def buildHan(uchHan):
Common.say('Creating Han Definition file for ' + uchHan)
hcf = Genome.HCF(Common.pathToURL(Common.makeHanPath(uchHan + Common.Constants.extHCF), Globals.urlHan))
aryGroups = [ _HAN_GROUP % (str(hcfG.bounds), hcfG.length, hcfG.ptCenter.x, hcfG.ptCenter.y,
' '.join([ str(i+1) for i in hcfG.containedStrokes])) for hcfG in hcf.aryGroups ]
aryStrokes = [ _HAN_STROKE % (str(hcfS.bounds),
hcfS.length,
'\n'.join([ _HAN_POINT % (ptd.x, ptd.y, ptd.distance) for ptd in hcfS.aryPointsForward]),
'\n'.join([ _HAN_POINT % (ptd.x, ptd.y, ptd.distance) for ptd in hcfS.aryPointsReverse]) ) for hcfS in hcf.aryStrokes ]
aryOverlaps = [ _HAN_OVERLAP % (hcfO.firstStroke, hcfO.secondStroke, hcfO.fRequired and 'true' or 'false') for hcfO in hcf.aryOverlaps ]
strHan = _HAN_DEFINITION % (str(uuid.uuid4()).upper(), hcf.unicode, datetime.datetime.utcnow().isoformat(), _NAME,
str(hcf.bounds), hcf.length, hcf.minimumStrokeLength,
'\n'.join(aryGroups),
'\n'.join(aryStrokes),
aryOverlaps and ('<overlaps>%s</overlaps>' % '\n'.join(aryOverlaps)) or '')
strPath = Common.resolvePath(os.path.join(Globals.strArchetypePath, Common.makeHanPath(hcf.unicode + Common.Constants.extHan)))
strDir = os.path.dirname(strPath)
if not os.path.exists(strDir):
try: os.makedirs(os.path.dirname(strPath))
except OSError, err: raise Common.BiologicError('Unable to create %s - %s' % (strDir, str(err)))
try:
fileHan = os.open(strPath, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileHan, strHan)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (strPath, str(err)))
os.close(fileHan)
Common.say('Han definition written to ' + strPath)
return
def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_GRIDARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.strLocalPath = Common.resolvePath(os.path.dirname(sys.argv[0]))
Globals.strXgridVolume = Common.readEnvironment('$STYLUS_XGRID_VOLUME')
Globals.strXgridNotify = Common.readEnvironment('$STYLUS_XGRID_EMAIL')
Globals.strXgridShell = Common.readEnvironment('$STYLUS_XGRID_SHELL')
Globals.strXgridController = Common.readEnvironment('$XGRID_CONTROLLER_HOSTNAME')
Globals.strXgridPassword = Common.readEnvironment('$XGRID_CONTROLLER_PASSWORD')
try:
opts, Globals.aryArgs = getopt.getopt(argv,
'erj:lg:p:xv:n:s:c:h',
[ 'exec', 'report', 'job=', 'launch', 'genomes=', 'plans=', 'xgrid', 'volume=', 'notify=', 'shell=', 'controller=', 'help' ])
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def main():
form = cgi.FieldStorage()
if not 'code' in form or not form['code']:
raise Common.BiologicError('Han unicode value is missing')
uchHan = form.getfirst('code').upper()
if 'hcf' in form:
pathHCF = Common.resolvePath('./../../Archetypes/' + Common.makeHanPath(uchHan + Common.Constants.extHCF))
try:
fileHCF = os.open(pathHCF, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileHCF, form['hcf'].value)
os.close(fileHCF)
except IOError, err:
raise Common.BiologicError('Unable to write %s - %s' % (pathHCF, str(err)))
inscribe.setGlobals([ '-d', './../../Archetypes/', '-u', './../../Archetypes/' ])
inscribe.buildHan(uchHan)
inscribe.setGlobals([ '-o', './../../Genes/', '-u', './../../Archetypes/' ])
aryGeneNames = inscribe.buildGenes(uchHan, [ 'default' ])
returnMsg('Successfully created Han definition and default gene (%s) for %s' % (aryGeneNames[0], uchHan))
def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_GRIDARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.strLocalPath = Common.resolvePath(os.path.dirname(sys.argv[0]))
Globals.strXgridVolume = Common.readEnvironment('$STYLUS_XGRID_VOLUME')
Globals.strXgridNotify = Common.readEnvironment('$STYLUS_XGRID_EMAIL')
Globals.strXgridShell = Common.readEnvironment('$STYLUS_XGRID_SHELL')
Globals.strXgridController = Common.readEnvironment(
'$XGRID_CONTROLLER_HOSTNAME')
Globals.strXgridPassword = Common.readEnvironment(
'$XGRID_CONTROLLER_PASSWORD')
try:
opts, Globals.aryArgs = getopt.getopt(argv, 'erj:lg:p:xv:n:s:c:h', [
'exec', 'report', 'job=', 'launch', 'genomes=', 'plans=', 'xgrid',
'volume=', 'notify=', 'shell=', 'controller=', 'help'
])
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
raise Usage('Xgrid does not support both exec and report -- run with exec first followed by report once completed')
if not Globals.strXgridVolume:
raise Usage('Xgrid requires the full path to the Stylus working directoryon an Xgrid client (e.g., /Stylus)')
if not Globals.strXgridShell:
raise Usage('Xgrid requires the full path to the shell within which to spawn Stylus on an Xgrid client')
if not Globals.strXgridController:
raise Usage('Xgrid requires the controller hostname')
if not Globals.fLaunchJobs:
Globals.fLaunchJobs = not Globals.strGenomes and not Globals.strPlans
else:
Globals.fLaunchJobs = True
if Globals.strGenomes and Globals.fLaunchJobs:
Globals.strGenomes = Common.resolvePath(Globals.strGenomes)
if Globals.fUseXgrid and not os.path.isabs(Globals.strGenomes):
Globals.strGenomes = os.path.join(Globals.strXgridVolume, Globals.strGenomes)
if Globals.strPlans and Globals.fLaunchJobs:
Globals.strPath = Common.resolvePath(Globals.strPlans)
if Globals.fUseXgrid and not os.path.isabs(Globals.strPlans):
Globals.strPlans = os.path.join(Globals.strXgridVolume, Globals.strPlans)
#------------------------------------------------------------------------------
# Function: spawnStylus
#
# Spawn one or more instances of a Stylus script
#------------------------------------------------------------------------------
def spawnStylus(fScript, dictEnv):
if (Globals.strGenomes or Globals.strPlans) and Globals.fLaunchJobs:
if option in ('-f', '--folders'):
Globals.aryFolders = value
if option in ('-r', '--removeage'):
nDays = int(value)
if nDays <= 0:
raise Usage('%s is an illegal value for removeage')
Globals.nRemoveAge = nDays
if option in ('-h', '--help'):
raise Usage('')
if not Globals.pathSrc:
raise Usage('Required source path was not specified')
Globals.pathSrc = os.path.abspath(Common.resolvePath(Globals.pathSrc))
if not os.path.exists(Globals.pathSrc) or not os.path.isdir(Globals.pathSrc):
raise Usage('Source path - %s - does not exist or is not a directory' % Globals.pathSrc)
if not Globals.pathDst:
raise Usage('Required destination path was not specified')
Globals.pathDst = os.path.abspath(Common.resolvePath(Globals.pathDst))
if not os.path.exists(Globals.pathDst) or not os.path.isdir(Globals.pathSrc):
raise Usage('Destination path - %s - does not exist or is not a directory' % Globals.pathDst)
if not Globals.aryFolders:
raise Usage('Required folders were not supplied')
Globals.aryFolders = Globals.aryFolders.split(':')
for folder in Globals.aryFolders:
pathFolder = os.path.abspath(os.path.join(Globals.pathSrc, folder))
if not os.path.exists(pathFolder) or not os.path.isdir(pathFolder):
def buildGenes(uchHan, aryGenes):
Common.say('Creating %d gene(s)' % len(aryGenes))
han = loadHan(uchHan)
strAuthor = Globals.strAuthor and (" author='%s'" % Globals.strAuthor) or ''
aryGeneNames = []
for specification in aryGenes:
Common.say('Creating gene from specification ' + specification)
gs = GeneSpecification(specification != Constants.strDefault and specification or '', han)
gsName = gs.toName(han.unicode) + Common.Constants.extGene
gsPoints = gs.getPoints()
Common.say('Gene to be named ' + gsName)
ptCurrent = Genome.Point(pt=gsPoints[0][1][0])
arySegments = []
# Convert each set of points into a list of vectors
for iSegment in xrange(len(gsPoints)):
fCoherent, aryPoints = gsPoints[iSegment]
# Build the segment starting from the current location
# - Ensure incoherent segments always begin at the current location
# (This causes moves to absorb the tracing error, effectively trading placement error for stroke fit error.)
if not fCoherent:
aryPoints[0].x = ptCurrent.x
aryPoints[0].y = ptCurrent.y
ptCurrent, aryVectors = buildSegment(ptCurrent, fCoherent, aryPoints)
if not fCoherent:
# If the segment contains too few vectors, pad it with an incoherent sequence
# - If there are no vectors, use No/So/Ea/We - binding code will ensure proper coherence at the endpoints
# - Otherwise, use the four points of the direction "compass" that are guaranteed incoherent with the last vector
if len(aryVectors) < 3:
iDirection = len(aryVectors) and Codons.Directions.add(Codons.Vectors.toDirection(aryVectors[-1]), 3) or Codons.Directions.North
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
iDirection = Codons.Directions.add(iDirection, 2)
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
# Inject vectors to force incoherency for incoherent segments
# - Essentially, add a vector pair to every two that forces incoherency
# - Walking the list must take into account injected vector pairs
else:
iVector = 0
while iVector < len(aryVectors):
if Codons.isCoherent([aryVectors[iVector-2], aryVectors[iVector-1], aryVectors[iVector+0]]):
idVector = aryVectors[iVector]
aryVectors.insert(iVector+0, Codons.Vectors.toOpposite(idVector))
aryVectors.insert(iVector+1, idVector)
iVector += 1
# Ensure the vectors "bind" without affecting the coherence of an adjoining segment
if iSegment:
fCoherencePrev, aryVectorsPrev = arySegments[-1]
if Codons.isCoherent([ aryVectorsPrev[-2], aryVectorsPrev[-1], aryVectors[0] ]) or Codons.isCoherent([ aryVectorsPrev[-1], aryVectors[0], aryVectors[1] ]):
if not fCoherencePrev:
aryVectorsPrev += [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
else:
aryVectors[:0] = [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
arySegments.append((fCoherent, aryVectors))
validateCoherence(arySegments)
aryCodons = [ Codons.Vectors.toVector(idVector).codon for fCoherent, aryVectors in arySegments for idVector in aryVectors ]
aryCodons[:0] = [ 'ATG' ]
aryCodons.append(Codons.Vectors.toVector(Codons.Vectors.create(Codons.Directions.Stop, Codons.Constants.iVectorShort)).codon)
aryStrokes = []
iStroke = 0
iBase = 4
for fCoherent, aryVectors in arySegments:
if fCoherent:
aryStrokes.append(_GENE_STROKE % (iBase, iBase+(len(aryVectors)*3-1), gs.mapStrokeToHan(iStroke)+1))
iStroke += 1
iBase += len(aryVectors) * 3
strGene = _GENE_DEFINITION % (str(uuid.uuid4()).upper(), strAuthor, datetime.datetime.utcnow().isoformat(), _NAME, str(gs),
''.join(aryCodons), len(aryCodons)*3,
gsPoints[0][1][0].x, gsPoints[0][1][0].y,
han.unicode,
'\n'.join(aryStrokes))
strPath = Common.resolvePath(os.path.join(Globals.strGenePath, Common.makeHanPath(gsName)))
strDir = os.path.dirname(strPath)
if not os.path.exists(strDir):
try: os.makedirs(os.path.dirname(strPath))
except OSError, err: raise Common.BiologicError('Unable to create %s - %s' % (strDir, str(err)))
try:
fileGene = os.open(strPath, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileGene, strGene)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (strPath, str(err)))
os.close(fileGene)
Common.say('\tWrote %s - %d codons, %d bases' % (strPath, len(aryCodons), len(aryCodons)*3))
aryGeneNames.append(gsName)
return aryGeneNames
Globals.strAuthor = value
if option in ('-q', '--quiet'):
Common.Globals.fQuiet = True
if option in ('-h', '--help'):
raise Usage('')
if Globals.fInteractive and not Globals.uchHan:
raise Usage('Required code was not specified')
if Globals.fBuildArchetype and not Globals.strArchetypePath:
raise Usage('Required archetype path was not specified')
if Globals.fBuildArchetype:
Globals.strArchetypePath = Common.resolvePath(Globals.strArchetypePath)
if not os.path.exists(Globals.strArchetypePath):
try: os.makedirs(Globals.strArchetypePath)
except OSError: raise Usage('Unable to create ' + Globals.strArchetypePath)
if len(Globals.aryGenes) > 0 and not Globals.strGenePath:
raise Usage('Required gene output path was not specified')
if len(Globals.aryGenes) > 0:
Globals.strGenePath = Common.resolvePath(Globals.strGenePath)
if not os.path.exists(Globals.strGenePath):
try: os.makedirs(Globals.strGenePath)
except OSError: raise Usage('Unable to create ' + Globals.strGenePath)
if not Globals.urlHan:
raise Usage('Required Han URL was not specified')
)
if not Globals.strXgridShell:
raise Usage(
'Xgrid requires the full path to the shell within which to spawn Stylus on an Xgrid client'
)
if not Globals.strXgridController:
raise Usage('Xgrid requires the controller hostname')
if not Globals.fLaunchJobs:
Globals.fLaunchJobs = not Globals.strGenomes and not Globals.strPlans
else:
Globals.fLaunchJobs = True
if Globals.strGenomes and Globals.fLaunchJobs:
Globals.strGenomes = Common.resolvePath(Globals.strGenomes)
if Globals.fUseXgrid and not os.path.isabs(Globals.strGenomes):
Globals.strGenomes = os.path.join(Globals.strXgridVolume,
Globals.strGenomes)
if Globals.strPlans and Globals.fLaunchJobs:
Globals.strPath = Common.resolvePath(Globals.strPlans)
if Globals.fUseXgrid and not os.path.isabs(Globals.strPlans):
Globals.strPlans = os.path.join(Globals.strXgridVolume,
Globals.strPlans)
#------------------------------------------------------------------------------
# Function: spawnStylus
#
# Spawn one or more instances of a Stylus script
% (Globals.cmd == Constants.cmdCreate and 'create' or 'validate'))
if Globals.cmd == Constants.cmdValidate and not Globals.strGenome and not Globals.strCodonTable:
raise Usage(
'validate takes either the genome or codon table as its source')
if Globals.cmd == Constants.cmdTranslate and (not Globals.strGenome or
not Globals.strCodonTable):
raise Usage(
'translate requires both the genome to translate and the codon table to use'
)
if Globals.cmd <> Constants.cmdValidate:
Globals.uuid = str(uuid.uuid4()).upper()
if Globals.strGenome:
Globals.urlGenome = Common.pathToURL(
Common.makeHanPath(Common.resolvePath(Globals.strGenome)),
Globals.urlGenomeBase)
if Globals.strCodonTable:
Globals.urlCodonTable = Common.pathToURL(Globals.strCodonTable,
Globals.urlCodonTableBase)
if Globals.cmd <> Constants.cmdValidate and Globals.pathOutput:
Globals.pathOutput = Common.resolvePath(Globals.pathOutput)
Common.ensurePath(os.path.dirname(Globals.pathOutput))
Globals.pathOutput = os.path.join(
Globals.pathOutput,
('%s%s' %
(Globals.uuid,
(Globals.cmd == Constants.cmdTranslate and
Common.Constants.extGene or Common.Constants.extCodonTable))))
return
if option in ('-f', '--folders'):
Globals.aryFolders = value
if option in ('-r', '--removeage'):
nDays = int(value)
if nDays <= 0:
raise Usage('%s is an illegal value for removeage')
Globals.nRemoveAge = nDays
if option in ('-h', '--help'):
raise Usage('')
if not Globals.pathSrc:
raise Usage('Required source path was not specified')
Globals.pathSrc = os.path.abspath(Common.resolvePath(Globals.pathSrc))
if not os.path.exists(Globals.pathSrc) or not os.path.isdir(
Globals.pathSrc):
raise Usage('Source path - %s - does not exist or is not a directory' %
Globals.pathSrc)
if not Globals.pathDst:
raise Usage('Required destination path was not specified')
Globals.pathDst = os.path.abspath(Common.resolvePath(Globals.pathDst))
if not os.path.exists(Globals.pathDst) or not os.path.isdir(
Globals.pathSrc):
raise Usage(
'Destination path - %s - does not exist or is not a directory' %
Globals.pathDst)
if not Globals.aryFolders:
Globals.urlCodonTableBase = Common.pathToURL(Globals.urlCodonTableBase, Common.Constants.schemeFile)
if Globals.urlCodonTableBase[len(Globals.urlCodonTableBase)-1] <> Common.Constants.urlSeparator:
Globals.urlCodonTableBase += Common.Constants.urlSeparator
if Globals.cmd <> Constants.cmdTranslate and Globals.strGenome and Globals.strCodonTable:
raise Usage('%s takes either the genome or codon table as its source - not both' % (Globals.cmd == Constants.cmdCreate and 'create' or 'validate'))
if Globals.cmd == Constants.cmdValidate and not Globals.strGenome and not Globals.strCodonTable:
raise Usage('validate takes either the genome or codon table as its source')
if Globals.cmd == Constants.cmdTranslate and (not Globals.strGenome or not Globals.strCodonTable):
raise Usage('translate requires both the genome to translate and the codon table to use')
if Globals.cmd <> Constants.cmdValidate:
Globals.uuid = str(uuid.uuid4()).upper()
if Globals.strGenome:
Globals.urlGenome = Common.pathToURL(Common.makeHanPath(Common.resolvePath(Globals.strGenome)), Globals.urlGenomeBase)
if Globals.strCodonTable:
Globals.urlCodonTable = Common.pathToURL(Globals.strCodonTable, Globals.urlCodonTableBase)
if Globals.cmd <> Constants.cmdValidate and Globals.pathOutput:
Globals.pathOutput = Common.resolvePath(Globals.pathOutput)
Common.ensurePath(os.path.dirname(Globals.pathOutput))
Globals.pathOutput = os.path.join(Globals.pathOutput, ('%s%s' % (Globals.uuid, (Globals.cmd == Constants.cmdTranslate and Common.Constants.extGene or Common.Constants.extCodonTable))))
return
#------------------------------------------------------------------------------
# Function: createTable
#
#------------------------------------------------------------------------------
def createTable():
aryEntries = [ _CODONTABLE_ENTRY % (codon, vector, (_CODONTABLE_ISSTANDARD % (Globals.codonTable.hasStandardMapping(codon) and 'true' or 'false'))) for codon, vector in Globals.codonTable.entries() ]
