Merge pull request #946 from AtlasOfLivingAustralia/feature/issue945

Optionally adds species URL to download #945

grails-app/conf/application.groovy

@@ -501,6 +501,9 @@ app {
 if (!ala.baseURL) {
     ala.baseURL = "https://www.ala.org.au"
 }
+bie.ws.url = "https://bie-ws.ala.org.au/"
+bie.url = "https://bie.ala.org.au/"
+
 if (!collectory.baseURL) {
     //collectory.baseURL = "https://collectory-dev.ala.org.au/"
     collectory.baseURL = "https://collections-test.ala.org.au/"

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

@@ -6,6 +6,8 @@ import org.bson.types.ObjectId
 
 class Record {
  //   def grailsApplication
+    /** Represents a species guid that was unable to be matched against the ALA names list */
+    static final String UNMATCHED_GUID = "A_GUID"
 
     static mapping = {
         occurrenceID index: true

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

@@ -2052,7 +2052,7 @@ class ParatooService {
         }
 
         // record is only created if guid is present
-        result.guid = result.guid ?: "A_GUID"
+        result.guid = result.guid ?: Record.UNMATCHED_GUID
         result
     }
 }

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

@@ -85,7 +85,7 @@ class SpeciesReMatchService {
         name = name?.toLowerCase() ?: ""
         cacheService.get('bie-search-auto-' + name, {
             def encodedQuery = URLEncoder.encode(name ?: '', "UTF-8")
-            def url = "${grailsApplication.config.getProperty('bie.url')}ws/search/auto.jsonp?q=${encodedQuery}&limit=${limit}&idxType=TAXON"
+            def url = "${grailsApplication.config.getProperty('bie.ws.url')}ws/search/auto.jsonp?q=${encodedQuery}&limit=${limit}&idxType=TAXON"
 
             webService.getJson(url)
         })

src/main/groovy/au/org/ala/ecodata/metadata/SpeciesUrlGetter.groovy

@@ -0,0 +1,26 @@
+package au.org.ala.ecodata.metadata
+
+import pl.touk.excel.export.getters.Getter
+import au.org.ala.ecodata.Record
+
+class SpeciesUrlGetter extends OutputDataGetter implements Getter<String> {
+    String biePrefix
+    SpeciesUrlGetter(String propertyName, Map dataNode, Map<String, Object> documentMap, TimeZone timeZone, String biePrefix) {
+        super(propertyName, dataNode, documentMap, timeZone)
+        this.biePrefix = biePrefix
+    }
+
+    @Override
+    def species(Object node, Value outputValue) {
+        def val = outputValue.value
+        if (!val?.name) {
+            return ""
+        }
+        if (!val?.guid || val.guid == Record.UNMATCHED_GUID) {
+            return "Unmatched name"
+        }
+        return biePrefix+val.guid
+    }
+
+
+}

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

@@ -176,6 +176,7 @@ class ProjectXlsExporter extends ProjectExporter {
         super(exporter)
         this.projectService = projectService
         distinctElectorates = new ArrayList()
+        useSpeciesUrlGetter = true
         setupManagementUnits(managementUnitService)
         setupFundingAbn(organisationService)
         setupProgramData(programService)
@@ -185,6 +186,7 @@ class ProjectXlsExporter extends ProjectExporter {
         super(exporter, tabsToExport, [:], TimeZone.default)
         this.projectService = projectService
         this.formSectionPerTab = formSectionPerTab
+        useSpeciesUrlGetter = true
         addDataDescriptionToDownload(downloadMetadata)
         distinctElectorates = new ArrayList(electorates?:[])
         distinctElectorates.sort()

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

@@ -6,6 +6,7 @@ import au.org.ala.ecodata.metadata.OutputDateGetter
 import au.org.ala.ecodata.metadata.OutputMetadata
 import au.org.ala.ecodata.metadata.OutputModelProcessor
 import au.org.ala.ecodata.metadata.OutputNumberGetter
+import au.org.ala.ecodata.metadata.SpeciesUrlGetter
 import grails.util.Holders
 import org.apache.commons.logging.Log
 import org.apache.commons.logging.LogFactory
@@ -26,6 +27,7 @@ class TabbedExporter {
     ReportingService reportingService =  Holders.grailsApplication.mainContext.getBean("reportingService")
     ActivityFormService activityFormService = Holders.grailsApplication.mainContext.getBean("activityFormService")
     OutputModelProcessor processor = new OutputModelProcessor()
+    String biePrefix = Holders.grailsApplication.config.getProperty("bie.url")+'species/'
 
     static String DATE_CELL_FORMAT = "dd/MM/yyyy"
     Map<String, AdditionalSheet> sheets
@@ -35,6 +37,7 @@ class TabbedExporter {
     TimeZone timeZone
     Boolean useDateGetter = false
     Boolean useNumberGetter = false
+    boolean useSpeciesUrlGetter = false
     // These fields map full activity names to shortened names that are compatible with Excel tabs.
     protected Map<String, String> activitySheetNames = [:]
     protected Map<String, List<AdditionalSheet>> typedActivitySheets = [:]
@@ -232,6 +235,22 @@ class TabbedExporter {
                             getter:new OutputNumberGetter(propertyPath, dataNode, documentMap, timeZone)]
                     fieldConfiguration << field
                 }
+                else if ((dataNode.dataType == 'species') && useSpeciesUrlGetter) {
+                    // Return a property for the species name and a property for the species URL
+                    Map nameField = field + [
+                            header:outputMetadata.getLabel(viewNode, dataNode),
+                            property:propertyPath,
+                            getter:new OutputDataGetter(propertyPath, dataNode, documentMap, timeZone)]
+                    fieldConfiguration << nameField
+
+                    Map urlField = field + [
+                            description: "Link to species in the ALA",
+                            header:outputMetadata.getLabel(viewNode, dataNode),
+                            property:propertyPath,
+                            getter:new SpeciesUrlGetter(propertyPath, dataNode, documentMap, timeZone, biePrefix)
+                    ]
+                    fieldConfiguration << urlField
+                }
                 else {
                     field += [
                             header:outputMetadata.getLabel(viewNode, dataNode),

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

@@ -1,6 +1,8 @@
 package au.org.ala.ecodata.reporting
 
 import au.org.ala.ecodata.*
+import au.org.ala.ecodata.metadata.OutputDataGetter
+import au.org.ala.ecodata.metadata.SpeciesUrlGetter
 import grails.testing.gorm.DomainUnitTest
 import grails.testing.web.GrailsWebUnitTest
 import grails.util.Holders
@@ -97,6 +99,49 @@ class TabbedExporterSpec extends Specification implements GrailsWebUnitTest, Dom
 
     }
 
+    def "Species data types will be expanded into two export columns if useSpeciesUrlGetter is true"() {
+        setup:
+        String type = 'form'
+        ActivityForm form = buildMockForm(type, buildFormTemplateWithSpecies())
+
+        when:
+        tabbedExporter.useSpeciesUrlGetter = true
+        List config = tabbedExporter.getActivityExportConfig(type, true)
+
+        then:
+        1 * activityFormService.findVersionedActivityForm(type) >> [form]
+
+        config.size() == 3
+        config[1].header == 'Species label'
+        config[1].property == 'form.species'
+        config[1].getter instanceof OutputDataGetter
+
+        config[2].header == 'Species label'
+        config[2].property == 'form.species'
+        config[2].getter instanceof SpeciesUrlGetter
+
+    }
+
+    def "Species data types will only export the species name if useSpeciesUrlGetter is false"() {
+        setup:
+        String type = 'form'
+        ActivityForm form = buildMockForm(type, buildFormTemplateWithSpecies())
+
+        when:
+        tabbedExporter.useSpeciesUrlGetter = false
+        List config = tabbedExporter.getActivityExportConfig(type, true)
+
+        then:
+        1 * activityFormService.findVersionedActivityForm(type) >> [form]
+
+        config.size() == 2
+        config[1].header == 'Species label'
+        config[1].property == 'form.species'
+        config[1].getter instanceof OutputDataGetter
+    }
+
+
+
     private ActivityForm buildMockForm(String name, Map template) {
         ActivityForm form = new ActivityForm(name:name, formVersion:1)
         FormSection section = new FormSection(name:name, template:template)
@@ -142,4 +187,25 @@ class TabbedExporterSpec extends Specification implements GrailsWebUnitTest, Dom
                 ]
         ]
     }
+
+    private Map buildFormTemplateWithSpecies() {
+        [
+                dataModel:[
+                        [
+                                name:"species",
+                                dataType:"species"
+                        ]
+                ],
+                viewModel:[
+                        [type:'row', items:[
+                                [
+                                        type:'speciesSelect',
+                                        source:'species',
+                                        preLabel:'Species label'
+                                ]
+                        ]]
+
+                ]
+        ]
+    }
 }