Development

.github/workflows/main.yml

@@ -1,13 +1,11 @@
 name: Main import action
 
 on:
-    push:
-      branches:
-        - "*"
-
+  push:
 jobs:
-  docker:
-    uses: Gravitate-Health/reusable-workflows/.github/workflows/main.yml@main
-    secrets:
-      REGISTRY_TOKEN: ${{ secrets.REGISTRY_TOKEN }}
-      REGISTRY_USERNAME: ${{ secrets.REGISTRY_USERNAME }}
+    main-GH-workflow:
+      uses: Gravitate-Health/reusable-workflows/.github/workflows/main.yml@main
+      secrets: 
+        REGISTRY_TOKEN: ${{ secrets.REGISTRY_TOKEN }}
+        REGISTRY_USERNAME: ${{ secrets.REGISTRY_USERNAME }}
+        KUBECONFIG_DEV: ${{ secrets.KUBECONFIG_DEV }}

src/lenses/lens-selector-mvp2_allergy.js → src/lenses/lens-selector-mvp2_allergyintollerance.js

@@ -8,6 +8,75 @@ let getSpecification = () => {
     return "1.0.0";
 };
 
+let enhance = async () => {
+    // Proves that IPS exists
+    if (ips == "" || ips == null) {
+        throw new Error("Failed to load IPS: the LEE is getting a empty IPS");
+    }
+
+    // Instantiates the array of condition codes
+    let arrayOfConditionCodes = [];
+
+    // Iterates through the IPS entry searching for conditions
+    ips.entry.forEach((element) => {
+        if (element.resource.resourceType == "AllergyIntolerance") {
+            if (element.resource.code != undefined) {
+                element.resource.code.coding.forEach((coding) => {
+                    arrayOfConditionCodes.push({
+                        code: coding.code,
+                        system: coding.system,
+                    });
+                });
+            }
+        }
+    });
+
+    // If there are no conditions, return the ePI as it is
+    if (arrayOfConditionCodes.length == 0) {
+        return htmlData;
+    }
+
+    // ePI traslation from terminology codes to their human redable translations in the sections
+    let compositions = 0;
+    let categories = [];
+    epi.entry.forEach((entry) => {
+        if (entry.resource.resourceType == "Composition") {
+            compositions++;
+            //Iterated through the Condition element searching for conditions
+            entry.resource.extension.forEach((element) => {
+
+                // Check if the position of the extension[1] is correct
+                if (element.extension[1].url == "concept") {
+                    // Search through the different terminologies that may be avaible to check in the condition
+                    if (element.extension[1].valueCodeableReference.concept != undefined) {
+                        element.extension[1].valueCodeableReference.concept.coding.forEach(
+                            (coding) => {
+                                console.log("Extension: " + element.extension[0].valueString + ":" + coding.code + " - " + coding.system)
+                                // Check if the code is in the list of categories to search
+                                if (equals(arrayOfConditionCodes, { code: coding.code, system: coding.system })) {
+                                    // Check if the category is already in the list of categories
+                                    categories.push(element.extension[0].valueString);
+                                }
+                            }
+                        );
+                    }
+                }
+            });
+        }
+    });
+
+    if (compositions == 0) {
+        throw new Error('Bad ePI: no category "Composition" found');
+    }
+
+    if (categories.length == 0) {
+        return htmlData;
+    }
+
+    //Focus (adds highlight class) the html applying every category found
+    return await annotateHTMLsection(categories, "highlight");
+};
+
 let annotationProcess = (listOfCategories, enhanceTag, document, response) => {
     listOfCategories.forEach((check) => {
         if (response.includes(check)) {
@@ -55,67 +124,11 @@ let annotateHTMLsection = async (listOfCategories, enhanceTag) => {
     }
 };
 
-let enhance = async () => {
-
-    let listOfCategoriesToSearch = [
-        "NUT-ALLERGY" // dummy allergy
-    ];
-
-    // Get IPS gender and check if is female
-    let gender;
-
-    if (ips == "" || ips == null) {
-        throw new Error("Failed to load IPS: the LEE is getting a empty IPS");
-    }
-    ips.entry.forEach((element) => {
-        if (element.resource.resourceType == "Patient") {
-            gender = element.resource.gender;
-            if (gender != "female") {
-                return htmlData;
-            }
-        }
+let equals = (array, object) => {
+    return array.some((element) => {
+        return (element.code === object.code) && (element.system === object.system);
     });
-
-    // ePI traslation from terminology codes to their human redable translations in the sections
-    let compositions = 0;
-    let categories = [];
-    epi.entry.forEach((entry) => {
-        if (entry.resource.resourceType == "Composition") {
-            compositions++;
-            //Iterated through the Condition element searching for conditions
-            entry.resource.extension.forEach((element) => {
-
-                // Check if the position of the extension[1] is correct
-                if (element.extension[1].url == "concept") {
-                    // Search through the different terminologies that may be avaible to check in the condition
-                    if (element.extension[1].valueCodeableReference.concept != undefined) {
-                        element.extension[1].valueCodeableReference.concept.coding.forEach(
-                            (coding) => {
-                                console.log("Extension: " + element.extension[0].valueString + ":" + coding.code)
-                                // Check if the code is in the list of categories to search
-                                if (listOfCategoriesToSearch.includes(coding.code)) {
-                                    // Check if the category is already in the list of categories
-                                    categories.push(element.extension[0].valueString);
-                                }
-                            }
-                        );
-                    }
-                }
-            });
-        }
-    });
-
-    if (compositions == 0) {
-        throw new Error('Bad ePI: no category "Composition" found');
-    }
-
-    if (categories.length == 0) {
-        // throw new Error("No categories found", categories);
-        return htmlData;
-    }
-    //Focus (adds highlight class) the html applying every category found
-    return await annotateHTMLsection(categories, "highlight");
-};
+}
 
 return {
     enhance: enhance,

src/lenses/lens-selector-mvp2_HIV.js → src/lenses/lens-selector-mvp2_conditions.js

@@ -8,75 +8,31 @@ let getSpecification = () => {
     return "1.0.0";
 };
 
-let annotationProcess = (listOfCategories, enhanceTag, document, response) => {
-    listOfCategories.forEach((check) => {
-        if (response.includes(check)) {
-            let elements = document.getElementsByClassName(check);
-            for (let i = 0; i < elements.length; i++) {
-                elements[i].classList.add(enhanceTag);
-            }
-            if (document.getElementsByTagName("head").length > 0) {
-                document.getElementsByTagName("head")[0].remove();
-            }
-            if (document.getElementsByTagName("body").length > 0) {
-                response = document.getElementsByTagName("body")[0].innerHTML;
-                console.log("Response: " + response);
-            } else {
-                console.log("Response: " + document.documentElement.innerHTML);
-                response = document.documentElement.innerHTML;
-            }
-        }
-    });
-
-    if (response == null || response == "") {
-        throw new Error(
-            "Annotation proccess failed: Returned empty or null response"
-        );
-        //return htmlData
-    } else {
-        console.log("Response: " + response);
-        return response;
-    }
-}
-
-let annotateHTMLsection = async (listOfCategories, enhanceTag) => {
-    let response = htmlData;
-    let document;
-
-    if (typeof window === "undefined") {
-        let jsdom = await import("jsdom");
-        let { JSDOM } = jsdom;
-        let dom = new JSDOM(htmlData);
-        document = dom.window.document;
-        return annotationProcess(listOfCategories, enhanceTag, document, response);
-    } else {
-        document = window.document;
-        return annotationProcess(listOfCategories, enhanceTag, document, response);
-    }
-};
-
 let enhance = async () => {
-    let listOfCategoriesToSearch = ["B90", "86406008"];
-
+    // Proves that IPS exists
     if (ips == "" || ips == null) {
         throw new Error("Failed to load IPS: the LEE is getting a empty IPS");
     }
 
-    //Search for the condition in the IPS
-    let patientHasCondition = false;
+    // Instantiates the array of condition codes
+    let arrayOfConditionCodes = [];
+
+    // Iterates through the IPS entry searching for conditions
     ips.entry.forEach((element) => {
         if (element.resource.resourceType == "Condition") {
             if (element.resource.code != undefined) {
                 element.resource.code.coding.forEach((coding) => {
-                    if (listOfCategoriesToSearch.includes(coding.code)) {
-                        patientHasCondition = true;
-                    }
+                    arrayOfConditionCodes.push({
+                        code: coding.code,
+                        system: coding.system,
+                    });
                 });
             }
         }
     });
 
-    if (!patientHasCondition) {
+    // If there are no conditions, return the ePI as it is
+    if (arrayOfConditionCodes.length == 0) {
         return htmlData;
     }
 
@@ -95,9 +51,9 @@ let enhance = async () => {
                     if (element.extension[1].valueCodeableReference.concept != undefined) {
                         element.extension[1].valueCodeableReference.concept.coding.forEach(
                             (coding) => {
-                                console.log("Extension: " + element.extension[0].valueString + ":" + coding.code)
+                                console.log("Extension: " + element.extension[0].valueString + ":" + coding.code + " - " + coding.system)
                                 // Check if the code is in the list of categories to search
-                                if (listOfCategoriesToSearch.includes(coding.code)) {
+                                if (equals(arrayOfConditionCodes, { code: coding.code, system: coding.system })) {
                                     // Check if the category is already in the list of categories
                                     categories.push(element.extension[0].valueString);
                                 }
@@ -114,12 +70,66 @@ let enhance = async () => {
     }
 
     if (categories.length == 0) {
-        //throw new Error("No categories found", categories);
         return htmlData;
     }
+
     //Focus (adds highlight class) the html applying every category found
     return await annotateHTMLsection(categories, "highlight");
 };
+
+let annotationProcess = (listOfCategories, enhanceTag, document, response) => {
+    listOfCategories.forEach((check) => {
+        if (response.includes(check)) {
+            let elements = document.getElementsByClassName(check);
+            for (let i = 0; i < elements.length; i++) {
+                elements[i].classList.add(enhanceTag);
+            }
+            if (document.getElementsByTagName("head").length > 0) {
+                document.getElementsByTagName("head")[0].remove();
+            }
+            if (document.getElementsByTagName("body").length > 0) {
+                response = document.getElementsByTagName("body")[0].innerHTML;
+                console.log("Response: " + response);
+            } else {
+                console.log("Response: " + document.documentElement.innerHTML);
+                response = document.documentElement.innerHTML;
+            }
+        }
+    });
+
+    if (response == null || response == "") {
+        throw new Error(
+            "Annotation proccess failed: Returned empty or null response"
+        );
+        //return htmlData
+    } else {
+        console.log("Response: " + response);
+        return response;
+    }
+}
+
+let annotateHTMLsection = async (listOfCategories, enhanceTag) => {
+    let response = htmlData;
+    let document;
+
+    if (typeof window === "undefined") {
+        let jsdom = await import("jsdom");
+        let { JSDOM } = jsdom;
+        let dom = new JSDOM(htmlData);
+        document = dom.window.document;
+        return annotationProcess(listOfCategories, enhanceTag, document, response);
+    } else {
+        document = window.document;
+        return annotationProcess(listOfCategories, enhanceTag, document, response);
+    }
+};
+
+let equals = (array, object) => {
+    return array.some((element) => {
+        return (element.code === object.code) && (element.system === object.system);
+    });
+}
+
 return {
     enhance: enhance,
     getSpecification: getSpecification,