os.path.join(strWorkingDir, "HDF5_1")
if os.path.exists(processDirectory):
self.dataOutput.addProcessDirectory(XSDataFile(XSDataString(processDirectory)))
else:
for identifier in self.dataInput.identifier:
processDirectory = os.path.join(strWorkingDir, identifier.idN.value)
if os.path.exists(processDirectory):
self.dataOutput.addProcessDirectory(XSDataFile(XSDataString(processDirectory)))
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatGnomv1_0.postProcess")
# Create some output data
if not os.path.isfile(self.outFile):
self.error("EDPluginExecDatGnomv1_0 did not produce output file %s as expected !" % self.outFile)
self.setFailure()
self.dataOutput = XSDataResultDatGnom()
return
gnom = XSDataGnom(gnomFile=XSDataFile(XSDataString(self.outFile)))
logfile = os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
out = open(logfile, "r").read().split()
for key, val, typ in (("Dmax", "dmax", XSDataLength),
("Guinier", "rgGuinier", XSDataLength),
("Gnom", "rgGnom", XSDataLength),
("Total", "total", XSDataDouble)):
if key in out:
idx = out.index(key)
res = out[idx + 2]
gnom.__setattr__(val, typ(float(res)))
else:
self.error("EDPluginExecDatGnomv1_0.postProcess No key %s in file %s" % (key, logfile))
self.setFailure()
self.dataOutput = XSDataResultDatGnom(gnom=gnom)
def postProcess(self, _oedObject=None):
EDPluginExecProcessScript.postProcess(self, _oedObject)
# Fill in file paths
xsDataXDSFilePaths = XSDataXDSFilePaths()
xparmXds = os.path.join(self.getWorkingDirectory(), "XPARM.XDS")
if os.path.exists(xparmXds):
xsDataXDSFilePaths.xparmXds = XSDataFile(XSDataString(xparmXds))
xCorrectionsCbf = os.path.join(self.getWorkingDirectory(),
"X-CORRECTIONS.cbf")
if os.path.exists(xCorrectionsCbf):
xsDataXDSFilePaths.xCorrectionsCbf = XSDataFile(
XSDataString(xCorrectionsCbf))
yCorrectionsCbf = os.path.join(self.getWorkingDirectory(),
"Y-CORRECTIONS.cbf")
if os.path.exists(yCorrectionsCbf):
xsDataXDSFilePaths.yCorrectionsCbf = XSDataFile(
XSDataString(yCorrectionsCbf))
bkginitCbf = os.path.join(self.getWorkingDirectory(), "BKGINIT.cbf")
if os.path.exists(bkginitCbf):
xsDataXDSFilePaths.bkginitCbf = XSDataFile(
XSDataString(bkginitCbf))
gainCbf = os.path.join(self.getWorkingDirectory(), "GAIN.cbf")
if os.path.exists(gainCbf):
xsDataXDSFilePaths.gainCbf = XSDataFile(XSDataString(gainCbf))
blankCbf = os.path.join(self.getWorkingDirectory(), "BLANK.cbf")
if os.path.exists(blankCbf):
xsDataXDSFilePaths.blankCbf = XSDataFile(XSDataString(blankCbf))
self.dataOutput.filePaths = xsDataXDSFilePaths
def postProcess(self, _oedObject=None):
EDPluginExecProcessScript.postProcess(self, _oedObject)
# Fill in file paths
xsDataXDSFilePaths = XSDataXDSFilePaths()
xparmXds = os.path.join(self.getWorkingDirectory(), "XPARM.XDS")
if os.path.exists(xparmXds):
xsDataXDSFilePaths.xparmXds = XSDataFile(XSDataString(xparmXds))
xCorrectionsCbf = os.path.join(self.getWorkingDirectory(), "X-CORRECTIONS.cbf")
if os.path.exists(xCorrectionsCbf):
xsDataXDSFilePaths.xCorrectionsCbf = XSDataFile(XSDataString(xCorrectionsCbf))
yCorrectionsCbf = os.path.join(self.getWorkingDirectory(), "Y-CORRECTIONS.cbf")
if os.path.exists(yCorrectionsCbf):
xsDataXDSFilePaths.yCorrectionsCbf = XSDataFile(XSDataString(yCorrectionsCbf))
bkginitCbf = os.path.join(self.getWorkingDirectory(), "BKGINIT.cbf")
if os.path.exists(bkginitCbf):
xsDataXDSFilePaths.bkginitCbf = XSDataFile(XSDataString(bkginitCbf))
gainCbf = os.path.join(self.getWorkingDirectory(), "GAIN.cbf")
if os.path.exists(gainCbf):
xsDataXDSFilePaths.gainCbf = XSDataFile(XSDataString(gainCbf))
blankCbf = os.path.join(self.getWorkingDirectory(), "BLANK.cbf")
if os.path.exists(blankCbf):
xsDataXDSFilePaths.blankCbf = XSDataFile(XSDataString(blankCbf))
self.dataOutput.filePaths = xsDataXDSFilePaths
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecXDSAPPv1_0.postProcess")
# Populate the results
prefixRunNumber = EDUtilsImage.getPrefix(self.dataInput.image.path.value)
xsDataResultXDSAPP = self.parseOutputDirectory(self.getWorkingDirectory(), prefixRunNumber)
self.dataOutput = xsDataResultXDSAPP
def postProcess(self):
self.DEBUG('Pointless: postProcess')
EDPluginExecProcessScript.postProcess(self)
outputFile = self.dataInput.output_file.value
self.dataOutput = self.parsePointlessOutput(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName()))
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatopv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultDatop(
outputCurve=self.dataInput.outputCurve)
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginH5ToCBFv1_0.postProcess")
if self.dataInput.dataCollection is None:
shutil.copy(self.tmpCBFFile, self.CBFFile)
else:
# Fill in metadata
fileTmpCBF = open(self.tmpCBFFile)
tmpCBF = fileTmpCBF.read()
fileTmpCBF.close()
# Replace opening line
tmpCBF = tmpCBF.replace("CBF: VERSION 1.5, CBFlib v0.7.8 - SLS/DECTRIS PILATUS detectors",
"CBF: VERSION 1.5, CBFlib v0.7.8")
index1 = tmpCBF.find("# WARNING: FOR XDS PROCESSING ONLY.")
string2 = "# SOFTWARE VERSION: 1.1.0-RELEASE"
index2 = tmpCBF.find(string2) + len(string2)
miniCBFHeader = self.generateMiniCBFHeader(self.dataInput)
newCBF = tmpCBF[:index1] + miniCBFHeader + tmpCBF[index2:]
newCBFFile = open(self.CBFFile, "w")
newCBFFile.write(newCBF)
newCBFFile.close()
def postProcess(self, _edObject = None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDIMPLEPHASERv10.postProcess")
self.programTermination()
# Create some output data
xsDataResult = CCP4DataResultPhaser(
HKLOUT = HKL(self._hklout),
XYZOUT = XYZ(self._xyzout),
returnStatus = CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
xyzout = None
for record in self.readProcessLogFile().split('\n'):
if 'Solution' in record and 'written to PDB file:' in record and ".pdb" in record:
xyzout = record.split()[-1]
assert(xyzout)
shutil.copyfile(os.path.join(self.getWorkingDirectory(), xyzout),
self._xyzout)
if not os.path.isfile(self._xyzout):
raise RuntimeError, 'File %s does not exist' % self._xyzout
return
def postProcess(self, _edObject = None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG(
'*** EDPluginExecDIMPLEREFMACRestrainedRefinementv10.postProcess')
init_r, init_r_free, final_r, final_r_free = self.parse_refmac_log()
xsDataResult = CCP4DataResultREFMACRestrainedRefinement(
HKLOUT = HKL(self._hklout),
XYZOUT = XYZ(self._xyzout),
initialR = XSDataFloat(init_r),
initialRFree = XSDataFloat(init_r_free),
finalR = XSDataFloat(final_r),
finalRFree = XSDataFloat(final_r_free),
returnStatus = CCP4ReturnStatus())
self.setDataOutput(xsDataResult)
if not os.path.isfile(self.getDataOutput().getHKLOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput().getHKLOUT().getPath().getValue()
if not os.path.isfile(self.getDataOutput().getXYZOUT().getPath().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput().getXYZOUT().getPath().getValue()
return
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecSaxsDelMetadatav1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultSaxsDelMetadatav1_0()
xsDataResult.setOutputImage(self.getDataInput().getInputImage())
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatPorodv1_0.postProcess")
# Create some output data
logfile = os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName())
out = open(logfile, "r").read().split()
if self.atsasVersion < "2.6":
try:
res = float(out[0])
except (ValueError, IndexError):
self.error("Unable to read porod log file: " + logfile)
self.setFailure()
else:
xsDataResult = XSDataResultDatPorod(
volume=XSDataDoubleWithUnit(value=res))
self.setDataOutput(xsDataResult)
else:
try:
res = float(out[2])
except (ValueError, IndexError):
self.error("Unable to read porod log file: " + logfile)
self.setFailure()
else:
xsDataResult = XSDataResultDatPorod(
volume=XSDataDoubleWithUnit(value=res))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatcmpv2_0.postProcess")
strResultFile = os.path.join(os.path.dirname(self.getScriptFilePath()), self.getScriptLogFileName())
if os.path.isfile(strResultFile):
for line in open(strResultFile):
words = line.split()
if (self.atsasVersion == "2.5.2") and (len(words) == 5):
try:
self.fChi = float(words[-2])
self.fFidelity = float(words[-1])
except ValueError:
self.WARNING("Strange ouptut from %s:%s %s" % (strResultFile, os.linesep, line))
else:
break
if (self.atsasVersion == "2.6.1") and (len(words) == 6):
try:
self.fChi = float(words[-3]) ** 0.5
self.fFidelity = float(words[-1].strip('*'))
except ValueError:
self.DEBUG("Strange ouptut from %s:%s %s" % (strResultFile, os.linesep, line))
else:
break
# Create some output data
xsDataResult = XSDataResultDatcmp()
if self.fChi is not None:
xsDataResult.chi = XSDataDouble(self.fChi)
if self.fFidelity is not None:
xsDataResult.fidelity = XSDataDouble(self.fFidelity)
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("*** EDPluginExecDIMPLEPDBSETv10.postProcess")
self.programTermination()
# Create some output data
# xsDataResult = CCP4DataResultPDBSET()
# self.setDataOutput( xsDataResult )
strLog = self.readProcessLogFile()
ccp4ReturnStatus = self.getPDBSETReturnStatus(strLog)
ccp4DataResultPDBSET = CCP4DataResultPDBSET()
# Set the output PDB file
ccp4DataResultPDBSET.setXYZOUT(
XSDataString(self.getDataInput().getXYZOUT().getPath().getValue()))
# Set the output log file
ccp4DataResultPDBSET.setOutputLogFile(
XSDataString(self.getScriptLogFileName()))
# Set the return status
ccp4DataResultPDBSET.setReturnStatus(ccp4ReturnStatus)
# Set the data output for the job
self.setDataOutput(ccp4DataResultPDBSET)
if not os.path.isfile(self.getDataOutput().getXYZOUT().getValue()):
raise RuntimeError, 'File %s does not exist' % self.getDataOutput(
).getXYZOUT().getValue()
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatcmpv1_0.postProcess")
strResultFile = os.path.join(os.path.dirname(self.getScriptFilePath()),
self.getScriptLogFileName())
if os.path.isfile(strResultFile):
for line in open(strResultFile):
words = line.split()
if len(words) == 2:
try:
self.fChi = float(words[0])
self.fFidelity = float(words[1])
except ValueError:
self.WARNING("Strange ouptut from %s:%s %s" %
(strResultFile, os.linesep, line))
else:
break
# Create some output data
xsDataResult = XSDataResultDatcmp()
if self.fChi is not None:
xsDataResult.chi = XSDataDouble(self.fChi)
if self.fFidelity is not None:
xsDataResult.fidelity = XSDataDouble(self.fFidelity)
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginH5ToCBFv1_0.postProcess")
if self.dataInput.dataCollection is None:
shutil.copy(self.tmpCBFFile, self.CBFFile)
else:
# Fill in metadata
fileTmpCBF = open(self.tmpCBFFile)
tmpCBF = fileTmpCBF.read()
fileTmpCBF.close()
# Replace opening line
tmpCBF = tmpCBF.replace(
"CBF: VERSION 1.5, CBFlib v0.7.8 - SLS/DECTRIS PILATUS detectors",
"CBF: VERSION 1.5, CBFlib v0.7.8")
index1 = tmpCBF.find("# WARNING: FOR XDS PROCESSING ONLY.")
string2 = "# SOFTWARE VERSION: 1.1.0-RELEASE"
index2 = tmpCBF.find(string2) + len(string2)
miniCBFHeader = self.generateMiniCBFHeader(self.dataInput)
newCBF = tmpCBF[:index1] + miniCBFHeader + tmpCBF[index2:]
newCBFFile = open(self.CBFFile, "w")
newCBFFile.write(newCBF)
newCBFFile.close()
def postProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginExecProcessScript.postProcess(self, _edObject)
self.DEBUG("EDPluginLabelitv10.postProcess...")
strLabelitLog = self.readProcessLogFile()
if strLabelitLog is None:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginLabelitv10.postProcess",
self.getClassName(),
"Could not read the Labelit log file",
)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
xsDataLabelitScreenOutput = self.parseLabelitScreenOutput(strLabelitLog)
xsDataIntegerSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber()
if xsDataIntegerSelectedSolutionNumber is None:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginLabelitv10.postProcess",
self.getClassName(),
"No selected solution",
)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
strLabelitMosflmScriptsOutput = self.readProcessFile(
self.generateMosflmScriptName(xsDataIntegerSelectedSolutionNumber.getValue())
)
xsDataLabelitMosflmScriptsOutput = self.parseMosflmScriptsOutput(strLabelitMosflmScriptsOutput)
xsDataResultLabelit = XSDataResultLabelit()
xsDataResultLabelit.setLabelitScreenOutput(xsDataLabelitScreenOutput)
xsDataResultLabelit.setLabelitMosflmScriptsOutput(xsDataLabelitMosflmScriptsOutput)
self.setDataOutput(xsDataResultLabelit)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDamminv0_1.postProcess")
# Create some output data
pathLogFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "dammin.log"))
pathFitFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "dammin.fit"))
pathMoleculeFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "dammin-1.pdb"))
pathSolventFile = XSDataString(
os.path.join(self.getWorkingDirectory(), "dammin-0.pdb"))
xsLogFile = XSDataFile(pathLogFile)
xsFitFile = XSDataFile(pathFitFile)
xsMoleculeFile = XSDataFile(pathMoleculeFile)
xsSolventFile = XSDataFile(pathSolventFile)
xsDataResult = XSDataResultDammin()
if os.path.exists(pathLogFile.getValue()):
xsDataResult.setLogFile(xsLogFile)
if os.path.exists(pathFitFile.getValue()):
xsDataResult.setFitFile(xsFitFile)
if os.path.exists(pathMoleculeFile.getValue()):
xsDataResult.setPdbMoleculeFile(xsMoleculeFile)
if os.path.exists(pathSolventFile.getValue()):
xsDataResult.setPdbSolventFile(xsSolventFile)
xsDataResult.setChiSqrt(self.returnDamminChiSqrt())
xsDataResult.setRfactor(self.returnDamminRFactor())
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginMinimalXds.postProcess")
# Check log for warning and errors
strPathToLogFile = os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
self.checkLogForWarningAndErrors(strPathToLogFile)
# XDS is considered to have succeeded iff CORRECT.LP has been created
outfile = os.path.join(self.getWorkingDirectory(), 'CORRECT.LP')
self.DEBUG('looking for {0}'.format(outfile))
if not os.path.isfile(outfile):
self.DEBUG('NOT FOUND')
self.dataOutput.succeeded = XSDataBoolean(False)
strErrorMessage = "Cannot find CORRECT.LP output file"
self.ERROR(strErrorMessage)
if len(self.getListOfErrorMessages()) == 0:
self.addErrorMessage(strErrorMessage)
else:
self.addWarningMessage(strErrorMessage)
self.setFailure()
return
else:
self.DEBUG('FOUND')
self.dataOutput.succeeded = XSDataBoolean(True)
self.DEBUG('succeeded is {0} and succeeded.value is {1}'.format(self.dataOutput.succeeded,
self.dataOutput.succeeded.value))
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecProcessScriptAutoRgv1_0.postProcess")
# Create some output data
# 2.83326 0.011646 2.04258e+07 18565.3 47 81 0.783626 1 bioSaxsMerged.dat
strOutput = self.readProcessLogFile()
xsDataResult = XSDataResultAutoRg()
listXSDOut = []
for line in strOutput.split(os.linesep):
words = line.split(None, 8)
if len(words) < 8:
break
try:
xsData = XSDataAutoRg()
xsData.filename = XSDataFile(XSDataString(words[-1]))
xsData.rg = XSDataLength(float(words[0]))
xsData.rgStdev = XSDataLength(float(words[1]))
xsData.i0 = XSDataDouble(float(words[2]))
xsData.i0Stdev = XSDataDouble(float(words[3]))
xsData.firstPointUsed = XSDataInteger(int(words[4]))
xsData.lastPointUsed = XSDataInteger(int(words[5]))
xsData.quality = XSDataDouble(float(words[6]))
xsData.isagregated = XSDataBoolean(bool(int(words[7])))
except Exception:
strError = "Error in parsing output:" + line
self.error(strError)
self.setFailure()
listXSDOut.append(xsData)
xsDataResult.autoRgOut = listXSDOut
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginExecProcessScript.postProcess(self, _edObject)
self.DEBUG("EDPluginLabelitv10.postProcess...")
strLabelitLog = self.readProcessLogFile()
if (strLabelitLog is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginLabelitv10.postProcess", self.getClassName(), "Could not read the Labelit log file")
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
xsDataLabelitScreenOutput = self.parseLabelitScreenOutput(strLabelitLog)
xsDataIntegerSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber()
if (xsDataIntegerSelectedSolutionNumber is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginLabelitv10.postProcess", self.getClassName(), "No selected solution")
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
strLabelitMosflmScriptsOutput = self.readProcessFile(self.generateMosflmScriptName(xsDataIntegerSelectedSolutionNumber.getValue()))
xsDataLabelitMosflmScriptsOutput = self.parseMosflmScriptsOutput(strLabelitMosflmScriptsOutput)
xsDataResultLabelit = XSDataResultLabelit()
xsDataResultLabelit.setLabelitScreenOutput(xsDataLabelitScreenOutput)
xsDataResultLabelit.setLabelitMosflmScriptsOutput(xsDataLabelitMosflmScriptsOutput)
self.setDataOutput(xsDataResultLabelit)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginMinimalXds.postProcess")
# Check log for warning and errors
strPathToLogFile = os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName())
self.checkLogForWarningAndErrors(strPathToLogFile)
# XDS is considered to have succeeded iff CORRECT.LP has been created
outfile = os.path.join(self.getWorkingDirectory(), 'CORRECT.LP')
self.DEBUG('looking for {0}'.format(outfile))
if not os.path.isfile(outfile):
self.DEBUG('NOT FOUND')
self.dataOutput.succeeded = XSDataBoolean(False)
strErrorMessage = "Cannot find CORRECT.LP output file"
self.ERROR(strErrorMessage)
if len(self.getListOfErrorMessages()) == 0:
self.addErrorMessage(strErrorMessage)
else:
self.addWarningMessage(strErrorMessage)
self.setFailure()
return
else:
self.DEBUG('FOUND')
self.dataOutput.succeeded = XSDataBoolean(True)
self.DEBUG('succeeded is {0} and succeeded.value is {1}'.format(
self.dataOutput.succeeded, self.dataOutput.succeeded.value))
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDatGnomv1_1.postProcess")
# Create some output data
cwd = self.getWorkingDirectory()
outfile = os.path.join(cwd, os.path.basename(self.outFile))
if not os.path.isfile(outfile):
self.error("EDPluginExecDatGnomv1_1 did not produce output file %s as expected !" % self.outFile)
self.setFailure()
self.dataOutput = XSDataResultDatGnom()
return
try:
os.rename(outfile, self.outFile)
except OSError: # may fail if src and dst on different filesystem
shutil.copy(outfile, self.outFile)
gnom = XSDataGnom(gnomFile=XSDataFile(XSDataString(self.outFile)))
logfile = os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
out = open(logfile, "r").read().split()
for key, val, typ in (("dmax:", "dmax", XSDataLength),
("Guinier:", "rgGuinier", XSDataLength),
("Gnom:", "rgGnom", XSDataLength),
("Total:", "total", XSDataDouble)):
if key in out:
idx = out.index(key)
res = out[idx + 1]
gnom.__setattr__(val, typ(float(res)))
else:
self.error("EDPluginExecDatGnomv1_1.postProcess No key %s in file %s" % (key, logfile))
self.setFailure()
self.dataOutput = XSDataResultDatGnom(gnom=gnom)
self.dataOutput.status = XSDataStatus(message=self.getXSDataMessage())
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDataverv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultDataver()
xsDataResult.outputCurve = XSDataFile(XSDataString(self.strOutFile))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecMTZDUMPUnitCellSpaceGroupv10.postProcess")
# Create some output data
pyStrLog = self.readProcessLogFile()
xsDataResultMTZDUMPUnitCellSpaceGroup = self.parseMTZDUMPLog(pyStrLog)
self.setDataOutput(xsDataResultMTZDUMPUnitCellSpaceGroup)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecSaxsAddMetadatav1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultSaxsAddMetadatav1_0()
xsDataResult.setOutputImage(self.getDataInput().getInputImage())
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecCrystFELIndexv1_0.postProcess")
# Populate the results
xsDataResultCrystFEL = self.parseOutputDirectory(
self.getWorkingDirectory())
self.dataOutput = xsDataResultCrystFEL
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDammifv0_1.postProcess")
# Create some output data
pathLogFile = XSDataString(os.path.join(self.getWorkingDirectory(), "dammif.log"))
pathFitFile = XSDataString(os.path.join(self.getWorkingDirectory(), "dammif.fit"))
pathMoleculeFile = XSDataString(os.path.join(self.getWorkingDirectory(), "dammif-1.pdb"))
pathSolventFile = XSDataString(os.path.join(self.getWorkingDirectory(), "dammif-0.pdb"))
xsLogFile = XSDataFile(pathLogFile)
xsFitFile = XSDataFile(pathFitFile)
xsMoleculeFile = XSDataFile(pathMoleculeFile)
xsSolventFile = XSDataFile(pathSolventFile)
xsDataResult = XSDataResultDammif()
if os.path.exists(pathLogFile.getValue()):
xsDataResult.setLogFile(xsLogFile)
if os.path.exists(pathFitFile.getValue()):
xsDataResult.setFitFile(xsFitFile)
if os.path.exists(pathMoleculeFile.getValue()):
xsDataResult.setPdbMoleculeFile(xsMoleculeFile)
if os.path.exists(pathSolventFile.getValue()):
xsDataResult.setPdbSolventFile(xsSolventFile)
xsDataResult.setChiSqrt(self.returnDammifChiSqrt())
xsDataResult.setRfactor(self.returnDammifRFactor())
self.setDataOutput(xsDataResult)
def postProcess(self):
self.DEBUG('Pointless: postProcess')
EDPluginExecProcessScript.postProcess(self)
output_file = self.dataInput.output_file.value
sgre = re.compile(""" \* Space group = '(?P<sgstr>.*)' \(number\s+(?P<sgnumber>\d+)\)""")
sgnumber = sgstr = None
# returns None if the file does not exist...
log = self.readProcessLogFile()
if log is not None:
# we'll apply the regexp to the whole file contents which
# hopefully won't be that long.
m = sgre.search(log)
if m is not None:
d = m.groupdict()
sgnumber = d['sgnumber']
sgstr = d['sgstr']
res = XSDataPointlessOut()
if sgnumber is not None:
res.sgnumber = XSDataInteger(sgnumber)
if sgstr is not None:
res.sgstr = XSDataString(sgstr)
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(output_file))
res.status = status
self.dataOutput = res
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecRsync.postProcess")
# Create some output data
xsDataResult = XSDataResultRsync(log=XSDataString(""))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
strRaddoseError = self.readProcessErrorLogFile()
if((strRaddoseError is not None) and (strRaddoseError != "")):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', 'EDPluginRaddosev10', strRaddoseError)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
resultDict = self.analyseScriptLogFileName(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()))
strSolvent = self.__dictResults[ EDPluginRaddosev10.__strSOLVENT ]
# ugly workaround while waiting for RADDOSE XML output file
strAbsorbedDose = None
for strAbsorbedDoseKeyword in EDPluginRaddosev10.__listABSORBED_DOSE:
strAbsorbedDose = self.__dictResults[ strAbsorbedDoseKeyword ]
if (strAbsorbedDose is not None):
break
if(strSolvent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', "Raddose", "No Result for Keyword [" + EDPluginRaddosev10.__strSOLVENT + "] see: " + self.getScriptLogFileName())
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if(strAbsorbedDose is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginRaddosev10.postProcess', "Raddose", "No Result for Keyword [" + strAbsorbedDoseKeyword + "] see: " + self.getScriptLogFileName())
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
self.__fSolvent = float(strSolvent)
if(self.__fSolvent < EDPluginRaddosev10.__iMIN_SOLVENT_PERCENTAGE or self.__fSolvent > EDPluginRaddosev10.__iMAX_SOLVENT_PERCENTAGE):
warningMessage = "Inconsistent solvent percentage value: %.1f" % self.__fSolvent
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
iNumberOfImages = self.getDataInput().getNumberOfImages().getValue()
fExposureTimePerImageInSec = self.getDataInput().getBeamExposureTime().getValue()
fTotalExposureTime = iNumberOfImages * fExposureTimePerImageInSec
fAbsorbedDoseSpeed = float(strAbsorbedDose) / fTotalExposureTime
xsDataAbsorbedDoseRate = XSDataAbsorbedDoseRate(fAbsorbedDoseSpeed)
xsDataAbsorbedDose = XSDataDouble(float(strAbsorbedDose))
self.__fTimeToReachHendersonLimit = EDPluginRaddosev10.__fHENDERSON_LIMIT / fAbsorbedDoseSpeed
xsDataRaddosev10Output = XSDataRaddoseOutput()
xsDataRaddosev10Output.setAbsorbedDose(xsDataAbsorbedDose)
xsDataRaddosev10Output.setAbsorbedDoseRate(xsDataAbsorbedDoseRate)
xsDataRaddosev10Output.setTimeToReachHendersonLimit(XSDataTime(self.__fTimeToReachHendersonLimit))
xsDataFilePathToLog = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))
xsDataRaddosev10Output.setPathToLogFile(xsDataFilePathToLog)
self.setDataOutput(xsDataRaddosev10Output)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginXOalignv1_0.postProcess")
strPathLogFile = os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
if os.path.exists(strPathLogFile):
xsDataResultXOalign = self.parseLogFile(strPathLogFile)
xsDataResultXOalign.logFile = XSDataFile(XSDataString(strPathLogFile))
self.dataOutput = xsDataResultXOalign
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecSupcombv0_3.postProcess")
try:
self.dataOutput = self.parseSupcombOutputFile()
except Exception as error:
self.ERROR("Error in supcomb: parseSupcombOutputFile: %s" % error)
self.setFailure()
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecXDSAPPv1_0.postProcess")
# Populate the results
prefixRunNumber = EDUtilsImage.getPrefix(
self.dataInput.image.path.value)
xsDataResultXDSAPP = self.parseOutputDirectory(
self.getWorkingDirectory(), prefixRunNumber)
self.dataOutput = xsDataResultXDSAPP
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecAbsCalcv0_1.postProcess")
# Create some output data
self.__xsDataResult = XSDataResultAbsCalc()
self.parseAbsCalcOutputFile()
self.setDataOutput(self.__xsDataResult)
def postProcess(self, _edObject = None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecAbsCalcv0_1.postProcess")
# Create some output data
self.__xsDataResult = XSDataResultAbsCalc()
self.parseAbsCalcOutputFile()
self.setDataOutput(self.__xsDataResult)
def postProcess( self, _edObject = None ):
EDPluginExecProcessScript.postProcess( self )
EDVerbose.DEBUG( "*** EDPluginExecDIMPLEMTZDUMPv10.postProcess")
# check to see if the program terminated normally
self.programTermination()
# Create some output data
strLog=self.readProcessLogFile()
dataResultFromMTZDUMP=self.parseDIMPLEMTZDUMP(strLog)
self.setDataOutput(dataResultFromMTZDUMP)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamminv0_2.postProcess")
# Create some output data
cwd = self.getWorkingDirectory()
model = XSDataSaxsModel(name=XSDataString("dammin"))
xsDataResult = XSDataResultDammin(model=model)
pathLogFile = os.path.join(cwd, "dammin.log")
pathFitFile = os.path.join(cwd, "dammin.fit")
pathFirFile = os.path.join(cwd, "dammin.fir")
pathMoleculeFile = os.path.join(cwd, "dammin-1.pdb")
pathSolventFile = os.path.join(cwd, "dammin-0.pdb")
try:
res = parse_atsas.parsePDB(pathMoleculeFile, pathMoleculeFile)
except Exception as error:
self.ERROR("EDPluginExecDamminv0_2:parsePDB: %s" % error)
else:
for k in res:
self.__setattr__(k, res[k])
if os.path.exists(pathLogFile):
xsDataResult.logFile = model.logFile = XSDataFile(
XSDataString(pathLogFile))
if not self.Rfactor:
self.Rfactor = self.returnDamminRFactor()
if self.Rfactor:
xsDataResult.rfactor = model.rfactor = XSDataDouble(
self.Rfactor)
if os.path.exists(pathFitFile):
xsDataResult.fitFile = model.fitFile = XSDataFile(
XSDataString(pathFitFile))
if os.path.exists(pathFirFile):
model.firFile = XSDataFile(XSDataString(pathFirFile))
xsDataResult.chiSqrt = model.chiSqrt = self.returnDamminChiSqrt()
if os.path.exists(pathMoleculeFile):
xsDataResult.pdbMoleculeFile = model.pdbFile = XSDataFile(
XSDataString(pathMoleculeFile))
if os.path.exists(pathSolventFile):
xsDataResult.pdbSolventFile = XSDataFile(
XSDataString(pathSolventFile))
if self.volume:
model.volume = XSDataDouble(self.volume)
if self.Rg:
model.rg = XSDataDouble(self.Rg)
if self.Dmax:
model.dmax = XSDataDouble(self.Dmax)
self.generateExecutiveSummary()
xsDataResult.status = XSDataStatus(
message=self.getXSDataMessage(),
executiveSummary=XSDataString(
os.linesep.join(self.getListExecutiveSummaryLines())))
self.dataOutput = xsDataResult
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("*** EDPluginFIT2DCakev1_0.postProcess")
# Create the output data
xsDataResultFIT2DCake = XSDataResultFIT2DCake()
if (self.m_strOutputFilePath is not None):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.m_strOutputFilePath))
xsDataResultFIT2DCake.setResultFile(xsDataFile)
self.setDataOutput(xsDataResultFIT2DCake)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamstartv0_2.postProcess")
model = XSDataSaxsModel(name=XSDataString("damstart"))
xsDataResult = XSDataResultDamstart(model=model)
xsDataResult.outputPdbFile = model.pdbFile = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.__strOutputPdbFileName)))
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecSiftDescriptorv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultSiftDescriptor()
if os.path.isfile(self.strKeys):
xsdFile = XSDataFile()
xsdFile.setPath(XSDataString(self.strKeys))
xsDataResult.setDescriptorFile(xsdFile)
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecSiftDescriptorv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultSiftDescriptor()
if os.path.isfile(self.strKeys):
xsdFile = XSDataFile()
xsdFile.setPath(XSDataString(self.strKeys))
xsDataResult.setDescriptorFile(xsdFile)
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("*** EDPluginFIT2DCakev1_0.postProcess")
# Create the output data
xsDataResultFIT2DCake = XSDataResultFIT2DCake()
if (self.m_strOutputFilePath is not None):
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.m_strOutputFilePath))
xsDataResultFIT2DCake.setResultFile(xsDataFile)
self.setDataOutput(xsDataResultFIT2DCake)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecDamfiltv0_1.postProcess")
xsDataResult = XSDataResultDamfilt()
pathOutputFile = XSDataString(os.path.join(self.getWorkingDirectory(), self.__strOutputPdbFileName))
xsDataResult.setOutputPdbFile(XSDataFile(pathOutputFile))
self.setDataOutput(xsDataResult)
def postProcess(self):
self.DEBUG('Truncate: postProcess')
EDPluginExecProcessScript.postProcess(self)
output_file = self.dataInput.output_file.value
res = XSDataResult()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(output_file))
res.status = status
self.dataOutput = res
def postProcess(self, _edObject=None):
"""
reading back and genericly process the output
"""
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginSTACv2_0.postProcess")
OutputData = self.fetchOutput()
self.DEBUG("EDPluginSTACv2_0.postProcess: " + str(OutputData))
if (OutputData is not None):
self.setDataOutput(OutputData)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecVideov10.postProcess")
# Create some output data
xsDataResult = XSDataResultExecVideo()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.videoFile))
xsDataResult.setVideoPath(xsDataFile)
xsDataResult.setVideoPath(xsDataFile)
xsDataResult.setVideoCodec(XSDataString(self.codec))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
EDVerbose.DEBUG("EDPluginExecVideov10.postProcess")
# Create some output data
xsDataResult = XSDataResultExecVideo()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(self.videoFile))
xsDataResult.setVideoPath(xsDataFile)
xsDataResult.setVideoPath(xsDataFile)
xsDataResult.setVideoCodec(XSDataString(self.codec))
self.setDataOutput(xsDataResult)
def postProcess(self):
self.DEBUG('Uniqueify: postProcess')
EDPluginExecProcessScript.postProcess(self)
output_file = self.dataInput.output_file.value
res = XSDataResult()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(output_file))
res.status = status
self.dataOutput = res
