def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_EXECARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.strAuthor = Common.readEnvironment('$STYLUS_AUTHOR')
try:
opts, remaining = getopt.getopt(argv, Common.Constants.strShortArgs, Common.Constants.aryLongArgs)
if len(remaining) > 0:
remaining[0].strip()
if len(remaining) > 1 or remaining[0]:
raise Usage(' '.join(remaining) + ' contains unexpected arguments')
except getopt.GetoptError, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def main(argv=None):
try:
getArguments()
if Globals.aryXgridJob:
queryXgrid()
if Globals.fRunExec:
os.environ['STYLUS_EXECARGS'] = Common.readEnvironment('$STYLUS_EXECARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_EXEC, os.environ)
if Globals.fRunReport:
os.environ['STYLUS_RPTARGS'] = Common.readEnvironment('$STYLUS_RPTARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_REPORT, os.environ)
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_BACKUPARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.pathSrc = Common.readEnvironment('$STYLUS_BACKUPSRC') or Constants.pathDefaultSrc
Globals.pathDst = Common.readEnvironment('$STYLUS_BACKUPDST') or Constants.pathDefaultDst
Globals.aryFolders = Common.readEnvironment('$STYLUS_BACKUPFOLDERS') or Constants.strDefaultFolders
try:
opts, Globals.aryArgs = getopt.getopt(argv,
's:d:f:r:h',
[ 'src=', 'dst=', 'folders=', 'removeage=', 'help' ])
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_EXECARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.strAuthor = Common.readEnvironment('$STYLUS_AUTHOR')
try:
opts, remaining = getopt.getopt(argv, Common.Constants.strShortArgs,
Common.Constants.aryLongArgs)
if len(remaining) > 0:
remaining[0].strip()
if len(remaining) > 1 or remaining[0]:
raise Usage(' '.join(remaining) +
' contains unexpected arguments')
except getopt.GetoptError, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def getArguments():
argv = sys.argv[1:]
Globals.strAuthor = Common.readEnvironment('$STYLUS_AUTHOR')
Globals.urlGenomeBase = Common.readEnvironment('$STYLUS_GENOMEURL')
if not Globals.urlGenomeBase:
Globals.urlGenomeBase = './'
Globals.urlCodonTableBase = Common.readEnvironment('$STYLUS_CODONTABLEURL')
if not Globals.urlCodonTableBase:
Globals.urlCodonTableBase = './'
try:
opts, remaining = getopt.getopt(argv, Constants.strShortArgs, Constants.aryLongArgs)
if len(remaining) > 0:
remaining[0].strip()
if len(remaining) > 1 or remaining[0]:
raise Usage(' '.join(remaining) + ' contains unexpected arguments')
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def setGlobals(aryArgs=[], strArgs=''):
envArgs = Common.readEnvironment('$STYLUS_INSCRIBEARGS')
argv = envArgs and envArgs.split() or []
argv += aryArgs
argv += strArgs.split()
Globals.strGenePath = Common.readEnvironment('$STYLUS_INSCRIBEOUT')
Globals.urlHan = Common.readEnvironment('$STYLUS_HANURL')
Globals.strAuthor = Common.readEnvironment('$STYLUS_AUTHOR')
try:
opts, remaining = getopt.getopt(argv,
'c:d:g:o:u:a:qh',
[ 'code=', 'definition', 'gene=', 'output=', 'urls=', 'author=', 'quiet', 'help' ])
if len(remaining) > 0:
remaining[0].strip()
if len(remaining) > 1 or remaining[0]:
raise Usage(' '.join(remaining) + ' contains unexpected arguments')
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def main(argv=None):
try:
getArguments()
if Globals.aryXgridJob:
queryXgrid()
if Globals.fRunExec:
os.environ['STYLUS_EXECARGS'] = Common.readEnvironment(
'$STYLUS_EXECARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_EXEC, os.environ)
if Globals.fRunReport:
os.environ['STYLUS_RPTARGS'] = Common.readEnvironment(
'$STYLUS_RPTARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_REPORT, os.environ)
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def getArguments():
argv = sys.argv[1:]
Globals.strAuthor = Common.readEnvironment('$STYLUS_AUTHOR')
Globals.urlGenomeBase = Common.readEnvironment('$STYLUS_GENOMEURL')
if not Globals.urlGenomeBase:
Globals.urlGenomeBase = './'
Globals.urlCodonTableBase = Common.readEnvironment('$STYLUS_CODONTABLEURL')
if not Globals.urlCodonTableBase:
Globals.urlCodonTableBase = './'
try:
opts, remaining = getopt.getopt(argv, Constants.strShortArgs,
Constants.aryLongArgs)
if len(remaining) > 0:
remaining[0].strip()
if len(remaining) > 1 or remaining[0]:
raise Usage(' '.join(remaining) +
' contains unexpected arguments')
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
def getArguments():
# Start with command-line arguments and append those passed via the environment
# (The command-line overrides the environment)
args = Common.readEnvironment('$STYLUS_BACKUPARGS')
argv = args and args.split() or []
argv += sys.argv[1:]
Globals.pathSrc = Common.readEnvironment(
'$STYLUS_BACKUPSRC') or Constants.pathDefaultSrc
Globals.pathDst = Common.readEnvironment(
'$STYLUS_BACKUPDST') or Constants.pathDefaultDst
Globals.aryFolders = Common.readEnvironment(
'$STYLUS_BACKUPFOLDERS') or Constants.strDefaultFolders
try:
opts, Globals.aryArgs = getopt.getopt(
argv, 's:d:f:r:h',
['src=', 'dst=', 'folders=', 'removeage=', 'help'])
except getopt.error, err:
raise Usage(' '.join(argv[1:]) + ' contains unknown arguments')
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 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')
