Additional labels and consistency requested by functional recview

build.gradle

@@ -71,14 +71,12 @@ dependencies {
  compile "org.jsoup:jsoup:1.8.3"
 
  compile group: 'org.grails.plugins', name: 'ala-bootstrap3', version: '3.0.6'
- compile group: 'org.grails.plugins', name: 'ala-auth', version:'3.1.2', changing: true
+ compile group: 'org.grails.plugins', name: 'ala-auth', version:'3.1.3', changing: true
  compile group: 'au.org.ala.plugins.grails', name: 'ala-citation-plugin', version: '1.0'
  runtime group: 'au.org.ala.plugins.grails', name: 'ala-charts-plugin', version: '2.0.1'
  compile group: 'au.org.ala.plugins.grails', name: 'images-client-plugin', version: '1.2'
- //runtime group: 'org.grails.plugins', name: 'ala-charts-plugin', version: '1.3', changing: true
- //compile (group: 'org.grails.plugins', name: 'images-client-plugin', version: '0.8', changing: true) {
- // exclude group: 'org.grails.plugins', module: 'ala-auth'
- //}
+ runtime group: 'xml-apis', name: 'xml-apis', version: '1.4.01'
+ runtime "org.hibernate:hibernate-validator:5.4.2.Final"
 }
 
 bootRun {

grails-app/conf/application.yml

@@ -94,6 +94,9 @@ endpoints:
 app:
  name: bie-plugin
  dataDir: /tmp/gbif-ecat
+security:
+ cas:
+ appServerName: http:https://dev.ala.org.au:8080
 skin:
  layout: generic
  orgNameLong: BIE Plugin
@@ -111,7 +114,7 @@ projectNameShort: ALA
 projectName: Atlas of Living Australia
 languageCodesUrl: /languages.json
 biocache:
- baseURL: "http:https://biocache.ala.org.au"
+ baseURL: http:https://biocache.ala.org.au
 biocacheService:
  baseURL: http:https://biocache.ala.org.au/ws
  queryContext:

grails-app/i18n/messages.properties

@@ -118,48 +118,74 @@ imageAvailable.false=No
 imageAvailable.yes=Yes
 imageAvailable.true=Yes
 
-rank.kingdom=Kingdom
-rank.phylum=Phylum
-rank.order=Order
-rank.family=Family
-rank.genus=Genus
-rank.species=Species
-rank.subspecies=Subspecies
-rank.variety=Variety
 rank.(rank\ not\ specified)=(Rank not specified)
-rank.subgenus=Subgenus
+rank.Incertae\ Sedis\ (uncertain\ rank)=Incertae Sedis (uncertain rank)
+rank.Species\ Inquirenda\ (doubtful\ identity)=Species Inquirenda (doubtful identity)
+rank.anamorph=Anamorph
+rank.biovar=Biovar
+rank.class=Class
+rank.cohort=Cohort
 rank.cultivar=Cultivar
+rank.division=Division
+rank.division\ zoology=Division (Zoology)
+rank.family=Family
+rank.form=Form
+rank.forma\ specialis=Forma Specialis
+rank.genus=Genus
+rank.genus\ group=Genus Group
+rank.incertae\ sedis=Incertae Sedis (uncertain rank)
+rank.informal=Informal
+rank.infraclass=Infraclass
+rank.infrafamily=Infrafamily
+rank.infraorder=Infraorder
+rank.infraspecific=Infraspecific
+rank.infraspecificname=Infraspecific Name
+rank.kingdom=Kingdom
+rank.nothovariety=Nothovariety
+rank.null=(not specified)
+rank.order=Order
+rank.pathovar=Pathovar
+rank.phylum/division=Phylum/Division
+rank.phylum=Phylum
 rank.section=Section
-rank.subfamily=Subfamily
-rank.tribe=Tribe
+rank.section\ botany=Section (Botany)
+rank.section\ zoology=Section (Zoology)
 rank.series=Series
-rank.superfamily=Superfamily
-rank.subtribe=Subtribe
-rank.subsection=Subsection
+rank.series\ botany=Series (Botany)
+rank.serovar=Serovar
+rank.species=Species
+rank.species\ group=Species Group
+rank.species\ inquirenda=Species Inquirenda (doubtful identity)
+rank.subclass=Subclass
+rank.subdivision\ zoology=Subdivision (Zoology)
+rank.subfamily=Subfamily
+rank.subform=Subform
+rank.subgenus=Subgenus
+rank.subinfraclass=Subinfraclass
+rank.subkingdom=Subkingdom
 rank.suborder=Suborder
+rank.subphylum/subdivision=Subphylum/Subdivision
+rank.subphylum=Subphylum
+rank.subsection=Subsection
+rank.subsection\ botany=Subsection (Botany)
+rank.subsection\ zoology=Subsection (Zoology)
 rank.subseries=Subseries
+rank.subseries\ botany=Subseries (Botany)
+rank.subspecies=Subspecies
+rank.subspecies\ aggregate=Subspecies Aggregate
+rank.subtribe=Subtribe
 rank.subvariety=Subvariety
-rank.subclass=Subclass
-rank.class=Class
-rank.suprageneric\ tax_\ of\ undefined\ rank=Suprageneric taxon of undefined rank
+rank.superclass=Superclass
+rank.superfamily=Superfamily
+rank.superorder=Superorder
+rank.superspecies=Superspecies
+rank.supertribe=Supertribe
 rank.suprageneric\ tax.\ of\ undefined\ rank=Suprageneric taxon of undefined rank
+rank.suprageneric\ tax_\ of\ undefined\ rank=Suprageneric taxon of undefined rank
 rank.supragenericname=Subfamily
-rank.infraorder=Infraorder
-rank.infraspecific=Infraspecific
-rank.infraspecificname=Infraspecific Name
-rank.subspecies\ aggregate=Subspecies Aggregate
-rank.supertribe=Supertribe
-rank.phylum/division=Phylum/Division
-rank.superorder=Superorder
-rank.subphylum/subdivision=Subphylum/Subdivision
-rank.infraclass=Infraclass
-rank.null=(not specified)
-rank.superclass=Superclass
-rank.form=Form
-rank.Incertae\ Sedis\ (uncertain\ rank)=Incertae Sedis (uncertain rank)
-rank.Species\ Inquirenda\ (doubtful\ identity)=Species Inquirenda (doubtful identity)
-rank.cohort=Cohort
-rank.division=Division
+rank.tribe=Tribe
+rank.unranked=Unranked
+rank.variety=Variety
 
 idxtype.TAXON=Species
 idxtype.INSTITUTION=Institution

grails-app/services/au/org/ala/bie/UtilityService.groovy

@@ -54,6 +54,14 @@ class UtilityService {
  namesSet
  }
 
+ def stripQuotes(String str) {
+ if (str == null || str.length() < 2)
+ return str
+ if (str.startsWith('"') && str.endsWith('"'))
+ str = str.substring(1, str.length() - 1)
+ return str.trim()
+ }
+
  /**
  * Group names which are equivalent into a map with a list of their name objects.
  * <p>
@@ -103,7 +111,7 @@ class UtilityService {
  if (term.contains(":")) {
  String[] fqBits = StringUtils.split(term, ":", 2);
  def values = facetMap.get(fqBits[0], [])
- values << fqBits[-1] ?: ""
+ values << this.stripQuotes(fqBits[-1]) ?: ""
  }
  }
  }
@@ -202,4 +210,5 @@ class UtilityService {
  }
  log.debug "synonyms = ${synonyms}"
  synonyms
- }}
+ }
+}

grails-app/views/species/_literature.gsp

@@ -5,8 +5,8 @@
  <div class="side-menu" id="sidebar">
  <nav class="navbar navbar-default" role="navigation">
  <ul class="nav nav-stacked">
- <li><a href="#bhl-integration">Biodiversity Heritage Library</a></li>
- <li><a href="#trove-integration">Trove</a></li>
+ <li><a href="#bhl-integration"><g:message code="bhl.title.bhl"/></a></li>
+ <li><a href="#trove-integration"><g:message code="bhl.title.trove"/></a></li>
  </ul>
  </nav>
  </div>
@@ -17,7 +17,7 @@
 
  <div id="bhl-integration">
  <%-- Scientific name search --%>
- <h3><g:message code="bhl.reference.found.bhl"/> <a href="${grailsApplication.config.literature.bhl.url}/search?SearchTerm=%22${synonyms?.join('%22+OR+%22')}%22&SearchCat=M#/names" target="_blank">Biodiversity Heritage Library</a></h3>
+ <h3><g:message code="bhl.reference.found.bhl"/> <a href="${grailsApplication.config.literature.bhl.url}/search?SearchTerm=%22${synonyms?.join('%22+OR+%22')}%22&SearchCat=M#/names" target="_blank"><g:message code="bhl.title.bhl"/></a></h3>
  <div id="bhl-results-list" class="result-list">
  <!-- Search results go here -->
  </div>
@@ -26,7 +26,7 @@
  <div id="trove-integration" class="column-wrap" style="padding-top:50px;">
  %{--<h2>&nbsp;</h2>--}%
  <hr />
- <h3><g:message code="bhl.reference.found.trove"/> <a href="${grailsApplication.config.literature.trove.url}/result?q=%22${synonyms?.join('%22+OR+%22')}%22" target="_trove">Trove - NLA</a></h3>
+ <h3><g:message code="bhl.reference.found.trove"/> <a href="${grailsApplication.config.literature.trove.url}/result?q=%22${synonyms?.join('%22+OR+%22')}%22" target="_trove"><g:message code="bhl.title.trove"/></a></h3>
 
  <div id="trove-result-list" class="result-list">
  <!-- Search results go here -->