def get_tool_link(self, exposure_object):
# TODO figure out how to do user-side customization on the type
# of files that can be added. Although this might better be
# done on the comparison page as that is the centralized place
# for all forms of comparison (i.e. CellML or SBML, etc).
if IExposureFile.providedBy(exposure_object):
return exposure_object.absolute_url() + '/bives_pick_file'
def getMenuItems(self, context, request):
# Have to set the context to the root.
if (IExposureFile.providedBy(context) or
IExposureFolder.providedBy(context)):
helper = zope.component.queryAdapter(
context, IExposureSourceAdapter)
exposure, workspace, path = helper.source()
context = exposure
return WorkflowMenu.getMenuItems(self, context, request)
def pmr1_citation_authors_sortable(context):
if IExposure.providedBy(context):
s = pmr1_citation_authors_exposure(context)()
elif IExposureFile.providedBy(context):
s = pmr1_citation_authors_exposurefile(context)()
else:
# well, this is either not an exposure type, or one that is
# sitting in some place wrong - we ignore it.
return ''
if isinstance(s, basestring):
return s.lower()
return ''
def generateTitle(self):
# the fallbacks assume context is an atct type.
if IExposureFile.providedBy(self.context):
# since this is an exposure file, we will need to derive the
# model/citation file as this should be the actual file that
# contain the documentation.
return self.findModelTitle() or self.context.Title()
# otherwise, we just use the list of authors if citation is
# found, for there are expectations for the listing to be the
# same as how PMR1 did it.
return self.findCitationAuthors() or self.context.Title()
def get_download_link(self, exposure_object):
if not IExposureFile.providedBy(exposure_object):
return
try:
exposure, workspace, path = getAdapter(exposure_object,
IExposureSourceAdapter).source()
except:
return
return '%s/@@%s/%s/%s' % (
workspace.absolute_url(), 'rawfile', exposure.commit_id, path
)
def available(self):
return IExposureFile.providedBy(self.context) and self.context.views
def moldExposure(exposure_context, request, exported):
"""\
Mold an exposure structure at the exposure context, using the
structure provided by the exported dictionary.
"""
def caststr(s):
# as the exported structure could be a json structure, according
# to that spec, all strings will be in unicode, however some of
# the internal types have been defined to be of type str. This
# method provides a way to properly cast them, maybe extended to
# provide the correct encoding while retaining undefined types
# (such as null/None).
if not isinstance(s, basestring):
return s
# XXX forced casting for now
return str(s)
for items in exported:
if len(items) != 2:
raise ProcessingError('Invalid entry')
path, fields = items
if path is None:
# due to wizard.
continue
path = caststr(path)
# We will be calling methods that modify internal states of that
# form, so we will require fresh instances for every file.
fgen = zope.component.getMultiAdapter(
(exposure_context, request), name='filegen')
if 'views' in fields:
# since we may use this in a regenerative context, check
# whether file had been created.
try:
ctxobj = fgen.resolve_file(path)
except ValueError:
# I guess not.
d = {
'filename': path,
}
fgen.createAndAdd(d)
# XXX using something that is magic in nature
# <form>.ctxobj is created by our customized object
# creation method for the form, and we are using
# this informally declared object.
ctxobj = fgen.ctxobj
views = []
for view, view_fields in fields['views']:
# generate views
annotatorFactory = zope.component.getUtility(
IExposureFileAnnotator,
name=view,
)
# pass in the view_fields regardless whether it is
# editable or not because editable notes will have
# data ignored.
data = view_fields and view_fields.items() or None
try:
# Annotator factory can expect request to be
# present. Refer to commit d5d308226767
annotator = annotatorFactory(ctxobj, request)
annotator(data)
views.append(view)
except RequiredMissing:
# this does not cover cases where schema have
# changed, or the old scheme into the new scheme.
note = zope.component.queryAdapter(
ctxobj,
name=view
)
if note:
# This editable note is missing some data,
# probably because it never existed, bad
# export data, updated schema or other
# errors. We ignore it for now, and purge
# the stillborn note from the new object.
del_note(ctxobj, view)
else:
# However, the automatic generated ones we
# will continue to raise errors. Maybe in
# the future we group these together, or
# make some way to adapt this to something
# that will handle the migration case.
raise
except Exception, err:
# XXX trap all here.
raise ProcessingError(str(err))
# only ExposureFiles have this
if IExposureFile.providedBy(ctxobj):
# The annotator handles the appending of the view to the
# final list of views that are to be made visible, but
# it does not care about the order. This corrects the
# order based on the order we append it here.
views = [view for view in views if view in ctxobj.views]
ctxobj.views = views
ctxobj.selected_view = fields['selected_view']
ctxobj.file_type = caststr(fields['file_type'])
ctxobj.setSubject(fields['Subject'])
ctxobj.reindexObject()
else:
# XXX couldn't this just create the folder first for out
# of order exports?
container = fgen.resolve_folder(path)
if fields['docview_gensource']:
# there is a source
# XXX I have unicode/str confusion
gensource = unicode(fields['docview_gensource'])
container.docview_gensource = gensource
viewgen = zope.component.queryUtility(
IDocViewGen,
name=fields['docview_generator']
)
if viewgen:
# and the view generator is still available
try:
viewgen(container)()
except Exception, err:
# XXX trap all here.
raise ProcessingError(str(err))
if IExposure.providedBy(container):
# only copy curation over, until this becomes an
# annotation.
container.curation = fields['curation']
container.setSubject(fields['Subject'])
container.reindexObject()
def available(self):
return (IExposureFile.providedBy(self.context)
and self.note
and self.note.flags)
def moldExposure(exposure_context, request, exported):
"""\
Mold an exposure structure at the exposure context, using the
structure provided by the exported dictionary.
"""
def caststr(s):
# as the exported structure could be a json structure, according
# to that spec, all strings will be in unicode, however some of
# the internal types have been defined to be of type str. This
# method provides a way to properly cast them, maybe extended to
# provide the correct encoding while retaining undefined types
# (such as null/None).
if not isinstance(s, basestring):
return s
# XXX forced casting for now
return str(s)
for items in exported:
if len(items) != 2:
raise ProcessingError('Invalid entry')
path, fields = items
if path is None:
# due to wizard.
continue
path = caststr(path)
# We will be calling methods that modify internal states of that
# form, so we will require fresh instances for every file.
fgen = zope.component.getMultiAdapter(
(exposure_context, request), name='filegen')
if 'views' in fields:
# since we may use this in a regenerative context, check
# whether file had been created.
try:
ctxobj = fgen.resolve_file(path)
except ValueError:
# I guess not.
d = {
'filename': path,
}
fgen.createAndAdd(d)
# XXX using something that is magic in nature
# <form>.ctxobj is created by our customized object
# creation method for the form, and we are using
# this informally declared object.
ctxobj = fgen.ctxobj
views, hidden_views = _mold_views(ctxobj, request, fields)
# only ExposureFiles have this
if IExposureFile.providedBy(ctxobj):
# The annotator handles the appending of the view to the
# final list of views that are to be made visible, but
# it does not care about the order. This corrects the
# order based on the order we append it here.
views = [view for view in views if view in ctxobj.views]
ctxobj.views = views
ctxobj.selected_view = fields['selected_view']
ctxobj.file_type = caststr(fields['file_type'])
ctxobj.hidden_views = hidden_views
ctxobj.setSubject(fields['Subject'])
ctxobj.reindexObject()
else:
# XXX couldn't this just create the folder first for out
# of order exports?
container = fgen.resolve_folder(path)
if fields['docview_gensource']:
# there is a source
# XXX I have unicode/str confusion
gensource = unicode(fields['docview_gensource'])
container.docview_gensource = gensource
viewgen = zope.component.queryUtility(
IDocViewGen,
name=fields['docview_generator']
)
if viewgen:
# and the view generator is still available
try:
viewgen(container)()
except Exception, err:
# XXX trap all here.
qi = getToolByName(ctxobj, 'portal_quickinstaller')
if qi.isDevelopmentMode():
logger.exception('Error molding exposure')
raise ProcessingError(str(err))
if IExposure.providedBy(container):
# only copy curation over, until this becomes an
# annotation.
container.curation = fields['curation']
container.setSubject(fields['Subject'])
container.reindexObject()