def test__get_html():
b = Builder(map_json='"useless_map"', model_json='"useless_model"',
embedded_css='')
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' % (substring, st))
# no static parse, local
html = b._get_html(js_source='local')
look_for_string(html, 'map_data: JSON.parse(\'"useless_map"\'),')
look_for_string(html, 'model_data: JSON.parse(\'"useless_model"\'),')
look_for_string(html, 'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,')
# static parse, not dev
static_index = '{"my": ["useless", "index"]}'
html = b._get_html(static_site_index_json=static_index, protocol='https')
look_for_string(html, 'map_data: JSON.parse(\'"useless_map"\'),')
look_for_string(html, 'model_data: JSON.parse(\'"useless_model"\'),')
look_for_string(html, 'map_download_url: JSON.parse(\'"https://escher.github.io/%s/%s/maps/"\'),' % (__schema_version__, __map_model_version__))
look_for_string(html, 'model_download_url: JSON.parse(\'"https://escher.github.io/%s/%s/models/"\'),' % (__schema_version__, __map_model_version__))
look_for_string(html, static_index)
look_for_string(html, 'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,')
def test_save_html(tmpdir):
# ok with embedded_css arg
b = Builder(map_json='"useless_map"',
model_json='"useless_model"',
embedded_css='')
filepath = join(str(tmpdir), 'builder.html')
b.save_html(filepath)
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' %
(substring, st))
# no static parse, local
with open(filepath, 'r') as f:
html = f.read()
look_for_string(
html,
'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),',
)
look_for_string(
html,
'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),',
)
look_for_string(
html,
'escher.Builder(data.map_data, data.model_data, ',
)
def test__draw_js():
b = Builder(map_json='"useless_map"', model_json='"useless_model"',
embedded_css='')
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' % (substring, st))
# no static parse, dev
ijs = b._initialize_javascript('id', 'local')
js = b._draw_js('id', True, 'all', True, True, True, 'pan', True, None)
look_for_string(ijs, 'var map_data_id = "useless_map";')
look_for_string(ijs, 'var model_data_id = "useless_model";')
look_for_string(js, 'Builder(map_data_id, model_data_id, embedded_css_id, d3.select("#id"), options);')
# static parse, not dev
ijs = b._initialize_javascript('id', 'local')
static_index = '{"my": ["useless", "index"]}'
js = b._draw_js('id', True, 'all', True, False, True, 'pan', True, static_index)
look_for_string(ijs, 'var map_data_id = "useless_map";')
look_for_string(ijs, 'var model_data_id = "useless_model";')
look_for_string(js, 'escher.static.load_map_model_from_url("{0}/{1}/maps/", "{0}/{1}/models/",'.format(__schema_version__, __map_model_version__))
look_for_string(js, static_index)
look_for_string(js, 'options, function(map_data_id, model_data_id, options) {')
look_for_string(js, 'escher.Builder(map_data_id, model_data_id, embedded_css_id, d3.select("#id"), options);')
def test_Builder_download():
# download
b = Builder(map_name='iJO1366.Central metabolism', model_name='iJO1366')
assert b.loaded_map_json is not None
assert b.loaded_model_json is not None
b._get_html(js_source='web')
# b.display_in_notebook(height=200)
# data
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
reaction_data=[{
'GAPD': 123
}, {
'GAPD': 123
}])
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
metabolite_data=[{
'nadh_c': 123
}, {
'nadh_c': 123
}])
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
gene_data=[{
'gapA': 123
}, {
'adhE': 123
}])
assert type(b.the_id) is unicode_type
assert len(b.the_id) == 10
def test__get_html():
b = Builder(map_json='"useless_map"', model_json='"useless_model"', embedded_css="")
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError("Could not find\n\n%s\n\nin\n\n%s" % (substring, st))
# no static parse, local
html = b._get_html(js_source="local")
look_for_string(html, "map_data: JSON.parse('\"useless_map\"'),")
look_for_string(html, "model_data: JSON.parse('\"useless_model\"'),")
look_for_string(html, "escher.Builder(t_map_data, t_model_data, data.builder_embed_css,")
# static parse, not dev
static_index = '{"my": ["useless", "index"]}'
html = b._get_html(static_site_index_json=static_index, protocol="https")
look_for_string(html, "map_data: JSON.parse('\"useless_map\"'),")
look_for_string(html, "model_data: JSON.parse('\"useless_model\"'),")
look_for_string(
html,
"map_download_url: JSON.parse('\"https://escher.github.io/%s/%s/maps/\"'),"
% (__schema_version__, __map_model_version__),
)
look_for_string(
html,
"model_download_url: JSON.parse('\"https://escher.github.io/%s/%s/models/\"'),"
% (__schema_version__, __map_model_version__),
)
look_for_string(html, static_index)
look_for_string(html, "escher.Builder(t_map_data, t_model_data, data.builder_embed_css,")
def test__get_html():
b = Builder(map_json='"useless_map"',
model_json='"useless_model"',
embedded_css='')
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' %
(substring, st))
# no static parse, local
html = b._get_html(js_source='local')
look_for_string(
html,
'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),')
look_for_string(
html,
'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),')
look_for_string(
html,
'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,')
# static parse, not dev
static_index = '{"my": ["useless", "index"]}'
html = b._get_html(static_site_index_json=static_index, protocol='https')
look_for_string(
html,
'map_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbWFwIg==\')),')
look_for_string(
html,
'model_data: JSON.parse(b64DecodeUnicode(\'InVzZWxlc3NfbW9kZWwi\')),')
map_download_url = base64.b64encode(
("https://escher.github.io/%s/%s/maps/" %
(__schema_version__,
__map_model_version__)).encode('utf-8')).decode('utf-8')
look_for_string(
html, 'map_download_url: b64DecodeUnicode(\'%s\'),' % map_download_url)
model_download_url = base64.b64encode(
("https://escher.github.io/%s/%s/models/" %
(__schema_version__,
__map_model_version__)).encode('utf-8')).decode('utf-8')
look_for_string(
html,
'model_download_url: b64DecodeUnicode(\'%s\'),' % model_download_url)
look_for_string(html,
'eyJteSI6IFsidXNlbGVzcyIsICJpbmRleCJdfQ==') # static_index
look_for_string(
html,
'escher.Builder(t_map_data, t_model_data, data.builder_embed_css,')
def test_save_html_embedded_css(tmpdir):
# ok with embedded_css arg
b = Builder(embedded_css='useless_css')
filepath = join(str(tmpdir), 'builder.html')
b.save_html(filepath)
with open(filepath, 'r') as f:
html = f.read()
look_for_string(
html,
"embedded_css = b64DecodeUnicode('dXNlbGVzc19jc3M=')",
)
def test_save_html_embedded_css(tmpdir):
# ok with embedded_css arg
b = Builder(embedded_css='useless_css')
filepath = join(str(tmpdir), 'builder.html')
b.save_html(filepath)
with open(filepath, 'r') as f:
html = f.read()
look_for_string(
html,
"embedded_css = b64DecodeUnicode('dXNlbGVzc19jc3M=')",
)
def draw_knockout_result(model, map_name, simulation_method, knockouts, *args,
**kwargs):
with model:
for reaction in model.reactions.get_by_any(knockouts):
reaction.knock_out()
solution = simulation_method(model, *args, **kwargs).fluxes
return Builder(map_name, reaction_data=solution)
def test_save_html(tmpdir):
b = Builder(map_json='"useless_map"', model_json='"useless_model"')
filepath = join(str(tmpdir), 'builder.html')
b.save_html(filepath)
with open(filepath, 'r') as f:
html = f.read()
look_for_string(
html,
'escher.Builder(data.map_data, data.model_data, ',
)
look_for_string(
html,
"map_data = JSON.parse(b64DecodeUnicode('InVzZWxlc3NfbWFwIg=='))",
)
look_for_string(
html,
"model_data = JSON.parse(b64DecodeUnicode('InVzZWxlc3NfbW9kZWwi'))",
)
assert 'embedded_css =' not in html
def test_save_html(tmpdir):
b = Builder(map_json='"useless_map"', model_json='"useless_model"')
filepath = join(str(tmpdir), 'builder.html')
b.save_html(filepath)
with open(filepath, 'r') as f:
html = f.read()
look_for_string(
html,
'escher.Builder(data.map_data, data.model_data, ',
)
look_for_string(
html,
"map_data = JSON.parse(b64DecodeUnicode('InVzZWxlc3NfbWFwIg=='))",
)
look_for_string(
html,
"model_data = JSON.parse(b64DecodeUnicode('InVzZWxlc3NfbW9kZWwi'))",
)
assert 'embedded_css =' not in html
def test__draw_js():
b = Builder(map_json='"useless_map"', model_json='"useless_model"',
embedded_css='')
def look_for_string(st, substring):
"""Look for the string in the substring. This solves a bug in py.test
for these cases"""
try:
found = st.find(substring)
assert found > -1
except AssertionError:
raise AssertionError('Could not find\n\n%s\n\nin\n\n%s' % (substring, st))
# no static parse, dev
ijs = b._initialize_javascript('id', 'local')
js = b._draw_js('id', True, 'all', True, True, True, 'pan', True, None)
look_for_string(ijs, 'var map_data_id = "useless_map";')
look_for_string(ijs, 'var model_data_id = "useless_model";')
look_for_string(js, 'Builder(map_data_id, model_data_id, embedded_css_id, d3.select("#id"), options);')
# static parse, not dev
ijs = b._initialize_javascript('id', 'local')
static_index = '{"my": ["useless", "index"]}'
js = b._draw_js('id', True, 'all', True, False, True, 'pan', True, static_index)
look_for_string(ijs, 'var map_data_id = "useless_map";')
look_for_string(ijs, 'var model_data_id = "useless_model";')
look_for_string(js, 'escher.static.load_map_model_from_url("%s/maps/", "%s/models/",' % (__schema_version__, __schema_version__))
look_for_string(js, static_index)
look_for_string(js, 'options, function(map_data_id, model_data_id, options) {')
look_for_string(js, 'escher.Builder(map_data_id, model_data_id, embedded_css_id, d3.select("#id"), options);')
def test_Builder_download():
# download
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366')
assert b.loaded_map_json is not None
assert b.loaded_model_json is not None
b._get_html(js_source='web')
b.display_in_notebook(height=200)
# data
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
reaction_data=[{'GAPD': 123}, {'GAPD': 123}])
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
metabolite_data=[{'nadh_c': 123}, {'nadh_c': 123}])
b = Builder(map_name='iJO1366.Central metabolism',
model_name='iJO1366',
gene_data=[{'gapA': 123}, {'adhE': 123}])
assert type(b.the_id) is unicode_type
assert len(b.the_id) == 10
def draw_knockout_result(model, map_name, simulation_method, knockouts, *args,
**kwargs):
tm = TimeMachine()
try:
for reaction in model._ids_to_reactions(knockouts):
tm(do=partial(setattr, reaction, 'lower_bound', 0),
undo=partial(setattr, reaction, 'lower_bound',
reaction.lower_bound))
tm(do=partial(setattr, reaction, 'upper_bound', 0),
undo=partial(setattr, reaction, 'upper_bound',
reaction.upper_bound))
solution = simulation_method(model, *args, **kwargs).x_dict
tm.reset()
return Builder(map_name, reaction_data=solution)
except Exception as e:
tm.reset()
raise e
def plot_fluxes(
flux_dict,
escher_map,
output_file='map.html',
height=600,
width=800,
reaction_scale=None,
min_flux=-10,
max_flux=10,
):
if min_flux is None:
min_flux = min(flux_dict)
if max_flux is None:
max_flux = max(flux_dict)
if reaction_scale is None:
reaction_scale = [{
'type': 'value',
'value': min_flux,
'color': 'red',
'size': 32
}, {
'type': 'value',
'value': 0,
'color': '#c8c8c8',
'size': 12
}, {
'type': 'value',
'value': max_flux,
'color': 'green',
'size': 32
}]
builder = Builder(height=height,
width=width,
map_json=escher_map,
reaction_scale=reaction_scale)
builder.reaction_data = flux_dict
builder.save_html(output_file)
builder.close()
def test_Builder_download():
# download
b = Builder(map_name="iJO1366.Central metabolism", model_name="iJO1366")
assert b.loaded_map_json is not None
assert b.loaded_model_json is not None
b._get_html(js_source="web")
# b.display_in_notebook(height=200)
# data
b = Builder(
map_name="iJO1366.Central metabolism", model_name="iJO1366", reaction_data=[{"GAPD": 123}, {"GAPD": 123}]
)
b = Builder(
map_name="iJO1366.Central metabolism", model_name="iJO1366", metabolite_data=[{"nadh_c": 123}, {"nadh_c": 123}]
)
b = Builder(map_name="iJO1366.Central metabolism", model_name="iJO1366", gene_data=[{"gapA": 123}, {"adhE": 123}])
assert type(b.the_id) is unicode_type
assert len(b.the_id) == 10
def animate_fluxes(
flux_time_data,
escher_map,
outputfile='animation.mp4',
height=600,
width=800,
time_interval_ms=100,
chrome=DEFAULT_CHROME,
reaction_scale=None,
min_flux=None,
max_flux=None,
time_size=12,
time_unit='h',
x_time=0.95,
y_time=0.9,
):
if min_flux is None:
min_flux = flux_time_data.min().min()
if max_flux is None:
max_flux = flux_time_data.max().max()
if reaction_scale is None:
reaction_scale = [{
'type': 'value',
'value': min_flux,
'color': 'red',
'size': 32
}, {
'type': 'value',
'value': 0,
'color': '#c8c8c8',
'size': 12
}, {
'type': 'value',
'value': max_flux,
'color': 'green',
'size': 32
}]
builder = Builder(height=height,
width=width,
map_json=escher_map,
embedd_css=EMBEDD_CSS,
menu='none',
reaction_scale=reaction_scale)
myimages = []
fig = plt.figure()
XVFB_DOCKER = '/usr/bin/xvfb-run -a -s \"-screen 0 {}x{}x24\"'.format(
width, height)
SCREENSHOT = "--headless --disable-gpu --no-sandbox --virtual-time-budget=10000 --screenshot=\'{}\' {}"
for t, fluxes in flux_time_data.iterrows():
builder.reaction_data = fluxes
builder.save_html('tmp.html', )
# Hacky hack hack ...
# Use chrome to make a screenshot
cmd = "{} {} {}".format(XVFB_DOCKER, chrome,
SCREENSHOT.format('tmp.png', 'tmp.html'))
os.system(cmd)
# Add time text
ylim = plt.gca().get_ylim()
xlim = plt.gca().get_xlim()
y = (ylim[1] - ylim[0]) * y_time + ylim[0]
x = (xlim[1] - xlim[0]) * x_time + xlim[0]
text = plt.text(x,
y,
'{:.1f} {}'.format(t, time_unit),
horizontalalignment='right',
fontsize=time_size)
img = mgimg.imread('tmp.png')
imgplot = plt.imshow(img)
# append AxesImage object to the list
myimages.append([imgplot, text])
plt.axis('off')
fig.tight_layout()
anim = animation.ArtistAnimation(fig, myimages, interval=time_interval_ms)
anim.save(outputfile, dpi=300)
builder.close()
def test_Builder_options():
b = Builder(metabolite_no_data_color='blue')
assert b.metabolite_no_data_color == 'blue'
b.metabolite_no_data_color = 'white'
assert b.metabolite_no_data_color == 'white'
import escher
from escher import Builder
import cobra
from time import sleep
escher.rc['never_ask_before_quit'] = True
Core = Builder(
map_name='e_coli_core.Core metabolism',
model_name='e_coli_core',
)
Core.save_html("Core.html")
CarbonMeta = Builder(model_json="Recon3D.json",
map_name='RECON1.Carbohydrate metabolism')
CarbonMeta.save_html("CarbonMeta.html")
FattyAcid = Builder(
model_name='iMM904',
map_name='iJO1366.Fatty acid beta-oxidation',
)
FattyAcid.save_html("FattyAcid.html")
EMP_TCA_PPP = Builder(map_name='RECON1.Glycolysis TCA PPP')
EMP_TCA_PPP.save_html
def test_Builder_options():
b = Builder(embedded_css='')
b.set_metabolite_no_data_color('white')
assert b.metabolite_no_data_color == 'white'
def test_Builder(tmpdir):
# ok with embedded_css arg
b = Builder(map_json='{"r": "val"}',
model_json='{"r": "val"}',
embedded_css='')
# b.display_in_notebook(js_source='local')
b.save_html(join(str(tmpdir), 'Builder.html'), js_source='local')
# test options
with raises(Exception):
b._get_html(js_source='devv')
with raises(Exception):
b._get_html(menu='')
with raises(Exception):
b._get_html(scroll_behavior='asdf')
b._get_html(js_source='local')
b._get_html(menu='all')
b._get_html(scroll_behavior='zoom')
import escher
from escher import Builder
import cobra
from time import sleep
escher.rc['never_ask_before_quit'] = True
Core = Builder(
map_name='e_coli_core.Core metabolism',
model_name='e_coli_core',
)
Core
model = cobra.io.load_json_model('e_coli_core.json')
reverse = True
step = 0.1
timestep = 0.1
duration = 1500 # seconds
lim = [0, 0.5]
val = lim[-1]
for _ in range(int(duration / timestep)):
model.reactions.EX_o2_e.lower_bound = -val
solution = model.optimize()
Core.reaction_data = solution.fluxes
if val <= lim[0]:
reverse = True
if val >= lim[1]:
reverse = False
if reverse:
val += step
else:
val -= step
# installed, escher makes downloading and viewing metabolic maps from a
# [repository](https://github.com/zakandrewking/escher/tree/gh-pages/maps)
# extremely simple. For more information, view the escher documentation.
#
# This example is also available as an IPython [notebook](http://nbviewer.ipyth
# on.org/github/opencobra/cobrapy/blob/master/documentation_builder/escher.ipyn
# b)
from escher import Builder
import cobra.test
model = cobra.test.create_test_model(cobra.test.ecoli_pickle)
cobra.flux_analysis.parsimonious.optimize_minimal_flux(model)
wt_solution = model.solution.x_dict
# mutant flux has PGI knocked out
model.reactions.PGI.lower_bound = 0
model.reactions.PGI.upper_bound = 0
cobra.flux_analysis.parsimonious.optimize_minimal_flux(model)
mutant_solution = model.solution.x_dict
wt_map = Builder("iJO1366_central_metabolism", reaction_data=wt_solution)
wt_map.display_in_notebook()
wt_map = Builder("iJO1366_central_metabolism", reaction_data=mutant_solution)
wt_map.display_in_notebook()
# In a non-notebook environment, metabolic maps can still be viewed by running
mutant_map.display_in_browser()
def test_Builder(tmpdir):
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}')
# Cannot load dev/local version without an explicit css string property.
# TODO include a test where these do not raise.
with raises(Exception):
b.display_in_notebook(js_source='dev')
with raises(Exception):
b.display_in_notebook(js_source='local')
# ok with embedded_css arg
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}', embedded_css='')
b.display_in_notebook(js_source='dev')
b.save_html(join(str(tmpdir), 'Builder.html'), js_source='dev')
# test options
with raises(Exception):
b._get_html(js_source='devv')
with raises(Exception):
b._get_html(menu='')
with raises(Exception):
b._get_html(scroll_behavior='asdf')
b._get_html(js_source='local')
b._get_html(menu='all')
b._get_html(scroll_behavior='zoom')
def test_Builder_options():
b = Builder(embedded_css="")
b.set_metabolite_no_data_color("white")
assert b.metabolite_no_data_color == "white"
html = b._get_html(js_source="local")
assert '"metabolite_no_data_color": "white"' in html
def test_Builder(tmpdir):
# ok with embedded_css arg
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}', embedded_css="")
# b.display_in_notebook(js_source='local')
b.save_html(join(str(tmpdir), "Builder.html"), js_source="local")
# test options
with raises(Exception):
b._get_html(js_source="devv")
with raises(Exception):
b._get_html(menu="")
with raises(Exception):
b._get_html(scroll_behavior="asdf")
b._get_html(js_source="local")
b._get_html(menu="all")
b._get_html(scroll_behavior="zoom")
def test_Builder(tmpdir):
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}')
# Cannot load dev/local version without an explicit css string property.
# TODO include a test where these do not raise.
with raises(Exception):
b.display_in_notebook(js_source='dev')
with raises(Exception):
b.display_in_notebook(js_source='local')
# ok with embedded_css arg
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}', embedded_css='')
b.display_in_notebook(js_source='dev')
b.save_html(join(str(tmpdir), 'Builder.html'), js_source='dev')
# test options
with raises(Exception):
b._get_html(js_source='devv')
with raises(Exception):
b._get_html(menu='')
with raises(Exception):
b._get_html(scroll_behavior='asdf')
b._get_html(js_source='local')
b._get_html(menu='all')
b._get_html(scroll_behavior='zoom')
import escher
from escher import Builder
import cobra
from time import sleep
escher.rc['never_ask_before_quit'] = True
builder = Builder()
builder
get_ipython().getoutput("wget -nc http://bigg.ucsd.edu/static/models/iAB_RBC_283.json")
builder = Builder(
model_json='iAB_RBC_283.json'
)
builder
escher.list_available_maps()
escher.list_available_models()
def test_Builder_options():
b = Builder(embedded_css='')
b.set_metabolite_no_data_color('white')
assert b.metabolite_no_data_color=='white'
html = b._get_html(js_source='local')
assert 'metabolite_no_data_color: "white"' in html
def test_Builder(tmpdir):
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}')
# Cannot load dev/local version without an explicit css string property.
# TODO include a test where these do not raise.
with raises(Exception):
b.display_in_notebook(js_source='dev')
with raises(Exception):
b.display_in_notebook(js_source='local')
b.display_in_notebook(js_source='web')
b.display_in_notebook(height=200)
# b.display_in_browser()
b.save_html(join(str(tmpdir), 'Builder.html'))
# test options
with raises(Exception):
b._get_html(js_source='devv')
with raises(Exception):
b._get_html(menu='')
with raises(Exception):
b._get_html(scroll_behavior='asdf')
b._get_html(js_source='web')
b._get_html(menu='all')
b._get_html(scroll_behavior='zoom')
# download
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366')
assert b.loaded_map_json is not None
assert b.loaded_model_json is not None
b.display_in_notebook(height=200)
# data
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366',
reaction_data=[{'GAPD': 123}, {'GAPD': 123}])
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366',
metabolite_data=[{'nadh_c': 123}, {'nadh_c': 123}])
assert type(b.the_id) is unicode
assert len(b.the_id) == 10
def test_Builder():
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}')
b.embedded_html(dev=True, enable_editing=True, height=100)
b.standalone_html(dev=True)
b.display_in_notebook(height=200)
# download
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366')
assert b.loaded_map_json is not None
assert b.loaded_model_json is not None
b.embedded_html(dev=True, enable_editing=True, height=100)
b.standalone_html(dev=True)
b.display_in_notebook(height=200)
# data
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366',
reaction_data=[{'GAPD': 123}, {'GAPD': 123}])
b = Builder(map_name='iJO1366_central_metabolism', model_name='iJO1366',
metabolite_data=[{'nadh_c': 123}, {'nadh_c': 123}])
assert type(b.the_id) is unicode
assert len(b.the_id) == 10
def test_Builder_options():
b = Builder(metabolite_no_data_color='blue')
assert b.metabolite_no_data_color == 'blue'
b.metabolite_no_data_color = 'white'
assert b.metabolite_no_data_color == 'white'
import escher
from escher import Builder
import cobra
from time import sleep
escher.rc['never_ask_before_quit'] = True
builder = Builder(
map_name='e_coli_core.Core metabolism',
model_name='e_coli_core',
)
builder
builder = Builder(
map_name='iMM904.Central carbon metabolism',
model_name='iMM904',
)
builder
builder = Builder(map_name= 'iJO1366.Fatty acid beta-oxidation')
builder
builder = Builder(model_json="Recon3D.json",
map_name= 'RECON1.Carbohydrate metabolism')
builder.save
def test_handling_cobra_fluxes(data, expected):
b = Builder(reaction_data=data, gene_data=data, metabolite_data=data)
assert b.reaction_data == expected
assert b.gene_data == expected
assert b.metabolite_data == expected
def test_Builder(tmpdir):
# ok with embedded_css arg
b = Builder(map_json='{"r": "val"}', model_json='{"r": "val"}', embedded_css='')
b.display_in_notebook(js_source='local')
b.save_html(join(str(tmpdir), 'Builder.html'), js_source='local')
# test options
with raises(Exception):
b._get_html(js_source='devv')
with raises(Exception):
b._get_html(menu='')
with raises(Exception):
b._get_html(scroll_behavior='asdf')
b._get_html(js_source='local')
b._get_html(menu='all')
b._get_html(scroll_behavior='zoom')
def test_Builder_options():
b = Builder(embedded_css='')
b.set_metabolite_no_data_color('white')
assert b.metabolite_no_data_color=='white'
html = b._get_html(js_source='local')
assert 'metabolite_no_data_color: "white"' in html
