python virtual environment; remove natural product

.gitignore

@@ -1,11 +1,33 @@
-# Python Interpreter #
+# python environment #
 ######################
-desktopApp/app/src/python/*
+desktopApp/env/*
+
+# electron #
+######################
+desktopApp/electron-*/*
 
 # desktop application node_modules #
 ####################################
 desktopApp/node_modules/*
 
+# desktopApp jobs #
+###################
+desktopApp/app/jobs/*
+
+
 # web application node_modules #
 ################################
 webApp/node_modules/*
+
+
+# webApp jobs #
+###############
+webApp/src/public/results/*
+
+# releases #
+############
+releases/*
+
+# __pycache__ #
+###############
+*/__pycache__/*

desktopApp/TurboPutative.bat

@@ -5,8 +5,13 @@ SET SRC_HOME=%~dp0
 SET SRC_HOME=%SRC_HOME:"=%
 SET SRC_HOME=%SRC_HOME:~0,-1%
 
+:: CHECK PYTHON ENVIRONMENT
+IF NOT EXIST "%SRC_HOME%\env" (
+    CMD /C " "%SRC_HOME%\install\install_win64.bat" "
+)
+
 :: ELECTRON DIRECTORY
-SET SRC_ELECTRON=%SRC_HOME%\node_modules\electron\dist\electron.exe
+SET SRC_ELECTRON=%SRC_HOME%\electron-v11.0.1-win32-x64\electron.exe
 
 :: APP DIRECTORY
 SET SRC_APP=%SRC_HOME%\app

desktopApp/app/sections/execute/tagger.html

@@ -179,12 +179,12 @@ <h3 style="color:white; font-size: 1.5em; font-weight: 300; font-family: Arial;"
                     <input class="cbTag" type="checkbox" id="drug" name="drug" value="true">
                     <span class="checkmark"></span>                
                 </label>
-
+                <!--
                 <label class="cbContainer">Natural Product
                     <input class="cbTag" type="checkbox" id="naturalProduct" name="naturalProduct" value="true">
                     <span class="checkmark"></span>                
                 </label>
-                <!--
+                
                 <label class="cbContainer">Microbial Compound
                     <input class="cbTag" type="checkbox" id="microbialCompound" name="microbialCompound" value="true">
                     <span class="checkmark"></span>                
@@ -379,8 +379,8 @@ <h3 style="color:white; font-size: 1.5em; font-weight: 300; font-family: Arial;"
             // iniContent += "###";
             iniContent += "Halogenated = " + document.getElementById('halogenated').checked;
             iniContent += "###";
-            iniContent += "NaturalProduct = " + document.getElementById('naturalProduct').checked;
-            iniContent += "###";
+            // iniContent += "NaturalProduct = " + document.getElementById('naturalProduct').checked;
+            // iniContent += "###";
             iniContent += "Peptide = " + document.getElementById('peptide').checked;
             iniContent += "###";
 

desktopApp/app/src/integrator.bat

@@ -6,7 +6,8 @@ SET SRC_HOME=%SRC_HOME:"=%
 SET SRC_HOME=%SRC_HOME:~0, -1%
 
 :: PYTHON EXE
-SET PYTHON="%SRC_HOME%\python\python.3.6.7\tools\python.exe"
+REM SET PYTHON="%SRC_HOME%\python\python.3.6.7\tools\python.exe"
+SET PYTHON=%SRC_HOME%\..\..\env\Scripts\python.exe
 
 :: INPUT VARIABLES
 SET WORKFLOW=%~1

desktopApp/app/src/pyModules/Tagger.py

@@ -547,8 +547,8 @@ def main(args):
     if re.search('(?i)true', config_param['TagSelection']['Drug']):
         df = drugTagger(df, n_cores)
 
-    if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
-        df = npTagger(df, n_cores)
+    # if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
+    #    df = npTagger(df, n_cores)
 
     if re.search('(?i)true', config_param['TagSelection']['Halogenated']):
         df = halogenatedTagger(df, n_cores)

desktopApp/install/install_win64.bat

@@ -0,0 +1,111 @@
+@ECHO OFF
+
+ECHO **
+ECHO ** CREATION OF PYTHON VIRTUAL ENVIRONMENT
+ECHO **
+
+:: SET WORKING DIRECTORY
+SET SRC_HOME="%~dp0"
+SET SRC_HOME=%SRC_HOME:"=%
+SET SRC_HOME=%SRC_HOME:~0,-1%
+
+:: SET env FOLDER
+SET SRC_ENV=%SRC_HOME%\..\env
+
+SETLOCAL EnableDelayedExpansion
+
+:: CHECK IF env FOLDER EXISTS
+:CHECK_ENV
+IF EXIST "%SRC_ENV%" (
+
+    GOTO ENV_CREATED
+
+) ELSE (
+
+    ECHO ** Check if Python is installed  
+    SET PYTHON=py
+
+    WHERE !PYTHON! > NUL 2>&1
+
+    IF ERRORLEVEL 1 (
+        ECHO ** !PYTHON! was not found in PATH...
+        GOTO USER_PYTHON
+    ) ELSE (
+        GOTO CREATE_ENV
+    )
+
+)
+
+
+:: USER PYTHON INTRODUCTION
+:USER_PYTHON
+
+SET /P PYTHON="** Enter path to python.exe or 'q' to exit installation: "
+IF %PYTHON% == q GOTO END
+GOTO ASSERT_PYTHON
+
+
+:: CHECK IF PYTHON IS INSTALLED
+:ASSERT_PYTHON
+
+IF EXIST %PYTHON% (
+
+    GOTO CREATE_ENV
+
+) ELSE (
+
+    ECHO ** Python could not be found: %PYTHON%
+    GOTO USER_PYTHON
+
+)
+
+
+:: CREATE VIRTUAL ENVIRONMENT
+:CREATE_ENV
+ECHO ** Check Python version
+
+FOR /F "useback delims=. tokens=1,2" %%I IN (`%PYTHON% --version`) DO (
+
+    IF NOT "%%I" == "Python 3" (
+        ECHO ** ERROR: Using %%I instead of Python 3
+        GOTO USER_PYTHON
+    )
+
+    IF NOT %%J GEQ 6 (
+        ECHO ** ERROR: Using %%I.%%J instead of Python 3.6 or greater
+        GOTO USER_PYTHON
+    )
+
+)
+
+ECHO ** Creating virtual environment
+CMD /C " "%PYTHON%" -m venv "%SRC_ENV%" "
+
+IF ERRORLEVEL 1 GOTO END
+
+SET SRC_SCRIPTS=%SRC_ENV%\Scripts
+
+REM UPGRADE PIP
+ECHO ** Upgrading pip
+CMD /C  " "%SRC_SCRIPTS%\python.exe" -m pip install --upgrade pip "
+
+IF ERRORLEVEL 1 GOTO END
+
+REM INSTALAR NUMPY y PANDAS
+ECHO ** Installing modules
+CMD /C " "%SRC_SCRIPTS%\pip.exe" install numpy pandas xlrd xlwt "
+
+IF ERRORLEVEL 1 GOTO END
+
+GOTO ENV_CREATED
+
+
+
+:ENV_CREATED
+ECHO ** Virtual environment created
+GOTO END
+
+
+:END
+ECHO ** Installation process finished. Press ENTER to close...
+PAUSE

tools/Tagger/Tagger.py

@@ -547,8 +547,8 @@ def main(args):
     if re.search('(?i)true', config_param['TagSelection']['Drug']):
         df = drugTagger(df, n_cores)
 
-    if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
-        df = npTagger(df, n_cores)
+    # if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
+    #    df = npTagger(df, n_cores)
 
     if re.search('(?i)true', config_param['TagSelection']['Halogenated']):
         df = halogenatedTagger(df, n_cores)

tools/Tagger/configTagger.ini

@@ -5,10 +5,6 @@ Food = True
 
 Drug = True
 
-NaturalProduct = True
-
-# MicrobialCompound = True
-
 Halogenated = True
 
 Peptide = True

webApp/src/public/assets/js/iniStringMaker.js

@@ -26,7 +26,7 @@ function iniTagger() {
     TaggerJSON['Drug'] = "";
     // TaggerJSON['MicrobialCompound'] = "";
     TaggerJSON['Halogenated'] = "";
-    TaggerJSON['NaturalProduct'] = "";
+    // TaggerJSON['NaturalProduct'] = "";
     TaggerJSON['Peptide'] = "";
 
     if(document.getElementById("Food").checked == true) {
@@ -47,9 +47,11 @@ function iniTagger() {
         TaggerJSON['Halogenated'] = "True";
     }
 
+    /*
     if(document.getElementById("NaturalProduct").checked == true) {
         TaggerJSON['NaturalProduct'] = "True";
     }
+    */
 
     if(document.getElementById("Peptide").checked == true) {
         TaggerJSON['Peptide'] = "True";
@@ -66,8 +68,8 @@ function iniTagger() {
     // iniContent += "###";
     iniContent += "Halogenated = " + TaggerJSON['Halogenated'];
     iniContent += "###";
-    iniContent += "NaturalProduct = " + TaggerJSON['NaturalProduct'];
-    iniContent += "###";
+    // iniContent += "NaturalProduct = " + TaggerJSON['NaturalProduct'];
+    // iniContent += "###";
     iniContent += "Peptide = " + TaggerJSON['Peptide'];
     iniContent += "###";
 

webApp/src/public/turboputative.html

@@ -295,11 +295,12 @@ <h3>Tagger settings</h3>
                         <input type="checkbox" id="Drug" name="Drug" value="True">
                         <label for="Drug"> Drug</label>
                     </div>
+                    <!--
                     <div class="check">
                         <input type="checkbox" id="NaturalProduct" name="NaturalProduct" value="True">
                         <label for="NaturalProduct"> Natural Product</label>                         
                     </div>
-                    <!--
+                    
                     <div class="check">
                         <input type="checkbox" id="MicrobialCompound" name="MicrobialCompound" value="True">
                         <label for="MicrobialCompound"> Microbial Compound</label><br>
@@ -641,7 +642,7 @@ <h3>TableMerger settings</h3>
             if (document.getElementById("workflow").value.search('1') != -1 &&
                 !document.getElementById('Food').checked &&
                 !document.getElementById('Drug').checked &&
-                !document.getElementById('NaturalProduct').checked &&
+                /*!document.getElementById('NaturalProduct').checked &&*/
                 !document.getElementById('Halogenated').checked &&
                 !document.getElementById('Peptide').checked /*&&
                 !document.getElementById('MicrobialCompound').checked*/) {

webApp/src/tools/pyModules/Tagger.py

@@ -547,8 +547,8 @@ def main(args):
     if re.search('(?i)true', config_param['TagSelection']['Drug']):
         df = drugTagger(df, n_cores)
 
-    if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
-        df = npTagger(df, n_cores)
+    # if re.search('(?i)true', config_param['TagSelection']['NaturalProduct']):
+    #    df = npTagger(df, n_cores)
 
     if re.search('(?i)true', config_param['TagSelection']['Halogenated']):
         df = halogenatedTagger(df, n_cores)