fix(RDF API): Incorrect internal IRIs

[svandenhoek]

What are the main changes you did:

• Some changes due to chore(emx2): spark to javalin migration #4165:
  • Removed unused return values
  • Refactored code to better make use of Context
• Closes RDF API output generates incorrect internal IRIs #4382: RDFService expects base URL of installation only:

  • molgenis-emx2/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java

    Lines 100 to 102 in 9b22e28

    	* The baseURL is the URL at which MOLGENIS is deployed, include protocol and port (if deviating
    	* from the protocol default port). This is used because we need to be able to refer to different
    	* schemas.

  • molgenis-emx2/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/RDFService.java

    Line 109 in 9b22e28

    * @param baseURL the base URL of the MOLGENIS installation

how to test:

• See if behaviour of RDF API output generates incorrect internal IRIs #4382 does not occur anymore
• Check if URL still correct regarding presence/absence port:
  • On local server: curl http://localhost:8080/pet%20store/api/rdf should contain <http://localhost:8080/pet%20store/api/rdf/User/column/username>
  • On preview server: curl https://preview-emx2-pr-4383.dev.molgenis.org/pet%20store/api/rdf should contain <http://preview-emx2-pr-4383.dev.molgenis.org/pet%20store/api/rdf/User/column/username>

todo:

• updated docs in case of new feature
• added/updated tests
• added/updated testplan to include a test for this fix, including ref to bug using # notation

[harmbrugge]

I think using contextPath wil fix the issue, but indeed a test would be nice

[esthervanenckevort]

• In general the code looks fine
• As already mentioned it would be good to add a test for the change in extractBaseUrl
• Update with main first

[esthervanenckevort]

I thought it is not preferable to use * imports

[svandenhoek]

IDEA did that automatically after I made some changes, I'll make sure to revert it.

[svandenhoek]

Seems config.router.contextPath (as stated in the Javalin docs) is currently not being configured in:

molgenis-emx2/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisWebservice.java

Lines 43 to 52 in a5e8310

	Javalin app =
	Javalin.create(
	config -> {
	config.http.maxRequestSize = MAX_REQUEST_SIZE;
	config.router.ignoreTrailingSlashes = true;
	config.router.treatMultipleSlashesAsSingleSlash = true;
	config.jetty.modifyServletContextHandler(
	handler -> handler.setSessionHandler(sessionManager.getSessionHandler()));
	})
	.start(port);

So the current fix might not work yet anyhow (or any other places that depend on a defined contextPath)...

[svandenhoek]

Tests were added where config.contextResolver.host & config.router.contextPath are set to test the behaviour. In my initial feedback processing (510b1b5) Javalin actually used the said port (and locally all tests worked), but the Azure build failed due to java.net.BindException: Permission denied on port 80.

So currently using the Javalin test framework that uses a random uncommon port and simply overriding the defined host. This means some of the tests were removed though that used the actual port.

[sonarcloud]

Quality Gate passed

Issues
6 New issues
0 Accepted issues

Measures
0 Security Hotspots
92.9% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud