Merge pull request #196 from AtlasOfLivingAustralia/experimental/bulk-annotations

Work for #195 and #194

Author: sughics

Diff for: grails-app/conf/application.yml

@@ -245,6 +245,8 @@ dataResource:
         - "document"
         - "uploads"
         - "species-list"
+        - "publications"
+        - "events"
     permissionsDocumentTypes:
         - ""
         - "Email"

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

@@ -500,7 +500,7 @@ class DataController {
 
         // suppress 'declined' data resources
         if (urlForm == 'dataResource' && params.public == "true") {
-            list = list.findAll { it.status != 'declined' }
+            list = list.findAll { it.status != 'declined' && it.isPrivate == false }
         }
 
         // init results with total

Diff for: grails-app/controllers/au/org/ala/collectory/PublicController.groovy

@@ -464,6 +464,9 @@ class PublicController {
         else if (instance.status == "declined") {
             render "This resource has decided to not contribute to the Atlas."
         }
+        else if (instance.isPrivate) {
+            render "This resource is private."
+        }
         else {
             def suitableFor = providerGroupService.getSuitableFor()
             activityLogService.log collectoryAuthService?.username(), collectoryAuthService?.userInRole(grailsApplication.config.ROLE_ADMIN), instance.uid, Action.VIEW
@@ -527,15 +530,15 @@ class PublicController {
     def dataSets = {}
 
     def dataSetSearch = {
-        def drs = DataResource.findAllByNameLikeAndStatusNotEqual('%' + params.q + '%', 'declined').collect {
+        def drs = DataResource.findAllByNameLikeAndStatusNotEqualAndIsPrivate('%' + params.q + '%', 'declined', false).collect {
            it.uid
         }
         render drs as JSON
     }
 
     def resources = {
         cache shared:true, validFor: 3600*24
-        def drs = DataResource.findAllByStatusNotEqual('declined', [sort:'name']).collect {
+        def drs = DataResource.findAllByStatusNotEqualAndIsPrivate('declined', false, [sort:'name']).collect {
         //def drs = DataResource.list([sort:'name']).collect {
             def pdesc = it.pubDescription ? cl.formattedText(dummy:'1',limit(it.pubDescription,1000)) : ""
             def tdesc = it.techDescription ? cl.formattedText(dummy:'1',limit(it.techDescription,1000)) : ""
@@ -551,7 +554,7 @@ class PublicController {
     }
 
     def condensed = {
-        def drs = DataResource.findAllByStatusNotEqual('declined',  [sort:'name'] ).collect {
+        def drs = DataResource.findAllByStatusNotEqualAndIsPrivate('declined', false, [sort:'name'] ).collect {
             //def drs = DataResource.list([sort:'name']).collect {
             def inst = it.institution
             def instName = (inst && inst.name.size() > 36 && inst.acronym) ? inst.acronym : inst?.name

Diff for: grails-app/i18n/messages.properties

@@ -22,7 +22,7 @@ public.chart.radio.onf=Other named facet
 public.chart.radio.el=Environmental layer
 
 public.datasets.title=Datasets
-public.datasets.header.title.param={0} data sets
+public.datasets.header.title.param={0} datasets
 public.datasets.header.message.param=Much of the content in the {0}, such as occurrence records, environmental data, images and the conservation status of species, comes from data sets provided by collecting institutions, individual collectors and community groups. These data sets are listed on this page.
 public.datasets.header.message03=Refine the list of data sets by clicking on a filter in the left hand list. Click the
 public.datasets.header.message04=toggle to see a description of the data set. To find out more, go to the data set's full metadata page by clicking on its name
@@ -99,7 +99,7 @@ public.purpose=Purpose
 public.geographicDescription = Geographic Description
 public.methodStepDescription = Methods
 public.location=Location
-public.website=Web site
+public.website=Website
 public.numbrs.des01=Looking up... the number of records that
 public.numbrs.des02=can be accessed through the {0}
 public.numbrs.link=Click to view records for the
@@ -198,8 +198,10 @@ public.sdr.content.link01=Click to view records for the
 public.sdr.content.link02=resource
 public.sdr.content.label10=Map of records
 public.sdr.content.label12=Species lists
+public.sdr.content.label13=Publication details
 public.sdr.content.link03=View this species list in species list tool
 public.sdr.content.link04=Visit the data resource's website
+public.sdr.content.link05=Visit the publication's website
 public.sdr.infosourcelist.title=Contributors to this page
 public.sdr.externalIdentifiers.title=Other Identifiers
 
@@ -526,6 +528,7 @@ collection.acronym.label=Acronym
 collection.resourceType.label=Resource type
 collection.institution.label=Institution
 collection.gbifDoi.label=DOI
+collection.isPrivate.label=Is private ?
 dataprovider.gbif.country=GBIF Attribution
 
 dataResource.dataProvider.label=Data provider
@@ -1091,6 +1094,7 @@ dataresource.show.sor=Source of records
 dataresource.show.guid=GUID
 dataresource.show.doi=DOI
 dataresource.show.resourcetype=Resource type
+dataresource.show.isprivate=Is private
 dataresource.show.website=Website
 dataresource.show.dg=Data generalisations
 dataresource.show.iw=Information withheld
@@ -1710,7 +1714,6 @@ licence.url.list.label=URL
 licence.acronym.list.label=Acronym
 licence.version.list.label=Version
 licence.image.list.label=Image
-licence.name.label=Name
 licence.acronym.label=Acronym
 licence.version.label=Version
 licence.url.label=URL
@@ -1862,6 +1865,7 @@ metadata.last.updated=Metadata last updated on
 
 dataAccess.title=Data access
 dataAccess.view.records=View records
+dataAccess.view.annotated.records=View referenced records
 dataAccess.download.stats=Download usage stats
 dataAccess.download.records=Download records
 dataAccess.alert.records=Create an email alert for new records for
@@ -2109,9 +2113,6 @@ datasets.js.appendresource10=View records
 datasets.js.appendresource11=Website
 datasets.js.appendresource09=Content includes
 
-datasets.js.lastUpdated=Last updated
-datasets.js.numRecords=Records
-
 datasets.js.updatetotal03=Showing
 datasets.js.updatetotal04=data
 datasets.js.updatetotal05=set.
@@ -2251,6 +2252,9 @@ dataset.result.records = records
 dataset.result.species-list = species-list
 dataset.result.website = website
 dataset.result.document = document
+dataset.result.annotations = annotations
+dataset.result.events = events
+dataset.result.publications = publication
 public.datasets.search.btn.title=Only show data sets which contain the search term
 citations.available = citations for these data
 collectory.tag.lib.the.collection.was.established.in=The collection was established in {0} and ceased acquisitions in {1}.
@@ -2288,4 +2292,22 @@ collectory.tag.lib.states.covered.include=States covered include: {0}.
 public.show.collection.has.an.estimated=has an estimated {0} {1}
 public.show.percent.over=over 100
 images.available.count={0} images
-images.available.count.available=have been made available from the {0}.
+images.available.count.available=have been made available from the {0}.
+
+resourceType.publications.list=Publications
+resourceType.annotations.list=Annotations
+resourceType.records.list=Occurrences
+resourceType.events.list=Events
+resourceType.species-list.list=Species lists
+
+resourceType.publications=Publication
+resourceType.annotations=Annotations dataset
+resourceType.records=Occurrence dataset
+resourceType.events=Events based data
+resourceType.species-list=Species list
+
+resourceType.publications.description=This publication references data from other datasets (occurrence or event based datasets). It may also include some modifications to the data as it is presented by the Atlas.
+resourceType.annotations.description=This dataset references data from other datasets (occurrence or event based datasets). It may also include some modifications to the data as it is presented by the Atlas.
+resourceType.records.description=This dataset that contains primary occurrence data for species.
+resourceType.events.description=This dataset that contains event based data for species which may include sampling information
+resourceType.species-list.description=This dataset contains a list of species with an associated trait.

Diff for: grails-app/views/dataResource/show.gsp

@@ -34,7 +34,9 @@
                 <li class="btn btn-default"><span class="glyphicon glyphicon-plus"></span><g:link class="create" action="create"> <g:message code="default.new.label" args="[entityName]"/></g:link></li>
             </ul>
             <ul class="btn-group pull-right">
-                <li class="btn btn-default"><cl:viewPublicLink uid="${instance?.uid}"/></li>
+                <g:if test="${!instance?.isPrivate}">
+                    <li class="btn btn-default"><cl:viewPublicLink uid="${instance?.uid}"/></li>
+                </g:if>
                 <li class="btn btn-default"><cl:jsonSummaryLink uid="${instance.uid}"/></li>
                 <li class="btn btn-default"><cl:jsonDataLink uid="${instance.uid}"/></li>
                 <li class="btn btn-default"><cl:emlDataLink uid="${instance.uid}"/></li>
@@ -76,6 +78,10 @@
                 <!-- type -->
                 <p><span class="category"><g:message code="dataresource.show.resourcetype" />: </span> ${fieldValue(bean: instance, field: "resourceType")}</p>
 
+                <!-- is private -->
+                <p><span class="category"><g:message code="dataresource.show.isprivate" />: </span> ${fieldValue(bean: instance, field: "isPrivate")}</p>
+
+
                 <!-- Web site -->
                 <p><span class="category"><g:message code="dataresource.show.website" />: </span> <cl:externalLink href="${fieldValue(bean:instance, field:'websiteUrl')}"/></p>
 

Diff for: grails-app/views/public/_dataLinks.gsp

@@ -0,0 +1,8 @@
+<%@ page import="au.org.ala.collectory.CollectoryTagLib" %>
+<div class="public-metadata">
+    <h4><g:message code="dataAccess.title"/></h4>
+    <div class="dataAccess btn-group-vertical">
+        <a href="${grailsApplication.config.biocacheUiURL}/occurrences/search?fq=annotationsUid:${instance.uid}" class="btn btn-default">
+            <i class="glyphicon glyphicon-list"></i> <g:message code="dataAccess.view.annotated.records"/></a>
+    </div>
+</div>

Diff for: grails-app/views/public/showDataResource.gsp

@@ -7,6 +7,9 @@
     <meta name="breadcrumbParent"
           content="${createLink(action: 'datasets', controller: 'public')},${message(code: 'breadcrumb.datasets')}"
     />
+    <meta name="breadcrumbs"
+          content="${createLink(action: 'datasets', controller: 'public')}#filters=resourceType:${instance.resourceType},${message(code: 'resourceType.' + instance.resourceType + '.list')}"
+    />
     <title>${fieldValue(bean: instance, field: "name")}</title>
     <script type="text/javascript">
         var COLLECTORY_CONF = {
@@ -42,7 +45,7 @@
             <div class="tabbable">
                 <ul class="nav nav-tabs" id="home-tabs">
                     <li class="active"><a href="#basicMetadata" data-toggle="tab"><g:message code="show.tab.metadata" /></a></li>
-                    <g:if test="${instance.resourceType=='records'}">
+                    <g:if test="${instance.resourceType=='records' || instance.resourceType=='events'}">
                         <li><a href="#usage-stats" data-toggle="tab"><g:message code="show.tab.usage.stats" /></a></li>
                         <li><a href="#metrics" data-toggle="tab"><g:message code="show.tab.metrics" /></a></li>
                     </g:if>
@@ -51,6 +54,12 @@
 
             <div class="tab-content">
                 <div id="basicMetadata" class="tab-pane active">
+
+                    <h3 class="dataResourceProviderLink">Dataset type</h3>
+                    <p>
+                        <g:message code="resourceType.${instance.resourceType}.description" default="${instance.resourceType}" />
+                    </p>
+
                     <g:if test="${instance.pubDescription || instance.techDescription || instance.focus}">
                         <h3><g:message code="public.des" /></h3>
                     </g:if>
@@ -138,7 +147,7 @@
                             <cl:dataCurrency date="${instance.dataCurrency}"/></p>
                     </g:if>
 
-                    <g:if test="${instance.resourceType == 'records'}">
+                    <g:if test="${instance.resourceType == 'records' || instance.resourceType=='events'}">
                         <h2><g:message code="public.sdr.content.label09" /></h2>
                         <div>
                             <p><span
@@ -155,7 +164,7 @@
                     <cl:lastUpdated date="${instance.lastUpdated}"/>
                 </div>
 
-                <g:if test="${!grailsApplication.config.disableLoggerLinks.toBoolean() && (instance.resourceType == 'website' || instance.resourceType == 'records')}">
+                <g:if test="${!grailsApplication.config.disableLoggerLinks.toBoolean() && (instance.resourceType == 'website' || instance.resourceType == 'records'  || instance.resourceType=='events')}">
                     <div id="usage-stats" class="tab-pane">
                         <div id='usage'>
                             <p><g:message code="public.usage.des" />...</p>
@@ -166,7 +175,7 @@
                     </div>
                 </g:if>
 
-                <g:if test="${instance.resourceType == 'records'}">
+                <g:if test="${instance.resourceType == 'records' || instance.resourceType=='events' || instance.resourceType=='publications'}">
                     <div id="metrics" class="section vertical-charts tab-pane">
                         <div id="charts"></div>
                     </div>
@@ -186,6 +195,10 @@
                 <img class="institutionImage" src='${resource(absolute:"true", dir:"data/dataResource/",file:instance.logoRef.file)}' />
             </g:elseif>
 
+            <section class="public-metadata">
+                <h3><g:message code="resourceType.${instance.resourceType}" default="${instance.resourceType}"/></h3>
+            </section>
+
             <g:if test="${fieldValue(bean: instance, field: 'imageRef') && fieldValue(bean: instance, field: 'imageRef.file')}">
                 <section>
                     <img alt="${fieldValue(bean: instance, field: "imageRef.file")}"
@@ -199,6 +212,10 @@
                 </section>
             </g:if>
 
+            <g:if test="${instance.resourceType == "publications"}">
+                <g:render template="dataLinks" model="[instance:instance]"/>
+            </g:if>
+
             <div id="dataAccessWrapper" style="display:none;">
                 <g:render template="dataAccess" model="[instance:instance]"/>
             </div>
@@ -229,7 +246,7 @@
             <g:if test="${instance.licenseType}">
                 <section class="public-metadata">
                 <h4><g:message code="public.license" default="Licence" /></h4>
-                <p><cl:displayLicenseType type="${instance.licenseType}" version="${instance.licenseVersion}"/></p>
+                <p style="margin-top: 10px; margin-bottom:10px;"><cl:displayLicenseType type="${instance.licenseType}" version="${instance.licenseVersion}"/></p>
                 </section>
             </g:if>
 
@@ -294,6 +311,15 @@
                     </div>
                 </section>
             </g:if>
+            <g:elseif test="${instance.resourceType == 'publications'}">
+                <section class="public-metadata">
+                    <h4><g:message code="public.website" /></h4>
+                    <div class="webSite">
+                        <a class='external_icon' target="_blank"
+                           href="${instance.websiteUrl}"><g:message code="public.sdr.content.link05" /></a>
+                    </div>
+                </section>
+            </g:elseif>
             <g:elseif test="${instance.websiteUrl}">
                 <section class="public-metadata">
                     <h4><g:message code="public.website" /></h4>
@@ -355,7 +381,13 @@
                   }
                 }
             </asset:script>
-            <g:render template="charts" model="[facet:'data_resource_uid', instance: instance]" />
+
+            <g:if test="${instance.resourceType == 'records' || instance.resourceType == 'events'}">
+                 <g:render template="charts" model="[facet:'dataResourceUid', instance: instance]" />
+            </g:if>
+            <g:if test="${instance.resourceType == 'publications'}">
+                <g:render template="charts" model="[facet:'annotationsUid', instance: instance]" />
+            </g:if>
     </div>
 </div>
 

Diff for: grails-app/views/shared/base.gsp

@@ -43,6 +43,10 @@
 
                 </div>
                 <g:if test="${command.ENTITY_TYPE == 'DataResource'}">
+                    <div class="form-group">
+                        <label for="isPrivate"><g:message code="collection.isPrivate.label" default="isPrivate"/></label>
+                        <g:checkBox name="isPrivate" value="${command?.isPrivate}"/>
+                    </div>
                     <div class="form-group">
                         <label for="gbifDoi"><g:message code="collection.gbifDoi.label" default="DOI"/></label>
                         <g:textField name="gbifDoi" class="form-control" maxlength="45" value="${command?.gbifDoi}" />