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):
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('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.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('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 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):
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 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('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):
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):
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
