Merge pull request #21 from Gravitate-Health/18-change-lens-selector-…

…to-fhir-ips-server

18 change lens selector to fhir ips server

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:16-slim as buildstage
+FROM node:20-slim as buildstage
 
 WORKDIR /usr/src/app
 

README.md

@@ -99,7 +99,8 @@ limitations under the License.
 ## Authors and history
 
 - Guillermo Mejías ([@gmej](https://github.com/gmej))
-- Alejo Esteban ([@10alejopain](https://github.com/))
+- Alejo Esteban ([@10alejospain](https://github.com/10alejospain))
+- Alejandro Alonso ([@aalonsolopez](https://github.com/aalonsolopez))
 
 
 ---

kubernetes/002_lens-selector-example-deployment.yaml

@@ -28,14 +28,16 @@ spec:
         app: lens-selector-mvp2
     spec:
       containers:
-        - name: lens-selector-mvp2
-          image: gravitate-registry.cr.de-fra.ionos.com/lens-selector-mvp2:latest
-          imagePullPolicy: Always
-          env:
-            - name: ENVIRONMENT
-              value: "prod"
-          ports:
-            - containerPort: 3000
-              protocol: TCP
+      - name: lens-selector-mvp2
+        image: gravitate-registry.cr.de-fra.ionos.com/lens-selector-mvp2:dev
+        imagePullPolicy: Always
+        env:
+        - name: ENVIRONMENT
+          value: "prod"
+        - name: BASE_URL
+          value: "http://gravitate-health.lst.tfo.upm.es"
+        ports:
+        - containerPort: 3000
+          protocol: TCP
       restartPolicy: Always
 status: {}

openapi.yaml

@@ -5,12 +5,12 @@ info:
   description: Gravitate Health Focusing Service. Focuses a Focused ePI.
   contact: {}
 servers:
-  - url: https://fosps.gravitatehealth.eu
+- url: https://fosps.gravitatehealth.eu
 paths:
   /lenses:
     get:
       tags:
-        - Lenses
+      - Lenses
       description: Returns all lenses IDs.
       responses:
         "200":
@@ -26,10 +26,10 @@ paths:
                       type: string
                     example: ["lense1", "lense2", "lense3"]
 
-  /lenses/{id}:
+  /lenses/{name}:
     get:
       tags:
-        - Lenses
+      - Lenses
       description: Returns the lense itself.
       responses:
         "200":
@@ -39,9 +39,83 @@ paths:
               schema:
                 type: object
                 properties:
-                  metadata:
+                  resourceType:
+                    type: string
+                    example: "Library"
+                  id:
+                    type: string
+                    example: "588"
+                  meta:
+                    type: object
+                  extension:
+                    type: array
+                    items:
+                      type: object
+                  url:
+                    type: string
+                    example: "http://hl7.eu/fhir/ig/gravitate-health/Library/mock-lib"
+                  identifier:
+                    type: array
+                    items:
+                      type: object
+                  version:
+                    type: string
+                    example: "0.0.1"
+                  name:
+                    type: string
+                    example: "pregnancy-lens"
+                  title:
+                    type: string
+                    example: "pregnancy-lens"
+                  status:
+                    type: string
+                    example: "draft"
+                  experimental:
+                    type: boolean
+                    example: true
+                  type:
                     type: object
-                  lense:
+                  date:
+                    type: string
+                    example: "2024-06-12T12:23:10.005Z"
+                  publisher:
                     type: string
-                    example: "console.log('Hello World!')"
+                    example: "Gravitate Health Project - UPM Team"
+                  contact:
+                    type: array
+                    items:
+                      type: object
+                  description:
+                    type: string
+                    example: "Lens that highlight or collapses pregnancy related information"
+                  jurisdiction:
+                    type: array
+                    items:
+                      type: object
+                  purpose:
+                    type: string
+                    example: "Collapse or highlight pregnancy related information on a preprocessed ePI."
+                  usage:
+                    type: string
+                    example: "You can import this lens directly to your FHIR Server which suports Library Resource type."
+                  copiright:
+                    type: string
+                    example: "© 2024 Gravitate Health"
+                  parameter:
+                    type: array
+                    items:
+                      type: object
+                  content:
+                    type: array
+                    items:
+                      type: object
+
+    parameters:
+    - name: name
+      in: path
+      required: true
+      schema:
+        type: string
+      description: The name of the lense to return.
+
 

package.json

@@ -6,7 +6,7 @@
   "scripts": {
     "test": "echo \"Error: no test specified\" && exit 1",
     "dev": "ts-node-dev ./src/index.ts",
-    "build": "if [ -d \"$PWD/build\" ]; then rm -r \"$PWD/build\"; fi && tsc --incremental && cp -r ./src/lenses ./build",
+    "build": "if [ -d \"$PWD/build\" ]; then rm -r \"$PWD/build\"; fi && tsc --incremental",
     "start": "node build/index.js"
   },
   "repository": {

src/controllers/lensesController.ts

@@ -1,52 +1,40 @@
 import { Response, Request } from "express";
 import { Logger } from "../utils/Logger";
-import fs, { readFile, readdir } from "fs"
 
-const readLensesDir = async () => {
-  try {
-    let path = `${process.cwd()}/build/lenses/`
-    console.log(`Looking for lenses in path: ${path}`);
-    let discoveredLenses = await fs.promises.readdir(path);
-    console.log(`Discovered the following files in dir: ${discoveredLenses || "None"}`);
-    return discoveredLenses
-  } catch (err) {
-    console.error('Error occurred while reading directory!', err);
-  }
-}
-
-const readLensFile = async (path: string) => {
-  try {
-    return await fs.promises.readFile(path, 'utf-8');
-  } catch (err) {
-    console.error('Error occurred while reading file!', err);
-  }
-}
+const fhirIpsURL = process.env.BASE_URL + "/ips/api/fhir"
 
 const retrieveLensesNames = async () => {
   try {
-    let lensesNames = await readLensesDir()
-    console.log(`Found the following lenses: ${lensesNames || "None"}`);
-    return await lensesNames
+    let response = []
+    let lensPath = "/Library"
+    let lenses = await fetch(`${fhirIpsURL}${lensPath}`)
+
+    let lensesBundle = await lenses.json()
+    if (lensesBundle.total === 0) {
+      return []
+    }
+    for (let entry of lensesBundle.entry) {
+      response.push(entry.resource.name)
+    }
+    return response
   } catch (error) {
     console.log(error);
     return null
   }
 }
 
-const retrieveLense = async (lenseId: string) => {
-  let lensFilename: string = lenseId + ".js"
-  let lensPath = `${process.cwd()}/build/lenses/${lensFilename}`
-
-  let lensesNames = await retrieveLensesNames()
-  console.log(`Looking for lens: ${lensFilename}`);
-  if (lensesNames?.includes(lensFilename)) {
-    try {
-      return await readLensFile(lensPath)
-    } catch (error) {
-      console.log(error);
+const retrieveLense = async (lenseId: string): Promise<Object | null> => {
+  let lensPath = `/Library?name:exact=${lenseId}`
+  try {
+    let lenses = await fetch(`${fhirIpsURL}${lensPath}`)
+    let lensesBundle = await lenses.json()
+    if (lensesBundle.total === 0) {
+      return `No lens found with ${lenseId} name`
     }
-  } else {
-    return null
+    return lensesBundle.entry[0].resource
+  } catch (error) {
+    console.log(error);
+    return null 
   }
 }
 
@@ -60,12 +48,15 @@ export const getLens = async (req: Request, res: Response) => {
   }
   try {
     let lens = await retrieveLense(reqlens)
-    let lensObject = {
-      metadata: {},
-      lens: lens
+
+    if (lens === null) {
+      console.log(`Lens ${reqlens} not found.`);
+      res.status(404).send({
+        message: `Lens ${reqlens} not found.`
+      })
     }
-    console.log(`Sending lens: ${JSON.stringify(lensObject)}`);
-    res.status(200).send(lensObject)
+    console.log(`Sending lens: ${JSON.stringify(lens)}`);
+    res.status(200).send(lens)
     return
   } catch (error) {
     console.log(error);