Merge pull request #217 from broadinstitute/develop

Patch Release 10/18

consent-ws/src/main/java/org/broadinstitute/consent/http/ConsentApplication.java

@@ -18,13 +18,20 @@
 import io.dropwizard.setup.Bootstrap;
 import io.dropwizard.setup.Environment;
 import jersey.repackaged.com.google.common.collect.Lists;
-import org.broadinstitute.consent.http.authentication.*;
+import org.broadinstitute.consent.http.authentication.AbstractOAuthAuthenticator;
+import org.broadinstitute.consent.http.authentication.BasicAuthenticator;
+import org.broadinstitute.consent.http.authentication.BasicCustomAuthFilter;
+import org.broadinstitute.consent.http.authentication.DefaultAuthFilter;
+import org.broadinstitute.consent.http.authentication.DefaultAuthenticator;
+import org.broadinstitute.consent.http.authentication.OAuthAuthenticator;
+import org.broadinstitute.consent.http.authentication.OAuthCustomAuthFilter;
 import org.broadinstitute.consent.http.cloudstore.GCSStore;
 import org.broadinstitute.consent.http.configurations.ConsentConfiguration;
 import org.broadinstitute.consent.http.configurations.ElasticSearchConfiguration;
 import org.broadinstitute.consent.http.configurations.MongoConfiguration;
 import org.broadinstitute.consent.http.configurations.StoreConfiguration;
 import org.broadinstitute.consent.http.db.ApprovalExpirationTimeDAO;
+import org.broadinstitute.consent.http.db.AssociationDAO;
 import org.broadinstitute.consent.http.db.ConsentDAO;
 import org.broadinstitute.consent.http.db.DACUserDAO;
 import org.broadinstitute.consent.http.db.DACUserRoleDAO;
@@ -38,6 +45,7 @@
 import org.broadinstitute.consent.http.db.MatchDAO;
 import org.broadinstitute.consent.http.db.ResearcherPropertyDAO;
 import org.broadinstitute.consent.http.db.VoteDAO;
+import org.broadinstitute.consent.http.db.WorkspaceAuditDAO;
 import org.broadinstitute.consent.http.db.mongo.MongoConsentDB;
 import org.broadinstitute.consent.http.mail.AbstractMailServiceAPI;
 import org.broadinstitute.consent.http.mail.MailService;
@@ -68,7 +76,9 @@
 import org.broadinstitute.consent.http.resources.MatchResource;
 import org.broadinstitute.consent.http.resources.ResearcherResource;
 import org.broadinstitute.consent.http.resources.UserResource;
+import org.broadinstitute.consent.http.resources.WorkspaceResource;
 import org.broadinstitute.consent.http.service.AbstractApprovalExpirationTimeAPI;
+import org.broadinstitute.consent.http.service.AbstractAuditServiceAPI;
 import org.broadinstitute.consent.http.service.AbstractConsentAPI;
 import org.broadinstitute.consent.http.service.AbstractDataAccessRequestAPI;
 import org.broadinstitute.consent.http.service.AbstractDataSetAPI;
@@ -85,6 +95,7 @@
 import org.broadinstitute.consent.http.service.AbstractTranslateServiceAPI;
 import org.broadinstitute.consent.http.service.AbstractVoteAPI;
 import org.broadinstitute.consent.http.service.DatabaseApprovalExpirationTimeAPI;
+import org.broadinstitute.consent.http.service.DatabaseAuditServiceAPI;
 import org.broadinstitute.consent.http.service.DatabaseConsentAPI;
 import org.broadinstitute.consent.http.service.DatabaseDataAccessRequestAPI;
 import org.broadinstitute.consent.http.service.DatabaseDataSetAPI;
@@ -187,11 +198,14 @@ public void run(ConsentConfiguration config, Environment env) {
         final DataSetAuditDAO dataSetAuditDAO = jdbi.onDemand(DataSetAuditDAO.class);
         final MailServiceDAO mailServiceDAO = jdbi.onDemand(MailServiceDAO.class);
         final ResearcherPropertyDAO  researcherPropertyDAO = jdbi.onDemand(ResearcherPropertyDAO.class);
+        final WorkspaceAuditDAO workspaceAuditDAO = jdbi.onDemand(WorkspaceAuditDAO.class);
+        final AssociationDAO associationDAO = jdbi.onDemand(AssociationDAO.class);
 
+        DatabaseAuditServiceAPI.initInstance(workspaceAuditDAO, dacUserDAO, associationDAO);
         UseRestrictionConverter structResearchPurposeConv = new UseRestrictionConverter(config.getUseRestrictionConfiguration());
         DatabaseDataAccessRequestAPI.initInstance(mongoInstance, structResearchPurposeConv, electionDAO, consentDAO, voteDAO, dacUserDAO, dataSetDAO);
 
-        DatabaseConsentAPI.initInstance(jdbi, consentDAO, electionDAO, mongoInstance);
+        DatabaseConsentAPI.initInstance(jdbi, consentDAO, electionDAO, associationDAO, mongoInstance);
 
         DatabaseMatchAPI.initInstance(matchDAO, consentDAO);
         DatabaseDataSetAPI.initInstance(dataSetDAO, dataSetAssociationDAO, dacUserRoleDAO, consentDAO, dataSetAuditDAO, electionDAO);
@@ -269,6 +283,7 @@ public void run(ConsentConfiguration config, Environment env) {
         env.jersey().register(ApprovalExpirationTimeResource.class);
         env.jersey().register(new UserResource(userAPI));
         env.jersey().register(new ResearcherResource(researcherAPI));
+        env.jersey().register(WorkspaceResource.class);
 
         //Authentication filters
         AuthFilter defaultAuthFilter = new DefaultAuthFilter.Builder<User>()
@@ -310,6 +325,7 @@ public void lifeCycleStopped(LifeCycle event) {
                 AbstractUseRestrictionValidatorAPI.clearInstance();
                 AbstractUserRolesHandler.clearInstance();
                 AbstractOAuthAuthenticator.clearInstance();
+                AbstractAuditServiceAPI.clearInstance();
                 super.lifeCycleStopped(event);
             }
         });

consent-ws/src/main/java/org/broadinstitute/consent/http/authentication/BasicAuthenticator.java

@@ -5,9 +5,6 @@
 import io.dropwizard.auth.basic.BasicCredentials;
 import org.broadinstitute.consent.http.configurations.BasicAuthConfig;
 import org.broadinstitute.consent.http.models.User;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
@@ -17,8 +14,6 @@ public class BasicAuthenticator implements Authenticator<BasicCredentials, User>
 
     BasicAuthConfig basicAuthentication;
 
-    private static final Logger logger = LoggerFactory.getLogger(BasicAuthenticator.class);
-
     public BasicAuthenticator(BasicAuthConfig basicAuthentication) {
         this.basicAuthentication = basicAuthentication;
     }

consent-ws/src/main/java/org/broadinstitute/consent/http/cloudstore/CloudStore.java

@@ -22,4 +22,4 @@ public interface CloudStore {
 
     String postOntologyDocument(InputStream stream, String type, String fileName) throws IOException, GeneralSecurityException, URISyntaxException;
 
-    }
+}

consent-ws/src/main/java/org/broadinstitute/consent/http/db/AssociationDAO.java

@@ -0,0 +1,13 @@
+package org.broadinstitute.consent.http.db;
+
+
+import org.skife.jdbi.v2.sqlobject.Bind;
+import org.skife.jdbi.v2.sqlobject.SqlQuery;
+
+
+public interface AssociationDAO {
+
+    @SqlQuery("select associationId from consentassociations where associationType = :associationType and objectId = :objectId")
+    Integer findAssociationIdByTypeAndObjectId(@Bind("associationType") String associationType,
+                                                @Bind("objectId") String objectId);
+}

consent-ws/src/main/java/org/broadinstitute/consent/http/db/ConsentDAO.java

@@ -5,14 +5,14 @@
 import org.broadinstitute.consent.http.models.ConsentManage;
 import org.broadinstitute.consent.http.models.dto.UseRestrictionDTO;
 import org.skife.jdbi.v2.sqlobject.Bind;
-import org.skife.jdbi.v2.sqlobject.SqlBatch;
 import org.skife.jdbi.v2.sqlobject.SqlQuery;
 import org.skife.jdbi.v2.sqlobject.SqlUpdate;
 import org.skife.jdbi.v2.sqlobject.customizers.Mapper;
 import org.skife.jdbi.v2.sqlobject.customizers.RegisterMapper;
 import org.skife.jdbi.v2.sqlobject.mixins.Transactional;
 import org.skife.jdbi.v2.sqlobject.stringtemplate.UseStringTemplate3StatementLocator;
 import org.skife.jdbi.v2.unstable.BindIn;
+
 import java.util.Collection;
 import java.util.Date;
 import java.util.List;
@@ -34,11 +34,6 @@ public interface ConsentDAO extends Transactional<ConsentDAO> {
     @SqlQuery("select * from consents  where consentId in (<consentIds>)")
     Collection<Consent> findConsentsFromConsentsIDs(@BindIn("consentIds") List<String> consentIds);
 
-    @SqlQuery("SELECT * " +
-            "FROM consents c INNER JOIN consentassociations cs ON c.consentId = cs.consentId "+
-            "WHERE cs.objectId IN (<datasetId>)")
-    Collection<Consent> findConsentsFromDatasetIDs(@BindIn("datasetId") List<String> datasetId);
-
     @Mapper(ConsentDataSetMapper.class)
     @SqlQuery("SELECT c.consentId, cs.objectId, ds.name " +
             "FROM consents c INNER JOIN consentassociations cs ON c.consentId = cs.consentId " +
@@ -113,16 +108,6 @@ String findAssociationByTypeAndId(@Bind("consentId") String consentId,
                                       @Bind("associationType") String associationType,
                                       @Bind("objectId") String objectId);
 
-    @SqlBatch("insert into consentassociations (consentId, associationType, objectId) values (:consentId, :associationType, :objectId)")
-    void insertAssociations(@Bind("consentId") String consentId,
-                            @Bind("associationType") String associationType,
-                            @Bind("objectId") List<String> ids);
-
-    @SqlBatch("delete from consentassociations where consentId = :consentId and associationType = :associationType and objectId =: objectId")
-    void deleteAssociations(@Bind("consentId") String consentId,
-                            @Bind("associationType") String associationType,
-                            @Bind("objectId") List<String> ids);
-
     @SqlUpdate("delete from consentassociations where consentId = :consentId and associationType = :associationType and objectId = :objectId")
     void deleteOneAssociation(@Bind("consentId") String consentId,
                               @Bind("associationType") String associationType,
@@ -143,6 +128,9 @@ void deleteAllAssociationsForType(@Bind("consentId") String consentId,
     List<String> findConsentsForAssociation(@Bind("associationType") String associationType,
                                             @Bind("objectId") String objectId);
 
+    @SqlQuery("select c.* from consentassociations ca inner join consents c on c.consentId = ca.consentId where associationType = :associationType and objectId= :objectId")
+    Consent findConsentByAssociationAndObjectId(@Bind("associationType") String associationType,
+                                            @Bind("objectId") String objectId);
 
     @SqlQuery("select * from consents where consentId not in (select c.consentId from consents c  inner join election e on e.referenceId = c.consentId )")
     List<Consent> findUnreviewedConsents();

consent-ws/src/main/java/org/broadinstitute/consent/http/db/DACUserMapper.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.consent.http.db;
 
-import org.broadinstitute.consent.http.enumeration.RoleStatus;
 import org.broadinstitute.consent.http.models.DACUser;
 import org.skife.jdbi.v2.StatementContext;
 import org.skife.jdbi.v2.tweak.ResultSetMapper;

consent-ws/src/main/java/org/broadinstitute/consent/http/db/DataSetAssociationDAO.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.consent.http.db;
 
 import org.broadinstitute.consent.http.db.mongo.DatasetAssociationMapper;
-import org.broadinstitute.consent.http.models.DataSet;
 import org.broadinstitute.consent.http.models.DatasetAssociation;
 import org.skife.jdbi.v2.exceptions.UnableToExecuteStatementException;
 import org.skife.jdbi.v2.sqlobject.*;
@@ -49,9 +48,5 @@ public interface DataSetAssociationDAO extends Transactional<DataSetAssociationD
 
     @SqlUpdate("delete from dataset_user_association where dacuserId = :ownerId")
     void deleteDatasetRelationshipsForUser(@Bind("ownerId") Integer ownerId);
-
-    @SqlBatch("update dataset_user_association set dacuserId = : toDataOwnerId, createDate = now() " +
-            " where dacUserId = :fromDataOwnerId")
-    void changeDatasetUserAssociation(@Bind("fromDataOwnerId") Integer fromDataOwnerId, @Bind("toDataOwnerId") Integer tDataOwnerId) throws UnableToExecuteStatementException;
 
 }

consent-ws/src/main/java/org/broadinstitute/consent/http/db/DataSetDAO.java

@@ -27,9 +27,6 @@ public interface DataSetDAO extends Transactional<DataSetDAO> {
 
     String CHAIRPERSON = "CHAIRPERSON";
 
-    @SqlQuery("select dataSetId from dataset where dataSetId = :dataSetId")
-    Integer checkDataSetbyId(@Bind("dataSetId") Integer dataSetId);
-
     @SqlQuery("select * from dataset where dataSetId = :dataSetId")
     DataSet findDataSetById(@Bind("dataSetId") Integer dataSetId);
 

consent-ws/src/main/java/org/broadinstitute/consent/http/db/ElectionDAO.java

@@ -241,4 +241,9 @@ void updateElectionById(@Bind("electionId") Integer electionId,
             " and e.status = '" + OPEN +"' and v.vote is null and v.dacUserId = :dacUserId")
     List<Election> findAccessRpOpenElectionIds(@Bind("dacUserId")Integer dacUserId);
 
+    @SqlQuery("select e.electionId,  e.datasetId, v.vote finalVote, e.status, e.createDate, e.referenceId, e.useRestriction, e.translatedUseRestriction, v.rationale finalRationale, v.createDate finalVoteDate, " +
+            "e.lastUpdate, e.finalAccessVote, e.electionType from election e inner join vote v  on v.electionId = e.electionId where e.electionType = 'DataAccess' "+
+            " and v.type = 'FINAL'  and e.referenceId in (<darIds>) order by e.createDate asc")
+    List<Election> findRequestElectionsByReferenceIds(@BindIn("darIds") List<String> darIds);
+
 }

consent-ws/src/main/java/org/broadinstitute/consent/http/db/ElectionMapper.java

@@ -9,7 +9,6 @@
 import java.io.IOException;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-import java.util.Objects;
 
 public class ElectionMapper implements ResultSetMapper<Election> {
 

consent-ws/src/main/java/org/broadinstitute/consent/http/db/ElectionReviewVoteMapper.java

@@ -5,7 +5,6 @@
 import org.broadinstitute.consent.http.models.Vote;
 import org.skife.jdbi.v2.StatementContext;
 import org.skife.jdbi.v2.tweak.ResultSetMapper;
-
 import java.sql.ResultSet;
 import java.sql.SQLException;
 

consent-ws/src/main/java/org/broadinstitute/consent/http/db/MailMessageDAO.java

@@ -14,9 +14,6 @@
 @RegisterMapper(MailMessageMapper.class)
 public interface MailMessageDAO extends Transactional<MailMessageDAO> {
 
-    @SqlQuery("select e.*, et.type from email_entity inner join email_type et ON e.emailType = et.emailType e where emailEntityId = :emailEntityId")
-    MailMessage findEmailById(@Bind("emailEntityId") String consentId);
-
     @SqlQuery("Select emailEntityId FROM email_entity e WHERE (e.entityReferenceId = :darElectionId or  e.entityReferenceId = :rpElectionId) AND e.emailType = 1 LIMIT 1")
     Integer existsCollectDAREmail(@Bind("darElectionId") Integer darElectionId, @Bind("rpElectionId") Integer rpElectionId);
 
@@ -30,16 +27,6 @@ void insertEmail(@Bind("voteId") Integer voteId,
                      @Bind("dateSent") Date dateSent,
                      @Bind("emailText") String emailText);
 
-    @SqlBatch("insert into email_entity " +
-            "(voteId, entityReferenceId, dacUserId, emailType, dateSent, emailText) values " +
-            "(:voteId, :entityReferenceId, :dacUserId, :emailType, :dateSent, :emailText)")
-    void insertBulkEmail(@Bind("voteId") List<Integer> voteIds,
-                     @Bind("dacUserId") List<Integer> userIds,
-                     @Bind("entityReferenceId") String entityReferenceId,
-                     @Bind("emailType") Integer emailType,
-                     @Bind("dateSent") Date dateSent,
-                     @Bind("emailText") String emailText);
-
     @SqlBatch("insert into email_entity " +
             "(entityReferenceId, dacUserId, emailType, dateSent, emailText) values " +
             "(:entityReferenceId, :dacUserId, :emailType, :dateSent, :emailText)")

consent-ws/src/main/java/org/broadinstitute/consent/http/db/MatchDAO.java

@@ -56,11 +56,6 @@ void updateMatch(@BindIn("match") Boolean match,
     @SqlUpdate("delete from match_entity where matchId = :id")
     void deleteMatch(@Bind("id") Integer matchId);
 
-    @SqlQuery("delete match_entity where name in (<matchIds>)")
-    List<Integer> matchBulkDeleteByIds(@BindIn("matchIds") List<String> matchIds);
-
     @SqlQuery("SELECT COUNT(*) FROM match_entity where matchEntity = :matchEntity and failed ='FALSE' ")
     Integer countMatchesByResult(@Bind("matchEntity") Boolean matchEntity);
-
-
 }

consent-ws/src/main/java/org/broadinstitute/consent/http/db/ResearcherPropertyDAO.java

@@ -1,7 +1,5 @@
 package org.broadinstitute.consent.http.db;
 
-
-import org.broadinstitute.consent.http.enumeration.ResearcherFields;
 import org.broadinstitute.consent.http.models.ResearcherProperty;
 import org.skife.jdbi.v2.sqlobject.Bind;
 import org.skife.jdbi.v2.sqlobject.BindBean;

consent-ws/src/main/java/org/broadinstitute/consent/http/db/RoleMapper.java

@@ -5,7 +5,6 @@
 import org.broadinstitute.consent.http.models.DACUserRole;
 import org.skife.jdbi.v2.StatementContext;
 import org.skife.jdbi.v2.tweak.ResultSetMapper;
-
 import java.sql.ResultSet;
 import java.sql.SQLException;
 

consent-ws/src/main/java/org/broadinstitute/consent/http/db/WorkspaceAuditDAO.java

@@ -0,0 +1,21 @@
+package org.broadinstitute.consent.http.db;
+
+import org.broadinstitute.consent.http.models.WorkspaceAudit;
+import org.skife.jdbi.v2.sqlobject.BindBean;
+import org.skife.jdbi.v2.sqlobject.SqlBatch;
+import org.skife.jdbi.v2.sqlobject.SqlUpdate;
+import org.skife.jdbi.v2.sqlobject.stringtemplate.UseStringTemplate3StatementLocator;
+import java.util.List;
+
+@UseStringTemplate3StatementLocator
+public interface WorkspaceAuditDAO {
+
+    @SqlUpdate("insert into workspace_audit (modifiedObjectId, modifiedTable, changeAction, modifiedByUserId, modificationDate) " +
+            " values (:modifiedObjectId, :modifiedTable, :changeAction, :modifiedByUserId, :modificationDate)")
+    void insertWorkspaceAudit(@BindBean WorkspaceAudit workspaceAudit);
+
+    @SqlBatch("insert into workspace_audit (modifiedObjectId, modifiedTable, changeAction, modifiedByUserId, modificationDate) " +
+            " values (:modifiedObjectId, :modifiedTable, :changeAction, :modifiedByUserId, :modificationDate)")
+    void batchInsertWorkspaceAudit(@BindBean List<WorkspaceAudit> workspaceAudits);
+
+}

consent-ws/src/main/java/org/broadinstitute/consent/http/enumeration/Actions.java

@@ -3,7 +3,7 @@
 
 public enum Actions {
 
-    REPLACE("replace"), ADD("add"), REMOVE("remove");
+    REPLACE("replace"), ADD("add"), REMOVE("remove"), CREATE("create");
 
     private String value;
 

consent-ws/src/main/java/org/broadinstitute/consent/http/enumeration/AssociationType.java

@@ -0,0 +1,17 @@
+package org.broadinstitute.consent.http.enumeration;
+
+public enum AssociationType {
+
+    SAMPLE("sample"), SAMPLESET("sampleSet"), WORKSPACE("workspace");
+
+    private String value;
+
+    AssociationType(String value) {
+        this.value = value;
+    }
+
+    public String getValue() {
+        return value;
+    }
+
+}