diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5b59984..8be6d79 100644
--- a/.github/workflows/main.yml
+++ b/.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 }}
\ No newline at end of file
+ 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 }}
\ No newline at end of file
diff --git a/src/lenses/lens-selector-mvp2_allergy.js b/src/lenses/lens-selector-mvp2_allergyintollerance.js
similarity index 78%
rename from src/lenses/lens-selector-mvp2_allergy.js
rename to src/lenses/lens-selector-mvp2_allergyintollerance.js
index 04030eb..76f6c06 100644
--- a/src/lenses/lens-selector-mvp2_allergy.js
+++ b/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,
diff --git a/src/lenses/lens-selector-mvp2_HIV.js b/src/lenses/lens-selector-mvp2_conditions.js
similarity index 83%
rename from src/lenses/lens-selector-mvp2_HIV.js
rename to src/lenses/lens-selector-mvp2_conditions.js
index bd98779..f5b92dd 100644
--- a/src/lenses/lens-selector-mvp2_HIV.js
+++ b/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,
diff --git a/src/lenses/lens-selector-mvp2_interaction.js b/src/lenses/lens-selector-mvp2_interaction.js
index 60138b6..0cce3d5 100644
--- a/src/lenses/lens-selector-mvp2_interaction.js
+++ b/src/lenses/lens-selector-mvp2_interaction.js
@@ -8,6 +8,80 @@ 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 arrayOfIngredientCodes = [];
+
+ // Iterates through the IPS entry searching for conditions
+ ips.entry.forEach((element) => {
+ if (element.resource.resourceType == "Medication") {
+ if (element.resource.ingredient != undefined) {
+ element.resource.ingredient.forEach((ingredient) => {
+ if (ingredient.itemCodeableConcept != undefined) {
+ ingredient.itemCodeableConcept.coding.forEach((coding) => {
+ console.log("Ingredient: " + coding.code + " - " + coding.system)
+ arrayOfIngredientCodes.push({
+ code: coding.code,
+ system: "",
+ });
+ });
+ }
+ })
+ }
+ }
+ });
+
+ // If there are no conditions, return the ePI as it is
+ if (arrayOfIngredientCodes.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(arrayOfIngredientCodes, { code: coding.code, 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)) {
@@ -55,68 +129,11 @@ let annotateHTMLsection = async (listOfCategories, enhanceTag) => {
}
};
-let enhance = async () => {
-
- let listOfCategoriesToSearch = [
- "XK4IUX8MNB", // contra-indication-hypericum
- "SY7Q814VUP", // contra-indication-calcium
- ];
-
- // 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,
diff --git a/src/lenses/lens-selector-mvp2_intolerance.js b/src/lenses/lens-selector-mvp2_intolerance.js
deleted file mode 100644
index 4e596f4..0000000
--- a/src/lenses/lens-selector-mvp2_intolerance.js
+++ /dev/null
@@ -1,123 +0,0 @@
-let pvData = pv;
-let htmlData = html;
-
-let epiData = epi;
-let ipsData = ips;
-
-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 = [
- "190751001" // lactose intolerance
- ];
-
- // 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;
- }
- }
- });
-
- // 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,
- getSpecification: getSpecification,
-};
diff --git a/target/fhir-lens-HIV.json b/target/fhir-lens-HIV.json
new file mode 100644
index 0000000..dfd507c
--- /dev/null
+++ b/target/fhir-lens-HIV.json
@@ -0,0 +1,65 @@
+{
+ "resourceType" : "Library",
+ "id" : "fhir-lens-HIV",
+ "meta" : {
+ "profile" : ["http://hl7.eu/fhir/ig/gravitate-health/StructureDefinition/lens"]
+ },
+ "text" : {
+ "status" : "generated",
+ "div" : "Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens
Parameters
| in | | | CodeableConcept | parameter documentation |
Contents
application/javascript
Classic Pregnancy Lens