Merge branch 'develop'

AtlasOfLivingAustralia · Aug 17, 2021 · 13c698b · 13c698b
2 parents cddc05b + 4ab83e5
commit 13c698b
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Showing 21 changed files with 322 additions and 56 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -8,6 +8,7 @@ branches:
   only:
   - master
   - dev
+  - develop
   - /^feature\/.*$/
   - /^hotfix\/.*$/
 before_cache:

diff --git a/build.gradle b/build.gradle
@@ -15,7 +15,7 @@ buildscript {
 plugins {
     id 'war'
 }
-version "5.2"
+version "5.2.1-SNAPSHOT"
 
 group "au.org.ala"
 
@@ -107,7 +107,7 @@ dependencies {
 
     if (!inplace) {
         compile "org.grails.plugins:ala-map-plugin:3.0"
-        compile "org.grails.plugins:ecodata-client-plugin:3.0.5"
+        compile "org.grails.plugins:ecodata-client-plugin:3.1"
     }
 }
 

diff --git a/grails-app/assets/javascripts/chartjsManager.js b/grails-app/assets/javascripts/chartjsManager.js
@@ -11,7 +11,14 @@ function ChartjsManagerViewModel() {
      * Whether to show the list of charts.
      */
     self.chartjsListShow = ko.computed(function () {
-        return self.chartjsList().length > 0;
+        var ifChartjsListShow = self.chartjsList().length > 0
+        if(ifChartjsListShow){
+            $('#chartGraphTab').show()
+        }
+        else {
+            $('#chartGraphTab').hide()
+        }
+        return ifChartjsListShow;
     });
 
     /**

diff --git a/grails-app/assets/javascripts/facets.js b/grails-app/assets/javascripts/facets.js
@@ -926,6 +926,9 @@ function decodeCamelCase(text) {
         var result = text.replace( /([A-Z])/g, " $1" );
         return result.charAt(0).toUpperCase() + result.slice(1); // capitalize the first letter - as an example.
     }
+    else{
+        return text
+    }
 }
 
 function cleanName(text) {

diff --git a/grails-app/assets/javascripts/projectActivities.js b/grails-app/assets/javascripts/projectActivities.js
@@ -230,12 +230,8 @@ var ProjectActivitiesSettingsViewModel = function (pActivitiesVM, placeHolder) {
     };
 
     self.saveForm = function () {
-        return self.genericUpdate("form");
-    };
-
-    self.saveSpecies = function () {
         if(self.current().areSpeciesValid()) {
-            self.genericUpdate("species");
+            self.genericUpdate("form");
         } else {
             showAlert("All species field(s) must be configured before saving.", "alert-error", self.placeHolder);
         }

diff --git a/grails-app/assets/javascripts/projectActivity.js b/grails-app/assets/javascripts/projectActivity.js
@@ -687,6 +687,9 @@ var ProjectActivity = function (params) {
         if (by == "form") {
             jsData = {};
             jsData.pActivityFormName = self.pActivityFormName();
+            jsData.speciesFields = $.map(self.speciesFields(), function (obj, i) {
+                return obj.asJson();
+            });
         }
         else if (by == "info") {
             var ignore = self.ignore.concat(['current',
@@ -698,13 +701,6 @@ var ProjectActivity = function (params) {
             jsData = ko.mapping.toJS(self, {ignore: ignore});
             jsData.endDate = moment(self.endDate(), 'YYYY-MM-DDThh:mm:ssZ').isValid() ? self.endDate() : "";
         }
-        else if (by == "species") {
-            jsData = {};
-
-            jsData.speciesFields = $.map(self.speciesFields(), function (obj, i) {
-                return obj.asJson();
-            });
-        }
         else if (by == "sites") {
             jsData = {};
             var sites = [];

diff --git a/grails-app/conf/application.groovy b/grails-app/conf/application.groovy
@@ -512,4 +512,8 @@ if(!map.overlays) {
         ]
 }
 
-settings.surveyMethods="fielddata.survey.methods"
+settings.surveyMethods="fielddata.survey.methods"
+if (!app.file.script.path) {
+        app.file.script.path = "/data/biocollect/scripts"
+}
+script.read.extensions.list = ['js','min.js','png']
diff --git a/grails-app/controllers/au/org/ala/biocollect/BioActivityController.groovy b/grails-app/controllers/au/org/ala/biocollect/BioActivityController.groovy
@@ -2,6 +2,7 @@ package au.org.ala.biocollect
 
 import au.org.ala.biocollect.merit.*
 import au.org.ala.biocollect.merit.hub.HubSettings
+import au.org.ala.ecodata.forms.ActivityFormService
 import au.org.ala.web.AuthService
 import au.org.ala.web.UserDetails
 import grails.converters.JSON
@@ -33,6 +34,7 @@ class BioActivityController {
     SettingService settingService
     AuthService authService
     UtilService utilService
+    ActivityFormService activityFormService
 
     static int MAX_FLIMIT = 500
     static allowedMethods = ['bulkDelete': 'POST', bulkRelease: 'POST', bulkEmbargo: 'POST']
@@ -883,10 +885,8 @@ class BioActivityController {
     }
 
     def addOutputModel(model) {
-        model.metaModel = metadataService.getActivityModel(model.activity.type)
-        model.outputModels = model.metaModel?.outputs?.collectEntries {
-            [it, metadataService.getDataModelFromOutputName(it)]
-        }
+        model.putAll(activityFormService.getActivityAndOutputMetadata(model.activity.type))
+        model
     }
 
     def defaultData

diff --git a/grails-app/controllers/au/org/ala/biocollect/DownloadController.groovy b/grails-app/controllers/au/org/ala/biocollect/DownloadController.groovy
@@ -3,6 +3,8 @@ package au.org.ala.biocollect
 import au.org.ala.biocollect.merit.CommonService
 import au.org.ala.biocollect.merit.UserService
 import au.org.ala.biocollect.merit.WebService
+import org.apache.commons.io.FilenameUtils
+
 class DownloadController {
 
     WebService webService
@@ -38,4 +40,50 @@ class DownloadController {
             }
         }
     }
+
+    /***
+     * This method is used to read custom Js files under /data/scripts directory.
+     * @return
+     */
+    def getScriptFile() {
+        if (params.filename && params.hub && params.model) {
+            log.debug("Script name: " + params.filename)
+            log.debug("Hub: " + params.hub)
+            log.debug("Model: " + params.model)
+            String filename = FilenameUtils.getName(params.filename)
+
+            if (filename != params.filename) {
+                response.status = 404
+                return
+            }
+
+            def extension = FilenameUtils.getExtension(params.filename)?.toLowerCase()
+            if (extension && !grailsApplication.config.script.read.extensions.list.contains(extension)){
+                response.status = 404
+                return
+            }
+
+            String path = "${grailsApplication.config.app.file.script.path}${File.separator}${params.hub}${File.separator}${params.model}${File.separator}${params.filename}"
+            log.debug("Script path: " + path)
+
+            File file = new File(path)
+
+            if (!file.exists()) {
+                response.status = 404
+                return null
+            }
+
+            if(extension == 'js' || extension == 'min.js') {
+                response.setContentType('text/javascript')
+            }
+            response.outputStream << new FileInputStream(file)
+            response.outputStream.flush()
+
+            return null
+
+        } else {
+            response.status = 400
+            render status:400, text: 'filename, hub or model is missing'
+        }
+    }
 }
diff --git a/grails-app/controllers/au/org/ala/biocollect/UrlMappings.groovy b/grails-app/controllers/au/org/ala/biocollect/UrlMappings.groovy
@@ -110,6 +110,7 @@ class UrlMappings {
                 }
                 "/download/file"(controller: "download", action: [GET: "file"])
                 "/download/$id"(controller: "download", action: [GET: "downloadProjectDataFile"])
+                "/download/getScriptFile"(controller: "download", action: [GET: "getScriptFile"])
                 "500"(controller:'error', action:'response500')
                 "404"(controller:'error', action:'response404')
 

diff --git a/grails-app/controllers/au/org/ala/biocollect/merit/ProxyController.groovy b/grails-app/controllers/au/org/ala/biocollect/merit/ProxyController.groovy
@@ -127,13 +127,17 @@ class ProxyController {
     def excelOutputTemplate() {
         String url =  "${grailsApplication.config.ecodata.service.url}/metadata/excelOutputTemplate"
         String expandList = params.expandList?:""
+        String listName = params.listName?:null
 
         if (params.data) {
             webService.proxyPostRequest(response, url,
                     [listName:params.listName, type:params.type, data:params.data, editMode:params.editMode, allowExtraRows:params.allowExtraRows, autosizeColumns:false, expandList: expandList])
         }
         else {
-            url += "?type=${params.type?.encodeAsURL()}&listName=${params.listName?.encodeAsURL()}&listName=${expandList?.encodeAsURL()}"
+            url += "?type=${params.type?.encodeAsURL()}&expandList=${expandList?.encodeAsURL()}"
+            if(listName){
+                url += "&listName=${params.listName.encodeAsURL()}"
+            }
             webService.proxyGetRequest(response, url)
         }
 

diff --git a/grails-app/i18n/messages.properties b/grails-app/i18n/messages.properties
@@ -691,7 +691,7 @@ project.myrecords.title=My sightings
 project.userrecords.title=Sightings of
 allrecords.title=All records
 myrecords.title=My records
-record.create.title=Record a sighting
+record.create.title=Create a record
 record.edit.title=Edit a sighting
 record.view.title=View a sighting
 record.edit.map.latLon=Latitude/longitude

diff --git a/grails-app/services/au/org/ala/biocollect/merit/FormSpeciesFieldParserService.groovy b/grails-app/services/au/org/ala/biocollect/merit/FormSpeciesFieldParserService.groovy
@@ -1,7 +1,10 @@
 package au.org.ala.biocollect.merit
 
+import au.org.ala.ecodata.forms.ActivityFormService
+
 class FormSpeciesFieldParserService {
     MetadataService metadataService
+    ActivityFormService activityFormService
 
     /**
      * Get the list of species fields, for the specified survey, grouped by outputs
@@ -13,15 +16,7 @@ class FormSpeciesFieldParserService {
      * @return the list of species fields
      */
     Map getSpeciesFieldsForSurvey(String id) {
-        def model = [:]
-
-        // the activity meta-model
-        model.metaModel = metadataService.getActivityModel(id)
-        // the array of output models
-        model.outputModels = model.metaModel?.outputs?.collectEntries {
-            [it, metadataService.getDataModelFromOutputName(it)]
-        }
-
+        def model = activityFormService.getActivityAndOutputMetadata(id)
 
         def fields = []
 

diff --git a/grails-app/services/au/org/ala/biocollect/merit/MetadataService.groovy b/grails-app/services/au/org/ala/biocollect/merit/MetadataService.groovy
@@ -205,7 +205,7 @@ class MetadataService {
 
 
     def clearEcodataCache() {
-        webService.get(grailsApplication.config.ecodata.service.url + "/admin/clearMetadataCache")
+        webService.doGet(grailsApplication.config.ecodata.service.url + "/admin/clearMetadataCache" , null)
     }
 
     def outputTypesList() {

diff --git a/grails-app/services/au/org/ala/biocollect/merit/SpeciesService.groovy b/grails-app/services/au/org/ala/biocollect/merit/SpeciesService.groovy
@@ -154,30 +154,14 @@ class SpeciesService {
 
     def searchSpeciesList(String sort = 'listName', Integer max = 100, Integer offset = 0, String guid = null, String order = "asc", String searchTerm = null) {
         def list
-        String url = "${grailsApplication.config.lists.baseURL}/ws/speciesList?sort=${sort}&max=${max}&offset=${offset}&order=${order}"
+        String url = "${grailsApplication.config.lists.baseURL}/ws/speciesList?sort=${sort}&max=${max}&offset=${offset}&order=${order}&q=${searchTerm?:''}"
 
-        if (!guid & !searchTerm) {
+        if (!guid) {
             list = webService.getJson(url)
         } else {
-            if (guid) {
-                // Search List by species in the list
-                url = "${url}&items=createAlias:items&items.guid=eq:${guid}"
-                list = webService.getJson(url)
-            }
-            if (searchTerm) {
-                // Search list by list name
-                def searchList = getAllSpeciesList()
-                def toLowerSearchTerm = searchTerm.toLowerCase()
-                // remove list that don't match the name
-                searchList.lists.removeAll { !(it.listName.toLowerCase() =~ /\A${toLowerSearchTerm}/) }
-                if (list) {
-                    list.lists.addAll(searchList.lists)
-                } else {
-                    list = searchList
-                }
-                list.lists.unique()
-                list.listCount = list.lists.size()
-            }
+            // Search List by species in the list
+            url = "${url}&items=createAlias:items&items.guid=eq:${guid}"
+            list = webService.getJson(url)
         }
 
         list

diff --git a/grails-app/views/projectActivity/_species.gsp b/grails-app/views/projectActivity/_species.gsp
@@ -85,7 +85,7 @@
 
                 <div class="span12">
                     <button class="btn-primary btn block btn-small"
-                            data-bind="click: $parent.saveSpecies"><i class="icon-white  icon-hdd" ></i>Save</button>
+                            data-bind="click: $parent.saveForm"><i class="icon-white  icon-hdd" ></i>Save</button>
                     <button class="btn-primary btn btn-small block" data-bind="showTabOrRedirect: {url:'', tabId: '#survey-form-tab'}"><i class="icon-white icon-chevron-left" ></i>Back</button>
                     <button class="btn-primary btn btn-small block" data-bind="showTabOrRedirect: {url:'', tabId: '#survey-locations-tab'}">Next <i class="icon-white icon-chevron-right" ></i></button>
                 </div>

diff --git a/src/test/groovy/au/org/ala/biocollect/DownloadControllerSpec.groovy b/src/test/groovy/au/org/ala/biocollect/DownloadControllerSpec.groovy
@@ -0,0 +1,84 @@
+package au.org.ala.biocollect
+
+import grails.test.mixin.TestFor
+import org.apache.http.HttpStatus
+import spock.lang.Specification
+
+@TestFor(DownloadController)
+class DownloadControllerSpec extends Specification {
+
+    File scriptsPath
+    File temp
+    File hubPath
+    File modelPath
+
+    void setup() {
+
+        temp = File.createTempDir("tmp", "")
+        scriptsPath = new File(temp, "scripts")
+        scriptsPath.mkdir()
+        hubPath = new File(scriptsPath, "tempHub")
+        hubPath.mkdir()
+        modelPath = new File(hubPath, "tempModel")
+        modelPath.mkdir()
+
+        controller.grailsApplication.config.app.file.script.path = scriptsPath.getAbsolutePath()
+
+        // Setup three files, one that should be accessible, and others that should not
+        File validFile =  new File(modelPath, "validFile.js")
+        validFile.createNewFile()
+
+        File jsonFile =  new File(modelPath, "validFile.json")
+        jsonFile.createNewFile()
+
+        File privateFile = new File(temp, "privateFile.js")
+        privateFile.createNewFile()
+    }
+
+    void "Files can be retrieved from the temporary scripts directory by filename"() {
+        when:
+        params.hub = "tempHub"
+        params.filename = "validFile.js"
+        params.model = "tempModel"
+        controller.getScriptFile()
+
+        then:
+        response.contentType == "text/javascript"
+        response.status == HttpStatus.SC_OK
+    }
+
+    void "If a file doesn't exist, a 404 will be returned"() {
+        when:
+        params.hub = "tempHub"
+        params.filename = "missingFile.js"
+        params.model = "tempModel"
+        controller.getScriptFile()
+
+        then:
+        response.status == HttpStatus.SC_NOT_FOUND
+    }
+
+    void "A file cannot be retrieved from outside the designated scripts directory"() {
+        when:
+        params.hub = "tempHub"
+        params.filename = "../../../privateFile.js"
+        params.model = "tempModel"
+        controller.getScriptFile()
+
+        then:
+        new File(modelPath, params.filename).exists()
+        response.status == HttpStatus.SC_NOT_FOUND
+    }
+
+    void "Tyring to read a file with extension which are not allowed to read"() {
+        when:
+        params.hub = "tempHub"
+        params.filename = "validFile.json"
+        params.model = "tempModel"
+        controller.getScriptFile()
+
+        then:
+        new File(modelPath, params.filename).exists()
+        response.status == HttpStatus.SC_NOT_FOUND
+    }
+}