catalog: create Organization db adaptor, #TASK-4389

opencga-analysis/src/test/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisTest.java

@@ -38,7 +38,9 @@
 import org.opencb.opencga.core.models.alignment.AlignmentGeneCoverageStatsParams;
 import org.opencb.opencga.core.models.file.File;
 import org.opencb.opencga.core.models.file.FileLinkParams;
-import org.opencb.opencga.core.models.user.Account;
+import org.opencb.opencga.core.models.organizations.OrganizationCreateParams;
+import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams;
+import org.opencb.opencga.core.models.user.User;
 import org.opencb.opencga.core.testclassification.duration.MediumTests;
 import org.opencb.opencga.storage.core.StorageEngineFactory;
 import org.opencb.opencga.storage.core.variant.VariantStorageEngine;
@@ -218,8 +220,11 @@ public static void afterClass() {
         opencga.after();
     }
 
-    public void setUpCatalogManager() throws IOException, CatalogException {
-        catalogManager.getUserManager().create(USER, "User Name", "[email protected]", PASSWORD, "", null, Account.AccountType.FULL, opencga.getAdminToken());
+    public void setUpCatalogManager() throws CatalogException {
+        catalogManager.getOrganizationManager().create(new OrganizationCreateParams().setId("test"), null, opencga.getAdminToken());
+        catalogManager.getUserManager().create("test", new User().setId(USER).setName("User Name").setEmail("[email protected]"), PASSWORD, opencga.getAdminToken());
+        catalogManager.getOrganizationManager().update("test", new OrganizationUpdateParams().setOwner(USER), null, opencga.getAdminToken());
+
         token = catalogManager.getUserManager().login("user", PASSWORD).getToken();
 
         String projectId = catalogManager.getProjectManager().create(PROJECT, "Project about some genomes", "", "Homo sapiens",

opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminCliOptionsParser.java

@@ -383,9 +383,6 @@ public class InstallCatalogCommandOptions extends CatalogDatabaseCommandOptions
         @Parameter(names = {"--email"}, description = "Administrator e-mail", arity = 1)
         public String email;
 
-        @Parameter(names = {"--organization"}, description = "Administrator organization", arity = 1)
-        public String organization;
-
         @Parameter(names = {"--secret-key"}, description = "Secret key needed to authenticate through OpenCGA (JWT).")
         public String secretKey;
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/CatalogCommandExecutor.java

@@ -186,7 +186,7 @@ private void install() throws CatalogException {
 
         try (CatalogManager catalogManager = new CatalogManager(configuration)) {
             catalogManager.installCatalogDB(configuration.getAdmin().getSecretKey(), commandOptions.commonOptions.adminPassword,
-                    commandOptions.email, commandOptions.organization, commandOptions.force);
+                    commandOptions.email, commandOptions.force);
         }
     }
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/AuthenticationManager.java

@@ -20,6 +20,7 @@
 import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.core.api.ParamConstants;
+import org.opencb.opencga.core.models.JwtPayload;
 import org.opencb.opencga.core.models.user.AuthenticationResponse;
 import org.opencb.opencga.core.models.user.User;
 import org.opencb.opencga.core.response.OpenCGAResult;
@@ -79,6 +80,14 @@ Key converStringToKeyObject(String keyString, String jcaAlgorithm) {
      */
     public abstract AuthenticationResponse refreshToken(String refreshToken) throws CatalogAuthenticationException;
 
+    public JwtPayload getPayload(String token) throws CatalogAuthenticationException {
+        if (StringUtils.isEmpty(token) || "null".equalsIgnoreCase(token)) {
+            return new JwtPayload().setUserId(ParamConstants.ANONYMOUS_USER_ID);
+        }
+
+        return jwtManager.getPayload(token);
+    }
+
     /**
      * Obtains the userId corresponding to the token.
      *
@@ -130,6 +139,16 @@ public String getUserId(String token) throws CatalogAuthenticationException {
      */
     public abstract void newPassword(String userId, String newPassword) throws CatalogException;
 
+    /**
+     * Create a token for the user with default expiration time.
+     *
+     * @param user user.
+     * @return A token.
+     */
+    public String createToken(User user) {
+        return createToken(user, Collections.emptyMap(), expiration);
+    }
+
     /**
      * Create a token for the user with default expiration time.
      *
@@ -172,6 +191,16 @@ public String createToken(String userId, Map<String, Object> claims) {
      */
     public abstract String createToken(String userId, Map<String, Object> claims, long expiration);
 
+    /**
+     * Create a token for the user.
+     *
+     * @param user user.
+     * @param claims claims.
+     * @param expiration Expiration time in seconds.
+     * @return A token.
+     */
+    public abstract String createToken(User user, Map<String, Object> claims, long expiration);
+
     /**
      * Create a token for the user with no expiration time.
      *

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/AzureADAuthenticationManager.java

@@ -408,6 +408,12 @@ public String createToken(String userId, Map<String, Object> claims, long expira
         throw new UnsupportedOperationException("Tokens are generated by Azure via authorization code or user-password");
     }
 
+    @Override
+    public String createToken(User user, Map<String, Object> claims, long expiration) {
+        // Tokens are generated by Azure via authorization code or user-password
+        throw new UnsupportedOperationException("Tokens are generated by Azure via authorization code or user-password");
+    }
+
     @Override
     public String createNonExpiringToken(String userId, Map<String, Object> claims) {
         // Tokens are generated by Azure via authorization code or user-password

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java

@@ -108,6 +108,11 @@ public String createToken(String userId, Map<String, Object> claims, long expira
         return jwtManager.createJWTToken(userId, claims, expiration);
     }
 
+    @Override
+    public String createToken(User user, Map<String, Object> claims, long expiration) {
+        return jwtManager.createJWTToken(user, claims, expiration);
+    }
+
     @Override
     public String createNonExpiringToken(String userId, Map<String, Object> claims) {
         return jwtManager.createJWTToken(userId, claims, 0L);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/JwtManager.java

@@ -18,6 +18,8 @@
 
 import io.jsonwebtoken.*;
 import org.opencb.opencga.catalog.exceptions.CatalogAuthenticationException;
+import org.opencb.opencga.core.models.JwtPayload;
+import org.opencb.opencga.core.models.user.User;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -87,6 +89,27 @@ public String createJWTToken(String userId, long expiration) {
         return createJWTToken(userId, Collections.emptyMap(), expiration);
     }
 
+    public String createJWTToken(User user, Map<String, Object> claims, long expiration) {
+        long currentTime = System.currentTimeMillis();
+
+        JwtBuilder jwtBuilder = Jwts.builder();
+        if (claims != null && !claims.isEmpty()) {
+            jwtBuilder.setClaims(claims);
+        }
+        jwtBuilder.setSubject(user.getId())
+                .setIssuer(user.getOrganization())
+                .setAudience("OpenCGA")
+                .setIssuedAt(new Date(currentTime))
+                .signWith(privateKey, algorithm);
+
+        // Set the expiration in number of seconds only if 'expiration' is greater than 0
+        if (expiration > 0) {
+            jwtBuilder.setExpiration(new Date(currentTime + expiration * 1000L));
+        }
+
+        return jwtBuilder.compact();
+    }
+
     public String createJWTToken(String userId, Map<String, Object> claims, long expiration) {
         long currentTime = System.currentTimeMillis();
 
@@ -115,6 +138,11 @@ public void validateToken(String token, Key publicKey) throws CatalogAuthenticat
         parseClaims(token, publicKey);
     }
 
+    public JwtPayload getPayload(String token) throws CatalogAuthenticationException {
+        Claims body = parseClaims(token, publicKey).getBody();
+        return new JwtPayload(body.getSubject(), body.getIssuer(), body.getAudience(), body.getIssuedAt(), body.getExpiration());
+    }
+
     public String getAudience(String token) throws CatalogAuthenticationException {
         return getAudience(token, this.publicKey);
     }

opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/LDAPAuthenticationManager.java

@@ -224,6 +224,11 @@ public String createToken(String userId, Map<String, Object> claims, long expira
         return jwtManager.createJWTToken(userId, claims, expiration);
     }
 
+    @Override
+    public String createToken(User user, Map<String, Object> claims, long expiration) {
+        return jwtManager.createJWTToken(user, claims, expiration);
+    }
+
     @Override
     public String createNonExpiringToken(String userId, Map<String, Object> claims) {
         return jwtManager.createJWTToken(userId, claims, 0L);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/AbstractDBAdaptor.java

@@ -16,17 +16,17 @@
 
 package org.opencb.opencga.catalog.db;
 
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.datastore.core.DataResult;
 import org.opencb.commons.datastore.core.Event;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.opencga.catalog.db.api.DBIterator;
 import org.opencb.opencga.catalog.exceptions.CatalogDBException;
+import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.slf4j.Logger;
 
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.List;
+import java.util.*;
 
 public abstract class AbstractDBAdaptor {
 
@@ -101,6 +101,21 @@ protected void checkParameter(Object param, String name) throws CatalogDBExcepti
         }
     }
 
+    protected void checkUpdatedParams(ObjectMap parameters, List<String> updateableKeys) throws CatalogParameterException {
+        Set<String> keysToUpdate = parameters.keySet();
+        Set<String> updateableKeysSet = new HashSet<>(updateableKeys);
+
+        List<String> unexpectedKeys = new ArrayList<>(keysToUpdate.size());
+        for (String key : keysToUpdate) {
+            if (!updateableKeysSet.contains(key)) {
+                unexpectedKeys.add(key);
+            }
+        }
+        if (!unexpectedKeys.isEmpty()) {
+            throw new CatalogParameterException("Unexpected fields passed to update: " + StringUtils.join(unexpectedKeys, ", "));
+        }
+    }
+
     public interface FilterOption {
         String getKey();
 

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/DBAdaptorFactory.java

@@ -76,6 +76,8 @@ public interface DBAdaptorFactory extends AutoCloseable {
 
     MetaDBAdaptor getCatalogMetaDBAdaptor();
 
+    OrganizationDBAdaptor getCatalogOrganizationDBAdaptor();
+
     UserDBAdaptor getCatalogUserDBAdaptor();
 
     ProjectDBAdaptor getCatalogProjectDbAdaptor();

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java

@@ -1,10 +1,14 @@
 package org.opencb.opencga.catalog.db.api;
 
+import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
 import org.opencb.commons.datastore.core.QueryParam;
+import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException;
 import org.opencb.opencga.catalog.exceptions.CatalogDBException;
+import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
 import org.opencb.opencga.core.models.organizations.Organization;
+import org.opencb.opencga.core.response.OpenCGAResult;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -85,12 +89,14 @@ public static QueryParams getParam(String key) {
 //
 //    OpenCGAResult nativeInsert(Map<String, Object> project, String userId) throws CatalogDBException;
 //
-//    OpenCGAResult insert(Project project, String userId, QueryOptions options)
-//            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
+    OpenCGAResult<Organization> insert(Organization organization, QueryOptions options)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 //
 //    OpenCGAResult<Project> get(String userId, QueryOptions options) throws CatalogDBException;
 //
-//    OpenCGAResult<Project> get(long project, QueryOptions options) throws CatalogDBException;
+    OpenCGAResult<Organization> get(long organization, QueryOptions options) throws CatalogDBException;
+
+    OpenCGAResult<Organization> get(Query query, QueryOptions options) throws CatalogDBException;
 //
 //    OpenCGAResult incrementCurrentRelease(long projectId) throws CatalogDBException;
 //
@@ -149,12 +155,12 @@ public static QueryParams getParam(String key) {
 //        return queryResults;
 //    }
 //
-//    OpenCGAResult<Project> update(long id, ObjectMap parameters, QueryOptions queryOptions)
-//            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
+    OpenCGAResult<Organization> update(long id, ObjectMap parameters, QueryOptions queryOptions)
+            throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 //
 //    OpenCGAResult<Long> update(Query query, ObjectMap parameters, QueryOptions queryOptions) throws CatalogDBException;
 //
-//    OpenCGAResult delete(Project project) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
+    OpenCGAResult<Organization> delete(Organization organization) throws CatalogDBException;
 //
 //    OpenCGAResult delete(Query query) throws CatalogDBException;
 //

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/ProjectDBAdaptor.java

@@ -136,7 +136,7 @@ default void checkId(long projectId) throws CatalogDBException {
 
     OpenCGAResult nativeInsert(Map<String, Object> project, String userId) throws CatalogDBException;
 
-    OpenCGAResult insert(Project project, String userId, QueryOptions options)
+    OpenCGAResult<Project> insert(String organizationId, Project project, QueryOptions options)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
 
     OpenCGAResult<Project> get(String userId, QueryOptions options) throws CatalogDBException;

opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptorFactory.java

@@ -29,6 +29,7 @@
 import org.opencb.commons.datastore.mongodb.MongoDataStoreManager;
 import org.opencb.opencga.catalog.db.DBAdaptorFactory;
 import org.opencb.opencga.catalog.db.api.MigrationDBAdaptor;
+import org.opencb.opencga.catalog.db.api.OrganizationDBAdaptor;
 import org.opencb.opencga.catalog.exceptions.CatalogDBException;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.core.config.Admin;
@@ -271,7 +272,8 @@ public MetaMongoDBAdaptor getCatalogMetaDBAdaptor() {
         return metaDBAdaptor;
     }
 
-    public OrganizationMongoDBAdaptor getOrganizationDBAdaptor() {
+    @Override
+    public OrganizationDBAdaptor getCatalogOrganizationDBAdaptor() {
         return organizationDBAdaptor;
     }