def createDictFromConfig():
""" Read the configuration from scipion/config/scipionbox.conf.
A dictionary will be created where each key will be a section starting
by MICROSCOPE:, all variables that are in the GLOBAL section will be
inherited by default.
"""
# Read from users' config file.
confGlobalDict = OrderedDict()
confDict = OrderedDict()
cp = ConfigParser()
cp.optionxform = str # keep case (stackoverflow.com/questions/1611799)
confFile = pw.getConfigPath("scipionbox.conf")
print "Reading conf file: ", confFile
cp.read(confFile)
GLOBAL = "GLOBAL"
MICROSCOPE = "MICROSCOPE:"
if not GLOBAL in cp.sections():
raise Exception("Missing section %s in %s" % (GLOBAL, confFile))
else:
for opt in cp.options(GLOBAL):
confGlobalDict[opt] = cp.get(GLOBAL, opt)
for section in cp.sections():
if section != GLOBAL and section.startswith(MICROSCOPE):
sectionDict = OrderedDict(confGlobalDict)
for opt in cp.options(section):
sectionDict[opt] = cp.get(section, opt)
confDict[section.replace(MICROSCOPE, '')] = sectionDict
return confDict
def createDictFromConfig():
""" Read the configuration from scipion/config/scipionbox.conf.
A dictionary will be created where each key will be a section starting
by MICROSCOPE:, all variables that are in the GLOBAL section will be
inherited by default.
"""
# Read from users' config file.
confGlobalDict = OrderedDict()
confDict = OrderedDict()
cp = ConfigParser()
cp.optionxform = str # keep case (stackoverflow.com/questions/1611799)
confFile = pw.getConfigPath("scipionbox.conf")
print "Reading conf file: ", confFile
cp.read(confFile)
GLOBAL = "GLOBAL"
MICROSCOPE = "MICROSCOPE:"
if not GLOBAL in cp.sections():
raise Exception("Missing section %s in %s" % (GLOBAL, confFile))
else:
for opt in cp.options(GLOBAL):
confGlobalDict[opt] = cp.get(GLOBAL, opt)
for section in cp.sections():
if section != GLOBAL and section.startswith(MICROSCOPE):
sectionDict = OrderedDict(confGlobalDict)
for opt in cp.options(section):
sectionDict[opt] = cp.get(section, opt)
confDict[section.replace(MICROSCOPE, '')] = sectionDict
return confDict
def _getHTMLTemplatePath(self):
""" Returns the path of the customized template at
config/execution.summary.html or the standard scipion HTML template"""
# Try if there is a customized template
template = getConfigPath('execution.summary.html')
if not os.path.exists(template):
template = getTemplatePath('execution.summary.template.html')
else:
print("Customized HTML template found at %s." % template)
return template
def _openConfigFile(self, configFile, userOnly=False):
""" Open an Scipion configuration file, if the user have one defined,
also open that one with the defined text editor.
"""
if not userOnly:
_open_cmd(pw.getConfigPath(configFile))
userHostConf = os.path.join(pwutils.getHomePath(), '.config',
'scipion', configFile)
if os.path.exists(userHostConf):
_open_cmd(userHostConf)
def _getHTMLTemplatePath(self):
""" Returns the path of the customized template at
config/execution.summary.html or the standard scipion HTML template"""
# Try if there is a customized template
template = getConfigPath('execution.summary.html')
if not os.path.exists(template):
template = getTemplatePath('execution.summary.template.html')
else:
print("Customized HTML template found at %s." % template)
return template
def _openConfigFile(self, configFile, userOnly=False):
""" Open an Scipion configuration file, if the user have one defined,
also open that one with the defined text editor.
"""
if not userOnly:
_open_cmd(pw.getConfigPath(configFile))
userHostConf = os.path.join(pwutils.getHomePath(),
'.config', 'scipion', configFile)
if os.path.exists(userHostConf):
_open_cmd(userHostConf)
def onGeneral(self):
# Config -> General
_open_cmd(pw.getConfigPath('scipion.conf'))
def getWorkflow(workflow):
""" Return the full workflow path from
the Scipion folder + config/workflows/
"""
return pw.getConfigPath('workflows', workflow)
def onGeneral(self):
# Config -> General
_open_cmd(pw.getConfigPath('scipion.conf'))
def getWorkflow(workflow):
""" Return the full workflow path from
the Scipion folder + config/workflows/
"""
return pw.getConfigPath('workflows', workflow)