def cv():
base = Path('cv')
with (base / 'content' / 'data.toml').open() as toml, \
(base / 'style' / 'index.css').open() as css:
data = loads(toml.read())
with html(lang='en') as document:
with head():
meta(charset='utf-8')
meta(name='description',
content=f'{SHARED.info.person_name} (engineer|designer)')
meta(name='keywords', content=','.join(SHARED.meta.keywords))
meta(name='author', content=f'{SHARED.info.person_name}')
title(SHARED.info.person_name)
style(raw(css.read()))
with body():
with table(id='content') as content:
with tr():
with td(id='image', colspan=4):
img(src='img/header.png', alt='...')
div('Curriculum Vitae')
for row in chain(
Basic(data['basic']).as_rows(),
Skills(data['skills']).as_rows(),
Experience(data['experience']).as_rows(),
Education(data['education']).as_rows()):
content.add(row)
copyright = comment(f'Copyright (C) 2015 - {datetime.now().year} '
f'{SHARED.info.person_name}. '
'All rights reserved.')
return f'<!DOCTYPE html>{copyright}{document.render(pretty=False)}'
def site():
base = Path('website')
with (base/'content'/'index.toml').open() as toml, \
(base/'style'/'index.css').open() as css:
data = loads(toml.read())
with html(lang='en') as document:
with head():
meta(charset='utf-8')
meta(name='description',
content=f'{SHARED.info.person_name} (engineer|designer)')
meta(name='keywords', content=','.join(SHARED.meta.keywords))
meta(name='author', content=f'{SHARED.info.person_name}')
title(SHARED.info.person_name)
link(rel='shortcut icon',
type='image/x-icon',
href='favicon.ico')
link(rel='icon', type='image/x-icon', href='favicon.ico')
style(raw(css.read()))
script(src='website/js/anim.js')
script(src='website/js/index.js')
with body():
_block('engineer', data['engineer'])
_block('designer', data['designer'])
with div(id='handler'):
div(raw('«»'))
script('main();', type='text/javascript')
copyright = comment(f'Copyright (C) 2015 - {datetime.now().year} '
f'{SHARED.info.person_name}. '
'All rights reserved.')
return f'<!DOCTYPE html>{copyright}{document.render(pretty=False)}'
def _common_meta(document):
with document:
H.attr(lang=u'en')
with document.head:
H.meta(charset=u'utf-8')
H.meta(name=u'generator', content=u'HTTPolice %s' % version)
H.style(type=u'text/css').add_raw_string(css_code)
def dominate_final_page():
"""
第四頁：感謝頁，
目標：利用dominate寫出 enter_page 的 html並在 templates 資料夾中存成 index4.html
分為三個區塊
doc = dominate.document()
with doc.head (包含css的style;meta確保中文可以運行在utf-8下)
with doc.body (h1)
最後寫入文件中(在templates資料夾中存成index4.html)
"""
doc = dominate.document(title="thank_you_page")
with doc.head:
tags.meta(name='charset', content="utf-8")
tags.style("""\
body {
background-color: #F9F8F1;
color: #2C232A;
font-family: sans-serif;
font-size: 14;
text-align: center;
}
""")
with doc.body:
tags.h1('Thank You!')
fn = 'templates/index4.html'
with open(file=fn, mode='w', encoding='utf-8') as f:
f.write(doc.render())
print(f)
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 _common_meta(document):
with document:
H.attr(lang=u'en')
with document.head:
H.meta(charset=u'utf-8')
H.meta(name=u'generator', content=u'HTTPolice %s' % version)
H.style(type=u'text/css').add_raw_string(css_code)
def add_head_style(this_urlpath=""):
"""Adds <link> tags for style files, assuming <head> context."""
tags.meta(charset="utf-8")
tags.meta(name="viewport", content="width=device-width, initial-scale=1.0")
emoji = urls.link(this_urlpath, "NotoColorEmoji.ttf")
tags.style(f"""
@font-face {{
font-family: 'Noto Color Emoji';
src: local('Noto Color Emoji'), url({emoji}) format("truetype");'
}}
""")
tags.link(
rel="icon",
type="image/png",
sizes="32x32",
href=urls.link(this_urlpath, "favicon-32x32.png"),
)
tags.link(
rel="icon",
type="image/png",
sizes="16x16",
href=urls.link(this_urlpath, "favicon-16x16.png"),
)
tags.link(
rel="stylesheet",
type="text/css",
href=urls.link(this_urlpath, "style.css"),
)
tags.script(src=urls.link(this_urlpath, "video.js"))
tags.script(src="https://kit.fontawesome.com/7e1cde4d00.js",
crossorigin="anonymous")
def __init__(self, title, css='splendor'):
self.doc = dominate.document(title=title)
self.has_widgets = False
self.has_tables = False
with self.doc.head:
link(rel='stylesheet', href=Journal.css[css], type='text/css')
# bokeh css/js
link_href, js_src = bu.get_bokeh_src()
link(rel='stylesheet', href=link_href, type="text/css")
script(type='text/javascript', src=js_src)
# css to center the bokeh plots
style("""
div.bk-grid {
margin: auto;
width: 50%;
}
div.bk-plot-layout {
margin: auto;
width: 50%;
}
div.bk-root {
margin: auto;
width: 50%;
}
div.bk-canvas-wrapper {
margin: auto;
width: 50%;
}
""")
def user_summary_for(rtype, storages, output_path: Path):
ustats = {}
def reg(user, query, stats):
if user not in ustats:
ustats[user] = {}
ustats[user][query] = stats
with ProcessPoolExecutor() as pp:
digests = pp.map(get_digest, [s.path for s in storages])
for s, digest in zip(storages, digests):
everything = flatten([ch for ch in digest.changes.values()])
for user, items in group_by_key(everything,
key=lambda x: x.user).items():
reg(user, s.name, len(items))
now = datetime.now()
doc = dominate.document(
title=
f'axol tags summary for {[s.name for s in storages]}, rendered at {fdate(now)}'
)
with doc.head:
T.style(STYLE)
raw_script(JS) # TODO necessary?
# TODO FIXME can't inline due to some utf shit
sortable_js = Path(__file__).absolute().parent / 'js' / 'sorttable.js'
T.script(src=str(sortable_js))
ft = FormatTrait.for_(rtype)
with doc.body:
with T.table(cls='sortable'):
emitted_head = False
for user, stats in sorted(ustats.items(),
key=lambda x: (-len(x[1]), x)):
if not emitted_head:
with T.thead():
T.td('user')
for q, _ in stats.items():
T.td(q)
emitted_head = True
with T.tr():
T.td(ft.user_link(user))
for q, st in stats.items():
with T.td(sorttable_customkey=str(st)):
# TODO I guess unclear which tag to choose though.
T.a(
q, href=f'summary/{q}.html'
) # TODO link to source in index? or on pinboard maybe
# TODO also project onto user's tags straight away
T.sup(
str(st) if st < 5 else T.b(
T.font(str(st), color='red'))) # TODO css
output_path.write_text(str(doc))
logger.info('Dumped user summary to %s', output_path)
def prepare_page():
page = dominate.document(title='parsePic')
with page.head:
style("""
img {
max-width: 1600px;
max-height: 800px;
}
""")
return page
def make_html(pixdir, route_name, results):
title = "Pictures from %s" % route_name
document = dominate.document(title=title)
with document.head:
meta(charset="UTF-8")
style("""
table { page-break-inside:auto; border-spacing:3px; padding:3px; }
table { margin-left:auto; margin-right:auto; }
table, td, th, tr { border:1px solid green; }
th { background-color: green; color: white; }
th.tiny { width:3%; }
th.narrow { width:47%; }
th.wide { width:50%; }
tr { page-break-inside:avoid; page-break-after:auto; }
tr.center { margin-left:auto; margin-right:auto; }
tr.alt { background-color: #f0f0f0; }
caption { background-color: #c0c040; font-size: 16px; \
font-family: "Courier New"; }
body { font-size: 16px; }
@media print {
body { font-size: 8px; font-family: "Courier New" }
caption { font-size: 10px }
a {
text-decoration: none; font-style: italic; font-weight: bold}
th { background-color: white; color: black; }
}
""")
with document.body:
with table():
caption(route_name)
tr(th("Name"), th("Description"), th("Imagefile"))
for time, filename, gc, tp in results:
pathname = os.path.join(pixdir, filename)
gcname, gcdesc = map(str, gc[1:])
gclink = "http://coord.info/%s" % quote(gcname)
with tr():
td(a(gcname, href=gclink))
td(gcdesc)
td(a(filename, href=quote(pathname)))
print >> open("make_html.html", "w"), document
def build_html(parsed_tokens, css_style):
with document(title="Code") as doc:
style(css_style)
for token in parsed_tokens:
if token.type == line_break:
br()
else:
lines = token.content.split('\n')
for j in range(len(lines)):
if j != 0:
br()
span(lines[j], cls=token.type)
return doc.render(pretty=False)
def dominate_enter_page():
"""
第三頁：確認資訊頁面，對應到 @app.route('/jump') 及其函數 registerpage_run [if request.method == 'POST']
目標：利用dominate寫出 enter_page 的 html並在 templates 資料夾中存成 index3.html
分為三個區塊
doc = dominate.document()
with doc.head (包含css的style;meta確保中文可以運行在utf-8下)
with doc.body (包含 6 information: name/ password/ student_id/
telephone_number/ school_bike_license/ bike_lock_number and a button confirm)
最後寫入文件中(在templates資料夾中存成index3.html)
"""
doc = dominate.document(title="entered")
with doc.head:
tags.meta(name='charset', content="utf-8")
tags.style("""\
body {
background-color: #F9F8F1;
color: #2C232A;
font-family: sans-serif;
font-size: 14;
text-align: center;
}
""")
with doc.body:
tags.h1('welcome' + str(name_list_temp[0]))
tags.h2('please confirm your information')
with tags.section(cls='information check'):
with tags.div(cls='name', style="text-align: center"):
tags.label('your name is ' + str(name_list_temp[0]))
with tags.div(cls='password', style="text-align: center"):
tags.label('your password is ' + str(password_temp[0]))
with tags.div(cls='student_id', style="text-align: center"):
tags.label('your student id is ' + str(student_id_temp[0]))
with tags.div(cls='telephone', style="text-align: center"):
tags.label('your telephone number is ' + str(telephone_number_temp[0]))
with tags.div(cls='license', style="text-align: center"):
tags.label('the status of your bike_lice ' + str(school_bike_license_temp[0]))
with tags.div(cls='lock_number', style="text-align: center"):
tags.label('your bike lock number is ' + str(bike_lock_number_temp[0]))
with tags.div(cls='button', style="margin:0 auto; width:250px;"):
tags.input(type='button', value='confirm', style="width:120px; background-color:pink;",
onclick="location.href='http://127.0.0.1:5000/entered'")
fn = 'templates/index3.html'
with open(file=fn, mode='w', encoding='utf-8') as f:
f.write(doc.render())
print(f)
def __init__(self, web_dir, title=None, refresh=0, overwrite=True, base_url='~/www', inverted=False):
"""Initialize the HTML classes
Parameters:
web_dir (str) -- a directory that stores the webpage. HTML file will be created at <web_dir>/index.html; images will be saved at <web_dir/images/
title (str) -- the webpage name
refresh (int) -- how often the website refresh itself; if 0; no refreshing
"""
if title is None:
title = web_dir.split('/')[-1]
self.title = title
self._url = web_dir
self.web_dir = web_dir
if base_url is not None:
self.web_dir = os.path.expanduser(base_url) + self.web_dir
self.img_dir = os.path.join(self.web_dir, 'images')
self.image_dir = self.img_dir
self.video_dir = os.path.join(self.web_dir, 'videos')
self.overwrite = overwrite
if not os.path.exists(self.web_dir):
os.makedirs(self.web_dir)
if not os.path.exists(self.img_dir):
os.makedirs(self.img_dir)
if not os.path.exists(self.video_dir):
os.makedirs(self.video_dir)
self.doc = dominate.document(title=title)
with self.doc.head:
link(rel='stylesheet', href='/css/main.css')
css = """
table { border-collapse: collapse; border: 1px solid #ccc; margin: auto !important; table-layout: fixed; margin-bottom: 10px; }
th, span { font-family: monospace; }
td { word-wrap: break-word; padding: 5px; }
caption { text-align: center; font-weight: 600; }
h1, h2, h3 { text-align: center; font-weight: normal; }
html, body { font-size: 18px; }
"""
if inverted:
css += """
html, body { background-color: #111; color: #eee; }
"""
style(css)
meta(charset='utf-8')
if refresh > 0:
with self.doc.head:
meta(http_equiv="refresh", content=str(refresh))
def dominate_homepage():
"""
第一頁：歡迎頁面，對應到 @app.route('/') 及其函數 homepage_run()
目標：利用dominate寫出homepage的html並在templates資料夾中存成index1.html
分為三個區塊
doc = dominate.document()
with doc.head (包含css的style;meta確保中文可以運行在utf-8下)
with doc.body (包含welcome words and a button)
最後寫入文件中(在templates資料夾中存成index1.html)
"""
doc = dominate.document(title='homepage')
with doc.head:
tags.meta(name='charset', content="utf-8")
tags.style("""\
body {
background-color: #F9F8F1;
color: #2C232A;
font-family: sans-serif;
font-size: 30;
text-align: center;
}
section{
width: 300px;
height: 300px;
position: absolute;
top: 50%;
left: 50%;
overflow: auto;
text-align: center;
margin-left:-150px;
margin-top:-150px;
}
""")
with doc.body:
with tags.section():
with tags.div(cls='headline', style='font-size: 30;'):
tags.h1('Find Your Bike')
tags.input(type='button', value='click me', onclick="location.href='http://127.0.0.1:5000/jump'",
style="width:120px; background-color:pink; font-size: 14;")
fn = 'templates/index1.html'
with open(file=fn, mode='w', encoding='utf-8') as f:
f.write(doc.render())
print(f)
def dominate_wrong_information_page():
"""
第五頁：資料庫連接錯誤頁面，對應到 @app.route('/entered') 及其函數 eneter_success()
目標：利用dominate寫出homepage的html並在templates資料夾中存成index5.html
分為三個區塊
doc = dominate.document()
with doc.head (包含css的style;meta確保中文可以運行在utf-8下)
with doc.body (包含 words and a button)
最後寫入文件中(在templates資料夾中存成index5.html)
"""
doc = dominate.document(title='error_page')
with doc.head:
tags.meta(name='charset', content="utf-8")
tags.style("""\
body {
background-color: #F9F8F1;
color: #2C232A;
font-family: sans-serif;
font-size: 30;
text-align: center;
}
section{
width: 300px;
height: 300px;
position: absolute;
top: 50%;
left: 50%;
overflow: auto;
text-align: center;
margin-left:-150px;
margin-top:-150px;
}
""")
with doc.body:
with tags.section():
with tags.div(cls='headline', style='font-size: 30;'):
tags.h2("wrong information! please try again")
tags.input(type='button', value='return back', onclick="location.href='http://127.0.0.1:5000/'",
style="width:120px; background-color:pink; font-size: 14;")
fn = 'templates/index6.html'
with open(file=fn, mode='w', encoding='utf-8') as f:
f.write(doc.render())
print(f)
def write_index(storages, output_dir: Path):
now = datetime.now()
doc = dominate.document(
title=
f'axol index for {[s.name for s in storages]}, rendered at {fdate(now)}'
)
# TODO don't need this anymore?
rss = True
if rss:
outlines = []
for storage in storages:
name = storage.name
htmlUrl = 'https://whatever'
url = f'https://unstable.beepb00p.xyz/atom/{name}.xml'
outlines.append(
f'<outline title="{name}" text="{name}" xmlUrl="{url}" htmlUrl="{htmlUrl}"></outline>'
)
outliness = "\n".join(outlines)
XML = f"""
<?xml version="1.0" encoding="UTF-8"?>
<opml version="2.0">
<body>
<outline text="All">
{outliness}
</outline>
</body>
</opml>
"""
(output_dir / 'rendered' / 'atom' / 'feeds.opml').write_text(XML)
with doc.head:
T.style(STYLE)
with doc.body:
with T.table():
for storage in storages:
with T.tr():
T.td(storage.name)
T.td(T.a('summary', href=f'summary/{storage.name}.html'))
T.td(T.a('history', href=f'rendered/{storage.name}.html'))
T.div(T.b(T.a('pinboard users summary', href=f'pinboard_users.html')))
T.div(T.b(T.a('reddit users summary', href=f'reddit_users.html')))
T.div(T.b(T.a('github users summary', href=f'github_users.html')))
T.div(T.b(T.a('twitter users summary', href=f'twitter_users.html')))
# TODO 'last updated'?
(output_dir / 'index.html').write_text(str(doc))
def dump_html_standalone(snippets, fname, webpage_style, include_banner,
include_vernums, html_assets, html_classes):
from dominate import tags, document
from dominate.util import raw
from . import GENERATOR
from .core import SerAPI
from .html import gen_banner, wrap_classes, ASSETS
from .pygments import HTML_FORMATTER
doc = document(title=fname)
doc.head.add(tags.meta(charset="utf-8"))
doc.head.add(tags.meta(name="generator", content=GENERATOR))
doc.set_attribute("class", "alectryon-standalone")
for css in ASSETS.ALECTRYON_CSS:
doc.head.add(tags.link(rel="stylesheet", href=css))
for link in (ASSETS.IBM_PLEX_CDN, ASSETS.FIRA_CODE_CDN):
doc.head.add(raw(link))
for js in ASSETS.ALECTRYON_JS:
doc.head.add(tags.script(src=js))
html_assets.extend(ASSETS.ALECTRYON_CSS)
html_assets.extend(ASSETS.ALECTRYON_JS)
pygments_css = HTML_FORMATTER.get_style_defs('.highlight')
doc.head.add(tags.style(pygments_css, type="text/css"))
cls = wrap_classes(webpage_style, *html_classes)
root = doc.body.add(tags.article(cls=cls))
if include_banner:
root.add(raw(gen_banner(SerAPI.version_info(), include_vernums)))
for snippet in snippets:
root.add(snippet)
return doc.render(pretty=False)
def get_html_str(self, list_pocket_items: List[PocketItem]) -> str:
"""Generate the HTML code of the report page
Args:
list_pocket_items (List[PocketItem]):
Returns:
str: The complete HTML code of the generated report as a string
"""
with self.doc.head:
tags.style(
".defaultfontfamily {font-family: Lucida Sans Unicode,Lucida Grande,sans-serif;}",
type="text/css",
)
for item in list_pocket_items:
self._add_item(item)
return self.doc.render()
def render_summary(repo: Path, digest: Changes[Any], rendered: Path) -> Path:
rtype = get_result_type(repo) # TODO ??
# ODO just get trait for type??
Cumulative = CumulativeBase.for_(rtype)
NOW = datetime.now()
name = repo.stem
everything = flatten([ch for ch in digest.changes.values()])
before = len(everything)
grouped = group_by_key(everything, key=Cumulative.cumkey)
print(f'before: {before}, after: {len(grouped)}')
cumulatives = list(map(Cumulative, grouped.values()))
cumulatives = list(sorted(cumulatives, key=Cumulative.sortkey))
doc = dominate.document(
title=f'axol results for {name}, rendered at {fdate(NOW)}')
with doc.head:
T.style(STYLE)
raw_script(JS)
with doc:
T.h3("This is axol search summary")
T.div(
"You can use 'hide' function in JS (chrome debugger) to hide certain tags/subreddits/users"
)
T.h4("Sources summary")
# TODO wrap in div?
with T.div():
Cumulative.sources_summary(everything)
for cc in cumulatives:
T.div(cc.format(), cls='item')
rendered.mkdir(exist_ok=True, parents=True)
sf = rendered.joinpath(name + '.html')
with sf.open('w') as fo:
fo.write(str(doc))
return sf
def page_a():
global widgets
init_widgets()
# Create a dominate document, see https://github.com/Knio/dominate
widgets.dominate_document()
with widgets.dom_doc.body: # add css elements here...
style(raw("""body {background-color:powderblue;}"""))
args, _redirect_page_metrics = widgets.process_req(request)
if not args: return _redirect_page_metrics
app.logger.info("{} : args {}".format(PAGE_URL, args))
# redirect to another page based on widget data...
_redirect = redirect_lookup_table(args.get("sel_nexturl", None))
if _redirect: return redirect(_redirect)
widgets.get("sel_nexturl").value = '99'
doc_layout = layout(sizing_mode='scale_width')
doc_layout.children.append(
row(Div(text="""<h1>pywrapBokeh</h1><h2>Page A</h2>"""),
Paragraph(text="""Play with all these widgets.""")))
source = AjaxDataSource(
data=dict(x=[], y=[]),
adapter=CustomJS(code="return cb_data.response"),
data_url="http://127.0.0.1:6800{}".format(PAGE_URL_GET_DATA),
polling_interval=1000,
mode='append')
fig = figure(title="Streaming Example")
fig.line('x', 'y', source=source)
doc_layout.children.append(fig)
doc_layout.children.append(row(widgets.get("sel_nexturl")))
return widgets.render(doc_layout)
def html(self):
""" Method to get the `dominate` HTML of the page. This HTML needs to be
rendered.
Returns:
dominate.document: HTML document corresponding to the page.
"""
doc = dominate.document(title=self.title)
# Add favicon
if self.favicon is not None:
with doc.head:
link(rel='icon', href=self.favicon)
# Add external files (Skin)
if self.skin is not None:
with doc.head:
for ref in self.skin.libs: # Libs
link(rel='stylesheet', crossorigin='anonymous', href=ref)
for ref in self.skin.fonts: # Fonts
link(rel='stylesheet', type='text/css', href=ref)
if self.skin.rules != "":
style(raw(self.skin.rules))
# Add Widgets HTML to the page
main_div = div(cls="container")
for w in self.widgets:
main_div.add(w.html())
main_div.add(br())
doc.add(main_div)
# Add Javascript code to the page
js_str = "\n\n".join([a.js() for a in self.ajax()])
if js_str != '':
doc.add(script(src=JQUERY_CDN))
doc.add(script(raw(js_str + "\n\n" + COMMON_JS)))
return doc
def parse(target='', source='', payload=''):
try:
with open(f'{lib_dir}/style.css') as s:
styles = s.read()
except FileNotFoundError:
styles = create_css()
doc = dominate.document(title=f'YAT')
with doc.head:
style(styles)
# link(rel='stylesheet', href=f'{lib_dir}/style.css')
with doc:
container = body(cls='body').add(div(cls='def_box'))
try:
payload[0]['translations'][0]['backTranslations']
query, dict_ = parse_dict(payload)
dict_html(container, query, dict_, source, target)
return doc
except (KeyError):
trans_html(container, payload, source)
return doc
def dominate_error_page():
"""
第五頁：資料庫連接錯誤頁面，對應到 @app.route('/entered') 及其函數 eneter_success()
目標：利用dominate寫出homepage的html並在templates資料夾中存成index5.html
分為三個區塊
doc = dominate.document()
with doc.head (包含css的style;meta確保中文可以運行在utf-8下)
with doc.body (包含 words and a button)
最後寫入文件中(在templates資料夾中存成index5.html)
"""
doc = dominate.document(title='error_page')
with doc.head:
tags.meta(name='charset', content="utf-8")
tags.style("""\
body {
background-color: #F9F8F1;
color: #2C232A;
font-family: sans-serif;
font-size: 30;
text-align: center;
}
""")
with doc.body:
with tags.section():
with tags.div(cls='headline', style='font-size: 30;'):
tags.h1('Register failed! You have registered before!')
tags.input(type='button', value='return back', onclick="location.href='http://127.0.0.1:5000/'",
style="width:120px; background-color:pink; font-size: 14;")
fn = 'templates/index5.html'
with open(file=fn, mode='w', encoding='utf-8') as f:
f.write(doc.render())
print(f)
def document(title, actual_hash=None, index=False):
doc = dominate.document(title=title)
style = t.style()
style.add_raw_string(STYLE)
script = t.script()
script.add_raw_string(SCRIPT)
doc.head.add(style, script)
if actual_hash is not None:
doc.body["data-actual-hash"] = actual_hash
if index:
doc.body["data-index"] = True
return doc
def make_page(app, uri):
doc = dominate.document()
inline = False
doc.head += tags.script(util.include(root / 'domx' / 'domx.js'))
doc.head += tags.style(util.include(root / 'domx' / 'domx.css'))
page = app(doc)
try:
# router
for p in uri.path.split('/'):
if p == '':
continue
if p == '_domx':
inline = True
continue
page = getattr(page, p)
except AttributeError:
raise ValueError(404)
# render page
tags.pre(repr(page))
with doc:
page()
# dxify
def walk(node):
for i in node.children:
if not isinstance(i, tags.dom_tag):
continue
if not isinstance(i, x):
walk(i)
continue
# it's a x() marker
# todo onsubmit, etc for different types
node['onclick'] = "dx.replace('{}', '{}');".format(
i['target'],
'/_domx' + i['get'],
)
node.children.remove(i)
walk(doc.body)
if inline:
return doc.body.children[0]
else:
return doc
t.meta(charset="utf-8")
t.style("""\
span, a {
font-family: monospace;
color: black;
text-decoration: none;
margin: 0;
}
a {
color: darkblue;
}
.entry a:target {
display: block;
background-color: navy;
}
#memorymap a:target {
color: red;
}
span.leadin {
margin-right: 1rem;
}
dl { border-left: 1px solid grey; padding-left: 0.4rem; }
dt { font-weight: bold }
div.
""")
def getHTML(title,
info=None,
body=None,
style=None,
state=None,
theme=None,
icon=None):
"""Provide HTML object
:param str title: short name of the notification, e.g.: server error
:param str info: some short description if needed, e.g.: It looks like the server is not responding
:param body: it can be string or dominate tag object, e.g.:
from dominate import tags as dom
return getHTML('server error', body=dom.pre(dom.code(result['Message']))
:param str style: additional css style if needed, e.g.: '.card{color:red;}'
:param int state: response state code, if needed, e.g.: 404
:param str theme: message color theme, the same that in bootstrap 5, e.g.: 'warning'
:param str icon: awesome icon name, e.g.: 'users'
:return: str -- HTML document
"""
html = document("DIRAC - %s" % title)
# select the color to the state code
if state in [400, 401, 403, 404]:
theme = theme or "warning"
elif state in [500]:
theme = theme or "danger"
elif state in [200]:
theme = theme or "success"
# select the icon to the theme
if theme in ["warning", "warn"]:
theme = "warning"
icon = icon or "exclamation-triangle"
elif theme == "info":
icon = icon or "info"
elif theme == "success":
icon = icon or "check"
elif theme in ["error", "danger"]:
theme = "danger"
icon = icon or "times"
else:
theme = theme or "secondary"
icon = icon or "flask"
# If body is text wrap it with tags
if body and isinstance(body, six.string_types):
body = dom.pre(
dom.code(traceback.format_exc() if body == "traceback" else body),
cls="mt-5")
try:
diracLogo = collectMetadata(ignoreErrors=True).get("logoURL", "")
except Exception:
diracLogo = ""
# Create head
with html.head:
# Meta tags
dom.meta(charset="utf-8")
dom.meta(name="viewport",
content="width=device-width, initial-scale=1")
# Favicon
dom.link(rel="shortcut icon",
href="/static/core/img/icons/system/favicon.ico",
type="image/x-icon")
# Provide awesome icons
# https://fontawesome.com/v4.7/license/
dom.script(
src=
"https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/js/all.min.js"
)
# Enable bootstrap 5
# https://getbootstrap.com/docs/5.0/getting-started/introduction/
# https://getbootstrap.com/docs/5.0/about/license/
dom.link(
rel="stylesheet",
integrity=
"sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC",
href=
"https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css",
crossorigin="anonymous",
)
dom.script(
src=
"https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js",
integrity=
"sha384-MrcW6ZMFYlzcLA8Nl+NtUVF0sA7MsXsP1UyJoMp4YLEuNSfAP+JcXn/tWtIaxVXM",
crossorigin="anonymous",
)
# Provide additional css
style = ".card{transition:.3s;}.card:hover{transform:scale(1.03);}" + (
style or "")
dom.style(style)
# Create body
with html:
# Background image
dom.i(
cls="position-absolute bottom-0 start-0 translate-middle-x m-5 fa "
"fa-%s text-%s" % (icon, theme),
style="font-size:40vw;z-index:-1;",
)
# A4 page with align center
with dom.div(
cls=
"row vh-100 vw-100 justify-content-md-center align-items-center m-0"
):
with dom.div(cls="container", style="max-width:600px;") as page:
# Main panel
with dom.div(cls="row align-items-center"):
# Logo
dom.div(dom.img(src=diracLogo, cls="card-img px-2"),
cls="col-md-6 my-3")
# Information card
with dom.div(cls="col-md-6 my-3"):
# Show response state number
if state and state != 200:
dom.div(dom.h1(
state,
cls="text-center badge bg-%s text-wrap" %
theme),
cls="row py-2")
# Message title
with dom.div(cls="row"):
dom.div(dom.i(cls="fa fa-%s text-%s" %
(icon, theme)),
cls="col-auto")
dom.div(title, cls="col-auto ps-0 pb-2 fw-bold")
# Description
if info:
dom.small(dom.i(cls="fa fa-info text-info"))
dom.small(info, cls="ps-1")
# Add content
if body:
page.add(body)
return html.render()
def test_main():
global widgets
init_widgets()
# Create a dominate document, see https://github.com/Knio/dominate
widgets.dominate_document()
with widgets.dom_doc.body: # add css elements here...
style(raw("""body {background-color:powderblue;}"""))
args, _redirect_page_metrics = widgets.process_req(request)
if not args: return _redirect_page_metrics
app.logger.info("{} : args {}".format(PAGE_URL, args))
# redirect to another page based on widget data...
_redirect = redirect_lookup_table(args.get("sel_nexturl", None))
if _redirect:
widgets.get("sel_nexturl").value = None
# TODO: make a widget set value method?
# TODO: or make a init function for all the widgets, and re-init them?
return redirect(_redirect)
# reset page to initial values, if there are no parms
# the widgets have state, so update if required
if not args:
widgets.get("sel_nexturl").value = '' # reset next url select
widgets.get("s_age").value = 25
widgets.get("s_amp").value = 1
text_age = "Please tell me how old you are..."
else:
text_age = "Wow, you are {} years old!".format(
widgets.get("s_age").value)
p_text_age = Paragraph(text=text_age, width=None, height=None)
# set various widget attributes
widgets.add_css(
"dp_birthday", {
'input': {
'background-color': '#98FB98'
},
'label': {
'background-color': '#98FB98',
'font-size': '16px'
}
})
widgets.add_css(
"s_age",
{'label': {
'background-color': '#98FB98',
'font-size': '16px'
}})
# make a graph, example at https://bokeh.pydata.org/en/latest/docs/user_guide/plotting.html
amplitude = float(args.get("s_amp", 1.0))
x = arange(-2 * pi, 2 * pi, 0.1)
y = amplitude * sin(x)
y2 = linspace(0, 100, len(y))
p = figure(x_range=(-6.5, 6.5), y_range=(-2.0, 2.0), width=600, height=200)
p.circle(x, y, color="red")
p.extra_y_ranges = {"foo": Range1d(start=0, end=100)}
p.circle(x, y2, color="blue", y_range_name="foo")
p.add_layout(LinearAxis(y_range_name="foo"), 'left')
doc_layout = layout(sizing_mode='scale_width')
doc_layout.children.append(
row(Div(text="""<h1>pywrapBokeh</h1>"""),
Paragraph(text="""Play with all these widgets.""")))
doc_layout.children.append(column(widgets.get("s_age"), p_text_age))
doc_layout.children.append(
row(widgets.get("dp_birthday"), widgets.get("msel_fruit"),
widgets.get("ds_birthday")))
doc_layout.children.append(column(widgets.get("s_amp"), p))
doc_layout.children.append(
row(widgets.get("b_test"), widgets.get("toggle_1"),
widgets.get("dropdn_1")))
doc_layout.children.append(
row(widgets.get("sel_nexturl"), widgets.get("cbbg_music"),
widgets.get("cbg_music")))
doc_layout.children.append(
row(widgets.get("rbg_music"), widgets.get("rg_music"),
widgets.get("rslider_amp")))
return widgets.render(doc_layout)
def process():
# doc = dominate.document(DOCNAME)
h = html(name=DOCNAME)
with h:
# _head = head()
_head = head()
with _head:
s = style()
s.add("\nh3, h4 {text-align:center;}")
s.add("\nth {background-color:yellow;}")
s.add("\ntr, td, th {text-align:center;}")
s.add("\ntd.left {text-align:left;}")
s.add("\n")
b = body()
b.add(h3(DOCNAME))
b.add(h4(asctime()))
b.add(hr())
t = table(border="1", cellpadding="3", cellspacing="3")
b.add(t)
r = tr()
t.add(r)
r.add(th("Code"))
r.add(th("Waypoint"))
r.add(th("Image"))
r.add(th("Note"))
f = open(FILENAME, "r")
for index, line in enumerate(f.readlines()):
if index == 0:
continue
code, waypoint_name, url = line.split('\t')
r = tr()
t.add(r)
r.add(td(code))
r.add(td(a(waypoint_name, href=url)))
if code in IMAGES:
link = IMAGES[code]
if isinstance(link, type([])):
images = table()
for link in link:
r2 = tr()
r2.add(td(a(link, href=link)))
images.add(r2)
else:
images = a(link, href=link)
else:
images = ""
r.add(td(images))
if code in NOTES:
note = NOTES[code]
else:
note = "TBD"
r.add(td(note, cls="left"))
outfile = open(OUTFILE, "wb")
print >> outfile, h
outfile.close()
print "Output is in %s" % OUTFILE
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))