class RDEFPermTab(SecurityViewMixIn, EntityView):
__regid__ = 'rdef-permissions'
__select__ = is_instance('CWRelation',
'CWAttribute') & authenticated_user()
def cell_call(self, row, col):
self.permissions_table(self.cw_rset.get_entity(row, col).yams_schema())
class TimeLeft(HeaderComponent):
""" Build a time left before session expiration display in the header.
"""
__regid__ = "time-left"
__select__ = authenticated_user()
context = u"header-right"
order = 3
def render(self, w):
# Get the expiration delay
expiration_delay = self._cw.vreg.config.get(
"apache-cleanup-session-time")
if expiration_delay is None:
expiration_delay = self._cw.vreg.config.get("cleanup-session-time")
if expiration_delay is None:
return
# Define the expiration delay div
w(u'<script>var cookie_name = "{0}clock";</script>'.format(
self._cw.session.sessionid))
w(u'<script>var expiration_time = {0};</script>'.format(
expiration_delay * 1000))
w(u'Auto logout in: <b id="timeh"></b>:<b id="timem"></b>:'
'<b id="times"></b>')
class CWRTypePermTab(SecurityViewMixIn, EntityView):
__regid__ = 'cwrtype-permissions'
__select__ = is_instance('CWRType') & authenticated_user()
def cell_call(self, row, col):
entity = self.cw_rset.get_entity(row, col)
rschema = self._cw.vreg.schema.rschema(entity.name)
self.grouped_permissions_table(rschema)
class SecurityManagementView(SecurityViewMixIn, EntityView):
"""display security information for a given entity"""
__regid__ = 'security'
__select__ = EntityView.__select__ & authenticated_user()
title = _('security')
def call(self):
self.w(u'<div id="progress">%s</div>' % self._cw._('validating...'))
super(SecurityManagementView, self).call()
def entity_call(self, entity):
self._cw.add_js('cubicweb.edition.js')
self._cw.add_css('cubicweb.acl.css')
w = self.w
_ = self._cw._
w(u'<h1><span class="etype">%s</span> <a href="%s">%s</a></h1>' %
(entity.dc_type().capitalize(), xml_escape(
entity.absolute_url()), xml_escape(entity.dc_title())))
# first show permissions defined by the schema
self.w('<h2>%s</h2>' % _('Schema\'s permissions definitions'))
self.permissions_table(entity.e_schema)
self.w('<h2>%s</h2>' % _('Manage security'))
# ownership information
if self._cw.vreg.schema.rschema('owned_by').has_perm(
self._cw, 'add', fromeid=entity.eid):
self.owned_by_edit_form(entity)
else:
self.owned_by_information(entity)
def owned_by_edit_form(self, entity):
self.w('<h3>%s</h3>' % self._cw._('Ownership'))
msg = self._cw._('ownerships have been changed')
form = self._cw.vreg['forms'].select(
'base',
self._cw,
entity=entity,
form_renderer_id='onerowtable',
submitmsg=msg,
form_buttons=[wdgs.SubmitButton()],
domid='ownership%s' % entity.eid,
__redirectvid='security',
__redirectpath=entity.rest_path())
field = guess_field(entity.e_schema,
self._cw.vreg.schema['owned_by'],
req=self._cw)
form.append_field(field)
form.render(w=self.w, display_progress_div=False)
def owned_by_information(self, entity):
ownersrset = entity.related('owned_by')
if ownersrset:
self.w('<h3>%s</h3>' % self._cw._('Ownership'))
self.w(u'<div class="ownerInfo">')
self.w(self._cw._('this entity is currently owned by') + ' ')
self.wview('csv', entity.related('owned_by'), 'null')
self.w(u'</div>')
class LogOutButton(AuthenticatedUserStatus):
""" Close the current session.
"""
__regid__ = "logout"
__select__ = authenticated_user()
order = 6
def attributes(self):
return (self._cw.build_url("logout"), "Sign-out", "fa-sign-out")
class LogoutAction(action.Action):
__regid__ = 'logout'
__select__ = authenticated_user()
title = _('logout')
category = 'useractions'
order = 30
def url(self):
return self._cw.build_url(self.__regid__)
class HomeButton(HeaderComponent):
""" Build a home button displayed in the header.
"""
__regid__ = "home-snapview"
__select__ = authenticated_user()
order = 0
context = u"header-right"
def attributes(self):
return self._cw.build_url("view", vid="index"), "Home", "fa-home"
class UserPreferencesAction(action.Action):
__regid__ = 'myprefs'
__select__ = authenticated_user()
title = _('user preferences')
category = 'useractions'
order = 10
def url(self):
return self._cw.build_url(self.__regid__)
class UserInfoAction(action.Action):
__regid__ = 'myinfos'
__select__ = authenticated_user()
title = _('profile')
category = 'useractions'
order = 20
def url(self):
return self._cw.build_url('cwuser/%s' % self._cw.user.login,
vid='edition')
class AdminGroupButton(HeaderComponent):
""" Build a create group button displayed in the header.
Only the managers have accessed to this functionality.
"""
__regid__ = "admin-status"
__select__ = match_user_groups("managers") & authenticated_user()
context = "header-right"
order = 4
def attributes(self):
return (self._cw.build_url("view", vid="shiirdor.groups-management"),
"Create groups", "fa-plus-square")
class AdminImportButton(HeaderComponent):
""" Build an importation button displayed in the header.
Only the managers have accessed to this functionality.
"""
__regid__ = "admin-import"
__select__ = match_user_groups("managers") & authenticated_user()
context = "header-right"
order = 5
def attributes(self):
return (self._cw.build_url("view", vid="shiirdor.users-groups-import"),
"Import users & groups", "fa-cloud-download")
class ManagerSyncButton(HeaderComponent):
""" Build a synchronisation button displayed in the header.
Only administrators and moderators will see this button.
"""
__regid__ = "manager-sync"
__select__ = match_user_groups("managers",
"moderators") & authenticated_user()
context = "header-right"
order = 3
def attributes(self):
return (self._cw.build_url("view", vid="schiirdor.sync-management"),
"Sync", "fa-exchange")
class ManagerManageButton(HeaderComponent):
""" Build a manage button displayed in the header.
Only administrators and moderators will see this button.
"""
__regid__ = "manager-manage"
__select__ = match_user_groups("managers",
"moderators") & authenticated_user()
context = "header-right"
order = 2
def attributes(self):
return (self._cw.build_url("view", vid="schiirdor.users-management"),
"Users & groups", "fa-users")
class ExpenseLineFilesComponent(component.EntityCtxComponent):
"""display the list of files attached to the expenselines"""
__regid__ = 'expenseline.attachments'
__select__ = (component.EntityCtxComponent.__select__
& authenticated_user() & is_instance('Expense')
& rql_condition('EXISTS(X has_lines Y, Y has_attachment F) '
'OR EXISTS(X has_attachment F)'))
title = _('has_attachment')
def render_body(self, w):
rset = self._cw.execute(
'(Any F WHERE X has_attachment F, X eid %(x)s)'
' UNION '
'(Any F WHERE X has_lines Y, Y has_attachment F, X eid %(x)s)',
dict(x=self.entity.eid))
self._cw.view('incontext', rset, 'null', w=w)
class History(NullView):
""" Create a view to display the history.
"""
__regid__ = "piws-history"
__select__ = authenticated_user()
templatable = False
div_id = "piws-history"
default_message = "Hostory has not been provided yet."
def __init__(self, *args, **kwargs):
""" Initialize the History class.
"""
super(History, self).__init__(*args, **kwargs)
def call(self, **kwargs):
""" Create the history page.
"""
# Get additional resources links
resources = {
"euaims-image": self._cw.data_url("startup/images/euaims.png"),
"pi-image": self._cw.data_url("startup/images/pi.png"),
"imagen-image": self._cw.data_url("startup/images/imagen.png"),
"fmri-image": self._cw.data_url("startup/images/fmri.png"),
"piws-image": self._cw.data_url("startup/images/piws-small.png"),
"nsap-image": self._cw.data_url("startup/images/nsap.png")
}
# Get local html startup
startup_html = os.path.join(os.path.dirname(__file__), "startup.html")
if os.path.isfile(startup_html):
links = (
u'<link rel="stylesheet" type="text/css" href="{0}"/>'.format(
self._cw.data_url("startup/css/style.css")))
for path in ("startup/js/jquery.js",
"startup/js/jquery-migrate.js", "startup/js/mezr.js",
"startup/js/public.js"):
links += (u'<script type="text/javascript" src="{0}"></script>'
.format(self._cw.data_url(path)))
with open(startup_html, "rt") as open_file:
html = open_file.readlines()
html = "\n".join(html[:8] + [links] + html[8:])
for key, value in resources.items():
html = html.replace("%({0})s".format(key), value)
self.w(unicode(html))
else:
self.w(unicode(self.default_message))
class AuthenticatedUserStatus(AnonUserStatusLink):
__select__ = authenticated_user()
def render(self, w):
# display useractions and siteactions
self._cw.add_css('cubicweb.pictograms.css')
actions = self._cw.vreg['actions'].possible_actions(self._cw, rset=self.cw_rset,
view=self.cw_extra_kwargs['view'])
box = MenuWidget('', 'userActionsBox', _class='', islist=False)
menu = PopupBoxMenu(self._cw.user.login, isitem=False, link_class='icon-user')
box.append(menu)
for action in actions.get('useractions', ()):
menu.append(self.action_link(action))
if actions.get('useractions') and actions.get('siteactions'):
menu.append(self.separator())
for action in actions.get('siteactions', ()):
menu.append(self.action_link(action))
box.render(w=w)
class SCHIIRDORModeratorIndexView(IndexView):
""" Class that defines the index view.
"""
__regid__ = "index"
__select__ = authenticated_user() & match_user_groups(
"managers", "moderators")
title = _("Index")
def call(self, **kwargs):
""" Create the loggedin 'index' page of our site.
"""
# Format template
template = self._cw.vreg.template_env.get_template(
"startup.logged.jinja2")
html = template.render(
header_url=self._cw.data_url("creative/img/neurospin.jpg"),
moderator=True)
self.w(html)
class CWETypePermTab(SecurityViewMixIn, EntityView):
__regid__ = 'cwetype-permissions'
__select__ = is_instance('CWEType') & authenticated_user()
def cell_call(self, row, col):
entity = self.cw_rset.get_entity(row, col)
eschema = self._cw.vreg.schema.eschema(entity.name)
self.w(u'<h4>%s</h4>' % self._cw._('This entity type permissions:'))
self.permissions_table(eschema)
self.w(u'<div style="margin: 0px 1.5em">')
self.w(u'<h4>%s</h4>' % self._cw._('Attributes permissions:'))
for attr, etype in eschema.attribute_definitions():
if attr not in META_RTYPES:
rdef = eschema.rdef(attr)
attrtype = str(rdef.rtype)
self.w(u'<h4 class="schema">%s (%s)</h4> ' %
(attrtype, self._cw._(attrtype)))
self.permissions_table(rdef)
self.w(u'</div>')
class UndoController(Controller):
__regid__ = 'undo'
__select__ = authenticated_user() & match_form_params('txuuid')
def publish(self, rset=None):
txuuid = self._cw.form['txuuid']
try:
self._cw.cnx.undo_transaction(txuuid)
except UndoTransactionException as exc:
errors = exc.errors
#This will cause a rollback in main_publish
raise ValidationError(None, {None: '\n'.join(errors)})
else:
self.redirect() # Will raise Redirect
def redirect(self, msg=None):
req = self._cw
msg = msg or req._("transaction undone")
self._redirect({'_cwmsgid': req.set_redirect_message(msg)})
class SCHIIRDORIndexView(IndexView):
""" Class that defines the index view.
"""
__regid__ = "index"
__select__ = ~authenticated_user()
title = _("Index")
templatable = False
def call(self, **kwargs):
""" Create the anonymous 'index' page of our site.
"""
# Get additional resources links
css = []
for path in ("creative/vendor/bootstrap/css/bootstrap.min.css",
"creative/vendor/font-awesome/css/font-awesome.min.css",
"creative/vendor/magnific-popup/magnific-popup.css",
"creative/css/creative.css"):
css.append(self._cw.data_url(path))
js = []
for path in (
"creative/vendor/jquery/jquery.min.js",
"creative/vendor/bootstrap/js/bootstrap.min.js",
"creative/vendor/scrollreveal/scrollreveal.min.js",
"creative/vendor/magnific-popup/jquery.magnific-popup.min.js",
"creative/js/creative.js"):
js.append(self._cw.data_url(path))
# Format template
template = self._cw.vreg.template_env.get_template("startup.jinja2")
html = template.render(
header_url=self._cw.data_url("creative/img/neurospin.jpg"),
login_url=self._cw.build_url(
"login", __message=u"Please login with your account."),
contact_email=self._cw.vreg.config.get("administrator-emails",
"*****@*****.**"),
css_url=css,
js_url=js)
self.w(html)
class MetaGenSearchAutoView(View):
""" Create a view to filter the PLINK genomic data from a metagen
reference.
"""
__regid__ = "metagen-search-auto"
__select__ = authenticated_user()
title = _("MetaGen Search")
paginable = False
div_id = "metagen-search-auto"
def call(self, measure=None, **kwargs):
""" Method that will create a filtered genomic measures table.
If no resultset are passed to this method, the current resultset is
used.
Parameters
----------
rset: resultset (optional, default None)
a cw resultset
patient_id: string (optional, default None)
the patient identifier.
"""
# Get the 'measure' parameter: if we use 'build_url' method, the data
# are in the form dictionary
measure = measure or self._cw.form.get("measure", None)
# Add css resources
self._cw.add_css(
"DataTables-1.10.10/media/css/jquery.dataTables.min.css")
self._cw.add_css("DataTables-1.10.10/extensions/FixedColumns/css/"
"fixedColumns.dataTables.min.css")
self._cw.add_css("DataTables-1.10.10/extensions/Scroller/css/"
"scroller.dataTables.min.css")
self._cw.add_css(
("https://code.jquery.com/ui/1.11.4/themes/smoothness/"
"jquery-ui.css"),
localfile=False)
# Add js resources
self._cw.add_js("DataTables-1.10.10/media/js/jquery.dataTables.min.js")
self._cw.add_js("DataTables-1.10.10/extensions/FixedColumns/js/"
"dataTables.fixedColumns.js")
self._cw.add_js("DataTables-1.10.10/extensions/fnSetFilteringDelay.js")
# Create a gene picker
genes = metagen_get_genes(
metagen_url=self._cw.vreg.config["metagen_url"])
genes_struct = {}
for gene in genes:
genes_struct.setdefault(gene.chromosome, []).append(gene.hgnc_name)
html = "<h1>PLINK Genomic Measures Search</h1>"
html += "<hr>"
html += ("<h2>Please select a gene of interest:</h2>")
html += "<select class='selectpicker' data-live-search='true'>"
html += "<option></option>"
for chromosome in sorted(genes_struct.keys()):
html += "<optgroup label='{0}' data-icon='glyphicon-heart'>".format(
chromosome)
for name in sorted(genes_struct[chromosome]):
html += "<option value='{0}'>{0}</option>".format(name)
html += "</optgroup>"
html += "</select>"
# Ceate a div to display the plots
html += "<div id='metagen-search-disp'></div>"
# Add an event when the selection change
search_url = self._cw.build_url(vid="metagen-search", measure=measure)
html += "<script type='text/javascript'>"
html += "$(function() {"
html += "$('.selectpicker').on('change', function(){"
html += "var selected = $(this).find('option:selected').val();"
html += "if (selected != ''){"
# > execute the ajax callback
html += "var request = $.ajax({"
html += "url: 'ajax?fname=get_metagen_search_body',"
html += "method: 'POST',"
html += "data: {{'measure': '{0}', 'gene': selected}},".format(measure)
html += "dataType: 'html'"
html += "}).done(function(html){$('#metagen-search-disp').html(html)});"
html += "}"
html += "});"
html += "});"
html += "</script>"
# Display the page content
self.w(unicode(html))
class ImageViewer(View):
""" Create an image viewer.
"""
__regid__ = "brainbrowser-image-viewer"
__select__ = authenticated_user()
title = _("Brainbrowser")
paginable = False
div_id = "brainbrowser-simple"
def __init__(self, *args, **kwargs):
""" Initialize the ImageViewer class.
If you want to construct the viewer manually in your view pass the
parent view in the 'parent_view' attribute.
"""
super(ImageViewer, self).__init__(*args, **kwargs)
if "parent_view" in kwargs:
self._cw = kwargs["parent_view"]._cw
self.w = kwargs["parent_view"].w
def call(self, imagefiles=None, **kwargs):
""" Method that will create a simple BrainBrowser image viewer.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the paths that will be rendered.
"""
# Get the parameters
imagefiles = imagefiles or self._cw.form.get("imagefiles", "")
# Guarantee that we have a list of paths
if not isinstance(imagefiles, list):
imagefiles = [imagefiles]
# Get the path to the in progress resource
wait_image_url = self._cw.data_url("images/please_wait.gif")
# Add css resources
self._cw.add_css("brainbrowser-2.3.0/css/ui-darkness/"
"jquery-ui-1.8.10.custom.css")
self._cw.add_css("brainbrowser-2.3.0/css/common.css")
self._cw.add_css("volume-viewer.css")
# Add js resources
self._cw.add_js("brainbrowser-2.3.0/src/jquery-1.6.4.min.js")
self._cw.add_js("brainbrowser-2.3.0/src/"
"jquery-ui-1.8.10.custom.min.js")
self._cw.add_js("brainbrowser-2.3.0/src/ui.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"brainbrowser.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/core/"
"tree-store.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/lib/" "config.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/lib/" "utils.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/lib/" "events.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/lib/" "loader.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/lib/"
"color-map.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/lib/display.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/lib/panel.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/lib/utils.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/modules/loading.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/modules/rendering.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/volume-loaders/overlay.js")
self._cw.add_js("brainbrowser-2.3.0/src/brainbrowser/"
"volume-viewer/volume-loaders/minc.js")
self._cw.add_js("image_viewer.js")
# Set the brainbrowser viewer navigation tools
html = self.build_brainbrowser_tools()
# Create a div for the in progress resource
html += ("<div id='loading' style='display:none' align='center'>"
"<img src='{0}'/></div>".format(wait_image_url))
# Build a brainborwser banner with tools
html += self.build_brainbrowser_banner(imagefiles)
# Set brainbrowser colormaps
html += self.build_color_maps()
# Define global javascript variables
html += "<script type='text/javascript'>"
html += "var quality = 50;"
html += "var ajaxcallback = 'get_brainbrowser_image';"
html += "</script>"
# Set brainbrowser nifti image loader
html += self.build_nifti_image_loader()
# Set a callback to select the qulity of the rendering
html += self.build_quality_callback(imagefiles)
# Set a callback to select an image to render
html += self.build_image_callback(imagefiles)
# Set a callback to select the rendering
html += self.build_rendering_callback(imagefiles)
# Set the cw brainbrowser image loader
html += self.build_cw_loader(imagefiles, 0, True)
html += '<strong>BrainBrowser© visualisation tool :</strong>'
html += '<dl class="dl-horizontal">'
html += '<dt>Lead Developer</dt><dd>Tarek Sherif</dd>'
html += '<dt>Full credits</dt><dd><a href="https://brainbrowser.cbrain.mcgill.ca/">BrainBrowser Website</a></dd>'
html += '</dl>'
# Creat the corresponding html page
self.w(unicode(html))
def build_nifti_image_loader(self):
""" Define a nifti image loader for BrainBrowser based on a CubicWeb
ajax callback.
Returns
-------
html: str
the nifti loader definition.
"""
# Add javascript
html = "<script type='text/javascript'>"
# And create the appropriate viewer
html += "var VolumeViewer = BrainBrowser.VolumeViewer;"
html += ("VolumeViewer.volume_loaders.nifti = "
"function(description, callback) {")
# Display wait message
html += "$('#loading').show();"
# Execute the ajax callback
html += "var postData = {};"
html += "postData.imagefile = description.data_file;"
html += "postData.dquality = quality;"
html += "var post = $.ajax({"
html += "url: '{0}ajax?fname=' + ajaxcallback,".format(
self._cw.base_url())
html += "type: 'POST',"
html += "data: postData"
html += "});"
# The ajax callback is done, get the result set
html += "post.done(function(p){"
html += "$('#loading').hide();"
html += "var data = p.data;"
html += "var header_text = p.header;"
# Decode and display data: expect uint8 buffer
html += "if (ajaxcallback == 'get_encoded_brainbrowser_image') {"
# Create the flatten image array data
html += "var slice_cnt = 0;"
html += "var the_array = [];"
html += "data.forEach(function(slicedata, slice_cnt) {"
# Decode the image in a function where a callback is called and
# and executed when the buffer is properly filled
html += "var effect = function(slicedata, length, callback) {"
html += "var img = new Image();"
html += "img.onload = function() {"
html += "var canvas = document.createElement('canvas');"
html += "canvas.width = img.width;"
html += "canvas.height = img.height;"
html += "var ctx = canvas.getContext('2d');"
html += "ctx.drawImage(img, 0, 0);"
html += "var imageData = ctx.getImageData(0,0,canvas.width, canvas.height);"
html += "var slicedata = imageData.data;"
# Fill the buffer: use scale factor to match uint16 dynamic
html += "for (var j = 0; j < slicedata.length; j += 4) {"
html += "the_array.push(slicedata[j] * 257);"
html += "}"
# Call the callback that will render the image when the buffer is
# completed
html += "callback(the_array, (slice_cnt + 1) == length);"
# Close onload
html += "};"
# Set the current slice base64 source
html += "img.src = 'data:image/jpg;base64,' + slicedata;"
# Close effect
html += "};"
# Load the image and define the callback
html += "effect(slicedata, data.length, function(data, is_loaded) {"
# Test if all the slice have been loaded in the buffer
html += "if (is_loaded) {"
# Load the image in BrainBrowsers
html += "var error_message;"
html += "if (description.data_file) {"
html += "BrainBrowser.parseHeader(header_text, function(header) {"
html += "BrainBrowser.createMincVolume(header, data, callback);"
html += "});"
html += "error_message = header.xspace.name;"
html += ("BrainBrowser.events.triggerEvent('error', "
"{ message: error_message });")
html += "throw new Error(error_message);"
html += "} else {"
html += "error_message = 'Error';"
html += ("BrainBrowser.events.triggerEvent('error', "
"{ message: error_message });")
html += "throw new Error(error_message);"
html += "}"
# Close callback
html += "};"
html += "});"
# Close foreach
html += "});"
# Close if encoded
html += "}"
# Display data: expect uint16 buffer
html += "else {"
# Load the image in BrainBrowsers
html += "var error_message;"
html += "if (description.data_file) {"
html += "BrainBrowser.parseHeader(header_text, function(header) {"
html += "BrainBrowser.createMincVolume(header, data, callback);"
html += "});"
html += "error_message = header.xspace.name;"
html += ("BrainBrowser.events.triggerEvent('error', "
"{ message: error_message });")
html += "throw new Error(error_message);"
html += "} else {"
html += "error_message = 'Error';"
html += ("BrainBrowser.events.triggerEvent('error', "
"{ message: error_message });")
html += "throw new Error(error_message);"
html += "}"
# Close else
html += "}"
# Close post
html += "});"
# Error when the loading failed
html += "post.fail(function(){"
html += "$('#loading').hide();"
html += " alert('Error : Image buffering failed!');"
html += "});"
html += "};"
# Close javascript
html += "</script>"
return html
def build_cw_loader(self,
imagefiles,
index=0,
decorated=False,
multiview=False):
""" Define the script that will load the image in BrainBrowser.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the paths that will be rendered.
index: int (optional, default 0)
the index of the image to render.
decorated: bool (optional, default False)
add the javascript tag.
multiview: bool (optional, default False)
display all the images at the same time.
Returns
-------
html: str
the loader definition.
"""
# Add javascript
html = ""
if decorated:
html += "<script type='text/javascript'>"
html += "$(document).ready(function() {"
# Load the volume
html += "var viewer = window.viewer;"
if multiview:
html += "viewer.loadVolumes({"
html += "volumes: ["
for path in imagefiles:
html += "{"
html += "type: 'nifti',"
html += "data_file: '{0}',".format(path)
html += "template: {"
html += "element_id: 'volume-ui-template',"
html += "viewer_insert_class: 'volume-viewer-display'"
html += "}"
html += "},"
html += "],"
html += "complete: function() {"
html += "$('#volume-type').hide();"
html += "$('.slice-display').css('display', 'inline');"
html += "$('.volume-controls').css('width', 'auto');"
html += "$('#loading').hide();"
html += "$('#brainbrowser-wrapper').slideDown({duration: 600});"
html += "}"
html += "});"
else:
html += "viewer.loadVolume({"
html += "type: 'nifti',"
html += "data_file: '{0}',".format(imagefiles[index])
html += "template: {"
html += "element_id: 'volume-ui-template',"
html += "viewer_insert_class: 'volume-viewer-display'"
html += "}"
html += "}, function() {"
html += "$('#volume-type').show();"
html += "$('.slice-display').css('display', 'inline');"
html += "$('.volume-controls').css('width', 'auto');"
html += "$('#loading').hide();"
html += "$('#brainbrowser-wrapper').slideDown({duration: 600});"
html += "});"
# Close function
html += "});"
# Close javascript
if decorated:
html += "</script>"
return html
def build_quality_callback(self, imagefiles):
""" Define the rendering quality callback.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the images that will be rendered.
Returns
-------
html: str
the quality definition.
"""
# Add javascript
html = "<script type='text/javascript'>"
# Define the callback
html += "$('#volume-quality').change(function() {"
# Raw data are requested
html += "if ($('#volume-quality').val() === 'RAW') {"
html += "ajaxcallback = 'get_brainbrowser_image';"
html += "}"
# Low quality encoded data are requested
html += "else if ($('#volume-quality').val() === 'LOW JPEG') {"
html += "ajaxcallback = 'get_encoded_brainbrowser_image';"
html += "quality = 50;"
html += "}"
# Add out of range event
html += "else {"
html += "ajaxcallback = 'get_brainbrowser_image';"
html += "}"
# Show the new image representation
html += self.build_image_callback(imagefiles, False)
# Close callback function
html += "});"
# Close javascript
html += "</script>"
return html
def build_rendering_callback(self, imagefiles):
""" Define the rendering callback.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the images that will be rendered.
Returns
-------
html: str
the rendering definition.
"""
# Add javascript
html = "<script type='text/javascript'>"
# Define the callback
html += "$('#volume-rendering').change(function() {"
# Add an event when an event occur
html += self.build_image_callback(imagefiles, False)
# Close callback function
html += "});"
# Close javascript
html += "</script>"
return html
def build_image_callback(self, imagefiles, decorated=True):
""" Define the on image change callback.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the paths that will be rendered.
decorated: bool (optional, default True)
add the javascript tag.
Returns
-------
html: str
the callback definition.
"""
# Add javascript
html = ""
if decorated:
html += "<script type='text/javascript'>"
# Define the callback
html += "$('#volume-type').change(function() {"
# Add an event for each image
for cnt in range(len(imagefiles)):
if cnt == 0:
html += "if ($('#volume-type').val() === '{0}') {{".format(cnt)
else:
html += "else if ($('#volume-type').val() === '{0}') {{".format(
cnt)
html += "viewer.clearVolumes();"
html += "if ($('#volume-rendering').val() == 'multi') {"
html += self.build_cw_loader(imagefiles, cnt, multiview=True)
html += "}"
html += "else {"
html += self.build_cw_loader(imagefiles, cnt, multiview=False)
html += "}"
html += "}"
# Add out of range event
html += "else {"
html += "viewer.clearVolumes();"
html += "}"
if decorated:
# Close callback function
html += "});"
# Close javascript
html += "</script>"
return html
def build_color_maps(self):
""" Define the BrainBrowser color-maps.
Returns
-------
html: str
the color-maps definition.
"""
# Go through colormaps
html = "<script>"
html += "BrainBrowser.config.set('color_maps', ["
baseurl = "brainbrowser-2.3.0/color-maps/"
for name, color in [("Gray", "#FF0000"), ("Spectral", "#FFFFFF"),
("Thermal", "#FFFFFF"), ("Blue", "#FFFFFF"),
("Green", "#FF0000")]:
resource = self._cw.data_url(
os.path.join(baseurl, "{0}.txt".format(name.lower())))
html += "{"
html += "name: '{0}',".format(name)
html += "url: '{0}',".format(resource)
html += "cursor_color: '{0}'".format(color)
html += "},"
html += "]);"
html += "</script>"
return html
def build_brainbrowser_tools(self,
time=True,
contrast=False,
brightness=False):
""" Define the default BrainBrowser tools.
Parameters
----------
time: bool (optional, default False)
add control to display time serie images.
contrast, brightness: bool (optional, default False)
add extra controls (not recommended).
Returns
-------
html: str
the tools definition.
"""
# Start javascript
html = "<script id='volume-ui-template' type='x-volume-ui-template'>"
# Define the image rendering location
html += "<div class='volume-viewer-display'>"
html += "</div>\n"
# Define control tools
html += "<div class='volume-viewer-controls volume-controls'>"
# Define a tool to display the voxel and world coordinates
html += "<div class='coords'>"
html += "<div class='control-container'>"
html += ("<div class='control-heading' "
"id='voxel-coordinates-heading-{{VOLID}}'>")
html += "Voxel Coordinates:"
html += "</div>"
html += "<div class='voxel-coords' data-volume-id='{{VOLID}}'>"
html += "I:<input id='voxel-i-{{VOLID}}' class='control-inputs'>"
html += "J:<input id='voxel-j-{{VOLID}}' class='control-inputs'>"
html += "K:<input id='voxel-k-{{VOLID}}' class='control-inputs'>"
html += "</div>"
html += ("<div class='control-heading' "
"id='world-coordinates-heading-{{VOLID}}'>")
html += "World Coordinates:"
html += "</div>"
html += "<div class='world-coords' data-volume-id='{{VOLID}}'>"
html += "X:<input id='world-x-{{VOLID}}' class='control-inputs'>"
html += "Y:<input id='world-y-{{VOLID}}' class='control-inputs'>"
html += "Z:<input id='world-z-{{VOLID}}' class='control-inputs'>"
html += "</div>"
# Define a tool to control different images in the volume
if time:
html += "<div id='time-{{VOLID}}' class='time-div' data-volume-id='{{VOLID}}' style='display:none'>"
html += "<div class='control-heading'>"
html += "<span>Time:</span>"
html += "</div>"
html += "<input class='control-inputs' value='0' id='time-val-{{VOLID}}'/>"
html += "<input type='checkbox' class='button' id='play-{{VOLID}}'><label for='play-{{VOLID}}'>Play</label>"
html += "<div class='slider volume-viewer-threshold' id='time-slider-{{VOLID}}'></div>"
html += "</div>"
html += "</div>"
else:
html += "</div>"
# Define a tool to change the colormap
html += "<div class='control-container'>"
html += "<div id='color-map-{{VOLID}}'>"
html += "<div class='control-heading'>"
html += "<span id='color-map-heading-{{VOLID}}'>"
html += "Color Map:"
html += "</span>"
html += "</div>"
html += "</div>"
# Define a tool to display the selected voxel intensity
html += "<div id='intensity-value-div-{{VOLID}}'>"
html += "<div class='control-heading'>"
html += "<span data-volume-id='{{VOLID}}'>"
html += "Value:"
html += "</span>"
html += "</div>"
html += ("<span id='intensity-value-{{VOLID}}' "
"class='intensity-value'></span>")
html += "</div>"
html += "</div>"
# Define a tool to threshold the image
html += "<div class='control-container'>"
html += "<div class='threshold-div' data-volume-id='{{VOLID}}'>"
html += "<div class='control-heading'>"
html += "Brightness/Contrast:"
html += "</div>"
html += "<div class='thresh-inputs'>"
html += ("<input id='min-threshold-{{VOLID}}' "
"class='control-inputs thresh-input-left' value='0'/>")
html += ("<input id='max-threshold-{{VOLID}}' "
"class='control-inputs thresh-input-right' value='65535'/>")
html += "</div>"
html += ("<div class='slider volume-viewer-threshold' "
"id='threshold-slider-{{VOLID}}'></div>")
html += "</div>"
# Define a complete slicer tool
html += ("<div id='slice-series-{{VOLID}}' "
"class='slice-series-div' data-volume-id='{{VOLID}}'>")
html += ("<div class='control-heading' "
"id='slice-series-heading-{{VOLID}}'>All slices: </div>")
html += ("<span class='slice-series-button button' "
"data-axis='xspace'>Sagittal</span>")
html += ("<span class='slice-series-button button' "
"data-axis='yspace'>Coronal</span>")
html += ("<span class='slice-series-button button' "
"data-axis='zspace'>Transverse</span>")
html += "</div>"
html += "</div>"
# Define a tool to control the image contrast
if contrast:
html += "<div class='control-container'>"
html += "<div class='contrast-div' data-volume-id='{{VOLID}}'>"
html += ("<span class='control-heading' "
"id='contrast-heading{{VOLID}}'>Contrast (0.0 to 2.0):"
"</span>")
html += ("<input class='control-inputs' value='1.0' "
"id='contrast-val'/>")
html += ("<div id='contrast-slider' "
"class='slider volume-viewer-contrast'></div>")
html += "</div>"
html += "</div>"
# Define a tool to control the image brightness
if brightness:
html += "<div class='control-container'>"
html += "<div class='brightness-div' data-volume-id='{{VOLID}}'>"
html += ("<span class='control-heading' "
"id='brightness-heading{{VOLID}}'>Brightness (-1 to 1):"
"</span>")
html += "<input class='control-inputs' value='0' id='brightness-val'/>"
html += ("<div id='brightness-slider' "
"class='slider volume-viewer-brightness'></div>")
html += "</div>"
html += "</div>"
# End controls
html += "</div>"
# End javascript
html += "</script>"
return html
def build_brainbrowser_banner(self, imagefiles):
""" Define the default BrainBrowser banner.
Parameters
----------
imagefiles: list of str (mandatory)
the path to the paths that will be rendered.
Returns
-------
html: str
the banner definition.
"""
# Define a banner divs
html = "<div id='brainbrowser-wrapper' style='display:none'>"
html += "<div id='volume-viewer'>"
html += "<div id='global-controls' class='volume-viewer-controls'>"
# Define item to select the image rendering
html += "<span class='control-heading'>Select rendering:</span>"
html += "<select id='volume-rendering'>"
html += "<option value='single'>Single</option>"
html += "<option value='multi'>Multi</option>"
html += "</select>"
# Define item to select the image to be displayed
html += "<select id='volume-type'>"
for cnt, path in enumerate(imagefiles):
html += "<option value='{0}'>{1}</option>".format(
cnt, os.path.basename(path))
html += "</select>"
# Define item to change the panle size
html += "<select id='volume-quality'>"
html += "<option value='RAW' SELECTED>RAW</option>"
# html += "<option value='LOW JPEG' SELECTED>LOW JPEG</option>"
html += "</select>"
# Define item to change the panel size
html += "<span class='control-heading'>Panel size:</span>"
html += "<select id='panel-size'>"
html += "<option value='128'>128</option>"
html += "<option value='256' SELECTED>256</option>"
html += "<option value='512'>512</option>"
html += "</select>"
# Define item to reset displayed views
# html += "<span id='sync-volumes-wrapper'>"
# html += ("<input type='checkbox' class='button' id='reset-volumes'>"
# "<label for='reset-volumes'>Reset</label>")
# html += "</span>"
# Define item to create a screenshot
html += "<span id='screenshot' class='button'>Screenshot</span>"
html += ("<div class='instructions'>Shift-click to drag. Hold ctrl "
"to measure distance.</div>")
# End divs
html += "</div>"
html += "<div id='brainbrowser'></div>"
html += "</div>"
html += "</div>"
return html
class MetaGenSearchView(View):
""" View to display the genomic measures store in PLINK format: bef/bim/fam
files.
The view id is 'metagen-search': .../view?vid=metagen-search&... . This
view accpets four parameters:
- measure (mandatory): specify the GenomicMeasure entity 'label' that
contains the PLINK file to be analysed: ...&measure=Chip1&...
- gene (manadatory): in order to filter the genomic dataset specify at
least one gene 'hgnc_name': ...&gene=CAMTA1&gene=EVI5...
- subject (optional, default all subjects): used to acces the data of
specific subjects only: ....&subject=iid1&subject=iid2...
- export (optional, default 'data'): the data export type: 'data' will
export the measured genomic data from the selected filtering options,
'metagen' will export the genomic metadata reference from the selected
genes only, 'ref' will export the genomic metadata reference from the
selected filtering options: ...&export=ref&...
"""
__regid__ = "metagen-search"
__select__ = authenticated_user()
title = _("MetaGen Search")
div_id = "metagen-search"
_display = True
def call(self, gene=None, measure=None, subjects=None, export_type=None):
""" Generate/display the genomic dataset of insterest.
"""
# Display header
if self._display:
self.w(u"<h1>MetaGen Search</h1>")
self.w(u"<hr>")
# Retrieve form parameters from the url
genes = gene or self._cw.form.get("gene", None)
if genes is not None and not isinstance(genes, list):
genes = [genes]
measure = measure or self._cw.form.get("measure", None)
subjects = subjects or self._cw.form.get("subject", None)
if subjects == "all":
subjects = None
if subjects is not None and not isinstance(subjects, list):
subjects = [subjects]
export_type = export_type or self._cw.form.get("export", "data")
# Check input parameters
if genes is None or measure is None:
msg = ("Need a gene name to perform a search and a valid "
"genomic measure name.")
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
if export_type not in ("data", "metagen", "ref"):
msg = ("'{0}' export type not recognize. Supported format are "
"'data', 'metagen' and 'ref'.".format(export_type))
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
# Display search parameters
if self._display:
self.w(u"<b>Gene Names</b>: {0}<br/>".format("; ".join(genes)))
self.w(u"<b>Genomic Measure</b>: {0}<br/>".format(measure))
self.w(u"<b>Subject</b>: {0}<br/>".format(
"; ".join(subjects) if subjects is not None else "all"))
self.w(u"<b>Export Type</b>: {0}<br/>".format(export_type))
# Get the genomic measure associated plink files
rset = self._cw.execute(
"Any G Where G is GenomicMeasure, G label '{0}'".format(measure))
if rset.rowcount != 1:
msg = u"'{0}' genomic measure(s) detected, one expected.".format(
rset.rowcount)
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
egmeasure = rset.get_entity(0, 0)
plinkfiles = []
for efset in egmeasure.filesets:
for efile in efset.external_files:
plinkfiles.append(efile.filepath)
if self._display:
self.w(u"<b>Plink Files</b>: {0}<br/>".format(
"; ".join(plinkfiles)))
self.w(u"<br/>")
roots = []
for path in plinkfiles:
root, ext = os.path.splitext(path)
if ext not in [".bed", ".bim", ".fam"]:
msg = u"'{0}' plink extension not supported.".format(ext)
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
roots.append(root)
if len(roots) != 3 or len(set(roots)) != 1:
msg = u"Three plink bed/bim/fam files expected in the same folder."
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
# Load the plink and the
try:
snp_data, metagen_snps_of_gene = genotype_measure(
path_dataset=root,
snp_ids=None,
gene_names=genes,
subject_ids=subjects,
count_A1=True,
path_log=None,
timeout=10,
nb_tries=3,
metagen_url=self._cw.vreg.config["metagen_url"])
except Exception as e:
msg = u"Can't acces the required genotype measure: {0}".format(e)
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
# Display result in a table view
# > export the measured genomic data from the selected filtering
# options
if export_type == "data":
labels = ["family_id"] + snp_data.sid.tolist()
records = numpy.concatenate((snp_data.iid, snp_data.val),
axis=1).tolist()
if self._display:
self.wview("jtable-hugetable-clientside",
None,
"null",
labels=labels,
records=records,
csv_export=True,
title="Genotypes",
timepoint="",
elts_to_sort=["ID", "family_id"],
tooltip_name=None,
use_scroller=False,
index=0)
else:
labels = ["subject_id"] + labels
self.w(
unicode(json.dumps({
"labels": labels,
"records": records
})))
# > export the genomic metadata reference from the selected filtering
# options
elif export_type == "ref":
labels = ["chromosome", "cM_position", "bp_position"]
snp_data.sid.shape += (1, )
records = numpy.concatenate((snp_data.sid, snp_data.pos),
axis=1).tolist()
if self._display:
self.wview("jtable-hugetable-clientside",
None,
"null",
labels=labels,
records=records,
csv_export=True,
title="Genotypes",
timepoint="",
elts_to_sort=[],
tooltip_name=None,
use_scroller=False,
index=1)
else:
labels = ["rs_id"] + labels
self.w(
unicode(json.dumps({
"labels": labels,
"records": records
})))
# > export the genomic metadata reference from the selected genes
# only
elif export_type == "metagen":
if metagen_snps_of_gene is not None:
labels = ["rs_id", "chromosome", "bp_position"]
records = []
for gname, snps in metagen_snps_of_gene.items():
for snp in snps:
records.append(
[gname, snp.rs_id, snp.chromosome, snp.bp_pos])
if self._display:
self.wview("jtable-hugetable-clientside",
None,
"null",
labels=labels,
records=records,
csv_export=True,
title="Genotypes",
timepoint="",
elts_to_sort=["ID", "rs_id", "chromosome"],
tooltip_name=None,
use_scroller=False,
index=2)
else:
labels = ["hgnc_name"] + labels
self.w(
unicode(
json.dumps({
"labels": labels,
"records": records
})))
else:
msg = (u"No genomic metadata found, please contact the "
"service administrator.")
if self._display:
self.error(msg)
else:
self.w(unicode(json.dumps({"error": msg})))
return
def error(self, msg):
""" Display an error message.
"""
self.w(u"<div class='panel panel-danger'>")
self.w(u"<div class='panel-heading'>")
self.w(u"<h2 class='panel-title'>ERROR</h2>")
self.w(u"</div>")
self.w(u"<div class='panel-body'>")
self.w(u"<h3>{0}</h3>".format(msg))
self.w(u"</div>")
self.w(u"</div>")
class DisplayDocumentation(NullView):
""" Create a view to display the documentation.
"""
__regid__ = "piws-documentation"
__select__ = authenticated_user()
templatable = False
div_id = "piws-documentation"
default_message = "Documentation has not been provided yet."
def __init__(self, *args, **kwargs):
""" Initialize the DisplayDocumentation class.
"""
super(DisplayDocumentation, self).__init__(*args, **kwargs)
def call(self, tooltip=None, tooltip_name=None, **kwargs):
""" Create the documentation page.
Parameters
----------
tooltip: str
a html formated string.
tooltip_name: str
the key of the item containing the html formated documentation.
"""
# Get the parameters
tooltip_name = tooltip_name or self._cw.form.get("tooltip_name", None)
if tooltip_name is not None:
tooltip = self._cw.vreg.docmap.get(tooltip_name, "")
page_title = tooltip_name
else:
tooltip = tooltip or self._cw.form.get("tooltip", "")
page_title = "Documentation"
# Set a default message if documentation is empty
if tooltip:
tooltip = tooltip
add_css = '<link rel="stylesheet" type="text/css" href="{0}"/>'\
.format(self._cw.data_url("doc.css"))
else:
image_url = self._cw.data_url("images/error.png")
error_html = '<div style="align: left; text-align:center;">'
error_html += '<img src="{0}"/>'.format(image_url)
error_html += '<div class="caption"><font size="7">{0}</font></div>'\
.format(self.default_message)
error_html += '</div>'
tooltip = "<div class='body'>{0}</div>".format(error_html)
add_css = ''
# Display documentation
self.w(u"<!DOCTYPE html>")
self.w(u"<html xmlns:cubicweb='http://www.cubicweb.org' lang='en'>")
self.w(u"<head>")
self.w(u"<meta http-equiv='content-type' content='text/html; charset=UTF-8'/>")
self.w(u"<meta http-equiv='X-UA-Compatible' content='IE=8' />")
self.w(u'{0}'.format(add_css))
self.w(u'<title>{0}</title>'.format(page_title))
self.w(u'<link rel="icon" href="{0}" />'.format(
self._cw.data_url("favicon.ico")))
self.w(u"</head>")
self.w(u"<body>")
tooltip = tooltip.replace('class="document"', 'class="body"')
self.w(unicode(tooltip))
self.w(u"</body>")
self.w(u"</html>")
