SpecimenClient | R Documentation |
This client connects to all Specimen-related endpoints of the NBA. Each endpoint is available as a class method (see section 'Methods' below). Optionally, a custom URL pointing to a NBA server and a user Agent can be specified by the user (see section 'Fields' below).
# client <- SpecimenClient$new()
R6 class
basePath
Stores url path of the request, defaults to http://api.biodiversitydata.nl/v2
userAgent
Set the user agent of the request, defaults to nbaR/0.1.0
count
Get the number of specimens matching a given condition; Conditions given as query parameters or a querySpec JSON.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
integer
count_distinct_values
Count the distinct number of values that exist for a given field; See also endpoint /getDistinctValues.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
field
: Name of field in the specimen object
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
integer
count_distinct_values_per_group
Count the distinct number of field values that exist per the given field to group by; See also endpoint /getDistinctValuesPerGroup.
Parameters:
group
: Name of field in the specimen object you want to group by
field
: Name of field in the specimen object
...
: additional parameters passed to httr::GET
Returns:
list
download_query
Dynamic download service: Query for specimens and return result as a stream ...; Query with query parameters or querySpec JSON. ....
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
Specimen
dwca_get_data_set
Download dataset as Darwin Core Archive File; Available datasets can be queried with /specimen/dwca/getDataSetNames. Response saved to <datasetname>-<yyyymmdd>.dwca.zip.
Parameters:
dataset
: name of dataset
filename
: location to save data, defaults to format(Sys.time(), "download-%Y-%m-%dT%H:%m.zip")
...
: additional parameters passed to httr::GET
Returns:
dwca_get_data_set_names
Retrieve the names of all available datasets; Individual datasets can then be downloaded with /dwca/getDataSet/dataset.
Parameters:
...
: additional parameters passed to httr::GET
Returns:
character
dwca_query
Dynamic download service: Query for specimens and return result as Darwin Core Archive File; Query with query parameters or querySpec JSON. Response saved to nba-specimens.dwca.zip.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
queryParams
: named list or vector with query parameters
filename
: location to save data, defaults to format(Sys.time(), "download-%Y-%m-%dT%H:%m.zip")
...
: additional parameters passed to httr::GET
Returns:
exists
Returns whether or not a unitID for a specimen exists; Returns either true or false.
Parameters:
unit_id
: the unitID of the specimen to query
...
: additional parameters passed to httr::GET
Returns:
logical
find
Find a specimen by id; If found, returns a single specimen.
Parameters:
id
: id of specimen
...
: additional parameters passed to httr::GET
Returns:
Specimen
find_by_ids
Find specimens by ids; Given multiple ids, returns a list of specimen.
Parameters:
ids
: ids of multiple specimen, separated by comma
...
: additional parameters passed to httr::GET
Returns:
Specimen
find_by_unit_id
Find a specimen by unitID; Get a specimen by its unitID. Returns a list of specimens since unitIDs are not strictly unique.
Parameters:
unit_id
: the unitID of the specimen to query
...
: additional parameters passed to httr::GET
Returns:
Specimen
get_distinct_values
Get all different values that exist for a field; A list of all fields for specimen documents can be retrieved with /metadata/getFieldInfo.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
field
: Name of field in specimen object
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
list
get_distinct_values_per_group
Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by; See also endpoint /getDistinctValues.
Parameters:
group
: Name of field in the specimen object you want to group by
field
: Name of field in the specimen object
...
: additional parameters passed to httr::GET
Returns:
list
get_field_info
Returns extended information for each field of a specimen document; Info consists of whether the fields is indexed, the ElasticSearch datatype and a list of allowed operators.
Parameters:
...
: additional parameters passed to httr::GET
Returns:
list
get_ids_in_collection
Retrieve all ids within a 'special collection' of specimens; Available collections can be queried with /getNamedCollections.
Parameters:
name
: name of dataset
...
: additional parameters passed to httr::GET
Returns:
character
get_named_collections
Retrieve the names of all 'special collections' of specimens; See also here: http://bioportal.naturalis.nl/collecties.
Parameters:
...
: additional parameters passed to httr::GET
Returns:
character
get_paths
Returns the full path of all fields within a document; See also metadata/getFieldInfo for all allowed operators per field.
Parameters:
...
: additional parameters passed to httr::GET
Returns:
character
get_setting
Get the value of an NBA setting; All settings can be queried with /metadata/getSettings.
Parameters:
name
: name of setting
...
: additional parameters passed to httr::GET
Returns:
list
get_settings
List all publicly available configuration settings for the NBA; The value of a specific setting can be queried with metadata/getSetting/name.
Parameters:
...
: additional parameters passed to httr::GET
Returns:
list
group_by_scientific_name
Aggregates Taxon and Specimen documents according to their scientific names; Returns a list with ScientificNameGroups, which contain Taxon and Specimen documents that share a scientific name.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
QueryResult
is_operator_allowed
Checks if a given operator is allowed for a given field; See also metadata/getFieldInfo.
Parameters:
field
: specimen document field
operator
: operator
...
: additional parameters passed to httr::GET
Returns:
logical
query
Query for specimens; Search for specimens (GET) using query parameters or a querySpec JSON.
Parameters:
query_spec
: Object of type QuerySpec or its JSON representation
queryParams
: named list or vector with query parameters
...
: additional parameters passed to httr::GET
Returns:
QueryResult
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