import zope.interface
import zope.component
from pmr2.app.factory import named_factory
from pmr2.app.annotation.interfaces import *
from pmr2.app.annotation.annotator import ExposureFileAnnotatorBase
from pmr2.annotation.shjs.interfaces import ISourceTextNote
class SourceTextAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator,
IExposureFileEditAnnotator)
title = u'Source Viewer'
label = u'Source View'
for_interface = ISourceTextNote
def generate(self):
return ()
SourceTextAnnotatorFactory = named_factory(SourceTextAnnotator)
from pmr2.app.exposure.interfaces import IExposureSourceAdapter
from pmr2.virtuoso.interfaces import IVirtuosoNote
from pmr2.virtuoso.interfaces import IExposureFileAnnotatorRDFIndexer
class VirtuosoAnnotator(ExposureFileAnnotatorBase):
"""
Mark this file as one containing RDF that is to be exported to
Virtuoso.
"""
zope.interface.implements(IExposureFileAnnotator,
IExposureFilePostEditAnnotator)
title = u'Export Semantic Metadata to Virtuoso'
label = u'Semantic Metadata'
description = u''
for_interface = IVirtuosoNote
edited_names = ('exclude_nav',)
def generate(self):
idx = zope.component.getAdapter(self, IExposureFileAnnotatorRDFIndexer)
idx()
if not self.data:
return {}
d = dict(self.data)
self.context.setExcludeFromNav(d.get('exclude_nav'))
return self.data
VirtuosoAnnotatorFactory = named_factory(VirtuosoAnnotator)
from pmr2.app.factory import named_factory
from pmr2.app.annotation import note_factory
from pmr2.app.annotation.interfaces import *
from pmr2.app.annotation.annotator import ExposureFileAnnotatorBase
from cellml.pmr2.note import CellMLCodegenNote
class DummyCodegenAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
title = u'Dummy Code'
description = u'A dummy code generator'
def generate(self):
return (
('code', {
'C': 'printf("this is a test\\n");',
'Python': 'print "this is a test"',
}),
)
DummyCodegenAnnotatorFactory = named_factory(DummyCodegenAnnotator)
DummyCodegenNoteFactory = note_factory(CellMLCodegenNote, 'dummy_code')
class HTMLDocViewGen(PortalTransformDocViewGenBase):
zope.interface.implements(IDocViewGen)
transform = 'safe_html'
title = u'HTML annotator'
description = u'This converts raw HTML files into a format suitable for ' \
'a Plone site.'
def generateTitle(self):
try:
tree = HTMLTreeBuilder.parse(StringIO(self.input), encoding='utf8')
result = tree.findtext("head/title")
except Exception:
result = None
return result or self.context.Title()
HTMLDocViewGenFactory = named_factory(HTMLDocViewGen)
class RSTDocViewGen(PortalTransformDocViewGenBase):
zope.interface.implements(IDocViewGen)
transform = 'rest_to_html'
title = u'reStructuredText annotator'
description = u'This converts raw RST files into a format suitable for ' \
'a Plone site.'
RSTDocViewGenFactory = named_factory(RSTDocViewGen)
# Supporting adapters
class ExposureFileNoteSourceAdapter(ExposureSourceAdapter):
model = doc.getModel()
pt = getToolByName(self.context, 'portal_transforms', None)
if pt:
stream = datastream('license_description')
pt.convert('safe_html', model.getNotesString(), stream)
text = stream.getData().decode('utf8', 'ignore')
else:
# XXX should warn unsafe
text = model.getNotesString()
return (
('text', text,),
)
SBMLNoteAnnotatorFactory = named_factory(SBMLNoteAnnotator)
class SBMLSpeciesAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
title = u'SBML Species'
label = u'Species'
description = u''
for_interface = ISBMLSpeciesNote
def generate(self):
reader = libsbml.SBMLReader()
doc = reader.readSBMLFromString(self.input)
model = doc.getModel()
result = [
(
"""
zope.interface.implements(IExposureFileAnnotator,
IExposureFileEditAnnotator)
title = u'Basic Model Curation'
label = u'Model Curation'
description = u'Basic curation flags assigned to this item.'
for_interface = IBasicCurationSet
def _annotate(self, data):
# XXX wholesale reimplementation of core method. Once a proper
# filter is implemented by parent class we can avoid doing this.
note = self.note
try:
for a, v in data:
# XXX figure out how to gracefully handle schema errors
# (such as missing values).
if a == 'flags':
v = scrub_json_unicode_to_string(v)
setattr(note, a, v)
except TypeError:
raise TypeError('%s.generate failed to return a list of ' \
'tuple(key, value)' % self.__class__)
except ValueError:
raise ValueError('%s.generate returned invalid values (not ' \
'list of tuple(key, value)' % self.__class__)
BasicCurationAnnotatorFactory = named_factory(BasicCurationAnnotator)
if isinstance(issued, basestring) and re_date.search(issued):
# Got everything.
return u'%s, %s' % (authors, issued[:4])
else:
# We could pull from workspace, but users can fix this on
# their own. Proper citation metadata spec, etc.
return u'%s, ' % (authors,)
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 generateDescription(self):
# the fallbacks assume context is an atct type.
# Since ExposureFiles don't usually show this field, the special
# rule here applies to Exposures. In the name of following the
# footsteps of PMR1, the description will be the title of the
# citation.
return self.findCitationTitle() or self.context.Description()
CellMLTmpDocViewGenFactory = named_factory(CellMLTmpDocViewGen)
from fieldml.pmr2.interfaces import *
from fieldml.pmr2.rdf import RdfExposureNoteHelper
class ZincViewerAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
for_interface = IZincViewerNote
title = u'Zinc Viewer (Original)'
label = u'Zinc Viewer'
def generate(self):
helper = RdfExposureNoteHelper()
helper.parse(self.input)
return helper.queryEFNote(self.__name__)
ZincViewerAnnotatorFactory = named_factory(ZincViewerAnnotator)
class JsonZincViewerAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
for_interface = IJsonZincViewerNote
title = u'Zinc Viewer (JSON)'
label = u'Zinc Viewer'
def generate(self):
helper = RdfExposureNoteHelper()
helper.parse(self.input)
return helper.queryEFNote(self.__name__)
JsonZincViewerAnnotatorFactory = named_factory(JsonZincViewerAnnotator)
description = u''
for_interface = IDocGenNote
edited_names = ('source', 'generator',)
def generate(self):
# XXX Should probably define the constraints better to make this
# look less hackish. Also tests?
if not self.data:
return {}
d = dict(self.data)
# XXX Fix the implementation of this to an adapter?
dvgu = zope.component.queryUtility(IDocViewGen, name=d['generator'])
if dvgu is None:
return self.data
exp, workspace, p = zope.component.getAdapter(self.context,
IExposureSourceAdapter).source()
storage = zope.component.queryAdapter(workspace, IStorage)
# should really use the adapter for this to avoid mistakes of
# forgetting this.
storage.checkout(exp.commit_id)
# XXX so we do all of this in one single step.
docviewgen = dvgu(self.context, storage.file(d['source']))
docviewgen()
# We don't need to change the data that got passed in.
return self.data
DocGenAnnotatorFactory = named_factory(DocGenAnnotator)
import zope.interface
import zope.component
from pmr2.app.factory import named_factory
from pmr2.app.annotation.interfaces import IExposureFileEditAnnotator
from pmr2.app.annotation.annotator import ExposureFileAnnotatorBase
from pmr2.app.annotation.annotator import PortalTransformAnnotatorBase
from pmr2.omex.interfaces import IOmexNote
@zope.interface.implementer(IExposureFileEditAnnotator)
class OmexAnnotator(ExposureFileAnnotatorBase):
title = u'COMBINE Archive Path'
label = u'COMBINE Archive'
description = u''
for_interface = IOmexNote
OmexAnnotatorFactory = named_factory(OmexAnnotator)
results = cu.extractMaths(model)
return results
def generate(self):
def mathc2p(s):
r = StringIO()
t = etree.parse(StringIO(s))
t.xslt(mathmlc2p_xslt).write(r)
return r.getvalue()
maths = self.maths()
maths = [(k, [mathc2p(m) for m in v]) for k, v in maths]
return (
('maths', maths),
)
CellMLMathAnnotatorFactory = named_factory(CellMLMathAnnotator)
class CellMLCodegenAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
title = u'CellML Code Generation'
label = u'Generated Code'
description = u''
for_interface = ICellMLCodegenNote
def codegen(self):
cu = zope.component.getUtility(ICellMLAPIUtility)
sa = zope.component.queryAdapter(
self.context, IExposureSourceAdapter)
exposure, workspace, path = sa.source()
modelfile = '%s/@@%s/%s/%s' % (workspace.absolute_url(),
import zope.interface
import zope.component
from pmr2.app.factory import named_factory
from pmr2.app.annotation.interfaces import *
from pmr2.app.annotation.annotator import ExposureFileAnnotatorBase
from pmr2.annotation.mathjax.interfaces import IMathJaxNote
class MathJaxAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
title = u'MathML Viewer'
label = u'MathML View'
for_interface = IMathJaxNote
def generate(self):
return ()
MathJaxAnnotatorFactory = named_factory(MathJaxAnnotator)
if 'error' in result:
raise KeyError("Flatmap server responded with an error: %s" %
result['error'])
if 'map' not in result:
raise KeyError(
"No `map_id` found in response provided by flatmap server")
# TODO deal with/wipe API key
return (
('flatmap_host', data['flatmap_host']),
('flatmap_host_root', flatmap_host_root),
('initial_response', r.text),
('map_id', result['map']),
)
FlatmapViewerAnnotatorFactory = named_factory(FlatmapViewerAnnotator)
class SDSAnnotator(ExposureFileAnnotatorBase):
zope.interface.implements(IExposureFileAnnotator)
for_interface = ISDSNote
title = u'Flatmap SDS'
label = u'Flatmap SDS Exporter'
def generate(self):
settings = zope.component.queryUtility(IPMR2GlobalSettings)
root = settings.dirOf(self.context)
view_root = join(root, self.__name__)
if not isdir(root):
makedirs(root)
if exists(view_root):
edited_names = set(ILicenseCitationNote.names())
def generate(self):
note = self.note
results = []
if note.format:
# a format is defined, we query for the selected utility to
# generate the values below.
u = zope.component.queryUtility(ICitationFormat, name=note.format)
if u is None:
# Something is wrong, either bad data or utility
# disappeared on us. Fallback to the next step.
pass
else:
# this may also provide the license_path if it has been
# correctly added to the site.
license_path, dcterms_license = u(self.context)()
results.append(('license_path', license_path,))
results.append(('dcterms_license', dcterms_license,))
return results
if note.license_path:
license = getLicenses(self.context, path=note.license_path)
if license:
results.append(('dcterms_license',
license[0].pmr2_license_uri,))
return results
LicenseCitationAnnotatorFactory = named_factory(LicenseCitationAnnotator)