From aa2806f34c592100085ada57df9b0c1e4f4744c1 Mon Sep 17 00:00:00 2001
From: chrisala <chris.godwin.ala@gmail.com>
Date: Fri, 24 May 2024 16:35:01 +1000
Subject: [PATCH 1/3] Record Monitor activities as finished #961

---
 grails-app/services/au/org/ala/ecodata/ParatooService.groovy | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
index d8b3077f2..158923b8e 100644
--- a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
+++ b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
@@ -479,12 +479,13 @@ class ParatooService {
                 formVersion      : activityForm.formVersion,
                 description      : "Activity submitted by monitor",
                 projectId        : collection.projectId,
-                publicationStatus: "published",
+                publicationStatus: PublicationStatus.PUBLISHED,
                 siteId           : dataSet.siteId,
                 startDate        : dataSet.startDate,
                 endDate          : dataSet.endDate,
                 plannedStartDate : dataSet.startDate,
                 plannedEndDate   : dataSet.endDate,
+                progress         : Activity.FINISHED,
                 externalIds      : [new ExternalId(idType: ExternalId.IdType.MONITOR_MINTED_COLLECTION_ID, externalId: dataSet.dataSetId)],
                 userId           : userId,
                 outputs          : [[

From 4c3ebedb67769129aaf3f7e41e42e37cb09e7488 Mon Sep 17 00:00:00 2001
From: temi <temi.varghese@csiro.au>
Date: Fri, 31 May 2024 06:45:44 +1000
Subject: [PATCH 2/3] #965 - do not create record for "Other" species

---
 grails-app/conf/application.groovy                   |  2 +-
 .../au/org/ala/ecodata/ParatooService.groovy         | 12 +++++++++---
 .../au/org/ala/ecodata/ParatooServiceSpec.groovy     | 12 ++++++++++++
 3 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/grails-app/conf/application.groovy b/grails-app/conf/application.groovy
index da139f946..3c186a923 100644
--- a/grails-app/conf/application.groovy
+++ b/grails-app/conf/application.groovy
@@ -1490,4 +1490,4 @@ paratoo.defaultPlotLayoutViewModels = [
                         ]
                 ]
         ]
-
+paratoo.species.specialCases = ["Other"]
diff --git a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
index d8b3077f2..15cd0dfd2 100644
--- a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
+++ b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
@@ -2097,9 +2097,15 @@ class ParatooService {
         }
 
         result.name = result.commonName ? result.scientificName ? "${result.scientificName} (${result.commonName})" : result.commonName : result.scientificName
-
-        // record is only created if guid is present
-        result.guid = result.guid ?: Record.UNMATCHED_GUID
+        List specialCases = grailsApplication.config.getProperty("paratoo.species.specialCases", List)
+        // do not create record for special cases
+        if (specialCases.contains(name)) {
+            result.remove("guid")
+        }
+        else {
+            // record is only created if guid is present
+            result.guid = result.guid ?: Record.UNMATCHED_GUID
+        }
         result
     }
 }
diff --git a/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy b/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
index 83f2c4f5c..046dade64 100644
--- a/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
+++ b/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
@@ -44,6 +44,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         setupData()
 
         grailsApplication.config.paratoo.location.excluded = ['location.vegetation-association-nvis']
+        grailsApplication.config.paratoo.species.specialCase = ["Other"]
         service.grailsApplication = grailsApplication
         service.webService = webService
         service.siteService = siteService
@@ -729,6 +730,17 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         result == [name: "Frogs", scientificName: "", guid: "A_GUID", commonName: "Frogs", taxonRank: "Class"]
         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: null, commonName: "Other", taxonRank: null]
+        1 * speciesReMatchService.searchByName(_) >> null
+        1 * speciesReMatchService.searchByName(_, false, true) >> null
+
     }
 
     void "buildTreeFromParentChildRelationships should build tree correctly"() {

From 50d4752e4c3af44283398dc29ced31a4086d36e9 Mon Sep 17 00:00:00 2001
From: temi <temi.varghese@csiro.au>
Date: Fri, 31 May 2024 07:06:09 +1000
Subject: [PATCH 3/3] #965 - adding N/A

---
 grails-app/conf/application.groovy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/grails-app/conf/application.groovy b/grails-app/conf/application.groovy
index 3c186a923..1abd9646f 100644
--- a/grails-app/conf/application.groovy
+++ b/grails-app/conf/application.groovy
@@ -1490,4 +1490,4 @@ paratoo.defaultPlotLayoutViewModels = [
                         ]
                 ]
         ]
-paratoo.species.specialCases = ["Other"]
+paratoo.species.specialCases = ["Other", "N/A"]