def visit_Navbar(self, node):
# create a navbar id that is somewhat fixed, but do not leak any
# information about memory contents to the outside
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav() if self.html5 else tags.div(
role='navigation')
root['class'] = 'navbar navbar-default'
cont = root.add(tags.div(_class='container-fluid'))
# collapse button
header = cont.add(tags.div(_class='navbar-header'))
btn = header.add(tags.button())
btn['type'] = 'button'
btn['class'] = 'navbar-toggle collapsed'
btn['data-toggle'] = 'collapse'
btn['data-target'] = '#' + node_id
btn['aria-expanded'] = 'false'
btn['aria-controls'] = 'navbar'
btn.add(tags.span('Toggle navigation', _class='sr-only'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
# title may also have a 'get_url()' method, in which case we render
# a brand-link
if node.title is not None:
if hasattr(node.title, 'get_url'):
header.add(
tags.a(node.title.text,
_class='navbar-brand',
href=node.title.get_url()))
else:
header.add(tags.span(node.title,
_class='navbar-brand'))
bar = cont.add(
tags.div(
_class='navbar-collapse collapse',
id=node_id,
))
bar_list = bar.add(tags.ul(_class='nav navbar-nav'))
bar_list_right = bar.add(
tags.ul(_class='nav navbar-nav navbar-right'))
to_right = False
for item in node.items:
if isinstance(item, SeparatorAlign):
to_right = True
continue
if not to_right:
bar_list.add(self.visit(item))
else:
bar_list_right.add(self.visit(item))
return root
def pager(self, *args, **kwargs):
with tags.div(cls=u"pagination-wrapper") as wrapper:
tags.ul(u"$link_previous ~2~ $link_next", cls=u"pagination")
kwargs.update(
format=text_type(wrapper),
symbol_previous=u"«",
symbol_next=u"»",
curpage_attr={u"class": u"active"},
link_attr={},
)
return super(Page, self).pager(*args, **kwargs)
def pager(self, *args: Any, **kwargs: Any) -> Markup:
with tags.div(cls=u"pagination-wrapper") as wrapper:
tags.ul(u"$link_previous ~2~ $link_next", cls=u"pagination")
params = dict(
format=str(wrapper),
symbol_previous=u"«",
symbol_next=u"»",
curpage_attr={u"class": u"active"},
link_attr={},
)
params.update(kwargs)
return super(Page, self).pager(*args, **params)
def visit_Navbar(self, node):
# create a navbar id that is somewhat fixed, but do not leak any
# information about memory contents to the outside
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav() if self.html5 else tags.div(role='navigation')
root['class'] = 'navbar navbar-default'
cont = root.add(tags.div(_class='container-fluid'))
# collapse button
header = cont.add(tags.div(_class='navbar-header'))
btn = header.add(tags.button())
btn['type'] = 'button'
btn['class'] = 'navbar-toggle collapsed'
btn['data-toggle'] = 'collapse'
btn['data-target'] = '#' + node_id
btn['aria-expanded'] = 'false'
btn['aria-controls'] = 'navbar'
btn.add(tags.span('Toggle navigation', _class='sr-only'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
# title may also have a 'get_url()' method, in which case we render
# a brand-link
if node.title is not None:
if hasattr(node.title, 'get_url'):
header.add(tags.a(node.title.text, _class='navbar-brand',
href=node.title.get_url()))
else:
header.add(tags.span(node.title, _class='navbar-brand'))
bar = cont.add(tags.div(
_class='navbar-collapse collapse',
id=node_id,
))
bar_list = bar.add(tags.ul(_class='nav navbar-nav'))
bar_list_right = bar.add(tags.ul(_class='nav navbar-nav navbar-right'))
to_right = False
for item in node.items:
if isinstance(item, SeparatorAlign):
to_right = True
continue
if not to_right:
bar_list.add(self.visit(item))
else:
bar_list_right.add(self.visit(item))
return root
def trans_html(container, payload, source):
container.add(div(f'{langs[source]} detected', cls='lang'))
trlns_box = container.add(div()).add(ul(cls='definition'))
for t in payload:
trlns_box.add(ul())
trlns_box.add(li(langs[t['to']]))
trln_text = trlns_box.add(div(cls='indent'))
trln_text.add(div(t['text'], cls='translation'))
try:
lit = t['transliteration']
trln_text.add(p(f"({lit['text']})", cls='lit'))
except KeyError:
continue
def visit_Navbar(self, node):
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav() if self.html5 else tags.div(role='navigation')
if hasattr(node, '_class'):
root['class'] = node._class
else:
root['class'] = 'navbar navbar-default'
cont = root.add(tags.div(_class='container-fluid'))
# collapse button
header = cont.add(tags.div(_class='navbar-header'))
btn = header.add(tags.button())
btn['type'] = 'button'
btn['class'] = 'navbar-toggle collapsed'
btn['data-toggle'] = 'collapse'
btn['data-target'] = '#' + node_id
btn['aria-expanded'] = 'false'
btn['aria-controls'] = 'navbar'
btn.add(tags.span('Toggle navigation', _class='sr-only'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
if node.title is not None:
if hasattr(node.title, 'get_url'):
header.add(tags.a(node.title.text, _class='navbar-brand',
href=node.title.get_url()))
elif hasattr(node.title, 'image'):
header.add(tags.span(tags.img(_src=node.title.image, _class='brand-img'), _class='navbar-brand'))
else:
header.add(tags.span(node.title, _class='navbar-brand'))
bar = cont.add(tags.div(
_class='navbar-collapse collapse',
id=node_id,
))
bar_list = bar.add(tags.ul(_class='nav navbar-nav'))
bar_list_right = bar.add(tags.ul(_class='nav navbar-nav navbar-right'))
for item in node.items:
if hasattr(item, 'right'):
bar_list_right.add(self.visit(item))
else:
bar_list.add(self.visit(item))
return root
def generateStatsHTML(graph,statsFilePath = "stats.html",postStatsFilePath = "postStats.html"): #Generates the Stats HTML section
firstLevel = checkFirstLevel(graph)
softwareLabelNum = queryVersionNum(graph)
softwareLabelNumList = addQueryToList(softwareLabelNum)
stats = document(title="FSL Viewer") #Creates initial html page (stats)
stats += h1("Sample FSL Viewer")
stats += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
stats += h2("Stats")
stats += hr()
stats += h3("Analysis Methods")
if askSpm(graph) == True: #Checks if SPM was used
stats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/)." % softwareLabelNumList[1])
elif askFsl(graph) == True: #Checks if FSL was used
fslFeatVersion = queryFslFeatVersion(graph)
stats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)." % (fslFeatVersion[0], softwareLabelNumList[1]))
stats += hr()
stats += h3("Design Matrix")
designMatrixLocation = queryDesignMatrixLocation(graph)
stats += a(img(src = designMatrixLocation[1], style = "border:5px solid black", border = 0), href = designMatrixLocation[0]) #Adds design matrix image (as a link) to html page
statsFile = open(statsFilePath, "x")
print(stats, file = statsFile) #Prints html page to a file
statsFile.close()
def render_comment(self, row: Row):
"""Render description column."""
comment = row.get('comment', '') or ''
if comment:
yield raw(comment)
if row['prov_value'] is None:
return
see_also_links = list(
map(
operator.itemgetter('link'),
self.query(
'''
SELECT ?link WHERE {
$node rdfs:seeAlso ?link .
OPTIONAL {
$node octa:position ?position .
}
}
ORDER BY ?position
''',
node=row['prov_value'],
),
), )
if see_also_links:
yield ul(
li(render(
node=link,
octiron=self.octiron,
), ) for link in see_also_links)
def get_html_forms(self, datatset_name_form=True):
"""generates html forms for all the metadata elements associated with this logical file
type
:param datatset_name_form If True then a form for editing dataset_name (title) attribute is
included
"""
root_div = div()
with root_div:
if datatset_name_form:
self._get_dataset_name_form()
keywords_div = div(cls="col-sm-12 content-block",
id="filetype-keywords")
action = "/hsapi/_internal/{0}/{1}/add-file-keyword-metadata/"
action = action.format(self.logical_file.__class__.__name__,
self.logical_file.id)
delete_action = "/hsapi/_internal/{0}/{1}/delete-file-keyword-metadata/"
delete_action = delete_action.format(
self.logical_file.__class__.__name__, self.logical_file.id)
with keywords_div:
legend("Keywords")
with form(id="id-keywords-filetype",
action=action,
method="post",
enctype="multipart/form-data"):
input(id="id-delete-keyword-filetype-action",
type="hidden",
value=delete_action)
with div(cls="tags"):
with div(id="add-keyword-wrapper", cls="input-group"):
input(id="txt-keyword-filetype",
cls="form-control",
placeholder="keyword",
type="text",
name="keywords")
with span(cls="input-group-btn"):
a("Add",
id="btn-add-keyword-filetype",
cls="btn btn-success",
type="button")
with ul(id="lst-tags-filetype",
cls="custom-well tag-list"):
for kw in self.keywords:
with li(cls="tag"):
span(kw)
with a():
span(
cls=
"glyphicon glyphicon-remove-circle icon-remove"
)
p("Duplicate. Keywords not added.",
id="id-keywords-filetype-msg",
cls="text-danger small",
style="display: none;")
self.get_extra_metadata_html_form()
self.get_temporal_coverage_html_form()
return root_div
def __init__(self, subtitle=''):
self.doc = dominate.document(self.site_name)
self.subtitle = subtitle if subtitle else self.__class__.__name__
self.on_ready_scriptage = []
with self.doc.head:
for css in self.cssfiles.split():
self._link_css(css)
for scripturl in self.scripturls:
tags.script(crossorigin="anonymous", src=scripturl)
self.script_list = tags.script().children
with self.doc.body.add(tags.div(cls="container")):
self.header = tags.div(id="header")
with self.header.add(tags.h2()):
tags.a(self.site_name, href='/', id="site_name")
tags.h3(self.subtitle, id="subtitle")
with tags.ul(id="status", style=self.status_style):
for msg in flask.get_flashed_messages():
tags.li(msg)
self.content = tags.div(id="content")
self.footer = tags.div(id="footer")
with self.footer:
tags.a("Latest", href=url_for("list_latest"))
tags.a("Back to the Front", href="/")
tags.a("Catalog",
href=url_for("show_catalog_page"),
onclick="shift_edit(event, this)")
tags.a("Register", href=url_for('loginbp.new_user'))
tags.label("")
if flask_login.current_user.is_authenticated:
tags.a(f"Log out", href=url_for('loginbp.logout'))
else:
tags.a(f"Login", href=url_for('loginbp.login'))
def _add_item(self, pocket_item: PocketItem) -> None:
"""Add a pocket item to the HTML report page
Args:
pocket_item (PocketItem):
Returns:
None
"""
self.doc.add(tags.h3(pocket_item.title, cls="defaultfontfamily"))
# Add bullets
pocket_item_description = tags.ul()
pocket_item_description += tags.li(
"Link: ",
tags.a(pocket_item.url, href=pocket_item.url),
cls="defaultfontfamily",
)
pocket_item_description += tags.li(
"Tags: ",
", ".join([elem for elem in pocket_item.tags]),
cls="defaultfontfamily",
)
pocket_item_description += tags.li(
"Time added: ",
pocket_item.convert_datetime_to_string(pocket_item.time_added),
cls="defaultfontfamily",
)
self.doc.add(pocket_item_description)
def visit_Navbar(self, node):
root = tags.ul(_class="nav nav-tabs nav-fill")
for item in node.items:
root.add(self.visit(item))
return root
def directory_list(octiron: Octiron, iri: Node) -> Union[html_tag, str]:
"""Render a list of subdirectories in given directory."""
links = map(
Prodict,
octiron.query(
'''
SELECT * WHERE {
?index_page octa:isChildOf ?directory .
?directory
octa:isParentOf /
octa:isParentOf /
octa:isParentOf ?link .
?link
a octa:IndexPage ;
octa:title ?title ;
octa:url ?url .
} ORDER BY ?title
''',
index_page=iri,
))
lis = [li(a(link.title, href=link.url)) for link in links]
return ul(*lis)
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(tags.a(href='#', _class='dropdown-toggle'))
if node.icon is not None:
a.add(tags.i(_class=str(node.icon)))
a.add(tags.span(node.title))
else:
a.add_raw_string(node.title)
a['data-toggle'] = 'dropdown'
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
a.add(tags.span(_class='caret'))
ul = li.add(tags.ul(_class='dropdown-menu'))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def visit_Subgroup(self, node):
if not self._in_dropdown:
node_id = sha1(str(id(node)).encode()).hexdigest()
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(
tags.a(href='javascript:void(0);', _class='dropdown-toggle'))
a.add(tags.i(_class='fa fa-fw fa-arrows-v'))
a.add(node.title)
a['data-toggle'] = 'collapse'
a['data-target'] = '#' + node_id
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
if hasattr(node, 'icon') and node.icon != None:
a.add(tags.i(_class='fa fa-fw fa-%s' % node.icon))
ul = li.add(tags.ul(_class='collapse', id=node_id))
active = node.active
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
if item.active:
active = True
self._in_dropdown = False
if active == True:
li['class'] = 'sub_active'
ul['class'] = 'collapse in'
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def open_html_doc(name, letter=None):
html_doc = dominate.document(title=u"מילון הראיה")
html_doc['dir'] = 'rtl'
with html_doc.head:
with tags.meta():
tags.attr(charset="utf-8")
with tags.meta():
tags.attr(name="viewport", content="width=device-width, initial-scale=1")
tags.script(src="jquery/dist/jquery.min.js")
tags.link(rel='stylesheet', href='bootstrap-3.3.6-dist/css/bootstrap.min.css')
tags.link(rel='stylesheet', href='style.css')
tags.script(src="bootstrap-3.3.6-dist/js/bootstrap.min.js")
tags.link(rel='stylesheet', href="bootstrap-rtl-3.3.4/dist/css/bootstrap-rtl.css")
tags.link(rel='stylesheet', href='html_demos-gh-pages/footnotes.css')
tags.script(src="milon.js")
tags.script(src="html_demos-gh-pages/footnotes.js")
tags.script(src="subjects_db.json")
html_doc.footnote_ids_of_this_html_doc = []
html_doc.name = name
if letter:
html_doc.letter = letter
html_doc.section = html_docs_l[-1].section
else:
html_doc.section = name
html_doc.index = len(html_docs_l) + 1
with html_doc.body:
with tags.div():
tags.attr(cls="container-fluid")
# TODO: call page_loaded to update saved URL also in other links
tags.script("page_loaded('%s.html')" % html_doc.index)
with tags.div():
tags.attr(cls="fixed_top_left", id="menu_bar")
with tags.div():
with tags.button(type="button"):
tags.attr(id="search_icon_button", type="button", cls="btn btn-default")
with tags.span():
tags.attr(cls="glyphicon glyphicon-search")
with tags.span():
tags.attr(cls="dropdown")
with tags.button(type="button", cls="btn btn-primary") as b:
tags.attr(href="#") #, cls="dropdown-toggle")
with tags.span():
tags.attr(cls="glyphicon glyphicon-menu-hamburger")
# b['data-toggle'] = "dropdown"
with tags.ul():
tags.attr(cls="dropdown-menu dropdown-menu-left scrollable-menu")
return html_doc
def visit_SuperGroup(self, node):
li = tags.li(_id=sanitise_for_css(node.title.text), _class="parent")
if node.title.active:
li['class'] = 'parent active'
a = li.add(tags.a(node.title.text, href=node.title.get_url()))
ul = tags.ul(*[self.visit(item) for item in node.items])
ul2 = li.add(ul)
return li
def generateMainHTML(graph,mainFilePath = "Main.html", statsFilePath = "stats.html", postStatsFilePath = "postStats.html"): #Generates the main HTML page
main = document(title="FSL Viewer")
main += h1("Sample FSL Viewer")
main += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
mainFile = open(mainFilePath, "x")
print(main, file = mainFile)
mainFile.close()
def append_list(self, *items):
with self.doc.body:
with ul() as unorderedList:
for item in items:
if type(item) is list:
self.append_list(*item)
else:
li(item)
def visit_Navbar(self, node):
nav = tags.nav(cls="navbar navbar-expand-lg navbar-dark bg-primary")
with nav:
tags.span(node.title, cls="navbar-brand")
with tags.div(id='navbarColor01', cls="collapse navbar-collapse"):
with tags.ul(cls='navbar-nav mr-auto'):
for item in node.items:
tags.li(self.visit(item))
return nav
def visit_Navbar(self, node):
# create a navbar id that is somewhat fixed, but do not leak any
# information about memory contents to the outside
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav() if self.html5 else tags.div(role='navigation')
root['class'] = 'navbar navbar-default'
cont = root.add(tags.div(_class='container-fluid'))
# collapse button
header = cont.add(tags.div(_class='navbar-header'))
btn = header.add(tags.button())
btn['type'] = 'button'
btn['class'] = 'navbar-toggle collapsed'
btn['data-toggle'] = 'collapse'
btn['data-target'] = '#' + node_id
btn['aria-expanded'] = 'false'
btn['aria-controls'] = 'navbar'
btn.add(tags.span('Toggle navigation', _class='sr-only'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
btn.add(tags.span(_class='icon-bar'))
# title may also have a 'get_url()' method, in which case we render
# a brand-link
if node.title is not None:
if hasattr(node.title, 'get_url'):
# a_tag = tags.a(node.title.text, _class='navbar-brand',
# href=node.title.get_url())
style = 'max-width:100px;margin-top: 18px;margin-right: 4px;'
header.add(
tags.span('pip install',
_class='navbar-left hidden-xs',
style=style))
a_tag = tags.a(_class='navbar-left',
title=node.title.text,
href=node.title.get_url())
a_tag.add(
tags.img(src='/images/logo_lofi.png',
style='max-width:100px;margin-top: 10px;'))
header.add(a_tag)
else:
header.add(tags.span(node.title, _class='navbar-brand'))
bar = cont.add(
tags.div(
_class='navbar-collapse collapse',
id=node_id,
))
bar_list = bar.add(tags.ul(_class='nav navbar-nav'))
for item in node.items:
bar_list.add(self.visit(item))
return root
def visit_Navbar(self, node):
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav(
_class='navbar navbar-expand-md navbar-dark bg-dark fixed-top')
# title may also have a 'get_url()' method, in which case we render
# a brand-link
if node.title is not None:
if hasattr(node.title, 'get_url'):
root.add(
tags.a(node.title.text,
_class='navbar-brand',
href=node.title.get_url()))
else:
root.add(tags.span(node.title, _class='navbar-brand'))
btn = root.add(tags.button())
btn['type'] = 'button'
btn['class'] = 'navbar-toggler'
btn['data-toggle'] = 'collapse'
btn['data-target'] = '#' + node_id
btn['aria-controls'] = 'navbarCollapse'
btn['aria-expanded'] = 'false'
btn['aria-label'] = "Toggle navigation"
btn.add(tags.span('', _class='navbar-toggler-icon'))
bar = root.add(
tags.div(
_class='navbar-collapse collapse',
id=node_id,
))
bar_list = bar.add(tags.ul(_class='navbar-nav mr-auto'))
for item in node.items:
bar_list.add(self.visit(item))
search_form = bar.add(tags.form(_class="form-inline mt-2 mt-md-0"))
# search_input = search_form.add(tags.input(_class="form-control mr-sm-2"))
# search_input['type'] = "text"
# search_input['placeholder'] = "Search"
# search_input['aria-label'] = "Search"
search_btn = search_form.add(
tags.button(_class="btn btn-success my-2 my-sm-0"))
search_btn['type'] = "submit"
search_btn.add_raw_string('+')
search_btn = search_form.add(
tags.button(_class="btn btn-success my-2 my-sm-0"))
search_btn['type'] = "submit"
search_btn.add_raw_string('Login')
return root
def report_list_group(self, items, **kwargs):
"""
Creates a list group. Each arg is a line
:param str title: Title of the section
:param list items: Each arg passed will be treated as a new list item
:param bool section: Kwarg Set to True to append the cards section to the preceding section. Default is false
:param tuple alert: Kwarg Create a dismissable alert box. First value of tuple is the color, and the second is the message
:param tuple reference: Kwarg Adds a small button which hrefs to a user supplied link. Is a tuple. First value is color, second is link
:param dict badge: Kwarg Adds badges. Key is the color, and value is the message.
:param str custom_html: Insert raw html to be added to the end of the section
:param dict modal: Create a modal. Is a dictionary. Valid keys are button, title and content
:raises NoValidTag: Raises not valid tag
Example:
>>> r += report.report_list_group('First entry', 'Second entry', ...)
"""
if not kwargs.get('title'):
raise rng.NotValidTag('Need a title')
title = kwargs.get('title')
if not isinstance(items, list):
raise rng.NotValidTag('Items have to be in the form of a list')
if 'section' in kwargs:
style = rng.CSSControl.sticky_section_css
else:
style = rng.CSSControl.css_overflow
with tag.div(
_class="jumbotron container context reportng-list-group-class",
style=style) as r:
t = tag.h1(title,
id="%s" % rng.HelperFunctions.id_with_random(5, title))
# creates a reference button with link
if 'reference' in kwargs:
t.add(rng.HelperFunctions.ref_button(kwargs.get('reference')))
# creates dismissable alert box
if 'alert' in kwargs:
rng.HelperFunctions.make_alert(kwargs.get('alert'))
with tag.ul(_class="list-group"):
for i in range(len(items)):
tag.li(
items[i],
_class=
"list-group-item d-flex justify-content-between align-items-center text-primary"
)
if 'badge' in kwargs:
rng.HelperFunctions.create_badges(kwargs.get('badge'))
if 'custom_html' in kwargs:
raw(kwargs.get('custom_html'))
if 'modal' in kwargs:
if isinstance(kwargs.get('modal'), dict):
rng.HelperFunctions.make_modals(title.replace(' ', ''),
kwargs.get('modal'))
return rng.HelperFunctions.convert_to_string(r)
def visit_Navbar(self, node):
kwargs = {'_class': 'navbar'}
kwargs.update(self.kwargs)
cont = tags.nav(**kwargs)
ul = cont.add(tags.ul())
for item in node.items:
ul.add(tags.li(self.visit(item)))
return cont
def visit_Subgroup(self, node):
group = tags.ul(_class='subgroup')
title = tags.span(node.title)
if node.active:
title.attributes['class'] = 'active'
for item in node.items:
group.add(tags.li(self.visit(item)))
return tags.div(title, group)
def visit_Navbar(self, node):
kwargs = {'_class': 'navbar'}
kwargs.update(self.kwargs)
cont = tags.nav(**kwargs)
ul = cont.add(tags.ul())
for item in node.items:
ul.add(tags.li(self.visit(item)))
return cont
def visit_Subgroup(self, node):
group = tags.ul(_class='subgroup')
title = tags.span(node.title)
if node.active:
title.attributes['class'] = 'active'
for item in node.items:
group.add(tags.li(self.visit(item)))
return tags.div(title, group)
def uniCourseList():
"""
Make a list of universities and their courses.
"""
results = g.query("""
select distinct ?courseName ?instructorFN ?instructorGN ?university where {
?id a ccso:Course .
?id ccso:csName ?courseName .
?id ccso:hasInstructor ?inst .
?inst foaf:familyName ?instructorFN .
?inst foaf:givenName ?instructorGN .
?id ccso:offeredBy ?dept .
?dept ccso:belongsTo ?uni .
?uni ccso:legalName ?university .
} limit 400""")
# Build up a dictionary with universities as keys,
# and courses as a list of values
byUniversity = {}
for courseName, instLast, instFirst, uni in results:
# print(line)
if uni in byUniversity:
byUniversity[uni].append((courseName, instLast, instFirst))
else:
byUniversity[uni] = [(courseName, instLast, instFirst)]
uniList = ul(cls="universities")
for uni in byUniversity:
courses = byUniversity[uni]
uniLi = uniList.add(li(uni, cls="university"))
courseList = uniLi.add(ul(cls="courseList"))
for course in courses:
courseName, instFN, instGN = course
name = f"{instGN} {instFN}"
courseList.add(
li(span(courseName, cls="courseName"),
span(", "),
span(name, cls="instName"),
cls="course"))
return h2("Courses by University"), uniList
def generateHtml():
with open(path.join(current_dir, '../changelog/', 'storage.json'),
'r') as f:
data = json.load(f)[::-1]
doc = document(title='Changelog - lkellar.org')
articles = []
with doc.head:
tags.link(rel='stylesheet', href='style.css')
tags.meta(charset="UTF-8")
tags.meta(name="description",
content="A log of all changes made on lkellar.org")
tags.meta(name="viewport",
content="width=device-width, initial-scale=1")
tags.link(rel="alternate",
title="Changelog Feed",
type="application/json",
href="https://lkellar.org/changelog/feed.json")
with doc:
with tags.nav().add(tags.ol()):
with tags.li():
tags.a("Home", href="../")
tags.li("Changelog")
with tags.main():
tags.h1('Changelog')
for entry in data:
tags.hr()
article_content = tags.article()
with article_content:
tags.h2(
f'{entry["title"]} - {entry["date"].split("T")[0]}',
id=f'{entry["title"]} - {entry["date"]}'.replace(
' ', ''.lower()))
list_content = tags.ul()
with list_content:
for line in entry['items']:
line = urls.sub(r'<a href="\2">\1</a>', line)
tags.li(raw(line))
articles.append((f'{entry["title"]} - {entry["date"]}'.replace(
' ', ''.lower()), list_content.render(), entry["date"],
entry['title']))
with open(path.join(current_dir, '../changelog/', 'index.html'), 'w') as f:
f.write(doc.render())
generateFeed(articles)
def _ul_right(self):
img_ = img(
_class="h-full w-full rounded-full mx-auto",
src=
("https://avatars.githubusercontent.com/u/54931660?s=400&u=dcf55"
"50498aee3550f2b2f835345d802fabe1833&v=4&_sm_au_=iNVf4trk1MFNLS"
"NnVsBFjK664v423"),
alt="profile boss",
)
li_ = li(img_, _class="h-10 w-10")
ul_right = ul(li_, _class="flex items-center")
return ul_right
def visit_Subgroup(self, node):
# 'a' tag required by smartmenus
title = tags.a(node.title, href="#")
group = tags.ul(_class='subgroup')
if node.active:
title.attributes['class'] = 'active'
for item in node.items:
group.add(tags.li(self.visit(item)))
return [title, group]
def add_nulls(self):
with self.doc:
dtg.h2("Null tests", id='nulls')
lst = dtg.ul()
sorter = self.s_null.sortTracers()
# All cross-correlations
xcorrs = np.array(["%d_%d" % (s[0], s[1]) for s in sorter])
# Unique cross-correlations
xc_un = np.unique(xcorrs)
cls_null = self.s_null.mean.vector
err_null = np.sqrt(self.s_null.precision.getCovarianceMatrix())
# Loop over unique correlations
for comb in xc_un:
t1, t2 = comb.split('_')
t1 = int(t1)
t2 = int(t2)
# Find all power spectra for this pair of tracers
ind_spectra = np.where(xcorrs == comb)[0]
# Plot title
title = self.s_null.tracers[t1].name[2:-1]
title += " x "
title += self.s_null.tracers[t2].name[2:-1]
# Plot file
fname = self.get_output('plots') + '/cls_null_'
fname += self.s_null.tracers[t1].name[2:-1]
fname += "_x_"
fname += self.s_null.tracers[t2].name[2:-1]
fname += ".png"
print(fname)
# Plot all power spectra
plt.figure()
plt.title(title, fontsize=15)
for ind in ind_spectra:
typ = sorter[ind][2].decode()
ndx = sorter[ind][4]
plt.errorbar(self.ells[self.msk],
(cls_null[ndx] / err_null[ndx])[self.msk],
yerr=np.ones(len(ndx))[self.msk],
fmt=self.cols_typ[typ] + '-',
label=typ)
plt.xlabel('$\\ell$', fontsize=15)
plt.ylabel('$C_\\ell/\\sigma_\\ell$', fontsize=15)
plt.legend()
plt.savefig(fname, bbox_index='tight')
plt.close()
lst += dtg.li(dtg.a(title, href=fname))
dtg.div(dtg.a('Back to TOC', href='#contents'))
def get_keywords_html(self):
"""generates html for viewing keywords"""
keywords_div = div()
if self.keywords:
keywords_div = div(cls="col-sm-12 content-block")
with keywords_div:
legend('Keywords')
with div(cls="tags"):
with ul(id="list-keywords-file-type",
cls="tag-list custom-well"):
for kw in self.keywords:
with li():
a(kw, cls="tag")
return keywords_div
def get_html(self):
"""Generates html for displaying all metadata elements associated with this logical file.
Subclass must override to include additional html for additional metadata it supports.
"""
root_div = div()
dataset_name_div = div()
if self.logical_file.dataset_name:
with dataset_name_div:
with table(cls='custom-table'):
with tbody():
with tr():
th("Title", cls="text-muted")
td(self.logical_file.dataset_name)
keywords_div = div()
if self.keywords:
keywords_div = div(cls="col-sm-12 content-block")
with keywords_div:
legend('Keywords')
with div(cls="tags"):
with ul(id="list-keywords-file-type",
cls="tag-list custom-well"):
for kw in self.keywords:
with li():
a(kw, cls="tag")
extra_metadata_div = div()
if self.extra_metadata:
extra_metadata_div = div(cls="col-sm-12 content-block")
with extra_metadata_div:
legend('Extended Metadata')
with table(cls="table table-striped funding-agencies-table",
style="width: 100%"):
with tbody():
with tr(cls="header-row"):
th("Key")
th("Value")
for k, v in self.extra_metadata.iteritems():
with tr(data_key=k):
td(k)
td(v)
if self.logical_file.dataset_name:
root_div.add(dataset_name_div)
if self.keywords:
root_div.add(keywords_div)
if self.extra_metadata:
root_div.add(extra_metadata_div)
return root_div.render()
def render_property_values(
property_values: List[Node],
octiron: Octiron,
) -> str:
rendered_values = [
render(
node=property_value,
octiron=octiron,
environments=[ADR.term('sidebar-property-value')],
) for property_value in property_values
]
if len(rendered_values) == 1:
return rendered_values[0]
return ul(*map(li, rendered_values))
def getTableTabsDiv(r):
table_tabs_div = div(['contentHolder', 'contentHolder'], cls='container')
tablist = ul(cls='nav nav-pills mb-3')
tablist.attributes['role'] = "tablist"
tab_names = list()
for count in range(len(r.report_df_list)):
tab_names.append(getFormattedName(r.alg_names_list[count]))
for count in range(len(r.report_df_list)):
if (count == 0):
tab = a(r.alg_names_list[count],
cls="nav-link active",
href='#' + tab_names[count] + "-tab-pane")
else:
tab = a(r.alg_names_list[count],
href='#' + tab_names[count] + "-tab-pane",
cls="nav-link")
tab.attributes['data-toggle'] = "pill"
li_element = li(tab, cls='nav-item')
tablist += li_element
table_tabs_div[0] = tablist
tabContentDiv = div(cls='tab-content')
for count in range(len(r.report_df_list)):
if (count == 0):
tabdiv = div(getDescriptionPills(
r.report_df_list[count]['Error'].describe()),
id=tab_names[count] + "-tab-pane",
cls='tab-pane active')
else:
tabdiv = div(getDescriptionPills(
r.report_df_list[count]['Error'].describe()),
id=tab_names[count] + "-tab-pane",
cls='tab-pane fade')
tabdiv.appendChild(
div('contentHolder', id=tab_names[count] + "-chart-div"))
tabdiv.appendChild(div(getErrorTableContent(r.report_df_list[count])))
tabContentDiv.appendChild(tabdiv)
table_tabs_div[1] = tabContentDiv
return table_tabs_div.render()
def visit_Navbar(self, node):
root = super(TwoSideRenderer, self).visit_Navbar(node)
# hack: add navbar-right block
collapse = root.children[0].children[1]
right = tags.ul(_class='nav navbar-nav navbar-right')
if hasattr(node, 'right_side_items'):
for item in node.right_side_items:
right.add(self.visit(item))
collapse.add(right)
# hack: logo
brand = root.children[0].children[0].children[1]
brand.attributes['class'] = ''
brand.add(self.visit(node.logo))
return root
def visit_Navbar(self, node):
# create a navbar id that is somewhat fixed, but do not leak any
# information about memory contents to the outside
node_id = self.id or sha1(str(id(node)).encode()).hexdigest()
root = tags.nav() if self.html5 else tags.div(role="navigation")
root["class"] = "navbar navbar-default"
cont = root.add(tags.div(_class="container-fluid"))
# collapse button
header = cont.add(tags.div(_class="navbar-header"))
btn = header.add(tags.button())
btn["type"] = "button"
btn["class"] = "navbar-toggle collapsed"
btn["data-toggle"] = "collapse"
btn["data-target"] = "#" + node_id
btn["aria-expanded"] = "false"
btn["aria-controls"] = "navbar"
btn.add(tags.span("Toggle navigation", _class="sr-only"))
btn.add(tags.span(_class="icon-bar"))
btn.add(tags.span(_class="icon-bar"))
btn.add(tags.span(_class="icon-bar"))
# title may also have a 'get_url()' method, in which case we render
# a brand-link
if node.title is not None:
if hasattr(node.title, "get_url"):
header.add(tags.a(node.title.text, _class="navbar-brand", href=node.title.get_url()))
else:
header.add(tags.span(node.title, _class="navbar-brand"))
bar = cont.add(tags.div(_class="navbar-collapse collapse", id=node_id))
bar_list = bar.add(tags.ul(_class="nav navbar-nav"))
for item in node.items:
bar_list.add(self.visit(item))
return root
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class="dropdown")
if node.active:
li["class"] = "active"
a = li.add(tags.a(node.title, href="#", _class="dropdown-toggle"))
a["data-toggle"] = "dropdown"
a["role"] = "button"
a["aria-haspopup"] = "true"
a["aria-expanded"] = "false"
a.add(tags.span(_class="caret"))
ul = li.add(tags.ul(_class="dropdown-menu"))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError("Cannot render nested Subgroups")
def visit_Subgroup(self, node):
if not self._in_dropdown:
li = tags.li(_class='dropdown')
if node.active:
li['class'] = 'active'
a = li.add(tags.a(node.title, href='#', _class='dropdown-toggle'))
a['data-toggle'] = 'dropdown'
a['role'] = 'button'
a['aria-haspopup'] = 'true'
a['aria-expanded'] = 'false'
a.add(tags.span(_class='caret'))
ul = li.add(tags.ul(_class='dropdown-menu'))
self._in_dropdown = True
for item in node.items:
ul.add(self.visit(item))
self._in_dropdown = False
return li
else:
raise RuntimeError('Cannot render nested Subgroups')
def fix_links(html_docs_l):
# fix outbound links
print "Fixing links"
for (doc) in html_docs_l:
for (child) in doc.body.children[0].children:
if 'definition' in child.attributes.get('class', ()):
href = ""
try:
href = child.children[0].attributes.get("href")
except AttributeError as e:
pass
# it's a link - try to update it
if href:
# first, strip it of weird chars
try:
href = clean_name(href)
updated = False
if update_values_for_href(child, href):
updated = True
else:
if href[0] in (u"ה", u"ו", u"ש", u"ב", u"כ", u"ל", u"מ"):
updated = update_values_for_href(child, href[1:])
if not updated:
# failed to update - it's not a real link...
update_href_no_link(child)
except Exception as e:
pass
print e, "Exception of HREF update", href
#TODO - investigate why it happens? (it's a single corner case, I think)
def sorter(html_doc):
if html_doc.name in [u"ערכים כלליים",]:
return "FIRST"
if html_doc.name in [u"נספחות",]:
return u"תתתתתתתתתת" #last
else:
return html_doc.name
# update sections menu
for (doc) in html_docs_l:
letters_l = []
# content_menu = doc.body.children[0].children[1].children[0].children[0].children[-1].children[0].children[1]
content_menu = doc.body.children[0].children[1].children[0].children[1].children[-1]
assert content_menu['class'] == 'dropdown-menu dropdown-menu-left scrollable-menu'
with content_menu:
with tags.li():
tags.a(u"אודות", href="index.html")
with tags.li():
tags.a(u"הקדמות", href="opening_intros.html")
with tags.li():
tags.a(u"הסכמות", href="opening_haskamot.html")
with tags.li():
tags.a(u"קיצורים", href="opening_abbrev.html")
with tags.li():
tags.a(u"סימנים", href="opening_signs.html")
# if you add more entries here, please update add_menu_to_apriory_htmls(..)
with tags.li():
tags.attr(cls="divider")
sorted_html_docs_l = sorted(html_docs_l, key=sorter)
for (html_doc) in sorted_html_docs_l:
# Only if this a 'high' heading, and not just a letter - include it in the TOC
if html_doc.name != "NEW_LETTER":
with tags.li():
tags.a(html_doc.name, href=str(html_doc.index)+".html")
if doc.section == html_doc.section:
tags.attr(cls="active")
else:
# it's a letter - if it's related to me, save it
if doc.section == html_doc.section:
letters_l.append(html_doc)
with doc.body.children[-1]:
assert doc.body.children[-1]['class'] == 'container-fluid'
with tags.ul():
tags.attr(cls="pagination")
for (html_doc) in letters_l:
tags.li(tags.a(html_doc.letter, href=str(html_doc.index)+".html"))
return html_docs_l
def generatePostStatsHTML(graph,statsFilePath = "stats.html",postStatsFilePath = "postStats.html"): #Generates Post-Stats page
voxelWise = checkHeightThreshold(graph)
clusterWise = checkExtentThreshold(graph)
softwareLabelNum = queryVersionNum(graph)
softwareLabelNumList = addQueryToList(softwareLabelNum)
statisticType = queryStatisticType(graph)
statisticType = statisticImage(statisticType[0])
statisticTypeString = statisticImageString(statisticType)
contrastName = queryContrastName(graph)
statisticMapImage = queryExcursionSetMap(graph)
postStats = document(title="FSL Viewer") #Creates initial HTML page (Post Stats)
postStats += h1("Sample FSL Viewer")
postStats += ul(li(a("Stats", href="stats.html")), li("-"),li(a("Post Stats", href = "postStats.html")))
postStats += h2("Post-stats")
postStats += hr()
postStats += h3("Analysis Methods")
if voxelWise == True: #If main threshold is Height Threshold
mainThreshValue = queryHeightThresholdValue(graph)
if askSpm(graph) == True:
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at P = %s (corrected)" % (softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askFsl(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at P = %s (corrected)"
%(fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif clusterWise == True: #If main threshold is extent threshold
mainThreshValue = queryClusterThresholdValue(graph)
heightThreshValue = queryUHeightThresholdValue(graph)
clusterThreshType = clusterFormingThreshType(graph, statisticType)
if askSpm(graph) == True:
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded using clusters determined by %s > %s and a (corrected) "
"cluster significance of P = %s "
% (softwareLabelNumList[1], statisticTypeString, clusterThreshType, heightThreshValue[0], mainThreshValue[0]))
elif askFsl(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl). %s statistic images were thresholded "
"using clusters determined by %s > %s and a (corrected) cluster significance of P = %s"
%(fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, clusterThreshType, heightThreshValue[0], mainThreshValue[0]))
else: #If there is no corrected threshold - assume voxel wise
mainThreshValue = queryUHeightThresholdValue(graph)
if askSpm(graph) == True and askIfPValueUncorrected(graph) == True: #SPM used and threshold type is nidm_PValueUncorrected
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at P = %s (uncorrected)" % (softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askSpm(graph) == True and askIfOboStatistic(graph) == True: #SPM used and threshold type is obo_statistic
postStats += p("FMRI data processing was carried out using SPM Version %s (SPM, http://www.fil.ion.ucl.ac.uk/spm/). %s statistic images were thresholded at %s = %s (uncorrected)" % (softwareLabelNumList[1], statisticTypeString, statisticType, mainThreshValue[0]))
elif askFsl(graph) == True and askIfPValueUncorrected(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at P = %s (uncorrected)." % (fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, mainThreshValue[0]))
elif askFsl(graph) == True and askIfOboStatistic(graph) == True:
fslFeatVersion = queryFslFeatVersion(graph)
postStats += p("FMRI data processing was carried out using FEAT (FMRI Expert Analysis Tool) Version %s, part of FSL %s (FMRIB's Software Library, www.fmrib.ox.ac.uk/fsl)."
"%s statistic images were thresholded at %s = %s (uncorrected)." % (fslFeatVersion[0], softwareLabelNumList[1], statisticTypeString, statisticType, mainThreshValue[0]))
postStats += hr()
postStats += h3("Thresholded Activation Images")
postStats += hr()
i = 0
if askFsl(graph) == True:
while i < len(contrastName):
postStats += p("%s" % contrastName[i])
postStats += img(src = statisticMapImage[i])
i = i + 1
postStatsFile = open(postStatsFilePath, "x")
print(postStats, file = postStatsFile)
postStatsFile.close()
