core: Fix cellbase validator to acknowledge tokens. #TASK-4913

opencb · Aug 30, 2023 · 4aeaa83 · 4aeaa83
1 parent a3de4e1
commit 4aeaa83
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Showing 2 changed files with 78 additions and 5 deletions.
diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java
@@ -1,23 +1,23 @@
 package org.opencb.opencga.core.cellbase;
 
+import io.jsonwebtoken.JwtException;
 import org.apache.commons.lang3.StringUtils;
+import org.opencb.biodata.models.variant.avro.VariantAnnotation;
 import org.opencb.cellbase.client.rest.CellBaseClient;
 import org.opencb.cellbase.core.config.SpeciesConfiguration;
 import org.opencb.cellbase.core.config.SpeciesProperties;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResponse;
 import org.opencb.cellbase.core.token.DataAccessTokenManager;
 import org.opencb.cellbase.core.token.DataAccessTokenSources;
+import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.opencga.core.common.VersionUtils;
 import org.opencb.opencga.core.config.storage.CellBaseConfiguration;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 
 public class CellBaseValidator {
 
@@ -46,6 +46,7 @@ private CellBaseClient newCellBaseClient(CellBaseConfiguration cellBaseConfigura
                 toCellBaseSpeciesName(species),
                 assembly,
                 cellBaseConfiguration.getDataRelease(),
+                cellBaseConfiguration.getToken(),
                 cellBaseConfiguration.toClientConfiguration());
     }
 
@@ -120,7 +121,7 @@ public void validate() throws IOException {
         validate(false);
     }
 
-    public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
+    private CellBaseConfiguration validate(boolean autoComplete) throws IOException {
         CellBaseConfiguration cellBaseConfiguration = getCellBaseConfiguration();
         String inputVersion = getVersion();
         CellBaseDataResponse<SpeciesProperties> species;
@@ -173,6 +174,38 @@ public CellBaseConfiguration validate(boolean autoComplete) throws IOException {
                 }
             }
         }
+        if (getToken() != null) {
+            // Check it's supported
+            if (!supportsToken(serverVersion)) {
+                throw new IllegalArgumentException("Token not supported for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion + "'");
+            }
+
+            // Check it's an actual token
+            DataAccessTokenManager tokenManager = new DataAccessTokenManager();
+            try {
+                tokenManager.decode(getToken());
+            } catch (JwtException e) {
+                throw new IllegalArgumentException("Malformed token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+
+            // Check it's a valid token
+            CellBaseDataResponse<VariantAnnotation> response = cellBaseClient.getVariantClient()
+                    .getAnnotationByVariantIds(Collections.singletonList("1:1:N:C"), new QueryOptions(), true);
+            if (response.firstResult() == null) {
+                throw new IllegalArgumentException("Invalid token for cellbase "
+                        + "url: '" + getURL() + "'"
+                        + ", version: '" + inputVersion
+                        + "', species: '" + getSpecies()
+                        + "', assembly: '" + getAssembly() + "'");
+            }
+        }
+
         return cellBaseConfiguration;
     }
 
@@ -206,6 +239,11 @@ public static boolean supportsDataRelease(String serverVersion) {
         return VersionUtils.isMinVersion("5.1.0", serverVersion);
     }
 
+    public static boolean supportsToken(String serverVersion) {
+        // Tokens support starts at version 5.4.0
+        return VersionUtils.isMinVersion("5.4.0", serverVersion);
+    }
+
     public String getVersionFromServerMajor() throws IOException {
         return major(getVersionFromServer());
     }

diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java
@@ -1,6 +1,8 @@
 package org.opencb.opencga.core.cellbase;
 
+import org.apache.commons.lang3.StringUtils;
 import org.junit.Assert;
+import org.junit.Assume;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
@@ -70,4 +72,37 @@ public void testNoActiveReleases() throws IOException {
         thrown.expectMessage("No active data releases found on cellbase");
         CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, null), "mmusculus", "GRCm38", true);
     }
+
+    @Test
+    public void testToken() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testTokenNotSupported() throws IOException {
+        String token = System.getenv("CELLBASE_HGMD_TOKEN");
+        Assume.assumeTrue(StringUtils.isNotEmpty(token));
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testMalformedToken() throws IOException {
+        thrown.expectMessage("Malformed token for cellbase");
+        String token = "MALFORMED_TOKEN";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
+    @Test
+    public void testUnsignedToken() throws IOException {
+        thrown.expectMessage("Invalid token for cellbase");
+        String token = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2OTMyMTY5MDd9.invalidsignature";
+        CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true);
+        Assert.assertNotNull(validated.getToken());
+    }
+
 }