def render(self):
if len(self.highlights) == 0 \
and len(self.notes) == 0 \
and len(self.bookmarks) == 0:
return
with div():
h2(self.title)
if self.authors is not None:
p(f'Authors: {self.authors}')
p(f'File: {self.file_name}')
if len(self.bookmarks) > 0:
h3('Bookmarks')
with ol():
for bookmark in self.bookmarks:
with li():
bookmark.render()
if len(self.highlights) > 0:
h3('Highlights')
with ol():
for highlight in self.highlights:
with li():
highlight.render()
if len(self.notes) > 0:
h3('Notes')
with ol():
for note in self.notes:
with li():
note.render()
def close_html_doc(html_doc):
with html_doc.body.children[-1]:
assert html_doc.body.children[-1]['class'] == 'container-fluid'
with tags.div(id="search_modal"):
tags.attr(cls="modal fade")
with html_doc:
# add footnotes content of this section:
with tags.ol(id="footnotes"):
for (id) in html_doc.footnote_ids_of_this_html_doc:
footnote = word_doc_footnotes.footnotes_part.notes[id + 1]
assert footnote.id == id
htmler.add_footnote_to_output(footnote.paragraphs)
# add placeholder for searching
tags.comment("search_placeholder")
place_holder = "<!--search_placeholder-->"
with open("input_web/stub_search.html", 'r') as file:
search_html = file.read()
html_doc_name = html_doc.index
name = "debug_%s.html" % html_doc_name
with open("output/" + name, 'w') as f:
f.write(html_doc.render(pretty=True).encode('utf8'))
replace_in_file("output/" + name, place_holder, search_html)
name = "%s.html" % html_doc_name
with open("output/" + name, 'w') as f:
f.write(html_doc.render(pretty=False).encode('utf8'))
print "Created ", name
replace_in_file("output/" + name, place_holder, search_html)
def makeHtml(path, fileName, sitename, authorname, usecss, usejs):
doc = dominate.document(title=sitename)
with doc.head:
if (usecss.lower() == "y"):
link(rel='stylesheet', href='style.css')
if (usejs.lower() == "y"):
script(type='text/javascript', src='script.js')
with meta():
attr(author=authorname)
with doc:
with div(id='header').add(ol()):
for i in ['home', 'about', 'contact']:
li(a(i.title(), href='/%s.html' % i))
with div():
attr(cls='body')
p('Lorem ipsum..')
if not os.path.exists("./" + path):
os.makedirs("./" + path)
f = open("./" + path + "/" + fileName, 'w+')
f.write(str(doc))
f.close()
if (usejs.lower() == "y"):
if not os.path.exists("./" + sitename + "/js"):
os.makedirs("./" + sitename + "/js")
if (usecss.lower() == "y"):
if not os.path.exists("./" + sitename + "/css"):
os.makedirs("./" + sitename + "/css")
def close_html_doc(html_doc):
with html_doc.body.children[-1]:
assert html_doc.body.children[-1]['class'] == 'container-fluid'
with tags.div(id="search_modal"):
tags.attr(cls="modal fade")
with html_doc:
# add footnotes content of this section:
with tags.ol(id="footnotes"):
for (id) in html_doc.footnote_ids_of_this_html_doc:
footnote = word_doc_footnotes.footnotes_part.notes[id + 1]
assert footnote.id == id
htmler.add_footnote_to_output(footnote.paragraphs)
# add placeholder for searching
tags.comment("search_placeholder")
place_holder = "<!--search_placeholder-->"
with open("input_web/stub_search.html", 'r') as file:
search_html = file.read()
html_doc_name = html_doc.index
name = "debug_%s.html" % html_doc_name
with open("output/" + name, 'w') as f:
f.write(html_doc.render(inline=False).encode('utf8'))
replace_in_file("output/" + name, place_holder, search_html)
name = "%s.html" % html_doc_name
with open("output/" + name, 'w') as f:
f.write(html_doc.render(inline=True).encode('utf8'))
print "Created ", name
replace_in_file("output/" + name, place_holder, search_html)
def new_user(form, ws_url, errors=None):
title = 'New User'
d = _doc(title)
with d:
with t.form(action=form.action, method='post'):
with t.fieldset():
t.legend(title)
_errors(errors)
with t.ol(cls='step_numbers'):
with t.li():
t.p('First, create a one-word username for yourself (lowercase, no spaces)...'
)
_text_input(
*form.nv('new_username'),
('required', 'autofocus'), {
'pattern': valid.re_username,
'oninput': 'check_username(this.value)'
}, 'Type new username here',
_invalid(valid.inv_username,
form.invalid('new_username')))
_invalid(valid.inv_username_exists, False,
'username_exists_message')
with t.li():
t.p("Next, invent a password; type it in twice to make sure you've got it..."
)
_text_input('password',
None, ('required', ),
{'pattern': valid.re_password},
'Type new password here',
_invalid(valid.inv_password,
form.invalid('password')),
type_='password')
_text_input('password_confirmation',
None, ('required', ),
None,
'Type password again for confirmation',
_invalid(
valid.inv_password_confirmation,
form.invalid('password_confirmation'),
'password_match_message'),
type_='password')
with t.li():
t.p("Finally, type in an email address that can be used if you ever need a password reset (optional, but this may be very useful someday!)..."
)
_text_input(
*form.nv('email'), None,
{'pattern': valid.re_email},
'Type email address here',
_invalid(valid.inv_email, form.invalid('email')))
t.input_(type="submit", value="Done!")
t.script(_js_validate_new_user_fields())
t.script(_js_check_username(ws_url))
return d.render()
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 slide_indicator(num):
"""
Helper function that controls how image slide count works
"""
with tag.ol(_class="carousel-indicators") as o:
for cnt in range(num):
if cnt == 0:
tag.li(data_target="#carousel_controls",
data_slide_to="0", _class="active")
else:
tag.li(data_target="#carousel_controls",
data_slide_to="%s" % str(cnt))
return o
def dict_html(container, query, dict_, source, target):
container.add(div(query, cls='word'))
container.add(div(raw(
f'{langs[source]} -> {langs[target[0]]}'), cls='lang'))
for w in dict_:
def_box = container.add(div()).add(ul())
defin = dict_[w]
def_box.add(li(f'{w} ({defin["word_type"]})'.lower(),
cls='definition'))
synonyms = def_box.add(ol())
for syn in defin['variants']:
if not syn[1]:
synonyms.add(li(syn[0], cls='synonyms'))
else:
syn_word = synonyms.add(li(f'{syn[0]} ',
cls='synonyms has_example'))
syn_word.add(sup(syn[1]))
def create_html_summary(n_genomes, n_clusters, n_big_clusters):
doc = dominate.document(title='Genomes mapping summary')
with doc.head:
tags.style("""
body {
background-color: #e1f5fe;
font-family: sans-serif;
font-size: 18px;
}
.container {
width: 80%;
margin: 0 auto;
background-color: white;
padding: 15px 30px;
}
span {
font-weight: 600;
}
cite {
border-left: solid black 3px;
font-size: 12px;
}
.big_img {
width: 100%;
}
""")
with doc.body:
with tags.div(cls='container'):
tags.h1('Creating the total list of genes for {}'.format(ORGANISM))
tags.p(
raw('Total list has <span>{} genomes</span>'.format(n_genomes)
+ ' and <span>{} clusters</span>.'.format(n_clusters)))
tags.img(src='../plots/clusters_sizes.png', alt='clusters sizes')
tags.p(
raw('There are <span>{} clusters</span>'.format(n_big_clusters)
+ ' of <span>size > 5</span>.'))
tags.img(src='../plots/n_clusters_by_threshold.png',
alt='N clusters by threshold')
tags.p(
raw('Check the <i>results/</i> folder for files, which you can use for the following analysis:'
))
with tags.ul():
tags.li(
raw('<i><b>proteome.faa</b></i> — fasta file with all the protein coding genes from'
+
'all the genomes. Gene names are concatenated with their genome ID. There is also'
+
'some extra information in brackets. Example of the header:<br> '
+
'<cite>>WP_000002298.1[genome:GCF_002741575.1_ASM274157v1_] MULTISPECIES: alpha-D-ribose'
+
' 1-methylphosphonate 5-phosphate C-P-lyase [Enterobacteriaceae]'
+
' [start:4548948] [end:4549793] [genome:GCF_002741575.1_ASM274157v1_]</cite>'
))
tags.li(
raw('<i><b>genes_info.tsv</b></i> — tab separated table with 2 columns: <b>gene</b> and'
+
' <b>info</b>. Contains information for each gene in the proteome. Information'
+ ' is extracted from fasta header.'))
tags.li(
raw('<i><b>cluster_info.json</b></i> — contains counted information about the genes in'
+
' each cluster. You can use it to take a look at what genes the cluster consists of'
+
', and to set a name for the cluster. Here is the example of visualisation'
+ ' of this information for 1 cluster:'))
tags.img(src='../images/cluster_names.png')
tags.li(
raw('<i><b>total_list.csv</b></i> — table with clusters in rows and genomes in columns. Number'
+
' on the intersection means, how many genes from this cluster the genome contains.'
))
with tags.li(
raw('<i><b>clusters.csv</b></i> — data frame with following columns:'
)):
with tags.ol():
tags.li(raw('<i>cluster</i> — cluster of a sequence'))
tags.li(
raw('<i>representative</i> — boolean variable, which indicates, if the given'
+ ' sequence is representative'))
tags.li(
raw('<i>gene</i> — name of the sequence from fasta header with appended genome ID'
))
tags.li(
raw('<i>length</i> — length of the gene\'s sequence'
))
tags.li(
raw('<i>identity</i> — identity of a sequence to representative sequence'
+ ' of its cluster'))
tags.li(
raw('<i>name</i> — name of the sequence from fasta header without appended genome ID'
))
tags.li(
raw('<i>genome</i> — genome id from fasta header'))
tags.li(
raw('<i>info</i> — information about gene from its fasta header'
))
tags.p(
raw('Visualisation of the total list of genes. Each row represents a genome. Each column'
+
' represents a cluster (only clusters with <b>size > 5</b> included).'
+
' If the genome has the gene, there is a white dot on the intersection.'
+ ' Otherwise — a black dot.'))
tags.img(src='../plots/genes_presence.png',
alt='genes presence',
cls='big_img')
tags.p(
raw('Clustering of genes. These illustrations are for you to take a look at the data.'
+
' For higher quality illustrations, and the following analysis it is recommended to perform '
+
'these operations in <a href="https://software.broadinstitute.org/morpheus/">Morpheus tool</a>'
+
' (also avialable as <a href="https://github.com/cmap/morpheus.R">R package</a>).'
))
tags.img(src='../plots/genes_presence_clustering.png',
alt='genes presence clustering')
tags.p(
raw('If you had any problems during the work of the program, or have any notes, please contact'
+
' <a href="mailto:[email protected]">[email protected]</a>'
))
with open('./results/summary.html', 'w') as f:
f.write(str(doc))
import dominate
from dominate import tags as dtags
doc = dominate.document(title="TKP")
with doc.head:
dtags.link(rel="stylesheet", href="style.css", type="text/css")
with open("gtag.html", "r") as gtag:
content = gtag.read()
# print(content)
dominate.util.raw(content)
with doc:
with dtags.div(id='header').add(dtags.ol()):
for i in ['home', 'about', 'contact']:
dtags.li(dtags.a(i.title(), href='/%s.html' % i))
with dtags.div():
dtags.attr(cls='body')
dtags.p('Lorem ipsum..')
print(doc)
def generate_html_document(trackers: List[Tracker], sequences: List[Sequence],
results, storage: Storage):
def insert_figure(figure):
buffer = io.StringIO()
figure.save(buffer, "SVG")
raw(buffer.getvalue())
def insert_mplfigure(figure):
buffer = io.StringIO()
figure.savefig(buffer,
format="SVG",
bbox_inches='tight',
pad_inches=0.01,
dpi=200)
raw(buffer.getvalue())
def add_style(name, linked=False):
if linked:
link(rel='stylesheet',
href='file://' +
os.path.join(os.path.dirname(__file__), name))
else:
style(read_resource(name))
def add_script(name, linked=False):
if linked:
script(type='text/javascript',
src='file://' +
os.path.join(os.path.dirname(__file__), name))
else:
with script(type='text/javascript'):
raw("//<![CDATA[\n" + read_resource(name) + "\n//]]>")
logger = logging.getLogger("vot")
table_header, table_data, table_order = extract_measures_table(
trackers, results)
plots = extract_plots(trackers, results)
legend = StyleManager.default().legend(Tracker)
doc = dominate.document(title='VOT report')
linked = check_debug()
with doc.head:
add_style("pure.css", linked)
add_style("report.css", linked)
add_script("jquery.js", linked)
add_script("table.js", linked)
add_script("report.js", linked)
with doc:
h1("VOT report")
with ol(cls="metadata"):
li('Toolkit version: ' + toolkit_version())
li('Created: ' + datetime.datetime.now().isoformat())
if len(table_header[2]) == 0:
logger.debug("No measures found, skipping table")
else:
with table(
cls=
"overview-table pure-table pure-table-horizontal pure-table-striped"
):
with thead():
with tr():
th()
[
th(c[0].identifier, colspan=c[1])
for c in merge_repeats(table_header[0])
]
with tr():
th()
[
th(c[0].title, colspan=c[1])
for c in merge_repeats(table_header[1])
]
with tr():
th("Trackers")
[
th(c.abbreviation,
data_sort="int" if order else "")
for c, order in zip(table_header[2], table_order)
]
with tbody():
for tracker, data in table_data.items():
with tr(data_tracker=tracker.reference):
with td():
insert_mplfigure(legend.figure(tracker))
span(tracker.label)
for value, order in zip(data, table_order):
insert_cell(
value, order[tracker]
if not order is None else None)
for experiment, experiment_plots in plots.items():
if len(experiment_plots) == 0:
continue
h2("Experiment {}".format(experiment.identifier), cls="experiment")
with div(cls="plots"):
for title, plot in experiment_plots:
with div(cls="plot"):
p(title)
insert_figure(plot)
with storage.write("report.html") as filehandle:
filehandle.write(doc.render())
def generate_html_document(trackers: List[Tracker], sequences: List[Sequence], results, storage: Storage):
import io
import dominate
from dominate.tags import h1, h2, table, thead, tbody, tr, th, td, div, p, li, ol, span, style, link, script
from dominate.util import raw
order_classes = {1: "first", 2: "second", 3: "third"}
def insert_figure():
buffer = io.StringIO()
plt.savefig(buffer, format="SVG", bbox_inches='tight', transparent=True)
raw(buffer.getvalue())
plt.close()
def insert_cell(value, order):
attrs = dict(data_sort_value=order, data_value=value)
if order in order_classes:
attrs["cls"] = order_classes[order]
td(_format_value(value), **attrs)
def add_style(name, linked=False):
if linked:
link(rel='stylesheet', href='file://' + os.path.join(os.path.dirname(__file__), name))
else:
style(_read_resource(name))
def add_script(name, linked=False):
if linked:
script(type='text/javascript', src='file://' + os.path.join(os.path.dirname(__file__), name))
else:
with script(type='text/javascript'):
raw("//<![CDATA[\n" + _read_resource(name) + "\n//]]>")
logger = logging.getLogger("vot")
legend = Legend()
table_header, table_data, table_order = _extract_measures_table(trackers, results)
graphs = _extract_graphs(trackers ,results, legend)
doc = dominate.document(title='VOT report')
linked = check_debug()
with doc.head:
add_style("pure.css", linked)
add_style("report.css", linked)
add_script("jquery.js", linked)
add_script("table.js", linked)
add_script("report.js", linked)
with doc:
h1("VOT report")
with ol(cls="metadata"):
li('Toolkit version: ' + version)
li('Created: ' + datetime.datetime.now().isoformat())
if len(table_header[2]) == 0:
logger.debug("No measures found, skipping table")
else:
with table(cls="measures pure-table pure-table-horizontal pure-table-striped"):
with thead():
with tr():
th()
[th(c[0].identifier, colspan=c[1]) for c in _merge_repeats(table_header[0])]
with tr():
th()
[th(c[0].name, colspan=c[1]) for c in _merge_repeats(table_header[1])]
with tr():
th("Trackers")
[th(c.abbreviation, data_sort="int" if order else "") for c, order in zip(table_header[2], table_order)]
with tbody():
for tracker, data in table_data.items():
with tr():
number = legend.number(tracker.identifier)
with td(id="legend_%d" % number):
legend.figure(tracker.identifier)
insert_figure()
span(tracker.label)
for value, order in zip(data, table_order):
insert_cell(value, order[tracker] if not order is None else None)
for experiment, experiment_graphs in graphs.items():
if len(experiment_graphs) == 0:
continue
h2("Experiment {}".format(experiment.identifier), cls="experiment")
with div(cls="graphs"):
for title, graph in experiment_graphs:
with graph, div(cls="graph"):
p(title)
insert_figure()
with storage.write("report.html") as filehandle:
filehandle.write(doc.render())
