server: add 3 new web services to handle events, #TASK-4178

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -89,7 +89,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-update","update-status-user","user-update","configuration-update","info","update")
+    private List<Candidate> organizationsList = asList( "create","notes-create","notes-search","notes-delete","notes-update","update-status-user","user-update","configuration-update","events-query","events-archive","events-retry","info","update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -276,6 +276,9 @@ public OpencgaCliOptionsParser() {
         organizationsSubCommands.addCommand("update-status-user", organizationsCommandOptions.userUpdateStatusCommandOptions);
         organizationsSubCommands.addCommand("user-update", organizationsCommandOptions.updateUserCommandOptions);
         organizationsSubCommands.addCommand("configuration-update", organizationsCommandOptions.updateConfigurationCommandOptions);
+        organizationsSubCommands.addCommand("events-query", organizationsCommandOptions.queryEventsCommandOptions);
+        organizationsSubCommands.addCommand("events-archive", organizationsCommandOptions.archiveEventsCommandOptions);
+        organizationsSubCommands.addCommand("events-retry", organizationsCommandOptions.retryEventsCommandOptions);
         organizationsSubCommands.addCommand("info", organizationsCommandOptions.infoCommandOptions);
         organizationsSubCommands.addCommand("update", organizationsCommandOptions.updateCommandOptions);
 

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

@@ -16,6 +16,7 @@
 import org.opencb.opencga.client.exceptions.ClientException;
 import org.opencb.opencga.core.common.JacksonUtils;
 import org.opencb.opencga.core.config.Optimizations;
+import org.opencb.opencga.core.models.event.CatalogEvent;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.models.notes.NoteCreateParams;
 import org.opencb.opencga.core.models.notes.NoteUpdateParams;
@@ -89,6 +90,15 @@ public void execute() throws Exception {
             case "configuration-update":
                 queryResponse = updateConfiguration();
                 break;
+            case "events-query":
+                queryResponse = queryEvents();
+                break;
+            case "events-archive":
+                queryResponse = archiveEvents();
+                break;
+            case "events-retry":
+                queryResponse = retryEvents();
+                break;
             case "info":
                 queryResponse = info();
                 break;
@@ -345,6 +355,37 @@ private RestResponse<OrganizationConfiguration> updateConfiguration() throws Exc
         return openCGAClient.getOrganizationClient().updateConfiguration(commandOptions.organization, organizationConfiguration, queryParams);
     }
 
+    private RestResponse<CatalogEvent> queryEvents() throws Exception {
+        logger.debug("Executing queryEvents in Organizations command line");
+
+        OrganizationsCommandOptions.QueryEventsCommandOptions commandOptions = organizationsCommandOptions.queryEventsCommandOptions;
+
+        ObjectMap queryParams = new ObjectMap();
+        queryParams.putIfNotEmpty("study", commandOptions.study);
+        queryParams.putIfNotEmpty("creationDate", commandOptions.creationDate);
+        queryParams.putIfNotEmpty("modificationDate", commandOptions.modificationDate);
+        queryParams.putIfNotNull("successful", commandOptions.successful);
+        if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
+            queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
+        }
+
+        return openCGAClient.getOrganizationClient().queryEvents(commandOptions.organization, queryParams);
+    }
+
+    private RestResponse<CatalogEvent> archiveEvents() throws Exception {
+        logger.debug("Executing archiveEvents in Organizations command line");
+
+        OrganizationsCommandOptions.ArchiveEventsCommandOptions commandOptions = organizationsCommandOptions.archiveEventsCommandOptions;
+        return openCGAClient.getOrganizationClient().archiveEvents(commandOptions.organization, commandOptions.eventId);
+    }
+
+    private RestResponse<CatalogEvent> retryEvents() throws Exception {
+        logger.debug("Executing retryEvents in Organizations command line");
+
+        OrganizationsCommandOptions.RetryEventsCommandOptions commandOptions = organizationsCommandOptions.retryEventsCommandOptions;
+        return openCGAClient.getOrganizationClient().retryEvents(commandOptions.organization, commandOptions.eventId);
+    }
+
     private RestResponse<Organization> info() throws Exception {
         logger.debug("Executing info in Organizations command line");
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OrganizationsCommandOptions.java

@@ -41,6 +41,9 @@ public class OrganizationsCommandOptions {
         public UserUpdateStatusCommandOptions userUpdateStatusCommandOptions;
         public UpdateUserCommandOptions updateUserCommandOptions;
         public UpdateConfigurationCommandOptions updateConfigurationCommandOptions;
+        public QueryEventsCommandOptions queryEventsCommandOptions;
+        public ArchiveEventsCommandOptions archiveEventsCommandOptions;
+        public RetryEventsCommandOptions retryEventsCommandOptions;
         public InfoCommandOptions infoCommandOptions;
         public UpdateCommandOptions updateCommandOptions;
 
@@ -57,6 +60,9 @@ public OrganizationsCommandOptions(CommonCommandOptions commonCommandOptions, JC
         this.userUpdateStatusCommandOptions = new UserUpdateStatusCommandOptions();
         this.updateUserCommandOptions = new UpdateUserCommandOptions();
         this.updateConfigurationCommandOptions = new UpdateConfigurationCommandOptions();
+        this.queryEventsCommandOptions = new QueryEventsCommandOptions();
+        this.archiveEventsCommandOptions = new ArchiveEventsCommandOptions();
+        this.retryEventsCommandOptions = new RetryEventsCommandOptions();
         this.infoCommandOptions = new InfoCommandOptions();
         this.updateCommandOptions = new UpdateCommandOptions();
 
@@ -354,6 +360,69 @@ public class UpdateConfigurationCommandOptions {
 
     }
 
+    @Parameters(commandNames = {"events-query"}, commandDescription ="Search events")
+    public class QueryEventsCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"--organization"}, description = "Organization id", required = true, arity = 1)
+        public String organization; 
+
+        @Parameter(names = {"--study", "-s"}, description = "Study [[organization@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
+        public String study; 
+
+        @Parameter(names = {"--creation-date", "--cd"}, description = "Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1)
+        public String creationDate; 
+
+        @Parameter(names = {"--modification-date", "--md"}, description = "Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1)
+        public String modificationDate; 
+
+        @Parameter(names = {"--successful"}, description = "Boolean indicating if the event was successful or not.", required = false, arity = 1)
+        public Boolean successful; 
+
+    }
+
+    @Parameters(commandNames = {"events-archive"}, commandDescription ="Archive an event")
+    public class ArchiveEventsCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1)
+        public String jsonFile;
+
+        @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0)
+        public Boolean jsonDataModel = false;
+
+        @Parameter(names = {"--organization"}, description = "Organization id", required = true, arity = 1)
+        public String organization; 
+
+        @Parameter(names = {"--event-id"}, description = "Event id.", required = true, arity = 1)
+        public String eventId; 
+
+    }
+
+    @Parameters(commandNames = {"events-retry"}, commandDescription ="Retry unsuccessful event")
+    public class RetryEventsCommandOptions {
+
+        @ParametersDelegate
+        public CommonCommandOptions commonOptions = commonCommandOptions;
+
+        @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1)
+        public String jsonFile;
+
+        @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0)
+        public Boolean jsonDataModel = false;
+
+        @Parameter(names = {"--organization"}, description = "Organization id", required = true, arity = 1)
+        public String organization; 
+
+        @Parameter(names = {"--event-id"}, description = "Event id.", required = true, arity = 1)
+        public String eventId; 
+
+    }
+
     @Parameters(commandNames = {"info"}, commandDescription ="Return the organization information")
     public class InfoCommandOptions {
 

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

@@ -24,7 +24,8 @@ enum QueryParams implements QueryParam {
         SUBSCRIBERS("subscribers", OBJECT, ""),
         SUCCESSFUL("successful", BOOLEAN, ""),
         CREATION_DATE("creationDate", STRING, ""),
-        MODIFICATION_DATE("modificationDate", STRING, "");
+        MODIFICATION_DATE("modificationDate", STRING, ""),
+        EVENT_STUDY_FQN("event.studyFqn", STRING, "");
 
         private static Map<String, QueryParams> map = new HashMap<>();
         static {

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

@@ -3,7 +3,6 @@
 import com.mongodb.client.ClientSession;
 import com.mongodb.client.model.Filters;
 import com.mongodb.client.model.Updates;
-import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.bson.Document;
 import org.bson.conversions.Bson;
@@ -50,7 +49,10 @@ public EventMongoDBAdaptor(MongoDBCollection eventCollection, MongoDBCollection
     @Override
     public OpenCGAResult<CatalogEvent> get(Query query, QueryOptions options)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
-        throw new NotImplementedException("Yet to implement");
+        long startTime = startQuery();
+        try (DBIterator<CatalogEvent> dbIterator = iterator(null, query, options)) {
+            return endQuery(startTime, dbIterator);
+        }
     }
 
     @Override
@@ -196,6 +198,7 @@ private Bson parseQuery(Query query) throws CatalogDBException {
                     case MODIFICATION_DATE:
                         addAutoOrQuery(PRIVATE_MODIFICATION_DATE, queryParam.key(), query, queryParam.type(), andBsonList);
                         break;
+                    case EVENT_STUDY_FQN:
                     case SUCCESSFUL:
                     case ID:
                     case UUID:

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/EventManager.java

@@ -1,5 +1,6 @@
 package org.opencb.opencga.catalog.managers;
 
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;
@@ -9,8 +10,10 @@
 import org.opencb.opencga.catalog.exceptions.CatalogDBException;
 import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.exceptions.CatalogParameterException;
+import org.opencb.opencga.catalog.utils.CatalogFqn;
 import org.opencb.opencga.catalog.utils.ParamUtils;
 import org.opencb.opencga.catalog.utils.UuidUtils;
+import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.common.TimeUtils;
 import org.opencb.opencga.core.events.EventFactory;
 import org.opencb.opencga.core.events.IEventHandler;
@@ -177,34 +180,25 @@ public CatalogEvent notify(String eventId, String organizationId, Supplier<Study
         return catalogEvent;
     }
 
-//    public CatalogEvent notify(String eventId, String organizationId, Study study, @Nullable String id, String userId,
-//                               QueryOptions queryOptions, ObjectMap params, JwtPayload payload, ExecuteOperation<?> executeOperation)
-//            throws CatalogException {
-//        CatalogEvent catalogEvent = new CatalogEvent(eventId, new OpencgaEvent(organizationId, eventId, params, userId, study.getFqn(),
-//        id, payload.getToken(), null));
-//        validateNewEvent(catalogEvent);
-//        try {
-//            logger.info("Executing '{}' event", eventId);
-//            OpenCGAResult<?> execute = executeOperation.execute(organizationId, study, userId, queryOptions, payload);
-//            catalogEvent.getEvent().setResult(execute);
-//        } catch (Exception e) {
-//            eventHandler.notify(catalogEvent, e);
-//            throw new CatalogException(e.getMessage(), e);
-//        }
-//
-//        logger.info("Notifying of event '{}'.", eventId);
-//        eventHandler.notify(catalogEvent);
-//        return catalogEvent;
-//    }
-
     public OpenCGAResult<CatalogEvent> search(String organizationId, Query query, String token) throws CatalogException {
         JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
         String userId = tokenPayload.getUserId(organizationId);
         catalogManager.getAuthorizationManager().checkIsAtLeastOrganizationOwnerOrAdmin(organizationId, userId);
+        fixQueryObject(query, tokenPayload);
 
         return dbAdaptorFactory.getEventDBAdaptor(organizationId).get(query, QueryOptions.empty());
     }
 
+    void fixQueryObject(Query query, JwtPayload tokenPayload) throws CatalogException {
+        String studyParam = query.getString(ParamConstants.STUDY_PARAM);
+        if (StringUtils.isNotEmpty(studyParam)) {
+            CatalogFqn catalogFqn = CatalogFqn.extractFqnFromStudy(studyParam, tokenPayload);
+            Study study = catalogManager.getStudyManager().resolveId(catalogFqn, QueryOptions.empty(), tokenPayload);
+            query.put(EventDBAdaptor.QueryParams.EVENT_STUDY_FQN.key(), study.getFqn());
+            query.remove(ParamConstants.STUDY_PARAM);
+        }
+    }
+
     public OpenCGAResult<CatalogEvent> archiveEvent(String organizationId, String eventId, String token) throws CatalogException {
         JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token);
         String userId = tokenPayload.getUserId(organizationId);

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,6 +1,6 @@
 # ##############################################################################
 ## OrganizationClient
-setGeneric("organizationClient", function(OpencgaR, id, organization, user, endpointName, params=NULL, ...)
+setGeneric("organizationClient", function(OpencgaR, eventId, id, organization, user, endpointName, params=NULL, ...)
     standardGeneric("organizationClient"))
 
 # ##############################################################################

opencga-client/src/main/R/R/Organization-methods.R

@@ -27,6 +27,9 @@
 #' | userUpdateStatus | /{apiVersion}/organizations/user/{user}/status/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateUser | /{apiVersion}/organizations/user/{user}/update | include, exclude, user[*], organization, includeResult, body[*] |
 #' | updateConfiguration | /{apiVersion}/organizations/{organization}/configuration/update | include, exclude, organization[*], includeResult, authenticationOriginsAction, body[*] |
+#' | queryEvents | /{apiVersion}/organizations/{organization}/events/query | organization[*], study, creationDate, modificationDate, successful |
+#' | archiveEvents | /{apiVersion}/organizations/{organization}/events/{eventId}/archive | organization[*], eventId[*] |
+#' | retryEvents | /{apiVersion}/organizations/{organization}/events/{eventId}/retry | organization[*], eventId[*] |
 #' | info | /{apiVersion}/organizations/{organization}/info | include, exclude, organization[*] |
 #' | update | /{apiVersion}/organizations/{organization}/update | include, exclude, organization[*], includeResult, adminsAction, body[*] |
 #'
@@ -36,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization, user, endpointName, params=NULL, ...) {
+setMethod("organizationClient", "OpencgaR", function(OpencgaR, eventId, id, organization, user, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/organizations/create:
@@ -125,6 +128,33 @@ setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization,
                 subcategory="configuration", subcategoryId=NULL, action="update", params=params, httpMethod="POST",
                 as.queryParam=NULL, ...),
 
+        #' @section Endpoint /{apiVersion}/organizations/{organization}/events/query:
+        #' Search events.
+        #' @param organization Organization id.
+        #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
+        #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
+        #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
+        #' @param successful Boolean indicating if the event was successful or not.
+        queryEvents=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=organization,
+                subcategory="events", subcategoryId=NULL, action="query", params=params, httpMethod="GET",
+                as.queryParam=NULL, ...),
+
+        #' @section Endpoint /{apiVersion}/organizations/{organization}/events/{eventId}/archive:
+        #' Archive an event.
+        #' @param organization Organization id.
+        #' @param eventId Event id.
+        archiveEvents=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=organization,
+                subcategory="events", subcategoryId=eventId, action="archive", params=params, httpMethod="POST",
+                as.queryParam=NULL, ...),
+
+        #' @section Endpoint /{apiVersion}/organizations/{organization}/events/{eventId}/retry:
+        #' Retry unsuccessful event.
+        #' @param organization Organization id.
+        #' @param eventId Event id.
+        retryEvents=fetchOpenCGA(object=OpencgaR, category="organizations", categoryId=organization,
+                subcategory="events", subcategoryId=eventId, action="retry", params=params, httpMethod="POST",
+                as.queryParam=NULL, ...),
+
         #' @section Endpoint /{apiVersion}/organizations/{organization}/info:
         #' Return the organization information.
         #' @param include Fields included in the response, whole JSON path must be provided.