Package {geoflow}

Version: 1.4.0
Date: 2026-09-04
Title: Orchestrate Geospatial (Meta)Data Management Workflows and Manage FAIR Services
Description: An engine to facilitate the orchestration and execution of metadata-driven data management workflows, in compliance with 'FAIR' (Findable, Accessible, Interoperable and Reusable) data management principles. By means of a pivot metadata model, relying on the 'DublinCore' standard (https://dublincore.org/), a unique source of metadata can be used to operate multiple and inter-connected data management actions. Users can also customise their own workflows by creating specific actions but the library comes with a set of native actions targeting common geographic information and data management, in particular actions oriented to the publication on the web of metadata and data resources to provide standard discovery and access services. At first, default actions of the library were meant to focus on providing turn-key actions for geospatial (meta)data: 1) by creating manage geospatial (meta)data complying with 'ISO/TC211' (https://committee.iso.org/home/tc211) and 'OGC' (https://www.ogc.org/standards/) geographic information standards (eg 19115/19119/19110/19139) and related best practices (eg. 'INSPIRE'); and 2) by facilitating extraction, reading and publishing of standard geospatial (meta)data within widely used software that compound a Spatial Data Infrastructure ('SDI'), including spatial databases (eg. 'PostGIS'), metadata catalogues (eg. 'GeoNetwork', 'CSW' servers), data servers (eg. 'GeoServer'). The library was then extended to actions for other domains: 1) biodiversity (meta)data standard management including handling of 'EML' metadata, and their management with 'DataOne' servers, 2) in situ sensors, remote sensing and model outputs (meta)data standard management by handling part of 'CF' conventions, 'NetCDF' data format and 'OPeNDAP' access protocol, and their management with 'Thredds' servers, 3) generic / domain agnostic (meta)data standard managers ('DublinCore', 'DataCite'), to facilitate the publication of data within (meta)data repositories such as 'Zenodo' (https://zenodo.org) or DataVerse (https://dataverse.org/). The execution of several actions will then allow to cross-reference (meta)data resources in each action performed, offering a way to bind resources between each other (eg. reference 'Zenodo' 'DOI' in 'GeoNetwork'/'GeoServer' metadata, or vice versa reference 'GeoNetwork'/'GeoServer' links in 'Zenodo' or 'EML' metadata). The use of standardized configuration files ('JSON' or 'YAML' formats) allow fully reproducible workflows to facilitate the work of data and information managers.
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Depends: R (≥ 3.3)
Imports: R6, methods, dotenv, benchmarkme, httr, mime, jsonlite, yaml, XML, xml2, rdflib, curl, whisker, digest, dplyr, readr, arrow, zip, png, uuid, sf, sfarrow, lwgeom, smoothr, terra, geometa (≥ 0.9), geosapi (≥ 0.8), geonapi (≥ 0.8-1), geonode4R (≥ 0.1-2), ows4R (≥ 0.5)
Suggests: testthat, readxl, gsheet, googledrive, DBI, rapiclient, RMariaDB, RPostgres, RPostgreSQL, RSQLite, ncdf4, thredds, EML, emld, datapack, dataone, rgbif, ocs4R (≥ 0.3), zen4R (≥ 0.10.4), atom4R (≥ 0.3-4), d4storagehub4R (≥ 0.4-5), rmarkdown, dataverse, blastula, waldo
License: MIT + file LICENSE
URL: https://github.com/r-geoflow/geoflow
BugReports: https://github.com/r-geoflow/geoflow/issues
LazyLoad: yes
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-09-04 19:28:14 UTC; emman
Author: Emmanuel Blondel ORCID iD [aut, cre, cph], Julien, Barde ORCID iD [aut], Wilfried Heintz ORCID iD [aut], Alexandre Bennici [ctb], Sylvain Poulain [ctb], Bastien Grasset [ctb], Mathias Rouan [ctb], Emilie Lerigoleur [ctb], Yvan Le Bras [ctb], Jeroen Ooms [ctb]
Repository: CRAN
Date/Publication: 2026-09-05 16:20:02 UTC

Tools to Orchestrate and Run (Meta)Data Management Workflows

Description

Provides an engine to manage Spatial Data Infrastructures (SDI) and to orchestrate, run and automate geospatial (meta)data workflows in compliance with international standards (ISO, OGC, INSPIRE) with a range of actions such as data upload in spatial databases, publication in GeoServer and metadata publication in GeoNetwork. It includes actions to manage domain-specific resources usch ecological metadata (EML) and its publication on tools such as Metacat. It also allows to publish data on cloud data infrastructures such as Zenodo or Dataverse. Through a pivot metadata model, geoflow allows to manage a unique source dataset metadata while offering a way to target various repositories for their publication. The execution of several actions will allow to cross-share (meta)data resources in each action performed, offering a way to bind resources between each other (eg. reference Zenodo DOIS in Geonetwork/Geoserver metadata, reference Geonetwork/Geoserver links in Zenodo or EML metadata). The use of standardized configuration files allows fully reproducible workflows, in compliance with FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Author(s)

Emmanuel Blondel emmanuel.blondel1@gmail.com

See Also

Useful links:

add_config_logger

Description

add_config_logger enables a logger (managed with the internal class geoflowLogger).

Usage

add_config_logger(config)

Arguments

config

object of class list

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

bbox_to_sf

Description

Creates a sf object out of a bounding box

Usage

bbox_to_sf(xmin, ymin, xmax, ymax, crs = 4326)

Arguments

xmin

xmin

ymin

ymin

xmax

xmax

ymax

ymax

crs

Defaut is 4326

Value

an object of class sf

Author(s)

Emmanuel Blondel emmanuel.blondel1@gmail.com

build_hierarchical_list

Description

build_hierarchical_list

Usage

build_hierarchical_list(parent, relationships)

Arguments

parent

parent

relationships

relationships

Value

a hierarchical list

check_packages

Description

check_packages checks availability of a list of R packages in R. This function is essentially used internally by geoflow in assocation to geoflow_software and geoflow_action that would need specific packages to be imported in R.

Usage

check_packages(pkgs)

Arguments

pkgs

a vector of package names

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

closeWorkflow

Description

closeWorkflow allows to close a workflow

Usage

closeWorkflow(config)

Arguments

config

a configuration object as read by closeWorkflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

create_geoflow_data_from_dbi

Description

create_geoflow_data_from_dbi

Usage

create_geoflow_data_from_dbi(dbi, schema, table)

Arguments

dbi

a dbi connection

schema

schema

table

table

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

create_object_identification_id

Description

create_object_identification_id

Usage

create_object_identification_id(prefix, str)

Arguments

prefix

a character string

str

a character string

Value

a digested character string

debugWorkflow

Description

debugWorkflow allows to initiate a workflow job for developers to work / debug on workflow actions.

Usage

debugWorkflow(
  file, dir, outdir, 
  entityIndex, copyData, 
  runSoftwareActions, runLocalActions
)

Arguments

file

configuration file

dir

a directory used to execute the workflow. This is the working directory, ie where local resources (data, metadata), should be located.

outdir

a directory where the geoflow will write the job outputs.

entityIndex

index of the entity within the list of loaded entities. Default is 1

copyData

whether data should be downloaded/copied to job data directory. Default is TRUE.

runSoftwareActions

whether software actions should be run. Default is TRUE.

runLocalActions

whether entity data local actions (if any) should be run. Default is TRUE

Value

a named list including the workflow config, the selected entity, the eventual options associated to the entity, and the output entity dir path of the selected entity.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

describeOGCRelation

Description

describeOGCRelation

Usage

describeOGCRelation(entity, data_object, service, download, format,
                          handle_category, handle_ogc_service_description, handle_format)

Arguments

entity

the entity considered

data_object

data object

service

service acronym

download

whether the relation should be a download one or not

format

format

handle_category

append the relation category

handle_ogc_service_description

append the OGC service description

handle_format

append the download format

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

enrich_text_from_entity

Description

enrich_text_from_entity will attempt to enrich an entity text property from other entity metadata, depending on text variables handled by a pattern in the form

- If the entity property is a text, only the name of the property name is required.

- If the entity property is a list, then 2 subcases can be distinguished:

If it is a named list (such as entity descriptions), the text variable will be compound by the entity property name and the element_property name, in the form

If it is a unnamed list (such as list of keywords, list of relations, etc), the text variable will handle four elements: property (entity property name to look at), a key value pair to use for search within the list, an element_property for which the value should be picked up to enrich the text. The variable willbe in the form

Usage

enrich_text_from_entity(str, entity)

Arguments

str

a text to be enriched

entity

an object of class geoflow_entity

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

executeWorkflow

Description

executeWorkflow allows to execute a workflow

Usage

executeWorkflow(file, dir, outdir, queue, 
                       on_initWorkflowJob, on_initWorkflow, on_closeWorkflow, 
                       monitor, session)

Arguments

file

a JSON geoflow configuration file

dir

a directory used to execute the workflow. This is the working directory, ie where local resources (data, metadata), should be located.

outdir

a directory where the geoflow will write the job outputs.

queue

an ipc queue to use geoflow in geoflow-shiny

on_initWorkflowJob

a function to trigger once initWorkflowJob is executed

on_initWorkflow

a function to trigger once initWorkflow is executed

on_closeWorkflow

a function to trigger once closeWorkflow is executed

monitor

a monitor function to increase progress bar

session

a shiny session object (optional) to run geoflow in a shiny context

Value

the path of the job directory

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

executeWorkflowJob

Description

executeWorkflowJob allows to execute a workflow job

Usage

executeWorkflowJob(config, jobdir, queue, monitor)

Arguments

config

a configuration object as read by initWorkflow

jobdir

the Job directory. Optional, by default inherited with the configuration.

queue

an ipc queue to use geoflow in geoflow-shiny

monitor

a monitor function to increase progress bar

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

extract_cell_components

Description

extract_cell_components extracts the components of a cell when using tabular data content handlers (for entity and contact).

Usage

extract_cell_components(str)

Arguments

str

a string as object of class character

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

extract_kvp

Description

extract_kvp parses a string into a key value pair represented by a geoflow_kvp object.

Usage

extract_kvp(str)

Arguments

str

a string as object of class character

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

extract_kvps

Description

extract_kvp parses a string into a key value pair represented by a geoflow_kvp object.

Usage

extract_kvps(strs, collapse)

Arguments

strs

a string as object of class character

collapse

collapse by. Default is NULL

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

fetch_layer_styles_from_dbi

Description

fetch_layer_styles_from_dbi

Usage

fetch_layer_styles_from_dbi(entity, dbi, schema, table)

Arguments

entity

a geoflow_entity to be used and enriched

dbi

a dbi connection

schema

schema

table

table

Value

the entity, enriched with layer styles

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

filter_sf_by_cqlfilter

Description

filter_sf_by_cqlfilter filters an object of class sf using a CQL syntax. This function is minimalistic and only basic CQL filters are supported.

Usage

filter_sf_by_cqlfilter(sfdata, cqlfilter)

Arguments

sfdata

object of class sf

cqlfilter

object of class character representing a CQL filter

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

geoflowLogger

Description

geoflowLogger

Format

R6Class object.

Value

Object of R6Class for modelling a simple logger

Public fields

verbose

verbose

debug

debug

Methods

Public methods

geoflowLogger$separator()

Util to separate chunks of logs of different natures

Usage
geoflowLogger$separator(char)
Arguments
char

A character to be used, eg '='

geoflowLogger$INFO()

Prints an INFO logger message

Usage
geoflowLogger$INFO(txt, ...)
Arguments
txt

logger message

...

values to be passed into txt. See sprintf

geoflowLogger$WARN()

Prints an WARN logger message

Usage
geoflowLogger$WARN(txt, ...)
Arguments
txt

logger message

...

values to be passed into txt. See sprintf

geoflowLogger$ERROR()

Prints an ERROR logger message

Usage
geoflowLogger$ERROR(txt, ...)
Arguments
txt

logger message

...

values to be passed into txt. See sprintf

geoflowLogger$DEBUG()

Prints an DEBUG logger message

Usage
geoflowLogger$DEBUG(txt, ...)
Arguments
txt

logger message

...

values to be passed into txt. See sprintf

geoflowLogger$new()

Initializes an object of class geoflowLogger

Usage
geoflowLogger$new(verbose = TRUE, debug = FALSE)
Arguments
verbose

TRUE if the logger is enabled, FALSE otherwise. Default is TRUE

debug

TRUE if the debugger is enabled, FALSE otherwise. Default is FALSE

geoflowLogger$clone()

The objects of this class are cloneable with this method.

Usage
geoflowLogger$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Logger class used internally by geoflow

Geoflow action class

Description

This class models an action to be executed by geoflow

Format

R6Class object.

Details

geoflow_action

Value

Object of R6Class for modelling an action

Super class

geoflowLogger -> geoflow_action

Public fields

id

action ID

enabled

enabled

funders

funders

authors

authors

maintainer

maintainer

scope

action scope

types

types of action

def

the action definition

target

the action target

target_dir

the action target directory

packages

list of packages required to perform the action

pid_generator

a name referencing the PID generator (if existing)

pid_types

types of PIDs to generate

generic_uploader

whether the action is a generic uploader or not.

fun

a function for the action

script

a script for the action

options

action options

available_options

a list of available options for the actions

status

status

notes

notes

Methods

Public methods

Inherited methods

geoflow_action$new()

Initialize a geoflow_action

Usage
geoflow_action$new(
  yaml = NULL,
  id = NULL,
  enabled = TRUE,
  funders = list(),
  authors = list(),
  maintainer = NULL,
  scope = "global",
  types = list(),
  def = "",
  target = NA,
  target_dir = NA,
  packages = list(),
  pid_generator = NULL,
  pid_types = list(),
  generic_uploader = FALSE,
  fun = NULL,
  script = NULL,
  options = list(),
  available_options = list(),
  status = "stable",
  notes = ""
)
Arguments
yaml

a yaml file

id

action id

enabled

enabled

funders

funders

authors

authors

maintainer

maintainer

scope

action scope "global" or "local"

types

action types

def

action definition

target

the action target, e.g. "entity"

target_dir

the action target directory

packages

list of packages required to perform the action

pid_generator

a name referencing the PID generator (if existing)

pid_types

types of PIDs to generate by the action

generic_uploader

whether the action is a generic uploader or not.

fun

action function

script

action script

options

action options

available_options

available options for the action

status

status of the action (experimental, stable, deprecated, superseded)

notes

notes

geoflow_action$fromYAML()

Reads action properties from YAML file

Usage
geoflow_action$fromYAML(file)
Arguments
file

file

geoflow_action$checkPackages()

Check that all packages required for the action are available, if yes, import them in the R session, and return a data.frame giving the packages names and version. If one or more packages are unavailable, an error is thrown and user informed of the missing packages.

Usage
geoflow_action$checkPackages()

geoflow_action$run()

Runs the action

Usage
geoflow_action$run(entity, config)
Arguments
entity

entity

config

config

geoflow_action$getOption()

Get action option value

Usage
geoflow_action$getOption(option)
Arguments
option

option id

Returns

the option value, either specified through a workflow, or the default value

geoflow_action$isPIDGenerator()

Indicates if the action is PID generator

Usage
geoflow_action$isPIDGenerator()
Returns

TRUE if the action is a PID generator, FALSE otherwise

geoflow_action$exportPIDs()

Exports PIDs for the action. This function will export the PIDs in several ways. First, a simple CSV file including the list of PIDs for each entity, and associated status (eg. draft/release) for the given PID resource. In addition, for each metadata entities file, an equivalent metadata table will be produced as CSV to handle entities enriched with the PID (added in the "Identifier" column), ready for use as workflow entities input. In addition, a new configuration file will be produced with name "<pid_generator>_geoflow_config_for_publication.json" turned as ready for publishing resources with PIDs (eg. publishing deposits in Zenodo).

Usage
geoflow_action$exportPIDs(config, entities)
Arguments
config

a geoflow configuration

entities

one or more objects of class geoflow_entity

geoflow_action$isGenericUploader()

Indicates if the action is a generic uploader

Usage
geoflow_action$isGenericUploader()
Returns

TRUE if the action is a generic uploader, FALSE otherwise

geoflow_action$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_action$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  action <- geoflow_action$new(
   id = "some-id",
   scope = "global",
   types = list("some purpose1", "some purpose2"),
   target = "entity",
   target_dir = "data",
   def = "some definition",
   packages = list(),
   pid_generator = NULL,
   generic_uploader = FALSE,
   fun = function(action, entity, config){},
   available_options = list(
     option_name = list(def = "option description", default = FALSE)
   ),
   options = list(option_name = TRUE)
 )

## End(Not run)

Geoflow contact class

Description

This class models a contact to be executed by geoflow

Format

R6Class object.

Details

geoflow_contact

Value

Object of R6Class for modelling a contact

Public fields

id

contact identifier

firstName

contact first name

lastName

contact lastname

organizationName

contact organization

positionName

contact position

role

contact role

voice

contact phone number

facsimile

contact facsimile

email

contact email

websiteUrl

contact website URL

websiteName

contact website name

postalAddress

contact postal address

postalCode

contact postal code

city

contact city

country

contact country

identifiers

contact identifiers

Methods

Public methods

geoflow_contact$new()

Initializes a geoflow_contact object

Usage
geoflow_contact$new()

geoflow_contact$setShinyEditorMode()

Set mode for geoflow-shiny

Usage
geoflow_contact$setShinyEditorMode(mode = c("creation", "edition"))
Arguments
mode

mode

geoflow_contact$getShinyEditorMode()

Get mode for geoflow-shiny

Usage
geoflow_contact$getShinyEditorMode()
Returns

the shiny editor mode

geoflow_contact$getAllowedKeyValuesFor()

Retrieves keys allowed for a given tabular field name. eg. "Identifier"

Usage
geoflow_contact$getAllowedKeyValuesFor(field)
Arguments
field

field name

Returns

the list of valid keys for the field considered

geoflow_contact$setIdentifier()

Sets an identifier by means of key

Usage
geoflow_contact$setIdentifier(key = "id", id)
Arguments
key

an identifier key. Default is "id"

id

the identifier

geoflow_contact$setId()

Sets an "id" identifier

Usage
geoflow_contact$setId(id)
Arguments
id

the identifier

geoflow_contact$setFirstName()

Sets contact first name

Usage
geoflow_contact$setFirstName(firstName)
Arguments
firstName

contact first name

geoflow_contact$setLastName()

Sets contact last name

Usage
geoflow_contact$setLastName(lastName)
Arguments
lastName

contact last name

geoflow_contact$setOrganizationName()

Sets contact organization name

Usage
geoflow_contact$setOrganizationName(organizationName)
Arguments
organizationName

contact organization name

geoflow_contact$setPositionName()

Sets contact position name

Usage
geoflow_contact$setPositionName(positionName)
Arguments
positionName

contact position name

geoflow_contact$setRole()

Sets contact role

Usage
geoflow_contact$setRole(role)
Arguments
role

the contact role

geoflow_contact$setVoice()

Sets contact voice (phone number)

Usage
geoflow_contact$setVoice(voice)
Arguments
voice

contact voice (phone number)

geoflow_contact$setFacsimile()

Sets contact facsimile

Usage
geoflow_contact$setFacsimile(facsimile)
Arguments
facsimile

contact facsimile

geoflow_contact$setEmail()

Sets contact email

Usage
geoflow_contact$setEmail(email)
Arguments
email

contact email

geoflow_contact$setWebsiteUrl()

Sets contact website URL

Usage
geoflow_contact$setWebsiteUrl(websiteUrl)
Arguments
websiteUrl

contact website URL

geoflow_contact$setWebsiteName()

Sets contact website name

Usage
geoflow_contact$setWebsiteName(websiteName)
Arguments
websiteName

contact website name

geoflow_contact$setPostalAddress()

Sets the contact postal address

Usage
geoflow_contact$setPostalAddress(postalAddress)
Arguments
postalAddress

contact postal address

geoflow_contact$setPostalCode()

Sets the contact postal code

Usage
geoflow_contact$setPostalCode(postalCode)
Arguments
postalCode

contact postalCode

geoflow_contact$setCity()

Sets the contact city

Usage
geoflow_contact$setCity(city)
Arguments
city

contact city

geoflow_contact$setCountry()

Sets the contact country

Usage
geoflow_contact$setCountry(country)
Arguments
country

contact country

geoflow_contact$asDataFrame()

Methods to export the geoflow_contact as data.frame using key-based syntax.

Usage
geoflow_contact$asDataFrame(line_separator = NULL)
Arguments
line_separator

a line separator. By default, the default line separator will be used.

Returns

an object of class data.frame giving the entities using key-based syntax

geoflow_contact$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_contact$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  contact <- geoflow_contact$new()
  contact$setId("john.doe@nowhere.org")
  contact$setFirstName("John")
  contact$setLastName("Doe")
  contact$setOrganizationName("Nowhere")
  contact$setPositionName("Wizard")
  contact$setRole("Manager")
  contact$setVoice("+9999000000000")
  contact$setFacsimile("+9999000000001")
  contact$setEmail("john.doe@nowhere.org")
  contact$setWebsiteUrl("www.nowhere.org")
  contact$setWebsiteName("Nowhere Inc.")
  contact$setPostalAddress("Nowhere street")
  contact$setPostalCode("Nowhere code")
  contact$setCity("Nowhere city")
  contact$setCountry("Nowhere country")

## End(Not run)

Geoflow data class

Description

This class models a data object

Format

R6Class object.

Details

geoflow_data

Value

Object of R6Class for modelling a data object

Public fields

dir

an object of class character giving a data directory

data

list of object of class geoflow_data in case we point to a data directory

restricted

indicates whether the data is under restricted access or not

access

accessor key for accessing sources. Default is 'default'

source

source

sourceFid

sourceFid

sourceSql

sourceSql

sourceType

source type

sourceZip

create a zip for the sources (DEPRECATED with #344)

sourceZipOnly

create a zip only for the sources, remove source files (DEPRECATED with #344)

sql

sql

upload

upload

uploadSource

upload source name

uploadType

upload type

cqlfilter

CQL filter for filtering data

workspaces

workspaces

store

store

layername

layer name

layertitle

layer title

layerdesc

layer description

layeruri

layer URI layeruri layer URI

styles

styles

styleUpload

upload styles

dimensions

dimensions

cloud_path

a relative path in a cloud storage (e.g., OCS)

spatialRepresentationType

spatial representation type eg. "vector", "grid"

ogc_dimensions

OGC dimensions

features

features

parameters

parameters

geometryField

geometry field

geometryType

geometry type

featureType

feature type name

featureTypeObj

feature type object

attributes

attributes

variables

variables

coverages

coverages

envelopeCompositionType

envelope composition type (for coverages)

selectedResolution

selected resolution (for coverages)

selectedResolutionIndex

selected resolution index (for coverages)

bands

list of bands

actions

local actions

run

whether to run local actions

Methods

Public methods

geoflow_data$new()

Initializes an object of class geoflow_data

Usage
geoflow_data$new(str = NULL, config = NULL)
Arguments
str

character string to initialize from, using key-based syntax

config

a geoflow config, if available and needed

geoflow_data$getDir()

Get data directory where datasets are scanned to build geoflow_data objects

Usage
geoflow_data$getDir()
Returns

an object of class character

geoflow_data$getData()

Get a lis tof geoflow_data objects built from a directory

Usage
geoflow_data$getData()
Returns

a list of objects of class geoflow_data

geoflow_data$getAllowedSourceValues()

Get allowed source values

Usage
geoflow_data$getAllowedSourceValues()
Returns

a vector of class character

geoflow_data$setAccess()

Set accessor id. See list_data_accessors() for available accessors

Usage
geoflow_data$setAccess(access)
Arguments
access

a data data accessor id

geoflow_data$getAllowedSourceTypes()

Get allowed source types

Usage
geoflow_data$getAllowedSourceTypes()
Returns

a vector of class character

geoflow_data$setSourceType()

Set the source type. The source type is a simplification of the data mime type and is used to identify the type of source set for the data object. By default it is assumed to be "other" (undefined). The source types currently allowed in geoflow can be listed with $getAllowedSourcedTypes().

Usage
geoflow_data$setSourceType(sourceType)
Arguments
sourceType

source type

geoflow_data$getAllowedGeomPossibleNames()

Get allowed Geometry possible names for coercing data to sf objects

Usage
geoflow_data$getAllowedGeomPossibleNames()

geoflow_data$getAllowedXPossibleNames()

Get allowed X possible names for coercing data to sf objects

Usage
geoflow_data$getAllowedXPossibleNames()

geoflow_data$getAllowedYPossibleNames()

Get allowed Y possible names for coercing data to sf objects

Usage
geoflow_data$getAllowedYPossibleNames()

geoflow_data$addSource()

Add source, object of class "character" (single source)

Usage
geoflow_data$addSource(source)
Arguments
source

source

geoflow_data$setSource()

Set source, object of class "character" (single source), or list. For spatial source, a single source will be used, while for sources of type 'other' (eg PDF files), multiple sources can be specified

Usage
geoflow_data$setSource(source)
Arguments
source

source

geoflow_data$setSourceFid()

Set source FID, object of class "character" (single source FID), or list.

Usage
geoflow_data$setSourceFid(sourceFid)
Arguments
sourceFid

sourceFid

geoflow_data$setSourceSql()

This is a convenience method for users that want to specify directly a SQL source. This method is called internally when a source SQL file has been set using setSource

Usage
geoflow_data$setSourceSql(sourceSql)
Arguments
sourceSql

a source SQL query

geoflow_data$setSourceZip()

Sets whether a zipped version of the data file(s) should be created from source files. Default is FALSE

Usage
geoflow_data$setSourceZip(sourceZip)
Arguments
sourceZip

zip sources, object of class logical

geoflow_data$setSourceZipOnly()

Sets whether a zipped version of the data file(s) only should be created from source files. Default is FALSE

Usage
geoflow_data$setSourceZipOnly(sourceZipOnly)
Arguments
sourceZipOnly

zip sources only, object of class logical

geoflow_data$setUploadSource()

Set the source to upload in output software, alternative to the source. If leave empty, the source will be used as uploadSource. A typical use case is when we want to get a CSV source to import in a database, and use the dbtable (or view/query) as upload source for publication in software like geoserver.

Usage
geoflow_data$setUploadSource(uploadSource)
Arguments
uploadSource

upload source

geoflow_data$getAllowedUploadTypes()

Get allowed upload types

Usage
geoflow_data$getAllowedUploadTypes()
Returns

the list of allowed upload types

geoflow_data$setUploadType()

The upload type is a simplification of the data mime type and is used to identify the type of data uploaded. By default it is assumed to be "other" (undefined). The upload types currently allowed in geoflow can be listed with $getAllowedUploadTypes().

Usage
geoflow_data$setUploadType(uploadType)
Arguments
uploadType

upload type

geoflow_data$setUpload()

Set whether the source data should be uploaded to the sofware output declared in the geoflow configuration or not. By default it is assumed that upload should be performed (upload TRUE).

Usage
geoflow_data$setUpload(upload)
Arguments
upload

upload

geoflow_data$setStyleUpload()

Set whether styles in source data should be uploaded, by default TRUE

Usage
geoflow_data$setStyleUpload(styleUpload)
Arguments
styleUpload

style upload

geoflow_data$setSql()

Sets SQL for publication purpose.

Usage
geoflow_data$setSql(sql)
Arguments
sql

sql

geoflow_data$setCqlFilter()

Sets a CQL filter. In case of spatial data, once the data is read by geoflow (during initialization phase), the CQL filter will be applied to the data.

Usage
geoflow_data$setCqlFilter(cqlfilter)
Arguments
cqlfilter

CQL filter

geoflow_data$setWorkspace()

Sets a workspace name, object of class character. A workspace must target a valid software type, object of class character, to be declared as first argument of this function, assuming the corresponding software is declared in the geoflow configuration.

Usage
geoflow_data$setWorkspace(software_type, workspace)
Arguments
software_type

sotware type where the workspace is identifier

workspace

workspace name

geoflow_data$setStore()

Sets a data/coverage store name, object of class character. Used as target data/coverage store name for GeoServer action.

Usage
geoflow_data$setStore(store)
Arguments
store

store

geoflow_data$setDatastore()

Sets a datastore name, object of class character. Used as target datastore name for GeoServer action. DEPRECATED, use setStore

Usage
geoflow_data$setDatastore(datastore)
Arguments
datastore

datastore

geoflow_data$setLayername()

Sets a layername, object of class character. Used as target layer name for Geoserver action.

Usage
geoflow_data$setLayername(layername)
Arguments
layername

layername

geoflow_data$setLayertitle()

Sets a layer title, object of class character. If available, used as target layer title in SDI-related action.

Usage
geoflow_data$setLayertitle(layertitle)
Arguments
layertitle

layertitle

geoflow_data$setLayerdesc()

Sets a layer description, object of class character. If available, used as target layer description/abstract in SDI-related actions.

Usage
geoflow_data$setLayerdesc(layerdesc)
Arguments
layerdesc

layerdesc

geoflow_data$setLayeruri()

Sets a layer URI, object of class character. If available, used as annotating URI for layer metadata (eg. in ISO 19115 action).

Usage
geoflow_data$setLayeruri(layeruri)
Arguments
layeruri

layeruri

geoflow_data$addStyle()

Adds a style name, object of class character. Used as layer style name(s) for GeoServer action.

Usage
geoflow_data$addStyle(style)
Arguments
style

style

geoflow_data$addDimension()

Adds a dimension

Usage
geoflow_data$addDimension(name, dimension)
Arguments
name

dimension name

dimension

object of class geoflow_dimension

geoflow_data$setCloudPath()

Set cloud path

Usage
geoflow_data$setCloudPath(cloud_path)
Arguments
cloud_path

cloud path

geoflow_data$getAllowedSpatialRepresentationTypes()

Get allowed spatial representation types, typically "vector" and "grid"

Usage
geoflow_data$getAllowedSpatialRepresentationTypes()
Returns

an object of class character

geoflow_data$setSpatialRepresentationType()

Set spatial representation type for the data considered

Usage
geoflow_data$setSpatialRepresentationType(spatialRepresentationType)
Arguments
spatialRepresentationType

spatial representation type

geoflow_data$setOgcDimensions()

Set OGC dimensions

Usage
geoflow_data$setOgcDimensions(name, values)
Arguments
name

dimension name

values

dimension values

geoflow_data$setFeatures()

Set data features

Usage
geoflow_data$setFeatures(features)
Arguments
features

features

geoflow_data$setParameter()

Set virtual parameter definition for setting virtual SQL view parametized layers in Geoserver, when uploadType is set to dbquery.The arguments here follow the definition of virtual parameters in GeoServer, ie a name (alias), the corresponding field name in the DBMS, a regular expression for validation of parameter values (required to prevent SQL injection risks), and a default value.

Usage
geoflow_data$setParameter(name, fieldname, regexp, defaultvalue)
Arguments
name

name

fieldname

fieldname

regexp

regexp

defaultvalue

default value

geoflow_data$setGeometryField()

Sets the name of the geometry field in the target GeoServer SQL view parametrized layer

Usage
geoflow_data$setGeometryField(geometryField)
Arguments
geometryField

geometry field

geoflow_data$setGeometryType()

Sets the name of the geometry field in the target GeoServer SQL view parametrized layer

Usage
geoflow_data$setGeometryType(geometryType)
Arguments
geometryType

geometry type

geoflow_data$setFeatureType()

Sets a feature type (ID) to link data with a dictionnary

Usage
geoflow_data$setFeatureType(featureType)
Arguments
featureType

feature type name

geoflow_data$setFeatureTypeObj()

Sets a feature type object

Usage
geoflow_data$setFeatureTypeObj(featureTypeObj)
Arguments
featureTypeObj

feature type object of class geoflow_featuretype

geoflow_data$setAttributes()

Set attributes, as simple way to describe attributes without binding to a proper geoflow_dictionary.

Usage
geoflow_data$setAttributes(attributes)
Arguments
attributes

attributes

geoflow_data$setVariables()

Set variables, as simple way to describe variables without binding to a proper geoflow_dictionary.

Usage
geoflow_data$setVariables(variables)
Arguments
variables

variables

geoflow_data$setCoverages()

Set coverages

Usage
geoflow_data$setCoverages(coverages)
Arguments
coverages

coverages

geoflow_data$getAllowedEnvelopeCompositionTypes()

Get allowed envelope composition types

Usage
geoflow_data$getAllowedEnvelopeCompositionTypes()
Returns

an object of class character

geoflow_data$setEnvelopeCompositionType()

Set envelope composition type

Usage
geoflow_data$setEnvelopeCompositionType(envelopeCompositionType)
Arguments
envelopeCompositionType

envelope composition type, either 'UNION' or 'INTERSECTION'

geoflow_data$setSelectedResolution()

Set selected resolution

Usage
geoflow_data$setSelectedResolution(selectedResolution)
Arguments
selectedResolution

selected resolution

geoflow_data$setSelectedResolutionIndex()

Set selected resolution index

Usage
geoflow_data$setSelectedResolutionIndex(selectedResolutionIndex)
Arguments
selectedResolutionIndex

selected resolution index

geoflow_data$setBand()

Set band

Usage
geoflow_data$setBand(name, index)
Arguments
name

band name

index

band index

geoflow_data$addAction()

Adds a local action

Usage
geoflow_data$addAction(action)
Arguments
action

object of class geoflow_action

geoflow_data$checkSoftwareProperties()

A function triggered when loading a data object to check eventual software dependent properties, to make sure the corresponding software are declared in the config.

Usage
geoflow_data$checkSoftwareProperties(config)
Arguments
config

geoflow config object

geoflow_data$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_data$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow data accessor class

Description

This class models a data accessor to be used by geoflow

Format

R6Class object.

Details

geoflow_data_accessor

Value

Object of R6Class for modelling a data accessor

Super class

geoflowLogger -> geoflow_data_accessor

Public fields

id

accessor ID

software_type

accessor software type

definition

accessor definition

packages

list of packages required for the accessor

download

a download function handler

list

a function handler to list resources in case of a data directory

Methods

Public methods

Inherited methods

geoflow_data_accessor$new()

Initializes the data ccessor

Usage
geoflow_data_accessor$new(
  id = NULL,
  software_type = NULL,
  definition,
  packages = list(),
  download,
  list = NULL
)
Arguments
id

accessor ID

software_type

accessor software type

definition

accessor definition

packages

list of packages required for the accessor

download

download function handler

list

list function handler

geoflow_data_accessor$setId()

Sets accessor ID

Usage
geoflow_data_accessor$setId(id)
Arguments
id

accessor ID to set

geoflow_data_accessor$setSoftwareType()

Sets software type

Usage
geoflow_data_accessor$setSoftwareType(software_type)
Arguments
software_type

software type

geoflow_data_accessor$setPackages()

Sets list of packages required for the accessor

Usage
geoflow_data_accessor$setPackages(packages)
Arguments
packages

a vecto of package names

geoflow_data_accessor$setDefinition()

Sets accessor definition

Usage
geoflow_data_accessor$setDefinition(definition)
Arguments
definition

accessor definition

geoflow_data_accessor$setDownload()

Set download handler (a function with arguments resource, file, path, unzip (TRUE/FALSE) and optional software)

Usage
geoflow_data_accessor$setDownload(download)
Arguments
download

an object of class function

geoflow_data_accessor$setList()

Set list handler (a function with no arguments)

Usage
geoflow_data_accessor$setList(list)
Arguments
list

an object of class function

geoflow_data_accessor$checkPackages()

Check that all packages required for the software are available, if yes, import them in the R session, and return a data.frame giving the packages names and version. If one or more packages are unavailable, an error is thrown and user informed of the missing packages.

Usage
geoflow_data_accessor$checkPackages()

geoflow_data_accessor$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_data_accessor$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  access <- geoflow_data_accessor$new(
   id = "some-id",
   software_type = "some-software",
   definition = "definition",
   packages = list(),
   download = function(resource, file, path, software, unzip){},
   list = function(resource, software){}
 )

## End(Not run)

Geoflow date class

Description

This class models an date

Format

R6Class object.

Details

geoflow_date

Value

Object of R6Class for modelling an date

Public fields

key

date key. Default is "creation"

value

date value. Default is generated with Sys.time()

Methods

Public methods

geoflow_date$new()

Initializes a geoflow_date

Usage
geoflow_date$new()

geoflow_date$setKey()

Sets the date key

Usage
geoflow_date$setKey(key)
Arguments
key

date key

geoflow_date$setValue()

Sets the date value. The method will check validity of date value.

Usage
geoflow_date$setValue(value)
Arguments
value

date value

geoflow_date$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_date$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  date <- geoflow_date$new()
  date$setKey("creation")
  date$setValue(Sys.time())

## End(Not run)

Geoflow dictionary class

Description

This class models a dictionary to be executed by geoflow

Format

R6Class object.

Details

geoflow_dictionary

Value

Object of R6Class for modelling a dictionary

Public fields

source

dictionary source, object of class data.frame

featuretypes

list of objects of class geoflow_featuretype

registers

list of objects of class geoflow_register

Methods

Public methods

geoflow_dictionary$new()

Initializes a geoflow_dictionary object

Usage
geoflow_dictionary$new()

geoflow_dictionary$setSource()

Sets dictionnary source

Usage
geoflow_dictionary$setSource(source)
Arguments
source

object of class data.frame

geoflow_dictionary$getFeatureTypes()

Get the list of geoflow_featuretype defined in the dictionary

Usage
geoflow_dictionary$getFeatureTypes()
Returns

a list of geoflow_featuretype

geoflow_dictionary$getFeatureTypeById()

Get an object of class geoflow_featuretype given an ID

Usage
geoflow_dictionary$getFeatureTypeById(id)
Arguments
id

id

Returns

an object of class geoflow_featuretype, otherwise NULL

geoflow_dictionary$addFeatureType()

Adds a feature type to the dictionnary

Usage
geoflow_dictionary$addFeatureType(ft)
Arguments
ft

object of class geoflow_featuretype

geoflow_dictionary$getRegisters()

Get the list of registers associated with the dictionnary

Usage
geoflow_dictionary$getRegisters()
Returns

a list of geoflow_register objects

geoflow_dictionary$getRegisterById()

Get register by ID

Usage
geoflow_dictionary$getRegisterById(id)
Arguments
id

id

Returns

an object of class geoflow_register, otherwise NULL

geoflow_dictionary$addRegister()

Adds a register to the dictionnary

Usage
geoflow_dictionary$addRegister(register)
Arguments
register

object of class geoflow_register

geoflow_dictionary$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_dictionary$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow dimension class

Description

This class models a dimension

Format

R6Class object.

Details

geoflow_dimension

Value

Object of R6Class for modelling a dimension

Public fields

longName

dimension longName

resolution

dimension resolution

size

dimension size

values

dimension values

minValue

dimension min value

maxValue

dimension max value

Methods

Public methods

geoflow_dimension$new()

Initializes the geoflow_dimension

Usage
geoflow_dimension$new()

geoflow_dimension$setLongName()

Sets the dimension long name

Usage
geoflow_dimension$setLongName(longName)
Arguments
longName

dimension long name

geoflow_dimension$setResolution()

Sets the resolution

Usage
geoflow_dimension$setResolution(uom, value)
Arguments
uom

unit of measure

value

resolution value

geoflow_dimension$setSize()

Sets the dimension size

Usage
geoflow_dimension$setSize(size)
Arguments
size

dimension size

geoflow_dimension$setValues()

Sets dimension values

Usage
geoflow_dimension$setValues(values)
Arguments
values

dimension values

geoflow_dimension$setMinValue()

Sets dimension min value

Usage
geoflow_dimension$setMinValue(minValue)
Arguments
minValue

min value

geoflow_dimension$setMaxValue()

Sets dimension max value

Usage
geoflow_dimension$setMaxValue(maxValue)
Arguments
maxValue

max value

geoflow_dimension$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_dimension$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

 ## Not run: 
  dimension <- geoflow_dimension$new()
  dimension$setLongName("longname")
  dimension$setResolution(uom="s",value=1)
  dimension$setSize(10)
  dimension$setValues(c(1,2,3))
  dimension$setMinValue(1)
  dimension$setMaxValue(3)
 
## End(Not run)

Geoflow entity class

Description

This class models a entity object

Format

R6Class object.

Details

geoflow_entity

Value

Object of R6Class for modelling a entity object

Public fields

identifiers

entity identifiers

dates

entity dates

language

entity language

types

entity types

titles

entity titles

descriptions

entity descriptions

subjects

entity subjects

formats

entity formats

contacts

entity contacts

relations

entity relations

rights

entity rights

spatial_extent

spatial extent

spatial_bbox

spatial bounding box

geo_bbox

geographic bounding box (in EPSG:4326 / WGS 84)

srid

entity srid

temporal_extent

entity temporal extent

provenance

entity provenance

data

entity data

status

entity status

resources

entity resources

locales

entity locales

Methods

Public methods

geoflow_entity$new()

Initializes an object of class geoflow_entity

Usage
geoflow_entity$new()

geoflow_entity$setShinyEditorMode()

Set mode for geoflow-shiny

Usage
geoflow_entity$setShinyEditorMode(mode = c("creation", "edition"))
Arguments
mode

mode

geoflow_entity$getShinyEditorMode()

Get mode for geoflow-shiny

Usage
geoflow_entity$getShinyEditorMode()
Returns

the shiny editor mode

geoflow_entity$getAllowedKeyValuesFor()

Retrieves keys allowed for a given tabular field name. eg. "Identifier"

Usage
geoflow_entity$getAllowedKeyValuesFor(field)
Arguments
field

field name

Returns

the list of valid keys for the field considered

geoflow_entity$addLocalesFromValues()

Adds locales to entity from kvp values

Usage
geoflow_entity$addLocalesFromValues(values)
Arguments
values

values

geoflow_entity$setIdentifier()

Set an identifier given a key. Default key is "id", but others can be specified, eg "doi".

Usage
geoflow_entity$setIdentifier(key = "id", id)
Arguments
key

identifier key. Default is "id"

id

identifier value

geoflow_entity$addDate()

Adds a date

Usage
geoflow_entity$addDate(dateType, date)
Arguments
dateType

date type, object of class character

date

date, object of class Date or POSIXt

geoflow_entity$setLanguage()

Set the language used for the entity description (metadata). Default is "eng".

Usage
geoflow_entity$setLanguage(language)
Arguments
language

language

geoflow_entity$writeDataResource()

writes a data resource. Deprecrated Note: TODO to review in line with 'writeWorkflowJobDataResource

Usage
geoflow_entity$writeDataResource(obj = NULL, resourcename, type = "shp")
Arguments
obj

object

resourcename

resource name

type

type of resosurce

geoflow_entity$setType()

Set the type of description. By default a generic type (key = "generic") is defined to "dataset", and will be used as default type for actions that perform metadata production / publication.

Usage
geoflow_entity$setType(key = "generic", type)
Arguments
key

type key. Default is "generic"

type

type value

geoflow_entity$setTitle()

Sets title

Usage
geoflow_entity$setTitle(key = "title", title)
Arguments
key

title key. Default is "title"

title

title value

geoflow_entity$setDescription()

Sets description

Usage
geoflow_entity$setDescription(key, description)
Arguments
key

description key. Default is "abstract"

description

description value

geoflow_entity$addSubject()

Adds a subject

Usage
geoflow_entity$addSubject(subject)
Arguments
subject

object of class geoflow_subject

geoflow_entity$addFormat()

Adds a format

Usage
geoflow_entity$addFormat(format)
Arguments
format

object of class geoflow_format

geoflow_entity$addContact()

Adds a contact

Usage
geoflow_entity$addContact(contact)
Arguments
contact

object of class geoflow_contact

geoflow_entity$addRelation()

Adds a relation

Usage
geoflow_entity$addRelation(relation)
Arguments
relation

object of class geoflow_relation

geoflow_entity$addRight()

Adds a right

Usage
geoflow_entity$addRight(right)
Arguments
right

object of class geoflow_right

geoflow_entity$setSpatialExtent()

Set spatial extent. Various ways can be used to set the spatial extent 1) with a WKT string, 2) with a bbox, object of class matrix, or 3) specifying a data object (from sf). The crs (coordinate reference system) should be specified with the crs SRID (number). The spatial extent is not necessarily a bounding box but can be one or more geometries.

Usage
geoflow_entity$setSpatialExtent(wkt = NULL, bbox = NULL, data = NULL, crs = NA)
Arguments
wkt

a WKT string

bbox

a bbox

data

an object of class sf

crs

crs

geoflow_entity$setSpatialBbox()

Set spatial bbox. Various ways can be used to set the spatial extent 1) with a WKT string, 2) with a bbox, object of class matrix, or 3) specifying a data object (from sf). The crs (coordinate reference system) should be specified with the crs SRID (number).

Usage
geoflow_entity$setSpatialBbox(wkt = NULL, bbox = NULL, data = NULL, crs = NA)
Arguments
wkt

a WKT string

bbox

a bbox

data

an object of class sf

crs

crs

geoflow_entity$setGeographicBbox()

Set geographic bbox (in EPGS:4326 / WGS 84), by converting (if needed) the spatial bbox

Usage
geoflow_entity$setGeographicBbox()

geoflow_entity$setSrid()

Sets entity SRID

Usage
geoflow_entity$setSrid(srid)
Arguments
srid

srid

geoflow_entity$setTemporalExtent()

Sets temporal extent. The temporal extent can be a year, date instant or interval

Usage
geoflow_entity$setTemporalExtent(str)
Arguments
str

object of class numeric (case of year) or character

geoflow_entity$setProvenance()

Sets entity provenance

Usage
geoflow_entity$setProvenance(provenance)
Arguments
provenance

object of class geoflow_provenance

geoflow_entity$setData()

Sets entity data object

Usage
geoflow_entity$setData(data)
Arguments
data

object of class geoflow_data

geoflow_entity$addData()

Adds entity data object

Usage
geoflow_entity$addData(data)
Arguments
data

object of class geoflow_data

geoflow_entity$getEntityJobDirname()

Gets entity job directory name. In case entity is identified with a DOI, the '/' (slash) will be replaced by '_' (underscore) to make sure directory is created.

Usage
geoflow_entity$getEntityJobDirname()
Returns

get the name of entity job directory that will be created for the entity

geoflow_entity$getEntityJobDirPath()

Gets entity job directory path. In the job directory, all entities subdirs will be created within a 'entities' directory.

Usage
geoflow_entity$getEntityJobDirPath(config, jobdir = NULL)
Arguments
config

geoflow configuration object

jobdir

relative path of the job directory

Returns

the entity job directory path

geoflow_entity$prepareEntityJobDir()

Function called internally by geoflow that creates the entity directory and relevant sub-directories. The default sub-directories will include 'data' and 'metadata'. Other sub-directories may be created depnding on the actions enabled in the workflow (and if their target directory is different from 'data'/'metadata').

Usage
geoflow_entity$prepareEntityJobDir(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$copyDataToJobDir()

This function will look at data object(s) associated to the entity (previously set with setData or added with addData), and will try to (download)/copy the data source to the geoflow job directory.

Usage
geoflow_entity$copyDataToJobDir(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$copyStylesToJobDir()

This function checks for the availability of layer styles (set as entity resource) that would have been added with DBI handlers from a special DB 'layer_styles' table

Usage
geoflow_entity$copyStylesToJobDir(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithDatatypes()

Function that will scan zip data files and resolve data objects sourceType and uploadType

Usage
geoflow_entity$enrichWithDatatypes(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$enrichWithData()

This function will enrich the entity data objects with data features (vector data) or coverages (grid data). This method will overwrite spatial metadata such as the bounding box (unless global option skipDynamicBbox is enabled). Note that the user spatial extent is not overwriten since it may contain finer geometries than a bounding box.

Usage
geoflow_entity$enrichWithData(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$enrichSpatialCoverageFromDB()

This function computes spatial coverage from DB (table, view or query) without having to deal with a full data download. It is triggered when the global option skipDataDownload is enabled.

Usage
geoflow_entity$enrichSpatialCoverageFromDB(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithFeatures()

This function will enrich the entity data objects with data features (vector data). This method will overwrite spatial metadata such as the bounding box (unless global option skipDynamicBbox is enabled). Note that the user spatial extent is not overwriten since it may contain finer geometries than a bounding box.

Usage
geoflow_entity$enrichWithFeatures(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$enrichWithCoverages()

This function will enrich the entity data objects with data coverages (grid data). This method will overwrite spatial metadata such as the bounding box (unless global option skipDynamicBbox is enabled). Note that the user spatial extent is not overwriten since it may contain finer geometries than a bounding box.

Usage
geoflow_entity$enrichWithCoverages(config, jobdir = NULL)
Arguments
config

geoflow config object

jobdir

relative path of the job directory

geoflow_entity$prepareFeaturesToUpload()

This function will 1) check (in case of upload is requested) if the type of source and upload are both different on files formats(eg. csv,shp,gpkg) and 2) process automatically to conversion from source to upload type.

Usage
geoflow_entity$prepareFeaturesToUpload(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithIdentifiers()

Function that will enrich entity with identifiers needed across multiple actions

Usage
geoflow_entity$enrichWithIdentifiers(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithRelations()

This function that will enrich the entity with relations. At now this is essentially related to adding relations if a Geoserver (geosapi) publishing action is enabled. Relations added will depend on the enrich_with_relation_* options set in a) the geosapi action, ie. 1) add WMS auto-generated thumbnail (if option enrich_with_relation_wms_thumbnail is TRUE) 2) add WMS base URL relation (if option enrich_with_relation_wms is TRUE) 3) for vector spatial representation type: - add WFS base URL relation (if option enrich_with_relation_wfs is TRUE) - add WFS auto-generated links as convenience for data download links (if option enrich_with_relation_wfs_download_links is TRUE) 4) for grid spatial representation type: - add WCS base URL relation (if option enrich_with_relation_wcs is TRUE) b) in the geonapi action (for adding a CSW metadata URL) b) in the ows4R action (for adding a CSW metadata URL)

Usage
geoflow_entity$enrichWithRelations(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithSubjects()

Enrichs the entity with subjects. If no subject specify in Subjects, automatically add keyword from dictionary to 'theme' category

Usage
geoflow_entity$enrichWithSubjects(config, exclusions = c())
Arguments
config

geoflow config object

exclusions

exclusions

geoflow_entity$enrichWithVocabularies()

Enrichs the entity with vocabularies

Usage
geoflow_entity$enrichWithVocabularies(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithFormats()

Enrichs the entity with formats

Usage
geoflow_entity$enrichWithFormats(config)
Arguments
config

geoflow config object

geoflow_entity$enrichWithMetadata()

Enrichs the entity properties with entity metadata from other properties.

Usage
geoflow_entity$enrichWithMetadata(config)
Arguments
config

geoflow config object

geoflow_entity$getContacts()

Get the entity contacts

Usage
geoflow_entity$getContacts(pretty = FALSE)
Arguments
pretty

to prettify the output as data.frame

Returns

a list of geoflow_contact or a data.frame

geoflow_entity$getSubjects()

Get the entity subjects

Usage
geoflow_entity$getSubjects(pretty = FALSE, keywords = FALSE)
Arguments
pretty

to prettify the output as data.frame

keywords

to add keywords to the output or not. Default is FALSE

Returns

a list of geoflow_subject or a data.frame

geoflow_entity$getRelations()

Get the entity relations

Usage
geoflow_entity$getRelations(pretty = FALSE)
Arguments
pretty

to prettify the output as data.frame

Returns

a list of geoflow_relation or a data.frame

geoflow_entity$setStatus()

Set a simple status either "draft" or "published". This method is required to deal with systems that manage DOIs, such as Zenodo (with zen4R) or Dataverse (with atom4R) publishing actions (Used internally by geoflow).

Usage
geoflow_entity$setStatus(system, status)
Arguments
system

a system name eg. "zenodo", "dataverse"

status

a status for entity resource "draft" or "published"

geoflow_entity$getJobResource()

Get an entity job resource path

Usage
geoflow_entity$getJobResource(config, resourceType, filename)
Arguments
config

a geoflow config object

resourceType

type of resource, matching a sub-directory within the entity job directory

filename

filename

Returns

the file path of the job resource

geoflow_entity$getJobDataResource()

Get an entity job data resource path

Usage
geoflow_entity$getJobDataResource(config, filename)
Arguments
config

a geoflow config object

filename

filename

Returns

the file path of the job data resource

geoflow_entity$getJobMetadataResource()

Get an entity job metadata resource path

Usage
geoflow_entity$getJobMetadataResource(config, filename)
Arguments
config

a geoflow config object

filename

filename

Returns

the file path of the job metadata resource

geoflow_entity$addResource()

Adds a resource to the entity

Usage
geoflow_entity$addResource(id, resource)
Arguments
id

id of the resource

resource

resource

geoflow_entity$asDataFrame()

Methods to export the geoflow_entity as data.frame using key-based syntax.

Usage
geoflow_entity$asDataFrame(line_separator = NULL)
Arguments
line_separator

a line separator. By default, the default line separator will be used.

Returns

an object of class data.frame giving the entities using key-based syntax

geoflow_entity$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_entity$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow feature type class

Description

This class models a feature type to be executed by geoflow

Format

R6Class object.

Details

geoflow_featuremember

Value

Object of R6Class for modelling a dictionary feature type member

Public fields

id

feature member ID

type

feature member type

code

feature member code

name

feature member name

def

feature member definition

defSource

feature member definition source

minOccurs

feature member minOccurs

maxOccurs

feature member maxOccurs

uom

feature member unit of measure (uom)

registerId

feature member register ID

registerScript

feature member register script

Methods

Public methods

geoflow_featuremember$new()

Initializes a geoflow_featuremember

Usage
geoflow_featuremember$new(
  type = "attribute",
  code = NULL,
  name = NULL,
  def = NULL,
  defSource = NULL,
  minOccurs = NULL,
  maxOccurs = NULL,
  uom = NULL,
  registerId = NULL,
  registerScript = NULL
)
Arguments
type

type

code

code

name

name

def

definition

defSource

definition source. Default is NULL

minOccurs

minOccurs. Default is NULL

maxOccurs

maxOccurs. Default is NULL

uom

unit of measure. Default is NULL

registerId

ID of the register associated to the feature type. Default is NULL

registerScript

source script providing the register functions. Default is NULL

geoflow_featuremember$asDataFrame()

Converts as data.frame

Usage
geoflow_featuremember$asDataFrame()
Returns

an object of class data.frame

geoflow_featuremember$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_featuremember$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow feature type class

Description

This class models a feature type to be executed by geoflow

Format

R6Class object.

Details

geoflow_featuretype

Value

Object of R6Class for modelling a dictionary feature type

Public fields

id

feature type ID

members

feature type members

Methods

Public methods

geoflow_featuretype$new()

Initializes a geoflow_featuretype

Usage
geoflow_featuretype$new(id = NULL)
Arguments
id

id

geoflow_featuretype$addMember()

Adds a member

Usage
geoflow_featuretype$addMember(fm)
Arguments
fm

object of class geoflow_featuremember

geoflow_featuretype$getMembers()

Get members

Usage
geoflow_featuretype$getMembers()
Returns

the list of members, as objects of class geoflow_featuremember

geoflow_featuretype$getMemberById()

Get member by ID

Usage
geoflow_featuretype$getMemberById(id)
Arguments
id

id

Returns

an object of class geoflow_featuremember, NULL otherwise

geoflow_featuretype$asDataFrame()

Converts to data frame

Usage
geoflow_featuretype$asDataFrame()
Returns

an object of class data.frame

geoflow_featuretype$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_featuretype$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow format class

Description

This class models a format

Format

R6Class object.

Details

geoflow_format

Value

Object of R6Class for modelling a format

Public fields

key

format key

name

key name

uri

key URI

description

key description

Methods

Public methods

geoflow_format$new()

Initializes a geoflow_format

Usage
geoflow_format$new(str = NULL)
Arguments
str

character string to initialize object using key-based syntax

geoflow_format$setKey()

Sets format key

Usage
geoflow_format$setKey(key)
Arguments
key

key

geoflow_format$setName()

Sets format name

Usage
geoflow_format$setName(name)
Arguments
name

name

geoflow_format$setUri()

Sets format URI

Usage
geoflow_format$setUri(uri)
Arguments
uri

URI

geoflow_format$setDescription()

Sets format description

Usage
geoflow_format$setDescription(description)
Arguments
description

description

geoflow_format$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_format$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  format <- geoflow_format$new()
  format$setKey("distribution")
  format$setName("text/csv")
  format$setUri("https://www.iana.org/assignments/media-types/text/csv")
  format$setDescription("CSV format")

## End(Not run)

Geoflow handler class

Description

This class models a content handler. An handler is a method to handle some content (eg entity or contact). It is mainly driven by a function that takes as argument the handler considered (as self accessible object), a source which identifiers the source to be handled, that can be of a different type (eg a URL, a file path) depending on the handler, and a config object, as the overall configuration created by geoflow initWorkflow function.

Format

R6Class object.

Details

geoflow_handler

Value

Object of R6Class for modelling a handler

Public fields

id

handler id

type

handler type (entity,contact,dictionary)

funders

funders

authors

authors

maintainer

maintainer

def

handler definition

packages

handler packages

fun

handler function

script

handler script

options

options

available_options

available options

status

status

notes

notes

Methods

Public methods

geoflow_handler$new()

Initializes a geoflow_handler

Usage
geoflow_handler$new(
  yaml = NULL,
  id = NULL,
  type = c("entity", "contact", "dictionary"),
  funders = list(),
  authors = list(),
  maintainer = NULL,
  def = "",
  packages = list(),
  fun = NULL,
  script = NULL,
  options = list(),
  available_options = list(),
  status = "stable",
  notes = ""
)
Arguments
yaml

a YAML file

id

id

type

type

funders

funders

authors

authors

maintainer

maintainer

def

def

packages

list of packages required for the handler

fun

the handler function having 2 arguments config and source

script

a handler script

options

action options

available_options

available options for the action

status

status (experimental/stable/deprecated/superseded)

notes

notes

geoflow_handler$fromYAML()

Reads handler properties from YAML file

Usage
geoflow_handler$fromYAML(file)
Arguments
file

file

geoflow_handler$checkPackages()

Check that all packages required for the handler are available, if yes, import them in the R session, and return a data.frame giving the packages names and version. If one or more packages are unavailable, an error is thrown and user informed of the missing packages.

Usage
geoflow_handler$checkPackages()

geoflow_handler$getOption()

Get handler option value

Usage
geoflow_handler$getOption(option)
Arguments
option

option id

Returns

the option value, either specified through a workflow, or the default value

geoflow_handler$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_handler$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

This class is essentially called internally by geoflow to register default handlers for entities and contacts.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  handler <- geoflow_handler$new(
   id = "some-id",
   def = "some definition",
   packages = list(),
   fun = function(handler, source, config){},
   available_options = list()
 )

## End(Not run)

Geoflow keyword class

Description

This class models a keyword

Format

R6Class object.

Details

geoflow_keyword

Value

Object of R6Class for modelling a keyword

Public fields

name

keyword

uri

keyword uri

Methods

Public methods

geoflow_keyword$new()

Initializes a geoflow_keyword

Usage
geoflow_keyword$new(name = NULL, uri = NULL)
Arguments
name

keyword name

uri

keyword URI

geoflow_keyword$setName()

Sets keyword

Usage
geoflow_keyword$setName(name)
Arguments
name

keyword name

geoflow_keyword$setUri()

Sets keyword URI

Usage
geoflow_keyword$setUri(uri)
Arguments
uri

keyword URI

geoflow_keyword$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_keyword$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  kwd <- geoflow_keyword$new()
  kwd$setName("keyword")
  kwd$setUri("http://somelink/keyword")

## End(Not run)

Geoflow kvp (Key Values pair) class

Description

This class models an kvp (Key Values pair)

Format

R6Class object.

Details

geoflow_kvp

Value

Object of R6Class for modelling an kvp (Key Values pair)

Public fields

key

the KVP key

values

the KVP values

locale

a locale definition for the KVP

Methods

Public methods

geoflow_kvp$new()

Initializes a Key-Value pair (KVP)

Usage
geoflow_kvp$new(key = NULL, values = NULL, locale = NULL)
Arguments
key

key

values

values

locale

locale

geoflow_kvp$setKey()

Set KVP key

Usage
geoflow_kvp$setKey(key)
Arguments
key

the key

geoflow_kvp$setValues()

Set KVP values

Usage
geoflow_kvp$setValues(values)
Arguments
values

the values

geoflow_kvp$setLocale()

Set KVP locale

Usage
geoflow_kvp$setLocale(locale)
Arguments
locale

locale

geoflow_kvp$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_kvp$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Geoflow process class

Description

This class models an process

Format

R6Class object.

Details

geoflow_process

Value

Object of R6Class for modelling an process

Public fields

rationale

process rationale

description

process description

processors

object of class list

Methods

Public methods

geoflow_process$new()

Initializes the geoflow_process

Usage
geoflow_process$new()

geoflow_process$setRationale()

Set process rationale

Usage
geoflow_process$setRationale(rationale)
Arguments
rationale

the process rationale

geoflow_process$setDescription()

Set process description

Usage
geoflow_process$setDescription(description)
Arguments
description

Set the process description

geoflow_process$addProcessor()

Adds processor

Usage
geoflow_process$addProcessor(processor)
Arguments
processor,

object of class geoflow_contact

geoflow_process$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_process$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  process <- geoflow_process$new()
  process$setRationale("rationale")
  process$setDescription("description")
  processor <- geoflow_contact$new()
  process$addProcessor(processor)

## End(Not run)

Geoflow profile class

Description

This class models an profile

Format

R6Class object.

Details

geoflow_profile

Value

Object of R6Class for modelling an profile

Public fields

id

profile id

name

profile name

project

profile project

organization

profile organization

logos

profile logo(s)

mode

mode of execution (Default is "raw")

options

global config options

Methods

Public methods

geoflow_profile$new()

Initializes an object of class geoflow_profile

Usage
geoflow_profile$new()

geoflow_profile$setId()

Sets profile ID

Usage
geoflow_profile$setId(id)
Arguments
id

id

geoflow_profile$setName()

Sets profile name

Usage
geoflow_profile$setName(name)
Arguments
name

name

geoflow_profile$setProject()

Sets profile project

Usage
geoflow_profile$setProject(project)
Arguments
project

project

geoflow_profile$setOrganization()

Sets profile organization

Usage
geoflow_profile$setOrganization(organization)
Arguments
organization

organization

geoflow_profile$addLogo()

Adds a profile organization

Usage
geoflow_profile$addLogo(logo)
Arguments
logo

logo

geoflow_profile$setMode()

Sets profile mode

Usage
geoflow_profile$setMode(mode)
Arguments
mode

profile mode

geoflow_profile$setOption()

Set global config option

Usage
geoflow_profile$setOption(name, value)
Arguments
name

option name

value

option value

geoflow_profile$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_profile$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  profile <- geoflow_profile$new()
  profile$setId("workflow1")
  profile$setName("Workflow 1")
  profile$setProject("My project")
  profile$setOrganization("My organization")
  provfile$addLogo("https://via.placeholder.com/300x150.png/09f/fff?text=geoflow")

## End(Not run)

Geoflow provenance class

Description

This class models an provenance

Format

R6Class object.

Details

geoflow_provenance

Value

Object of R6Class for modelling an provenance

Public fields

statement

provenance statement

processes

list of processes, as objects of class geoflow_process

Methods

Public methods

geoflow_provenance$new()

Initializes a geoflow_provenance

Usage
geoflow_provenance$new(str = NULL)
Arguments
str

character string to initialize a provenance using key-based syntax

geoflow_provenance$setStatement()

Set process statement

Usage
geoflow_provenance$setStatement(statement)
Arguments
statement

process statement

geoflow_provenance$addProcess()

Adds process

Usage
geoflow_provenance$addProcess(process)
Arguments
process,

object of class geoflow_process

geoflow_provenance$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_provenance$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  provenance <- geoflow_provenance$new()
  provenance$setStatement("statement")
  process1 <- geoflow_process$new()
  process1$setRationale("task 1")
  process1$setDescription("Performs task 1")
  provenance$addProcess(process1)
  process2 <- geoflow_process$new()
  process2$setRationale("task 2")
  process2$setDescription("Performs task 2")
  provenance$addProcess(process2)

## End(Not run)

Geoflow register class

Description

This class models a register to be used by geoflow

Format

R6Class object.

Details

geoflow_register

Value

Object of R6Class for modelling a register

Public fields

id

register id

def

register def

fun

register function

data

register data

Methods

Public methods

geoflow_register$new()

Initializes an object of class geoflow_register

Usage
geoflow_register$new(id, def, fun)
Arguments
id

id

def

def

fun

fun

geoflow_register$fetch()

Fetchs the register data using the register function

Usage
geoflow_register$fetch(config = NULL)
Arguments
config

a geoflow config object

geoflow_register$check()

Checks the register data structure. The structure of the data.frame returned by the register function should be of 4 columns including "code", "uri", "label", "definition". In case the data structure is not valid, the function throws an error.

Usage
geoflow_register$check(data)
Arguments
data

a register data structure

geoflow_register$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_register$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  register <- geoflow_register$new(
   id = "some-id",
   def = "definition",
   fun = function(){}
  )

## End(Not run)

Geoflow relation class

Description

This class models an relation

Format

R6Class object.

Details

geoflow_relation

Value

Object of R6Class for modelling an relation

Public fields

key

relation key

link

relation link

mimeType

relation mime

name

relation name

description

relation name

prov

provenance,

Methods

Public methods

geoflow_relation$new()

Initializes an object of class geoflow_relation

Usage
geoflow_relation$new(str = NULL)
Arguments
str

character string to initialize from using key-based syntax

geoflow_relation$setKey()

Set key

Usage
geoflow_relation$setKey(key)
Arguments
key

key

geoflow_relation$setLink()

Set link

Usage
geoflow_relation$setLink(link)
Arguments
link

link

geoflow_relation$setMimeType()

Set mime type

Usage
geoflow_relation$setMimeType(mimeType)
Arguments
mimeType

mime type

geoflow_relation$setName()

Set name

Usage
geoflow_relation$setName(name)
Arguments
name

name

geoflow_relation$setDescription()

Set description

Usage
geoflow_relation$setDescription(description)
Arguments
description

description

geoflow_relation$setProv()

Set provenance

Usage
geoflow_relation$setProv(prov = c("user", "geoflow"))
Arguments
prov

provenance

geoflow_relation$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_relation$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  relation <- geoflow_relation$new()
  relation$setProv("user")
  relation$setKey("wms")
  relation$setLink("http://somelink/wms")
  relation$setMimeType("application/xml")
  relation$setName("layername")
  relation$setDescription("layer description")

## End(Not run)

Geoflow right class

Description

This class models an right

Format

R6Class object.

Details

geoflow_right

Value

Object of R6Class for modelling an right

Public fields

key

right key

values

right values

Methods

Public methods

geoflow_right$new()

Initializes an object of class geoflow_right

Usage
geoflow_right$new(str = NULL, kvp = NULL)
Arguments
str

character string to initialize from using key-based syntax

kvp

an object of class geoflow_kvp

geoflow_right$setKey()

Sets key

Usage
geoflow_right$setKey(key)
Arguments
key

key

geoflow_right$setValues()

Sets values

Usage
geoflow_right$setValues(values)
Arguments
values

values

geoflow_right$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_right$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  right <- geoflow_right$new()
  right$setKey("use")
  right$setValues("No restrictions")

## End(Not run)

Geoflow SKOS vocabulary class

Description

This class models a SKOS vocabulary

Format

R6Class object.

Details

geoflow_skos_vocabulary

Value

Object of R6Class for modelling a SKOS vocabulary

Super class

geoflow_vocabulary -> geoflow_skos_vocabulary

Public fields

rdf

rdf

rdf_data

rdf_data

endpoint

endpoint

Methods

Public methods

Inherited methods

geoflow_skos_vocabulary$new()

Initializes a vocabulary

Usage
geoflow_skos_vocabulary$new(id, def, uri, endpoint = NULL, file = NULL)
Arguments
id

id

def

def

uri

uri

endpoint

A Sparql endpoint

file

a RDF file

geoflow_skos_vocabulary$query()

query

Usage
geoflow_skos_vocabulary$query(str, graphUri = NULL, mimetype = "text/csv")
Arguments
str

str

graphUri

graphUri

mimetype

mimetype

Returns

the response of the SPARQL query

geoflow_skos_vocabulary$query_full_dataset()

Queries full dataset

Usage
geoflow_skos_vocabulary$query_full_dataset()
Returns

an object of class tibble

geoflow_skos_vocabulary$ping()

Ping query

Usage
geoflow_skos_vocabulary$ping()

geoflow_skos_vocabulary$list_collections()

list_collections

Usage
geoflow_skos_vocabulary$list_collections(
  mimetype = "text/csv",
  count_sub_collections = TRUE,
  count_concepts = TRUE
)
Arguments
mimetype

mimetype

count_sub_collections

count_sub_collections. Default is TRUE

count_concepts

count_concepts. Default is TRUE

Returns

the response of the SPARQL query

geoflow_skos_vocabulary$get_concepts_hierarchy()

list_concepts

Usage
geoflow_skos_vocabulary$get_concepts_hierarchy(
  lang = "en",
  method = c("SPARQL", "R"),
  out_format = c("tibble", "list")
)
Arguments
lang

lang

method

method used to build the hierarchy, either "SPARQL" or "R"

out_format

output format (tibble or list). Default is "tibble"

Returns

the response of the SPARQL query

geoflow_skos_vocabulary$list_concepts()

list_concepts

Usage
geoflow_skos_vocabulary$list_concepts(lang = "en", mimetype = "text/csv")
Arguments
lang

lang

mimetype

mimetype

Returns

the response of the SPARQL query

geoflow_skos_vocabulary$query_from_uri()

query_from_uri

Usage
geoflow_skos_vocabulary$query_from_uri(
  uri,
  graphUri = NULL,
  mimetype = "text/csv"
)
Arguments
uri

uri

graphUri

graphUri

mimetype

mimetype

Returns

an object of class tibble

geoflow_skos_vocabulary$query_from_term()

query_from_term

Usage
geoflow_skos_vocabulary$query_from_term(
  term,
  graphUri = NULL,
  mimetype = "text/csv"
)
Arguments
term

term

graphUri

graphUri

mimetype

mimetype

Returns

an object of class tibble

geoflow_skos_vocabulary$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_skos_vocabulary$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Geoflow software class

Description

This class models a software to be used by geoflow

Format

R6Class object.

Details

geoflow_software

Value

Object of R6Class for modelling a software

Super class

geoflowLogger -> geoflow_software

Public fields

id

software id

type

software I/O type ("input" or "output")

software_type

type of software

definition

definition

packages

list of packages required for the software functioning

handler

software handler function

arguments

software arguments

parameters

software parameters

attributes

software attributes

properties

software properties

actions

actions associated with the software

Methods

Public methods

Inherited methods

geoflow_software$new()

Initializes a software

Usage
geoflow_software$new(
  id = NULL,
  type = NULL,
  software_type,
  packages = list(),
  definition,
  handler,
  arguments,
  attributes = list(),
  actions = list()
)
Arguments
id

id

type

type "input" or "output"

software_type

software type

packages

list of packages required for the software functioning

definition

software definition

handler

software handler function

arguments

software handler arguments

attributes

software attributes

actions

software actions

geoflow_software$setId()

Sets software ID

Usage
geoflow_software$setId(id)
Arguments
id

id

geoflow_software$setType()

Set type. Either "input" or "output"

Usage
geoflow_software$setType(type)
Arguments
type

software I/O type

geoflow_software$setSoftwareType()

Set software type

Usage
geoflow_software$setSoftwareType(software_type)
Arguments
software_type

software type

geoflow_software$setPackages()

Set software required packages

Usage
geoflow_software$setPackages(packages)
Arguments
packages

list of package names

geoflow_software$setDefinition()

Set software definition

Usage
geoflow_software$setDefinition(definition)
Arguments
definition

software definition

geoflow_software$setAttributes()

Set attributes. Function to call when creating an instance of geoflow_software

Usage
geoflow_software$setAttributes(attributes)
Arguments
attributes

named list of attributes

geoflow_software$setProperties()

Set properties. Function to call to pass argument values for a given geoflow_software

Usage
geoflow_software$setProperties(props)
Arguments
props

named list of properties

geoflow_software$setArguments()

Set software arguments. Function to call when creating an instance of geoflow_software

Usage
geoflow_software$setArguments(arguments)
Arguments
arguments

list of software arguments

geoflow_software$setParameters()

Set parameters. Function to call to pass argument values for a given geoflow_software

Usage
geoflow_software$setParameters(params)
Arguments
params

named list of parameters

geoflow_software$setActions()

Set software actions

Usage
geoflow_software$setActions(actions)
Arguments
actions

a list of geoflow_action

geoflow_software$setHandler()

Set the software handler function

Usage
geoflow_software$setHandler(handler)
Arguments
handler

object of class function

geoflow_software$checkPackages()

Check that all packages required for the software are available, if yes, import them in the R session, and return a data.frame giving the packages names and version. If one or more packages are unavailable, an error is thrown and user informed of the missing packages.

Usage
geoflow_software$checkPackages()

geoflow_software$getHandlerInstance()

Get the software handler instance

Usage
geoflow_software$getHandlerInstance()
Returns

an object instance of the software handler

geoflow_software$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_software$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  software<- geoflow_software$new(
   id = "some-id",
   type = "output",
   software_type = "software",
   definition = "definition",
   packages = list(),
   handler = function(){},
   arguments = list(
     url = list(def = "the software url")
   ),
   attributes = list(
     workspace = list(def = "a workspace name in the software")
   )
 )

## End(Not run)

Geoflow subject class

Description

This class models a subject

Format

R6Class object.

Details

geoflow_subject

Value

Object of R6Class for modelling a subject

Public fields

key

subject key

name

subject name

uri

subject URI

dates

subject date(s)

keywords

subject keywords

Methods

Public methods

geoflow_subject$new()

Initializes an object of class geoflow_subject

Usage
geoflow_subject$new(str = NULL, kvp = NULL)
Arguments
str

a character string to initialize from, using key-based syntax

kvp

an object of class geoflow_kvp

geoflow_subject$setKey()

Sets subject key

Usage
geoflow_subject$setKey(key)
Arguments
key

key

geoflow_subject$setName()

Sets subject name

Usage
geoflow_subject$setName(name)
Arguments
name

name

geoflow_subject$setUri()

Sets subject URI

Usage
geoflow_subject$setUri(uri)
Arguments
uri

uri

geoflow_subject$setDate()

Sets date

Usage
geoflow_subject$setDate(dateType, date)
Arguments
dateType

type of date

date

date

geoflow_subject$addKeyword()

Adds a keyword

Usage
geoflow_subject$addKeyword(keyword, uri = NULL)
Arguments
keyword

keyword

uri

keyword URI. Default is NULL

geoflow_subject$getKeywords()

Get keywords associated with the subject

Usage
geoflow_subject$getKeywords(pretty = FALSE)
Arguments
pretty

whether the output has to prettyfied as data.frame

Returns

the list of keywords as list of geoflow_keyword objects or data.frame

geoflow_subject$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_subject$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  subject <- geoflow_subject$new()
  subject$setKey("theme")
  subject$setName("General")
  subject$setUri("http://somelink/general")
  subject$addKeyword("keyword1", "http://somelink/keyword1")
  subject$addKeyword("keyword2", "http://somelink/keyword2")
  subject$addKeyword("keyword3", "http://somelink/keyword3")

## End(Not run)

geoflow_validator

Description

geoflow_validator

Public fields

source

object of class data.frame handling metadata objects to validate

Methods

Public methods

geoflow_validator$new()

Initializes a table validator for a given metadata model

Usage
geoflow_validator$new(model, valid_columns, source)
Arguments
model

the data model name, eg. "entity", "contact"

valid_columns

a vector of valid columns for the data model

source

an object of class data.frame handling the contacts

geoflow_validator$validate_structure()

Validates a source table against a data model structure

Usage
geoflow_validator$validate_structure()
Returns

TRUE if valid, FALSE otherwise.

geoflow_validator$validate_content()

Validates a source table using syntactic and content validation rules

Usage
geoflow_validator$validate_content(raw = FALSE)
Arguments
raw

indicates whether to return a list of geoflow_validator_cell objects or a data.frame

debug

debug validation

Returns

a list of geoflow_validator_cell objects, or data.frame

geoflow_validator$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_cell

Description

geoflow_validator_cell

Public fields

i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

Methods

Public methods

geoflow_validator_cell$new()

Initializes a geoflow_validator_cell

Usage
geoflow_validator_cell$new(
  na_authorized,
  use_key_syntax,
  key_required,
  valid_keys,
  default_key,
  error_if_invalid_key,
  exclude_http_keys,
  multiple,
  i,
  j,
  str
)
Arguments
na_authorized

if validator cell authorizes NAs or empty strings. Default is FALSE

use_key_syntax

if validator cell uses key-based syntax. Default is TRUE

key_required

if validator cell has a key required. Default is TRUE

valid_keys

valid keys for the validator cell. Default is an empty list

default_key

default_key to use if key is omitted. Default is NULL

error_if_invalid_key

raise an error if key is invalid. Default is TRUE

exclude_http_keys

if 'http' keys have to be excluded from validation checks. Default is TRUE

multiple

if cell may contain multiple values. Deprecated

i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

character string to validate

geoflow_validator_cell$isNaAuthorized()

Indicates if the validator cell authorizes NAs and empty strings

Usage
geoflow_validator_cell$isNaAuthorized()
Returns

TRUE if authorizes NAs and empty strings, FALSE otherwise

geoflow_validator_cell$isKeySynthaxUser()

Indicates if the validator cell makes use of key-based syntax

Usage
geoflow_validator_cell$isKeySynthaxUser()
Returns

TRUE if using key-based syntax, FALSE otherwise

geoflow_validator_cell$isKeyRequired()

Indicates if a key is required for the validator cell

Usage
geoflow_validator_cell$isKeyRequired()
Returns

TRUE if requires a key, FALSE otherwise

geoflow_validator_cell$getValidKeys()

Gives the list of valid keys for the validator cell

Usage
geoflow_validator_cell$getValidKeys()
Returns

the list of valid keys

geoflow_validator_cell$isErrorIfInvalidKey()

Indicates if a report error will be given in case of invalid key

Usage
geoflow_validator_cell$isErrorIfInvalidKey()
Returns

TRUE if a report error will be given in case of invalid key, FALSE otherwise

geoflow_validator_cell$getDefaultKey()

Gets the default key

Usage
geoflow_validator_cell$getDefaultKey()
Returns

the default key

geoflow_validator_cell$isExcludeHttpKeys()

Indicates if 'http' keys are excluded from the validation

Usage
geoflow_validator_cell$isExcludeHttpKeys()
Returns

TRUE if 'http' keys are excluded from the validation, FALSE otherwise

geoflow_validator_cell$isMultiple()

indicates if multiple key-based components can be used within a same cell

Usage
geoflow_validator_cell$isMultiple()
Returns

TRUE if supporting multiple key-based components by cell, FALSE otherwise

geoflow_validator_cell$validate()

Proceeds with syntactic validation for the cell considered

Usage
geoflow_validator_cell$validate()
Returns

an object of class data.frame including possible errors/warnings

geoflow_validator_cell$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_cell$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_contact_Identifier

Description

geoflow_validator_contact_Identifier

Super class

geoflow_validator_cell -> geoflow_validator_contact_Identifier

Methods

Public methods

Inherited methods

geoflow_validator_contact_Identifier$new()

Initializes a contact 'Identifier' cell

Usage
geoflow_validator_contact_Identifier$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_contact_Identifier$validate()

Validates a contact identifier. Proceeds with syntactic validation and content (ORCID) validation.

Usage
geoflow_validator_contact_Identifier$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_contact_Identifier$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_contact_Identifier$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_contacts

Description

geoflow_validator_contacts

Super class

geoflow_validator -> geoflow_validator_contacts

Methods

Public methods

Inherited methods

geoflow_validator_contacts$new()

Initializes a contacts table validator

Usage
geoflow_validator_contacts$new(source)
Arguments
source

an object of class data.frame handling the contacts

geoflow_validator_contacts$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_contacts$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entities

Description

geoflow_validator_entities

Super class

geoflow_validator -> geoflow_validator_entities

Methods

Public methods

Inherited methods

geoflow_validator_entities$new()

Initializes an entities table validator

Usage
geoflow_validator_entities$new(source)
Arguments
source

an object of class data.frame handling the entities

geoflow_validator_entities$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entities$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Creator

Description

geoflow_validator_entity_Creator

Super class

geoflow_validator_cell -> geoflow_validator_entity_Creator

Methods

Public methods

Inherited methods

geoflow_validator_entity_Creator$new()

Initializes an entity 'Creator' cell

Usage
geoflow_validator_entity_Creator$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Creator$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Creator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Data

Description

geoflow_validator_entity_Data

Super class

geoflow_validator_cell -> geoflow_validator_entity_Data

Methods

Public methods

Inherited methods

geoflow_validator_entity_Data$new()

Initializes an entity 'Data' cell

Usage
geoflow_validator_entity_Data$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Data$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Data$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Date

Description

geoflow_validator_entity_Date

Super class

geoflow_validator_cell -> geoflow_validator_entity_Date

Methods

Public methods

Inherited methods

geoflow_validator_entity_Date$new()

Initializes an entity 'Date' cell

Usage
geoflow_validator_entity_Date$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Date$validate()

Validates a date. Proceeds with syntactic validation and content validation.

Usage
geoflow_validator_entity_Date$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_Date$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Date$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Description

Description

geoflow_validator_entity_Description

Super class

geoflow_validator_cell -> geoflow_validator_entity_Description

Methods

Public methods

Inherited methods

geoflow_validator_entity_Description$new()

Initializes an entity 'Description' cell

Usage
geoflow_validator_entity_Description$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Description$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Description$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Format

Description

geoflow_validator_entity_Format

Super class

geoflow_validator_cell -> geoflow_validator_entity_Format

Methods

Public methods

Inherited methods

geoflow_validator_entity_Format$new()

Initializes an entity 'Format' cell

Usage
geoflow_validator_entity_Format$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Format$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Format$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Identifier

Description

geoflow_validator_entity_Identifier

Super class

geoflow_validator_cell -> geoflow_validator_entity_Identifier

Methods

Public methods

Inherited methods

geoflow_validator_entity_Identifier$new()

Initializes an entity 'Identifier' cell

Usage
geoflow_validator_entity_Identifier$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Identifier$validate()

Validates an entity identifier. Proceeds with syntactic validation and content validation for DOIs and UUIDs.

Usage
geoflow_validator_entity_Identifier$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_Identifier$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Identifier$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Language

Description

geoflow_validator_entity_Language

Super class

geoflow_validator_cell -> geoflow_validator_entity_Language

Methods

Public methods

Inherited methods

geoflow_validator_entity_Language$new()

Initializes an entity 'Language' cell

Usage
geoflow_validator_entity_Language$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Language$validate()

Validates a language. Proceeds with syntactic validation and language validation.

Usage
geoflow_validator_entity_Language$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_Language$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Language$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Provenance

Description

geoflow_validator_entity_Provenance

Super class

geoflow_validator_cell -> geoflow_validator_entity_Provenance

Methods

Public methods

Inherited methods

geoflow_validator_entity_Provenance$new()

Initializes an entity 'Provenance' cell

Usage
geoflow_validator_entity_Provenance$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Provenance$validate()

Validates a Provenance. Proceeds with syntactic validation and content validation.

Usage
geoflow_validator_entity_Provenance$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_Provenance$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Provenance$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Relation

Description

geoflow_validator_entity_Relation

Super class

geoflow_validator_cell -> geoflow_validator_entity_Relation

Methods

Public methods

Inherited methods

geoflow_validator_entity_Relation$new()

Initializes an entity 'Relation' cell

Usage
geoflow_validator_entity_Relation$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Relation$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Relation$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Rights

Description

geoflow_validator_entity_Rights

Super class

geoflow_validator_cell -> geoflow_validator_entity_Rights

Methods

Public methods

Inherited methods

geoflow_validator_entity_Rights$new()

Initializes an entity 'Rights' cell

Usage
geoflow_validator_entity_Rights$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Rights$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Rights$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_SpatialCoverage

Description

geoflow_validator_entity_SpatialCoverage

Super class

geoflow_validator_cell -> geoflow_validator_entity_SpatialCoverage

Methods

Public methods

Inherited methods

geoflow_validator_entity_SpatialCoverage$new()

Initializes an entity 'SpatialCoverage' cell

Usage
geoflow_validator_entity_SpatialCoverage$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_SpatialCoverage$validate()

Validates a spatial coverage. Proceeds with syntactic validation and spatial coverage validation (including EWKT, WKT and SRID).

Usage
geoflow_validator_entity_SpatialCoverage$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_SpatialCoverage$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_SpatialCoverage$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Subject

Description

geoflow_validator_entity_Subject

Super class

geoflow_validator_cell -> geoflow_validator_entity_Subject

Methods

Public methods

Inherited methods

geoflow_validator_entity_Subject$new()

Initializes an entity 'Subject' cell

Usage
geoflow_validator_entity_Subject$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Subject$validate()

Validates a Subject. Proceeds with syntactic validation and content validation.

Usage
geoflow_validator_entity_Subject$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_Subject$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Subject$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_TemporalCoverage

Description

geoflow_validator_entity_TemporalCoverage

Super class

geoflow_validator_cell -> geoflow_validator_entity_TemporalCoverage

Methods

Public methods

Inherited methods

geoflow_validator_entity_TemporalCoverage$new()

Initializes an entity 'TemporalCoverage' cell

Usage
geoflow_validator_entity_TemporalCoverage$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_TemporalCoverage$validate()

Validates temporal coverage. Proceeds with syntactic validation and temporal coverage validation.

Usage
geoflow_validator_entity_TemporalCoverage$validate()
Returns

an validation report, as object of class data.frame

geoflow_validator_entity_TemporalCoverage$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_TemporalCoverage$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Title

Description

geoflow_validator_entity_Title

Super class

geoflow_validator_cell -> geoflow_validator_entity_Title

Methods

Public methods

Inherited methods

geoflow_validator_entity_Title$new()

Initializes an entity 'Title' cell

Usage
geoflow_validator_entity_Title$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Title$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Title$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

geoflow_validator_entity_Type

Description

geoflow_validator_entity_Type

Super class

geoflow_validator_cell -> geoflow_validator_entity_Type

Methods

Public methods

Inherited methods

geoflow_validator_entity_Type$new()

Initializes an entity 'Type' cell

Usage
geoflow_validator_entity_Type$new(i, j, str)
Arguments
i

row index (internal index to be used for graphical geoflow validation handlers)

j

col index (internal index to be used for graphical geoflow validation handlers)

str

string to validate

geoflow_validator_entity_Type$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_validator_entity_Type$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Geoflow vocabulary class

Description

This class models a vocabulary

Format

R6Class object.

Details

geoflow_vocabulary

Value

Object of R6Class for modelling a vocabulary

Public fields

id

id

def

def

uri

uri

software_type

software_type

software

software

connection

connection

Methods

Public methods

geoflow_vocabulary$new()

Initializes a vocabulary

Usage
geoflow_vocabulary$new(id, def, uri, software_type, connection = "unknown")
Arguments
id

id

def

def

uri

uri

software_type

software type

connection

connection

geoflow_vocabulary$setSoftware()

Set software

Usage
geoflow_vocabulary$setSoftware(software)
Arguments
software

software

geoflow_vocabulary$clone()

The objects of this class are cloneable with this method.

Usage
geoflow_vocabulary$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

getDBTableColumnComment

Description

getDBTableColumnComment

Usage

getDBTableColumnComment(dbi, schema, table, column_index)

Arguments

dbi

a dbi connection

schema

schema

table

table

column_index

table column index

Value

the table comment

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

getDBTableComment

Description

getDBTableComment

Usage

getDBTableComment(dbi, schema, table)

Arguments

dbi

a dbi connection

schema

schema

table

table

Value

the table comment

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_absolute_path

Description

get_absolute_path allows to get the absolute path of a resource given a base directory

Usage

get_absolute_path(path, base, mustWork, expand_tilde)

Arguments

path

a path in character string

base

a base direcotry

mustWork

must work?

expand_tilde

expand tilde?

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_config_resource_path

Description

get_config_resource_path

Usage

get_config_resource_path(config, path)

Arguments

config

a geoflow config

path

a resource path to resolve vs. the config root dir

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_contact_handler

Description

get_contact_handler allows to get a contact handler

Usage

get_contact_handler(id)

Arguments

id

A contact handler identifier

Value

an object of class geoflow_handler

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_data_accessor

Description

get_data_accessor get a data accessor by ID.

Usage

get_data_accessor(id)

Arguments

id

an accessor ID

Value

an object of class geoflow_data_accessor, or NULL

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_dictionary_handler

Description

get_dictionary_handler allows to get a dictionary handler

Usage

get_dictionary_handler(id)

Arguments

id

A dictionary handler identifier

Value

an object of class geoflow_handler

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_entity_handler

Description

get_entity_handler allows to get an entity handler

Usage

get_entity_handler(id)

Arguments

id

An entity handler identifier

Value

an object of class geoflow_handler

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_epsg_code

Description

get_epsg_code is a consolidated method to get EPSG code (srid) from a CRS

Usage

get_epsg_code(x)

Arguments

x

an object of class 'sf'

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_line_separator

Description

get_line_separator get the line separator used by geoflow when extracting cell components for tabular data content handling. Default is set to an underscore followed by a line break.

Usage

get_line_separator()

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

get_locales_from

Description

Get locales from a property values set

Usage

get_locales_from(values)

Arguments

values

values

get_union_bbox

Description

get_union_bbox will build a unified bounding box from a list of geoflow_data objects

Usage

get_union_bbox(data_objects)

Arguments

data_objects

list of geoflow_data objects

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

initWorkflow

Description

initWorkflow allows to init a workflow

Usage

initWorkflow(file, dir, outdir, jobDirPath, handleMetadata, session)

Arguments

file

a JSON or YAML configuration file

dir

a directory used to execute the workflow. This is the working directory, ie where local resources (data, metadata), should be located.

outdir

a directory where the geoflow will write the job outputs.

jobDirPath

a directory set-up for the job. Default is NULL means it will be created during initialization of the workflow, otherwise the path provided will be used.

handleMetadata

Default is TRUE. Metadata contacts/entities/dictionary will be handled. If set to FALSE, they will not be handled. This is used for example in geoflow Shiny app where we want to initialize config without handling metadata to inherit software connections and test dynamically the metadata validity.

session

a shiny session object (optional) to run geoflow in a shiny context

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

initWorkflowJob

Description

initWorkflowJob allows to init a workflow job

Usage

initWorkflowJob(dir)

Arguments

dir

a directory where to initialize/execute the workflow

Value

the job directory path

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

is_absolute_path

Description

is_absolute_path evaluate if a ${{path}} expression is an absolute path, the function will return a boolean argument.

Usage

is_absolute_path(path)

Arguments

path

a path in character string

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_action_options

Description

list_action_options lists the options available for a given action supported by geoflow.

Usage

list_action_options(id, raw)

Arguments

id

An action identifier

raw

if raw list should be returned

Value

an object of class data.frame (or list if raw is TRUE) listing the available action options.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_actions

Description

list_actions lists the actions supported by geoflow.

Usage

list_actions(raw)

Arguments

raw

Default value is FALSE, meaning the actions will be listed as data.frame. The output If TRUE the raw list of geoflow_action is returned.

Value

an object of class data.frame (or list of geoflow_action if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_contact_handler_options

Description

list_contact_handler_options lists the options available for a given contact handler supported by geoflow.

Usage

list_contact_handler_options(id, raw)

Arguments

id

An contact handler identifier

raw

if raw list should be returned

Value

an object of class data.frame (or list if raw is TRUE) listing the available handler options.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_contact_handlers

Description

list_contact_handlers lists the contact handlers supported by geoflow.

Usage

list_contact_handlers(raw)

Arguments

raw

Default value is FALSE), meaning the handlers will be listed as data.frame. The output If TRUE the raw list of geoflow_handler is returned.

Value

an object of class data.frame (or list of geoflow_handler if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_data_accessors

Description

list_data_accessors lists the data accessors supported by geoflow.

Usage

list_data_accessors(raw)

Arguments

raw

Default value is FALSE, meaning the data accessors will be listed as data.frame. The output If TRUE the raw list of geoflow_data_accessor is returned.

Value

an object of class data.frame (or list of geoflow_data_accessor if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_dictionary_handler_options

Description

list_dictionary_handler_options lists the options available for a given dictionary handler supported by geoflow.

Usage

list_dictionary_handler_options(id, raw)

Arguments

id

An dictionary handler identifier

raw

if raw list should be returned

Value

an object of class data.frame (or list if raw is TRUE) listing the available handler options.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_dictionary_handlers

Description

list_dictionary_handlers lists the dictionary handlers supported by geoflow.

Usage

list_dictionary_handlers(raw)

Arguments

raw

Default value is FALSE, meaning the handlers will be listed as data.frame. The output If TRUE the raw list of geoflow_handler is returned.

Value

an object of class data.frame (or list of geoflow_handler if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_entity_handler_options

Description

list_entity_handler_options lists the options available for a given entity handler supported by geoflow.

Usage

list_entity_handler_options(id, raw)

Arguments

id

An entity handler identifier

raw

if raw list should be returned

Value

an object of class data.frame (or list if raw is TRUE) listing the available handler options.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_entity_handlers

Description

list_entity_handlers lists the entity handlers supported by geoflow.

Usage

list_entity_handlers(raw)

Arguments

raw

Default value is FALSE, meaning the handlers will be listed as data.frame. The output If TRUE the raw list of geoflow_handler is returned.

Value

an object of class data.frame (or list of geoflow_handler if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_registers

Description

list_registers lists the registers supported by geoflow.

Usage

list_registers(raw)

Arguments

raw

Default value is FALSE, meaning the registers will be listed as data.frame. The output If TRUE the raw list of geoflow_register is returned.

Value

an object of class data.frame (or list of geoflow_register if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_software

Description

list_software lists the software supported by geoflow.

Usage

list_software(raw)

Arguments

raw

Default value is FALSE, meaning the software will be listed as data.frame. The output If TRUE the raw list of geoflow_software is returned.

Value

an object of class data.frame (or list of geoflow_software if raw = FALSE)

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_software_parameters

Description

list_software_parameters lists the parameters of a given software supported by geoflow.

Usage

list_software_parameters(software_type, raw)

Arguments

software_type

A software type

raw

if raw list should be returned

Value

an object of class data.frame (or list if raw is TRUE) listing the software parameters

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_software_properties

Description

list_software_properties lists the properties of a given software supported by geoflow.

Usage

list_software_properties(software_type, raw)

Arguments

software_type

A software type

raw

if raw list should be returned

Value

an object of class data.frame listing the software properties

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

list_vocabularies

Description

list_vocabularies lists the vocabularies supported by geoflow.

Usage

list_vocabularies(raw)

Arguments

raw

Default value is FALSE, meaning the vocabularies will be listed as data.frame. The output If TRUE the raw list of geoflow_vocabulary is returned.

Value

an object of class data.frame (or list of geoflow_vocabulary if raw = FALSE)

loadMetadataHandler

Description

loadMetadataHandler allows to load a metadata handler

Usage

loadMetadataHandler(config, element, type)

Arguments

config

a geoflow configuration (as list). Only used to write logs, can be NULL.

element

a geoflow configuration metadata list element

type

either 'contacts', 'entities' or 'dictionnary'

Value

an object of class geoflow_handler

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

load_workflow_environment

Description

load_workflow_environment loads a workflow environment by evaluating variable expressions in the form ${{variable}}. If no variable expression pattern is identified in the string, the function will return the original string.

Usage

load_workflow_environment(config, session)

Arguments

config

object of class list

session

a shiny session object (optional) to run geoflow in a shiny context.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

posix_to_str

Description

posix_to_str converts a POSIX object to ISO string

Usage

posix_to_str(posix)

Arguments

posix

a POSIX object

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

precompute_relationships

Description

precompute_relationships

Usage

precompute_relationships(data, parent_key, child_key, child_label)

Arguments

data

data

parent_key

parent_key

child_key

child_key

child_label

child_label

Value

a list of relationships

read_contacts

Description

read_contacts allows to read contacts

Usage

read_contacts(id, source, config)

Arguments

id

a contact handler identifier

source

source

config

a geoflow config (output of initWorkflow). Default is NULL

Value

a list of object of class geoflow_contact

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

read_dictionary

Description

read_dictionary allows to read a dictionary

Usage

read_dictionary(id, source, config)

Arguments

id

a dictionary handler identifier

source

source

config

a geoflow config (output of initWorkflow). Default is NULL

Value

an object of class geoflow_dictionary

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

read_entities

Description

read_entities allows to read entities

Usage

read_entities(id, source, config)

Arguments

id

an entity handler identifier

source

source

config

a geoflow config (output of initWorkflow). Default is NULL

Value

a list of object of class geoflow_entity

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_actions

Description

register_actions registers default geoflow actions

Usage

register_actions()

Note

Function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_contact_handlers

Description

register_contact_handlers registers the default contact handlers for geoflow

Usage

register_contact_handlers()

Note

Internal function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_data_accessors

Description

register_data_accessors registers default geoflow data accessors

Usage

register_data_accessors()

Note

Function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_dictionary_handlers

Description

register_dictionary_handlers registers the default dictionary handlers for geoflow

Usage

register_dictionary_handlers()

Note

Internal function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_entity_handlers

Description

register_entity_handlers registers the default entity handlers for geoflow

Usage

register_entity_handlers()

Note

Internal function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_registers

Description

register_registers registers default geoflow registers

Usage

register_registers()

Note

Function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_software

Description

register_software registers default geoflow software

Usage

register_software()

Note

Function called on load by geoflow

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

register_vocabularies

Description

register_vocabularies registers default geoflow vocabularies

Usage

register_vocabularies()

Note

Function called on load by geoflow

sanitize_date

Description

sanitize_date sanitizes a date in geoflow

Usage

sanitize_date(date)

Arguments

date

an object o class character

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

sanitize_str

Description

sanitize_str sanitizes a string definition in geoflow

Usage

sanitize_str(str)

Arguments

str

a string as object of class character

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

set_i18n

Description

Set default locales to a property values set

Usage

set_i18n(term_key, default, expr, ...)

Arguments

term_key

term key

default

default

expr

expr

...

named values to be passed to expr

set_line_separator

Description

set_line_separator set the line separator to be used by geoflow when extracting cell components for tabular data content handling.

Usage

set_line_separator(x)

Arguments

x

a string as object of class character representing the line separator.

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

set_locales_to

Description

Set locales to a property values set

Usage

set_locales_to(values,locales)

Arguments

values

values

locales

locales

str_to_posix

Description

str_to_posix parses a string into a POSIX object

Usage

str_to_posix(str)

Arguments

str

a string as object of class character

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

unload_workflow_environment

Description

unload_workflow_environment unloads a workflow environment, in the case environment was provided by means of a dotenv file, and loaded using dotenv by geoflow. The function will recover the session environment variables values (useful in case an environment variable was overwriten for the workflow execution).

Usage

unload_workflow_environment(config)

Arguments

config

object of class list

Author(s)

Emmanuel Blondel, emmanuel.blondel1@gmail.com

writeWorkflowJobDataResource

Description

writeWorkflowJobDataResource allows to transform datasource into different formats

Usage

writeWorkflowJobDataResource(entity, config, obj, 
                                    useFeatures, resourcename, useUploadSource, 
                                    createIndexes, overwrite, append, chunk.size, 
                                    type)

Arguments

entity

a entity object as read by geoflow_entity

config

a configuration object as read by initWorkflow

obj

a sf file

useFeatures

a boolean condition to define if features must be attach to obj file

resourcename

name of data input

useUploadSource

a boolean condition to define if resourcename is same as uploadSource information

createIndexes

a boolean condition for possibility to create indexes for each column

overwrite

a boolean condition for writing to DB. Default is TRUE

append

a boolean condition for appending to DB existing table. Default is FALSE

chunk.size

an object of class integer giving the size of chunks to apply for DB upload. Default is equal to OL, meaning DB upload will be done without chunking.

type

format to convert into. Formats supported: shp, csv, gpkg, parquet, dbtable

Author(s)

Alexandre Bennici, bennicialexandre@gmail.com