Merge branch 'release/1.9.10'

CollectoryGrailsPlugin.groovy

@@ -9,7 +9,7 @@ class CollectoryGrailsPlugin {
     def authenticateService
 
     // the plugin version
-    def version = "1.9.9"
+    def version = "1.9.10"
     // the version or versions of Grails the plugin is designed for
     def grailsVersion = "2.5 > *"
     // resources that are excluded from plugin packaging

grails-app/controllers/au/org/ala/collectory/DataController.groovy

@@ -176,6 +176,24 @@ class DataController {
         render(status:403, text: 'You are not authorised to use this service')
     }
 
+    def checkApiKey = {
+        def apiKey = {
+            if(params.api_key){
+                params.api_key
+            } else {
+                request.getHeader("Authorization")
+            }
+        }.call()
+        def keyCheck
+        if (apiKey) {
+            keyCheck = collectoryAuthService?.checkApiKey(apiKey)
+        }
+        if (!keyCheck?.valid) {
+            return false
+        }
+        return true
+    }
+
     /**
      * Should be added for any uri that returns multiple formats based on content negotiation.
      * (So the content can be correctly cached by proxies.)
@@ -306,6 +324,7 @@ class DataController {
      * @param uid - optional uid of an instance of entity
      * @param pg - optional instance specified by uid (added in beforeInterceptor)
      * @param summary - any non-null value will cause a richer summary to be returned for entity lists
+     * @param api_key - optional param for displaying any sensitive data
      */
     def getEntity = {
         if (params.entity == 'tempDataResource') {
@@ -317,7 +336,13 @@ class DataController {
                 // return specified entity
                 addContentLocation "/ws/${urlForm}/${params.pg.uid}"
                 def eTag = (params.pg.uid + ":" + params.pg.lastUpdated).encodeAsMD5()
-                def entityInJson = crudService."read${clazz}"(params.pg)
+                def entityInJson
+                if (clazz == 'DataResource') {
+                    def keyCheck = checkApiKey()
+                    entityInJson = crudService."read${clazz}"(params.pg, keyCheck)
+                } else {
+                    entityInJson = crudService."read${clazz}"(params.pg)
+                }
                 entityInJson = metadataService.convertAnyLocalPaths(entityInJson)
                 response.setContentType("application/json")
                 response.setCharacterEncoding("UTF-8")
@@ -602,10 +627,16 @@ class DataController {
 
     /**
      * Returns a single contact (independent of any entity).
+     * A valid api key is needed to display contact information
      * URI form: /contacts/{id}
      * @param id the database id of the contact
      */
     def contacts = {
+
+        if (!checkApiKey()) {
+            unauthorised()
+            return
+        }
         if (params.id) {
             def c = Contact.get(params.id)
             if (c) {

grails-app/controllers/au/org/ala/collectory/IptController.groovy

@@ -39,6 +39,7 @@ class IptController {
         def create = params.create != null && params.create.equalsIgnoreCase("true")
         def check = params.check == null || !params.check.equalsIgnoreCase("false")
         def keyName = params.key ?: 'catalogNumber'
+        def isShareableWithGBIF = params.isShareableWithGBIF ? params.isShareableWithGBIF.toBoolean(): true
         def provider = ProviderGroup._get(params.uid)
         def apiKey = request.cookies.find { cookie -> cookie.name == API_KEY_COOKIE }
         def keyCheck = apiKey ? collectoryAuthService.checkApiKey(apiKey.value) : null
@@ -55,7 +56,7 @@ class IptController {
             return
         }
         try {
-            def updates = provider == null ? null : iptService.scan(provider, create, check, keyName, username, admin)
+            def updates = provider == null ? null : iptService.scan(provider, create, check, keyName, username, admin, isShareableWithGBIF)
             log.info "${updates.size()} data resources to update for ${params.uid}"
             response.addHeader HttpHeaders.VARY, HttpHeaders.ACCEPT
             withFormat {

grails-app/services/au/org/ala/collectory/CrudService.groovy

@@ -40,7 +40,7 @@ class CrudService {
     ]
     static dataResourceNumberProperties = ['harvestFrequency','downloadLimit']
     static dataResourceTimestampProperties = ['lastChecked','dataCurrency']
-    static dataResourceBooleanProperties = ['gbifDataset']
+    static dataResourceBooleanProperties = ['gbifDataset', 'isShareableWithGBIF']
     static dataResourceJSONArrays = ['connectionParameters', 'contentTypes', 'defaultDarwinCoreValues', 'imageMetadata']
     //static dataResourceObjectProperties = ['dataProvider']
 
@@ -269,7 +269,7 @@ class CrudService {
 
     /* data resource */
 
-    def readDataResource(DataResource p) {
+    def readDataResource(DataResource p, apiKey = null) {
         def builder = new JSONBuilder()
 
         def result = builder.build {
@@ -351,7 +351,7 @@ class CrudService {
                 if (p.listConsumers()) {
                     linkedRecordConsumers = p.listConsumers().formatEntitiesFromUids()
                 }
-                if (p.connectionParameters) {
+                if (p.connectionParameters && apiKey) {
                     connectionParameters = p.connectionParameters.formatJSON()
                 }
                 if (p.imageMetadata) {

grails-app/services/au/org/ala/collectory/IptService.groovy

@@ -81,9 +81,9 @@ class IptService {
      * @return A list of data resources that need re-loading
      */
     @org.springframework.transaction.annotation.Transactional(propagation = org.springframework.transaction.annotation.Propagation.REQUIRED)
-    def scan(DataProvider provider, boolean create, boolean check, String keyName, String username, boolean admin) {
+    def scan(DataProvider provider, boolean create, boolean check, String keyName, String username, boolean admin, boolean shareWithGbif) {
         ActivityLog.log username, admin, provider.uid, Action.SCAN
-        def updates = this.rss(provider, keyName)
+        def updates = this.rss(provider, keyName, shareWithGbif)
 
         return merge(provider, updates, create, check, username, admin)
     }
@@ -166,7 +166,7 @@ class IptService {
      *
      * @return A list of (possibly new providers)
      */
-    def rss(DataProvider provider, String keyName) {
+    def rss(DataProvider provider, String keyName, Boolean isShareableWithGBIF) {
 
         def url = provider.websiteUrl
         if(!url.endsWith("/")){
@@ -180,7 +180,7 @@ class IptService {
         rss.declareNamespace(NAMESPACES)
         def items = rss.channel.item
 
-        return items.collect { item -> this.createDataResource(provider, item, keyName) }
+        return items.collect { item -> this.createDataResource(provider, item, keyName, isShareableWithGBIF) }
     }
 
     /**
@@ -192,7 +192,7 @@ class IptService {
      *
      * @return A created resource matching the information provided
      */
-    def createDataResource(DataProvider provider, GPathResult rssItem, String keyName) {
+    def createDataResource(DataProvider provider, GPathResult rssItem, String keyName, Boolean isShareableWithGBIF) {
         def resource = new DataResource()
         def eml = rssItem."ipt:eml"?.text()
         def dwca = rssItem."ipt:dwca"?.text()
@@ -201,6 +201,7 @@ class IptService {
         rssFields.each { name, accessor -> resource.setProperty(name, accessor(rssItem))}
 
         resource.connectionParameters =  dwca == null || dwca.isEmpty() ? null : "{ \"protocol\": \"DwCA\", \"url\": \"${dwca}\", \"automation\": true, \"termsForUniqueKey\": [ \"${keyName}\" ] }";
+        resource.isShareableWithGBIF = isShareableWithGBIF
 
         def contacts = []
         if (eml != null) {

web-app/js/taxonTree.js

@@ -158,6 +158,5 @@ function showBie(node) {
     if (rank == 'kingdoms') return;
     var name = node.attr('id');
     var sppUrl = CHARTS_CONFIG.bieWebappUrl + "/species/" + name;
-    if (rank != 'species') { sppUrl += "_(" + rank + ")"; }
     document.location.href = sppUrl;
 }