Merge pull request #1011 from AtlasOfLivingAustralia/feature/issue1007

#1007 org method get all collections; requires database update

grails-app/controllers/au/org/ala/ecodata/ParatooController.groovy

@@ -119,6 +119,24 @@ class ParatooController {
         respond projects: paratooService.userProjects(userService.currentUserDetails.userId)
     }
 
+    @GET
+    @SecurityRequirements([@SecurityRequirement(name = "jwt"), @SecurityRequirement(name = "openIdConnect"), @SecurityRequirement(name = "oauth")])
+    @Path("/get-all-collections")
+    @Operation(
+            method = "GET",
+            summary = "Gets the list of all org minted uuids submitted by an authenticated user.",
+            description = "Gets the list of all org minted uuids submitted by an authenticated user.",
+            responses = [
+                    @ApiResponse(responseCode = "200", description = "Returns the list of all org minted uuids submitted by the user.", content = @Content(mediaType = "application/json", array = @ArraySchema(schema = @Schema(implementation = Map.class)))),
+                    @ApiResponse(responseCode = "403", description = "Forbidden"),
+                    @ApiResponse(responseCode = "404", description = "Not found")
+            ],
+            tags = "Org Interface"
+    )
+    def userCollections() {
+        respond collections: paratooService.userCollections(userService.currentUserDetails.userId)
+    }
+
     @SkipApiKeyCheck
     @POST
     @Path("/validate-token")

grails-app/controllers/au/org/ala/ecodata/UrlMappings.groovy

@@ -237,6 +237,12 @@ class UrlMappings {
             action = 'hasWriteAccess'
         }
 
+        "/ws/paratoo/get-all-collections" {
+            controller = 'paratoo'
+            action = [GET:'userCollections', OPTIONS:'options']
+        }
+
+
         "/ws/paratoo/validate-token" {
             controller = 'paratoo'
             action = [POST:'validateToken', OPTIONS:'options']

grails-app/domain/au/org/ala/ecodata/Activity.groovy

@@ -1,12 +1,7 @@
 package au.org.ala.ecodata
 
 import au.org.ala.ecodata.graphql.mappers.ActivityGraphQLMapper
-import grails.util.Holders
-import graphql.schema.DataFetcher
-import graphql.schema.DataFetchingEnvironment
 import org.bson.types.ObjectId
-import org.grails.gorm.graphql.entity.dsl.GraphQLMapping
-
 /**
  * Currently this holds both activities and assessments.
  */
@@ -44,6 +39,7 @@ class Activity {
     }
 
     static hasMany = [externalIds:ExternalId]
+    static embedded = ['externalIds']
 
     ObjectId id
     String activityId

grails-app/services/au/org/ala/ecodata/ParatooService.groovy

@@ -100,6 +100,23 @@ class ParatooService {
         projects.findAll { it.protocols }
     }
 
+    List<String> userCollections (String userId) {
+        Set<String> collectionIds = new HashSet<String>()
+        List<Activity> activities = Activity.createCriteria().list {
+            eq('userId', userId)
+            ne('status', Status.DELETED)
+            eq('externalIds.idType', ExternalId.IdType.MONITOR_MINTED_COLLECTION_ID)
+        }
+
+        activities?.each { Activity activity ->
+            ExternalId externalId = activity.externalIds?.find { it.idType == ExternalId.IdType.MONITOR_MINTED_COLLECTION_ID }
+            if (externalId?.externalId)
+                collectionIds.add(externalId.externalId)
+        }
+
+        collectionIds.toList()
+    }
+
     private List findProjectProtocols(ParatooProject project) {
         log.debug "Finding protocols for ${project.id} ${project.name}"
         List<ActivityForm> protocols = []

scripts/releases/5.0/updateMissingActivityExternalIds.js

@@ -0,0 +1,26 @@
+load('../../utils/audit.js');
+let adminUserId = 'system';
+let count = 0;
+db.activity.find({"description" : "Activity submitted by monitor"}).forEach(function(activity) {
+    if (!activity.externalIds || activity.externalIds.length == 0) {
+        var project = db.project.findOne({projectId: activity.projectId});
+        if (project && project.custom && project.custom.dataSets) {
+            var dataset = project.custom.dataSets.find(function(dataset) {
+                return dataset.activityId == activity.activityId;
+            });
+
+            if (dataset) {
+                activity.externalIds = [{idType: "MONITOR_MINTED_COLLECTION_ID", externalId: dataset.dataSetId}];
+                db.activity.replaceOne({activityId: activity.activityId}, activity);
+                audit(activity, activity.activityId, 'au.org.ala.ecodata.Activity', adminUserId);
+                print(`Updated activity:  + ${activity.activityId} +  with dataSetId: ${dataset.dataSetId}`);
+                count ++;
+            }
+            else {
+                print(`Activity: ${activity.activityId} does not have a dataset`);
+            }
+        }
+    }
+});
+
+print(`Updated ${count} activities`);

scripts/utils/audit.js

@@ -0,0 +1,88 @@
+/** Inserts a document into the auditMessage collection */
+function audit(entity, entityId, type, userId, projectId, eventType) {
+    var auditMessage = {
+        date: ISODate(),
+        entity: entity,
+        eventType: eventType || 'Update',
+        entityType: type,
+        entityId: entityId,
+        userId: userId
+    };
+    if (entity.projectId || projectId) {
+        auditMessage.projectId = (entity.projectId || projectId);
+    }
+    db.auditMessage.insertOne(auditMessage);
+}
+
+/** Updates the name and dates for a supplied report */
+function updateReportDetails(reportId, name, fromDate, toDate, userId, submissionDate, description) {
+    var now = ISODate();
+    var report = db.report.findOne({reportId:reportId});
+    report.fromDate = fromDate;
+    report.toDate = toDate;
+    report.lastUpdated = now;
+    report.name = name;
+    report.description = description || name;
+    report.submissionDate = submissionDate || toDate;
+
+    db.report.replaceOne({_id: report._id}, report);
+    audit(report, report.reportId, 'au.org.ala.ecodata.Report', userId);
+
+    updateActivity(report, userId);
+}
+
+/** Updates an activity to match the changes made to a supplied report and audits the change */
+function updateActivity(report, userId)  {
+    var activity = db.activity.findOne({activityId:report.activityId});
+    activity.plannedEndDate = report.toDate;
+    activity.endDate  =  report.toDate;
+    activity.plannedStartDate = report.fromDate;
+    activity.startDate = report.fromDate;
+    activity.description = report.name;
+
+    activity.lastUpdated = report.lastUpdated;
+
+    db.activity.replaceOne({_id:activity._id}, activity);
+    audit(activity, activity.activityId, 'au.org.ala.ecodata.Activity', userId);
+}
+
+function addProjectPermission(userId, projectId, accessLevel, adminUserId) {
+    addPermission(userId, projectId, accessLevel, 'au.org.ala.ecodata.Project', adminUserId);
+}
+
+function addPermission(userId, entityId, accessLevel, entityType, adminUserId) {
+    var userPermission = {
+        userId:userId,
+        entityType:entityType,
+        entityId:entityId,
+        accessLevel:accessLevel
+    };
+    if (db.userPermission.findOne({userId:userId, entityId:entityId})) {
+        print("Not adding permission for user: "+userId+" to entity: "+entityId+", permission already exists");
+    }
+    else {
+        print("Adding permission for user: "+userId+" to entity: "+entityId+" of type: "+entityType);
+        db.userPermission.insert(userPermission);
+        var id = db.userPermission.findOne({userId:userId, entityId:entityId})._id;
+        audit(userPermission, id, 'au.org.ala.ecodata.UserPermission', adminUserId, entityId);
+    }
+
+}
+
+
+function restoreRemovedPermissions(userId, removalDate, adminUserId) {
+    let messages = db.auditMessage.find(
+        {'entity.userId':userId,
+            userId:'<anon>',
+            entityType:'au.org.ala.ecodata.UserPermission',
+            date:{$gt:ISODate(removalDate)},
+            eventType:"Delete"
+        });
+    while (messages.hasNext()) {
+        let message = messages.next();
+        let permission = message.entity;
+
+        addProjectPermission(userId, permission.entityId, permission.accessLevel, permission.entityType, adminUserId);
+
+    }
+}

src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy

@@ -84,6 +84,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         UserPermission.findAll().each { it.delete() }
         Program.findAll().each { it.delete() }
         Site.findAll().each { it.delete() }
+        Activity.findAll().each { it.delete() }
     }
 
     def cleanup() {
@@ -666,6 +667,41 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         activityForm.externalIds = [new ExternalId(externalId: "guid-4", idType: ExternalId.IdType.MONITOR_PROTOCOL_GUID)]
         activityForm.save(failOnError: true, flush: true)
 
+        def activity = new Activity(
+                activityId: UUID.randomUUID().toString(),
+                type             : activityForm.name,
+                formVersion      : activityForm.formVersion,
+                description      : "Activity submitted by monitor",
+                projectId        : "p1",
+                publicationStatus: PublicationStatus.PUBLISHED,
+                siteId           : "s2",
+                startDate        : new Date(),
+                endDate          : new Date(),
+                plannedStartDate : new Date(),
+                plannedEndDate   : new Date(),
+                progress         : Activity.FINISHED,
+                userId           : 'user1'
+        )
+        activity.externalIds = [new ExternalId(idType: ExternalId.IdType.MONITOR_MINTED_COLLECTION_ID, externalId: 'abc')]
+        activity.save(failOnError: true, flush: true)
+
+        activity = new Activity (
+                activityId: UUID.randomUUID().toString(),
+                type             : activityForm.name,
+                formVersion      : activityForm.formVersion,
+                description      : "Activity submitted by monitor",
+                projectId        : "p2",
+                publicationStatus: PublicationStatus.PUBLISHED,
+                siteId           : "s1",
+                startDate        : new Date(),
+                endDate          : new Date(),
+                plannedStartDate : new Date(),
+                plannedEndDate   : new Date(),
+                progress         : Activity.FINISHED,
+                userId           : 'user1'
+        )
+        activity.externalIds = [new ExternalId(idType: ExternalId.IdType.MONITOR_MINTED_COLLECTION_ID, externalId: 'def')]
+        activity.save(failOnError: true, flush: true)
     }
 
     void "capitalizeModelName should convert hyphenated name to capitalised name"() {
@@ -1682,6 +1718,16 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         "DO NOT ADD" | true
     }
 
+    void "userCollection should return orgMintedId/dataSetId" (userId, expectedResult) {
+        expect:
+        service.userCollections(userId) == expectedResult
+
+        where:
+        userId | expectedResult
+        "user1" | ['abc', 'def']
+        "user2" | []
+    }
+
     private Map getNormalDefinition() {
         def input = """
 {