Entity Linker args, readme, license, fixes

LICENSE.MD

@@ -0,0 +1,18 @@
+Copyright 2024 Ensar Emir EROL
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the “Software”), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.MD

@@ -0,0 +1,44 @@
+# aidava-openrefine-tagger
+
+This is a simple OpenRefine extension that allows you to tag columns with dummy operations.
+It is useful when you want to keep extra information in operation history for other applications.
+
+## How to install
+
+Download the latest release from the [releases page](https://github.com/AIDAVA-DEV/aidava-openrefine-tagger/releases)
+and extract it to the `extensions` folder of your OpenRefine installation.
+
+**Note:** module folder should be in the following path: `extensions/aidava-openrefine-tagger/module`. Do not directly
+copy `module` folder to `extensions` folder. It should be in `aidava-openrefine-tagger` folder.
+
+## How to use
+
+After installing the extension, you will see a new option in the column menu called `Tag Column for ...`.
+
+(1) Click the arrow on the column header to open the column menu.
+(2) Go into the `Edit column` submenu.
+(3) Click on `Tag Column for ...`.
+(4) Select required arguments for the operation.
+(5) Click `Tag` button.
+
+## Current Tags
+
+```json
+[
+  {
+    "op": "aidava-tagger/tag-nlp-operation",
+    "columnName": "SUBTYPE",
+    "modelName": "model1",
+    "index": 2,
+    "description": "NLPTaggerOperation on SUBTYPE with model model1"
+  },
+  {
+    "op": "aidava-tagger/tag-entity-linking-operation",
+    "columnName": "SUBTYPE_NAME",
+    "language": "en",
+    "terminology": "snomed",
+    "index": 3,
+    "description": "EntityLinkingTaggerOperation on SUBTYPE_NAME with language en and terminology snomed"
+  }
+]
+```

src/main/java/org/aidava/openrefine/extension/tagger/commands/EntityLinkingTaggerCommand.java

@@ -15,15 +15,20 @@ protected AbstractOperation createOperation(Project project, HttpServletRequest
         final String columnName = httpServletRequest.getParameter("column");
         final Column column = project.columnModel.getColumnByName(columnName);
 
-        final String modelName = httpServletRequest.getParameter("model");
+        final String language = httpServletRequest.getParameter("language");
+        if (language == null) {
+            throw new Exception("Missing language parameter");
+        }
+        final String terminology = httpServletRequest.getParameter("terminology");
 
         if (column == null) {
             throw new Exception("Invalid column name: " + columnName);
         }
 
         return new EntityLinkingTaggerOperation(
                 column.getName(),
-                modelName,
+                language,
+                terminology,
                 column.getCellIndex()
         );
     }

src/main/java/org/aidava/openrefine/extension/tagger/operations/EntityLinkingTaggerOperation.java

@@ -7,16 +7,21 @@
 public class EntityLinkingTaggerOperation extends ColumnMoveOperation {
     private final String language;
 
+    private final String terminology;
+
     public EntityLinkingTaggerOperation(
             @JsonProperty("columnName")
             String columnName,
             @JsonProperty("language")
             String language,
+            @JsonProperty("terminology")
+            String terminology,
             @JsonProperty("index")
             int index
     ) {
         super(columnName, index);
         this.language = language;
+        this.terminology = terminology;
     }
 
 
@@ -25,8 +30,13 @@ public String getLanguage() {
         return language;
     }
 
+    @JsonProperty("terminology")
+    public String getTerminology() {
+        return terminology;
+    }
+
     @Override
     protected String getBriefDescription(Project project) {
-        return "EntityLinkingTaggerOperation on " + getColumnName() + " with language " + language;
+        return "EntityLinkingTaggerOperation on " + getColumnName() + " with language " + language + " and terminology " + terminology;
     }
 }

src/main/resources/module/dialogs/entity-linking-tagger-dialog.html

@@ -7,7 +7,14 @@
             <p>
                 Select the Language that is used in the column.
             </p>
-            <ol bind="el-langs"></ol>
+            <ol bind="el-langs" class="language"></ol>
+        </fieldset>
+        <br/>
+        <fieldset>
+            <p>
+                Select the Target Terminology for the column.
+            </p>
+            <ol bind="el-terminologies" class="terminology"></ol>
         </fieldset>
     </div>
     <div class="dialog-footer">

src/main/resources/module/dialogs/entity-linking-tagger-dialog.js

@@ -1,43 +1,27 @@
-// <div className="dialog-frame aidava-tagger">
-//     <div className="dialog-header">
-//         Tag column named "<span className="tagger-column-name">column</span>" for Entity Linking Workflow
+// <div class="dialog-frame aidava-tagger">
+//     <div class="dialog-header">
+//         Tag column named "<span class="tagger-column-name">column</span>" for Entity Linking Workflow
 //     </div>
-//     <div className="dialog-body">
+//     <div class="dialog-body">
 //         <fieldset>
 //             <p>
 //                 Select the Language that is used in the column.
 //             </p>
-//             <ol bind="el-langs"></ol>
+//             <ol bind="el-langs" class="language"></ol>
 //         </fieldset>
-//     </div>
-//     <div className="dialog-footer">
-//         <button bind="cancel" className="button">Cancel</button>
-//         <button bind="tag" className="button default" disabled>Tag</button>
-//     </div>
-// </div>
-
-//
-// JS File for Tagger Dialog
-// HTML: src/main/resources/module/dialogs/nlp-tagger-dialog.html
-// <div class="dialog-frame">
-//     <div class="dialog-header">
-//         Tag column named "<span class="tagger-column-name">column</span>" for NLP Workflow
-//     </div>
-//     <div class="dialog-body">
+//         <br/>
 //         <fieldset>
 //             <p>
-//                 Select the NLP model that needs to be used for this column.
+//                 Select the Target Terminology for the column.
 //             </p>
-//             <ol bind="nlp-models"></ol>
+//             <ol bind="el-terminologies" class="terminology"></ol>
 //         </fieldset>
 //     </div>
 //     <div class="dialog-footer">
-//         <button class="button" bind="cancel">Cancel</button>
-//         <button class="button default" bind="tag">Tag</button>
+//         <button bind="cancel" class="button">Cancel</button>
+//         <button bind="tag" class="button default" disabled>Tag</button>
 //     </div>
 // </div>
-//
-
 
 function EntityLinkingTaggerDialog(column) {
     this.column = column;
@@ -46,15 +30,16 @@ function EntityLinkingTaggerDialog(column) {
 EntityLinkingTaggerDialog.prototype = {
     init: function (callback) {
         let self = this,
-            selectedModel = null,
+            selectedLanguage = null,
+            selectedTerminology = null,
             dialogElement = this.dialogElement = $(DOM.loadHTML("aidava-tagger", "dialogs/entity-linking-tagger-dialog.html"));
         // Populate labels
         $(".tagger-column-name", dialogElement).text(this.column.name);
         // Bind controls
         let controls = DOM.bind(dialogElement);
         controls.cancel.click(this.bound("hide"));
         controls.tag.click(() => {
-            self.tag(selectedModel);
+            self.tag(selectedLanguage, selectedTerminology);
         });
 
         // Load NLP models
@@ -64,14 +49,35 @@ EntityLinkingTaggerDialog.prototype = {
             {name: "Estonian", value: "et"}
         ];
 
-        let modelList = $("ol", dialogElement);
+        let terminologies = [
+            {name: "Snomed CT", value: "snomed"},
+            {name: "ICD-10", value: "icd10"},
+            {name: "LOINC", value: "loinc"}
+        ];
+
+        let langList = $("ol.language", dialogElement);
+        let terminologyList = $("ol.terminology", dialogElement);
 
         langs.forEach((model) => {
-            let li = $("<li></li>").appendTo(modelList);
-            let radio = $('<input type="radio" name="nlp-model" value="' + model.value + '">').appendTo(li);
+            let li = $("<li></li>").appendTo(langList);
+            let radio = $('<input type="radio" name="language" value="' + model.value + '">').appendTo(li);
+            radio.click(() => {
+                selectedLanguage = model.value;
+                if (selectedTerminology) {
+                    controls.tag.prop("disabled", false);
+                }
+            });
+            $('<label>' + model.name + '</label>').appendTo(li);
+        });
+
+        terminologies.forEach((model) => {
+            let li = $("<li></li>").appendTo(terminologyList);
+            let radio = $('<input type="radio" name="terminology" value="' + model.value + '">').appendTo(li);
             radio.click(() => {
-                selectedModel = model.value;
-                controls.tag.prop("disabled", false);
+                selectedTerminology = model.value;
+                if (selectedLanguage) {
+                    controls.tag.prop("disabled", false);
+                }
             });
             $('<label>' + model.name + '</label>').appendTo(li);
         });
@@ -80,12 +86,15 @@ EntityLinkingTaggerDialog.prototype = {
         }
     },
 
-    tag: function (model) {
+    tag: function (
+        language,
+        terminology
+    ) {
         // Tag the column with the selected model
-        console.log("Tagging column", this.column.name, "with model", model);
         let data = {
             column: this.column.name,
-            model: model
+            language: language,
+            terminology: terminology
         }
         Refine.postProcess("aidava-tagger", "tag-entity-linking", data, {}, {rowsChanged: false, modelsChanged: false});
         this.hide();