def run_asm_stats(assembly, out_file):
os.environ["FASTA_FILE"] = assembly
notebook = read(open("masmvaliweb/notebooks/assembly-stats.ipynb"), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
os.remove(assembly)
exportHTML = HTMLExporter(config=Config({'HTMLExporter': {'default_template': 'basic'}}))
with open(out_file, 'w') as of:
of.write(exportHTML.from_notebook_node(r.nb)[0])
def convert_nb_html(nb):
"""
Convert a notebooks output to HTML
"""
nb = run_notebook(nb)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exportHtml = HTMLExporter(config=config)
html, resources = exportHtml.from_notebook_node(nb)
soup = BeautifulSoup(html)
return ''.join(map(str, soup.findAll("div", {"class": ["output", "text_cell_render border-box-sizing rendered_html"]})))
def convert_nb_html(nb):
"""
Convert a notebooks output to HTML
"""
nb = run_notebook(nb)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exportHtml = HTMLExporter(config=config)
html, resources = exportHtml.from_notebook_node(nb)
soup = BeautifulSoup(html)
filters = ["output", "text_cell_render border-box-sizing rendered_html"]
return ''.join(map(str, soup.findAll("div", {"class": filters})))
def html_conversion(nbjson, template=None):
"""
Input template file .tpl as string.
Provisionnally use the templates in class ezmarkdown.template.
e.g. 'ezmarkdown.template.TEMPLATE_OUTPUT_CELLS_ONLY'.
"""
tpl_loader = jinja2.FileSystemLoader(TEMPLATE_DIR)
html_config = Config({"HTMLExporter": {"default_template": 'full'}})
if template:
html_config = Config({"HTMLExporter": {"template_file": template}})
html_exporter = HTMLExporter(config=html_config, extra_loaders=[tpl_loader])
html, resources = html_exporter.from_notebook_node(nbjson)
return html
def export_unit_to_html(unit):
"""Export unit into html format."""
path = os.path.dirname(os.path.realpath(__file__))
cfg = Config({'HTMLExporter':{'template_file':'basic_reduced',
'template_path':['.',path],
'filters':{'markdown2html':
markdown2html_pandoc}}})
exportHtml = HTMLExporter(config=cfg)
(body, resources) = exportHtml.from_notebook_node(unit)
body = re.sub(r'\\begin\{ *equation *\}', '\[', body)
body = re.sub(r'\\end\{ *equation *\}', '\]', body)
return body
def display(user, path):
full_path = os.path.join('/home', user, 'notebooks', path + '.ipynb')
if not os.path.exists(full_path):
return "No such notebook", 404
mtime = str(os.stat(full_path).st_mtime)
key = cache_key(user, path, mtime)
cached = redis.get(key)
if cached:
return cached
exportHtml = HTMLExporter(config=Config({'HTMLExporter':{'default_template':'basic'}}))
notebook = nbformat.reads_json(open(full_path).read())
body, res = exportHtml.from_notebook_node(notebook)
redis.set(key, body)
redis.expire(key, app.config['REDIS_EXPIRY_SECONDS'])
return body
def export_html(nb, dest_path=None, image_dir=None, image_rel_dir=None):
"""Convert notebook to HTML.
Optionally saves HTML to dest_path.
"""
c = Config({'ExtractOutputPreprocessor': {'enabled': True}})
exporter = HTMLExporter(template_file='full', config=c)
output, resources = exporter.from_notebook_node(nb)
header = output.split('<head>', 1)[1].split('</head>', 1)[0]
body = output.split('<body>', 1)[1].split('</body>', 1)[0]
# Monkeypatch CSS
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace(
'body {\n overflow: visible;\n padding: 8px;\n}\n', '')
header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
bad_anywhere = [
'navbar', 'body{', 'alert{', 'uneditable-input{', 'collapse{'
]
bad_anywhere.extend(['h%s{' % (i + 1) for i in range(6)])
bad_beginning = ['pre{', 'p{margin']
header_lines = [
x for x in header.split('\n')
if (not any(x.startswith(s)
for s in bad_beginning) and not any(s in x
for s in bad_anywhere))
]
header = '\n'.join(header_lines)
# Concatenate raw html lines
lines = ['<div class="ipynotebook">']
lines.append(header)
lines.append(body)
lines.append('</div>')
html_out = '\n'.join(lines)
if image_dir is not None and image_rel_dir is not None:
html_out = export_images(resources, image_dir, image_rel_dir, html_out)
if dest_path is not None:
with io.open(dest_path, 'w', encoding='utf-8') as f:
f.write(html_out)
return html_out
def export_html(nb, dest_path=None, image_dir=None, image_rel_dir=None):
"""Convert notebook to HTML.
Optionally saves HTML to dest_path.
"""
c = Config({'ExtractOutputPreprocessor': {'enabled': True}})
exporter = HTMLExporter(template_file='full', config=c)
output, resources = exporter.from_notebook_node(nb)
header = output.split('<head>', 1)[1].split('</head>', 1)[0]
body = output.split('<body>', 1)[1].split('</body>', 1)[0]
# Monkeypatch CSS
header = header.replace('<style', '<style scoped="scoped"')
header = header.replace(
'body {\n overflow: visible;\n padding: 8px;\n}\n', '')
header = header.replace("code,pre{", "code{")
# Filter out styles that conflict with the sphinx theme.
bad_anywhere = ['navbar',
'body{',
'alert{',
'uneditable-input{',
'collapse{']
bad_anywhere.extend(['h%s{' % (i+1) for i in range(6)])
bad_beginning = ['pre{', 'p{margin']
header_lines = [x for x in header.split('\n')
if (not any(x.startswith(s) for s in bad_beginning)
and not any(s in x for s in bad_anywhere))]
header = '\n'.join(header_lines)
# Concatenate raw html lines
lines = ['<div class="ipynotebook">']
lines.append(header)
lines.append(body)
lines.append('</div>')
html_out = '\n'.join(lines)
if image_dir is not None and image_rel_dir is not None:
html_out = export_images(resources, image_dir, image_rel_dir, html_out)
if dest_path is not None:
with open(dest_path, 'w') as f:
f.write(html_out)
return html_out
def parse(path):
source = read_text_file(path)
if path.endswith('.rst'):
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {c.tagname: str(c.children[0])
for i in docinfos for c in i.children}
parts = publish_parts(source, writer_name='html')
return {'body': parts['body'],
'date': docinfo.get('date'),
'title': parts['title']}
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
exporter = HTMLExporter(config=None, extra_loaders=[dl])
body, resources = exporter.from_notebook_node(notebook)
return {'body': body,
'date': notebook['metadata']['date'],
'title': notebook['metadata']['name']}
def article_of(notebook_txt, HTMLExporter):
notebook = nbformat.reads(notebook_txt)
hide, meta = article_meta(notebook)
for ix in sorted(hide, reverse=True):
del notebook.cells[ix]
for n, v in meta:
yield '%s: %s\n' % (n, v)
yield '\n'
exportHtml = HTMLExporter(config=Config({'HTMLExporter':
{'default_template': 'basic'}}))
body, resources = exportHtml.from_notebook_node(notebook)
# [txt[:100] for txt in resources['inlining']['css']]
yield body
def article_of(notebook_txt, HTMLExporter):
notebook = nbformat.reads(notebook_txt)
hide, meta = article_meta(notebook)
for ix in sorted(hide, reverse=True):
del notebook.cells[ix]
for n, v in meta:
yield '%s: %s\n' % (n, v)
yield '\n'
exportHtml = HTMLExporter(
config=Config({'HTMLExporter': {
'default_template': 'basic'
}}))
body, resources = exportHtml.from_notebook_node(notebook)
# [txt[:100] for txt in resources['inlining']['css']]
yield body
def convert_to_html(notebook, resources, target_directory):
"""Return a list of strings representing the rst of the given notebook."""
exporter = HTMLExporter(
template_file='gallery_page',
template_path=[os.path.dirname(__file__)],
config={'ExtractOutputPreprocessor': {
'enabled': True
}})
resources.update({'output_files_dir': 'notebook_output'})
html, resources = exporter.from_notebook_node(notebook, resources)
# Convert linked resources (such as images) into actual files in the
# source directory.
for name, data in resources.get('outputs', {}).items():
name = os.path.join(target_directory, name)
if not os.path.exists(os.path.dirname(name)):
os.makedirs(os.path.dirname(name))
with io.open(name, 'wb') as f:
f.write(data)
return html, resources.get('outputs', {}).keys()
def _parse_ipynb(self):
notebook = nbformat.reads_json(self.source)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exporter = HTMLExporter(config=config)
body, resources = exporter.from_notebook_node(notebook)
body = body[body.index('\n<div class="cell'):-36] # excise template
body = self._decapitate(body)
body = body.replace('\n</pre>', '</pre>')
self.add_mathjax = r'\(' in body
fields = notebook['metadata']
if 'date' in fields:
self.date = datetime.strptime(fields['date'], '%d %B %Y').date()
else:
self.date = datetime.now().date()
self.tags = set()
if 'tags' in fields:
self.tags.update('-'.join(tag.strip().lower().split())
for tag in fields['tags'].split(','))
if self.date and self.tags:
heading = ':Date: {}\n:Tags: {}\n'.format(
self.date.strftime('%d %B %Y').lstrip('0'),
', '.join(sorted(self.tags)),
)
parts = parse_rst(heading)
body = parts['docinfo'] + body
self.add_disqus = fields.get('add_disqus', False)
self.body_html = body
self.next_link = None
self.previous_link = None
self.add_title = True
def _parse_ipynb(self):
notebook = nbformat.reads_json(self.source)
config = Config({'HTMLExporter': {'default_template': 'basic'}})
exporter = HTMLExporter(config=config)
body, resources = exporter.from_notebook_node(notebook)
body = body[body.index('\n<div class="cell'):-36] # excise template
body = self._decapitate(body)
body = body.replace('\n</pre>', '</pre>')
self.add_mathjax = r'\(' in body
fields = notebook['metadata']
if 'date' in fields:
self.date = datetime.strptime(fields['date'], '%d %B %Y').date()
else:
self.date = datetime.now().date()
self.tags = set()
if 'tags' in fields:
self.tags.update('-'.join(tag.strip().lower().split())
for tag in fields['tags'].split(','))
if self.date and self.tags:
heading = ':Date: {}\n:Tags: {}\n'.format(
self.date.strftime('%d %B %Y').lstrip('0'),
', '.join(sorted(self.tags)),
)
parts = parse_rst(heading)
body = parts['docinfo'] + body
self.add_disqus = fields.get('add_disqus', False)
self.body_html = body
self.next_link = None
self.previous_link = None
self.add_title = True
def inner():
# run MUMmer
mummer_cmd = "echo RUNNING NUCMER && bash -x ~/github/metassemble/scripts/validate/nucmer/run-nucmer.sh test/references/Mircea_07102013_selected_refs.fasta {0} /tmp/nucmer && echo SUCCESS!".format(save_path)
#mummer_cmd = "echo fakka"
proc = subprocess.Popen(mummer_cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
while True:
char = proc.stdout.read(1)
if char:
if str(char) != '\n':
yield str(char)
else:
yield '<br />\n'
else:
break
#TODO: not working, points to relative dir
yield '<a href="/tmp/nucmer/nucmer.coords">nucmer.coords</a>\n'
notebook = read(open("masmvaliweb/notebooks/mgcov-comparison-mpld3.ipynb"), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
exportHTML = HTMLExporter(config=Config({'HTMLExporter': {'default_template': 'basic'}}))
yield exportHTML.from_notebook_node(r.nb)[0]
def parse(path):
source = read_text_file(path)
if path.endswith('.rst'):
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {
c.tagname: str(c.children[0])
for i in docinfos for c in i.children
}
parts = publish_parts(source, writer_name='html')
return {
'body': parts['body'],
'date': docinfo.get('date'),
'title': parts['title']
}
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
exporter = HTMLExporter(config=None, extra_loaders=[dl])
body, resources = exporter.from_notebook_node(notebook)
return {
'body': body,
'date': notebook['metadata']['date'],
'title': notebook['metadata']['name']
}
def parse(path):
source = read_text_file(path)
result = {}
if path.endswith('.html'):
if utils.detect_blogofile(source):
heading, info, other_html = utils.convert_blogofile(source)
parts = utils.parse_rst(heading)
body_html = parts['docinfo'] + other_html
body_html = utils.pygmentize_pre_blocks(body_html)
body_html = body_html.replace('\n</pre>', '</pre>')
result['title'] = utils.html_parser.unescape(parts['title'])
result['needs_disqus'] = True
result['date'] = info['date']
result['tags'] = info['tags']
else:
result['title'] = utils.find_title_in_html(source)
body_html = SimpleTemplate(source)
result['needs_disqus'] = False
result['date'] = None
result['tags'] = ()
result['body'] = body_html
result['next_link'] = None
result['previous_link'] = None
elif path.endswith('.rst'):
if utils.detect_blogofile(source):
heading, info, body = utils.convert_blogofile(source)
source = heading + body
result['title'] = info['title']
del heading, info, body
result['needs_disqus'] = True
else:
result['needs_disqus'] = False
doctree = publish_doctree(source)
docinfos = doctree.traverse(nodes.docinfo)
docinfo = {c.tagname: str(c.children[0])
for i in docinfos for c in i.children}
parts = utils.parse_rst(source)
# parts = publish_from_doctree(source, writer_name='html',
# settings_overrides={'initial_header_level': 2})
body = parts['docinfo'] + utils.pygmentize_pre_blocks(parts['fragment'])
result['body'] = body
result['date'] = datetime.strptime(
docinfo.get('date'), '%d %B %Y').date()
if 'title' not in result:
result['title'] = parts['title']
elif path.endswith('.ipynb'):
notebook = nbformat.reads_json(source)
docinfo = utils.build_docinfo_block_for_notebook(notebook)
exporter = HTMLExporter(config=None, extra_loaders=[dl],
filters=filters)
body, resources = exporter.from_notebook_node(notebook)
body = body.replace('\n</pre>', '</pre>')
body = body.replace('</h1>', '</h1>\n' + docinfo.rstrip())
date = notebook['metadata']['date']
if date is not None:
date = datetime.strptime(date, '%d %B %Y').date()
result['body'] = body
result['date'] = date
result['needs_disqus'] = notebook['metadata'].get('needs_disqus')
result['title'] = (notebook['metadata']['name']
or utils.find_title_in_html(body))
return result
def _generate_html(self, node, substitutions): # pragma: no cover
exporter = HTMLExporter()
exporter.register_preprocessor(
Substitute(self.nbversion, substitutions))
html, _ = exporter.from_notebook_node(node)
return html
args = parser.parse_args()
host = default.host + "/blog"
exportHtml = HTMLExporter(config=Config({'HTMLExporter':{'default_template':'basic'}}))
f = open(args.rsakey,'r')
private_key = RSA.importKey(f.read())
signer = PKCS1_v1_5.new(private_key)
url = args.url
if url == "":
url = '-'.join((args.title).lower().split(" "))
notebook = nbformat.reads_json(open(os.path.join(args.directory, args.file), "r").read())
(body,resources) = exportHtml.from_notebook_node(notebook)
content = ((body.split("</body>")[0]).split('<div class="container" id="notebook-container">')[1])[0:-16]
category = ""
if args.title == "root":
category = "static"
else:
category = args.category
data = {"title": args.title,
"url": url,
"content": content,
"author": args.author,
"year": datetime.datetime.now().year,
"month": datetime.datetime.now().month,
def _generate_html(self, node, substitutions): # pragma: no cover
exporter = HTMLExporter()
exporter.register_preprocessor(Substitute(self.nbversion,
substitutions))
html,_ = exporter.from_notebook_node(node)
return html
