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_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_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 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):
# 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 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_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_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(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
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
get_ipython().getoutput("wget -nc http://bigg.ucsd.edu/static/models/e_coli_core.json")
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()
builder.reaction_data = solution.fluxes
if val <= lim[0]:
reverse = True
if val >= lim[1]:
reverse = False
if reverse:
val += step
else:
val -= step
sleep(timestep)
builder.save_html('example_map.svg')
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()
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
sleep(timestep)
Core.save_html("Core.html")
CarbonMeta = Builder(model_json="Recon3D.json",
map_name='RECON1.Carbohydrate metabolism')
CarbonMeta.save_html("CarbonMeta.html")
CarbonMeta.save_html("CarbonMeta.html")
model = cobra.io.load_json_model('Recon3D.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)):
