Merge pull request #912 from AtlasOfLivingAustralia/feature/paratoo

Feature/paratoo

build.gradle

@@ -17,6 +17,7 @@ buildscript {
 plugins {
     id "com.github.node-gradle.node" version "3.4.0"
     id 'jacoco'
+    id "com.gorylenko.gradle-git-properties" version "2.4.1"
 }
 
 version "4.4-SNAPSHOT"

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

@@ -22,6 +22,9 @@ import static au.org.ala.ecodata.Status.DELETED
 
 class MetadataService {
 
+    static final String BUILD_VERSION_PROPERTY = "git.build.version"
+    private static final String GIT_PROPERTIES_FILE = "git.properties"
+
     // The spatial portal returns n/a when the point does not intersect a layer.
     private static final String SPATIAL_PORTAL_NO_MATCH_VALUE = 'n/a'
 
@@ -1182,7 +1185,11 @@ class MetadataService {
 
     /** Returns a value from the gradle git plugin generated git.properties */
     String getGitProperty(String propertyName) {
-        getFromPropertyFile("git.properties", propertyName)
+        getFromPropertyFile(GIT_PROPERTIES_FILE, propertyName)
+    }
+
+    String getVersion() {
+        getGitProperty(BUILD_VERSION_PROPERTY)
     }
 
     /** Returns a value from the gradle/spring boot generated build-info.properties */

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

@@ -39,6 +39,7 @@ class ParatooService {
     SiteService siteService
     PermissionService permissionService
     TokenService tokenService
+    MetadataService metadataService
 
     /**
      * The rules we use to find projects eligible for use by paratoo are:
@@ -147,9 +148,12 @@ class ParatooService {
                 surveyId: paratooCollectionId.surveyId,
                 eventTime: new Date(),
                 userId: userId,
-                projectId: projectId
+                projectId: projectId,
+                system: "MERIT",
+                version: metadataService.getVersion()
         )
         dataSet.orgMintedIdentifier = orgMintedIdentifier.encodeAsMintedCollectionId()
+        log.info "Minting identifier for Monitor collection: ${paratooCollectionId}: ${dataSet.orgMintedIdentifier}"
         project.custom.dataSets << dataSet
         Map result = projectService.update([custom:project.custom], projectId, false)
 
@@ -272,9 +276,11 @@ class ParatooService {
     private Map syncParatooProtocols(List<Map> protocols) {
 
         Map result = [errors:[], messages:[]]
+        List guids = []
         protocols.each { Map protocol ->
             String id = protocol.id
             String guid = protocol.attributes.identifier
+            guids << guid
             String name = protocol.attributes.name
             ActivityForm form = ActivityForm.findByExternalId(guid)
             if (!form) {
@@ -295,12 +301,15 @@ class ParatooService {
                 if (paratooInternalId) {
                     String message = "Updating form with id: "+paratooInternalId.externalId+", guid: "+guid+", name: "+name+", new id: "+id
                     paratooInternalId.externalId = id
+                    result.messages << message
+                    log.info message
                 }
                 else {
-                    result.errors << "Error: Missing internal id for form with id: "+id+", name: "+name
+                    String error = "Error: Missing internal id for form with id: "+id+", name: "+name
+                    result.errors << error
+                    log.error error
                 }
-                result.messages << message
-                log.info message
+
             }
 
             mapProtocolToActivityForm(protocol, form)
@@ -311,6 +320,18 @@ class ParatooService {
                 log.warn "Error saving form with id: "+id+", name: "+name
             }
         }
+
+        List allProtocolForms = ActivityForm.findAll {
+            externalIds {
+                idType == ExternalId.IdType.MONITOR_PROTOCOL_GUID
+            }
+            status != Status.DELETED
+        }
+
+        List deletions = allProtocolForms.findAll{it.externalIds.find{it.idType == ExternalId.IdType.MONITOR_PROTOCOL_GUID && !(it.externalId in guids)}}
+        deletions.each { ActivityForm activityForm ->
+            result.messages << "Form ${activityForm.name} with guid: ${activityForm.externalIds.find{it.idType == ExternalId.IdType.MONITOR_PROTOCOL_GUID}.externalId} has been deleted"
+        }
         result
 
     }

src/main/groovy/au/org/ala/ecodata/paratoo/ParatooMintedIdentifier.groovy

@@ -4,6 +4,7 @@ import au.org.ala.ecodata.DateUtil
 import grails.converters.JSON
 import grails.databinding.BindingFormat
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties
+import org.springframework.beans.factory.annotation.Value
 
 @JsonIgnoreProperties(['metaClass', 'errors', 'expandoMetaClass'])
 class ParatooMintedIdentifier {
@@ -12,6 +13,8 @@ class ParatooMintedIdentifier {
     Date eventTime
     String userId
     String projectId
+    String system
+    String version
 
     String eventTimeAsISOString() {
         DateUtil.formatWithMilliseconds(eventTime)
@@ -24,7 +27,11 @@ class ParatooMintedIdentifier {
                 userId: userId,
                 projectId: projectId,
                 protocolId: surveyId.protocol.id,
-                protocolVersion: surveyId.protocol.version
+                protocolVersion: surveyId.protocol.version,
+                org_provenance: [
+                        system: system,
+                        version: version
+                ]
         ]
         String jsonString = (data as JSON).toString()
         jsonString.encodeAsBase64()

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

@@ -21,6 +21,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
     WebService webService = Mock(WebService)
     TokenService tokenService = Mock(TokenService)
     SettingService settingService = Mock(SettingService)
+    MetadataService metadataService = Mock(MetadataService)
 
     static Map DUMMY_POLYGON = [type:'Polygon', coordinates: [[[1,2], [2,2], [2, 1], [1,1], [1,2]]]]
 
@@ -35,6 +36,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         service.permissionService = new PermissionService() // Using the real permission service for this test
         service.tokenService = tokenService
         service.settingService = settingService
+        service.metadataService = metadataService
 
         JSON.registerObjectMarshaller(new MapMarshaller())
         JSON.registerObjectMarshaller(new CollectionMarshaller())