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SearchService.groovy
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SearchService.groovy
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package au.org.ala.bie
import au.org.ala.bie.search.IndexDocType
import au.org.ala.bie.util.Encoder
import grails.web.servlet.mvc.GrailsParameterMap
import org.apache.solr.client.solrj.SolrQuery
import org.apache.solr.client.solrj.response.FacetField
import org.apache.solr.common.SolrDocument
import org.apache.solr.common.params.MapSolrParams
import org.gbif.nameparser.PhraseNameParser
import java.text.MessageFormat
/**
* A set of search services for the BIE.
*/
class SearchService {
static BULK_BATCH_SIZE = 20
static GET_ALL_SIZE = 40
def grailsApplication
def conservationListsSource
def indexService
def biocacheService
def additionalResultFields = null
/**
* Retrieve species & subspecies for the supplied taxon which have images.
*
* @param taxonID
* @param start
* @param rows
* @return
*/
def imageSearch(taxonID, start, rows, queryContext, List<Locale> locales){
def query = "q=*:*"
if(taxonID){
//retrieve the taxon rank and then construct the query
def taxon = lookupTaxon(taxonID)
if(!taxon){
return []
}
def tid = Encoder.escapeSolr(taxon.guid)
query = "(guid:\"${tid}\" OR rkid_${taxon.rank.toLowerCase().replaceAll('\\s', '_')}:\"${tid}\")"
}
def response = indexService.query(true, query, ["rankID:[7000 TO *]", "imageAvailable:true"], rows, start, queryContext)
log.debug "imageSearch response json = ${response}"
[
totalRecords: response.results.numFound,
facetResults: formatFacets(response.facetFields),
results: formatDocs(response.results, null, null, locales)
]
}
/**
* Retrieve species & subspecies for the supplied taxon which have images.
*
* @param taxonID
* @param start
* @param rows
* @return
*/
def imageLinkSearch(taxonID, type, queryContext, List<Locale> locales){
def result = imageSearch(taxonID, 0, 1, queryContext, locales)
if (!result || result.isEmpty() || result.totalRecords == 0) {
return null
}
def taxon = result.results.get(0)
if (!taxon.image || taxon.image.isEmpty()) {
return null
}
if (type == 'thumbnail') {
return MessageFormat.format(grailsApplication.config.images.service.thumbnail, taxon.image)
} else if (type == 'small') {
return MessageFormat.format(grailsApplication.config.images.service.small, taxon.image)
} else if (type == 'large') {
return MessageFormat.format(grailsApplication.config.images.service.large, taxon.image)
} else {
return MessageFormat.format(grailsApplication.config.images.service.large, taxon.image)
}
}
/**
* General search service.
*
* @param q The search query
* @param params The request parameters
* @param requestedFacets The facets to use
* @param locale The preferred locale for common names
*
* @return
*/
def search(String q, GrailsParameterMap params, List requestedFacets, List<Locale> locales) {
params.remove("controller") // remove Grails stuff from query
params.remove("action") // remove Grails stuff from query
log.debug "params = ${params.toMapString()}"
def fqs = params.list('fq')
def queryTitle = null
def start = (params.start ?: 0) as Integer
def rows = (params.rows ?: params.pageSize ?: 10) as Integer
if (q) {
queryTitle = q
if (!q) {
q = q.replaceFirst("q=", "q=*:*")
} else if (q.trim() == "*") {
q = q.replaceFirst("q=*", "q=*:*")
}
// boost query syntax was removed from here. NdR.
// Add fuzzy search term modifier to simple queries with > 1 term (e.g. no braces)
q = q.trim()
if (!q.startsWith('(') && q.trim() =~ /\s+/) {
def qs = q.replaceAll(/[^\p{Alnum}]+/, " ").trim()
def queryArray = qs.split(/\s+/).findAll({ it.length() > 5}).collect({ it + "~0.8"})
def nq = queryArray.join(" ")
log.debug "fuzzy nq = ${nq}"
q = "\"${q}\"^100 ${nq}"
}
} else {
q = "*:*"
queryTitle = "all records"
}
def response = indexService.search(true, q, fqs, requestedFacets, start, rows, params.sort, params.dir)
if (response.results.numFound as Integer == 0) {
try {
//attempt to parse the name
def nameParser = new PhraseNameParser()
def parsedName = nameParser.parse(q)
if (parsedName && parsedName.canonicalName()) {
def canonical = parsedName.canonicalName()
// TODO test if this breaks paginating through results... looks like it will
response = indexService.search(true, "scientificName:\"${canonical}\"", fqs, requestedFacets, start, rows, params.sort, params.dir)
}
} catch(Exception e){
//expected behaviour for non scientific name matches
log.debug "expected behaviour for non scientific name matches: ${e}"
}
}
def matcher = ( queryTitle =~ /(rkid_)([a-z]{1,})(:)(.*)/ )
if(matcher.matches()){
try {
def rankName = matcher[0][2]
def guid = matcher[0][4]
def shortProfile = getShortProfile(guid)
if (shortProfile)
queryTitle = rankName + " " + shortProfile.scientificName
else
queryTitle = rankName + " " + guid
} catch (Exception e){
log.warn("Exception thrown parsing name..", e)
}
}
if(!queryTitle){
queryTitle = "all records"
}
log.debug("search called with q = ${q}, returning ${response.results.numFound}")
[
totalRecords: response.results.numFound,
facetResults: formatFacets(response.facetFields, requestedFacets),
results : formatDocs(response.results, response.highlighting, params, locales),
queryTitle : queryTitle
]
}
boolean isCollectionOrArray(object) {
[Collection, Object[]].any { it.isAssignableFrom(object.getClass()) }
}
def getHabitats(){
def children = []
def response = indexService.query(true, "idxtype:${IndexDocType.HABITAT.name()}", [], 1000)
return response.results.collect { taxon ->
[
guid:taxon.guid,
parentGuid: taxon.parentGuid,
name: taxon.name
]
}
}
def getHabitatsIDsByGuid(guid){
guid = Encoder.escapeSolr(guid)
def response = indexService.query(true, "guid:\"${guid}\"", [ "idxtype:${IndexDocType.HABITAT.name()}" ], 1, 0)
//construct a tree
def ids = []
if(response.results){
def doc = response.results.get(0)
ids << doc.name
ids << getChildHabitatIDs(doc.guid)
}
ids.flatten()
}
private def getChildHabitatIDs(guid){
guid = Encoder.escapeSolr(guid)
def response = indexService.query(true, "parentGuid:\"${guid}\"", [ "idxtype:${IndexDocType.HABITAT.name()}" ], 1000, 0)
def ids = []
//construct a tree
response.results.each {
ids << it.name
ids << getChildHabitatIDs(it.guid)
}
ids
}
def getHabitatByGuid(guid){
guid = Encoder.escapeSolr(guid)
def response = indexService.query(true, "guid:\"${guid}\"", [ "idxtype:${IndexDocType.HABITAT.name()}" ], 1, 0)
//construct a tree
def root = [:]
if(response.results){
def doc = response.results.get(0)
return [
guid:doc.guid,
name: doc.name,
children: getChildHabitats(doc.guid)
]
}
}
private def getChildHabitats(guid){
guid = Encoder.escapeSolr(guid)
def response = indexService.query(true, "parentGuid:\"${guid}\"", [ "idxtype:${IndexDocType.HABITAT.name()}" ], 1000, 0)
return response.results.collect {
[
guid:it.guid,
name: it.name,
children: getChildHabitats(it.guid)
]
}
}
def getHabitatsTree(){
def response = indexService.query(true, "idxtype:${IndexDocType.HABITAT.name()}", [], 1000, 0)
//construct a tree
def root = [:]
response.results.each {
if(!it.parentGuid){
root[it.guid] = [
guid:it.guid,
name: it.name
]
}
}
//look for children of the root
def nodes = root.values()
nodes.each { addChildren(response.results, it) }
root
}
private def addChildren(docs, node){
docs.each {
if(it.parentGuid && node.guid == it.parentGuid){
if(!node.children){
node.children = [:]
}
def childNode = [
guid:it.guid,
name: it.name
]
node.children[it.guid] = childNode
addChildren(docs, childNode)
}
}
}
private queryChildConcepts(q, fqs, queryString, children) {
def response = indexService.query(true, q, fqs, 1000, 0, queryString)
def taxa = response.results
taxa.each { taxon ->
children << [
guid : taxon.guid,
parentGuid : taxon.parentGuid,
name : taxon.scientificName,
nameComplete : taxon.nameComplete ?: taxon.scientificName,
nameFormatted: taxon.nameFormatted,
author : taxon.scientificNameAuthorship,
rank : taxon.rank,
rankID : taxon.rankID
]
}
}
def getChildConcepts(taxonID, queryString, within, unranked){
def baseTaxon = lookupTaxon(taxonID)
def baseRankID = baseTaxon?.rankID ?: -1
def baseFq = "idxtype:${IndexDocType.TAXON.name()}"
def fqs = [ baseFq ]
def q = "parentGuid:\"${ Encoder.escapeSolr(taxonID) }\""
def children = []
if (baseRankID > 0 && within) {
fqs << "rankID:[${unranked ? -1 : baseRankID + 1} TO ${baseRankID + within}]"
}
this.queryChildConcepts(q, fqs, queryString, children)
if (unranked && baseRankID > 0 && within) // Long running bug in SOLR unable to handle (- +) subqueries
this.queryChildConcepts(q, [ baseFq, "-rankID:*"], queryString, children)
if (children.isEmpty() && fqs.size() > 1)
this.queryChildConcepts(q, [ baseFq ], queryString, children)
children.sort { c1, c2 ->
def r1 = c1.rankID
def r2 = c2.rankID
if (r1 != null && r2 != null) {
if (r1 <= 0 && r2 > 0)
return 10000
if (r2 <= 0 && r1 > 0)
return -10000
if (r2 != r1)
return r1 - r2
}
return c1.name?.compareTo(c2.name) ?: 0
}
children
}
/**
* Retrieve details of a taxon by taxonID
*
* @param taxonID
* @param useOfflineIndex
* @return
*/
def lookupTaxon(String taxonID, Boolean useOfflineIndex = false){
def encID = Encoder.escapeSolr(taxonID)
def response = indexService.query(!useOfflineIndex, "guid:\"${encID}\" OR linkIdentifier:\"${encID}\"", [ "idxtype:${ IndexDocType.TAXON.name() }" ], 1, 0)
return response.results.isEmpty() ? null : response.results.get(0)
}
/**
* Retrieve details of a taxon by common name or scientific name.
* <p>
* If not found, try looking for a taxon variant
*
* @param taxonName The taxon name
* @param kingdom The kingdom, if available, to help disambiguate homonyms
* @param useOfflineIndex Use the offline index for lookups
* @return
*/
def lookupTaxonByName(String taxonName, String kingdom, Boolean useOfflineIndex = false){
taxonName = Encoder.escapeSolr(taxonName)
def q = "scientificName:\"${taxonName}\" OR nameComplete:\"${taxonName}\" OR commonName:\"${taxonName}\""
if (kingdom)
q = "(${q}) AND rk_kingdom:\"${ Encoder.escapeSolr(kingdom) }\""
def response = indexService.query(
!useOfflineIndex,
q,
[ "idxtype:${IndexDocType.TAXON.name()}" ],
1,
0,
null,
null,
null,
null,
true,
true
)
if (response.results.isEmpty()) {
q = "+scientificName:\"${taxonName}\" OR +nameComplete:\"${taxonName}\""
response = indexService.query(!useOfflineIndex, q, [ "idxtype:${ IndexDocType.TAXONVARIANT.name() }" ], 1, 0)
if (!response.results.isEmpty())
return lookupTaxon(response.results.get(0).taxonGuid, useOfflineIndex)
}
return response.results.isEmpty() ? null : response.results.get(0)
}
/**
* Request is for an old identifier - lookup current taxon
*
* @param identifier
* @param useOfflineIndex
* @return
* @throws Exception
*/
private def lookupTaxonByPreviousIdentifier(String identifier, Boolean useOfflineIndex = false) throws Exception {
identifier = Encoder.escapeSolr(identifier)
def response = indexService.query(!useOfflineIndex, "guid:\"${identifier}\"", [], 1, 0)
def taxonGuid = response.results.isEmpty() ? null : response.results.get(0).taxonGuid
def taxon = null
if (taxonGuid) {
taxon = lookupTaxon(taxonGuid, useOfflineIndex)
}
return taxon
}
/**
* Retrieve details of a specific vernacular name by taxonID
*
* @param taxonID The taxon identifier
* @param name The vernacular name
* @param useOfflineIndex
* @return
*/
def lookupVernacular(String taxonID, String vernacularName, Boolean useOfflineIndex = false){
taxonID = Encoder.escapeSolr(taxonID)
vernacularName = Encoder.escapeSolr(vernacularName)
def response = indexService.query(!useOfflineIndex, "taxonGuid:\"${taxonID}\"", [ "idxtype:${ IndexDocType.COMMON.name() }", "name:\"${vernacularName}\"" ], 1, 0)
return response.results.isEmpty() ? null : response.results.get(0)
}
/**
* Retrieve details of a specific identifier by taxonID
*
* @param taxonID The taxon identifier
* @param identifier The identifier
* @param useOfflineIndex
* @return
*/
def lookupIdentifier(String taxonID, String identifier, Boolean useOfflineIndex = false){
taxonID = Encoder.escapeSolr(taxonID)
identifier = Encoder.escapeSolr(identifier)
def response = indexService.query(!useOfflineIndex, "taxonGuid:\"${taxonID}\"", [ "idxtype:${ IndexDocType.IDENTIFIER.name() }", "guid:\"${identifier}\"" ], 1, 0)
return response.results.isEmpty() ? null : response.results.get(0)
}
/**
* Retrieve details of all vernacular names attached to a taxon.
*
* @param taxonID The taxon identifier
* @param useOfflineIndex
* @return
*/
def lookupVernacular(String taxonID, Boolean useOfflineIndex = false){
taxonID = Encoder.escapeSolr(taxonID)
def response = indexService.query(!useOfflineIndex, "taxonGuid:\"${taxonID}\"", [ "idxtype:${ IndexDocType.COMMON.name() }" ], GET_ALL_SIZE)
return response.results
}
/**
* Retrieve details of all identifiers attached to a taxon.
*
* @param taxonID The taxon identifier
* @param useOfflineIndex
* @return
*/
def lookupIdentifier(String taxonID, Boolean useOfflineIndex = false){
taxonID = Encoder.escapeSolr(taxonID)
def response = indexService.query(!useOfflineIndex, "taxonGuid:\"${taxonID}\"", [ "idxtype:${ IndexDocType.IDENTIFIER.name() }" ], GET_ALL_SIZE)
return response.results
}
/**
* Retrieve details of all name vairants attached to a taxon.
*
* @param taxonID The taxon identifier
* @param useOfflineIndex
* @return
*/
def lookupVariant(String taxonID, Boolean useOfflineIndex = false){
taxonID = Encoder.escapeSolr(taxonID)
def response = indexService.query(!useOfflineIndex, "taxonGuid:\"${taxonID}\"", [ "idxtype:${ IndexDocType.TAXONVARIANT.name() }" ], GET_ALL_SIZE)
return response.results
}
/**
* Return a simplified profile object for the docs that match the provided name
*
* @param name
* @return Map with 4 fields
*/
def getProfileForName(String name){
name = Encoder.escapeSolr(name)
def query = "scientificName:\"${name}\" OR nameComplete:\"${name}\" OR commonName:\"${name}\""
def response = indexService.query(
true,
query,
[ "idxtype:${IndexDocType.TAXON.name()}" ],
10,
0,
null,
null,
null,
null,
true,
true
)
def model = []
if (response.results.numFound > 0) {
response.results.each { result ->
model << [
"identifier": result.guid,
"name": result.scientificName,
"acceptedIdentifier": result.acceptedConceptID ?: (result.taxonomicStatus == "accepted" ? result.guid : ""),
"acceptedName": result.acceptedConceptName ?: (result.taxonomicStatus == "accepted" ? result.scientificName : "")
]
}
}
model
}
Map getLongProfileForName(String name, boolean includeVernacular){
name = Encoder.escapeSolr(name)
def query = "scientificName:\"${name}\" OR nameComplete:\"${name}\""
if (includeVernacular)
query = query + " OR commonName:\"${name}\""
def response = indexService.query(
true,
query,
[ "idxtype:${IndexDocType.TAXON.name()}" ],
1,
0,
null,
null,
null,
null,
true,
true
)
def model = [:]
if (response.results.numFound > 0) {
def result = response.results.get(0)
//json.response.docs.each { result ->
model = [
"identifier": result.guid,
"guid": result.guid,
"parentGuid": result.parentGuid,
"name": result.scientificName,
"nameComplete": result.nameComplete,
"commonName" : result.commonName,
"commonNameSingle" : result.commonNameSingle,
"rank" : result.rank,
"rankId" : result.rankID,
"acceptedConceptGuid": result.acceptedConceptID ?: result.guid,
"acceptedConceptName": result.acceptedConceptName ?: result.scientificName,
"taxonomicStatus": result.taxonomicStatus,
"imageId": result.image,
"imageUrl": (result.image) ? MessageFormat.format(grailsApplication.config.images.service.large, result.image) : "",
"thumbnailUrl": (result.image) ? MessageFormat.format(grailsApplication.config.images.service.thumbnail, result.image) : "",
"largeImageUrl": (result.image) ? MessageFormat.format(grailsApplication.config.images.service.large, result.image) : "",
"smallImageUrl": (result.image) ? MessageFormat.format(grailsApplication.config.images.service.small, result.image) : "",
"imageMetadataUrl": (result.image) ? MessageFormat.format(grailsApplication.config.images.service.metadata, result.image) : "",
"kingdom": result.rk_kingdom,
"phylum": result.rk_phylum,
"classs": result.rk_class,
"order":result.rk_order,
"family": result.rk_family,
"genus": result.rk_genus,
"author": result.scientificNameAuthorship,
"linkIdentifier": result.linkIdentifier
]
}
model
}
def getShortProfile(taxonID){
log.debug "getShortProfile taxonID = ${taxonID}"
def taxon = lookupTaxon(taxonID)
if(!taxon){
return null
}
def classification = extractClassification(taxon)
def model = [
taxonID:taxon.guid,
scientificName: taxon.scientificName,
scientificNameAuthorship: taxon.scientificNameAuthorship,
author: taxon.scientificNameAuthorship,
rank: taxon.rank,
rankID:taxon.rankID,
kingdom: classification.kingdom?:"",
family: classification.family?:""
]
if (taxon.commonNameSingle) {
model.put("commonName", taxon.commonNameSingle)
} else if (taxon.commonName){
model.put("commonName", taxon.commonName.first())
}
if(taxon.image){
model.put("thumbnail", MessageFormat.format(grailsApplication.config.images.service.thumbnail, taxon.image))
model.put("imageURL", MessageFormat.format(grailsApplication.config.images.service.large, taxon.image))
}
model
}
def getTaxa(List guidList){
def resultMap = [:]
def matchingTaxa = []
while (!guidList.isEmpty()) {
def batch = guidList.take(BULK_BATCH_SIZE)
def batchSet = (batch.findAll { !resultMap.containsKey(it) }) as Set
def matches = getTaxaBatch(batchSet)
if (!matches) // Error return
return null
matches.each { match ->
resultMap[match.guid] = match
if (match.linkIdentifier)
resultMap[match.linkIdentifier] = match
}
batch.each { guid ->
matchingTaxa << resultMap[guid]
}
guidList = guidList.drop(BULK_BATCH_SIZE)
}
return matchingTaxa
}
private getTaxaBatch(Collection guidList) {
if (!guidList)
return []
def queryList = guidList.collect({'"' + Encoder.escapeSolr(it) + '"'}).join(',')
def response = indexService.query(true, "guid:(${queryList}) OR linkIdentifier:(${queryList})", [ "idxtype:${IndexDocType.TAXON.name()}" ], BULK_BATCH_SIZE, 0)
//create the docs....
if(response.results.numFound > 0){
def matchingTaxa = []
response.results.each { doc ->
def taxon = [
guid: doc.guid,
name: doc.scientificName,
scientificName: doc.scientificName,
author: doc.scientificNameAuthorship,
nameComplete: doc.nameComplete?:doc.scientificName,
rank: doc.rank,
kingdom: doc.rk_kingdom,
phylum: doc.rk_phylum,
classs: doc.rk_class,
order: doc.rk_order,
family: doc.rk_family,
genus: doc.rk_genus,
datasetName: doc.datasetName,
datasetID: doc.datasetID
]
if(doc.image){
taxon.put("thumbnailUrl", MessageFormat.format(grailsApplication.config.images.service.thumbnail, doc.image))
taxon.put("smallImageUrl", MessageFormat.format(grailsApplication.config.images.service.small, doc.image))
taxon.put("largeImageUrl", MessageFormat.format(grailsApplication.config.images.service.large, doc.image))
}
if (doc.linkIdentifier)
taxon.put("linkIdentifier", doc.linkIdentifier)
if (doc.commonNameSingle) {
taxon.put("commonNameSingle", doc.commonNameSingle)
} else if (doc.commonName) {
taxon.put("commonNameSingle", doc.commonName.first())
}
matchingTaxa << taxon
}
return matchingTaxa
} else {
return null
}
}
def getTaxon(taxonLookup, List<Locale> locales){
def taxon = lookupTaxon(taxonLookup)
if(!taxon) {
taxon = lookupTaxonByName(taxonLookup, null)
}
if(!taxon) {
taxon = lookupTaxonByPreviousIdentifier(taxonLookup)
if(!taxon){
return null
}
}
//retrieve any synonyms
def encGuid = Encoder.escapeSolr(taxon.guid)
def response = indexService.query(true, "acceptedConceptID:\"${encGuid}\"", [ "idxtype:${IndexDocType.TAXON.name()}"], GET_ALL_SIZE)
def synonyms = response.results
def classification = extractClassification(taxon)
//retrieve any common names, ordered by priority and then language
response = indexService.query(true, "taxonGuid:\"${encGuid}\"", [ "idxtype:${IndexDocType.COMMON.name()}"], GET_ALL_SIZE)
def languages = Encoder.buildLanguageList(locales)
def commonNames = response.results.sort { n1, n2 ->
def s = n2.priority - n1.priority
if (s == 0) {
def s1 = languages.findIndexOf { it == n1.language }
if (s1 < 0) s1 = languages.size()
def s2 = languages.findIndexOf { it == n2.language }
if (s2 < 0) s2 = languages.size()
s = s1 - s2
}
if (s == 0) {
s = n1.name.compareTo(n2.name)
}
s
}
//retrieve any additional identifiers
response = indexService.query(true, "taxonGuid:\"${encGuid}\"", [ "idxtype:${IndexDocType.IDENTIFIER.name()}"], GET_ALL_SIZE)
def identifiers = response.results
// retrieve any variants
response = indexService.query(true, "taxonGuid:\"${encGuid}\"", [ "idxtype:${IndexDocType.TAXONVARIANT.name()}"], GET_ALL_SIZE)
def variants = response.results
//Dataset index
def datasetMap = [:]
def taxonDatasetURL = getDataset(taxon.datasetID, datasetMap)?.guid
def taxonDatasetName = getDataset(taxon.datasetID, datasetMap)?.name
// Conservation status map
def clists = conservationListsSource.lists ?: []
def conservationStatus = clists.inject([:], { ac, cl ->
final cs = taxon[cl.field]
if (cs)
ac.put(cl.label, [ dr: cl.uid, status: cs ])
ac
})
def model = [
taxonConcept:[
guid: taxon.guid,
parentGuid: taxon.parentGuid,
nameString: taxon.scientificName,
nameComplete: taxon.nameComplete,
nameFormatted: taxon.nameFormatted,
author: taxon.scientificNameAuthorship,
nomenclaturalCode: taxon.nomenclaturalCode,
taxonomicStatus: taxon.taxonomicStatus,
nomenclaturalStatus: taxon.nomenclaturalStatus,
rankString: taxon.rank,
nameAuthority: taxon.datasetName ?: taxonDatasetName ?: grailsApplication.config.attribution.default,
rankID:taxon.rankID,
nameAccordingTo: taxon.nameAccordingTo,
nameAccordingToID: taxon.nameAccordingToID,
namePublishedIn: taxon.namePublishedIn,
namePublishedInYear: taxon.namePublishedInYear,
namePublishedInID: taxon.namePublishedInID,
taxonRemarks: taxon.taxonRemarks,
provenance: taxon.provenance,
favourite: taxon.favourite,
infoSourceURL: taxon.source ?: taxonDatasetURL,
datasetURL: taxonDatasetURL
],
taxonName:[],
classification: classification,
synonyms:synonyms.collect { synonym ->
def datasetURL = getDataset(synonym.datasetID, datasetMap)?.guid
def datasetName = getDataset(synonym.datasetID, datasetMap)?.name
[
nameString: synonym.scientificName,
nameComplete: synonym.nameComplete,
nameFormatted: synonym.nameFormatted,
nameGuid: synonym.guid,
nomenclaturalCode: synonym.nomenclaturalCode,
taxonomicStatus: synonym.taxonomicStatus,
nomenclaturalStatus: synonym.nomenclaturalStatus,
nameAccordingTo: synonym.nameAccordingTo,
nameAccordingToID: synonym.nameAccordingToID,
namePublishedIn: synonym.namePublishedIn,
namePublishedInYear: synonym.namePublishedInYear,
namePublishedInID: synonym.namePublishedInID,
nameAuthority: synonym.datasetName ?: datasetName ?: grailsApplication.config.attribution.synonym ?: grailsApplication.config.attribution.default,
taxonRemarks: synonym.taxonRemarks,
provenance: synonym.provenance,
infoSourceURL: synonym.source ?: datasetURL,
datasetURL: datasetURL
]
},
commonNames: commonNames.collect { commonName ->
def datasetURL = getDataset(commonName.datasetID, datasetMap)?.guid
def datasetName = getDataset(commonName.datasetID, datasetMap)?.name
[
nameString: commonName.name,
status: commonName.status,
priority: commonName.priority,
language: commonName.language ?: grailsApplication.config.commonName.defaultLanguage,
temporal: commonName.temporal,
locationID: commonName.locationID,
locality: commonName.locality,
countryCode: commonName.countryCode,
sex: commonName.sex,
lifeStage: commonName.lifeStage,
isPlural: commonName.isPlural,
organismPart: commonName.organismPart,
taxonRemarks: commonName.taxonRemarks,
provenance: commonName.provenance,
labels: commonName.labels,
infoSourceName: commonName.datasetName ?: datasetName ?: grailsApplication.config.attribution.common ?: grailsApplication.config.attribution.default,
infoSourceURL: commonName.source ?: datasetURL,
datasetURL: datasetURL
]
},
imageIdentifier: taxon.image,
conservationStatuses:conservationStatus,
extantStatuses: [],
habitats: [],
categories: [],
simpleProperties: [],
images: [],
identifiers: identifiers.collect { identifier ->
def datasetURL = getDataset(identifier.datasetID, datasetMap)?.guid
def datasetName = getDataset(identifier.datasetID, datasetMap)?.name
[
identifier: identifier.guid,
nameString: identifier.name,
status: identifier.status,
subject: identifier.subject,
format: identifier.format,
provenance: identifier.provenance,
infoSourceName: identifier.datasetName ?: datasetName ?: grailsApplication.config.attribution.identifier ?: grailsApplication.config.attribution.default,
infoSourceURL: identifier.source ?: datasetURL,
datasetURL: datasetURL
]
},
variants: variants.collect { variant ->
def datasetURL = getDataset(variant.datasetID, datasetMap)?.guid
def datasetName = getDataset(variant.datasetID, datasetMap)?.name
[
nameString: variant.scientificName,
nameComplete: variant.nameComplete,
nameFormatted: variant.nameFormatted,
identifier: variant.guid,
nomenclaturalCode: variant.nomenclaturalCode,
taxonomicStatus: variant.taxonomicStatus,
nomenclaturalStatus: variant.nomenclaturalStatus,
nameAccordingTo: variant.nameAccordingTo,
nameAccordingToID: variant.nameAccordingToID,
namePublishedIn: variant.namePublishedIn,
namePublishedInYear: variant.namePublishedInYear,
namePublishedInID: variant.namePublishedInID,
nameAuthority: variant.datasetName ?: datasetName ?: grailsApplication.config.variantSourceAttribution,
taxonRemarks: variant.taxonRemarks,
provenance: variant.provenance,
infoSourceName: variant.datasetName ?: datasetName ?: grailsApplication.config.variantSourceAttribution,
infoSourceURL: variant.source ?: datasetURL,
datasetURL: datasetURL,
priority: variant.priority
]
}
]
if (taxon.taxonConceptID)
model.taxonConcept["taxonConceptID"] = taxon.taxonConceptID
if (taxon.scientificNameID)
model.taxonConcept["scientificNameID"] = taxon.scientificNameID
if (taxon.acceptedConceptID)
model.taxonConcept["acceptedConceptID"] = taxon.acceptedConceptID
if (taxon.acceptedConceptName)
model.taxonConcept["acceptedConceptName"] = taxon.acceptedConceptName
if(getAdditionalResultFields()) {
def doc = [:]
getAdditionalResultFields().each { field ->
if (taxon."${field}") {
doc.put(field, taxon."${field}")
}
}
model << doc
}
model
}
/**
* Retrieve a classification for the supplied taxonID.
*
* @param taxonID
*/
def getClassification(taxonID){
def classification = []
def taxon = retrieveTaxon(taxonID)
if (!taxon) return classification // empty list
classification.add(0, [
rank : taxon.rank,
rankID : taxon.rankID,
scientificName : taxon.scientificName,
guid:taxonID
])
//get parents
def parentGuid = taxon.parentGuid
def seen = [] as Set
def stop = false
while(parentGuid && !stop){
taxon = retrieveTaxon(parentGuid)
if(taxon && !seen.contains(taxon.guid)) {
classification.add(0, [
rank : taxon.rank,
rankID : taxon.rankID,
scientificName : taxon.scientificName,
guid : taxon.guid
])
seen.add(taxon.guid)
parentGuid = taxon.parentGuid
} else {
stop = true
}
}
classification
}
private def formatFacets(List<FacetField> facetFields, List requestedFacets = []){
def formatted = facetFields.collect { field ->
def values = field.values.collect { count ->
[ label: count.name, count: count.count, fieldValue: count.name, fq: count.asFilterQuery ]
}
[ fieldName: field.name, fieldResult: values ]
}
if (!requestedFacets)
return formatted
def ordered = []
requestedFacets.each { name ->
def facet = formatted.find { it.fieldName == name }
if (facet) {
formatted.remove(facet)
ordered << facet
}
}
ordered.addAll(formatted)
return ordered
}
/**
* Munge SOLR document set for output via JSON
*
* @param docs
* @param highlighting
* @return
*/
private List formatDocs(List<SolrDocument> docs, highlighting, params, List<Locale> locales) {
def formatted = []
def fields = params?.fields?.split(",")?.collect({ String f -> f.trim() }) as Set
// add occurrence counts
if(grailsApplication.config.biocache.occurrenceCount.enabled as Boolean){
docs = populateOccurrenceCounts(docs, params)
}
docs.each {
Map doc = null
if (it.idxtype == IndexDocType.TAXON.name()) {
def commonNameSingle = ""
def commonNames = ""
if (it.commonNameSingle)
commonNameSingle = it.commonNameSingle
if (it.commonName) {
commonNames = it.commonName.join(", ")
}
doc = [
"id" : it.id, // needed for highlighting
"guid" : it.guid,
"linkIdentifier" : it.linkIdentifier,
"idxtype" : it.idxtype,
"name" : it.scientificName,
"kingdom" : it.rk_kingdom,
"nomenclaturalCode" : it.nomenclaturalCode,
"scientificName" : it.scientificName,
"scientificNameAuthorship": it.scientificNameAuthorship,
"author" : it.scientificNameAuthorship,
"nameComplete" : it.nameComplete,
"nameFormatted" : it.nameFormatted,
"taxonomicStatus" : it.taxonomicStatus,
"nomenclaturalStatus" : it.nomenclaturalStatus,
"parentGuid" : it.parentGuid,
"rank" : it.rank,
"rankID" : it.rankID ?: -1,
"commonName" : commonNames,
"commonNameSingle" : commonNameSingle,
"occurrenceCount" : it.occurrenceCount,
"conservationStatus" : it.conservationStatus,
"favourite" : it.favourite,
"infoSourceName" : it.datasetName,
"infoSourceURL" : "${grailsApplication.config.collectory.base}/public/show/${it.datasetID}"
]
if (it.acceptedConceptID) {
doc.put("acceptedConceptID", it.acceptedConceptID)
if (it.acceptedConceptName)