A

activeProfile(String) - Method in QualityService

addAssertion() - Method in AssertionsController

Add a new assertion (POST).

addAssertion(String, String, String, String, String, String, String, String, String) - Method in WebServicesService

Perform POST for new assertion to biocache-service

addSpatialParams(String, Boolean) - Method in SpatialSearchRequestParams

Add the spatial params to the param string

AdminController - Class in au.org.ala.biocache.hubs

Admin functions - should be protected by login and ROLE_ADMIN or equiv.

AdminInterceptor - Class in au.org.ala.biocache.hubs

Interceptor for Admin controller, adapted from grails 2 `beforeInterceptor` code.

advancedSearch(AdvancedSearchParams) - Method in HomeController

AdvancedSearchParams - Class in au.org.ala.biocache.hubs

Request parameters for the advanced search form (form backing bean)

after() - Method in AdminInterceptor

afterPropertiesSet() - Method in ExtendedPluginAwareResourceBundleMessageSource

Overriding this method allows the i18n source via HTTP call to biocache-service

afterView() - Method in AdminInterceptor

allCodes() - Method in DataQualityController

Application - Class in biocache.hubs

assertions(String) - Method in AssertionsController

Create combined assertions JSON web service from the user and quality assertion services on biocache-service.

AssertionsController - Class in au.org.ala.biocache.hubs

augmentRecord(JSONObject) - Method in PostProcessingService

Add markup, links, etc., to certain field values.

B

before() - Method in AdminInterceptor

BiocacheHubsGrailsPlugin - Class in au.org.ala.biocache.hubs

Biocache-hubs plugin descriptor file

BiocacheHubsUrlMappings - Class in au.org.ala.biocache.hubs

BootStrap - Class in biocache.hubs

C

cachedFullTextSearch(SpatialSearchRequestParams) - Method in WebServicesService

canConvert(def) - Method in EnglishValueConverter

clearAllCaches() - Method in AdminController

clearCache() - Method in FacetsCacheService

Can be triggered from the admin page.

clearCollectoryCache() - Method in AdminController

clearFacetsCache() - Method in AdminController

clearLongTermCache() - Method in AdminController

clearMessageCache() - Method in MessageSourceCacheService

Trigger the message source cache to be reset (different to the @Cacheable cache) which effectively grabs a new copy from biocache-service (base properties) and then adds to that from the i18n messages in the local grails app.

clearPropertiesCache() - Method in AdminController

clearRecordCountCache() - Method in AdminController

clearRecordCountCache() - Method in QualityService

combineTermsWithAND(String, String) - Method in AdvancedSearchParams

Advanced search field "ALL of these words (full text)" assumes default Boolean operator will be AND but bugs happen and someone changed it to be OR.

conditionalEncode(String, Boolean) - Method in SearchRequestParams

URI encode the param value if isEncoded is true

CONTEXTUAL - Field in WebServicesService

convert(def) - Method in EnglishValueConverter

countTotalRecords(SpatialSearchRequestParams) - Method in QualityService

createQueryWithTaxaParam(List, List) - Method in PostProcessingService

Generate SOLR query from a taxa[] query

D

data() - Method in HelpController

DataQualityController - Class in au.org.ala.biocache.hubs

Generate codes and metadata for the data quality checks.

dataQualityExcludeCounts(SpatialSearchRequestParams) - Method in OccurrenceController

dataResource(SpatialSearchRequestParams) - Method in OccurrenceController

deleteAssertion() - Method in AssertionsController

Delete an assertion (POST).

deleteAssertion(String, String) - Method in WebServicesService

Perform POST to delete an assertion on biocache-service

detailsForUserId(String) - Method in UserService

Get both email and displayName for a numeric user id.

doClearCollectoryCache() - Method in WebServicesService

doClearFacetsCache() - Method in AdminController

doClearLongTermCache() - Method in WebServicesService

doClearPropertiesCache() - Method in AdminController

doGet(String) - Method in ProxyController

Performs an HTTP GET request

doPost(String) - Method in ProxyController

Performs an HTTP POST request

doWithSpring() - Method in BiocacheHubsGrailsPlugin

E

EnglishValueConverter - Class in au.org.ala.biocache.hubs

Custom ValueConverter to force double values to be read as EN locale values This fixes issues with non-EN locales removing dot/period (as a comma would be)

EnglishValueConverter() - Constructor in EnglishValueConverter

ENVIRONMENTAL - Field in WebServicesService

exists(String) - Method in OccurrenceController

exploreYourArea() - Method in OccurrenceController

Explore your area page Uses http://dev.maxmind.com/geoip/geoip2/geolite2/

ExtendedPluginAwareResourceBundleMessageSource - Class in au.org.ala.biocache.hubs

Extend PluginAwareResourceBundleMessageSource so we can access the (protected) getMergedProperties() method to export all i18n messages for JS usage.

F

facetCSVDownload(SearchRequestParams) - Method in WebServicesService

facets(SpatialSearchRequestParams) - Method in OccurrenceController

FacetsCacheService - Class in au.org.ala.biocache.hubs

Service to cache the facet values available from a given data hub.

facetsDownload(SpatialSearchRequestParams) - Method in OccurrenceController

facetSearch(SearchRequestParams) - Method in WebServicesService

FacetsName - Enum in au.org.ala.biocache.hubs

Enum for facet fields needed to populate drop-down lists in advanced search page, etc.

FacetsName(String) - Constructor in FacetsName

fieldGuideDownload(SpatialSearchRequestParams) - Method in OccurrenceController

Field guide download

FieldGuideDTO - Class in au.org.ala.biocache.hubs

Field Guide DTO

findAllEnabledCategories(String) - Method in QualityService

findAllEnabledProfiles(boolean) - Method in QualityService

formatDynamicLabel(def) - Method in OccurrenceTagLib

formatFieldName(def, def) - Method in OccurrenceTagLib

Format a dynamic field name.

fullTextSearch(SpatialSearchRequestParams) - Method in WebServicesService

G

GeoIpService - Class in au.org.ala.biocache.hubs

Provides methods to access MaxMind GeoIP2 API (http://maxmind.github.io/GeoIP2-java/) Some code for getIpAddress has been taken from https://github.com/donbeave/grails-geoip/ Download City DB from https://dev.maxmind.com/geoip/geoip2/geolite2/ DB Download is automated and installed to grailsApplication.config.geopip.database.path as part of ala-install ansible playbooks and roles (https://github.com/AtlasOfLivingAustralia/ala-install/blob/82d2f13e462680c20f805e0f5e061d21fbe8a352/ansible/roles/biocache-hub/tasks/main.yml#L137)

get(String) - Method in UserController

get(def, def) - Method in UserDataService

getAlerts() - Method in OccurrenceController

getAlerts(String) - Method in WebServicesService

getAllCodes() - Method in WebServicesService

getAllFacets(List) - Method in PostProcessingService

Build a LinkedHashMap form of the facets to display in the customise drop down div

getAllGroupedFacets(Map, def, def) - Method in PostProcessingService

Add any ungrouped facets from search results to the groupedFacetsMap used to construct the facets column in search results.

getAllInverseCategoryFiltersForProfile(QualityProfile) - Method in QualityService

getAllOccurrenceFields() - Method in WebServicesService

getAssertionCodeMap() - Method in WebServicesService

getCollectionContact(String) - Method in WebServicesService

getCollectionInfo(String) - Method in WebServicesService

getCompareRecord(String) - Method in WebServicesService

getCookieValue(Cookie, String, String) - Method in PostProcessingService

Utility method for getting a named cookie value from the HttpServletRepsonse cookies array

getCurrentPageUUIDs() - Method in OccurrenceNavigationDTO

getCurrentUUID() - Method in OccurrenceNavigationDTO

getDataQualityCsv() - Method in WebServicesService

Get the CSV for ALA data quality checks meta data

getDataresourceContact(String) - Method in WebServicesService

getDefaultFacets() - Method in WebServicesService

getDuplicateRecordDetails(JSONObject) - Method in WebServicesService

getDynamicFacets(String) - Method in WebServicesService

Get list of dynamic facets for a given query (Sandbox)

getEnabledFiltersByLabel(String) - Method in QualityService

getEnabledQualityFilters(String) - Method in QualityService

getEncodedParams() - Method in SearchRequestParams

Produce a URI encoded query string for use in java.util.URI, etc

getEncodedParams() - Method in SpatialSearchRequestParams

Produce a URI encoded query string for use in java.util.URI, etc

getErrorCodes() - Method in WebServicesService

getExcludeCount(String, List<QualityCategory>, SpatialSearchRequestParams) - Method in QualityService

getExcluded(SpatialSearchRequestParams) - Method in OccurrenceController

getFacetNamesFor(String) - Method in FacetsCacheService

Get the facets values (and labels if available) for the requested facet field.

getFacetsFromCookie(HttpServletRequest) - Method in PostProcessingService

Read the request cookie to determine which facets are active

getFilteredFacets(LinkedHashMap<String, Boolean>) - Method in PostProcessingService

Filter the Map of all facets to produce a list of only the "active" or selected facets

getGroupedAssertions(JSONArray, JSONArray, String) - Method in PostProcessingService

Get the assertions grouped by assertion code.

getGroupedEnabledFilters(String) - Method in QualityService

getGroupedFacets() - Method in WebServicesService

getGuidsForTaxa(List) - Method in WebServicesService

Query the BIE for GUIDs for a given list of names

getImageFileSizeInMb(JSONArray) - Method in WebServicesService

Generate a Map of image url (key) with image file size (like ls -h) (value)

getInverseCategoryFilter(QualityCategory) - Method in QualityService

getJoinedQualityFilter(String) - Method in QualityService

getJson() - Method in FieldGuideDTO

getJsonElements(String, String) - Method in WebServicesService

Perform HTTP GET on a JSON web service

getLayersMetaData() - Method in WebServicesService

getListFromGroupedFacets(Map) - Method in PostProcessingService

Extract list of facet fields from the grouped facets Map (json)

getListOfLayerIds(SpatialSearchRequestParams) - Method in PostProcessingService

Find any cl1234 or el1234 layer IDs in the q or fq params and return a list of layer IDs

getListOfLayerObjects(List) - Method in PostProcessingService

For a given list of layer IDs (el1234 or cl456) do a lookup against spatial service for metadata for the layer ID and return a list of layer objects.

getListOfLayers(SpatialSearchRequestParams) - Method in PostProcessingService

Find any cl1234 or el1234 layer IDs in the q or fq params and return a list of layer objects containing layer metadata

getLocation(HttpServletRequest) - Method in GeoIpService

gets Obtains the Location for a client request

getLoggerReasons() - Method in WebServicesService

getLoggerSources() - Method in WebServicesService

getMapLegend(String) - Method in WebServicesService

getMapOfFacetResults(JSONArray) - Method in PostProcessingService

Create a Map of facet fields for a "lookup" in _facets.gsp Also normalises some fields (decade)

getMessagesMap(Locale) - Method in MessageSourceCacheService

getMessagesPropertiesFile() - Method in WebServicesService

getMetadataForOutlierLayers(JSONObject, Map) - Method in PostProcessingService

Add layers metadata to outlier for layer record attributes

getQueryAssertions(String) - Method in WebServicesService

getRecord(String, Boolean) - Method in WebServicesService

getSearchRequestParams() - Method in OccurrenceNavigationDTO

getSearchRequestResultSize() - Method in OccurrenceNavigationDTO

getTargetType() - Method in EnglishValueConverter

getText(String) - Method in WebServicesService

Perform HTTP GET on a text-based web service

getUngroupedFacetsList(Map, def) - Method in PostProcessingService

Get a list of facet fields (from search results) that are NOT in the grouped facets Map.

getUrlParams() - Method in SearchRequestParams

Constructs the params to be returned in the result

getUrlParams() - Method in SpatialSearchRequestParams

getUserAssertions(String) - Method in WebServicesService

getUserPref(String, HttpServletRequest) - Method in UserService

gk - Field in SpatialSearchRequestParams

H

help() - Method in HelpController

HelpController - Class in au.org.ala.biocache.hubs

HomeController - Class in au.org.ala.biocache.hubs

I

i18n(String) - Method in MessagesController

Export raw i18n message properties as TEXT for use by JavaScript i18n library

index() - Method in AdminController

index() - Method in AssertionsController

index() - Method in DataQualityController

index() - Method in HelpController

index() - Method in HomeController

index() - Method in OccurrenceController

init() - Method in FacetsCacheService

Init method - load facetsList from config file

init() - Method in GeoIpService

init() - Method in QualityService

init() - Method in WebServicesService

isProfileEnabled(String) - Method in QualityService

isProfileValid(def) - Method in QualityService

J

K

L

lat - Field in SpatialSearchRequestParams

legend() - Method in OccurrenceController

AJAX webservice for legend data from SP

list(SpatialSearchRequestParams) - Method in OccurrenceController

Perform a full text search

listMessageCodes(Locale) - Method in ExtendedPluginAwareResourceBundleMessageSource

Provide a complete listing of properties for a given locale, as a Map Client app properties override those from this plugin

lon - Field in SpatialSearchRequestParams

M

main(String) - Method in Application

mergeRequestedFacets(List, List) - Method in PostProcessingService

Merge requested and custom facets

MessagesController - Class in au.org.ala.biocache.hubs

MessageSourceCacheService - Class in au.org.ala.biocache.hubs

A service that provides a java.util.Map representation of the i18n messages for a given locale (cached).

MoreWebUtils - Class in au.org.ala.biocache.hubs

moveCursorAndShow(int) - Method in OccurrenceController

N

next() - Method in OccurrenceController

Go to the next occurrences of the search results Use the Navigation DTO from session (if available)

O

OccurrenceController - Class in au.org.ala.biocache.hubs

Controller for occurrence searches and records

OccurrenceNavigationDTO - Class in au.org.ala.biocache.hubs

OccurrenceTagLib - Class in au.org.ala.biocache.hubs

Custom taglib for biocache-hubs

OutageBanner - Class in au.org.ala.biocache.hubs

Command object for outage banner (admin function)

P

populateProfile(def) - Method in WebServicesService

postFormData(String, Map, String) - Method in WebServicesService

Perform a POST with URL encoded params as POST body

postJsonElements(String, String) - Method in WebServicesService

PostProcessingService - Class in au.org.ala.biocache.hubs

Service to perform processing of data between the DAO and View layers

previous() - Method in OccurrenceController

Go to the previous occurrences of the search results Use the Navigation DTO from session (if available)

processUserFQInteraction(SpatialSearchRequestParams, def) - Method in PostProcessingService

ProxyController - Class in au.org.ala.biocache.hubs

Proxy Controller for AJAX requests to biocache-service

Q

QualityService - Class in au.org.ala.biocache.hubs

This service provides below functions 1. wrap API calls to data-quality-filter-service 2. get excluded counts of quality categories

R

radius - Field in SpatialSearchRequestParams

resultsHaveImages(JSONObject) - Method in PostProcessingService

Determine if the record contains images

S

sanitizeBodyText(String, Boolean) - Method in OccurrenceTagLib

Utility to sanitise HTML text and only allow links to be kept, removing any other HTML markup.

searchJson(SpatialSearchRequestParams) - Method in OccurrenceController

JSON webservices for debugging/testing

SearchRequestParams - Class in au.org.ala.biocache.hubs

Data Transfer Object to represent the request parameters required to search for occurrence records against biocache-service.

set(String) - Method in UserController

set(def, def, def) - Method in UserDataService

setCurrentPageUUIDs(List<String>) - Method in OccurrenceNavigationDTO

setCurrentUUID(String) - Method in OccurrenceNavigationDTO

setSearchRequestParams(SpatialSearchRequestParams) - Method in OccurrenceNavigationDTO

setSearchRequestResultSize(int) - Method in OccurrenceNavigationDTO

show(String) - Method in OccurrenceController

Display an occurrence record

showBanner() - Method in OutageBanner

Determine whether or not to display the banner

showCore(String) - Method in OccurrenceController

Display just the "core" section of an occurrence record.

showJson(String) - Method in OccurrenceController

JSON webservices for debugging/testing

SpatialSearchRequestParams - Class in au.org.ala.biocache.hubs

Created with IntelliJ IDEA.

subscribeMyAnnotation() - Method in OccurrenceController

subscribeMyAnnotation(String) - Method in WebServicesService

T

taxa(String) - Method in OccurrenceController

taxaPost() - Method in OccurrenceController

POST from taxa drop-down list of raw taxon names

termsOfUse() - Method in HelpController

time(String, Closure<V>) - Method in TimingUtils

TimingUtils - Class in au.org.ala.biocache.hubs

toMap() - Method in OutageBanner

toParamMap() - Method in AdvancedSearchParams

Get the queryString in the form of a Map - for use with 'params' attribute in redirect, etc.

toQueryString(Map) - Method in MoreWebUtils

Converts the given parameters to a query string using the default UTF-8 encoding

toString() - Method in AdvancedSearchParams

This custom toString method outputs a valid /occurrence/search query string.

toString() - Method in FieldGuideDTO

toString() - Method in OutageBanner

toString(Boolean) - Method in SearchRequestParams

Common code to output a param string with conditional encoding of values

toString() - Method in SpatialSearchRequestParams

Custom toString method to produce a String to be used as the request parameters for the Biocache Service webservices

translateValues(def, def, def) - Method in PostProcessingService

U

unsubscribeMyAnnotation() - Method in OccurrenceController

unsubscribeMyAnnotation(String) - Method in WebServicesService

UserController - Class in au.org.ala.biocache.hubs

Controller for occurrence searches and records

UserDataService - Class in au.org.ala.biocache.hubs

UserService - Class in au.org.ala.biocache.hubs

V

valueOfFieldName(String) - Method in FacetsName

Do a lookup on the fieldName field

W

WebServicesService - Class in au.org.ala.biocache.hubs

Service to perform web service DAO operations

wkt - Field in SpatialSearchRequestParams

X

Y

Z

_