def get(self):
# get the organisms, maps, and models
response = yield gen.Task(AsyncHTTPClient().fetch, get_url('server_index', protocol='http'))
if response.code == 200 and response.body is not None:
server_index_json = response.body.decode('utf-8')
else:
server_index_json = None
# get the cached maps and models
index = local_index()
# render the template
template = env.get_template('homepage.html')
data = template.render(escher=get_url('escher_min', 'local'),
homepage_css=get_url('homepage_css', 'local'),
favicon=get_url('favicon', 'local'),
logo=get_url('logo', 'local'),
documentation=get_url('documentation', protocol='https'),
github=get_url('github'),
github_releases=get_url('github_releases'),
homepage_js=get_url('homepage_js', 'local'),
map_download_url=get_url('map_download', 'local'),
server_index_json=b64dump(server_index_json),
local_index_json=b64dump(index),
version=__version__,
web_version=False)
self.set_header("Content-Type", "text/html")
self.serve(data)
def _draw_js(
self,
the_id,
enable_editing,
menu,
enable_keys,
dev,
fill_screen,
scroll_behavior,
never_ask_before_quit,
static_site_index_json,
):
draw = (
"options = {{ enable_editing: {enable_editing},\n"
"menu: {menu},\n"
"enable_keys: {enable_keys},\n"
"scroll_behavior: {scroll_behavior},\n"
"fill_screen: {fill_screen},\n"
"reaction_data: reaction_data_{the_id},\n"
"metabolite_data: metabolite_data_{the_id},\n"
"gene_data: gene_data_{the_id},\n"
"never_ask_before_quit: {never_ask_before_quit},\n"
).format(
the_id=the_id,
enable_editing=json.dumps(enable_editing),
menu=json.dumps(menu),
enable_keys=json.dumps(enable_keys),
scroll_behavior=json.dumps(scroll_behavior),
fill_screen=json.dumps(fill_screen),
never_ask_before_quit=json.dumps(never_ask_before_quit),
)
# Add the specified options
for option in self.options:
val = getattr(self, option)
if val is None:
continue
draw = draw + "{option}: {value},\n".format(option=option, value=json.dumps(val))
draw = draw + "};\n\n"
# dev needs escher.
dev_str = "" if dev else "escher."
# parse the url in javascript, for building a static site
if static_site_index_json:
# get the relative location of the escher_download urls
map_d = get_url("map_download", source="local")
model_d = get_url("model_download", source="local")
o = (
'%sstatic.load_map_model_from_url("%s", "%s", \n%s, \noptions, function(map_data_%s, model_data_%s, options) {\n'
% (dev_str, map_d, model_d, static_site_index_json, the_id, the_id)
)
draw = draw + o
# make the builder
draw = draw + (
"{dev_str}Builder(map_data_{the_id}, model_data_{the_id}, embedded_css_{the_id}, "
'd3.select("#{the_id}"), options);\n'.format(dev_str=dev_str, the_id=the_id)
)
if static_site_index_json:
draw = draw + "});\n"
return draw
def load_map(self):
"""Load the map from input map_json using load_resource, or, secondarily,
from map_name.
"""
map_json = self.map_json
if map_json is not None:
self.loaded_map_json = load_resource(self.map_json,
'map_json',
safe=self.safe)
elif self.map_name is not None:
# get the name
map_name = self.map_name
map_name = map_name.replace('.json', '')
# if the file is not present attempt to download
cache_dir = get_cache_dir(name='maps')
map_filename = join(cache_dir, map_name + '.json')
if not isfile(map_filename):
map_not_cached = 'Map "%s" not in cache. Attempting download from %s' % \
(map_name, get_url('escher_root'))
warn(map_not_cached)
try:
map_url = map_name_to_url(self.map_name)
download = urlopen(map_url)
with open(map_filename, 'w') as outfile:
outfile.write(download.read())
except HTTPError:
raise ValueError('No map named %s found in cache or at %s' % \
(map_name, map_url))
with open(map_filename) as f:
self.loaded_map_json = f.read()
def _json_for_name(name: str, kind: str):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name'])
for obj in index[kind + 's'] if obj[kind + '_name'] == name]
try:
index = server_index()
except URLError:
raise Exception('Could not connect to the Escher server')
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception('Could not find the %s %s on the server' %
(kind, name))
org, name = match[0]
url = (get_url(kind + '_download') +
'/'.join([url_escape(x, plus=False)
for x in [org, name + '.json']]))
print('Downloading %s from %s' % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in at %s' % (kind, url))
data = _decode_response(download)
return data
def _embedded_css(self, url_source):
"""Return a css string to be embedded in the SVG.
Returns self.embedded_css if it has been assigned. Otherwise, attempts
to download the css file.
Arguments
---------
url_source: Whether to load from 'web' or 'local'.
"""
if self.embedded_css is not None:
return self.embedded_css
loc = get_url('builder_embed_css', source=url_source,
local_host=self.local_host, protocol='https')
try:
download = urlopen(loc)
except URLError:
raise Exception(('Could not find builder_embed_css. Be sure to pass '
'a local_host argument to Builder if js_source is dev or local '
'and you are in an iPython notebook or a static html file.'))
data = _decode_response(download)
return data.replace('\n', ' ')
def _json_for_name(name: str, kind: str):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name'])
for obj in index[kind + 's']
if obj[kind + '_name'] == name]
try:
index = server_index()
except URLError:
raise Exception('Could not connect to the Escher server')
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception(f'Could not find the {kind} {name} on the server')
org, name = match[0]
url = (
get_url(kind + '_download') +
'/'.join([url_escape(x) for x in [org, name + '.json']])
)
print('Downloading %s from %s' % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in at %s' % (kind, url))
data = _decode_response(download)
return data
def save_html(self, filepath):
"""Save an HTML file containing the map.
:param string filepath:
The name of the HTML file.
TODO apply options from self
"""
# options = transform(self.options)
# get options
options = {}
for key in self.traits(option=True):
val = getattr(self, key)
if val is not None:
options[key] = val
options_json = json.dumps(options)
template = env.get_template('standalone.html')
embedded_css_b64 = (b64dump(self.embedded_css)
if self.embedded_css is not None else None)
html = template.render(
escher_url=get_url('escher_min'),
embedded_css_b64=embedded_css_b64,
map_data_json_b64=b64dump(self._loaded_map_json),
model_data_json_b64=b64dump(self._loaded_model_json),
options_json_b64=b64dump(options_json),
)
with open(expanduser(filepath), 'wb') as f:
f.write(html.encode('utf-8'))
def _embedded_css(self, url_source):
"""Return a css string to be embedded in the SVG.
Returns self.embedded_css if it has been assigned. Otherwise, attempts
to download the css file.
Arguments
---------
url_source: Whether to load from 'web' or 'local'.
"""
if self.embedded_css is not None:
return self.embedded_css
loc = get_url('builder_embed_css',
source=url_source,
local_host=self.local_host,
protocol='https')
try:
download = urlopen(loc)
except URLError:
raise Exception((
'Could not find builder_embed_css. Be sure to pass '
'a local_host argument to Builder if js_source is dev or local '
'and you are in an iPython notebook or a static html file.'))
data = _decode_response(download)
return data.replace('\n', ' ')
def load_map(self):
"""Load the map from input map_json using load_resource, or, secondarily,
from map_name.
"""
map_json = self.map_json
if map_json is not None:
self.loaded_map_json = load_resource(self.map_json,
'map_json',
safe=self.safe)
elif self.map_name is not None:
# get the name
map_name = self.map_name
map_name = map_name.replace('.json', '')
# if the file is not present attempt to download
cache_dir = get_cache_dir(name='maps')
map_filename = join(cache_dir, map_name + '.json')
if not isfile(map_filename):
map_not_cached = 'Map "%s" not in cache. Attempting download from %s' % \
(map_name, get_url('escher_root'))
warn(map_not_cached)
try:
map_url = map_name_to_url(self.map_name)
download = urlopen(map_url)
with open(map_filename, 'w') as outfile:
outfile.write(download.read())
except HTTPError:
raise ValueError('No map named %s found in cache or at %s' % \
(map_name, map_url))
with open(map_filename) as f:
self.loaded_map_json = f.read()
def save_html(self, filepath):
"""Save an HTML file containing the map.
:param string filepath:
The name of the HTML file.
TODO apply options from self
"""
# options = transform(self.options)
# get options
options = {}
for key in self.traits(option=True):
val = getattr(self, key)
if val is not None:
options[key] = val
options_json = json.dumps(options)
template = env.get_template('standalone.html')
embedded_css_b64 = (b64dump(self.embedded_css)
if self.embedded_css is not None else None)
html = template.render(
escher_url=get_url('escher_min'),
embedded_css_b64=embedded_css_b64,
map_data_json_b64=b64dump(self._loaded_map_json),
model_data_json_b64=b64dump(self._loaded_model_json),
options_json_b64=b64dump(options_json),
)
with open(expanduser(filepath), 'wb') as f:
f.write(html.encode('utf-8'))
def _draw_js(self, the_id, enable_editing, menu, enable_keys, dev,
fill_screen, scroll_behavior, never_ask_before_quit,
static_site_index_json):
draw = ("options = {{ enable_editing: {enable_editing},\n"
"menu: {menu},\n"
"enable_keys: {enable_keys},\n"
"scroll_behavior: {scroll_behavior},\n"
"fill_screen: {fill_screen},\n"
"reaction_data: reaction_data_{the_id},\n"
"metabolite_data: metabolite_data_{the_id},\n"
"gene_data: gene_data_{the_id},\n"
"never_ask_before_quit: {never_ask_before_quit},\n").format(
the_id=the_id,
enable_editing=json.dumps(enable_editing),
menu=json.dumps(menu),
enable_keys=json.dumps(enable_keys),
scroll_behavior=json.dumps(scroll_behavior),
fill_screen=json.dumps(fill_screen),
never_ask_before_quit=json.dumps(never_ask_before_quit))
# Add the specified options
for option in self.options:
val = getattr(self, option)
if val is None: continue
draw = draw + "{option}: {value},\n".format(option=option,
value=json.dumps(val))
draw = draw + "};\n\n"
# dev needs escher.
dev_str = '' if dev else 'escher.'
# parse the url in javascript, for building a static site
if static_site_index_json:
# get the relative location of the escher_download urls
map_d = get_url('map_download', source='local')
model_d = get_url('model_download', source='local')
o = (
'%sstatic.load_map_model_from_url("%s", "%s", \n%s, \noptions, function(map_data_%s, model_data_%s, options) {\n'
% (dev_str, map_d, model_d, static_site_index_json, the_id,
the_id))
draw = draw + o
# make the builder
draw = draw + (
'{dev_str}Builder(map_data_{the_id}, model_data_{the_id}, embedded_css_{the_id}, '
'd3.select("#{the_id}"), options);\n'.format(dev_str=dev_str,
the_id=the_id))
if static_site_index_json:
draw = draw + '});\n'
return draw
def server_index():
url = get_url('server_index', source='web', protocol='https')
try:
download = urlopen(url)
except URLError:
raise URLError('Could not contact Escher server')
index = json.loads(download.read())
return index
def server_index():
url = get_url("server_index", source="web", protocol="https")
try:
download = urlopen(url)
except URLError:
raise URLError("Could not contact Escher server")
data = _decode_response(download)
index = json.loads(data)
return index
def server_index():
url = get_url('server_index')
try:
download = urlopen(url)
except URLError:
raise URLError('Could not contact Escher server')
data = _decode_response(download)
index = json.loads(data)
return index
def server_index():
url = get_url('server_index', source='web', protocol='https')
try:
download = urlopen(url)
except URLError:
raise URLError('Could not contact Escher server')
data = _decode_response(download)
index = json.loads(data)
return index
def _json_for_name(name, kind, cache_dir):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name'])
for obj in index[kind + 's'] if obj[kind + '_name'] == name]
# first check the local index
match = match_in_index(name, local_index(cache_dir=cache_dir), kind)
if len(match) == 0:
path = None
else:
org, name = match[0]
path = join(cache_dir, kind + 's', org, name + '.json')
if path:
# load the file
with open(path, 'rb') as f:
return f.read().decode('utf-8')
# if the file is not present attempt to download
else:
try:
index = server_index()
except URLError:
raise Exception(
('Could not find the %s %s in the cache, and could '
'not connect to the Escher server' % (kind, name)))
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception(
'Could not find the %s %s in the cache or on the server' %
(kind, name))
org, name = match[0]
url = (get_url(kind + '_download', source='web', protocol='https') +
'/'.join(
[url_escape(x, plus=False) for x in [org, name + '.json']]))
warn('%s not in cache. Attempting download from %s' %
(kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in cache or at %s' % (kind, url))
data = _decode_response(download)
# save the file
org_path = join(cache_dir, kind + 's', org)
try:
os.makedirs(org_path)
except OSError:
pass
with open(join(org_path, name + '.json'), 'w') as outfile:
outfile.write(data)
return data
def test_bad_url():
with raises(Exception):
get_url('bad-name')
with raises(Exception):
get_url('d3', source='bad-source')
with raises(Exception):
get_url('d3', protocol='bad-protocol')
def test_bad_url():
with raises(Exception):
get_url('bad-name')
with raises(Exception):
get_url('d3', source='bad-source')
with raises(Exception):
get_url('d3', protocol='bad-protocol')
def _json_for_name(name, kind, cache_dir):
# check the name
name = name.replace(".json", "")
def match_in_index(name, index, kind):
return [(obj["organism"], obj[kind + "_name"]) for obj in index[kind + "s"] if obj[kind + "_name"] == name]
# first check the local index
match = match_in_index(name, local_index(cache_dir=cache_dir), kind)
if len(match) == 0:
path = None
else:
org, name = match[0]
path = join(cache_dir, kind + "s", org, name + ".json")
if path:
# load the file
with open(path, "rb") as f:
return f.read().decode("utf-8")
# if the file is not present attempt to download
else:
try:
index = server_index()
except URLError:
raise Exception(
("Could not find the %s %s in the cache, and could " "not connect to the Escher server" % (kind, name))
)
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception("Could not find the %s %s in the cache or on the server" % (kind, name))
org, name = match[0]
url = get_url(kind + "_download", source="web", protocol="https") + "/".join(
[url_escape(x, plus=False) for x in [org, name + ".json"]]
)
warn("%s not in cache. Attempting download from %s" % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError("No %s found in cache or at %s" % (kind, url))
data = _decode_response(download)
# save the file
org_path = join(cache_dir, kind + "s", org)
try:
os.makedirs(org_path)
except OSError:
pass
with open(join(org_path, name + ".json"), "w") as outfile:
outfile.write(data)
return data
def _json_for_name(name, kind, cache_dir):
# check the name
name = name.replace('.json', '')
def match_in_index(name, index, kind):
return [(obj['organism'], obj[kind + '_name']) for obj in index[kind + 's']
if obj[kind + '_name'] == name]
# first check the local index
match = match_in_index(name, local_index(cache_dir=cache_dir), kind)
if len(match) == 0:
path = None
else:
org, name = match[0]
path = join(cache_dir, kind + 's', org, name + '.json')
if path:
# load the file
with open(path, 'rb') as f:
return f.read().decode('utf-8')
# if the file is not present attempt to download
else:
try:
index = server_index()
except URLError:
raise Exception(('Could not find the %s %s in the cache, and could '
'not connect to the Escher server' % (kind, name)))
match = match_in_index(name, server_index(), kind)
if len(match) == 0:
raise Exception('Could not find the %s %s in the cache or on the server' % (kind, name))
org, name = match[0]
url = (get_url(kind + '_download', source='web', protocol='https') +
'/'.join([url_escape(x, plus=False) for x in [org, name + '.json']]))
warn('%s not in cache. Attempting download from %s' % (kind.title(), url))
try:
download = urlopen(url)
except URLError:
raise ValueError('No %s found in cache or at %s' % (kind, url))
data = _decode_response(download)
# save the file
org_path = join(cache_dir, kind + 's', org)
try:
os.makedirs(org_path)
except OSError:
pass
with open(join(org_path, name + '.json'), 'w') as outfile:
outfile.write(data)
return data
def generate_static_site():
print('Generating static site at %s' % top_directory)
# index file
template = env.get_template('homepage.html')
def static_rel(path):
return 'py/' + path
data = template.render(d3=static_rel(get_url('d3', 'local')),
boot_css=static_rel(get_url('boot_css', 'local')),
homepage_css=static_rel(get_url('homepage_css', 'local')),
favicon=static_rel(get_url('favicon', 'local')),
logo=static_rel(get_url('logo', 'local')),
documentation=get_url('documentation', protocol='https'),
github=get_url('github', protocol='https'),
github_releases=get_url('github_releases', protocol='https'),
homepage_js=static_rel(get_url('homepage_js', 'local')),
version=__version__,
map_download_url=get_url('map_download', 'local'),
web_version=True,
server_index_url=static_rel(get_url('server_index', 'local')))
with open(join(top_directory, 'index.html'), 'wb') as f:
f.write(data.encode('utf-8'))
# viewer and builder
# make the builder
builder = Builder(safe=True, id='static_map')
filepath = join(top_directory, 'builder')
with open(join(root_directory, get_url('server_index', source='local')), 'r') as f:
index_json = f.read()
html = builder.save_html(filepath=filepath,
overwrite=True,
js_source='local',
protocol=None,
minified_js=True,
static_site_index_json=index_json)
# copy over the source maps
escher_map = get_url('escher_min', 'local') + '.map'
builder_css_map = get_url('builder_css_min', 'local') + '.map'
shutil.copy(join(root_directory, escher_map), join(top_directory, 'builder', escher_map))
shutil.copy(join(root_directory, builder_css_map), join(top_directory, 'builder', builder_css_map))
def get(self, kind, path):
# builder vs. viewer
enable_editing = (kind=='builder')
# Builder options
builder_kwargs = {}
for a in ['starting_reaction', 'model_name', 'map_name', 'map_json',
'reaction_no_data_color', 'reaction_no_data_size',
'metabolite_no_data_color', 'metabolite_no_data_size',
'hide_secondary_nodes']:
args = self.get_arguments(a)
if len(args)==1:
builder_kwargs[a] = (True if args[0].lower()=='true' else
(False if args[0].lower()=='false' else
args[0]))
# array args
for a in ['quick_jump', 'metabolite_size_range', 'metabolite_color_range',
'reaction_size_range', 'reaction_color_range', 'gene_styles']:
args = self.get_arguments(a + '[]')
if len(args) > 0:
builder_kwargs[a] = args
# js source
args = self.get_arguments('js_source')
js_source = args[0] if len(args) == 1 else 'web'
# if the server is running locally, then the embedded css must be loaded
# asynchronously using the same server thread.
if js_source in ['dev', 'local']:
global PORT
url = get_url('builder_embed_css',
source='local',
local_host='http://localhost:%d' % PORT)
response = yield gen.Task(AsyncHTTPClient().fetch, url)
if response.code != 200 or response.body is None:
raise Exception('Could not load embedded_css from %s' % url)
builder_kwargs['embedded_css'] = (response.body
.decode('utf-8')
.replace('\n', ' '))
# example data
def load_data_file(rel_path):
"""Load a JSON file with relative path."""
try:
with open(join(root_directory, rel_path), 'r') as f:
return json.load(f)
except:
logging.warn('Could not load example_data file: %s' % rel_path)
if len(self.get_arguments('example_data')) > 0:
r_filepath = 'escher/example_data/reaction_data_iJO1366.json'
builder_kwargs['reaction_data'] = load_data_file(r_filepath)
m_filepath = 'escher/example_data/metabolite_data_iJO1366.json'
builder_kwargs['metabolite_data'] = load_data_file(m_filepath)
# make the builder
builder = Builder(safe=True, **builder_kwargs)
# display options
display_kwargs = {'minified_js': True,
'scroll_behavior': 'pan',
'menu': 'all'}
# keyword
for a in ['menu', 'scroll_behavior', 'minified_js',
'auto_set_data_domain', 'never_ask_before_quit']:
args = self.get_arguments(a)
if len(args)==1:
display_kwargs[a] = (True if args[0].lower()=='true' else
(False if args[0].lower()=='false' else
args[0]))
html = builder._get_html(js_source=js_source, enable_editing=enable_editing,
enable_keys=True, html_wrapper=True, fill_screen=True,
height='100%', **display_kwargs)
self.set_header("Content-Type", "text/html")
self.serve(html)
def test_map_json_for_name_web(tmpdir):
data = map_json_for_name("iJO1366.Central metabolism", cache_dir=str(tmpdir))
root = get_url("escher_root", protocol="https").rstrip("/")
assert json.loads(data)[0]["schema"] == "/".join([root, "escher", "jsonschema", __schema_version__ + "#"])
def test_cdn():
url = get_url('boot_js', 'web')
assert url == '//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.6/js/bootstrap.min.js'
def _get_html(self, js_source='web', menu='none', scroll_behavior='pan',
html_wrapper=False, enable_editing=False, enable_keys=False,
minified_js=True, fill_screen=False, height='800px',
never_ask_before_quit=False, static_site_index_json=None):
"""Generate the Escher HTML.
Arguments
--------
js_source: Can be one of the following:
'web' - (Default) use js files from escher.github.io.
'local' - use compiled js files in the local escher installation. Works offline.
'dev' - use the local, uncompiled development files. Works offline.
menu: Menu bar options include:
'none' - (Default) No menu or buttons.
'zoom' - Just zoom buttons (does not require bootstrap).
'all' - Menu and button bar (requires bootstrap).
scroll_behavior: Scroll behavior options:
'pan' - (Default) Pan the map.
'zoom' - Zoom the map.
'none' - No scroll events.
minified_js: If True, use the minified version of js files. If
js_source is 'dev', then this option is ignored.
html_wrapper: If True, return a standalone html file.
enable_editing: Enable the editing modes (build, rotate, etc.).
enable_keys: Enable keyboard shortcuts.
height: The height of the HTML container.
never_ask_before_quit: Never display an alert asking if you want to
leave the page. By default, this message is displayed if enable_editing
is True.
static_site_index_json: The index, as a JSON string, for the static
site. Use javascript to parse the URL options. Used for
generating static pages (see static_site.py).
"""
if js_source not in ['web', 'local', 'dev']:
raise Exception('Bad value for js_source: %s' % js_source)
if menu not in ['none', 'zoom', 'all']:
raise Exception('Bad value for menu: %s' % menu)
if scroll_behavior not in ['pan', 'zoom', 'none']:
raise Exception('Bad value for scroll_behavior: %s' % scroll_behavior)
content = env.get_template('content.html')
# if height is not a string
if type(height) is int:
height = "%dpx" % height
elif type(height) is float:
height = "%fpx" % height
elif type(height) is str:
height = str(height)
# set the proper urls
url_source = 'local' if (js_source=='local' or js_source=='dev') else 'web'
is_dev = (js_source=='dev')
d3_url = get_url('d3', url_source, self.local_host)
d3_rel_url = get_url('d3', url_source)
escher_url = ('' if js_source=='dev' else
get_url('escher_min' if minified_js else 'escher',
url_source, self.local_host))
jquery_url = ('' if not menu=='all' else
get_url('jquery', url_source, self.local_host))
boot_css_url = ('' if not menu=='all' else
get_url('boot_css', url_source, self.local_host))
boot_js_url = ('' if not menu=='all' else
get_url('boot_js', url_source, self.local_host))
require_js_url = get_url('require_js', url_source, self.local_host)
escher_css_url = get_url('builder_css', url_source, self.local_host)
favicon_url = get_url('favicon', url_source, self.local_host)
lh_string = ('' if self.local_host is None else
self.local_host.rstrip('/') + '/')
html = content.render(id=self.the_id,
height=height,
dev=is_dev,
d3=d3_url,
d3_rel=d3_rel_url,
escher=escher_url,
jquery=jquery_url,
boot_css=boot_css_url,
boot_js=boot_js_url,
require_js=require_js_url,
escher_css=escher_css_url,
wrapper=html_wrapper,
title='Escher ' + ('Builder' if enable_editing else 'Viewer'),
favicon=favicon_url,
host=lh_string,
initialize_js=self._initialize_javascript(self.the_id, url_source),
draw_js=self._draw_js(self.the_id, enable_editing,
menu, enable_keys, is_dev,
fill_screen, scroll_behavior,
never_ask_before_quit,
static_site_index_json))
return html
def test_load_resource_web(tmpdir):
url = "/".join([get_url("map_download", protocol="https"), "Escherichia%20coli/iJO1366.Central%20metabolism.json"])
_ = json.loads(_load_resource(url, "name"))
def save_html(self,
filepath=None,
overwrite=False,
js_source='web',
protocol='https',
menu='all',
scroll_behavior='pan',
enable_editing=True,
enable_keys=True,
minified_js=True,
never_ask_before_quit=False,
static_site_index_json=None):
"""Save an HTML file containing the map.
:param string filepath:
The HTML file will be saved to this location. When js_source is
'local', then a new directory will be created with this name.
:param Boolean overwrite:
Overwrite existing files.
:param string js_source:
Can be one of the following:
- *web* (Default) - Use JavaScript files from escher.github.io.
- *local* - Use compiled JavaScript files in the local Escher
installation. Works offline. To make the dependencies
available to the downloaded file, a new directory will
be made with the name specified by filepath.
- *dev* - No longer necessary with source maps. This now gives the
same behavior as 'local'.
:param string protocol:
The protocol can be 'http', 'https', or None which indicates a
'protocol relative URL', as in //escher.github.io. Ignored if source
is local.
:param string menu: Menu bar options include:
- *none* - No menu or buttons.
- *zoom* - Just zoom buttons.
- *all* (Default) - Menu and button bar.
:param string scroll_behavior: Scroll behavior options:
- *pan* - Pan the map.
- *zoom* - Zoom the map.
- *none* (Default) - No scroll events.
:param Boolean enable_editing: Enable the map editing modes.
:param Boolean enable_keys: Enable keyboard shortcuts.
:param Boolean minified_js:
If True, use the minified version of JavaScript and CSS files.
:param number height: Height of the HTML container.
:param Boolean never_ask_before_quit:
Never display an alert asking if you want to leave the page. By
default, this message is displayed if enable_editing is True.
:param string static_site_index_json:
The index, as a JSON string, for the static site. Use javascript
to parse the URL options. Used for generating static pages (see
static_site.py).
"""
filepath = expanduser(filepath)
if js_source in ['local', 'dev']:
if filepath is None:
raise Exception(
'Must provide a filepath when js_source is not "web"')
# make a directory
directory = re.sub(r'\.html$', '', filepath)
if exists(directory):
if not overwrite:
raise Exception('Directory already exists: %s' % directory)
else:
os.makedirs(directory)
# add dependencies to the directory
escher = get_url('escher_min' if minified_js else 'escher',
'local')
favicon = get_url('favicon', 'local')
for path in [escher, favicon]:
if path is None:
continue
src = join(root_directory, path)
dest = join(directory, path)
dest_dir = dirname(dest)
if not exists(dest_dir):
os.makedirs(dest_dir)
shutil.copy(src, dest)
filepath = join(directory, 'index.html')
else:
if not filepath.endswith('.html'):
filepath += '.html'
if exists(filepath) and not overwrite:
raise Exception('File already exists: %s' % filepath)
html = self._get_html(js_source=js_source,
menu=menu,
scroll_behavior=scroll_behavior,
html_wrapper=True,
enable_editing=enable_editing,
enable_keys=enable_keys,
minified_js=minified_js,
fill_screen=True,
height="100%",
never_ask_before_quit=never_ask_before_quit,
static_site_index_json=static_site_index_json,
protocol=protocol)
if filepath is not None:
with open(filepath, 'wb') as f:
f.write(html.encode('utf-8'))
return filepath
else:
from tempfile import mkstemp
from os import write, close
os_file, filename = mkstemp(suffix=".html", text=False) # binary
write(os_file, html.encode('utf-8'))
close(os_file)
return filename
def test_no_protocol():
url = get_url('escher', 'web')
assert url == '//unpkg.com/escher@%s/dist/escher.js' % __version__
def test_localhost():
url = get_url('escher',
source='local',
local_host='http://localhost:7778/')
assert url == 'http://localhost:7778/escher/static/escher/escher.js'
def test_map_download_url():
url = get_url('map_download')
assert url == ('https://escher.github.io/%s/%s/maps/' %
(__schema_version__, __map_model_version__))
def test_urls():
# online
url = get_url('builder_embed_css', source='web', protocol='https')
assert url == 'https://escher.github.io/builder-embed-%s.css' % __version__
# no protocol
url = get_url('escher', 'web')
assert url == '//escher.github.io/escher-%s.js' % __version__
# local
url = get_url('require_js', 'local')
assert url == 'escher/lib/require.min.js'
assert exists(join(root_directory, url))
# localhost
url = get_url('require_js',
source='local',
local_host='http://localhost:7778/')
assert url == 'http://localhost:7778/escher/lib/require.min.js'
# cdn
url = get_url('boot_js', 'web')
assert url == '//netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js'
# download
url = get_url('server_index', source='local')
assert url == __schema_version__ + '/' + __map_model_version__ + '/index.json'
url = get_url('map_download', protocol='https')
assert url == 'https://escher.github.io/%s/%s/maps/' % (
__schema_version__, __map_model_version__)
# raises
with raises(Exception):
get_url('bad-name')
with raises(Exception):
get_url('d3', source='bad-source')
with raises(Exception):
get_url('d3', protocol='bad-protocol')
def generate_static_site():
print('Generating static site at %s' % root_directory)
# index file
template = env.get_template('index.html')
data = template.render(d3=get_url('d3', 'local'),
boot_css=get_url('boot_css', 'local'),
index_css=get_url('index_css', 'local'),
favicon=get_url('favicon', 'local'),
logo=get_url('logo', 'local'),
documentation=get_url('documentation', protocol='https'),
github=get_url('github', protocol='https'),
github_releases=get_url('github_releases', protocol='https'),
index_js=get_url('index_js', 'local'),
index_gh_pages_js=get_url('index_gh_pages_js', 'local'),
version=__version__,
map_download=get_url('map_download', 'local'),
web_version=True,
server_index_url=get_url('server_index', 'local'),
# server_index=
# local_index=
can_dev=False,
# can_dev_js=
)
with open(join(root_directory, 'index.html'), 'w') as f:
f.write(data.encode('utf-8'))
# viewer and builder
for kind in ['viewer', 'builder']:
for minified_js in [True, False]:
js_source = 'local'
enable_editing = (kind=='builder')
# make the builder
with open(join(root_directory, get_url('builder_embed_css', 'local')), 'r') as f:
css = f.read()
builder = Builder(embedded_css=css, safe=True, id='static')
filepath = join(root_directory,
'%s%s.html' % (kind, '' if minified_js else '_not_minified'))
with open(join(root_directory, get_url('server_index', source='local')), 'r') as f:
index_json = f.read()
html = builder.save_html(filepath=filepath,
js_source=js_source,
minified_js=minified_js,
enable_editing=enable_editing,
static_site_index_json=index_json)
def test_bad_url():
with raises(Exception):
get_url('bad-name')
def _get_html(self,
js_source='web',
menu='none',
scroll_behavior='pan',
html_wrapper=False,
enable_editing=False,
enable_keys=False,
minified_js=True,
fill_screen=False,
height='800px',
never_ask_before_quit=False,
static_site_index_json=None,
protocol=None,
ignore_bootstrap=False):
"""Generate the Escher HTML.
Arguments
--------
js_source: Can be one of the following:
'web' - (Default) use js files from unpkg.
'local' - Use compiled js files in the local escher installation. Works offline.
'dev' - No longer necessary with source maps. This now gives the
same behavior as 'local'.
menu: Menu bar options include:
'none' - (Default) No menu or buttons.
'zoom' - Just zoom buttons (does not require bootstrap).
'all' - Menu and button bar (requires bootstrap).
scroll_behavior: Scroll behavior options:
'pan' - (Default) Pan the map.
'zoom' - Zoom the map.
'none' - No scroll events.
minified_js: If True, use the minified version of JavaScript files.
html_wrapper: If True, return a standalone html file.
enable_editing: Enable the editing modes (build, rotate, etc.).
enable_keys: Enable keyboard shortcuts.
height: The height of the HTML container.
never_ask_before_quit: Never display an alert asking if you want to
leave the page. By default, this message is displayed if enable_editing
is True.
static_site_index_json: The index, as a JSON string, for the static
site. Use javascript to parse the URL options. Used for
generating static pages (see static_site.py).
protocol: The protocol can be 'http', 'https', or None which indicates a
'protocol relative URL', as in //escher.github.io. Ignored if source is
local.
ignore_bootstrap: Deprecated
"""
if js_source not in ['web', 'local', 'dev']:
raise Exception('Bad value for js_source: %s' % js_source)
if menu not in ['none', 'zoom', 'all']:
raise Exception('Bad value for menu: %s' % menu)
if scroll_behavior not in ['pan', 'zoom', 'none']:
raise Exception('Bad value for scroll_behavior: %s' %
scroll_behavior)
content = env.get_template('content.html')
# if height is not a string
if type(height) is int:
height = "%dpx" % height
elif type(height) is float:
height = "%fpx" % height
elif type(height) is str:
height = str(height)
# set the proper urls
url_source = 'local' if (js_source == 'local'
or js_source == 'dev') else 'web'
local_host = self.local_host
# get the urls
escher_url = get_url(('escher_min' if minified_js else 'escher'),
url_source, local_host, protocol)
favicon_url = get_url('favicon', url_source, local_host, protocol)
# for static site
map_download_url = get_url('map_download', url_source, local_host,
protocol)
model_download_url = get_url('model_download', url_source, local_host,
protocol)
# local host
lh_string = ('' if local_host is None else local_host.rstrip('/') +
'/')
# options
options = {
'menu': menu,
'enable_keys': enable_keys,
'enable_editing': enable_editing,
'scroll_behavior': scroll_behavior,
'fill_screen': fill_screen,
'never_ask_before_quit': never_ask_before_quit,
'reaction_data': self.reaction_data,
'metabolite_data': self.metabolite_data,
'gene_data': self.gene_data,
}
# Add the specified options
for option in self.options:
val = getattr(self, option)
if val is None:
continue
options[option] = val
html = content.render(
# standalone
title='Escher ' + ('Builder' if enable_editing else 'Viewer'),
favicon_url=favicon_url,
# content
wrapper=html_wrapper,
height=height,
id=self.the_id,
escher_url=escher_url,
# dump json
id_json=json_dump_and_escape(self.the_id),
options_json=json_dump_and_escape(options),
map_download_url_json=json_dump_and_escape(map_download_url),
model_download_url_json=json_dump_and_escape(model_download_url),
builder_embed_css_json=json_dump_and_escape(self.embedded_css),
# alreay json
map_data_json=escape_json_or_null(self.loaded_map_json),
model_data_json=escape_json_or_null(self.loaded_model_json),
static_site_index_json=escape_json_or_null(static_site_index_json),
)
return html
def test_local():
url = get_url('escher_min', 'local')
assert url == 'escher/static/escher/escher.min.js'
assert exists(join(root_directory, url))
def save_html(self, filepath=None, overwrite=False, js_source='web',
protocol='https', menu='all', scroll_behavior='pan',
enable_editing=True, enable_keys=True, minified_js=True,
never_ask_before_quit=False, static_site_index_json=None):
"""Save an HTML file containing the map.
:param string filepath:
The HTML file will be saved to this location. When js_source is
'local', then a new directory will be created with this name.
:param Boolean overwrite:
Overwrite existing files.
:param string js_source:
Can be one of the following:
- *web* (Default) - Use JavaScript files from escher.github.io.
- *local* - Use compiled JavaScript files in the local Escher
installation. Works offline. To make the dependencies
available to the downloaded file, a new directory will
be made with the name specified by filepath.
- *dev* - No longer necessary with source maps. This now gives the
same behavior as 'local'.
:param string protocol:
The protocol can be 'http', 'https', or None which indicates a
'protocol relative URL', as in //escher.github.io. Ignored if source
is local.
:param string menu: Menu bar options include:
- *none* - No menu or buttons.
- *zoom* - Just zoom buttons.
- *all* (Default) - Menu and button bar (requires Bootstrap).
:param string scroll_behavior: Scroll behavior options:
- *pan* - Pan the map.
- *zoom* - Zoom the map.
- *none* (Default) - No scroll events.
:param Boolean enable_editing: Enable the map editing modes.
:param Boolean enable_keys: Enable keyboard shortcuts.
:param Boolean minified_js:
If True, use the minified version of JavaScript and CSS files.
:param number height: Height of the HTML container.
:param Boolean never_ask_before_quit:
Never display an alert asking if you want to leave the page. By
default, this message is displayed if enable_editing is True.
:param string static_site_index_json:
The index, as a JSON string, for the static site. Use javascript
to parse the URL options. Used for generating static pages (see
static_site.py).
"""
filepath = expanduser(filepath)
if js_source in ['local', 'dev']:
if filepath is None:
raise Exception('Must provide a filepath when js_source is not "web"')
# make a directory
directory = re.sub(r'\.html$', '', filepath)
if exists(directory):
if not overwrite:
raise Exception('Directory already exists: %s' % directory)
else:
os.makedirs(directory)
# add dependencies to the directory
escher = get_url('escher_min' if minified_js else 'escher', 'local')
builder_css = get_url('builder_css_min' if minified_js else 'builder_css', 'local')
d3 = get_url('d3', 'local')
favicon = get_url('favicon', 'local')
if menu == 'all':
boot_css = get_url('boot_css', 'local')
boot_js = get_url('boot_js', 'local')
jquery = get_url('jquery', 'local')
boot_font_eot = get_url('boot_font_eot', 'local')
boot_font_svg = get_url('boot_font_svg', 'local')
boot_font_woff = get_url('boot_font_woff', 'local')
boot_font_woff2 = get_url('boot_font_woff2', 'local')
boot_font_ttf = get_url('boot_font_ttf', 'local')
else:
boot_css = boot_js = jquery = None
boot_font_eot = boot_font_svg = None
boot_font_woff = boot_font_woff2 = boot_font_ttf = None
for path in [escher, builder_css, boot_css, boot_js, jquery, d3,
favicon, boot_font_eot, boot_font_svg, boot_font_woff,
boot_font_woff2, boot_font_ttf]:
if path is None:
continue
src = join(root_directory, path)
dest = join(directory, path)
dest_dir = dirname(dest)
if not exists(dest_dir):
os.makedirs(dest_dir)
shutil.copy(src, dest)
filepath = join(directory, 'index.html')
else:
if not filepath.endswith('.html'):
filepath += '.html'
if exists(filepath) and not overwrite:
raise Exception('File already exists: %s' % filepath)
html = self._get_html(js_source=js_source, menu=menu,
scroll_behavior=scroll_behavior,
html_wrapper=True, enable_editing=enable_editing,
enable_keys=enable_keys, minified_js=minified_js,
fill_screen=True, height="100%",
never_ask_before_quit=never_ask_before_quit,
static_site_index_json=static_site_index_json,
protocol=protocol)
if filepath is not None:
with open(filepath, 'wb') as f:
f.write(html.encode('utf-8'))
return filepath
else:
from tempfile import mkstemp
from os import write, close
os_file, filename = mkstemp(suffix=".html", text=False) # binary
write(os_file, html.encode('utf-8'))
close(os_file)
return filename
def test_download():
url = get_url('server_index', source='local')
assert url == '../' + __schema_version__ + '/' + __map_model_version__ + '/index.json'
url = get_url('map_download', protocol='https')
assert url == 'https://escher.github.io/%s/%s/maps/' % (
__schema_version__, __map_model_version__)
def test_load_resource_web(tmpdir):
url = '/'.join([
get_url('map_download', protocol='https'),
'Escherichia%20coli/iJO1366.Central%20metabolism.json'
])
_ = json.loads(_load_resource(url, 'name'))
def test_online():
url = get_url('escher', source='web', protocol='https')
assert url == 'https://unpkg.com/escher@%s/dist/escher.js' % __version__
def test_local():
url = get_url('boot_js', 'local')
assert url == 'escher/static/lib/bootstrap.min.js'
assert exists(join(root_directory, url))
def _get_html(self, js_source='web', menu='none', scroll_behavior='pan',
html_wrapper=False, enable_editing=False, enable_keys=False,
minified_js=True, fill_screen=False, height='800px',
never_ask_before_quit=False, static_site_index_json=None,
protocol=None, ignore_bootstrap=False):
"""Generate the Escher HTML.
Arguments
--------
js_source: Can be one of the following:
'web' - (Default) use js files from escher.github.io.
'local' - use compiled js files in the local escher installation. Works offline.
'dev' - use the local, uncompiled development files. Works offline.
menu: Menu bar options include:
'none' - (Default) No menu or buttons.
'zoom' - Just zoom buttons (does not require bootstrap).
'all' - Menu and button bar (requires bootstrap).
scroll_behavior: Scroll behavior options:
'pan' - (Default) Pan the map.
'zoom' - Zoom the map.
'none' - No scroll events.
minified_js: If True, use the minified version of JavaScript and CSS
files.
html_wrapper: If True, return a standalone html file.
enable_editing: Enable the editing modes (build, rotate, etc.).
enable_keys: Enable keyboard shortcuts.
height: The height of the HTML container.
never_ask_before_quit: Never display an alert asking if you want to
leave the page. By default, this message is displayed if enable_editing
is True.
static_site_index_json: The index, as a JSON string, for the static
site. Use javascript to parse the URL options. Used for
generating static pages (see static_site.py).
protocol: The protocol can be 'http', 'https', or None which indicates a
'protocol relative URL', as in //escher.github.io. Ignored if source is
local.
ignore_bootstrap: Do not use Bootstrap for buttons, even if it
available. This is used to embed Escher in a Jupyter notebook where it
conflicts with the Jupyter Boostrap installation.
"""
if js_source not in ['web', 'local', 'dev']:
raise Exception('Bad value for js_source: %s' % js_source)
if menu not in ['none', 'zoom', 'all']:
raise Exception('Bad value for menu: %s' % menu)
if scroll_behavior not in ['pan', 'zoom', 'none']:
raise Exception('Bad value for scroll_behavior: %s' % scroll_behavior)
content = env.get_template('content.html')
# if height is not a string
if type(height) is int:
height = "%dpx" % height
elif type(height) is float:
height = "%fpx" % height
elif type(height) is str:
height = str(height)
# set the proper urls
url_source = 'local' if (js_source=='local' or js_source=='dev') else 'web'
local_host = self.local_host
# get the urls
d3_url = get_url('d3', url_source, local_host, protocol)
escher_url = get_url(('escher_min' if minified_js else 'escher'),
url_source, local_host, protocol)
if menu == 'all' and not ignore_bootstrap:
jquery_url = get_url('jquery', url_source, local_host, protocol)
boot_css_url = get_url('boot_css', url_source, local_host, protocol)
boot_js_url = get_url('boot_js', url_source, local_host, protocol)
else:
jquery_url = boot_css_url = boot_js_url = None
escher_css_url = get_url(('builder_css_min' if minified_js else 'builder_css'),
url_source, local_host, protocol)
favicon_url = get_url('favicon', url_source, local_host, protocol)
# for static site
map_download_url = get_url('map_download', url_source, local_host, protocol)
model_download_url = get_url('model_download', url_source, local_host, protocol)
# local host
lh_string = ('' if local_host is None else
local_host.rstrip('/') + '/')
# options
options = {
'menu': menu,
'enable_keys': enable_keys,
'enable_editing': enable_editing,
'scroll_behavior': scroll_behavior,
'fill_screen': fill_screen,
'ignore_bootstrap': ignore_bootstrap,
'never_ask_before_quit': never_ask_before_quit,
'reaction_data': self.reaction_data,
'metabolite_data': self.metabolite_data,
'gene_data': self.gene_data,
}
# Add the specified options
for option in self.options:
val = getattr(self, option)
if val is None:
continue
options[option] = val
html = content.render(
# standalone
title='Escher ' + ('Builder' if enable_editing else 'Viewer'),
jquery_url=jquery_url,
boot_js_url=boot_js_url,
boot_css_url=boot_css_url,
escher_css_url=escher_css_url,
favicon_url=favicon_url,
# content
wrapper=html_wrapper,
height=height,
id=self.the_id,
d3_url=d3_url,
escher_url=escher_url,
# dump json
id_json=json_dump_and_escape(self.the_id),
options_json=json_dump_and_escape(options),
map_download_url_json=json_dump_and_escape(map_download_url),
model_download_url_json=json_dump_and_escape(model_download_url),
builder_embed_css_json=json_dump_and_escape(self.embedded_css),
# alreay json
map_data_json=escape_json_or_null(self.loaded_map_json),
model_data_json=escape_json_or_null(self.loaded_model_json),
static_site_index_json=escape_json_or_null(static_site_index_json),
)
return html
def test_index_url():
url = get_url('server_index')
assert url == ('https://escher.github.io/%s/%s/index.json' %
(__schema_version__, __map_model_version__))
def test_map_json_for_name_web(tmpdir):
data = map_json_for_name('iJO1366.Central metabolism',
cache_dir=str(tmpdir))
root = get_url('escher_root', protocol='https').rstrip('/')
assert json.loads(data)[0]['schema'] == '/'.join(
[root, 'escher', 'jsonschema', __schema_version__ + '#'])
def test_online():
url = get_url('escher')
assert url == 'https://unpkg.com/escher@%s/dist/escher.js' % __version__
def test_no_protocol():
url = get_url('escher', 'web')
assert url == '//npmcdn.com/escher-vis@%s/js/dist/escher.js' % __version__
def _get_html(self,
js_source='web',
menu='none',
scroll_behavior='pan',
html_wrapper=False,
enable_editing=False,
enable_keys=False,
minified_js=True,
fill_screen=False,
height='800px',
never_ask_before_quit=False,
static_site_index_json=None):
"""Generate the Escher HTML.
Arguments
--------
js_source: Can be one of the following:
'web' - (Default) use js files from escher.github.io.
'local' - use compiled js files in the local escher installation. Works offline.
'dev' - use the local, uncompiled development files. Works offline.
menu: Menu bar options include:
'none' - (Default) No menu or buttons.
'zoom' - Just zoom buttons (does not require bootstrap).
'all' - Menu and button bar (requires bootstrap).
scroll_behavior: Scroll behavior options:
'pan' - (Default) Pan the map.
'zoom' - Zoom the map.
'none' - No scroll events.
minified_js: If True, use the minified version of js files. If
js_source is 'dev', then this option is ignored.
html_wrapper: If True, return a standalone html file.
enable_editing: Enable the editing modes (build, rotate, etc.).
enable_keys: Enable keyboard shortcuts.
height: The height of the HTML container.
never_ask_before_quit: Never display an alert asking if you want to
leave the page. By default, this message is displayed if enable_editing
is True.
static_site_index_json: The index, as a JSON string, for the static
site. Use javascript to parse the URL options. Used for
generating static pages (see static_site.py).
"""
if js_source not in ['web', 'local', 'dev']:
raise Exception('Bad value for js_source: %s' % js_source)
if menu not in ['none', 'zoom', 'all']:
raise Exception('Bad value for menu: %s' % menu)
if scroll_behavior not in ['pan', 'zoom', 'none']:
raise Exception('Bad value for scroll_behavior: %s' %
scroll_behavior)
content = env.get_template('content.html')
# if height is not a string
if type(height) is int:
height = "%dpx" % height
elif type(height) is float:
height = "%fpx" % height
elif type(height) is str:
height = str(height)
# set the proper urls
url_source = 'local' if (js_source == 'local'
or js_source == 'dev') else 'web'
is_dev = (js_source == 'dev')
d3_url = get_url('d3', url_source, self.local_host)
d3_rel_url = get_url('d3', url_source)
escher_url = ('' if js_source == 'dev' else get_url(
'escher_min' if minified_js else 'escher', url_source,
self.local_host))
jquery_url = ('' if not menu == 'all' else get_url(
'jquery', url_source, self.local_host))
boot_css_url = ('' if not menu == 'all' else get_url(
'boot_css', url_source, self.local_host))
boot_js_url = ('' if not menu == 'all' else get_url(
'boot_js', url_source, self.local_host))
require_js_url = get_url('require_js', url_source, self.local_host)
escher_css_url = get_url('builder_css', url_source, self.local_host)
favicon_url = get_url('favicon', url_source, self.local_host)
lh_string = ('' if self.local_host is None else
self.local_host.rstrip('/') + '/')
html = content.render(
id=self.the_id,
height=height,
dev=is_dev,
d3=d3_url,
d3_rel=d3_rel_url,
escher=escher_url,
jquery=jquery_url,
boot_css=boot_css_url,
boot_js=boot_js_url,
require_js=require_js_url,
escher_css=escher_css_url,
wrapper=html_wrapper,
title='Escher ' + ('Builder' if enable_editing else 'Viewer'),
favicon=favicon_url,
host=lh_string,
initialize_js=self._initialize_javascript(self.the_id, url_source),
draw_js=self._draw_js(self.the_id, enable_editing, menu,
enable_keys, is_dev, fill_screen,
scroll_behavior, never_ask_before_quit,
static_site_index_json))
return html
def test_localhost():
url = get_url('boot_js', source='local', local_host='http://localhost:7778/')
assert url == 'http://localhost:7778/escher/static/lib/bootstrap.min.js'
def generate_static_site():
print('Generating static site at %s' % top_directory)
# index file
template = env.get_template('homepage.html')
def static_rel(path):
return 'py/' + path
data = template.render(
d3=static_rel(get_url('d3', 'local')),
boot_css=static_rel(get_url('boot_css', 'local')),
homepage_css=static_rel(get_url('homepage_css', 'local')),
favicon=static_rel(get_url('favicon', 'local')),
logo=static_rel(get_url('logo', 'local')),
documentation=get_url('documentation', protocol='https'),
github=get_url('github', protocol='https'),
github_releases=get_url('github_releases', protocol='https'),
homepage_js=static_rel(get_url('homepage_js', 'local')),
version=__version__,
map_download_url=get_url('map_download', 'local'),
web_version=True,
server_index_url=static_rel(get_url('server_index', 'local')))
with open(join(top_directory, 'index.html'), 'wb') as f:
f.write(data.encode('utf-8'))
# viewer and builder
# make the builder
builder = Builder(safe=True, id='static_map')
filepath = join(top_directory, 'builder')
with open(join(root_directory, get_url('server_index', source='local')),
'r') as f:
index_json = f.read()
html = builder.save_html(filepath=filepath,
overwrite=True,
js_source='local',
protocol=None,
minified_js=True,
static_site_index_json=index_json)
# copy over the source maps
escher_map = get_url('escher_min', 'local') + '.map'
builder_css_map = get_url('builder_css_min', 'local') + '.map'
shutil.copy(join(root_directory, escher_map),
join(top_directory, 'builder', escher_map))
shutil.copy(join(root_directory, builder_css_map),
join(top_directory, 'builder', builder_css_map))
def test_download():
url = get_url('server_index', source='local')
assert url == '../' + __schema_version__ + '/' + __map_model_version__ + '/index.json'
url = get_url('map_download', protocol='https')
assert url == 'https://escher.github.io/%s/%s/maps/' % (__schema_version__, __map_model_version__)
def test__load_resource_web(tmpdir):
url = '/'.join([get_url('map_download', protocol='https'),
'Escherichia%20coli/iJO1366.Central%20metabolism.json'])
_ = json.loads(_load_resource(url, 'name'))
def test_online():
url = get_url('builder_css', source='web', protocol='https')
assert url == 'https://npmcdn.com/escher-vis@%s/css/dist/builder.css' % __version__
def test_map_json_for_name_web(tmpdir):
data = map_json_for_name('iJO1366.Central metabolism', cache_dir=str(tmpdir))
root = get_url('escher_root', protocol='https').rstrip('/')
assert json.loads(data)[0]['schema'] == '/'.join([root, 'escher', 'jsonschema',
__schema_version__ + '#'])
def get(self):
# get the organisms, maps, and models
response = yield gen.Task(AsyncHTTPClient().fetch, get_url('server_index', protocol='http'))
if response.code == 200 and response.body is not None:
server_index = response.body.decode('utf-8')
else:
server_index = json.dumps(None)
# get the cached maps and models
index = local_index()
# render the template
template = env.get_template('index.html')
data = template.render(d3=get_url('d3', 'local'),
boot_css=get_url('boot_css', 'local'),
index_css=get_url('index_css', 'local'),
favicon=get_url('favicon', 'local'),
logo=get_url('logo', 'local'),
documentation=get_url('documentation', protocol='https'),
github=get_url('github'),
github_releases=get_url('github_releases'),
index_js=get_url('index_js', 'local'),
index_gh_pages_js=get_url('index_gh_pages_js', 'local'),
map_download=get_url('map_download', 'local'),
# server_index_url=
server_index=server_index,
local_index=json.dumps(index),
can_dev=CAN_DEV,
can_dev_js=json.dumps(CAN_DEV),
version=__version__,
web_version=False)
self.set_header("Content-Type", "text/html")
self.serve(data)
def test_urls():
# online
url = get_url('builder_embed_css', source='web', protocol='https')
assert url == 'https://escher.github.io/builder-embed-%s.css' % __version__
# no protocol
url = get_url('escher', 'web')
assert url == '//escher.github.io/escher-%s.js' % __version__
# local
url = get_url('require_js', 'local')
assert url == 'escher/lib/require.min.js'
assert exists(join(root_directory, url))
# localhost
url = get_url('require_js', source='local', local_host='http://localhost:7778/')
assert url == 'http://localhost:7778/escher/lib/require.min.js'
# cdn
url = get_url('boot_js', 'web')
assert url == '//netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js'
# download
url = get_url('server_index', source='local')
assert url == __schema_version__ + '/index.json'
url = get_url('map_download', protocol='https')
assert url == 'https://escher.github.io/%s/maps/' % __schema_version__
# raises
with raises(Exception):
get_url('bad-name')
with raises(Exception):
get_url('d3', source='bad-source')
with raises(Exception):
get_url('d3', protocol='bad-protocol')
