Merge branch 'dev'

gradle.properties

@@ -5,7 +5,7 @@ groovyVersion=3.0.11
 mongodbDriverVersion=4.5.1
 grailsGradlePluginVersion=5.2.3
 gormMongoVersion=7.3.0
-alaSecurityLibsVersion=6.0.0
+alaSecurityLibsVersion=6.2.0
 org.gradle.daemon=true
 org.gradle.parallel=true
 org.gradle.jvmargs=-Dfile.encoding=UTF-8 -Xmx1024M

grails-app/conf/application.groovy

@@ -161,3 +161,13 @@ elasticSearch {
     maxBulkRequest = 250
 }
 
+attachement {
+    categories = [
+                  [key:"General", value:"General"],
+                  [key:"Management", value:"Management"],
+                  [key:"National Best Practice Manual", value:"National Best Practice Manual"],
+                  [key:"National Strategic Plan", value:"National Strategic Plan"],
+                  [key:"National Weed Management Guide", value:"National Weed Management Guide"],
+                  [key:"Other Management Resources", value:"Other Management Resources"]
+    ]
+}

grails-app/controllers/au/org/ala/profile/OpusController.groovy

@@ -438,6 +438,11 @@ class OpusController extends BaseController {
         }
     }
 
+    def getCategories() {
+        def categories = grailsApplication.config.getProperty('attachement.categories', List)
+        render(categories as JSON)
+    }
+
     def getTags() {
         render([tags: Tag.list()] as JSON)
     }

grails-app/controllers/au/org/ala/profile/UrlMappings.groovy

@@ -54,6 +54,7 @@ class UrlMappings {
         "/opus/$opusId/attachment/$attachmentId/download" controller: "opus", action: [GET: "downloadAttachment"]
         "/opus/$opusId/attachment/$attachmentId" controller: "opus", action: [GET: "getAttachmentMetadata", DELETE: "deleteAttachment"]
         "/opus/$opusId/attachment/" controller: "opus", action: [GET: "getAttachmentMetadata", POST: "saveAttachment"]
+        "/attachment/categories" controller: "opus", action: [GET: "getCategories"]
 
         "/opus/$opusId" controller: "opus", action: [GET: "show", POST: "updateOpus", DELETE: "deleteOpus"]
 
@@ -99,8 +100,7 @@ class UrlMappings {
         "/opus/$opusId/profile/$profileId/specimen" controller: "profile", action: [POST: "saveSpecimens"]
 
         "/opus/$opusId/profile/$profileId/classification" controller: "profile", action: [GET: "classification"]
-
-        "/opus/$opusId/profile/$profileId/publication" controller: "profile", action: [GET: "listPublications", POST: "savePublication"]
+        "/opus/$opusId/profile/$profileId/publication" controller: "profile", action: [GET: "listPublications"]
         "/opus/$opusId/profile/$profileId/publication/$publicationId/file" controller: "profile", action: [GET: "getPublicationFile"]
 
         "/opus/$opusId/profile/$profileId/profileSettings" controller: "profile", action: [GET: "getProfileSettings", POST: "saveProfileSettings"]

grails-app/domain/au/org/ala/profile/Attachment.groovy

@@ -39,6 +39,6 @@ class Attachment {
     }
 
     static constraints = {
-        category blank: true,  inList: ['Management', 'General']
+        category blank: true,  validator: {grailsApplication.config.getProperty('attachement.categories',List).value.contains(val)}
     }
 }

grails-app/services/au/org/ala/profile/OpusService.groovy

@@ -72,6 +72,8 @@ class OpusService extends BaseDataAccessService {
                 opus.markDirty('approvedLists')
             }
             opus.approvedLists.addAll(json.approvedLists)
+        } else {
+            opus.approvedLists.removeAll(opus.approvedLists)
         }
 
         if (json.featureLists) {
@@ -82,6 +84,8 @@ class OpusService extends BaseDataAccessService {
                 opus.markDirty('featureLists')
             }
             opus.featureLists.addAll(json.featureLists)
+        } else {
+            opus.featureLists.removeAll(opus.featureLists)
         }
         opus.featureListSectionName = json.featureListSectionName ? json.featureListSectionName : null;
 

grails-app/services/au/org/ala/profile/SearchService.groovy

@@ -49,16 +49,16 @@ class SearchService extends BaseDataAccessService {
 
     Map search(List<String> opusIds, String term, int offset, int pageSize, SearchOptions options) {
         log.debug("Searching for ${term} in collection(s) ${opusIds} with options ${options}")
-
-        List<Opus> opusList = getAccessibleCollections(opusIds)
+        List<Opus> opusList = getAccessibleCollections(opusIds, isAlaAdmin())
         String[] accessibleCollections = opusList?.collect { it.uuid } as String[]
+        boolean isAccessible = alaAdmin? true : (accessibleCollections? true : false)
         List<Vocab> vocabs = Vocab.findAllByUuidInList(opusList*.attributeVocabUuid)
         String[] summaryTerms = Term.findAllByVocabInListAndSummary(vocabs, true)*.uuid
         String[] nameTerms = Term.findAllByVocabInListAndContainsName(vocabs, true)*.uuid
         Map<String, List<String>> filterLists = opusList.collectEntries { [(it.uuid) : masterListService.getCombinedLowerCaseNamesListForUser(it) ]}
 
         Map results = [:]
-        if (accessibleCollections) {
+        if (isAccessible) {
             Map params = [
                     indices:  Profile,
                     types: Profile,
@@ -123,6 +123,11 @@ class SearchService extends BaseDataAccessService {
         results
     }
 
+    private boolean isAlaAdmin() {
+        boolean alaAdmin = userService.userInRole("ROLE_ADMIN")
+        return alaAdmin
+    }
+
     private Map getProfileMatchReason (String term, Profile profile, Map nslResult) {
         Map matchReason = [:]
         if (profile.scientificNameLower == term.toLowerCase()) {
@@ -287,7 +292,7 @@ class SearchService extends BaseDataAccessService {
             wildcard = '\\s*$' // regex end of line to ensure full word matching
         }
 
-        List<Opus> accessibleCollections = getAccessibleCollections(opusIds)
+        List<Opus> accessibleCollections = getAccessibleCollections(opusIds, isAlaAdmin())
         Map<Long, Opus> opusMap = accessibleCollections?.collectEntries { [(it.id): it] }
 
         if (max == -1) {
@@ -729,11 +734,10 @@ class SearchService extends BaseDataAccessService {
         match
     }
 
-    private List<Opus> getAccessibleCollections(List<String> opusIds) {
+    private List<Opus> getAccessibleCollections(List<String> opusIds, boolean alaAdmin) {
         List<Opus> opusList = opusIds?.findResults { Opus.findByUuidOrShortName(it, it) }
 
         // search results from private collections can only be seen by ALA Admins or users registered with the collection
-        boolean alaAdmin = userService.userInRole("ROLE_ADMIN")
         String userId = userService.getCurrentUserDetails()?.userId
 
         // if the user is ala admin, do nothing
@@ -746,6 +750,8 @@ class SearchService extends BaseDataAccessService {
             filteredOpusList = (opusList ?: Opus.list()).findAll {
                 !it?.privateCollection || it?.authorities?.find { auth -> auth.user.userId == userId }
             }
+        } else if (alaAdmin && !opusList) {
+            filteredOpusList = Opus.list()
         }
 
         filteredOpusList

src/integration-test/groovy/au/org/ala/profile/OpusServiceSpec.groovy

@@ -7,6 +7,7 @@ import au.org.ala.web.UserDetails
 import grails.gorm.transactions.Rollback
 import grails.gsp.PageRenderer
 import grails.testing.mixin.integration.Integration
+import net.sf.json.JSONObject
 import org.springframework.beans.factory.annotation.Autowired
 import org.springframework.web.multipart.commons.CommonsMultipartFile
 
@@ -271,4 +272,92 @@ class OpusServiceSpec extends BaseIntegrationSpec {
         1 * service.attachmentService.saveAttachment(_, _, _, _, _)
         0 * service.attachmentService.deleteAttachment(_, _, _, _)
     }
-}
+
+    def "update opus for approved lists"() {
+        given:
+        Opus opus1 = new Opus(title: "opus1", dataResourceUid: "123", glossary: new Glossary(), approvedLists: ["dr123", "dr345"])
+
+        def opus2 = [
+                title         : "opus1",
+                dataResourceUid      : "123",
+                approvedLists        : ["dr123"],
+        ]
+
+
+        JSONObject json1 = new JSONObject(opus2)
+        save opus1
+
+        when:
+        Opus updateOpus = service.updateOpus(opus1.uuid, json1)
+
+        then:
+        updateOpus.approvedLists.size() == json1.approvedLists.size()
+    }
+
+    def "update opus for featured lists"() {
+        given:
+        Opus opus1 = new Opus(title: "opus1", dataResourceUid: "123", glossary: new Glossary(), featureLists: ["dr123", "dr345", "dr678"])
+
+        def opus2 = [
+                title         : "opus1",
+                dataResourceUid      : "123",
+                featureLists        : ["dr345"],
+        ]
+
+
+        JSONObject json1 = new JSONObject(opus2)
+        save opus1
+
+        when:
+        Opus updateOpus = service.updateOpus(opus1.uuid, json1)
+
+        then:
+        updateOpus.featureLists.size() == json1.featureLists.size()
+    }
+
+    def "update opus for approved lists and feature lists"() {
+        given:
+        Opus opus1 = new Opus(title: "opus1", dataResourceUid: "123", glossary: new Glossary(), approvedLists: ["dr123", "dr345"], featureLists: ["fl123","fl456","fl789"])
+
+        def opus2 = [
+                title         : "opus1",
+                dataResourceUid      : "123",
+                approvedLists        : ["dr123"],
+                featureLists         : ["fl123", "fl456"]
+         ]
+
+
+        JSONObject json1 = new JSONObject(opus2)
+        save opus1
+
+        when:
+        Opus updateOpus = service.updateOpus(opus1.uuid, json1)
+
+        then:
+        updateOpus.approvedLists.size() == json1.approvedLists.size()
+        updateOpus.featureLists.size() == json1.featureLists.size()
+    }
+
+    def "update opus for approved lists and feature lists are empty"() {
+        given:
+        Opus opus1 = new Opus(title: "opus1", dataResourceUid: "123", glossary: new Glossary(), approvedLists: [], featureLists: [])
+
+        def opus2 = [
+                title         : "opus1",
+                dataResourceUid      : "123",
+                approvedLists        : [],
+                featureLists         : []
+        ]
+
+
+        JSONObject json1 = new JSONObject(opus2)
+        save opus1
+
+        when:
+        Opus updateOpus = service.updateOpus(opus1.uuid, json1)
+
+        then:
+        updateOpus.approvedLists.size() == json1.approvedLists.size()
+        updateOpus.featureLists.size() == json1.featureLists.size()
+    }
+}

src/scripts/mangrove-watch-images/package.json

@@ -1,7 +1,7 @@
 {
   "name": "profiles-image-upload",
   "dependencies": {
-    "axios": "^1.4.0",
+    "axios": "^1.6.0",
     "csvtojson": "^2.0.10",
     "form-data": "^4.0.0",
     "yargs": "^17.7.2"