Merge pull request #199 from EGA-archive/bugfix/EE-1919

Ignore duplicates when producing map using streams

.gitlab-ci.yml

@@ -16,7 +16,6 @@ services:
 ## List of jobs:
 stages:
   - unitTest
-  - integrationTest
   - imageBuild
 
 # Cache downloaded dependencies and plugins between builds.
@@ -35,27 +34,6 @@ unitTest:
   script:
     - mvn test
 
-integrationTest:
-  stage: integrationTest
-  before_script:
-    - mvn install -DskipTests=true -P production -Dmaven.javadoc.skip=true -B -V -DskipDockerPush
-#    - sudo service postgresql stop
-    - mkdir -p /usr/local/share/ca-certificates/
-    - cp extras/certificate/rootCA.pem /usr/local/share/ca-certificates/CA.crt
-    - chmod 644 /usr/local/share/ca-certificates/CA.crt
-    - update-ca-certificates
-    - docker build -t ega-data-api/ega-dataedge  --file Dockerfile.dataedge .
-    - docker build -t ega-data-api/ega-res  --file Dockerfile.res .
-    - docker build -t ega-data-api/ega-keyserver  --file Dockerfile.keyserver .
-    - docker build -t ega-data-api/ega-filedatabase  --file Dockerfile.filedatabase .
-    - docker build -t ega-data-api/ega-postgres --file extras/postgresdb/Dockerfile .
-    - cd extras && source ./variables.sh
-    - docker-compose up -d
-    - sleep 90
-    - cd ../ega-data-api-it
-  script:
-    - mvn test "-Dkey.url=https://dataedge" "-Dfile.url=https://dataedge" "-Dres.url=https://dataedge" "-Ddataedge.url=https://dataedge"
-
 imageBuild:
   stage: imageBuild
   script:

ega-data-api-commons/src/main/java/eu/elixir/ega/ebi/commons/config/MyAccessTokenConverter.java

@@ -238,7 +238,7 @@ public class MyAccessTokenConverter implements AccessTokenConverter {
                         .orElse(null));
     }
 
-    private Map<String, List<String>> getDatasetFileMap(final List<String> ga4ghDatasets) {
+    protected Map<String, List<String>> getDatasetFileMap(final List<String> ga4ghDatasets) {
         return ga4ghDatasets
                 .parallelStream()
                 .map(jwtService::parse)
@@ -249,7 +249,7 @@ public class MyAccessTokenConverter implements AccessTokenConverter {
                 .map(this::getDatasetId)
                 .filter(Optional::isPresent)
                 .map(Optional::get)
-                .collect(toMap(datasetId -> datasetId, fileDatasetService::getFileIds));
+                .collect(toMap(datasetId -> datasetId, fileDatasetService::getFileIds, (d1, d2) -> d2));
     }
 
     private boolean isValidToken(final SignedJWT signedJWT) {

ega-data-api-commons/src/test/java/eu/elixir/ega/ebi/commons/config/MyAccessTokenConverterTest.java

+package eu.elixir.ega.ebi.commons.config;
+
+import static java.lang.System.currentTimeMillis;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.nimbusds.jose.JOSEObjectType;
+import com.nimbusds.jose.JWSAlgorithm;
+import com.nimbusds.jose.JWSHeader;
+import com.nimbusds.jwt.JWTClaimsSet;
+import com.nimbusds.jwt.SignedJWT;
+
+import eu.elixir.ega.ebi.commons.shared.service.FileDatasetService;
+import eu.elixir.ega.ebi.commons.shared.service.Ga4ghService;
+import eu.elixir.ega.ebi.commons.shared.service.JWTService;
+import eu.elixir.ega.ebi.commons.shared.service.UserDetailsService;
+
+@RunWith(SpringRunner.class)
+public class MyAccessTokenConverterTest {
+
+	private MyAccessTokenConverter accessTokenConverter;
+
+	@MockBean
+	private JWTService jwtService;
+
+	@MockBean
+	private Ga4ghService ga4ghService;
+
+	@MockBean
+	private FileDatasetService fileDatasetService;
+
+	@MockBean
+	private UserDetailsService userDetailsService;
+
+	private final String dataset1 = "EGAD00001";
+	private final String dataset2 = "EGAD00002";
+
+	@Before
+	public void before() {
+		accessTokenConverter = new MyAccessTokenConverter(jwtService, ga4ghService, fileDatasetService,
+				userDetailsService);
+	}
+
+	@Test
+	public void getDatasetFileMap_whenPassDuplicateDatasets_thenReturnWithoutDuplicates()
+			throws JsonProcessingException, IOException, ParseException, URISyntaxException {
+		commonMock();
+
+		Map<String, List<String>> userDatasets = accessTokenConverter.getDatasetFileMap(get3Ga4GhDatasets());
+		assertEquals(2, userDatasets.size());
+		assertTrue(userDatasets.containsKey(dataset1));
+		assertTrue(userDatasets.containsKey(dataset2));
+	}
+
+	@Test
+	public void getDatasetFileMap_whenPassNoDatasets_thenReturnZeroDatasets()
+			throws JsonProcessingException, IOException, ParseException, URISyntaxException {
+		commonMock();
+
+		Map<String, List<String>> userDatasets = accessTokenConverter.getDatasetFileMap(new ArrayList<>());
+		assertEquals(0, userDatasets.size());
+	}
+
+	private List<String> get3Ga4GhDatasets() {
+		List<String> ga4ghDatasets = new ArrayList<>();
+		ga4ghDatasets.add("header1." + dataset1 + ".signature1");
+		ga4ghDatasets.add("header2." + dataset2 + ".signature2");
+		ga4ghDatasets.add("header3." + dataset2 + ".signature3");
+		return ga4ghDatasets;
+	}
+
+	private SignedJWT getSignedJWT(String dataset)
+			throws JsonProcessingException, IOException, ParseException, URISyntaxException {
+		ObjectMapper mapper = new ObjectMapper();
+		String PassportVisaObjectJson = "{ \"type\":\"ControlledAccessGrants\", \"value\":\"" + dataset + "\" }";
+		String json = "{ \"exp\":" + (currentTimeMillis() + 9000) + " , \"ga4gh_visa_v1\":" + PassportVisaObjectJson + " }";
+		JsonNode node = mapper.readTree(json);
+
+		final JWTClaimsSet jwtClaimsSet = JWTClaimsSet.parse(node.toString());
+		return new SignedJWT(getJWSHeader(), jwtClaimsSet);
+	}
+
+	private JWSHeader getJWSHeader() throws URISyntaxException {
+		return new JWSHeader.Builder(JWSAlgorithm.parse("RS256"))
+				.keyID("test")
+				.type(JOSEObjectType.JWT)
+				.jwkURL(new URI("http://example.com/"))
+				.build();
+	}
+
+	private void commonMock() throws IOException, ParseException, URISyntaxException {
+		when(jwtService.parse(get3Ga4GhDatasets().get(0))).thenReturn(Optional.of(getSignedJWT(dataset1)));
+		when(jwtService.parse(get3Ga4GhDatasets().get(1))).thenReturn(Optional.of(getSignedJWT(dataset2)));
+		when(jwtService.parse(get3Ga4GhDatasets().get(2))).thenReturn(Optional.of(getSignedJWT(dataset2)));
+		when(jwtService.isValidSignature(any())).thenReturn(true);
+		when(fileDatasetService.getFileIds(anyString())).thenReturn(new ArrayList<>());
+	}
+}