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_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')
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_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_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')
# 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()
