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Merge pull request #20 from Gravitate-Health/development
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Development
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@aalonsolopez
aalonsolopez authored Jun 12, 2024
2 parents cce36cb + c37b5c5 commit 7e83c2d
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Showing 12 changed files with 681 additions and 311 deletions.
16 changes: 7 additions & 9 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
@@ -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 }}
133 changes: 73 additions & 60 deletions src/lenses/lens-selector-mvp2_allergy.js → ...lens-selector-mvp2_allergyintollerance.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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)) {
Expand Down Expand Up @@ -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,
Expand Down
126 changes: 68 additions & 58 deletions src/lenses/lens-selector-mvp2_HIV.js → src/lenses/lens-selector-mvp2_conditions.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}

Expand All @@ -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);
}
Expand All @@ -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,
Expand Down
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