#941

- added fauna plot to site - site with features are now of compound type - plot update will now create new site
AtlasOfLivingAustralia · May 15, 2024 · dc6099e · dc6099e
1 parent 8933698
commit dc6099e
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Showing 3 changed files with 70 additions and 24 deletions.
diff --git a/grails-app/domain/au/org/ala/ecodata/Site.groovy b/grails-app/domain/au/org/ala/ecodata/Site.groovy
@@ -181,4 +181,14 @@ class Site {
             status != Status.DELETED
         }.find()
     }
+
+    static List<Site> findAllByExternalId(ExternalId.IdType idType, String externalId, Map params) {
+        where {
+            externalIds {
+                idType == idType
+                externalId == externalId
+            }
+            status != Status.DELETED
+        }.list(params)
+    }
 }
diff --git a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
@@ -588,7 +588,10 @@ class ParatooService {
             List features = geoJson?.features ?: []
             geoJson.remove('features')
             siteProps.features = features
-            siteProps.type = Site.TYPE_SURVEY_AREA
+            if (features)
+                siteProps.type = Site.TYPE_COMPOUND
+            else
+                siteProps.type = Site.TYPE_SURVEY_AREA
             siteProps.publicationStatus = PublicationStatus.PUBLISHED
             siteProps.projects = [project.projectId]
             String externalId = geoJson.properties?.externalId
@@ -598,18 +601,19 @@ class ParatooService {
             Site site
             // create new site for every non-plot submission
             if (config.usesPlotLayout) {
-                site = Site.findByExternalId(ExternalId.IdType.MONITOR_PLOT_GUID, externalId)
-                if (site?.features) {
-                    siteProps.features?.addAll(site.features)
-                }
+                List sites = Site.findAllByExternalId(ExternalId.IdType.MONITOR_PLOT_GUID, externalId, [sort: "lastUpdated", order: "desc"])
+                if (sites)
+                    site = sites.first()
             }
 
             Map result
-            if (!site) {
+            // If the plot layout has been updated, create a new site
+            if (!site || isUpdatedPlotLayout(site, observation, config)) {
                 result = siteService.create(siteProps)
             } else {
                 result = [siteId: site.siteId]
             }
+
             if (result.error) {
                 // Don't treat this as a fatal error for the purposes of responding to the paratoo request
                 log.error("Error creating a site for survey " + collection.orgMintedUUID + ", project " + project.projectId + ": " + result.error)
@@ -619,6 +623,12 @@ class ParatooService {
         [siteId:siteId, name:siteProps?.name]
     }
 
+    private static boolean isUpdatedPlotLayout (Site site, Map observation, ParatooProtocolConfig config) {
+        Date localSiteUpdated = site.lastUpdated
+        Date plotLayoutUpdated = config.getPlotLayoutUpdatedAt(observation)
+        plotLayoutUpdated?.after(localSiteUpdated) ?: false
+    }
+
     private Map syncParatooProtocols(List<Map> protocols) {
         Map result = [errors: [], messages: []]
         List guids = []

diff --git a/src/main/groovy/au/org/ala/ecodata/paratoo/ParatooProtocolConfig.groovy b/src/main/groovy/au/org/ala/ecodata/paratoo/ParatooProtocolConfig.groovy
@@ -12,7 +12,8 @@ import org.locationtech.jts.geom.Geometry
 @Slf4j
 @JsonIgnoreProperties(['metaClass', 'errors', 'expandoMetaClass'])
 class ParatooProtocolConfig {
-
+    static final String FAUNA_PLOT = 'Fauna plot'
+    static final String CORE_PLOT = 'Core monitoring plot'
     String name
     String apiEndpoint
     boolean usesPlotLayout = true
@@ -26,7 +27,9 @@ class ParatooProtocolConfig {
     String plotVisitPath = 'plot_visit'
     String plotLayoutPath = "${plotVisitPath}.plot_layout"
     String plotLayoutIdPath = "${plotLayoutPath}.id"
+    String plotLayoutUpdatedAtPath = "${plotLayoutPath}.updatedAt"
     String plotLayoutPointsPath = "${plotLayoutPath}.plot_points"
+    String faunaPlotPointPath = "${plotLayoutPath}.fauna_plot_point"
     String plotSelectionPath = "${plotLayoutPath}.plot_selection"
     String plotLayoutDimensionLabelPath = "${plotLayoutPath}.plot_dimensions.label"
     String plotLayoutTypeLabelPath = "${plotLayoutPath}.plot_type.label"
@@ -79,6 +82,16 @@ class ParatooProtocolConfig {
         return removeMilliseconds(date)
     }
 
+    Date getPlotLayoutUpdatedAt(Map surveyData) {
+        def date = getProperty(surveyData, plotLayoutUpdatedAtPath)
+        if (!date) {
+            date = getPropertyFromSurvey(surveyData, plotLayoutUpdatedAtPath)
+        }
+
+        date = getFirst(date)
+        date ? DateUtil.parseWithMilliseconds(date) : null
+    }
+
     Map getSurveyId(Map surveyData) {
         if(surveyIdPath == null || surveyData == null) {
             return null
@@ -203,7 +216,11 @@ class ParatooProtocolConfig {
             geoJson = extractSiteDataFromPlotVisit(output)
             // get list of all features associated with observation
             if (geoJson && form && output) {
-                geoJson.features = extractFeatures(output, form)
+                List features = extractFeatures(output, form)
+                if (features) {
+                    features.addAll(geoJson.features?:[])
+                    geoJson = createConvexHullGeoJSON(features, geoJson.properties.name, geoJson.properties.externalId)
+                }
             }
         }
         else if (geometryPath) {
@@ -212,20 +229,10 @@ class ParatooProtocolConfig {
         else if (form && output) {
             List features = extractFeatures(output, form)
             if (features) {
-                List featureGeometries = features.collect { it.geometry }
-                Geometry geometry = GeometryUtils.getFeatureCollectionConvexHull(featureGeometries)
                 String startDateInString = getStartDate(output)
                 startDateInString = DateUtil.convertUTCDateToStringInTimeZone(startDateInString, clientTimeZone?:TimeZone.default)
                 String name = "${form.name} site - ${startDateInString}"
-                geoJson = [
-                    type: 'Feature',
-                    geometry: GeometryUtils.geometryToGeoJsonMap(geometry),
-                    properties: [
-                            name: name,
-                            description: "${name} (convex hull of all features)",
-                    ],
-                    features: features
-                ]
+                geoJson = createConvexHullGeoJSON(features, name)
             }
         }
 
@@ -313,6 +320,8 @@ class ParatooProtocolConfig {
             log.warn("No plot_layout found in survey at path ${plotLayoutIdPath}")
             return null
         }
+        else
+            plotLayoutId = plotLayoutId.toString()
         List plotLayoutPoints = getProperty(surveyData, plotLayoutPointsPath)
         Map plotSelection = getProperty(surveyData, plotSelectionPath)
         Map plotSelectionGeoJson = plotSelectionToGeoJson(plotSelection)
@@ -322,16 +331,33 @@ class ParatooProtocolConfig {
 
         String name = plotSelectionGeoJson.properties.name + ' - ' + plotLayoutTypeLabel + ' (' + plotLayoutDimensionLabel + ')'
 
-        Map plotGeoJson = createFeatureFromGeoJSON(plotLayoutPoints, name, plotLayoutId, plotSelectionGeoJson?.properties?.notes)
-
-        //Map faunaPlotGeoJson = toGeometry(plotLayout.fauna_plot_point)
+        Map plotGeoJson = createFeatureFromGeoJSON(plotLayoutPoints, name, plotLayoutId, "${CORE_PLOT} ${plotSelectionGeoJson?.properties?.notes?:""}")
+        List faunaPlotPoints = getProperty(surveyData, faunaPlotPointPath)
+        Map faunaPlotGeoJson = createFeatureFromGeoJSON(faunaPlotPoints, name, plotLayoutId, "${FAUNA_PLOT} ${plotSelectionGeoJson?.properties?.notes?:""}")
 
-        // TODO maybe turn this into a feature with properties to distinguish the fauna plot?
-        // Or a multi-polygon?
+        if (faunaPlotGeoJson) {
+            List features = [plotGeoJson, faunaPlotGeoJson]
+            plotGeoJson = createConvexHullGeoJSON(features, name, plotLayoutId)
+        }
 
         plotGeoJson
     }
 
+    static Map createConvexHullGeoJSON (List features, String name, String externalId = "") {
+        List featureGeometries = features.collect { it.geometry }
+        Geometry geometry = GeometryUtils.getFeatureCollectionConvexHull(featureGeometries)
+        [
+                type: 'Feature',
+                geometry: GeometryUtils.geometryToGeoJsonMap(geometry),
+                properties: [
+                        name: name,
+                        externalId: externalId,
+                        description: "${name} (convex hull of all features)",
+                ],
+                features: features
+        ]
+    }
+
     static Map createFeatureFromGeoJSON(List plotLayoutPoints, String name, def plotLayoutId, String notes  = "") {
         Map plotGeometry = toGeometry(plotLayoutPoints)
         createFeatureObject(plotGeometry, name, plotLayoutId, notes)