Merge branch 'dev' into feature/extended-data

grails-app/conf/data/mapping.json

@@ -220,11 +220,27 @@
           "type": "text",
           "index": "false"
         },
+        "services": {
+          "type": "keyword"
+        },
+        "projectElectFacet": {
+          "type": "keyword"
+        },
+        "projectStateFacet": {
+          "type": "keyword"
+        },
         "extent":{
           "properties": {
             "geometry": {
               "properties": {
-
+                "geometry": {
+                  "properties": {
+                    "intersectionAreaByFacets": {
+                      "type": "object",
+                      "enabled": false
+                    }
+                  }
+                }
 
               }
             }
@@ -236,7 +252,10 @@
               "properties": {
                 "geometry": {
                   "properties": {
-
+                    "intersectionAreaByFacets": {
+                      "type": "object",
+                      "enabled": false
+                    }
                   }
                 }
               }

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

@@ -30,7 +30,7 @@ class ActivityController {
     }
 
     def get(String id) {
-        def detail = params.view == SCORES ? [SCORES] : []
+        def detail = params.view == SCORES ? [SCORES] : params.view
         if (!id) {
 
             def list = activityService.getAll(params.boolean('includeDeleted'), params.view)

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

@@ -329,7 +329,7 @@ class ProjectController {
             render status:400, text: "projectId is a required parameter"
         } else {
             Map project = projectService.get(params.projectId)
-            asJson projectService.findStateAndElectorateForProject(project)
+            asJson projectService.findAndFormatStatesAndElectoratesForProject(project)
         }
     }
 

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

@@ -1167,6 +1167,9 @@ class ElasticSearchService {
                 it.remove('periodTargets')
                 it.remove('outcomeTargets')
             } // Not useful for searching and is causing issues with the current mapping.
+
+            // add algorithmically generated or manually selected states and electorates of a project
+            projectMap << projectService.findStateAndElectorateForProject(projectMap)
         } else {
             projectMap.sites = siteService.findAllNonPrivateSitesForProjectId(project.projectId, SiteService.FLAT)
             // GeoServer requires a single attribute with project area. Cannot use `sites` property (above) since it has
@@ -1233,6 +1236,16 @@ class ElasticSearchService {
                 if (!projectMap.visibility && program.inheritedConfig?.visibility) {
                     projectMap.visibility = program.inheritedConfig.visibility
                 }
+                List services = project.findProjectServices()
+
+                if (services) {
+                    projectMap.services = services?.collect{
+                        it.getProgramLabels()?[project.programId]?.label ?: it.name
+                    }
+                }
+
+
+
             }
             else {
                 log.error("Project "+project.projectId+" references invalid program with programId = "+project.programId)

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

@@ -2128,7 +2128,9 @@ class ParatooService {
             result.name = result.commonName ? result.scientificName ? "${result.scientificName} (${result.commonName})" : result.commonName : result.scientificName
         }
         else {
-            result.name = result.scientificName ?: result.commonName
+            result.name = result.scientificName
+            // clear common name if it is same as scientific name
+            result.commonName = null
         }
 
         List specialCases = grailsApplication.config.getProperty("paratoo.species.specialCases", List)

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

@@ -244,6 +244,8 @@ class ProjectService {
                     mapOfProperties.sites = siteService.findAllForProjectId(project.projectId, [SiteService.FLAT], version)
                 }
 
+                // add geographic info attributes such as primarystate, otherstate, primaryelect and otherelect
+                mapOfProperties << findAndFormatStatesAndElectoratesForProject(mapOfProperties)
                 mapOfProperties.documents = documentService.findAllForProjectId(project.projectId, levelOfDetail, version)
                 mapOfProperties.links = documentService.findAllLinksForProjectId(project.projectId, levelOfDetail, version)
                 Lock lock = lockService.get(project.projectId)
@@ -1206,10 +1208,10 @@ class ProjectService {
         Map<String,Map<String,Double>> sumOfIntersectionsByLayer = [:].withDefault { [:].withDefault { 0 } }
         Map orderedIntersectionsByArea = [:]
         Map config = metadataService.getGeographicConfig(project.hubId)
-        List layers = config.checkForBoundaryIntersectionInLayers
+        List layers = config?.checkForBoundaryIntersectionInLayers
         List projectSites = getRepresentativeSitesOfProject(project)
         projectSites?.each { Map site ->
-            layers.each { String layer ->
+            layers?.each { String layer ->
                 Map facet = metadataService.getGeographicFacetConfig(layer, project.hubId)
                 site.extent?.geometry?.get(SpatialService.INTERSECTION_AREA)?.get(facet.name)?.get(SiteService.INTERSECTION_CURRENT)?.each { String layerValue, value ->
                     sumOfIntersectionsByLayer[layer][layerValue] += value
@@ -1260,13 +1262,35 @@ class ProjectService {
         []
     }
 
+    Map findAndFormatStatesAndElectoratesForProject(Map project) {
+        Map result = findStateAndElectorateForProject (project)
+        if(!result) {
+            return [:]
+        }
+
+        List elect = result.remove('projectElectFacet') as List
+        List state = result.remove('projectStateFacet') as List
+
+        if (state) {
+            result["primarystate"] = state.pop()
+            result["otherstate"] = state?.join("; ")
+        }
+
+        if (elect) {
+            result["primaryelect"] = elect.pop()
+            result["otherelect"] = elect.join("; ")
+        }
+
+        result
+    }
+
     /**
      * Find primary/other state(s)/electorate(s) for a project.
      * 1. If isDefault is true, use manually assigned state(s)/electorate(s) i.e project.geographicInfo.
      * 2. If isDefault is false or missing, use the state(s)/electorate(s) from sites using site precedence.
      * 3. If isDefault is false and there are no sites, use manual state(s)/electorate(s) in project.geographicInfo.
      */
-    Map findStateAndElectorateForProject(Map project) {
+    Map findStateAndElectorateForProject (Map project) {
         Map result = [:]
         if(project == null) {
             return result
@@ -1277,14 +1301,13 @@ class ProjectService {
         if (geographicInfo == null || (geographicInfo.isDefault == false)) {
             Map intersections = orderLayerIntersectionsByAreaOfProjectSites(project)
             Map config = metadataService.getGeographicConfig()
-            List intersectionLayers = config.checkForBoundaryIntersectionInLayers
+            List intersectionLayers = config?.checkForBoundaryIntersectionInLayers
             intersectionLayers?.each { layer ->
                 Map facetName = metadataService.getGeographicFacetConfig(layer)
                 if (facetName.name) {
                     List intersectionValues = intersections[layer]
                     if (intersectionValues) {
-                        result["primary${facetName.name}"] = intersectionValues.pop()
-                        result["other${facetName.name}"] = intersectionValues.join("; ")
+                        result["project${facetName.name.capitalize()}Facet"] = intersectionValues
                     }
                 }
                 else
@@ -1295,14 +1318,12 @@ class ProjectService {
         //isDefault is true or false and no sites.
         if (geographicInfo) {
             // load from manually assigned electorates/states
-            if (!result.containsKey("primaryelect")) {
-                result["primaryelect"] = geographicInfo.primaryElectorate
-                result["otherelect"] = geographicInfo.otherElectorates?.join("; ")
+            if (!result.containsKey("projectElectFacet")) {
+                result["projectElectFacet"] = (geographicInfo.primaryElectorate ? [geographicInfo.primaryElectorate] : []) + geographicInfo.otherElectorates
             }
 
-            if (!result.containsKey("primarystate")) {
-                result["primarystate"] = geographicInfo.primaryState
-                result["otherstate"] = geographicInfo.otherStates?.join("; ")
+            if (!result.containsKey("projectStateFacet")) {
+                result["projectStateFacet"] = (geographicInfo.primaryState ? [geographicInfo.primaryState] : []) + geographicInfo.otherStates
             }
         }
 

src/main/groovy/au/org/ala/ecodata/reporting/ProjectXlsExporter.groovy

@@ -336,7 +336,7 @@ class ProjectXlsExporter extends ProjectExporter {
     }
 
     private void addPrimaryAndOtherIntersections (Map project) {
-        Map result = projectService.findStateAndElectorateForProject(project) ?: [:]
+        Map result = projectService.findAndFormatStatesAndElectoratesForProject(project) ?: [:]
         project << result
     }
 

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

@@ -51,6 +51,7 @@ class ActivityControllerSpec extends Specification implements ControllerUnitTest
 
         when:
         params.id = '1'
+        params.view = []
         controller.get()
 
         then:
@@ -67,6 +68,7 @@ class ActivityControllerSpec extends Specification implements ControllerUnitTest
 
         when:
         params.id = '2'
+        params.view = []
         controller.get()
 
         then:

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

@@ -368,6 +368,7 @@ class ElasticSearchIndexServiceSpec extends MongoSpec implements ServiceUnitTest
         then:
         1 * client.index({ IndexRequest index -> index.index() == ElasticIndex.HOMEPAGE_INDEX && index.id() == projectProps.projectId}, RequestOptions.DEFAULT) >>
                 { index, options -> result = new JsonSlurper().parseText(index.source().utf8ToString()); Mock(IndexResponse) }
+        1 * projectService.findStateAndElectorateForProject(_) >> [:]
         1 * projectService.toMap(project, ProjectService.FLAT) >> projectProps
 
         and:
@@ -396,6 +397,7 @@ class ElasticSearchIndexServiceSpec extends MongoSpec implements ServiceUnitTest
         then:
         1 * client.index({ IndexRequest index -> index.index() == ElasticIndex.HOMEPAGE_INDEX && index.id() == meritProjectProps.projectId}, RequestOptions.DEFAULT) >>
                 { index, options  -> meritResult = new JsonSlurper().parseText(index.source().utf8ToString()); Mock(IndexResponse) }
+        1 * projectService.findStateAndElectorateForProject(_) >> [:]
         1 * projectService.toMap(meritProject, ProjectService.FLAT) >> meritProjectProps
         1 * siteService.findAllForProjectId(meritProject.projectId, SiteService.FLAT) >> [site1]
 
@@ -492,7 +494,7 @@ class ElasticSearchIndexServiceSpec extends MongoSpec implements ServiceUnitTest
 
         then:
         1 * projectService.toMap(project, ProjectService.FLAT) >> meritProjectProps
-
+        1 * projectService.findStateAndElectorateForProject(_) >> [:]
         1 * client.get(_, _) >> getResponse
         1 * getResponse.exists >> true
         1 * client.delete(_, _)

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

@@ -815,13 +815,23 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         ]
         0 * speciesReMatchService.searchByName(_, false, true)
 
+        when: // user inputs scientific name to field and ALA cannot match the name
+        result = service.transformSpeciesName("Centipeda cunninghamii")
+        outputSpeciesId = result.remove("outputSpeciesId")
+
+        then:
+        outputSpeciesId != null
+        result == [name: "Centipeda cunninghamii", scientificName: "Centipeda cunninghamii", commonName: null, taxonRank: null, guid: "A_GUID"]
+        1 * speciesReMatchService.searchByName(_) >> null
+        1 * speciesReMatchService.searchByName(_, false, true) >> null
+
         when: // Do not create record when value equals special cases. Therefore, removes guid.
         result = service.transformSpeciesName("Other")
         outputSpeciesId = result.remove("outputSpeciesId")
 
         then:
         outputSpeciesId != null
-        result == [name: "Other", scientificName: "Other", commonName: "Other", taxonRank: null]
+        result == [name: "Other", scientificName: "Other", commonName: null, taxonRank: null]
         1 * speciesReMatchService.searchByName(_) >> null
         1 * speciesReMatchService.searchByName(_, false, true) >> null
 

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

@@ -965,6 +965,49 @@ class ProjectServiceSpec extends MongoSpec implements ServiceUnitTest<ProjectSer
         result["cl11163"][2] == "canberra"
     }
 
+    void "orderLayerIntersectionsByAreaOfProjectSites should order shapes over points"() {
+        setup:
+        Map projectMap
+        Map result
+        Project project1
+        Site site1, site2, site3
+        Site.metaClass.getDbo = {
+            delegate.properties
+        }
+        metadataService.getGeographicConfig(_) >> [
+                contextual: [
+                        elect : 'cl11163'
+                ],
+                "checkForBoundaryIntersectionInLayers" : [ "cl11163" ]
+        ]
+        metadataService.getGeographicFacetConfig("cl11163", "12345") >> [name: "elect", grouped: true]
+        project1 = new Project(projectId: '111', name: "Project 111", hubId:"12345", isMERIT: true)
+        site1 = new Site(siteId: 's1', name: "Site 1", type: "surveyArea", status: 'active', projects: ['111'], extent: [ source: "point", geometry: [intersectionAreaByFacets: ["elect": ["CURRENT": ["fenner": 0]]]]])
+        site2 = new Site(siteId: 's2', name: "Site 2", type: "surveyArea", status: 'active', projects: ['111'], extent: [ source: "drawn", geometry: [intersectionAreaByFacets: ["elect": ["CURRENT": ["bean": 0.7, "canberra": 0.4]]]]])
+        site3 = new Site(siteId: 's3', name: "Site 3", type: "surveyArea", status: 'active', projects: ['111'], extent: [ source: "point", geometry: [intersectionAreaByFacets: ["elect": ["CURRENT": ["adelaide": 0]]]]])
+        Project.withTransaction {
+            project1.save(flush: true, failOnError: true)
+            site1.save(flush: true, failOnError: true)
+            site2.save(flush: true, failOnError: true)
+            site3.save(flush: true, failOnError: true)
+        }
+        project1.metaClass.getDbo = { new BasicDBObject(project1.properties) }
+
+        when:
+        Project.withTransaction {
+            projectMap = service.toMap(project1, ProjectService.ALL)
+        }
+
+        result = service.orderLayerIntersectionsByAreaOfProjectSites(projectMap)
+
+        then:
+        result.size() == 1
+        result["cl11163"][0] == "bean"
+        result["cl11163"][1] == "canberra"
+        ["fenner", "adelaide"].contains(result["cl11163"][2])
+        ["fenner", "adelaide"].contains(result["cl11163"][3])
+    }
+
 
     void "getRepresentativeSitesOfProject should get EMSA site or Reporting sites only" () {
         setup:
@@ -1118,7 +1161,7 @@ class ProjectServiceSpec extends MongoSpec implements ServiceUnitTest<ProjectSer
         metadataService.getGeographicFacetConfig("layer2", _) >> [name: "elect", grouped: false]
 
         when:
-        Map result = service.findStateAndElectorateForProject(project)
+        Map result = service.findAndFormatStatesAndElectoratesForProject(project)
 
         then:
         result.primarystate == "state1"
@@ -1142,7 +1185,7 @@ class ProjectServiceSpec extends MongoSpec implements ServiceUnitTest<ProjectSer
 
 
         when:
-        Map result = service.findStateAndElectorateForProject(project)
+        Map result = service.findAndFormatStatesAndElectoratesForProject(project)
 
         then:
         result.primarystate == "ACT"
@@ -1157,7 +1200,7 @@ class ProjectServiceSpec extends MongoSpec implements ServiceUnitTest<ProjectSer
         Map project = [geographicInfo: [isDefault: true, primaryState: "ACT", otherStates: ['NSW', 'VIC'], primaryElectorate: "Bean", otherElectorates: ['Canberra', 'Fenner']]]
 
         when:
-        Map result = service.findStateAndElectorateForProject(project)
+        Map result = service.findAndFormatStatesAndElectoratesForProject(project)
 
         then:
         result.primarystate == "ACT"
@@ -1169,7 +1212,7 @@ class ProjectServiceSpec extends MongoSpec implements ServiceUnitTest<ProjectSer
     def "findStateAndElectorateForProject should return empty map if project is null"() {
         when:
         Map project = null
-        Map result = service.findStateAndElectorateForProject(project)
+        Map result = service.findAndFormatStatesAndElectoratesForProject(project)
 
         then:
         result.isEmpty()

src/test/groovy/au/org/ala/ecodata/reporting/ProjectXlsExporterSpec.groovy

@@ -230,7 +230,7 @@ class ProjectXlsExporterSpec extends Specification implements GrailsUnitTest {
         setup:
         String sheet = "Electorate Coord"
         Map project = project()
-        projectService.findStateAndElectorateForProject(_) >> ["primarystate": "ACT", "otherstate": null, "primaryelect": "bean", "otherelect": "fenner; canberra"]
+        projectService.findAndFormatStatesAndElectoratesForProject(_) >> ["primarystate": "ACT", "otherstate": null, "primaryelect": "bean", "otherelect": "fenner; canberra"]
 
         when:
         projectXlsExporter.export(project)