Merge remote-tracking branch 'origin/dev' into feature/paratoo

gradle.properties

@@ -6,7 +6,7 @@ gormMongoVersion=7.3.0
 grailsViewsVersion=2.3.2
 assetPipelineVersion=3.3.4
 elasticsearchVersion=7.17.9
-alaSecurityLibsVersion=6.1.0
+alaSecurityLibsVersion=6.2.0
 mongoDBVersion=7.3.2
 #22.x+ causes issues with mongo / GORM javax.validation.spi, might need grails 5
 geoToolsVersion=21.5

grails-app/conf/application.groovy

@@ -526,9 +526,6 @@ if (!security.cas.adminRole) {
 if (!ecodata.use.uuids) {
     ecodata.use.uuids = false
 }
-if (!userDetails.url) {
-    userDetails.url = "https://auth-test.ala.org.au/userdetails/"
-}
 
 if (!authGetKeyUrl) {
     authGetKeyUrl = "https://m.ala.org.au/mobileauth/mobileKey/generateKey"
@@ -542,6 +539,10 @@ ecodata.documentation.exampleProjectUrl = 'http://ecodata-test.ala.org.au/ws/act
 // Used by ParatooService to sync available protocols
 paratoo.core.baseUrl = 'https://merit-test.core-api.paratoo.tern.org.au/api'
 
+auth.baseUrl = 'https://auth-test.ala.org.au'
+userDetails.web.url = "${auth.baseUrl}/userdetails/"
+userDetails.api.url = "${auth.baseUrl}/userdetails/userDetails/"
+
 if (!grails.cache.ehcache) {
     grails {
         cache {

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

@@ -1,13 +1,5 @@
 package au.org.ala.ecodata
 
-import au.org.ala.ecodata.reporting.ManagementUnitXlsExporter
-import au.org.ala.ecodata.reporting.XlsExporter
-import org.apache.http.HttpStatus
-
-import java.text.ParseException
-import java.time.Instant
-
-
 @RequireApiKey
 class ManagementUnitController {
 
@@ -98,24 +90,6 @@ class ManagementUnitController {
         respond managementUnitService.managementUnitSiteMap(ids)
     }
 
-
-    /**
-     * startDate and endDate need to be ISO 8601
-     *
-     * Get reports of all management units in a given period
-     */
-    def generateReportsInPeriod(){
-        try{
-            Map message = managementUnitService.generateReportsInPeriods(params.startDate, params.endDate, params.reportDownloadBaseUrl, params.senderEmail, params.systemEmail,params.email,params.getBoolean("summaryFlag", false))
-            respond(message, status:200)
-       }catch ( ParseException e){
-            def message = [message: 'Error: You need to provide startDate and endDate in the format of ISO 8601']
-            respond(message, status:HttpStatus.SC_NOT_ACCEPTABLE)
-       }catch(Exception e){
-            def message = [message: 'Fatal: ' + e.message]
-            respond(message, status:HttpStatus.SC_NOT_ACCEPTABLE)
-        }
-    }
     /**
      * Get financial years of managment unit reports cover
      * @return

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

@@ -3,12 +3,11 @@ package au.org.ala.ecodata
 import grails.converters.JSON
 
 import static au.org.ala.ecodata.ElasticIndex.DEFAULT_INDEX
-
 /**
  * Exposes web services to perform CRUD operations on an organisation.
  */
 class OrganisationController {
-
+    static responseFormats = ['json', 'xml']
     OrganisationService organisationService
     ElasticSearchService elasticSearchService
 
@@ -96,7 +95,6 @@ class OrganisationController {
         }
     }
 
-
     private Map buildParams(Map params) {
 
         Map values = [:]

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

@@ -422,8 +422,26 @@ class ParatooController {
     }
 
     @PUT
-    @Path("/projects")
-    def updateProjectSites(String id) {
+    @Path("/projects/{id}")
+    @SecurityRequirements([@SecurityRequirement(name = "jwt"), @SecurityRequirement(name = "openIdConnect"), @SecurityRequirement(name = "oauth")])
+    @Operation(
+            method = "PUT",
+            responses = [
+                    @ApiResponse(responseCode = "200", description = "Updated project", content = @Content(mediaType = "application/json", schema = @Schema(implementation = Map.class))),
+                    @ApiResponse(responseCode = "403", description = "Forbidden"),
+                    @ApiResponse(responseCode = "500", description = "Internal server error")
+            ],
+            requestBody = @RequestBody(
+                    description = "Project sites to update",
+                    required = true,
+                    content = @Content(
+                            mediaType = 'application/json',
+                            schema = @Schema(implementation = Map.class)
+                    )
+            ),
+            tags = "Org Interface"
+    )
+    def updateProjectSites(@Parameter(name = "id", description = "Project id", required = true, in = ParameterIn.PATH, schema = @Schema(type = "string"))String id) {
         String userId = userService.currentUserDetails.userId
         List projects = paratooService.userProjects(userId)
         ParatooProject project = projects?.find { it.id == id }

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

@@ -1,13 +1,15 @@
 package au.org.ala.ecodata
 
 import grails.converters.JSON
-import org.grails.web.json.JSONObject
+import org.apache.http.HttpStatus
 
+import java.text.ParseException
 
 class ReportController {
 
     static responseFormats = ['json', 'xml']
     def reportingService
+    ReportService reportService
 
     def get(String id) {
         respond reportingService.get(id, false)
@@ -89,4 +91,23 @@ class ReportController {
 
         render reportingService.aggregateReports(params.searchCriteria, params.reportConfig) as JSON
     }
+
+    /**
+     * startDate and endDate need to be ISO 8601
+     *
+     * Get reports of all management units in a given period
+     */
+    @RequireApiKey
+    def generateReportsInPeriod(){
+        try{
+            Map message = reportService.generateReportsInPeriods(params.startDate, params.endDate, params.reportDownloadBaseUrl, params.senderEmail, params.systemEmail,params.email,params.getBoolean("summaryFlag", false), params.entity, params.hubId)
+            respond(message, status:200)
+        }catch ( ParseException e){
+            def message = [message: 'Error: You need to provide startDate and endDate in the format of ISO 8601']
+            respond(message, status: HttpStatus.SC_NOT_ACCEPTABLE)
+        }catch(Exception e){
+            def message = [message: 'Fatal: ' + e.message]
+            respond(message, status:HttpStatus.SC_NOT_ACCEPTABLE)
+        }
+    }
 }

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

@@ -183,6 +183,7 @@ class UrlMappings {
 
 
         "/ws/report/runReport"(controller:"report", action:"runReport")
+        "/ws/report/generateReportsInPeriod"(controller:"report", action:"generateReportsInPeriod")
 
         "/ws/project/findByName"(controller: "project"){ action = [GET:"findByName"] }
         "/ws/project/importProjectsFromSciStarter"(controller: "project", action: "importProjectsFromSciStarter")

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

@@ -192,45 +192,6 @@ class ManagementUnitService {
         return [count: countOfReports, downloadId: downloadId]
     }
 
-    /**
-     *
-     * @param startDate
-     * @param endDate
-     * @param reportDownloadBaseUrl  Base url of downloading generated report
-     * @param senderEmail
-     * @param systemEmail
-     * @param receiverEmail
-     * @return
-     */
-    Map generateReportsInPeriods(String startDate, String endDate, String reportDownloadBaseUrl, String senderEmail, String systemEmail, String receiverEmail, boolean isSummary ){
-        List<Map> reports =  getReportingActivities(startDate,endDate)
-        int countOfReports = reports.sum{it.activities?.count{it.progress!=Activity.PLANNED}}
-
-        Map params = [:]
-        params.fileExtension = "xlsx"
-        params.reportDownloadBaseUrl = reportDownloadBaseUrl
-        params.senderEmail = senderEmail
-        params.systemEmail = systemEmail
-        params.email = receiverEmail
-
-        Closure doDownload = { File file ->
-            XlsExporter exporter = new XlsExporter(file.absolutePath)
-            ManagementUnitXlsExporter  muXlsExporter = new ManagementUnitXlsExporter(exporter)
-            muXlsExporter.export(reports, isSummary)
-            exporter.sizeColumns()
-            exporter.save()
-        }
-        String downloadId = downloadService.generateReports(params, doDownload)
-        Map message =[:]
-        if (countOfReports>0){
-            message = [message:"Your will receive an email notification when report is generated", details:downloadId]
-        }else{
-            message = [message:"Your download will be emailed to you when it is complete. <p> WARNING, the period you requested may not have reports.", details: downloadId]
-        }
-        return message
-    }
-
-
     /**
      *  Get reports of all management units in a period
      *

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

@@ -1,11 +1,10 @@
 package au.org.ala.ecodata
 
-
 import com.mongodb.client.model.Filters
 import grails.validation.ValidationException
 import org.bson.conversions.Bson
 
-import static au.org.ala.ecodata.Status.*
+import static au.org.ala.ecodata.Status.DELETED
 
 /**
  * Works with Organisations, mostly CRUD operations at this point.
@@ -18,6 +17,8 @@ class OrganisationService {
     static transactional = 'mongo'
 
     def commonService, projectService, userService, permissionService, documentService, collectoryService, messageSource, emailService, grailsApplication
+    ReportingService reportingService
+    ActivityService activityService
 
     def get(String id, levelOfDetail = [], includeDeleted = false) {
         Organisation organisation
@@ -174,17 +175,46 @@ class OrganisationService {
      * significant memory and performance overhead when dealing with so many entities
      * at once.
      * @param action the action to be performed on each Organisation.
+     * @param filters list of filters
      */
-    void doWithAllOrganisations(Closure action) {
+    void doWithAllOrganisations(Closure action, List<Filters> filters = []) {
         // Due to various memory & performance issues with GORM mongo plugin 1.3, this method uses the native API.
         def collection = Organisation.getCollection()
         //DBObject siteQuery = new QueryBuilder().start('status').notEquals(DELETED).get()
-        Bson query = Filters.ne("status", DELETED);
+        Bson query = Filters.ne("status", DELETED)
+        filters.add(query)
+        query = Filters.and(filters)
         def results = collection.find(query).batchSize(100)
 
         results.each { dbObject ->
             action.call(dbObject)
         }
     }
 
+    /**
+     *  Get reports of all management units in a period
+     *
+     * @param start
+     * @param end
+     * @param hubId
+     * @return
+     */
+    List<Map> getReportingActivities (String startDate, String endDate, String hubId) {
+        List<Map> organisationDetails = []
+        doWithAllOrganisations({ org ->
+            List<Report> reports = reportingService.search([organisationId: org.organisationId, dateProperty:'toDate', startDate:startDate, endDate:endDate])
+
+             List<Map> activities = activityService.search([activityId:reports.activityId], ['all'])
+
+            Map result = new HashMap(org)
+            result.reports = reports
+            result.activities = activities
+
+            organisationDetails << result
+
+        }, [Filters.eq("hubId", hubId)])
+
+        organisationDetails
+    }
+
 }

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

@@ -17,6 +17,7 @@ import static au.org.ala.ecodata.ElasticIndex.HOMEPAGE_INDEX
  */
 @Slf4j
 class ReportService {
+    static final String MU = 'managementUnit', ORG = 'organisation'
 
     ActivityService activityService
     ElasticSearchService elasticSearchService
@@ -26,6 +27,9 @@ class ReportService {
     MetadataService metadataService
     UserService userService
     AuthService authService
+    DownloadService downloadService
+    ManagementUnitService managementUnitService
+    OrganisationService organisationService
 
     def findScoresByLabel(List labels) {
         Score.findAllByLabelInList(labels)
@@ -463,4 +467,63 @@ class ReportService {
         List<String> activityIds = Report.findAllByManagementUnitIdInList(muIds.toList()).activityId
         Date[] period = activityService.getPeriod(activityIds)
     }
+
+    /**
+     * Generate report for entity
+     * @param startDate
+     * @param endDate
+     * @param reportDownloadBaseUrl  Base url of downloading generated report
+     * @param senderEmail
+     * @param systemEmail
+     * @param receiverEmail
+     * @param entity managementUnit or organisation
+     * @param hubId
+     * @return
+     */
+    Map generateReportsInPeriods(String startDate, String endDate, String reportDownloadBaseUrl, String senderEmail, String systemEmail, String receiverEmail, boolean isSummary, String entity, String hubId ){
+        List<Map> reports
+        switch (entity) {
+            case ORG:
+                reports =  organisationService.getReportingActivities(startDate, endDate, hubId)
+                break
+            case MU:
+            default:
+                reports =  managementUnitService.getReportingActivities(startDate, endDate)
+                break
+        }
+
+        int countOfReports = reports ? reports.sum{it.activities?.count{it.progress!=Activity.PLANNED}} : 0
+
+        Map params = [:]
+        params.fileExtension = "xlsx"
+        params.reportDownloadBaseUrl = reportDownloadBaseUrl
+        params.senderEmail = senderEmail
+        params.systemEmail = systemEmail
+        params.email = receiverEmail
+
+        Closure doDownload = { File file ->
+            XlsExporter exporter = new XlsExporter(file.absolutePath)
+            switch (entity) {
+                case ORG:
+                    OrganisationXlsExporter orgXlsExporter = new OrganisationXlsExporter(exporter, [], [:])
+                    orgXlsExporter.export(reports, isSummary)
+                    break
+                case MU:
+                default:
+                    ManagementUnitXlsExporter muXlsExporter = new ManagementUnitXlsExporter(exporter)
+                    muXlsExporter.export(reports, isSummary)
+                    break
+            }
+            exporter.sizeColumns()
+            exporter.save()
+        }
+        String downloadId = downloadService.generateReports(params, doDownload)
+        Map message =[:]
+        if (countOfReports>0){
+            message = [message:"Your will receive an email notification when report is generated", details:downloadId]
+        }else{
+            message = [message:"Your download will be emailed to you when it is complete. <p> WARNING, the period you requested may not have reports.", details: downloadId]
+        }
+        return message
+    }
 }