Update essential reactions in spreadsheets. Include online web docs

README.md

@@ -35,6 +35,7 @@ The computation of vulnerabilities can also be exploited programmatically via th
 
 ## Table of Contents
 - [License](#license)
+- [Online Web](#online-web)
 - [Install](#Install)
 - [Quickstart](#Quickstart)
 - [Documentation](#documentation)
@@ -48,6 +49,10 @@ The computation of vulnerabilities can also be exploited programmatically via th
 
 CONTRABASS is released under [GPLv3 license](LICENSE).
 
+## Online Web
+
+CONTRABASS can also be executed through the [CONTRABASS Online Web App (http://contrabass.unizar.es)](http://contrabass.unizar.es).
+
 ## Install
 ```CONTRABASS``` can be installed via **pip** package manager:
 ```shell
@@ -59,7 +64,7 @@ CONTRABASS is released under [GPLv3 license](LICENSE).
 Generate report on vulnerabilities on input model ```MODEL.xml```
 
 ```shell
-  $ contrabass report critial-reactions MODEL.xml
+  $ contrabass report critical-reactions MODEL.xml
 ```
 
 Generate report on growth-dependent reactions on input model ```MODEL.xml```

docs/source/ComputeGrowthDependent.rst

@@ -1,3 +1,5 @@
+.. _growth-op-documentation:
+
 5. Compute growth dependent reactions
 ========================================
 .

docs/source/License.rst

@@ -1,5 +1,5 @@
 
-9. License
+10. License
 ===============
 
 CONTRABASS is released under GPLv3_.

docs/source/OnlineWebApp.rst

@@ -0,0 +1,65 @@
+
+9. Online Web App
+===============
+
+CONTRABASS can also be executed though the online web application at CONTRABASS-Online_.
+
+9.1. Usage
+------------
+
+9.1.1. Submit model
+*********************
+
+To load a model in the web app drag-and-drop a valid SBML model to the box on the left (see image below).
+CONTRABASS also comes with 4 sample models to try out the tool. To use one of the 4 sample models, simply click on one
+of the ```Try this model``` buttons in the box on the right (see image below). (see image below).
+
+.. image:: _static/step1.png
+    :align: center
+    :alt: step 1
+
+9.1.2. Run operation
+************************
+
+If the model is correctly formatted, CONTRABASS will read the model and notify when it is ready.
+When the read completes successfully, a row similar to the following with the model data will appear on the page:
+
+.. image:: _static/step2.png
+    :align: center
+    :alt: step 2
+.
+CONTRABASS allows you to execute the two operations explained above in the documentation, that is:
+    - **Compute growth dependent reactions**: produce an overview of the critical reactions in the model and explore how they vary when the growth constraints vary (See :ref:`growth-op-documentation`).
+    - **Compute critical reactions**: compute sets of critical reactions and their intersections for a given growth rate (See :ref:`vulnerabilities-documentation`).
+
+If we click on one of the 2 accordions showing the 2 possible operations, they will expand showing the optional parameters
+that we can adjust before starting the execution (see image below).
+Once we are done with the parameters, to start the execution simply click the ```Execute``` button.
+
+.. image:: _static/step3.png
+    :align: center
+    :alt: step 3
+
+While the selected operation is being executed, the page will show feedback on the computations performed:
+
+.. image:: _static/step4.png
+    :align: center
+    :alt: step 4
+
+9.1.3. Download reports
+************************
+
+Once the selected operation ends its execution, the web will display 2 buttons (see image below) to download different reports:
+
+    - **Download spreadsheet**: Download the spreadsheet report of the computation.
+    - **View report**: View and online interactive report with the result of the computation.
+
+
+.. image:: _static/step5.png
+    :align: center
+    :alt: step 5
+
+
+
+.. _CONTRABASS-Online: https://github.com/openCONTRABASS/CONTRABASS/blob/master/LICENSE
+

docs/source/index.rst

@@ -3,14 +3,15 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to CONRTABASS's documentation!
+Welcome to CONTRABASS's documentation!
 ========================================
 
 .. toctree::
     :maxdepth: 4
     :glob:
 
     Introduction
+    OnlineWebApp
     Installation
     ToolCommands
     ComputeVulnerabilities

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 name = contrabass
 url = https://github.com/openCONTRABASS/CONTRABASS
-version = 0.2.0
+version = 0.2.1
 author = Alex Oarga
 author_email = [email protected]
 description = Constraint-based model vulnerabilities analysis

src/contrabass/core/Spreadsheet.py

@@ -834,24 +834,7 @@ def __aux_spreadsheet_get_data(self, state):
         if state.essential_genes() is not None:
             essential_genes = [g.id for g in state.essential_genes()]
 
-        er_g0 = []
-        er_g005 = []
-        objective_value = state.objective_value()
-        if state.objective_value() is not None:
-            if not isnan(state.objective_value()):
-                objective_value_005 = state.objective_value() * 0.05
-            else:
-                objective_value_005 = 0
-            for reaction, value in knockout_growth.items():
-                if not isnan(objective_value):
-                    if isnan(value) or value == 0:
-                        er_g0.append(reaction)
-                        er_g005.append(reaction)
-                    elif value < objective_value_005:
-                        er_g005.append(reaction)
-                else:
-                    er_g0.append(reaction)
-                    er_g005.append(reaction)
+        essential_reactions = state.essential_reactions()
 
         reversibles = state.reversible_reactions()
 
@@ -862,9 +845,7 @@ def __aux_spreadsheet_get_data(self, state):
             list(chokepoints_dict.keys()),
             essential_genes,
             genes_reactions_dict,
-            knockout_growth,
-            er_g0,
-            er_g005,
+            essential_reactions,
             reversibles,
             dead_reactions,
         ]
@@ -878,15 +859,9 @@ def __aux_spreadsheet_write_two_model_summary(
         sheet.write(x + 3, y + 1, "Chokepoint reactions", style=style)
         sheet.write(x + 4, y + 1, "Essential genes", style=style)
         sheet.write(x + 5, y + 1, "Essential genes reactions", style=style)
-        sheet.write(x + 6, y + 1, "Essential reactions (objective=0)", style=style)
-        sheet.write(
-            x + 7,
-            y + 1,
-            "Essential reactions (objective < 5% max objective)",
-            style=style,
-        )
-        sheet.write(x + 8, y + 1, "Reversible reactions", style=style)
-        sheet.write(x + 9, y + 1, "Dead reactions", style=style)
+        sheet.write(x + 6, y + 1, "Essential reactions", style=style)
+        sheet.write(x + 7, y + 1, "Reversible reactions", style=style)
+        sheet.write(x + 8, y + 1, "Dead reactions", style=style)
         sheet.write(x + 1, y + 2, "Before", style=style)
         sheet.write(x + 1, y + 3, "After", style=style)
         sheet.write(x + 1, y + 5, "Only before", style=style)
@@ -951,15 +926,9 @@ def __aux_spreadsheet_write_four_model_summary(
         sheet.write(x + 3, y + 1, "Chokepoint reactions", style=style)
         sheet.write(x + 4, y + 1, "Essential genes", style=style)
         sheet.write(x + 5, y + 1, "Essential genes reactions", style=style)
-        sheet.write(x + 6, y + 1, "Essential reactions (objective=0)", style=style)
-        sheet.write(
-            x + 7,
-            y + 1,
-            "Essential reactions (objective < 5% max objective)",
-            style=style,
-        )
-        sheet.write(x + 8, y + 1, "Reversible reactions", style=style)
-        sheet.write(x + 9, y + 1, "Dead reactions", style=style)
+        sheet.write(x + 6, y + 1, "Essential reactions", style=style)
+        sheet.write(x + 7, y + 1, "Reversible reactions", style=style)
+        sheet.write(x + 8, y + 1, "Dead reactions", style=style)
 
         sheet.write(x + 1, y + 2, "Only: M0", style=style)
         sheet.write(x + 1, y + 3, "Only: MNODEM", style=style)
@@ -984,8 +953,6 @@ def __aux_spreadsheet_write_four_model_summary(
                 model_results[2][i],
                 model_results[3][i],
             ]
-            if i == 8:
-                print(set_list)
             self.__aux_write_sets(sheet, x + i + 2, y, set_list)
 
     #
@@ -1100,10 +1067,6 @@ def spreadsheet_write_summary(
             list_model_fvadem_results,
         ]
 
-        # remove essential_reactions list with objective values
-        for m in models:
-            del m[4]
-
         list_metabolites = [
             len(state_initial.metabolites()),
             len(state_dem.metabolites()),
@@ -1119,9 +1082,9 @@ def spreadsheet_write_summary(
 
         # 1: list(chokepoints_dict.keys()),
         # 3: genes_reactions_dict,
-        # 5: er_g0
+        # 4: essential_reactions
         reactions_data = []
-        for i in [1, 3, 5]:
+        for i in [1, 3, 4]:
             rdl = [
                 list_model_initial_results[i],
                 list_model_dem_results[i],
@@ -1223,7 +1186,7 @@ def spreadsheet_write_summary(
             style,
             y,
             0,
-            "CHOKEPOINT REACTIONS - ESSENTIAL REACTIONS (objectite value < 5% max objective value)",
+            "CHOKEPOINT REACTIONS - ESSENTIAL REACTIONS",
             "Only chokepoints",
             reactions_data[0],
             "Only essential reactions",
@@ -1236,7 +1199,7 @@ def spreadsheet_write_summary(
             style,
             y,
             0,
-            "ESSENTIAL GENES REACTIONS - ESSENTIAL REACTIONS (objectite value < 5% max objective value)",
+            "ESSENTIAL GENES REACTIONS - ESSENTIAL REACTIONS",
             "Only essential genes reactions",
             reactions_data[1],
             "Only essential reactions",
@@ -1249,7 +1212,7 @@ def spreadsheet_write_summary(
             style,
             y,
             0,
-            "CHOKEPOINT REACTIONS - ESSENTIAL GENES REACTIONS - ESSENTIAL REACTIONS (objectite value < 5% max objective value)",
+            "CHOKEPOINT REACTIONS - ESSENTIAL GENES REACTIONS - ESSENTIAL REACTIONS",
             "Only chokepoints reactions",
             reactions_data[0],
             "Only essential genes reactions",