def postProcess(self):
self.DEBUG('Import: postProcess')
EDPluginControl.postProcess(self)
res = XSDataEDNAprocImportOut()
status = XSDataStatus()
res.status = status
if self.dataInput.input_noanom:
all_good = not self.anom.isFailure() and not self.noanom.isFailure()
else:
all_good = not self.anom.isFailure()
status.isSuccess = XSDataBoolean(all_good)
files = list()
if not self.anom.isFailure():
files.append(self.anom.dataInput.output_file)
if self.dataInput.input_noanom and not self.noanom.isFailure():
files.append(self.noanom.dataInput.output_file)
res.files = files
if self.dataInput.input_noanom:
res.pointless_sgnumber = self.noanom.dataOutput.pointless_sgnumber
res.pointless_sgstring = self.noanom.dataOutput.pointless_sgstring
res.pointless_cell = self.noanom.dataOutput.pointless_cell
else:
res.pointless_sgnumber = self.anom.dataOutput.pointless_sgnumber
res.pointless_sgstring = self.anom.dataOutput.pointless_sgstring
res.pointless_cell = self.anom.dataOutput.pointless_cell
res.aimless_log_anom = self.anom.dataOutput.aimless_log
if self.dataInput.input_noanom:
res.aimless_log_noanom = self.noanom.dataOutput.aimless_log
self.dataOutput = res
def postProcess(self):
self.DEBUG('Import: postProcess')
EDPluginControl.postProcess(self)
res = XSDataEDNAprocImportOut()
status = XSDataStatus()
res.status = status
if self.dataInput.input_noanom:
all_good = not self.anom.isFailure() and not self.noanom.isFailure(
)
else:
all_good = not self.anom.isFailure()
status.isSuccess = XSDataBoolean(all_good)
files = list()
if not self.anom.isFailure():
files.append(self.anom.dataInput.output_file)
if self.dataInput.input_noanom and not self.noanom.isFailure():
files.append(self.noanom.dataInput.output_file)
res.files = files
if self.dataInput.input_noanom:
res.pointless_sgnumber = self.noanom.dataOutput.pointless_sgnumber
res.pointless_sgstring = self.noanom.dataOutput.pointless_sgstring
res.pointless_cell = self.noanom.dataOutput.pointless_cell
else:
res.pointless_sgnumber = self.anom.dataOutput.pointless_sgnumber
res.pointless_sgstring = self.anom.dataOutput.pointless_sgstring
res.pointless_cell = self.anom.dataOutput.pointless_cell
res.aimless_log_anom = self.anom.dataOutput.aimless_log
if self.dataInput.input_noanom:
res.aimless_log_noanom = self.noanom.dataOutput.aimless_log
self.dataOutput = res
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.match(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):
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):
self.DEBUG('FileConversion: postProcess')
EDPluginControl.postProcess(self)
output_file = self.dataInput.output_file.value
res = XSDataResult()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(self.uniqueify.dataInput.output_file.value))
res.status = status
self.dataOutput = res
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):
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
def postProcess(self):
self.DEBUG('FileConversion: postProcess')
EDPluginControl.postProcess(self)
output_file = self.dataInput.output_file.value
res = XSDataResult()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(
os.path.exists(self.uniqueify.dataInput.output_file.value))
res.status = status
self.dataOutput = res
def parsePointlessOutput(self, _outputFile):
sgre = re.compile(
""" \* Space group = '(?P<sgstr>.*)' \(number\s+(?P<sgnumber>\d+)\)"""
)
sgnumber = sgstr = None
res = XSDataPointlessOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(False)
if os.path.exists(_outputFile):
res.status = status
strLog = EDUtilsFile.readFile(_outputFile)
if strLog is not None:
# we'll apply the regexp to the whole file contents which
# hopefully won't be that long.
m = sgre.search(strLog)
if m is not None:
d = m.groupdict()
sgnumber = d['sgnumber']
sgstr = d['sgstr']
res.sgnumber = XSDataInteger(sgnumber)
res.sgstr = XSDataString(sgstr)
status.isSuccess = XSDataBoolean(True)
# Search first for unit cell after the Laue group...
unitCellRe = re.compile(
""" Laue group confidence.+\\n\\n\s+Unit cell:(.+)""")
m2 = unitCellRe.search(strLog)
if m2 is None:
# Then search it from the end...
unitCellRe = re.compile(
""" \* Cell Dimensions : \(obsolete \- refer to dataset cell dimensions above\)\\n\\n(.+)"""
)
m2 = unitCellRe.search(strLog)
if m2 is not None:
listCell = m2.groups()[0].split()
xsDataCCP4Cell = XSDataCCP4Cell()
xsDataCCP4Cell.length_a = XSDataLength(listCell[0])
xsDataCCP4Cell.length_b = XSDataLength(listCell[1])
xsDataCCP4Cell.length_c = XSDataLength(listCell[2])
xsDataCCP4Cell.angle_alpha = XSDataAngle(listCell[3])
xsDataCCP4Cell.angle_beta = XSDataAngle(listCell[4])
xsDataCCP4Cell.angle_gamma = XSDataAngle(listCell[5])
res.cell = xsDataCCP4Cell
return res
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
executiveSummary = os.linesep.join(self.lstExecutiveSummary)
self.xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(executiveSummary))
self.dataOutput = self.xsDataResult
if self.frame:
self.frame.processing = False
def postProcess(self):
self.DEBUG('Import: postProcess')
EDPluginControl.postProcess(self)
res = XSDataAutoprocImportOut()
status = XSDataStatus()
res.status = status
all_good = not self.anom.isFailure() and not self.noanom.isFailure()
status.isSuccess = XSDataBoolean(all_good)
files = list()
for p in [self.anom, self.noanom]:
if not p.isFailure():
files.append(p.dataInput.output_file)
res.files = files
self.dataOutput = res
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsNormalizev1_0.postProcess")
# Create some output data
self.xsdResult.status = XSDataStatus(
executiveSummary=XSDataString(os.linesep.join(self.lstProcessLog)))
self.setDataOutput(self.xsdResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlSaxsAnalysisv1_0.postProcess")
# Create some output data
strLog = """Rg = %.2f +/- %2f
I(0) = %.2e +/- %.2e
Points %i to %i
Quality: %4.2f%% Aggregated: %s""" % (
self.autoRg.rg.value, self.autoRg.rgStdev.value,
self.autoRg.i0.value, self.autoRg.i0Stdev.value,
self.autoRg.firstPointUsed.value, self.autoRg.lastPointUsed.value,
self.autoRg.quality.value * 100., self.autoRg.isagregated.value)
if self.gnom is None:
strLog += """
datGnom failed"""
else:
strLog += """
Dmax = %12.2f Total = %12.2f
Guinier = %12.2f Gnom = %12.2f""" % (
self.gnom.dmax.value, self.gnom.total.value,
self.gnom.rgGuinier.value, self.gnom.rgGnom.value)
if self.xVolume is None:
strLog += """
datPorod failed"""
else:
strLog += """
Volume = %12.2f""" % (self.xVolume.value)
xsDataResult = XSDataResultSaxsAnalysis(
autoRg=self.autoRg,
gnom=self.gnom,
volume=self.xVolume,
status=XSDataStatus(executiveSummary=XSDataString(strLog)))
self.setDataOutput(xsDataResult)
def postProcess(self):
self.DEBUG('Import: postProcess')
EDPluginControl.postProcess(self)
res = XSDataAutoprocImportOut()
status = XSDataStatus()
res.status = status
all_good = not self.anom.isFailure() and not self.noanom.isFailure()
status.isSuccess = XSDataBoolean(all_good)
files = list()
for p in [self.anom, self.noanom]:
if not p.isFailure():
files.append(p.dataInput.output_file)
res.files = files
self.dataOutput = res
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
executiveSummary = os.linesep.join(self.lstExecutiveSummary)
self.xsDataResult.status = XSDataStatus(
executiveSummary=XSDataString(executiveSummary))
self.dataOutput = self.xsDataResult
EDPluginBioSaxsHPLCv1_3.dictHPLC[self.runId].reset()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsISPyBModellingv1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsISPyBModellingv1_0(status=XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstError))))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlSingleSamplev1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsSingleSamplev1_0()
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(self.strExecutiveSummary))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
xsDataResult = XSDataResultBioSaxsSolutionScatteringISPyBv1_0(
status=XSDataStatus(
executiveSummary=XSDataString(os.linesep.join(self.lstError))))
self.setDataOutput(xsDataResult)
self.DEBUG("EDPluginBioSaxsSolutionScatteringISPyBv1_0.postProcess")
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginAutoSubv1_0.postProcess")
# Create some output data
self.xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstProcessLog)))
self.xsDataResult.subtractedCurve = XSDataFile(XSDataString(self.subtractedCurve))
self.dataOutput = self.xsDataResult
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self)
self.xsDataResult.status = XSDataStatus(
message=self.getXSDataMessage(),
executiveSummary=XSDataString(
os.linesep.join(self.getListExecutiveSummaryLines())))
self.dataOutput = self.xsDataResult
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsProcessOneFilev1_4.postProcess")
# Create some output data
if os.path.exists(self.integratedCurve):
self.xsDataResult.integratedCurve = XSDataFile(XSDataString(self.integratedCurve))
self.xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstExecutiveSummary)))
self.setDataOutput(self.xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsAzimutIntv1_1.postProcess")
# Create some output data
strLog = os.linesep.join(self.lstProcessLog)
self.xsdResult.status = XSDataStatus(executiveSummary=XSDataString(strLog))
self.setDataOutput(self.xsdResult)
EDVerbose.DEBUG("EDPluginBioSaxsAzimutIntv1_1.postProces: Comments generated: " + os.linesep + strLog)
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 parsePointlessOutput(self, _outputFile):
sgre = re.compile(""" \* Space group = '(?P<sgstr>.*)' \(number\s+(?P<sgnumber>\d+)\)""")
sgnumber = sgstr = None
res = XSDataPointlessOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(False)
if os.path.exists(_outputFile):
res.status = status
strLog = EDUtilsFile.readFile(_outputFile)
if strLog is not None:
# we'll apply the regexp to the whole file contents which
# hopefully won't be that long.
m = sgre.search(strLog)
if m is not None:
d = m.groupdict()
sgnumber = d['sgnumber']
sgstr = d['sgstr']
res.sgnumber = XSDataInteger(sgnumber)
res.sgstr = XSDataString(sgstr)
status.isSuccess = XSDataBoolean(True)
# Search first for unit cell after the Laue group...
unitCellRe = re.compile(""" Laue group confidence.+\\n\\n\s+Unit cell:(.+)""")
m2 = unitCellRe.search(strLog)
if m2 is None:
# Then search it from the end...
unitCellRe = re.compile(""" \* Cell Dimensions : \(obsolete \- refer to dataset cell dimensions above\)\\n\\n(.+)""")
m2 = unitCellRe.search(strLog)
if m2 is not None:
listCell = m2.groups()[0].split()
xsDataCCP4Cell = XSDataCCP4Cell()
xsDataCCP4Cell.length_a = XSDataLength(listCell[0])
xsDataCCP4Cell.length_b = XSDataLength(listCell[1])
xsDataCCP4Cell.length_c = XSDataLength(listCell[2])
xsDataCCP4Cell.angle_alpha = XSDataAngle(listCell[3])
xsDataCCP4Cell.angle_beta = XSDataAngle(listCell[4])
xsDataCCP4Cell.angle_gamma = XSDataAngle(listCell[5])
res.cell = xsDataCCP4Cell
return res
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):
EDPluginControl.postProcess(self)
EDVerbose.DEBUG("EDPluginBioSaxsAzimutIntv1_0.postProcess")
#remove the terminal carriage return
if self.strProcessLog.endswith("\n"):
self.strProcessLog = self.strProcessLog[:-1]
# Create some output data
self.xsdResult.setStatus(XSDataStatus(executiveSummary=XSDataString(self.strProcessLog)))
self.setDataOutput(self.xsdResult)
EDVerbose.DEBUG("Comment generated ...\n" + self.strProcessLog)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_0.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsSmartMergev1_0()
xsDataResult.mergedCurve = self.dataInput.mergedCurve
executiveSummary = os.linesep.join(self.lstSummary)
xsDataResult.status = XSDataStatus(
executiveSummary=XSDataString(executiveSummary))
self.setDataOutput(xsDataResult)
self.DEBUG(executiveSummary)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsProcessOneFilev1_1.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsProcessOneFilev1_0()
xsDataResult.normalizedImage = self.normalizedImage
xsDataResult.integratedImage = self.integratedImage
xsDataResult.integratedCurve = self.integratedCurve
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstExecutiveSummary)))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsNormalizev1_1.postProcess")
if os.path.isfile(self.strNormalizedImage):
xsNormFile = XSDataImage()
xsNormFile.setPath(XSDataString(self.strNormalizedImage))
self.xsdResult.setNormalizedImage(xsNormFile)
self.xsdResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstProcessLog)))
# Create some output data
self.setDataOutput(self.xsdResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsProcessOneFilev1_3.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsProcessOneFilev1_0()
if os.path.exists(self.integratedCurve):
xsDataResult.integratedCurve = XSDataFile(XSDataString(self.integratedCurve))
xsDataResult.sample = self.sample
xsDataResult.experimentSetup = self.experimentSetup
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(os.linesep.join(self.lstExecutiveSummary)))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsSmartMergev1_3.postProcess")
# Create some output data
xsDataResult = XSDataResultBioSaxsSmartMergev1_0()
xsDataResult.mergedCurve = self.dataInput.mergedCurve
executiveSummary = os.linesep.join(self.lstSummary)
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(executiveSummary))
if self.autoRg is not None:
xsDataResult.autoRg = self.autoRg
if self.strSubFile is not None and os.path.isfile(self.strSubFile):
xsDataResult.subtractedCurve = XSDataFile(XSDataString(self.strSubFile))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginBioSaxsReduceFileSeriev1_0.postProcess")
# Create some output data
executiveSummary = os.linesep.join(self.lstSummary)
xsDataResult = XSDataResultBioSaxsReduceFileSeriev1_0()
xsDataResult.status = XSDataStatus(executiveSummary=XSDataString(executiveSummary))
xsDataResult.directory1D = XSDataFile(XSDataString(self.directory1D))
xsDataResult.directory2D = XSDataFile(XSDataString(self.directory2D))
xsDataResult.directoryMisc = XSDataFile(XSDataString(self.directoryMisc))
xsDataResult.mergedCurve = XSDataFile(XSDataString(self.strMergedCurve))
self.setDataOutput(xsDataResult)
self.DEBUG(executiveSummary)
def postProcess(self):
self.DEBUG('FileConversion: postProcess')
EDPluginControl.postProcess(self)
output_file = self.dataInput.output_file.value
# gzip the pointless multirecord file
pointless_out = os.path.join(os.path.dirname(self.dataInput.output_file.value),
self.pointless_out)
try:
self.DEBUG("gzip'ing pointless multirecord file {0}".format(pointless_out))
subprocess.call(['gzip', pointless_out])
except Exception:
self.DEBUG("gzip'ing the file failed: {0}".format(traceback.format_exc()))
res = XSDataFileConversionOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(self.uniqueify.dataInput.output_file.value))
res.status = status
res.pointless_sgnumber = self.pointless.dataOutput.sgnumber
res.pointless_sgstring = self.pointless.dataOutput.sgstr
res.aimless_log = XSDataString(self.aimless_log)
self.dataOutput = res
def postProcess(self):
self.DEBUG('FileConversion: postProcess')
EDPluginControl.postProcess(self)
output_file = self.dataInput.output_file.value
# gzip the aimless unmerged file
aimless_unmerged_out = 'ep_{0}{1}_aimless_unmerged.mtz'.format(self.image_prefix, self.strAnomSuffix)
aimless_unmerged_path = os.path.join(os.path.dirname(self.dataInput.output_file.value),
aimless_unmerged_out)
try:
self.DEBUG("gzip'ing aimless unmerged file {0}".format(aimless_unmerged_path))
subprocess.call(['gzip', aimless_unmerged_path])
except Exception:
self.DEBUG("gzip'ing the file failed: {0}".format(traceback.format_exc()))
# gzip the pointless multirecord file
pointless_out = os.path.join(os.path.dirname(self.dataInput.output_file.value),
self.pointless_out)
try:
self.DEBUG("gzip'ing pointless multirecord file {0}".format(pointless_out))
subprocess.call(['gzip', pointless_out])
except Exception:
self.DEBUG("gzip'ing the file failed: {0}".format(traceback.format_exc()))
res = XSDataFileConversionOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(self.uniqueify.dataInput.output_file.value))
res.status = status
res.pointless_sgnumber = self.pointless.dataOutput.sgnumber
res.pointless_sgstring = self.pointless.dataOutput.sgstr
res.pointless_cell = [XSDataDouble(self.pointless.dataOutput.cell.length_a.value),
XSDataDouble(self.pointless.dataOutput.cell.length_b.value),
XSDataDouble(self.pointless.dataOutput.cell.length_c.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_alpha.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_beta.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_gamma.value)]
res.aimless_log = XSDataString(self.aimless_log)
self.dataOutput = res
def postProcess(self):
self.DEBUG('FileConversion: postProcess')
EDPluginControl.postProcess(self)
output_file = self.dataInput.output_file.value
# gzip the aimless unmerged file
aimless_unmerged_out = 'ep_{0}{1}_aimless_unmerged.mtz'.format(self.image_prefix, self.strAnomSuffix)
aimless_unmerged_path = os.path.join(os.path.dirname(self.dataInput.output_file.value),
aimless_unmerged_out)
try:
self.DEBUG("gzip'ing aimless unmerged file {0}".format(aimless_unmerged_path))
subprocess.call(['gzip', aimless_unmerged_path])
except Exception:
self.DEBUG("gzip'ing the file failed: {0}".format(traceback.format_exc()))
# gzip the pointless multirecord file
pointless_out = os.path.join(os.path.dirname(self.dataInput.output_file.value),
self.pointless_out)
try:
self.DEBUG("gzip'ing pointless multirecord file {0}".format(pointless_out))
subprocess.call(['gzip', pointless_out])
except Exception:
self.DEBUG("gzip'ing the file failed: {0}".format(traceback.format_exc()))
res = XSDataFileConversionOut()
status = XSDataStatus()
status.isSuccess = XSDataBoolean(os.path.exists(self.uniqueify.dataInput.output_file.value))
res.status = status
res.pointless_sgnumber = self.pointless.dataOutput.sgnumber
res.pointless_sgstring = self.pointless.dataOutput.sgstr
res.pointless_cell = [XSDataDouble(self.pointless.dataOutput.cell.length_a.value),
XSDataDouble(self.pointless.dataOutput.cell.length_b.value),
XSDataDouble(self.pointless.dataOutput.cell.length_c.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_alpha.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_beta.value),
XSDataDouble(self.pointless.dataOutput.cell.angle_gamma.value)]
res.aimless_log = XSDataString(self.aimless_log)
self.dataOutput = res
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamaverv0_2.postProcess")
# Create some output data
self.outputDamaverPdbFiles()
if self.__bAutomatic:
self.parseDamselLog()
self.generateExecutiveSummary()
self.__xsDataResult.status = XSDataStatus(
message=self.getXSDataMessage(),
executiveSummary=XSDataString(
os.linesep.join(self.getListExecutiveSummaryLines())))
self.dataOutput = self.__xsDataResult
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlSaxsAnalysisModelingv1_0.postProcess")
# Create some output data
self.xsDataResult.autoRg = self.autoRg
self.xsDataResult.gnom = self.gnom
self.xsDataResult.volume = self.xVolume
self.xsDataResult.status = XSDataStatus(
message=self.getXSDataMessage(),
executiveSummary=XSDataString(
os.linesep.join(self.getListExecutiveSummaryLines())))
self.setDataOutput(self.xsDataResult)
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self)
self.DEBUG("EDPluginControlXdsBest.postProcess")
self.dataOutput = XSDataOutputXdsBurnStrategy()
self.dataOutput.status = XSDataStatus()
# check if a XDS.HKL file has been generated
expected = os.path.join(self._xds.getWorkingDirectory(),
'XDS_ASCII.HKL')
if os.path.exists(expected):
self.dataOutput.status.isSuccess = XSDataBoolean(True)
self.dataOutput.xds_hkl = XSDataString(expected)
else:
self.dataOutput.status.isSuccess = XSDataBoolean(False)
