Add microbial database & Handle file extension

CNIC-Proteomics · Dec 18, 2020 · c3298cf · c3298cf
1 parent 4a27cab
commit c3298cf
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Showing 20 changed files with 21,068 additions and 38 deletions.
diff --git a/.gitignore b/.gitignore
@@ -23,7 +23,7 @@ webApp/node_modules/*
 
 # webApp jobs #
 ###############
-webApp/src/public/results/*/*
+webApp/src/public/jobs/*/*
 
 # releases #
 ############
@@ -44,9 +44,9 @@ desktopApp/app/src/pyModules/pygoslin/domain/__pycache__/*
 ##################
 desktopApp/app/src/pyModules/pygoslin/*
 desktopApp/app/src/pyModules/pygoslin_library/*
-webApp/src/TurboPutative/pyModules/pygoslinn/*
-webApp/src/TurboPutative/pyModules/pygoslinn_library/*
-webApp/src/TurboPutative/pyModules/pygoslinn_library.zip
+webApp/src/TurboPutative/pyModules/pygoslin/*
+webApp/src/TurboPutative/pyModules/pygoslin_library/*
+webApp/src/TurboPutative/pyModules/pygoslin_library.zip
 
 # Jupyter Notebook scripts #
 ############################

diff --git a/desktopApp/app/assets/files/errorCode.json b/desktopApp/app/assets/files/errorCode.json
@@ -102,5 +102,19 @@
 		"module": "TableMerger",
 		"description": "An error occurred when writing output file.",
 		"code": "42"
-	}
+	},
+	"50": {
+		"module": "TableMerger",
+		"description": "File with feature information could not be copied",
+		"code": "50"
+	},
+	"51": {
+		"module": "search",
+		"description": "The requested job was not found",
+		"code": "51"
+	},
+	"52": {
+		"module": "workflow",
+		"description": "Input file extension error"
+	} 
 }
diff --git a/desktopApp/app/assets/files/tests/test10/additional_information.xls b/desktopApp/app/assets/files/tests/test10/additional_information.xls
diff --git a/desktopApp/app/assets/files/tests/test10/annotations.xls b/desktopApp/app/assets/files/tests/test10/annotations.xls
diff --git a/desktopApp/app/assets/files/tests/test3/MS_experiment_log.txt b/desktopApp/app/assets/files/tests/test3/MS_experiment_log.txt
@@ -37,3 +37,22 @@
 11/05/2020 06:12:47 PM - INFO - Removing rows identified by RemoveRow parameter
 11/05/2020 06:12:47 PM - INFO - Synonyms substitution prior to parsing
 11/05/2020 06:12:50 PM - INFO - Applying regular expression from regex.ini and sorting peptide aminoacids alphabetically
+12/17/2020 07:01:39 PM - INFO - start script: Tagger.py -i ../../assets/files/tests/test3/MS_experiment.xls
+12/17/2020 07:01:39 PM - INFO - Using 1 cores
+12/17/2020 07:01:39 PM - INFO - Reading input file: ..\..\assets\files\tests\test3\MS_experiment.xls
+12/17/2020 07:01:40 PM - INFO - ..\..\assets\files\tests\test3\MS_experiment.xls was read
+12/17/2020 07:01:40 PM - INFO - Start food tagging
+12/17/2020 07:01:40 PM - INFO - Reading Food Table: C:\Users\Rafael\CNIC\Metabolomica\TurboPutative_GitHub_TFM\desktopApp\app\src\pyModules\..\Data\food_database.tsv
+12/17/2020 07:01:55 PM - INFO - Finished food tagging
+12/17/2020 07:01:55 PM - INFO - Start drug tagging
+12/17/2020 07:01:55 PM - INFO - Reading Drug Table: C:\Users\Rafael\CNIC\Metabolomica\TurboPutative_GitHub_TFM\desktopApp\app\src\pyModules\..\Data\drug_database.tsv
+12/17/2020 07:02:15 PM - INFO - Finished drug tagging
+12/17/2020 07:02:15 PM - INFO - Start microbial compound tagging
+12/17/2020 07:02:15 PM - INFO - Reading Microbial Table: C:\Users\Rafael\CNIC\Metabolomica\TurboPutative_GitHub_TFM\desktopApp\app\src\pyModules\..\Data\microbial_database.tsv
+12/17/2020 07:02:15 PM - INFO - Finished microbial tagging
+12/17/2020 07:02:15 PM - INFO - Start halogenated compounds tagging
+12/17/2020 07:02:15 PM - INFO - Finished halogenated compounds tagging
+12/17/2020 07:02:15 PM - INFO - Start peptide compounds tagging
+12/17/2020 07:02:15 PM - INFO - Finished peptide tagging
+12/17/2020 07:02:21 PM - INFO - Write Output Table: tagged_MS_experiment.xls
+12/17/2020 07:02:21 PM - INFO - end script
diff --git a/desktopApp/app/sections/execute/tagger.html b/desktopApp/app/sections/execute/tagger.html
@@ -184,12 +184,12 @@ <h3 style="color:white; font-size: 1.5em; font-weight: 300; font-family: Arial;"
                     <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>                
                 </label>
-                -->
+
                 <label class="cbContainer">Halogenated
                     <input class="cbTag" type="checkbox" id="halogenated" name="halogenated" value="true">
                     <span class="checkmark"></span>                
@@ -375,8 +375,8 @@ <h3 style="color:white; font-size: 1.5em; font-weight: 300; font-family: Arial;"
             iniContent += "###";
             iniContent += "Drug = " + document.getElementById('drug').checked;
             iniContent += "###";
-            // iniContent += "MicrobialCompound = " + document.getElementById('microbialCompound').checked;
-            // iniContent += "###";
+            iniContent += "MicrobialCompound = " + document.getElementById('microbialCompound').checked;
+            iniContent += "###";
             iniContent += "Halogenated = " + document.getElementById('halogenated').checked;
             iniContent += "###";
             // iniContent += "NaturalProduct = " + document.getElementById('naturalProduct').checked;