def base(request, context):
# Keep existing service name previously set by any of the webtools
serviceName = getVarFromRequest(request, SERVICE_NAME)
if serviceName is None and SERVICE_NAME in context:
serviceName = context[SERVICE_NAME]
context_base = {
# ICON
'favicon': getResourceIcon('favicon'),
'logo_scipion': getResourceIcon('logo_scipion'),
'logo_scipion_transparent':
getResourceIcon('logo_scipion_transparent'),
# CSS
'general_css': getResourceCss('general'),
'messi_css': getResourceCss('messi'),
'font_awesome': getResourceCss('font_awesome'),
# JS
'jquery': getResourceJs('jquery'),
'messi_js': getResourceJs('messi'),
# JS
'utils': getResourceJs('utils'),
"projectName": getVarFromRequest(request, PROJECT_NAME),
SERVICE_NAME: serviceName
}
context = VARS_base(request, context)
context.update(context_base)
return context
def contentContext(request, project):
from pyworkflow.gui.tree import ProjectRunsTreeProvider
projectName = project.getShortName()
print "ProjectName: ", projectName
project_settings = project.getSettings()
request.session['projectPath'] = project.getPath()
request.session['projectName'] = projectName
provider = ProjectRunsTreeProvider(project)
runs = formatProvider(provider, "runs")
request.session['runs'] = runs
# Get the selected runs stored in BD
selectedRuns = project_settings.runSelection
# Get the run mode view (0:list / 1:graph / 2:small graph) stored in BD
runsView = project_settings.runsView.get()
# load the protocol tree current active
htmlTree = loadProtTree(project)
# get the choices to load protocol trees
choices = project.getProtocolViews()
# get the choice current
choiceSelected = choices.index(project.getCurrentProtocolView().text.get())
# show the project name in the header.html
projectNameHeader = 'Project ' + str(projectName)
context = {
'projectName': projectName,
'view': 'protocols',
'editTool': getResourceIcon('edit_toolbar'),
'copyTool': getResourceIcon('copy_toolbar'),
'deleteTool': getResourceIcon('delete_toolbar'),
'browseTool': getResourceIcon('browse_toolbar'),
'stopTool': getResourceIcon('stop_toolbar'),
'analyzeTool': getResourceIcon('analyze_toolbar'),
'treeTool': getResourceIcon('tree_toolbar'),
'listTool': getResourceIcon('list_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css': getResourceCss('project_content'),
'protTreeHtml': htmlTree,
'choices': choices,
'choiceSelected': choiceSelected,
'runs': runs,
'columns': provider.getColumns(),
'projectNameHeader': projectNameHeader,
'runsView': runsView,
'selectedRuns': selectedRuns
}
context = base_flex(request, context)
return context
def contentContext(request, project):
from pyworkflow.gui.tree import ProjectRunsTreeProvider
projectName = project.getShortName()
print "ProjectName: ", projectName
project_settings = project.getSettings()
request.session['projectPath'] = project.getPath()
request.session['projectName'] = projectName
provider = ProjectRunsTreeProvider(project)
runs = formatProvider(provider, "runs")
request.session['runs'] = runs
# Get the selected runs stored in BD
selectedRuns = project_settings.runSelection
# Get the run mode view (0:list / 1:graph / 2:small graph) stored in BD
runsView = project_settings.runsView.get()
# load the protocol tree current active
htmlTree = loadProtTree(project)
# get the choices to load protocol trees
choices = project.getProtocolViews()
# get the choice current
choiceSelected = choices.index(project.getCurrentProtocolView().text.get())
# show the project name in the header.html
projectNameHeader = 'Project '+ str(projectName)
context = {'projectName': projectName,
'view':'protocols',
'editTool': getResourceIcon('edit_toolbar'),
'copyTool': getResourceIcon('copy_toolbar'),
'deleteTool': getResourceIcon('delete_toolbar'),
'browseTool': getResourceIcon('browse_toolbar'),
'stopTool': getResourceIcon('stop_toolbar'),
'analyzeTool': getResourceIcon('analyze_toolbar'),
'treeTool': getResourceIcon('tree_toolbar'),
'listTool': getResourceIcon('list_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css':getResourceCss('project_content'),
'protTreeHtml': htmlTree,
'choices':choices,
'choiceSelected': choiceSelected,
'runs': runs,
'columns': provider.getColumns(),
'projectNameHeader': projectNameHeader,
'runsView': runsView,
'selectedRuns': selectedRuns
}
context = base_flex(request, context)
return context
def contentContext(request, project, serviceName=None):
from pyworkflow.gui.tree import ProjectRunsTreeProvider
projectName = project.getShortName()
if serviceName is None:
serviceName = getVarFromRequest(request, SERVICE_NAME)
project_settings = project.getSettings()
request.session[CTX_PROJECT_PATH] = project.getPath()
request.session[PROJECT_NAME] = projectName
provider = ProjectRunsTreeProvider(project)
runs = formatProvider(provider, "runs")
request.session['runs'] = runs
# Get the selected runs stored in BD
selectedRuns = project_settings.runSelection
# Get the run mode view (0:list / 1:graph / 2:small graph) stored in BD
runsView = project_settings.runsView.get()
# load the protocol tree current active
htmlTree = loadProtTree(project, serviceName)
# get the choices to load protocol trees
choices = project.getProtocolViews()
# get the choice current
choiceSelected = choices.index(project.getCurrentProtocolView().text.get())
context = {
CTX_PROJECT_NAME: projectName,
'view': 'protocols',
'editTool': getResourceIcon('edit_toolbar'),
'copyTool': getResourceIcon('copy_toolbar'),
'deleteTool': getResourceIcon('delete_toolbar'),
'browseTool': getResourceIcon('browse_toolbar'),
'stopTool': getResourceIcon('stop_toolbar'),
'analyzeTool': getResourceIcon('analyze_toolbar'),
'treeTool': getResourceIcon('tree_toolbar'),
'listTool': getResourceIcon('list_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css': getResourceCss('project_content'),
'protTreeHtml': htmlTree,
'choices': choices,
'choiceSelected': choiceSelected,
'runs': runs,
'columns': provider.getColumns(),
'runsView': runsView,
'selectedRuns': selectedRuns,
SERVICE_NAME: serviceName
}
context = base_flex(request, context)
return context
def base(request, context):
context_base = {
#ICON
'favicon': getResourceIcon('favicon'),
'logo_scipion': getResourceIcon('logo_scipion'),
'logo_scipion_transparent' : getResourceIcon('logo_scipion_transparent'),
#CSS
'general_css': getResourceCss('general'),
'messi_css': getResourceCss('messi'),
'font_awesome': getResourceCss('font_awesome'),
#JS
'jquery': getResourceJs('jquery'),
'messi_js': getResourceJs('messi'),
#JS
'utils': getResourceJs('utils'),
}
context = VARS_base(request, context)
context.update(context_base)
return context
def getExtIconPath(ext):
txt = {'txt', 'log', 'out', 'err', 'stdout', 'stderr', 'emx'}
img = {'png', 'gif', 'jpg', 'jpeg'}
py = {'py', 'pyc'}
java = {'java'}
md = {'xmd', 'star', 'pos'}
sqlite = {'sqlite', 'db'}
particle = {
'xmp', 'tif', 'tiff', 'spi', 'mrc', 'map', 'raw', 'inf', 'dm3', '.em',
'pif', 'psd', 'spe', 'ser', 'img', 'hed'
}
vol = {'vol'}
stk = {'stk', 'mrcs', 'st', 'pif'}
if ext == 'folder':
res = getResourceIcon('folder')
# elif ext == 'unknown':
# res = getResourceIcon('file_normal')
else:
if ext in txt:
res = getResourceIcon('file_text')
elif ext in img or ext in particle:
res = getResourceIcon('file_image')
elif ext in py:
res = getResourceIcon('file_python')
elif ext in java:
res = getResourceIcon('file_java')
elif ext in md:
res = getResourceIcon('file_md')
elif ext in sqlite:
res = getResourceIcon('file_sqlite')
elif ext in vol:
res = getResourceIcon('file_vol')
elif ext in stk:
res = getResourceIcon('file_stack')
else:
res = getResourceIcon('file_normal')
return res
def getExtIconPath(ext):
txt = {'txt', 'log', 'out', 'err', 'stdout', 'stderr', 'emx'}
img = {'png', 'gif', 'jpg', 'jpeg'}
py = {'py', 'pyc'}
java = {'java'}
md = {'xmd', 'star', 'pos'}
sqlite = {'sqlite', 'db'}
particle = {'xmp', 'tif', 'tiff', 'spi', 'mrc', 'map', 'raw',
'inf', 'dm3', '.em', 'pif', 'psd', 'spe',
'ser', 'img', 'hed'}
vol = {'vol'}
stk = {'stk', 'mrcs', 'st', 'pif'}
if ext == 'folder':
res = getResourceIcon('folder')
# elif ext == 'unknown':
# res = getResourceIcon('file_normal')
else:
if ext in txt:
res = getResourceIcon('file_text')
elif ext in img or ext in particle:
res = getResourceIcon('file_image')
elif ext in py:
res = getResourceIcon('file_python')
elif ext in java:
res = getResourceIcon('file_java')
elif ext in md:
res = getResourceIcon('file_md')
elif ext in sqlite:
res = getResourceIcon('file_sqlite')
elif ext in vol:
res = getResourceIcon('file_vol')
elif ext in stk:
res = getResourceIcon('file_stack')
else:
res = getResourceIcon('file_normal')
return res
def base(request, context):
context_base = {
#ICON
'favicon': getResourceIcon('favicon'),
'logo_scipion': getResourceIcon('logo_scipion'),
'logo_scipion_transparent':
getResourceIcon('logo_scipion_transparent'),
#CSS
'general_css': getResourceCss('general'),
'messi_css': getResourceCss('messi'),
'font_awesome': getResourceCss('font_awesome'),
#JS
'jquery': getResourceJs('jquery'),
'messi_js': getResourceJs('messi'),
#JS
'utils': getResourceJs('utils'),
}
context = VARS_base(request, context)
context.update(context_base)
return context
def base_wiz(request, context):
context_base = {'general_style': getResourceCss('general'),
'wizard_style': getResourceCss('wizard'),
'jquery_ui_style': getResourceCss('jquery_ui'),
'font_awesome': getResourceCss('font_awesome'),
'jquery': getResourceJs('jquery'),
'jquery_ui': getResourceJs('jquery_ui'),
'jquery_ui_touch': getResourceJs('jquery_ui_touch'),
'wizard_utils': getResourceJs('wizard_utils'),
'raphael':getResourceJs('raphael'),
'projectName': request.session['projectName'],
'loading' : getResourceIcon('loading'),
}
context = VARS_base(request, context)
context.update(context_base)
return context
def upload(request, form=None):
# Load documents for the list page
mode = request.GET.get('mode', None)
path = os.path.join(request.session['projectPath'],'Uploads')
split_path = path.split("/ScipionUserData/")
relative_path = "ScipionUserData/" + split_path[1]
context = {'relative_path': relative_path,
'form': DocumentForm(),
'logo_scipion_small': getResourceIcon('logo_scipion_small'),
"upload_utils": getResourceJs('upload_utils'),
"mode": mode,
}
context = base_form(request, context)
# Render list page with the documents and the form
return render_to_response('upload/upload.html', context,
context_instance=RequestContext(request))
def base_wiz(request, context):
context_base = {
'general_style': getResourceCss('general'),
'wizard_style': getResourceCss('wizard'),
'jquery_ui_style': getResourceCss('jquery_ui'),
'font_awesome': getResourceCss('font_awesome'),
'jquery': getResourceJs('jquery'),
'jquery_ui': getResourceJs('jquery_ui'),
'jquery_ui_touch': getResourceJs('jquery_ui_touch'),
'wizard_utils': getResourceJs('wizard_utils'),
'raphael': getResourceJs('raphael'),
'projectName': request.session['projectName'],
'loading': getResourceIcon('loading'),
}
context = VARS_base(request, context)
context.update(context_base)
return context
def base_wiz(request, context):
context_base = {
'general_style': getResourceCss('general'),
'wizard_style': getResourceCss('wizard'),
'jquery_ui_style': getResourceCss('jquery_ui'),
'font_awesome': getResourceCss('font_awesome'),
'jquery': getResourceJs('jquery'),
'jquery_ui': getResourceJs('jquery_ui'),
'jquery_ui_touch': getResourceJs('jquery_ui_touch'),
'wizard_utils': getResourceJs('wizard_utils'),
'raphael': getResourceJs('raphael'),
'utils': getResourceJs('utils'),
CTX_PROJECT_NAME: getVarFromRequest(request, PROJECT_NAME),
SERVICE_NAME: getVarFromRequest(request, SERVICE_NAME),
'loading': getResourceIcon('loading'),
}
context = VARS_base(request, context)
context.update(context_base)
return context
def contextForm(request):
from views_base import base_form
from django.core.context_processors import csrf
from views_util import getResourceCss, getResourceIcon, getResourceJs, getResourceLogo
from pyworkflow.protocol.params import Group, Line
project, protocol = loadProtocolProject(request, requestType='GET')
action = request.GET.get('action', None)
paramProt = request.GET.get('paramProt', None)
protRunIdViewer = request.GET.get('protRunIdViewer', None)
# Patch : to fix the relion dynamic way to generate the viewer form
# For this is necessary to call setProtocol method
if protRunIdViewer is not None:
protocol_parent = project.getProtocol(int(protRunIdViewer))
protocol.setProtocol(protocol_parent)
hosts = project.getHostNames()
print "Host in the project: ", hosts
visualize = 0
viewerDict = None
if action == 'visualize':
visualize = 1
viewerDict = protocol._getVisualizeDict()
elif action == 'protSimple':
visualize = 2
elif action == 'copy':
protocol = project.copyProtocol(protocol)
package = protocol.getClassPackage()
logoPath = ''
path = getattr(package, '_logo', '')
if path != '':
logoPath = getResourceLogo(path)
wizards = findWizardsWeb(protocol)
protocol.htmlCitations = parseText(protocol.citations())
protocol.htmlDoc = parseText(protocol.getDoc())
for section in protocol._definition.iterSections():
for paramName, param in section.iterParams():
protVar = getattr(protocol, paramName, None)
if protVar is None:
# raise Exception("_fillSection: param '%s' not found in protocol" % paramName)
# GROUP PARAM
if isinstance(param, Group):
for paramGroupName, paramGroup in param.iterParams():
protVar = getattr(protocol, paramGroupName, None)
# LINE PARAM
if isinstance(paramGroup, Line):
for paramLineName, paramLine in paramGroup.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in paramGroup.iterParams():
wizParamName = name
if wizParamName in wizards:
paramGroup.hasWizard = True
paramGroup.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramGroupName in viewerDict:
paramGroup.hasViewer = True
if not paramGroup.help.empty():
paramGroup.htmlHelp = parseText(paramGroup.help.get())
paramGroup.htmlCond = paramGroup.condition.get()
paramGroup.htmlDepend = ','.join(paramGroup._dependants)
paramGroup.htmlCondParams = ','.join(paramGroup._conditionParams)
elif protVar is None:
pass
else:
paramGroup = PreprocessParamForm(request, paramGroup, paramGroupName, wizards, viewerDict, visualize, protVar)
param.htmlCond = param.condition.get()
param.htmlDepend = ','.join(param._dependants)
param.htmlCondParams = ','.join(param._conditionParams)
# LINE PARAM
if isinstance(param, Line):
for paramLineName, paramLine in param.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in param.iterParams():
wizParamName = name
if wizParamName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
param.htmlCond = param.condition.get()
param.htmlDepend = ','.join(param._dependants)
param.htmlCondParams = ','.join(param._conditionParams)
else:
# OTHER PARAM
param = PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar)
context = {SERVICE_NAME: getVarFromRequest(request, SERVICE_NAME),
CTX_PROJECT_NAME: project.getShortName(),
'protocol': protocol,
'package_logo': logoPath,
'protRunIdViewer': protRunIdViewer,
'definition': protocol._definition,
'visualize': visualize,
'paramProt': paramProt,
'favicon': getResourceIcon('favicon'),
'comment': getResourceIcon('edit_toolbar'),
'jquery_ui_css': getResourceCss('jquery_ui'),
'wizard': getResourceIcon('wizard'),
'protocol_form_utils': getResourceJs('protocol_form_utils'),
'hosts': hosts,
'comment': parseText(protocol.getObjComment()),
'showHost': True,
'showParallel': True
}
# Update the context dictionary with the special params
for paramName in SPECIAL_PARAMS:
context[paramName] = protocol.getAttributeValue(paramName, '')
# Cross Site Request Forgery protection is need it
context.update(csrf(request))
context = base_form(request, context)
return context
def contextForm(request):
from views_base import base_form
from django.core.context_processors import csrf
from views_util import getResourceCss, getResourceIcon, getResourceJs, getResourceLogo
from pyworkflow.protocol.params import Group, Line
project, protocol = loadProtocolProject(request, requestType="GET")
action = request.GET.get("action", None)
paramProt = request.GET.get("paramProt", None)
protRunIdViewer = request.GET.get("protRunIdViewer", None)
# Patch : to fix the relion dynamic way to generate the viewer form
# For this is necessary to call setProtocol method
if protRunIdViewer is not None:
protocol_parent = project.getProtocol(int(protRunIdViewer))
protocol.setProtocol(protocol_parent)
hosts = project.getHostNames()
print "Host in the project: ", hosts
visualize = 0
viewerDict = None
if action == "visualize":
visualize = 1
viewerDict = protocol._getVisualizeDict()
elif action == "protSimple":
visualize = 2
elif action == "copy":
protocol = project.copyProtocol(protocol)
package = protocol.getClassPackage()
logoPath = ""
path = getattr(package, "_logo", "")
if path != "":
logoPath = getResourceLogo(path)
wizards = findWizardsWeb(protocol)
protocol.htmlCitations = parseText(protocol.citations())
protocol.htmlDoc = parseText(protocol.getDoc())
for section in protocol._definition.iterSections():
for paramName, param in section.iterParams():
protVar = getattr(protocol, paramName, None)
if protVar is None:
# raise Exception("_fillSection: param '%s' not found in protocol" % paramName)
# GROUP PARAM
if isinstance(param, Group):
for paramGroupName, paramGroup in param.iterParams():
protVar = getattr(protocol, paramGroupName, None)
# LINE PARAM
if isinstance(paramGroup, Line):
for paramLineName, paramLine in paramGroup.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(
request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar
)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in paramGroup.iterParams():
wizParamName = name
if wizParamName in wizards:
paramGroup.hasWizard = True
paramGroup.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramGroupName in viewerDict:
paramGroup.hasViewer = True
if not paramGroup.help.empty():
paramGroup.htmlHelp = parseText(paramGroup.help.get())
paramGroup.htmlCond = paramGroup.condition.get()
paramGroup.htmlDepend = ",".join(paramGroup._dependants)
paramGroup.htmlCondParams = ",".join(paramGroup._conditionParams)
elif protVar is None:
pass
else:
paramGroup = PreprocessParamForm(
request, paramGroup, paramGroupName, wizards, viewerDict, visualize, protVar
)
param.htmlCond = param.condition.get()
param.htmlDepend = ",".join(param._dependants)
param.htmlCondParams = ",".join(param._conditionParams)
# LINE PARAM
if isinstance(param, Line):
for paramLineName, paramLine in param.iterParams():
protVar = getattr(protocol, paramLineName, None)
if protVar is None:
pass
else:
paramLine = PreprocessParamForm(
request, paramLine, paramLineName, wizards, viewerDict, visualize, protVar
)
# PATCH: This is applied to all the params in the line, maybe just need for the first one.
for name, _ in param.iterParams():
wizParamName = name
if wizParamName in wizards:
param.hasWizard = True
param.wizardClassName = wizards[wizParamName].__name__
if visualize == 1:
if paramName in viewerDict:
param.hasViewer = True
if not param.help.empty():
param.htmlHelp = parseText(param.help.get())
param.htmlCond = param.condition.get()
param.htmlDepend = ",".join(param._dependants)
param.htmlCondParams = ",".join(param._conditionParams)
else:
# OTHER PARAM
param = PreprocessParamForm(request, param, paramName, wizards, viewerDict, visualize, protVar)
context = {
"projectName": project.getName(),
"package_logo": logoPath,
"protocol": protocol,
"protRunIdViewer": protRunIdViewer,
"definition": protocol._definition,
"visualize": visualize,
"paramProt": paramProt,
"favicon": getResourceIcon("favicon"),
"comment": getResourceIcon("edit_toolbar"),
"jquery_ui_css": getResourceCss("jquery_ui"),
"wizard": getResourceIcon("wizard"),
"protocol_form_utils": getResourceJs("protocol_form_utils"),
"hosts": hosts,
"comment": parseText(protocol.getObjComment()),
"showHost": True,
"showParallel": True,
}
# Update the context dictionary with the special params
for paramName in SPECIAL_PARAMS:
context[paramName] = protocol.getAttributeValue(paramName, "")
# Cross Site Request Forgery protection is need it
context.update(csrf(request))
context = base_form(request, context)
return context
