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 _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 __init__(self, protocol, ctfMonitor, sysMonitor, publishCmd=None,
**kwargs):
# The CTF protocol to monitor
self.protocol = protocol
self.provider = SummaryProvider(protocol)
self.ctfMonitor = ctfMonitor
self.sysMonitor = sysMonitor
# Get the html template to be used, by default use the one
# in scipion/config/templates
defaultTemplate = getTemplatePath('execution.summary.template.html')
self.template = kwargs.get('template', defaultTemplate)
self.publishCmd = publishCmd
self.refreshSecs = kwargs.get('refreshSecs', 60)
def __init__(self,
protocol,
ctfMonitor,
sysMonitor,
movieGainMonitor,
publishCmd=None,
**kwargs):
# The CTF protocol to monitor
self.protocol = protocol
self.ctfProtocol = protocol._getCtfProtocol()
self.alignProtocol = protocol._getAlignProtocol()
self.micThumbSymlinks = False
self.reportPath = protocol.reportPath
self.reportDir = protocol.reportDir
self.provider = SummaryProvider(protocol)
self.ctfMonitor = ctfMonitor
self.sysMonitor = sysMonitor
self.movieGainMonitor = movieGainMonitor
self.lastThumbIndex = 0
self.thumbsReady = 0
self.thumbPaths = {
MIC_THUMBS: [],
PSD_THUMBS: [],
SHIFT_THUMBS: [],
MIC_PATH: [],
SHIFT_PATH: [],
PSD_PATH: [],
MIC_ID: []
}
# Get the html template to be used, by default use the one
# in scipion/config/templates
defaultTemplate = getTemplatePath('execution.summary.template.html')
self.template = kwargs.get('template', defaultTemplate)
self.publishCmd = publishCmd
self.refreshSecs = kwargs.get('refreshSecs', 60)
def getTemplate(root):
# Check if there is any .json.template in the template folder
# get the template folder
templateFolder = pw.getTemplatePath()
# Get all ".json.template" there
templates = []
for file in glob.glob1(templateFolder, "*.json.template"):
templates.append(String(file))
if len(templates):
if len(templates) == 1:
chosen = templates[0].get()
else:
provider = ListTreeProviderString(templates)
dlg = dialog.ListDialog(root, "Workflow templates", provider,
"Select one of the templates.")
chosen = dlg.values[0].get()
chosen = os.path.join(templateFolder, chosen)
print("Template to use: %s" % chosen)
with open(chosen, 'r') as myfile:
template = myfile.read()
# Replace environment variables
template = template % os.environ
return template
else:
raise Exception("There isn't any *.json.template at %s" % templates)