def preProcess(self, _oedObject=None):
EDPluginSTACv2_0.preProcess(self)
EDVerbose.DEBUG("EDPluginSTACAlignmentv2_0.preProcess")
#bestfile.par
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "bestfile.par" ), self.m_xsDataInput.getBestFileContentPar().getValue())
#self.writeBestfilePar( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "bestfile.par" ), self.getDataInput()[0].getBestFileContentPar().getValue() )
self.writeBestfilePar(
os.path.join(self.getWorkingDirectory(), "bestfile.par"),
self.getDataInput("inputBest")[0].getBestFileContentPar().
getValue())
#self.writeAlignmentRequest() - for now use a predefined request
if (self.getDataInput("kappa_alignment_request") is not None):
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
"DNA_kappa_alignment_request"),
self.getDataInput("kappa_alignment_request")[0].marshal())
else:
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
"DNA_kappa_alignment_request"),
"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_alignment_request><desired_orientation><v1>a*</v1><v2>b*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>a*</v1><v2>c*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>b*</v1><v2>a*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>b*</v1><v2>c*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>c*</v1><v2>a*</v2><close>true</close><comment></comment></desired_orientation><desired_orientation><v1>c*</v1><v2>b*</v2><close>false</close><comment></comment></desired_orientation><comment>First test parameter passed</comment></kappa_alignment_request>"
)
#self.writeKappaSettings() - for now use a predefined datum (0;0;0)
#EDUtilsFile.writeFile( os.path.join( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
self.writeKappaSettings()
def preProcess( self, _oedObject=None ):
EDPluginSTACv2_0.preProcess( self )
self.DEBUG( "EDPluginSTACStrategyv2_0.preProcess" )
#bestfile.par
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "bestfile.par" ), self.m_oxsDataBestFileContentPar.getValue())
#self.writeBestfilePar( os.path.join( self.getWorkingDirectory(), "bestfile.par" ), self.m_oxsDataBestFileContentPar.getValue() )
self.writeBestfilePar( os.path.join( self.getWorkingDirectory(), "bestfile.par" ), self.getDataInput( "inputBest" )[0].getBestFileContentPar().getValue() )
self.writeStrategyRequest()
self.writeKappaSettings()
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
EDFactoryPluginStatic.loadModule( "XSDataSTACv2_0" )
from XSDataSTACv2_0 import kappa_alignment_request
self.setXSDataInputClass(kappa_alignment_request, "kappa_alignment_request")
def preProcess(self, _oedObject=None):
EDPluginSTACv2_0.preProcess(self)
self.DEBUG("EDPluginSTACAlignmentv2_0.preProcess")
#bestfile.par
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "bestfile.par" ), self.m_xsDataInput.getBestFileContentPar().getValue())
#self.writeBestfilePar( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "bestfile.par" ), self.getDataInput()[0].getBestFileContentPar().getValue() )
self.writeBestfilePar(os.path.join(self.getWorkingDirectory(), "bestfile.par"), self.getDataInput("inputBest")[0].getBestFileContentPar().getValue())
#self.writeAlignmentRequest() - for now use a predefined request
if (self.getDataInput( "kappa_alignment_request" ) is not None):
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "DNA_kappa_alignment_request"), self.getDataInput( "kappa_alignment_request" )[0].marshal() )
else:
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "DNA_kappa_alignment_request"), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_alignment_request><desired_orientation><v1>a*</v1><v2>b*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>a*</v1><v2>c*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>b*</v1><v2>a*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>b*</v1><v2>c*</v2><close>false</close><comment></comment></desired_orientation><desired_orientation><v1>c*</v1><v2>a*</v2><close>true</close><comment></comment></desired_orientation><desired_orientation><v1>c*</v1><v2>b*</v2><close>false</close><comment></comment></desired_orientation><comment>First test parameter passed</comment></kappa_alignment_request>")
#self.writeKappaSettings() - for now use a predefined datum (0;0;0)
#EDUtilsFile.writeFile( os.path.join( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
self.writeKappaSettings()
def __init__( self ):
"""
"""
EDPluginSTACv2_0.__init__( self )
EDFactoryPluginStatic.loadModule( "XSDataMXv1" )
EDFactoryPluginStatic.loadModule( "XSDataMXv2" )
EDFactoryPluginStatic.loadModule( "XSDataSTACv2_0" )
EDFactoryPluginStatic.loadModule( "XSDataBestv1_2" )
from XSDataMXv1 import XSDataIndexingResult
from XSDataMXv1 import XSDataInputStrategy
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass( kappa_strategy_request, "kappa_strategy_request" )
import XSDataMXv2
self.setXSDataInputClass( XSDataMXv2.XSDataCollection, "mxv2DataCollection" )
# not used: self.setXSDataInputClass( XSDataIndexingResult, "indexingResult" )
self.setXSDataInputClass( XSDataInputStrategy, "inputBest" )
