Package 'geonapi'

Description

Provides an R interface to the 'GeoNetwork' API (<https://geonetwork-opensource.org/#api>) allowing to upload and publish metadata in a 'GeoNetwork' web-application and expose it to OGC CSW Web-Services (Catalogue Service for the Web).

Author(s)

Emmanuel Blondel [email protected]

Description

GNAbstractManager

GNAbstractManager

Format

R6Class object.

Value

Object of R6Class with methods for communication with the REST API of a GeoNetwork instance.

Public fields

Methods

Public methods

• GNAbstractManager$logger()

• GNAbstractManager$INFO()

• GNAbstractManager$WARN()

• GNAbstractManager$ERROR()

• GNAbstractManager$new()

• GNAbstractManager$getUrl()

• GNAbstractManager$getLang()

• GNAbstractManager$login()

• GNAbstractManager$getClassName()

• GNAbstractManager$clone()

Method logger()

Provides log messages

Usage

GNAbstractManager$logger(type, text)

Arguments

Method INFO()

Provides INFO log messages

Usage

GNAbstractManager$INFO(text)

Arguments

Method WARN()

Provides WARN log messages

Usage

GNAbstractManager$WARN(text)

Arguments

Method ERROR()

Provides ERROR log messages

Usage

GNAbstractManager$ERROR(text)

Arguments

Method new()

This method is used to instantiate a GNAbstractManager with the url of the GeoNetwork and credentials to authenticate (user/pwd). By default, the logger argument will be set to NULL (no logger).

The keyring_backend can be set to use a different backend for storing the Geonetwork password/token with keyring (Default value is 'env').

The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Usage

GNAbstractManager$new(
  url,
  user = NULL,
  pwd = NULL,
  version,
  logger = NULL,
  keyring_backend = "env"
)

Arguments

Method getUrl()

Get URL

Usage

GNAbstractManager$getUrl()

Returns

an object of class character

Method getLang()

Get service language

Usage

GNAbstractManager$getLang()

Returns

an object of class character

Method login()

Log-ins. This methods (here abstract) attempts a connection to GeoNetwork API. Used internally by subclasses of GNAbstractManager to login Geonetwork.

Usage

GNAbstractManager$login(user, pwd)

Arguments

Method getClassName()

Get class name

Usage

GNAbstractManager$getClassName()

Returns

an object of class character

Method clone()

The objects of this class are cloneable with this method.

Usage

GNAbstractManager$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Description

GNLegacyAPIManager

GNLegacyAPIManager

Format

R6Class object.

Value

Object of R6Class with methods for communication with the REST API of a GeoNetwork instance using the legacy API.

Super class

geonapi::GNAbstractManager -> GNLegacyAPIManager

Methods

Public methods

• GNLegacyAPIManager$new()

• GNLegacyAPIManager$login()

• GNLegacyAPIManager$getGroups()

• GNLegacyAPIManager$getCategories()

• GNLegacyAPIManager$insertMetadata()

• GNLegacyAPIManager$setPrivConfiguration()

• GNLegacyAPIManager$get()

• GNLegacyAPIManager$getMetadataByID()

• GNLegacyAPIManager$getMetadataByUUID()

• GNLegacyAPIManager$getInfoByID()

• GNLegacyAPIManager$getInfoByUUID()

• GNLegacyAPIManager$updateMetadata()

• GNLegacyAPIManager$deleteMetadata()

• GNLegacyAPIManager$deleteMetadataAll()

• GNLegacyAPIManager$clone()

Method new()

This method is used to instantiate a GNLegacyAPIManager with the url of the GeoNetwork and credentials to authenticate (user/pwd).

The keyring_backend can be set to use a different backend for storing the Geonetwork password/token with keyring (Default value is 'env').

The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Usage

GNLegacyAPIManager$new(
  url,
  user = NULL,
  pwd = NULL,
  version,
  logger = NULL,
  keyring_backend = "env"
)

Arguments

Method login()

#' This methods attempts a connection to GeoNetwork REST API. User internally during initialization of GNLegacyAPIManager.

Usage

GNLegacyAPIManager$login(user, pwd)

Arguments

Method getGroups()

Retrieves the list of user groups available in Geonetwork

Usage

GNLegacyAPIManager$getGroups()

Returns

an object of class data.frame

Method getCategories()

Retrieves the list of categories available in Geonetwork

Usage

GNLegacyAPIManager$getCategories()

Returns

an object of class data.frame

Method insertMetadata()

Inserts a metadata by file, XML object or geometa object of class ISOMetadata or ISOFeatureCatalogue. If successful, returns the Geonetwork metadata internal identifier (integer). Extra parameters geometa_validate (TRUE by default) and geometa_inspire (FALSE by default) can be used with geometa objects for perform ISO and INSPIRE validation respectively. In that case on object of class geometa::INSPIREMetadataValidator, with a proper user API key, should be specified as geometa_inspireValidator argument.

Usage

GNLegacyAPIManager$insertMetadata(
  xml = NULL,
  file = NULL,
  geometa = NULL,
  group,
  category = NULL,
  stylesheet = NULL,
  validate = FALSE,
  geometa_validate = TRUE,
  geometa_inspire = FALSE,
  geometa_inspireValidator = NULL
)

Arguments

Method setPrivConfiguration()

Set the privilege configuration for a metadata. 'id' is the metadata integer id. 'config' is an object of class "GNPrivConfiguration".

Usage

GNLegacyAPIManager$setPrivConfiguration(id, config)

Arguments

Method get()

Generic getter for metadata. Possible values for by are 'id', 'uuid'. Used internally only. The 'output' argument gives the type of output to return, with possible values "id", "metadata", "info".

Usage

GNLegacyAPIManager$get(id, by, output)

Arguments

Method getMetadataByID()

Get a metadata by Id

Usage

GNLegacyAPIManager$getMetadataByID(id)

Arguments

Returns

an object of class ISOMetadata (ISO 19115) or ISOFeatureCatalogue (ISO 19110) (from geometa package)

Method getMetadataByUUID()

Get a metadata by UUID

Usage

GNLegacyAPIManager$getMetadataByUUID(uuid)

Arguments

Returns

an object of class ISOMetadata (ISO 19115) or ISOFeatureCatalogue (ISO 19110) (from geometa package)

Method getInfoByID()

Get a metadata Info by Id.

Usage

GNLegacyAPIManager$getInfoByID(id)

Arguments

Returns

an XML document object

Method getInfoByUUID()

Get a metadata Info by UUID

Usage

GNLegacyAPIManager$getInfoByUUID(uuid)

Arguments

Returns

an XML document object

Method updateMetadata()

Updates a metadata by file, XML object or geometa object of class 'ISOMetadata' or 'ISOFeatureCatalogue'. Extra parameters geometa_validate (TRUE by default) and geometa_inspire (FALSE by default) can be used with geometa objects for perform ISO and INSPIRE validation respectively. In that case on object of class geometa::INSPIREMetadataValidator, with a proper user API key, should be specified as geometa_inspireValidator argument.

Usage

GNLegacyAPIManager$updateMetadata(
  id,
  xml = NULL,
  file = NULL,
  geometa = NULL,
  geometa_validate = TRUE,
  geometa_inspire = FALSE,
  geometa_inspireValidator = NULL
)

Arguments

Method deleteMetadata()

Deletes metadata by Id.

Usage

GNLegacyAPIManager$deleteMetadata(id)

Arguments

Returns

the id of the record deleted, NULL otherwise

Method deleteMetadataAll()

Deletes all metadata

Usage

GNLegacyAPIManager$deleteMetadataAll()

Method clone()

The objects of this class are cloneable with this method.

Usage

GNLegacyAPIManager$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
   GNLegacyAPIManager$new("http://localhost:8080/geonetwork", "admin", "geonetwork", "3.0.0")

## End(Not run)

Description

The function GNManager$new will set-up the right Geonetwork manager depending on the GeoNetwork version specified by the user. For the time-being, GeoNetwork with version < 4 will be interfaced with the GeoNetwork legacy API (see detailed documentation at GNLegacyAPIManager), while starting with GeoNetwork 3.2, the new GeoNetwork OpenAPI will be used.

Format

R6Class object.

Value

Object of R6Class with methods for communication with the API of a GeoNetwork instance.

Super class

geonapi::GNAbstractManager -> GNManager

Methods

Public methods

• GNManager$new()

• GNManager$clone()

Method new()

Initializes a GNManager

Usage

GNManager$new(url, user = NULL, pwd = NULL, version, logger = NULL)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

GNManager$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
   GMManager$new("http://localhost:8080/geonetwork", "admin", "geonetwork", "3.0.0")

## End(Not run)

Description

GNOpenAPIManager

GNOpenAPIManager

Format

R6Class object.

Value

Object of R6Class with methods for communication with the REST API of a GeoNetwork instance using the legacy API.

Super class

geonapi::GNAbstractManager -> GNOpenAPIManager

Methods

Public methods

• GNOpenAPIManager$new()

• GNOpenAPIManager$login()

• GNOpenAPIManager$getGroups()

• GNOpenAPIManager$getTags()

• GNOpenAPIManager$getCategories()

• GNOpenAPIManager$getMetadataByUUID()

• GNOpenAPIManager$insertRecord()

• GNOpenAPIManager$insertMetadata()

• GNOpenAPIManager$updateMetadata()

• GNOpenAPIManager$deleteMetadata()

• GNOpenAPIManager$uploadAttachment()

• GNOpenAPIManager$publishThumbnail()

• GNOpenAPIManager$doiCheckPreConditions()

• GNOpenAPIManager$createDOI()

• GNOpenAPIManager$deleteDOI()

• GNOpenAPIManager$clone()

Method new()

This method is used to instantiate a GNOpenAPIManager with the url of the GeoNetwork and credentials to authenticate (user/pwd).

The keyring_backend can be set to use a different backend for storing the Geonetwork password/token with keyring (Default value is 'env').

The logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

Usage

GNOpenAPIManager$new(
  url,
  user = NULL,
  pwd = NULL,
  version,
  logger = NULL,
  keyring_backend = "env"
)

Arguments

Method login()

This methods attempts a connection to GeoNetwork REST API. User internally during initialization of GNLegacyAPIManager.

Usage

GNOpenAPIManager$login(user, pwd)

Arguments

Method getGroups()

Retrieves the list of user groups available in Geonetwork

Usage

GNOpenAPIManager$getGroups()

Returns

an object of class data.frame

Method getTags()

Retrieves the list of tags (categories) available in Geonetwork

Usage

GNOpenAPIManager$getTags()

Returns

an object of class data.frame

Method getCategories()

Retrieves the list of categories (same as tags) available in Geonetwork

Usage

GNOpenAPIManager$getCategories()

Returns

an object of class data.frame

Method getMetadataByUUID()

Get a metadata by UUID.

Usage

GNOpenAPIManager$getMetadataByUUID(
  uuid,
  addSchemaLocation = TRUE,
  increasePopularity = TRUE,
  approved = TRUE
)

Arguments

Returns

Returns an object of class ISOMetadata (ISO 19115) or ISOFeatureCatalogue (ISO 19110) (from geometa package)

Method insertRecord()

Inserts a record by file, XML object or geometa object of class ISOMetadata or ISOFeatureCatalogue. Extra parameters related to geometa objects: geometa_validate (TRUE by default) and geometa_inspire (FALSE by default) can be used to perform ISO and INSPIRE validation respectively. In that case on object of class geometa::INSPIREMetadataValidator, with a proper user API key, should be specified as geometa_inspireValidator argument.

Usage

GNOpenAPIManager$insertRecord(
  xml = NULL,
  file = NULL,
  geometa = NULL,
  metadataType = "METADATA",
  uuidProcessing = "NOTHING",
  group,
  category = NULL,
  rejectIfInvalid = FALSE,
  publishToAll = TRUE,
  transformWith = "_none_",
  schema = NULL,
  extra = NULL,
  geometa_validate = TRUE,
  geometa_inspire = FALSE,
  geometa_inspireValidator = NULL
)

Arguments

Method insertMetadata()

Inserts a metadata by file, XML object or geometa object of class ISOMetadata or ISOFeatureCatalogue. Extra parameters related to geometa objects: geometa_validate (TRUE by default) and geometa_inspire (FALSE by default) can be used to perform ISO and INSPIRE validation respectively. In that case on object of class geometa::INSPIREMetadataValidator, with a proper user API key, should be specified as geometa_inspireValidator argument.

Usage

GNOpenAPIManager$insertMetadata(
  xml = NULL,
  file = NULL,
  geometa = NULL,
  metadataType = "METADATA",
  uuidProcessing = "NOTHING",
  group,
  category = NULL,
  rejectIfInvalid = FALSE,
  publishToAll = TRUE,
  transformWith = "_none_",
  schema = NULL,
  extra = NULL,
  geometa_validate = TRUE,
  geometa_inspire = FALSE,
  geometa_inspireValidator = NULL
)

Arguments

Method updateMetadata()

Inserts a metadata by file, XML object or geometa object of class ISOMetadata or ISOFeatureCatalogue. Extra parameters related to geometa objects: geometa_validate (TRUE by default) and geometa_inspire (FALSE by default) can be used to perform ISO and INSPIRE validation respectively. In that case on object of class geometa::INSPIREMetadataValidator, with a proper user API key, should be specified as geometa_inspireValidator argument.

Usage

GNOpenAPIManager$updateMetadata(
  xml = NULL,
  file = NULL,
  geometa = NULL,
  metadataType = "METADATA",
  group,
  category = NULL,
  rejectIfInvalid = FALSE,
  publishToAll = TRUE,
  transformWith = "_none_",
  schema = NULL,
  extra = NULL,
  geometa_validate = TRUE,
  geometa_inspire = FALSE,
  geometa_inspireValidator = NULL
)

Arguments

Method deleteMetadata()

Deletes a metadata by ID

Usage

GNOpenAPIManager$deleteMetadata(id, withBackup = TRUE)

Arguments

Method uploadAttachment()

Uploads attachment

Usage

GNOpenAPIManager$uploadAttachment(
  id,
  file,
  visibility = "public",
  approved = TRUE
)

Arguments

Returns

a named list of the uploaded attachment, including the url, size, id and type, NULL otherwise

Method publishThumbnail()

Publishes thumbnail based on URL

Usage

GNOpenAPIManager$publishThumbnail(id, url, desc = "")

Arguments

Returns

TRUE if published, FALSE otherwise

Method doiCheckPreConditions()

Checks pre-conditions to publish DOI

Usage

GNOpenAPIManager$doiCheckPreConditions(id)

Arguments

Returns

TRUE if DOI pre-conditions are fulfiled, FALSE otherwise

Method createDOI()

Submit a record to the Datacite metadata store in order to create a DOI.

Usage

GNOpenAPIManager$createDOI(id)

Arguments

Returns

TRUE if metadata record has been submitted with DOI created, FALSE otherwise

Method deleteDOI()

Remove a DOI (this is not recommended, DOI are supposed to be persistent once created. This is mainly here for testing).

Usage

GNOpenAPIManager$deleteDOI(id)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

GNOpenAPIManager$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
   GNOpenAPIManager$new("http://localhost:8080/geonetwork", "admin", "geonetwork", "4.0.5")

## End(Not run)

Description

This class is an utility to configure privileges

This class is an utility to configure privileges

Format

R6Class object.

R6Class object.

Details

GeoNetwork REST API - GeoNetwork privilege configuration

GeoNetwork REST API - GeoNetwork privilege configuration

Value

Object of R6Class for modelling a GeoNetwork Privilege configuration

Object of R6Class for modelling a GeoNetwork Privilege configuration

Public fields

Methods

Public methods

• GNPriv$new()

• GNPriv$clone()

Method new()

Initializes a GNPriv object

Usage

GNPriv$new(group, privileges)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

GNPriv$clone(deep = FALSE)

Arguments

Public fields

Methods

Public methods

• GNPrivConfiguration$new()

• GNPrivConfiguration$setPrivileges()

• GNPrivConfiguration$clone()

Method new()

Initializes an object of class GNPrivConfiguration

Usage

GNPrivConfiguration$new()

Method setPrivileges()

Sets the operation privileges for a particular group. Allowed group values are "guest","intranet" and "all". Allowed values for operation privileges are "view", "download", "editing", "notify", "dynamic" and "featured".

Usage

GNPrivConfiguration$setPrivileges(group, privileges)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

GNPrivConfiguration$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
 priv <- GNPriv$new(group="all", privileges=c("view","dynamic","featured"))

## End(Not run)

## Not run: 
 pcfg <- GNPrivConfiguration$new()
 pcfg$setPrivileges("all", c("view","dynamic","featured"))

## End(Not run)

Description

GeoNetwork REST API REST Request

GeoNetwork REST API REST Request

Format

R6Class object.

Value

Object of R6Class for modelling a GeoNetwork REST request

Public fields

Methods

Public methods

• GNRESTRequest$new()

• GNRESTRequest$setChild()

• GNRESTRequest$encode()

• GNRESTRequest$clone()

Method new()

Initializes a GNRESTRequest

Usage

GNRESTRequest$new(...)

Arguments

Method setChild()

Set child

Usage

GNRESTRequest$setChild(key, value)

Arguments

Method encode()

Encodes request as XML

Usage

GNRESTRequest$encode()

Returns

an object of class character representing the XML

Method clone()

The objects of this class are cloneable with this method.

Usage

GNRESTRequest$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Description

GeoNetwork REST API Manager Utils

GeoNetwork REST API Manager Utils

Format

R6Class object.

Value

Object of R6Class with static util methods for communication with the REST API of a GeoNetwork instance.

Static methods

getUserAgent()

This method is used to get the user agent for performing GeoNetwork API requests. Here the user agent will be compound by geonapi package name and version.

getUserToken(user, pwd)

This method is used to get the user authentication token for performing GeoNetwork API requests. Token is given a Base64 encoded string.

GET(url, path, token, verbose)

This method performs a GET request for a given path to GeoNetwork REST API

PUT(url, path, token, filename, contentType, verbose)

This method performs a PUT request for a given path to GeoNetwork REST API, to upload a file of name filename with given contentType

POST(url, path, token, content, contentType, encode, verbose)

This method performs a POST request for a given path to GeoNetwork REST API, to post content of given contentType

DELETE(url, path, token, verbose)

This method performs a DELETE request for a given GeoNetwork resource identified by a path in GeoNetwork REST API

parseResponseXML(req)

Convenience method to parse XML response from GeoNetwork REST API. Although package httr suggests the use of xml2 package for handling XML, geonapi still relies on the package XML. Response from httr is retrieved as text, and then parsed as XML 'xmlParse' function.

getPayloadXML(obj)

Convenience method to create payload XML to send to GeoNetwork.

Methods

Public methods

• GNUtils$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

GNUtils$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Description

This class is an utility wrap the Geonetwork version

Format

R6Class object.

Details

GeoNetwork REST API - GeoNetwork Version

Value

Object of R6Class for modelling a GeoNetwork version

Public fields

Methods

Public methods

• GNVersion$new()

• GNVersion$lowerThan()

• GNVersion$greaterThan()

• GNVersion$equalTo()

• GNVersion$clone()

Method new()

Initializes an object of class GNVersion

Usage

GNVersion$new(version)

Arguments

Method lowerThan()

Compares to a version and returns TRUE if it is lower, FALSE otherwise

Usage

GNVersion$lowerThan(version)

Arguments

Returns

TRUE if lower, FALSE otherwise

Method greaterThan()

Compares to a version and returns TRUE if it is greater, FALSE otherwise

Usage

GNVersion$greaterThan(version)

Arguments

Returns

TRUE if lower, FALSE otherwise

Method equalTo()

Compares to a version and returns TRUE if it is equal, FALSE otherwise

Usage

GNVersion$equalTo(version)

Arguments

Returns

TRUE if lower, FALSE otherwise

Method clone()

The objects of this class are cloneable with this method.

Usage

GNVersion$clone(deep = FALSE)

Arguments

Author(s)

Emmanuel Blondel <[email protected]>

Examples

## Not run: 
version <- GNVersion$new("2.6.4")

## End(Not run)