class GroupSpaceIndex(base.ATCTContent):
'''A group space'''
implements(IGroupSpaceIndex)
schema = GroupSpaceIndexSchema
portal_type = 'Group Space Index'
chair = atapi.ATReferenceFieldProperty('chair')
coChair = atapi.ATReferenceFieldProperty('coChair')
description = atapi.ATFieldProperty('description')
members = atapi.ATReferenceFieldProperty('members')
title = atapi.ATFieldProperty('title')
class BiomarkerPanel(Biomarker):
'''Biomarker panel.'''
implements(IBiomarkerPanel)
schema = BiomarkerPanelSchema
portal_type = 'Biomarker Panel'
members = atapi.ATReferenceFieldProperty('members')
qaState = atapi.ATFieldProperty('qaState')
class BiomarkerBodySystem(ATFolder, KnowledgeObject):
'''Biomarker body system.'''
implements(IBiomarkerBodySystem)
schema = BiomarkerBodySystemSchema
portal_type = 'Biomarker Body System'
bodySystem = atapi.ATReferenceFieldProperty('bodySystem')
phase = atapi.ATFieldProperty('phase')
protocols = atapi.ATReferenceFieldProperty('protocols')
publications = atapi.ATReferenceFieldProperty('publications')
qaState = atapi.ATFieldProperty('qaState')
resources = atapi.ATReferenceFieldProperty('resources')
datasets = atapi.ATReferenceFieldProperty('datasets')
description = atapi.ATFieldProperty('description')
performanceComment = atapi.ATFieldProperty('performanceComment')
cliaCertification = atapi.ATFieldProperty('cliaCertification')
fdaCertification = atapi.ATFieldProperty('fdaCertification')
class TokenRoleMailerAdapter(FormMailerAdapter):
"""Token role mailer adapter"""
implements(ITokenRoleMailerAdapter)
meta_type = "TokenRoleMailerAdapter"
content_icon = 'mailaction.gif'
schema = TokenRoleMailerAdapterSchema
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
security = ClassSecurityInfo()
# -*- Your ATSchema to Python Property Bridges Here ... -*-
private_doc = atapi.ATReferenceFieldProperty('private_doc')
minutes = atapi.ATFieldProperty('minutes')
security.declarePrivate('onSuccess')
def onSuccess(self, fields, REQUEST=None):
"""
e-mails data.
"""
REQUEST['form.widgets.token_id'] = self.generate_token()
super(TokenRoleMailerAdapter, self).onSuccess(fields, REQUEST)
security.declarePrivate('_dreplace')
def _dreplace(self, s):
form = getattr(self.REQUEST, 'form', {})
if form and self.REQUEST.get('form.widgets.token_id'):
form['TOKEN_URL'] = self.REQUEST.get('form.widgets.token_id')
return dollarReplace.DollarVarReplacer(form).sub(s)
def generate_token(self):
""" Generate a new token """
minutes = self.getMinutes()
token_roles = ['Reader']
private_doc = self.getPrivate_doc()
if private_doc:
token_id = make_uuid(private_doc.getId())
token_end = datetime.datetime.now() + datetime.timedelta(
minutes=minutes)
private_doc.REQUEST.set('form.widgets.token_id', token_id)
ITokenInfoSchema(private_doc).token_id = token_id
ITokenInfoSchema(private_doc).token_end = token_end
ITokenInfoSchema(private_doc).token_roles = token_roles
return "%s?token=%s" % (private_doc.absolute_url(), token_id)
def startupDirectoryMethod(self):
return "/".join(self.getPhysicalPath()[:-2])
class Group(base.ATCTContent):
"""Let you have several persons together"""
implements(IGroup)
portal_type = "Group"
schema = GroupSchema
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
persons = atapi.ATReferenceFieldProperty('persons')
class HomeBox(folder.ATFolder):
"""Description of the Example Type"""
implements(IHomeBox)
meta_type = "HomeBox"
schema = HomeBoxSchema
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
text = atapi.ATFieldProperty('text')
style = atapi.ATFieldProperty('style')
resource = atapi.ATReferenceFieldProperty('resource')
appearance = atapi.ATFieldProperty('appearance')
width = atapi.ATFieldProperty('width')
height = atapi.ATFieldProperty('height')
showControls = atapi.ATFieldProperty('showControls')
class BodySystemStudy(ATFolder, KnowledgeObject):
'''Body system study.'''
implements(IBodySystemStudy)
schema = BodySystemStudySchema
portal_type = 'Body System Study'
protocol = atapi.ATReferenceFieldProperty('protocol')
protocols = atapi.ATReferenceFieldProperty('protocols')
publications = atapi.ATReferenceFieldProperty('publications')
resources = atapi.ATReferenceFieldProperty('resources')
datasets = atapi.ATReferenceFieldProperty('datasets')
study = atapi.ATReferenceFieldProperty('study')
decisionRule = atapi.ATFieldProperty('decisionRule')
class SCALDS(base.ATCTContent):
"""Interface to the SCALDS Model."""
implements(ISCALDS, IModel)
meta_type = "SCALDS"
schema = SCALDSSchema
security = ClassSecurityInfo()
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
template = atapi.ATReferenceFieldProperty('template')
scenario = atapi.ATReferenceFieldProperty('scenario')
vmt = atapi.ATReferenceFieldProperty('vmt')
water = atapi.ATReferenceFieldProperty('water')
end_time = atapi.ATFieldProperty('end_time')
start_time = atapi.ATFieldProperty('start_time')
runstatus = atapi.ATFieldProperty('runstatus')
security.declarePublic('requeue')
def requeue(self):
"""simple method to requeue the scenario"""
self.runstatus = 'queued'
self.reindexObject([
'runstatus',
])
return "requeue"
security.declarePublic('end_run')
def end_run(self):
"""Mark the run as complete, set the end time, and set default
page to summary.
NEEDS WORK -- should set the endtime field, should set the
default page to the summary doc, should pass an arg that
selects 'complete' or 'terminated'.
"""
self.runstatus = 'complete'
self.reindexObject([
'runstatus',
])
#self.setDefaultPage(obj)
return
security.declarePublic('getConfig')
def getConfig(self):
"""Returns the cconfiguration necessary for running the model"""
#import pdb; pdb.set_trace()
model = Element('model')
tree = SubElement(model, 'scenario')
SubElement(tree, 'id').text = self.id
SubElement(tree, 'title').text = self.title
SubElement(tree, 'repository').text = \
'http://svn.leamgroup.com/desktop/ccrpc_scalds/trunk'
SubElement(tree, 'cmdline').text = \
'python startup -c config.xml'
el = SubElement(tree, 'template')
SubElement(el, 'title').text = self.getTemplate().title
SubElement(el, 'download').text = self.getTemplate().absolute_url() + \
'/at_download/file'
el = SubElement(tree, 'scenario')
SubElement(el, 'title').text = self.getScenario().title
SubElement(el, 'url').text = self.getScenario().absolute_url()
SubElement(el, 'config').text = self.getScenario().absolute_url() + \
'/getConfig'
el = SubElement(tree, 'vmt')
SubElement(el, 'title').text = self.getVmt().title
SubElement(el, 'download').text = self.getVmt().absolute_url() + \
'/at_download/simImage'
el = SubElement(tree, 'water')
SubElement(el, 'title').text = self.getWater().title
SubElement(el, 'download').text = self.getWater().absolute_url() + \
'/at_download/simImage'
self.REQUEST.RESPONSE.setHeader('Content-Type',
'application/xml; charset=UTF-8')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition', 'attachment; filename="%s.xml"' % self.id)
return tostring(model, encoding='UTF-8')
class SmartLink(ATLink):
"""A link to an internal or external resource."""
interface.implements(ISmartLink, IImageContent)
meta_type = "ATLink"
schema = LinkSchema
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
internalLink = atapi.ATReferenceFieldProperty('internalLink')
security = ClassSecurityInfo()
security.declareProtected(permissions.View, 'size')
def size(self):
"""Get size of the content
"""
return self.get_size()
security.declareProtected(permissions.View, 'get_size')
def get_size(self):
"""ZMI / Plone get size method
Size is given from the sum of the two image field
"""
size = 0
f = self.getField('image')
if f is not None:
size += f.get_size(self)
f = self.getField('favicon')
if f is not None:
size += f.get_size(self)
return size
security.declareProtected(permissions.View, 'tag')
def tag(self, **kwargs):
"""Generate image tag using the api of the ImageField
"""
if 'title' not in kwargs:
kwargs['title'] = self.getImageCaption()
return self.getField('image').tag(self, **kwargs)
def __bobo_traverse__(self, REQUEST, name):
"""Transparent access to image scales
"""
if name.startswith('image'):
field = self.getField('image')
image = None
if name == 'image':
image = field.getScale(self)
else:
scalename = name[len('image_'):]
if scalename in field.getAvailableSizes(self):
image = field.getScale(self, scale=scalename)
if image is not None and not isinstance(image, basestring):
# image might be None or '' for empty images
return image
elif name == 'favicon':
field = self.getField('favicon')
image = field.getScale(self)
if image is not None and not isinstance(image, basestring):
# image might be None or '' for empty images
return image
return ATLink.__bobo_traverse__(self, REQUEST, name)
security.declareProtected(permissions.ModifyPortalContent,
'setExternalLink')
def setExternalLink(self, value, **kwargs):
"""remote url mutator
Use urlparse to sanify the url
Also see http://dev.plone.org/plone/ticket/3296
"""
if value:
value = urlparse.urlunparse(urlparse.urlparse(value))
self.getField('externalLink').set(self, value, **kwargs)
self.setRemoteUrl(self.getRemoteUrl())
security.declareProtected(permissions.ModifyPortalContent,
'setInternalLink')
def setInternalLink(self, value, **kwargs):
self.getField('internalLink').set(self, value, **kwargs)
self.setRemoteUrl(self.getRemoteUrl())
security.declareProtected(permissions.View, 'getRemoteUrl')
def getRemoteUrl(self):
"""Return the URL of the link from the appropriate field, internal or external."""
# We need to check if the self object has the reference_catalog attribute.
# It's an integration problem with p4a that call this method when we don't have an internal link.
if hasattr(self, 'reference_catalog'):
ilink = self.getInternalLink()
else:
ilink = None
# If we are using an internal link
if ilink:
anchor = self.getAnchor() or ''
if anchor and not anchor.startswith("#"):
anchor = '#' + anchor
smartlink_config = queryUtility(ISmartlinkConfig,
name="smartlink_config")
if smartlink_config:
if smartlink_config.relativelink:
object = self.getField('internalLink').get(self)
remote = '/'.join(object.getPhysicalPath())
return quote(remote + anchor, safe='?$#@/:=+;$,&%')
remote = ilink.absolute_url() + anchor
else:
remote = self.getExternalLink()
remote = getUtility(ILinkNormalizerUtility).toFrontEnd(remote)
# If we still haven't remote value now, let's return the "normal" field value
if not remote:
remote = self.getField('remoteUrl').get(self)
return quote(remote, safe='?$#@/:=+;$,&%')
security.declarePrivate('cmf_edit')
def cmf_edit(self, remote_url=None, **kwargs):
if not remote_url:
remote_url = kwargs.get('remote_url', None)
self.update(externalLink=remote_url, **kwargs)
security.declareProtected(permissions.View, 'post_validate')
def post_validate(self, REQUEST, errors):
"""Check to make sure that either an internal or external link was supplied."""
if not REQUEST.form.get('externalLink') and not REQUEST.form.get(
'internalLink'):
xlink = REQUEST.get('externalLink', None)
ilink = REQUEST.get('internalLink', None)
if (not xlink and not ilink):
errors['externalLink'] = _(
"error_externallink_internallink_required",
default=
u'Please provide the external URL, or fill the "Internal link" field'
)
errors['internalLink'] = _(
"error_internallink_externallink_required",
default=
u'Please provide the internal link, or fill the "External link" field'
)
return errors
if REQUEST.form.get('externalLink') and REQUEST.form.get(
'internalLink'):
errors['externalLink'] = _(
"error_internallink_externallink_doubled",
default=
u'You must select an internal link or enter an external link. You cannot have both.'
)
return errors
security.declarePrivate('_processForm')
def _processForm(self, data=1, metadata=None, REQUEST=None, values=None):
"""BBB: I need to check old value before change it...
I don't find a good place where to put this code. Zope3 events don't help me"""
form = self.REQUEST.form
target = self.getInternalLink()
if target and target.UID() != form.get(
'internalLink') and ISmartLinked.providedBy(target):
interface.noLongerProvides(target, ISmartLinked)
ATLink._processForm(self,
data=data,
metadata=metadata,
REQUEST=REQUEST,
values=values)
security.declareProtected(permissions.View, 'getIcon')
def getIcon(self, relative_to_portal=0):
"""If a favicon was provided, show it"""
if not self.getFavicon():
return ATLink.getIcon(self, relative_to_portal)
utool = getToolByName(self, 'portal_url')
if relative_to_portal:
return self.absolute_url().replace(utool() + '/', "") + '/favicon'
# Relative to REQUEST['BASEPATH1']
res = utool(relative=1) + self.absolute_url().replace(utool(),
"") + '/favicon'
while res[:1] == '/':
res = res[1:]
return res
security.declareProtected(permissions.View, 'getInternalLinkPath')
def getInternalLinkPath(self):
"""Get database path to the internally linked content"""
ilink = self.getInternalLink()
if ilink:
return '/'.join(ilink.getPhysicalPath())
if not ilink and not self.getExternalLink():
# Try this way... this seems the only way to get the referenced object when we are deleting
# No event will help us... neither OFS.interfaces.IObjectWillBeRemovedEvent
portal_url = getToolByName(self, 'portal_url')
internalPath = self.getRemoteUrl().replace(
getUtility(ILinkNormalizerUtility).toFrontEnd(portal_url()),
'')
if not internalPath.startswith(
'/' + portal_url.getPortalObject().getId()):
internalPath = '/' + portal_url.getPortalObject().getId(
) + internalPath
return internalPath
return None
# Proxy data
@property
def proxy_enabled(self):
""" Global check if proxy is enabled in the site """
smartlink_config = queryUtility(ISmartlinkConfig,
name="smartlink_config")
if not smartlink_config:
return False
return getattr(smartlink_config, 'proxy_enabled', False)
security.declarePrivate('check_proxy_status')
def check_proxy_status(self):
""" Returns True is we can proxy reference content's data """
internal = self.getInternalLink()
return internal and self.getInternalProxy() and self.proxy_enabled
# Proxy data
# NB: can't proxy title and description with property due to Archetypes internals # noqa
def Title(self):
internal = self.getInternalLink()
if internal and self.check_proxy_status():
return internal.Title()
return self.getField('title').get(self)
def Description(self):
internal = self.getInternalLink()
if internal and self.check_proxy_status:
return internal.Description()
return self.getField('description').get(self)
class Contact(base.ATCTContent):
""" Describe a contact.
"""
implements(IContact)
portal_type = "Contact"
_at_rename_after_creation = True
schema = ContactSchema
title = atapi.ATFieldProperty('title')
firstname = atapi.ATFieldProperty('firstname')
lastname = atapi.ATFieldProperty('lastname')
job_title = atapi.ATFieldProperty('job_title')
organization = atapi.ATReferenceFieldProperty('organization')
department = atapi.ATFieldProperty('department')
address = atapi.ATFieldProperty('address')
address_complement = atapi.ATFieldProperty('address_complement')
postcode = atapi.ATFieldProperty('postcode')
city = atapi.ATFieldProperty('city')
country = atapi.ATFieldProperty('country')
email = atapi.ATFieldProperty('email')
website = atapi.ATFieldProperty('website')
office_phone = atapi.ATFieldProperty('office_phone')
mobile_phone = atapi.ATFieldProperty('mobile_phone')
private_phone = atapi.ATFieldProperty('private_phone')
fax_number = atapi.ATFieldProperty('fax_number')
description = atapi.ATFieldProperty('description')
def generateNewId(self):
return self.id
def Title(self):
title = ('%s %s' % (
self.getFirstname(),
self.getLastname(),
)).strip()
if title:
return title
else:
return "---"
def setTitle(self, title):
"""
Don't ever touch this method!!!
It's existence prevent the parent's method to be called!
"""
pass
def Description(self):
return ' '.join(
[' / '.join([self.getOffice_phone(),
self.getEmail()])])
def setDescription(self, description):
"""
Don't ever touch this method!!!
It's existence prevent the parent's method to be called!
"""
pass
def getOrganizationUID(self):
return self.getOrganization().UID()
def SearchableText(self):
collec = []
for name in ('firstname', 'lastname', 'job_title', 'organization',
'department', 'address', 'address_complement', 'city',
'country', 'email', 'website'):
text = self.schema[name].get(self)
if not isinstance(text, str):
text = getattr(text, 'title', str(text))
collec.append(text)
return " ".join(collec)
def sortable_title(self):
return self.Title().lower()
def directoryUID(self):
return self.aq_inner.aq_parent.UID()
class Probmap(base.ATCTContent):
"""a Land Use Change probability map"""
implements(IProbmap)
meta_type = "Probmap"
schema = ProbmapSchema
security = ClassSecurityInfo()
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
year = atapi.ATFieldProperty('year')
roads = atapi.ATReferenceFieldProperty('roads')
#transit = atapi.ATReferenceFieldProperty('transit')
tdm = atapi.ATReferenceFieldProperty('tdm')
trans_w = atapi.ATReferenceFieldProperty('trans_w')
drivers = atapi.ATReferenceFieldProperty('drivers')
nogrowth = atapi.ATReferenceFieldProperty('nogrowth')
empcenters = atapi.ATReferenceFieldProperty('empcenters')
emp_w = atapi.ATReferenceFieldProperty('emp_w')
popcenters = atapi.ATReferenceFieldProperty('popcenters')
pop_w = atapi.ATReferenceFieldProperty('pop_w')
dem = atapi.ATReferenceFieldProperty('dem')
landuse = atapi.ATReferenceFieldProperty('landuse')
probview = atapi.ATReferenceFieldProperty('probview')
probfile = atapi.ATFieldProperty('probfile')
def _simmap(self, obj):
"""returns URL of the simImage download"""
return obj.absolute_url() + '/at_download/simImage'
security.declarePublic('getConfig')
def getConfig(self):
"""Generate a configuration file for the Probmap"""
#import pdb; pdb.set_trace()
tree = Element('probmap')
SubElement(tree, 'id').text = self.id
SubElement(tree, 'title').text = self.title
SubElement(tree, 'year').text = str(self.year)
SubElement(tree, 'trans_w').text = str(self.trans_w)
SubElement(tree, 'pop_w').text = str(self.pop_w)
SubElement(tree, 'emp_w').text = str(self.emp_w)
SubElement(tree, 'url').text = self.absolute_url()
SubElement(tree, 'download').text = self.absolute_url() + \
'/at_download/probfile'
e = SubElement(tree, 'tdm')
if self.tdm:
e.text = self._simmap(self.tdm)
e = SubElement(tree, 'roads')
if self.roads:
e.text = self._simmap(self.roads)
e = SubElement(tree, 'drivers')
for s in self.drivers:
SubElement(e, 'driver').text = self._simmap(s)
e = SubElement(tree, 'nogrowth_maps')
for s in self.nogrowth:
SubElement(e, 'nogrowth').text = self._simmap(s)
e = SubElement(tree, 'empcenters')
for s in self.empcenters:
SubElement(e, 'empcenter').text = self._simmap(s)
e = SubElement(tree, 'popcenters')
for s in self.popcenters:
SubElement(e, 'popcenter').text = self._simmap(s)
e = SubElement(tree, 'landuse')
if self.landuse:
e.text = self._simmap(self.landuse)
e = SubElement(tree, 'dem')
if self.dem:
e.text = self._simmap(self.dem)
self.REQUEST.RESPONSE.setHeader('Content-Type',
'application/xml;;charset=UTF-8')
self.REQUEST.RESPONSE.setHeader('Content-Disposition',
'attachment; filename="%s_probmap.xml"' % self.title)
return tostring(tree, encoding='UTF-8')
class Person(base.ATCTContent):
"""Contact information of a person"""
implements(IPerson)
portal_type = 'Person'
schema = PersonSchema
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
shortName = atapi.ATFieldProperty('shortName')
lastName = atapi.ATFieldProperty('lastName')
firstName = atapi.ATFieldProperty('firstName')
birthdate = atapi.ATFieldProperty('birthdate')
organization = atapi.ATReferenceFieldProperty('organization')
position = atapi.ATFieldProperty('position')
department = atapi.ATFieldProperty('department')
workPhone = atapi.ATFieldProperty('workPhone')
workPhoneInternal = atapi.ATFieldProperty('workPhoneInternal')
workMobilePhone = atapi.ATFieldProperty('workMobilePhone')
workFax = atapi.ATFieldProperty('workFax')
workEmail = atapi.ATFieldProperty('workEmail')
workEmail2 = atapi.ATFieldProperty('workEmail2')
workEmail3 = atapi.ATFieldProperty('workEmail3')
photo = atapi.ATFieldProperty('photo')
address = atapi.ATFieldProperty('address')
country = atapi.ATFieldProperty('country')
state = atapi.ATFieldProperty('state')
city = atapi.ATFieldProperty('city')
zip = atapi.ATFieldProperty('zip')
phone = atapi.ATFieldProperty('phone')
mobilePhone = atapi.ATFieldProperty('mobilePhone')
email = atapi.ATFieldProperty('email')
web = atapi.ATFieldProperty('web')
text = atapi.ATFieldProperty('text')
# deprecated properties
short_name = DeprecatedATFieldProperty('shortName', 'short_name')
last_name = DeprecatedATFieldProperty('lastName', 'last_name')
first_name = DeprecatedATFieldProperty('firstName', 'first_name')
work_phone = DeprecatedATFieldProperty('workPhone', 'work_phone')
work_mobile_phone = DeprecatedATFieldProperty('workMobilePhone',
'work_mobile_phone')
work_email = DeprecatedATFieldProperty('workEmail', 'work_email')
work_email2 = DeprecatedATFieldProperty('workEmail2', 'work_email2')
work_email3 = DeprecatedATFieldProperty('workEmail3', 'work_email3')
mobile_phone = DeprecatedATFieldProperty('mobilePhone', 'mobile_phone')
def _compute_title(self):
"""Compute title from last and first name"""
names = []
if self.lastName:
names.append(self.lastName)
if self.firstName:
names.append(self.firstName)
return safe_unicode(', '.join(names))
def tag(self, **kwargs):
"""Generate image tag using the api of the ImageField
"""
return self.getField('photo').tag(self, **kwargs)
def __bobo_traverse__(self, REQUEST, name):
"""
Transparent access to image scales.
Taken from http://www.unc.edu/~jj/plone/#imagefieldscales
"""
if name.startswith('photo'):
field = self.getField('photo')
image = None
if name == 'photo':
image = field.getScale(self)
else:
scalename = name[len('photo_'):]
if scalename in field.getAvailableSizes(self):
image = field.getScale(self, scale=scalename)
if image is not None and not isinstance(image, basestring):
# image might be None or '' for empty images
return image
return super(Person, self).__bobo_traverse__(REQUEST, name)
class Protocol(folder.ATFolder, knowledgeobject.KnowledgeObject):
'''Protocol.'''
implements(IProtocol)
schema = ProtocolSchema
portal_type = 'Protocol'
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
abstract = atapi.ATFieldProperty('abstract')
involvedInvestigatorSites = atapi.ATReferenceFieldProperty(
'involvedInvestigatorSites')
coordinatingInvestigatorSite = atapi.ATReferenceFieldProperty(
'coordinatingInvestigatorSite')
leadInvestigatorSite = atapi.ATReferenceFieldProperty(
'leadInvestigatorSite')
bmName = atapi.ATFieldProperty('bmName')
collaborativeGroupText = atapi.ATFieldProperty('collaborativeGroupText')
phasedStatus = atapi.ATFieldProperty('phasedStatus')
aims = atapi.ATFieldProperty('aims')
analyticMethod = atapi.ATFieldProperty('analyticMethod')
blinding = atapi.ATFieldProperty('blinding')
cancerTypes = atapi.ATReferenceFieldProperty('cancerTypes')
comments = atapi.ATFieldProperty('comments')
dataSharingPlan = atapi.ATFieldProperty('dataSharingPlan')
inSituDataSharingPlan = atapi.ATFieldProperty('inSituDataSharingPlan')
startDate = atapi.ATFieldProperty('startDate')
estimatedFinishDate = atapi.ATFieldProperty('estimatedFinishDate')
finishDate = atapi.ATFieldProperty('finishDate')
design = atapi.ATFieldProperty('design')
fieldOfResearch = atapi.ATFieldProperty('fieldOfResearch')
abbrevName = atapi.ATFieldProperty('abbrevName')
objective = atapi.ATFieldProperty('objective')
project = atapi.ATFieldProperty('project')
protocolType = atapi.ATFieldProperty('protocolType')
publications = atapi.ATReferenceFieldProperty('publications')
outcome = atapi.ATFieldProperty('outcome')
secureOutcome = atapi.ATFieldProperty('secureOutcome')
plannedSampleSize = atapi.ATFieldProperty('plannedSampleSize')
finalSampleSize = atapi.ATFieldProperty('finalSampleSize')
isAPilotFor = atapi.ATReferenceFieldProperty('isAPilotFor')
obtainsData = atapi.ATReferenceFieldProperty('obtainsData')
providesData = atapi.ATReferenceFieldProperty('providesData')
obtainsSpecimens = atapi.ATReferenceFieldProperty('obtainsSpecimens')
providesSpecimens = atapi.ATReferenceFieldProperty('providesSpecimens')
relatedProtocols = atapi.ATReferenceFieldProperty('relatedProtocols')
animalSubjectTraining = atapi.ATFieldProperty('animalSubjectTraining')
humanSubjectTraining = atapi.ATFieldProperty('humanSubjectTraining')
irbApproval = atapi.ATFieldProperty('irbApproval')
originalIRBApprovalDate = atapi.ATFieldProperty('originalIRBApprovalDate')
currentIRBApprovalDate = atapi.ATFieldProperty('currentIRBApprovalDate')
currentIRBExpirationDate = atapi.ATFieldProperty(
'currentIRBExpirationDate')
irbNotes = atapi.ATFieldProperty('irbNotes')
irbNumber = atapi.ATFieldProperty('irbNumber')
siteRoles = atapi.ATFieldProperty('siteRoles')
reportingStage = atapi.ATFieldProperty('reportingStage')
biomarkers = atapi.ATReferenceFieldProperty('biomarkers')
datasets = atapi.ATReferenceFieldProperty('datasets')
piName = atapi.ATFieldProperty('piName')
datasetNames = atapi.ATFieldProperty('datasetNames')
involvedInvestigatorUID = atapi.ATFieldProperty('involvedInvestigatorUID')
involvedSiteNames = atapi.ATFieldProperty('involvedSiteNames')
def _computePIName(self):
if not self.leadInvestigatorSite:
return None
if not self.leadInvestigatorSite.principalInvestigator:
return None
return self.leadInvestigatorSite.principalInvestigator.title
def _computeDatasetNames(self):
if not self.datasets:
return []
return [i.title for i in self.datasets if i and i.title]
def _computeInvolvedSiteNames(self):
if not self.involvedInvestigatorSites:
return []
return [
i.title for i in self.involvedInvestigatorSites if i and i.title
]
def _computeDescription(self):
# CA-580 order: abstract is most important; then objective, then aims, finally outcome.
# If none of those have any text, punt.
for fieldName in ('abstract', 'objective', 'aims', 'outcome'):
value = getattr(self, fieldName, None)
if value:
filterer = MarkupFilterer()
filterer.feed(safe_unicode(value))
return filterer.getResult()
return u''
def _computePIUID(self):
return self.leadInvestigatorSite is not None and self.leadInvestigatorSite.getPiUID(
) or None
def _computeInvolvedSitePIUID(self):
if not self.involvedInvestigatorSites:
return None
return [
i.getPiUID() for i in self.involvedInvestigatorSites
if i and i.getPiUID()
]
class StressAnalysis(base.ATCTContent):
"""Frontend to the LEAM Stress Analysis Model"""
implements(IStressAnalysis, IModel)
meta_type = "StressAnalysis"
schema = StressAnalysisSchema
security = ClassSecurityInfo()
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
layer = atapi.ATReferenceFieldProperty('layer')
scenario = atapi.ATReferenceFieldProperty('scenario')
section = atapi.ATReferenceFieldProperty('section')
runstatus = atapi.ATFieldProperty('runstatus')
end_time = atapi.ATFieldProperty('end_time')
start_time = atapi.ATFieldProperty('start_time')
def checkDependencies(self):
"""Checks that all necessary impacts are ready for use."""
pass
security.declarePublic('requeue')
def requeue(self):
"""simple method to requeue the scenario"""
self.runstatus = 'queued'
self.reindexObject([
'runstatus',
])
return "requeue"
security.declarePublic('getConfig')
def getConfig(self):
"""Generates a configuration file for this analysis."""
model = Element('model')
tree = SubElement(model, 'scenario')
SubElement(tree, 'id').text = self.id
SubElement(tree, 'title').text = self.title
SubElement(tree, 'repository').text = \
'http://datacenter.leamgroup.com/svn/desktop/ccrpc_sa/trunk'
SubElement(tree, 'cmdline').text = \
'python startup.py -c config.xml'
for p in self.getLayer():
reg = SubElement(tree, 'zonemap')
SubElement(reg, 'title').text = p.title
SubElement(reg, 'layer').text = p.absolute_url() + \
'/at_download/simImage'
SubElement(tree, 'scenario').text = self.getScenario().absolute_url()
SubElement(tree, 'section').text = ''
self.REQUEST.RESPONSE.setHeader('Content-Type',
'application/xml; charset=UTF-8')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition', 'attachment; filename="%s.xml"' % self.id)
return tostring(model, encoding='UTF-8')
class Projection(base.ATCTContent):
"""A population and employment projection used within the LEAM model"""
implements(IProjection)
meta_type = "Projection"
schema = ProjectionSchema
security = ClassSecurityInfo()
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
projection = atapi.ATFieldProperty('projection')
zone = atapi.ATReferenceFieldProperty('zone')
pop_density = atapi.ATReferenceFieldProperty('pop_density')
emp_density = atapi.ATReferenceFieldProperty('emp_density')
redevelopment = atapi.ATFieldProperty('redevelopment')
security.declarePublic('config')
def config(self):
"""return projection configuration"""
url = self.absolute_url()
p = self.getProjection()
year = [rec['year'] for rec in p]
pop = [rec['pop'] for rec in p]
emp = [rec['emp'] for rec in p]
r = {
'@context': 'http://leamgroup.com/contexts/projections.jsonld',
'@id': url,
'title': self.title,
'shortname': self.id,
'startyear': p[0]['year'],
'endyear': p[-1]['year'],
'value': {
'years': year,
'population': pop,
'employment': emp,
},
'zone': {
'@id': self.zone.absolute_url(),
'@type': 'simmap',
'layer': self.zone.absolute_url() + '/at_download/simImage',
'mapfile': self.zone.absolute_url() + '/at_download/mapFile',
},
# deprecated
'graph': url + '/getGraph',
}
if self.pop_density:
url = self.pop_density.absolute_url()
r['pop_density'] = {
'@id': url,
'@type': 'simmap',
'layer': url + '/at_download/simImage',
'mapfile': url + '/at_download/mapFile',
}
if self.emp_density:
url = self.emp_density.absolute_url()
r['pop_density'] = {
'@id': url,
'@type': 'simmap',
'layer': url + '/at_download/simImage',
'mapfile': url + '/at_download/mapFile',
}
self.REQUEST.RESPONSE.setHeader('Content-type', 'application/json')
return json.dumps(r)
security.declarePublic('getConfig')
def getConfig(self):
"""Generates a configuration file for this projection"""
tree = Element('projection')
SubElement(tree, 'id').text = self.id
SubElement(tree, 'title').text = self.title
SubElement(tree, 'startyear').text = self.getProjection()[0]['year']
SubElement(tree, 'endyear').text = self.getProjection()[-1]['year']
SubElement(tree, 'graph').text = self.absolute_url() + '/getGraph'
SubElement(tree, 'layer').text = self.zone.absolute_url() + \
'/at_download/simImage'
SubElement(tree, 'redevelopment').text = str(self.redevelopment)
e = SubElement(tree, 'pop_density')
if self.pop_density:
e.text = self.pop_density.absolute_url() + '/at_download/simImage'
e = SubElement(tree, 'emp_density')
if self.emp_density:
e.text = self.emp_density.absolute_url() + '/at_download/simImage'
self.REQUEST.RESPONSE.setHeader('Content-Type', 'text/plain')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition',
'attachment; filename="%s_demand.xml"' % self.title)
return tostring(tree, encoding='UTF-8')
security.declarePublic('getGraph')
def getGraph(self):
"""Generates a the projection in the LEAM land use models
required format.
"""
proj = StringIO()
proj.write('# population and employment graph\n')
proj.write('# title: %s\n' % self.title)
proj.write('# url: %s\n' % self.absolute_url())
proj.write('# spatial area: %s\n' % self.getZone().absolute_url())
if self.pop_density:
proj.write('# population density: %s\n' % \
self.pop_density.absolute_url())
if self.emp_density:
proj.write('# employment density: %s\n\n' % \
self.emp_density.absolute_url())
proj.write('Population\n')
for p in self.getProjection():
proj.write('%s, %s\n' % (p['year'], p['pop'].replace(',', '')))
proj.write('\nEmployment\n')
for p in self.getProjection():
proj.write('%s, %s\n' % (p['year'], p['emp'].replace(',', '')))
# need to specify the encoding
#self.REQUEST.RESPONSE.setHeader('Content-Type',
# 'text/plain;;charset=UTF-8')
self.REQUEST.RESPONSE.setHeader('Content-Type', 'text/plain')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition',
'attachment; filename="%s_demand.txt"' % self.title)
#return unicode(proj.getvalue())
return proj.getvalue()
security.declarePublic('getDecline')
def getDecline(self):
"""Generates a the projection in the LEAM land use models
required format normalized for decline.
"""
proj = StringIO()
proj.write('# population and employment graph\n')
proj.write('# title: %s\n' % self.title)
proj.write('# url: %s\n' % self.absolute_url())
proj.write('# spatial area: %s\n' % self.getZone().absolute_url())
if self.pop_density:
proj.write('# population density: %s\n' % \
self.pop_density.absolute_url())
if self.emp_density:
proj.write('# employment density: %s\n\n' % \
self.emp_density.absolute_url())
p = self.getProjection()[0]
startpop = int(p['pop'].replace(',', ''))
startemp = int(p['emp'].replace(',', ''))
proj.write('Population\n')
for p in self.getProjection():
pop = int(p['pop'].replace(',', '')) - startpop
if pop < 0:
pop = -1 * pop
else:
pop = 0
proj.write('%s, %d\n' % (p['year'], pop))
proj.write('\nEmployment\n')
for p in self.getProjection():
emp = int(p['emp'].replace(',', '')) - startemp
if emp < 0:
emp = -1 * emp
else:
emp = 0
proj.write('%s, %s\n' % (p['year'], emp))
# need to specify the encoding
#self.REQUEST.RESPONSE.setHeader('Content-Type',
# 'text/plain;;charset=UTF-8')
self.REQUEST.RESPONSE.setHeader('Content-Type', 'text/plain')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition',
'attachment; filename="%s_demand.txt"' % self.title)
#return unicode(proj.getvalue())
return proj.getvalue()
security.declarePublic('csv')
def csv(self):
"""return the projection in 3-column CSV format"""
proj = StringIO()
proj.write('# population and employment projection\n')
proj.write('# title: %s\n' % self.title)
proj.write('# url: %s/csv\n' % self.absolute_url())
for p in self.getProjection():
proj.write(', '.join(
(p['year'], p['pop'].replace(',',
''), p['emp'].replace(',', ''))))
self.REQUEST.RESPONSE.setHeader('Content-Type', 'text/csv')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition',
'attachment; filename="%s.csv"' % self.title)
return proj.getvalue()
class LUCScenario(folder.ATFolder):
"""LEAM Land Use Change (LUC) Scenario"""
implements(ILUCScenario, IModel)
meta_type = "LUCScenario"
schema = LUCScenarioSchema
security = ClassSecurityInfo()
title = atapi.ATFieldProperty('title')
description = atapi.ATFieldProperty('description')
# -*- Your ATSchema to Python Property Bridges Here ... -*-
end_time = atapi.ATFieldProperty('end_time')
start_time = atapi.ATFieldProperty('start_time')
runstatus = atapi.ATFieldProperty('runstatus')
command = atapi.ATFieldProperty('command')
growth = atapi.ATReferenceFieldProperty('growth')
growthmap = atapi.ATReferenceFieldProperty('growthmap')
decline = atapi.ATReferenceFieldProperty('decline')
declinemap = atapi.ATReferenceFieldProperty('declinemap')
def cmdline(self):
url = self.absolute_url()
cmd = api.portal.get_registry_record(
'leam.luc.interfaces.settings.ILUCSettings.scenario_cmd')
return cmd.format(id=self.id, url=url)
def repository(self):
url = self.absolute_url()
repo = api.portal.get_registry_record(
'leam.luc.interfaces.settings.ILUCSettings.scenario_repo')
return repo.format(id=self.id, url=url)
security.declarePublic('end_run')
def end_run(self):
"""Mark the run as complete, set the end time, and set
default page to summary.
NEEDS WORK -- should set the endtime field, should set the
default page to the summary doc, should pass an arg that
selects 'complete' or 'terminated'.
more on setDefaultPage at https://svn.plone.org/svn/collective/CMFDynamicViewFTI/trunk/Products/CMFDynamicViewFTI/interfaces.py#L84
"""
#import pdb; pdb.set_trace()
self.runstatus = 'complete'
self.reindexObject([
'runstatus',
])
#self.setDefaultPage(obj)
return
security.declarePublic('requeue')
def requeue(self):
"""simple method to requeue the current scenario"""
self.runstatus = 'queued'
self.reindexObject([
'runstatus',
])
return "requeue"
security.declarePublic('queue_post')
def queue_post(self):
"""Create queued versions of any post-processing jobs found
in the post-processing folder.
Note: Is this the appropriate place for this funcntionality?
How much model support logic should be in the interface code and
should this call be part of the API or triggered by a call
to the model success API call and should it be called by the model
directly, the jobserver, be Plone interface code?
"""
#import pdb; pdb.set_trace()
context = aq_inner(self)
portal = api.portal.get()
portal_path = '/'.join(portal.getPhysicalPath())
# if a post-processing folder exists then delete contents
if 'post-processing' in context:
localpp = context.get('post-processing')
for ids in localpp.keys():
api.content.delete(obj=localpp[ids])
# otherwise create post-processing folder
else:
localpp = api.content.create(type='Folder',
title='Post Processing',
container=context)
# get the LUC post-processing folder
# TODO: this path shouldn't be hard-coded
pp_path = portal_path + '/luc/post-processing'
pp = api.content.get(path=pp_path)
for ids in pp.keys():
api.content.copy(source=pp[ids], target=localpp)
# update the variable in the newly created post-processing jobs
intids = getUtility(IIntIds)
scenario_id = intids.getId(context)
for ids in localpp.keys():
localpp[ids].scenario = RelationValue(scenario_id)
localpp[ids].runstatus = 'queued'
localpp[ids].reindexObject([
'runstatus',
])
return '%d jobs queued' % len(localpp.keys())
security.declarePublic('config')
def config(self):
"""return the scenario configuration"""
#import pdb; pdb.set_trace()
context = aq_inner(self)
portal = api.portal.get()
r = {
'@context': 'http://leamgroup.com/contexts/scenario.jsonld',
'@id': context.absolute_url(),
'shortname': self.id,
'title': context.title,
'results': context.absolute_url(),
'config': context.absolute_url()+'/config',
'resources': {
'grass': context.luc.resources.grass.absolute_url() \
+ '/at_download/file',
},
'projections': [],
'drivers': [],
#deprecated
'grass_loc': context.luc.resources.grass.absolute_url() \
+ '/at_download/file',
}
for p in self.getGrowth():
d = {
'@id': p.absolute_url(),
'config': p.absolute_url() + '/config',
'mode': 'growth',
}
r['projections'].append(d)
for p in self.getDecline():
d = {
'@id': p.absolute_url(),
'config': p.absolute_url() + '/config',
'mode': 'decline',
}
r['projections'].append(d)
for p in self.getGrowthmap():
d = {
'@id': p.absolute_url(),
'config': p.absolute_url() + '/getConfig',
'cache': p.absolute_url() + '/at_download/probfile',
'mode': 'growth',
}
r['drivers'].append(d)
for p in self.getDeclinemap():
d = {
'@id': p.absolute_url(),
'config': p.absolute_url() + '/getConfig',
'cache': p.absolute_url() + '/at_download/probfile',
'mode': 'decline',
}
r['drivers'].append(d)
self.REQUEST.RESPONSE.setHeader("Content-type", "application/json")
return json.dumps(r)
security.declarePublic('getConfig')
def getConfig(self):
"""Returns the configuration necessary for running the model"""
#import pdb; pdb.set_trace()
portal = api.portal.get()
portal_url = portal.absolute_url()
context = aq_inner(self)
model = Element('model')
tree = SubElement(model, 'scenario')
SubElement(tree, 'id').text = context.id
SubElement(tree, 'title').text = context.title
SubElement(tree, 'portal').text = portal_url
SubElement(tree, 'results').text = context.absolute_url()
SubElement(tree, 'grass_loc').text = \
context.luc.resources.grass.absolute_url() + '/at_download/file'
# get the repository from registry
registry = getUtility(IRegistry)
settings = registry.forInterface(ILUCSettings)
SubElement(tree, 'repository').text = settings.scenario_repo
SubElement(tree, 'cmdline').text = settings.scenario_cmd
# regions to be modeled
reg = SubElement(tree, 'growth')
for p in self.getGrowth():
reg.append(fromstring(p.getConfig()))
reg = SubElement(tree, 'growthmap')
for p in self.getGrowthmap():
reg.append(fromstring(p.getConfig()))
reg = SubElement(tree, 'decline')
for p in self.getDecline():
reg.append(fromstring(p.getConfig()))
reg = SubElement(tree, 'declinemap')
for p in self.getDeclinemap():
reg.append(fromstring(p.getConfig()))
SubElement(tree, 'post-processing').text = context.absolute_url() + \
'/queue_post'
self.REQUEST.RESPONSE.setHeader('Content-Type',
'application/xml;;charset=UTF-8')
self.REQUEST.RESPONSE.setHeader(
'Content-Disposition',
'attachment; filename="%s_scenario.xml"' % self.title)
return tostring(model, encoding='UTF-8')
security.declarePublic('get_results')
def get_results(self):
"""Returns the scenarios results to enable further processing"""
#import pdb; pdb.set_trace()
# context is the scenario object
context = aq_inner(self)
results = getattr(context, 'model-results', None)
if results:
url = context.absolute_url()
d = dict(
status=0,
errmsg='',
short_name=context.id,
title=context.title,
context=url,
config=url + '/getConfig',
results=url + '/at_download/file',
)
else:
d = dict(
status=1,
errmsg='results not available',
short_name=context.id,
title=context.title,
context=url,
)
self.REQUEST.RESPONSE.setHeader("Content-type", "application/json")
return json.dumps(d)
security.declarePublic('set_view')
def set_view(self):
"""set the default content on scenario folder view"""
#import pdb; pdb.set_trace()
context = aq_inner(self)
view_id = self.REQUEST.get('view_id', None)
if not view_id:
return "FAIL: view_id parameter required"
view_obj = getattr(context, view_id, None)
if not view_obj:
return "FAIL: id %s not found in folder" % self
context.default_page = view_id
return "SUCCESS: default page = " + view_id
class Biomarker(ATFolder, knowledgeobject.KnowledgeObject):
'''Biomarker.'''
implements(IBiomarker)
schema = BiomarkerSchema
accessGroups = atapi.ATFieldProperty('accessGroups')
biomarkerKind = atapi.ATFieldProperty('biomarkerKind')
bmAliases = atapi.ATFieldProperty('bmAliases')
description = atapi.ATFieldProperty('description')
indicatedBodySystems = atapi.ATFieldProperty('indicatedBodySystems')
protocols = atapi.ATReferenceFieldProperty('protocols')
publications = atapi.ATReferenceFieldProperty('publications')
resources = atapi.ATReferenceFieldProperty('resources')
datasets = atapi.ATReferenceFieldProperty('datasets')
shortName = atapi.ATFieldProperty('shortName')
hgncName = atapi.ATFieldProperty('hgncName')
geneName = atapi.ATFieldProperty('geneName')
uniProtAC = atapi.ATFieldProperty('uniProtAC')
mutCount = atapi.ATFieldProperty('mutCount')
pmidCount = atapi.ATFieldProperty('pmidCount')
cancerDOCount = atapi.ATFieldProperty('cancerDOCount')
affProtFuncSiteCount = atapi.ATFieldProperty('affProtFuncSiteCount')
reshgnc = atapi.ATFieldProperty('reshgnc')
reskegg = atapi.ATFieldProperty('reskegg')
resentrez = atapi.ATFieldProperty('resentrez')
geoprofile = atapi.ATFieldProperty('geoprofile')
geodataset = atapi.ATFieldProperty('geodataset')
ressnp = atapi.ATFieldProperty('ressnp')
gwasref = atapi.ATFieldProperty('gwasref')
resgene = atapi.ATFieldProperty('resgene')
generef = atapi.ATFieldProperty('generef')
resuniprot = atapi.ATFieldProperty('resuniprot')
proteinref = atapi.ATFieldProperty('proteinref')
resfda = atapi.ATFieldProperty('resfda')
resgenecard = atapi.ATFieldProperty('resgenecard')
resensembl = atapi.ATFieldProperty('resensembl')
resprobeid = atapi.ATFieldProperty('resprobeid')
respdb = atapi.ATFieldProperty('respdb')
respfam = atapi.ATFieldProperty('respfam')
reskeggpathway = atapi.ATFieldProperty('reskeggpathway')
reskeggpathwayname = atapi.ATFieldProperty('reskeggpathwayname')
resgenename = atapi.ATFieldProperty('resgenename')
resrnaseq = atapi.ATFieldProperty('resrnaseq')
resentrezgene = atapi.ATFieldProperty('resentrezgene')
restrembl = atapi.ATFieldProperty('restrembl')
resbiosummary = atapi.ATFieldProperty('resbiosummary')
piUIDs = atapi.ATFieldProperty('piUIDs')
def _computeIndicatedBodySystems(self):
return [i.capitalize() for i in self.objectIds()]
def updatedIndicatedBodySystems(self):
self.indicatedBodySystems = self._computeIndicatedBodySystems()
def SearchableText(self):
txt = super(Biomarker, self).SearchableText()
certifications = ''
for objID, obj in self.contentItems():
if obj.cliaCertification:
certifications += 'CLIA ' * 5
if obj.fdaCertification:
certifications += 'FDA ' * 20
return certifications + txt