From 19b2f901c7940b4988ff307b24f6f48f22a5f88f Mon Sep 17 00:00:00 2001
From: Carlo Minotti <50220438+minottic@users.noreply.github.com>
Date: Tue, 30 Jul 2024 20:01:58 +0200
Subject: [PATCH] Change response type to octet/stream parsing

* Change response type to octet/stream parsing

* Add contentType to avoid selfclosing manipulation
---
 .../acceptance/technique.controller.acceptance.ts  |  2 +-
 src/__tests__/fixtures/MockStubs.ts                | 14 +++++++++++++-
 .../fixtures/responses/github.response.ts          |  4 +++-
 src/__tests__/unit/technique-getter.unit.ts        |  2 +-
 src/misc/technique-getter.ts                       |  6 ++++--
 5 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/__tests__/acceptance/technique.controller.acceptance.ts b/src/__tests__/acceptance/technique.controller.acceptance.ts
index 1d764bf..6c906ec 100644
--- a/src/__tests__/acceptance/technique.controller.acceptance.ts
+++ b/src/__tests__/acceptance/technique.controller.acceptance.ts
@@ -30,7 +30,7 @@ configs.forEach(conf => {
           .stub(BioPortalTechniques.prototype, 'getCollection')
           .resolves(bioportalResponse);
       // eslint-disable-next-line  @typescript-eslint/no-explicit-any
-      else sandbox.stub(superagent, 'get').resolves(githubRespone as any);
+      else sandbox.stub(superagent, 'get').returns(githubRespone as any);
       ({app, client} = await setupApplication({
         technique: {class: conf, cache: cache},
       }));
diff --git a/src/__tests__/fixtures/MockStubs.ts b/src/__tests__/fixtures/MockStubs.ts
index e1a5657..1adf209 100644
--- a/src/__tests__/fixtures/MockStubs.ts
+++ b/src/__tests__/fixtures/MockStubs.ts
@@ -1,7 +1,19 @@
 import {JSDOM} from 'jsdom';
 
 export const xmlContent = `<?xml version="1.0"?>
-<rdf:RDF xmlns="aXML">
+<rdf:RDF xmlns="http://purl.org/pan-science/PaNET/PaNET.owl#"
+     xml:base="http://purl.org/pan-science/PaNET/PaNET.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:foaf="http://xmlns.com/foaf/0.1/"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:skos="http://www.w3.org/2004/02/skos/core#"
+     xmlns:vann="http://purl.org/vocab/vann/"
+     xmlns:PaNET="PaNET:"
+     xmlns:terms="http://purl.org/dc/terms/">
 
     <owl:Class rdf:about="class1">
         <owl:equivalentClass rdf:resource="http://class2/label2"/>
diff --git a/src/__tests__/fixtures/responses/github.response.ts b/src/__tests__/fixtures/responses/github.response.ts
index 03a4319..8e27d0c 100644
--- a/src/__tests__/fixtures/responses/github.response.ts
+++ b/src/__tests__/fixtures/responses/github.response.ts
@@ -1,5 +1,6 @@
 export const githubRespone = {
-  text: `<?xml version="1.0"?>
+  responseType: (value: string) => ({
+    body: `<?xml version="1.0"?>
 <rdf:RDF xmlns="http://purl.org/pan-science/PaNET/PaNET.owl#"
      xml:base="http://purl.org/pan-science/PaNET/PaNET.owl"
      xmlns:obo="http://purl.obolibrary.org/obo/"
@@ -4256,4 +4257,5 @@ export const githubRespone = {
 
 
 <!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->`,
+  }),
 };
diff --git a/src/__tests__/unit/technique-getter.unit.ts b/src/__tests__/unit/technique-getter.unit.ts
index 110e4ad..919dbe0 100644
--- a/src/__tests__/unit/technique-getter.unit.ts
+++ b/src/__tests__/unit/technique-getter.unit.ts
@@ -299,7 +299,7 @@ describe('GitHubOwlTechnique', () => {
       sandbox
         .stub(superagent, 'get')
         // eslint-disable-next-line  @typescript-eslint/no-explicit-any
-        .returns({text: xmlContent} as any);
+        .returns({responseType: () => ({body: xmlContent})} as any);
       const data = await GitHubOwlTechnique.getCollection();
       expect(data.length).to.be.eql(3);
     });
diff --git a/src/misc/technique-getter.ts b/src/misc/technique-getter.ts
index 52f76d8..d565c90 100644
--- a/src/misc/technique-getter.ts
+++ b/src/misc/technique-getter.ts
@@ -145,8 +145,10 @@ export class GitHubOwlTechnique extends OntologyTechnique {
   }
 
   async getCollection(): Promise<NodeList> {
-    const xmlFile = await superagent.get(this.url);
-    const xmlParsed = new jsdom.JSDOM(xmlFile.text);
+    const xmlFile = await superagent.get(this.url).responseType('blob');
+    const xmlParsed = new jsdom.JSDOM(xmlFile.body.toString('utf-8'), {
+      contentType: 'application/xml',
+    });
     return xmlParsed.window.document.querySelectorAll(
       'owl\\:Class[rdf\\:about]',
     );