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
# 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()