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fix(RDF API): Incorrect internal IRIs #4383

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merged 16 commits into from
Oct 28, 2024
Merged

fix(RDF API): Incorrect internal IRIs #4383

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77c5c38
Possible fix for RDF API using incorrect base URL
svandenhoek Oct 21, 2024
879d675
Revert "Possible fix for RDF API using incorrect base URL"
svandenhoek Oct 21, 2024
4cd2ab3
Removed unused returns
svandenhoek Oct 21, 2024
de0650c
fixed variable naming
svandenhoek Oct 21, 2024
4715f3f
Updated tests to validate on bug
svandenhoek Oct 21, 2024
4bb13ee
fix for incorrect internal IRI + some refactoring
svandenhoek Oct 21, 2024
652e154
Removed unneeded code (test on PR server shows no port in IRI while l…
svandenhoek Oct 21, 2024
b3fe982
Revert "fixed variable naming"
svandenhoek Oct 21, 2024
856c269
Reverted wildcard imports done by IDE
svandenhoek Oct 22, 2024
551160e
Added test (+ some refactoring to add tests properly)
svandenhoek Oct 24, 2024
fb5fd95
Merge branch 'master' into fix/rdf_api_base_url
svandenhoek Oct 24, 2024
0d44a6f
formatting
svandenhoek Oct 24, 2024
510b1b5
auto-formatting
svandenhoek Oct 24, 2024
7a46997
Tests do not use actual ports but only override value due to failing …
svandenhoek Oct 24, 2024
8651f33
Merge branch 'master' into fix/rdf_api_base_url
svandenhoek Oct 28, 2024
13605a0
Some code adjustments for more coverage
svandenhoek Oct 28, 2024
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45 changes: 10 additions & 35 deletions backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/RDFApi.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,7 @@
import io.javalin.Javalin;
import io.javalin.http.Context;
import java.io.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.*;
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I thought it is not preferable to use * imports

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

import org.eclipse.rdf4j.rio.RDFFormat;
import org.molgenis.emx2.Database;
import org.molgenis.emx2.MolgenisException;
Expand Down Expand Up @@ -58,12 +55,11 @@ private static void defineApiRoutes(Javalin app, String apiLocation, RDFFormat f
app.head("{schema}" + apiLocation + "/{table}column/{column}/", (ctx) -> rdfHead(ctx, format));
}

private static String rdfHead(Context ctx, RDFFormat format) {
private static void rdfHead(Context ctx, RDFFormat format) {
ctx.contentType(selectFormat(ctx, format).getDefaultMIMEType());
return "";
}

private static int rdfForDatabase(Context ctx, RDFFormat format) throws IOException {
private static void rdfForDatabase(Context ctx, RDFFormat format) throws IOException {
format = selectFormat(ctx, format); // defines format if null

Database db = sessionManager.getSession(ctx.req()).getDatabase();
Expand Down Expand Up @@ -99,10 +95,9 @@ private static int rdfForDatabase(Context ctx, RDFFormat format) throws IOExcept

outputStream.flush();
outputStream.close();
return 200;
}

private static int rdfForSchema(Context ctx, RDFFormat format) throws IOException {
private static void rdfForSchema(Context ctx, RDFFormat format) throws IOException {
format = selectFormat(ctx, format); // defines format if null

Schema schema = getSchema(ctx);
Expand All @@ -118,10 +113,9 @@ private static int rdfForSchema(Context ctx, RDFFormat format) throws IOExceptio
rdf.describeAsRDF(outputStream, null, null, null, schema);
outputStream.flush();
outputStream.close();
return 200;
}

private static int rdfForTable(Context ctx, RDFFormat format) throws IOException {
private static void rdfForTable(Context ctx, RDFFormat format) throws IOException {
format = selectFormat(ctx, format); // defines format if null

Table table = getTableByIdOrName(ctx);
Expand All @@ -138,10 +132,9 @@ private static int rdfForTable(Context ctx, RDFFormat format) throws IOException
rdf.describeAsRDF(outputStream, table, rowId, null, table.getSchema());
outputStream.flush();
outputStream.close();
return 200;
}

private static int rdfForRow(Context ctx, RDFFormat format) throws IOException {
private static void rdfForRow(Context ctx, RDFFormat format) throws IOException {
format = selectFormat(ctx, format); // defines format if null
Table table = getTableByIdOrName(ctx);
String rowId = sanitize(ctx.pathParam("row"));
Expand All @@ -154,10 +147,9 @@ private static int rdfForRow(Context ctx, RDFFormat format) throws IOException {
rdf.describeAsRDF(outputStream, table, rowId, null, table.getSchema());
outputStream.flush();
outputStream.close();
return 200;
}

private static int rdfForColumn(Context ctx, RDFFormat format) throws IOException {
private static void rdfForColumn(Context ctx, RDFFormat format) throws IOException {
format = selectFormat(ctx, format); // defines format if null

Table table = getTableByIdOrName(ctx);
Expand All @@ -172,30 +164,13 @@ private static int rdfForColumn(Context ctx, RDFFormat format) throws IOExceptio
rdf.describeAsRDF(outputStream, table, null, columnName, table.getSchema());
outputStream.flush();
outputStream.close();
return 200;
}

private static String extractBaseURL(Context ctx) {
// NOTE: The request.host() already includes the server port!
String scheme = ctx.scheme();
String port = null;
var parts = ctx.host().split(":", 2);
String host = parts[0];
if (parts.length == 2) {
if (!isWellKnownPort(scheme, parts[1])) {
port = parts[1];
}
}
return scheme
return ctx.scheme()
+ "://"
+ host
+ (port != null ? ":" + port : "")
+ (!ctx.path().isEmpty() ? "/" + ctx.path() + "/" : "/");
}

private static boolean isWellKnownPort(String scheme, String port) {
return (scheme.equals("http") && port.equals("80"))
|| (scheme.equals("https") && port.equals("443"));
+ ctx.host()
+ (!ctx.contextPath().isEmpty() ? "/" + ctx.contextPath() + "/" : "/");
}

private static RDFFormat selectFormat(Context ctx, RDFFormat format) {
Expand Down
32 changes: 28 additions & 4 deletions backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -822,7 +822,7 @@ public void testMolgenisWebservice_robotsDotTxt() {
}

@Test
public void testRdfApi() {
public void testRdfApiRequest() {
final String urlPrefix = "http://localhost:" + PORT;

final String defaultContentType = "text/turtle";
Expand Down Expand Up @@ -865,16 +865,40 @@ public void testRdfApi() {
.head(urlPrefix + "/pet store/api/jsonld");
rdfApiContentTypeRequest(200, jsonldContentType, ttlContentType)
.head(urlPrefix + "/pet store/api/ttl");
}

// Validate actual output.
String result =
@Test
void testRdfApiContent() {
// Output from global API call.
String resultBase =
given()
.sessionId(SESSION_ID)
.when()
.get("http://localhost:" + PORT + "/api/rdf?schemas=pet store")
.getBody()
.asString();
assertFalse(result.contains("CatalogueOntologies"));

// Output schema API call.
String resultSchema =
given()
.sessionId(SESSION_ID)
.when()
.get("http://localhost:" + PORT + "/pet store/api/rdf")
.getBody()
.asString();

assertAll(
// Validate base API.
() -> assertFalse(resultBase.contains("CatalogueOntologies")),
() ->
assertTrue(
resultBase.contains(
"http://localhost:" + PORT + "/pet%20store/api/rdf/Category/column/name")),
// Validate schema API.
() ->
assertTrue(
resultSchema.contains(
"http://localhost:" + PORT + "/pet%20store/api/rdf/Category/column/name")));
}

/**
Expand Down