Angular service

BiocacheService source

Description

Methods to interact with ALA biocache-service

Methods

bbox (query) -> Promise(List)

Get query longitude and latitude bounding box

Example

Input:
- query
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
Output:
[[-180, -90], [180, 90]]

Parameters

NameTypeDescription
query Query

Biocache query

Returns

TypeDescription
Promise(List)

southWest corner and northEast corner as decimal latitude and longitude

constructSearchResultUrl (query, fqs, pageSize, offset, facet) -> Promise(String)

General search query URL

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 "http://biocache-ws.ala.org.au/ws/occurrences/search?q=Macropus&fq=geospatial_kosher:true&pageSize=1&offset=0&facet=false"

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms
pageSize Integer

(Optional) page size (default=1)
offset Integer

(Optional) offset (default=0)
facet Boolean

(Optional) include server default facets (default=false)

Returns

TypeDescription
Promise(String)

search URL

count (query, fqs) -> Promise(Integer)

Get number of occurrences

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 500

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(Integer)

number of occurrences

dataProviderList (query, fqs) -> Promise(List)

List data providers

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 []

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(List)

List of data proviers

facet (facet, query) -> Promise(List)

Get facet list

Example

Input:
- facet
 "taxon_name"
- query
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
Output:
[{
                    "name": "Macropus giganteus",
                    "count": 70654,
                    "colour": 0,
                    "fq": "taxon_name:\"Macropus giganteus\"",
                    "red": 51,
                    "blue": 204,
                    "green": 102,
                    "displayname": "Macropus giganteus"
                    },
                 {
                 "name": "Osphranter rufus",
                 "count": 47542,
                 "colour": 0,
                 "fq": "taxon_name:\"Osphranter rufus\"",
                  "red": 220,
                  "blue": 18,
                  "green": 57
                  }]

Parameters

NameTypeDescription
facet String

Facet name
query Query

Biocache query

Returns

TypeDescription
Promise(List)

facets

facetGeneral (facet, query, pageSize, offset, prefixFilter, sortBy, config) -> Promise(List)

Get pageable facet list

Example

Input:
- facet
 "taxon_name"
- query
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
Output:
[{
                     "fieldName": "taxon_name",
                     "fieldResult":
                        [{
                         "label": "Macropus giganteus",
                         "count": 70654,
                         "fq": "taxon_name:\"Macropus giganteus\"",
                         "displaylabel": "Macropus giganteus"
                         },
                         {
                         "label": "Osphranter rufus",
                         "count": 47542,
                         "fq": "taxon_name:\"Osphranter rufus\"",
                         "displaylabel": "Osphranter rufus"
                         }]
                     }]

Parameters

NameTypeDescription
facet String

Facet name
query Query

Biocache query
pageSize Integer

(Optional) page size (default=1)
offset Integer

(Optional) offset (default=0)
prefixFilter String

(Optional) keywords
sortBy String

(Optional) sorted by field (default=count)
config List

(Optional) parameters for $http#get

Returns

TypeDescription
Promise(List)

facets

joinAndEncode (list) -> String

Encode and join a list of q and fq terms

Parameters

NameTypeDescription
list List

q and fqs

Returns

TypeDescription
String

query parameters as a string

newLayer (query, area, name) -> Promise(Layer)

Create a new #Layer suitable for adding to #MapService

Example

Input:
- q
 ["taxon_name:Macropus"]
Output:
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au",
     "name": ""
 }

Parameters

NameTypeDescription
query List

q and fq terms
area Area

(optional) area to limit the query
name newName

(optional) name for display

Returns

TypeDescription
Promise(Layer)

newLayerAddFq (query, fq, name) -> Promise(Layer)

Create a new query #Layer

Example

Input:
- q
 ["taxon_name:Macropus"]
Output:
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au",
     "name": ""
 }

Parameters

NameTypeDescription
query List

q and fq terms
fq String

(optional) one fq term
name newName

(optional) name for display

Returns

TypeDescription
Promise(Layer)

newQuery (query, name, wkt) -> Query

Create a new #Query

Example

Input:
- q
 ["taxon_name:Macropus"]
Output:
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au",
     "name": ""
 }

Parameters

NameTypeDescription
query List

q and fq terms
name name

(optional) name for display
wkt String

(optional) WKT search value

Returns

TypeDescription
Query

queryTitle (query, fqs) -> Promise(String)

Get the default query title

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 "<span>Macropus</span>"

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(String)

formatted biocache-service query title

registerLayer (wsUrl, hubUrl, fqs, wkt, qualityProfile, disableQualityFilter, disableAllQualityFilters, name) -> Promise(Layer)

Create a layer and register for qid

Example

Input:
- bs
 "https://biocache-ws.ala.org.au/ws"
- ws
 "https://biocache.ala.org.au"
- fq
 ["taxon_name:Macropus"]
Output:
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au",
     "name": ""
 }

Parameters

NameTypeDescription
wsUrl String

biocache-service URL
hubUrl String

biocache-hub URL
fqs List

q and fq terms
wkt String

(optional) WKT
qualityProfile String

(optional) quality profile
disableQualityFilter Array

(optional) quality filters to disable
disableAllQualityFilters Boolean

(optional) whether to disable all quality filters
name newName

(optional) name for display

Returns

TypeDescription
Promise(Layer)

registerParam (url, query, fq, wkt, qualityProfile, disableQualityFilter, disableAllQualityFilters) -> Promise(Integer)

Get qid for a query

Example

Input:
- bs
 "https://biocache-ws.ala.org.au/ws"
- q
 ["taxon_name:Macropus"]
Output:
1234

Parameters

NameTypeDescription
url String

biocache-service URL
query List

q and fq terms
fq List

(optional) one fq term
wkt String

(optional) WKT search value
qualityProfile String

(optional) quality profile
disableQualityFilter Array

(optional) quality filters to disable
disableAllQualityFilters Boolean

(optional) whether to disable all quality filters

Returns

TypeDescription
Promise(Integer)

qid

registerQuery (query) -> Promise(Query)

Shorten a query

Example

Input:
- query
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
Output:
{
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au",
     "qid": 1234
 }

Parameters

NameTypeDescription
query Query

Biocache query

Returns

TypeDescription
Promise(Query)

qid

searchForOccurrences (query, fqs, pageSize, offset, facet) -> Promise(Map)

Get search query output

Example

Input:
- query
 {
     "q": ["taxon_name:Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- pageSize
 0
Output:
{
 "pageSize": 0,
 "startIndex": 0,
 "totalRecords": 736,
 "sort": "score",
 "dir": "asc",
 "status": "OK",
 "occurrences": [],
 "facetResults": [],
 "query": "?q=taxon_name%3AMacropus",
 "urlParameters": "?q=taxon_name%3AMacropus",
 "queryTitle": "Scientific name:Macropus",
 "activeFacetMap": {}
 }

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms
pageSize Integer

(Optional) page size (default=1)
offset Integer

(Optional) offset (default=0)
facet Boolean

(Optional) include server default facets (default=false)

Returns

TypeDescription
Promise(Map)

search results

speciesCount (query, fqs) -> Promise(Integer)

Get the number of unique species (by facet names_and_lsid)

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Ouput:
 10

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(Integer)

Number of unique species

speciesCountEndemic (query, fqs) -> Promise(Integer)

Get the number of unique endemic species (by facet names_and_lsid)

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Ouput:
 2

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(Integer)

Number of unique endemic species

speciesList (query, fqs, config) -> Promise(String)

Get species list CSV

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
- config
Ouput:
 "names_and_lsid","Species Name","Scientific Name Authorship","Taxon Rank","Kingdom","Phylum","Class","Order","Family","Genus","Vernacular Name","Number of records","Conservation","Invasive"
 "Macropus giganteus|urn:lsid:biodiversity.org.au:afd.taxon:23f4784e-1116-482c-8e3e-b6b12733f588|Eastern Grey Kangaroo|Animalia|Macropodidae","Macropus giganteus","Shaw, 1790","species","ANIMALIA","CHORDATA","MAMMALIA","DIPROTODONTIA","MACROPODIDAE","Macropus","Eastern Grey Kangaroo","70654","South Australia : Conservation Status",""
 "Osphranter rufus|urn:lsid:biodiversity.org.au:afd.taxon:e6aff6af-ff36-4ad5-95f2-2dfdcca8caff|Red Kangaroo|Animalia|Macropodidae","Osphranter rufus","(Desmarest, 1822)","species","ANIMALIA","CHORDATA","MAMMALIA","DIPROTODONTIA","MACROPODIDAE","Osphranter","Red Kangaroo","47542","Northern Territory : Conservation Status",""

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms
config Map

(Optional) parameters for $http#get

Returns

TypeDescription
Promise(String)

Species list CSV

speciesListEndemic (query, fqs) -> Promise(String)

Get the endemic species list as CSV

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 ```
 names_and_lsid    Species Name    Scientific Name Authorship    Taxon Rank    Kingdom    Phylum    Class    Order    Family    Genus    Vernacular Name    Number of records
 Notamacropus agilis agilis|urn:lsid:biodiversity.org.au:afd.taxon:471127b3-a2c1-430e-931d-938cce4e58e8||Animalia|Macropodidae"    Notamacropus agilis agilis    (Gould, 1842)    subspecies    ANIMALIA    CHORDATA    MAMMALIA    DIPROTODONTIA    MACROPODIDAE    Notamacropus        130
 Notamacropus agilis jardinii|urn:lsid:biodiversity.org.au:afd.taxon:bfe816bf-2b7e-47cb-87f8-ac386af751ab||Animalia|Macropodidae"    Notamacropus agilis jardinii    (De Vis, 1884)    subspecies    ANIMALIA    CHORDATA    MAMMALIA    DIPROTODONTIA    MACROPODIDAE    Notamacropus        451
 ```

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(String)

CSV of endemic species list

speciesListEndemicUrl (query, fqs) -> Promise(String)

Build URL to GET endemic species list CSV

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 "http://biocache.ala.org.au/ws/explore/endemic/species/1234.csv?facets=names_and_lsid&lookup=true&count=true&lists=true"

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(String)

GET URL to endemic species list CSV

speciesListUrl (query, fqs) -> Promise(String)

Build URL to GET species list CSV

Example

Input:
- query
 {
     "q": ["Macropus"],
     "bs": "https://biocache-ws.ala.org.au/ws",
     "ws": "https://biocache.ala.org.au"
 }
- fqs
 ["geospatial_kosher:true"]
Output:
 "https://biocache-ws.ala.org.au/ws/occurrences/facets/download?facets=names_and_lsid&lookup=true&count=true&lists=true&q=Macropus&fq=geospatial_kosher:true"

Parameters

NameTypeDescription
query Query

Biocache query
fqs List

(Optional) additional fq terms

Returns

TypeDescription
Promise(String)

GET URL to species list CSV