def get(self):
# 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'
# 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 testing_data file: %s' % rel_path)
if len(self.get_arguments('testing_data')) > 0:
r_filepath = 'escher/testing_data/reaction_data_iJO1366.json'
builder_kwargs['reaction_data'] = load_data_file(r_filepath)
m_filepath = 'escher/testing_data/metabolite_data_iJO1366.json'
builder_kwargs['metabolite_data'] = load_data_file(m_filepath)
# 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',
'enable_editing']:
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]))
# make the builder
builder = Builder(safe=True, **builder_kwargs)
html = builder._get_html(js_source=js_source, enable_keys=True,
html_wrapper=True, fill_screen=True,
height='100%', **display_kwargs)
self.set_header("Content-Type", "text/html")
self.serve(html)
def get(self, dev_path, offline_path, kind, path):
# builder vs. viewer & dev vs. not dev
js_source = ('dev' if (dev_path is not None) else
('local' if (offline_path is not None) else
'web'))
enable_editing = (kind=='builder')
# Builder options
builder_kwargs = {}
for a in ['starting_reaction', 'model_name', 'map_name', 'map_json']:
args = self.get_arguments(a)
if len(args)==1:
builder_kwargs[a] = args[0]
# 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']:
args = self.get_arguments(a)
if len(args)==1:
display_kwargs[a] = args[0]
# get the html
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 get(self):
# 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'
# 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)
# 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',
'enable_editing']:
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]))
# make the builder
builder = Builder(safe=True, **builder_kwargs)
html = builder._get_html(js_source=js_source, enable_keys=True,
html_wrapper=True, fill_screen=True,
height='100%', **display_kwargs)
self.set_header("Content-Type", "text/html")
self.serve(html)
def get(self, path):
try:
kind, organism, name = path.strip('/').split('/')
except (TypeError, ValueError):
raise Exception('invalid path %s' % path)
if kind == 'maps':
b = Builder(map_name=name)
self.set_header('Content-Type', 'application/json')
self.serve(b.loaded_map_json)
else:
b = Builder(model_name=name)
self.set_header('Content-Type', 'application/json')
self.serve(b.loaded_model_json)
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 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 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 get(self, dev_path, offline_path, kind, path):
# builder vs. viewer & dev vs. not dev
js_source = ('dev' if (dev_path is not None) else
('local' if (offline_path is not None) else
'web'))
enable_editing = (kind=='builder')
# Builder options
builder_kwargs = {}
for a in ['starting_reaction', 'model_name', 'map_name', 'map_json']:
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]))
# 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
response = yield gen.Task(AsyncHTTPClient().fetch,
join('http://localhost:%d' % PORT, urls.builder_embed_css_local))
print response
builder_kwargs['embedded_css'] = response.body.replace('\n', ' ')
# example data
def load_data_file(rel_path):
"""Load a JSON file with relative path."""
try:
with open(join(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 = 'example_data/reaction_data_iJO1366.json'
builder_kwargs['reaction_data'] = load_data_file(r_filepath)
m_filepath = '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']:
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)
