Title:	Ecological Metadata as Linked Data
Version:	0.5.1
Description:	This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.
URL:	https://docs.ropensci.org/emld/, https://github.com/ropensci/emld
BugReports:	https://github.com/ropensci/emld/issues
Depends:	R (≥ 3.1.0)
License:	MIT + file LICENSE
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.1.1
Suggests:	spelling, testthat, magrittr, rmarkdown, covr, knitr, rdflib, jqr
Imports:	xml2, jsonlite, jsonld, methods, yaml
VignetteBuilder:	knitr
Language:	en-US
NeedsCompilation:	no
Packaged:	2020-09-27 02:57:18 UTC; cboettig
Author:	Carl Boettiger [aut, cre, cph], Matthew B. Jones [aut, cph], Bryce Mecum [aut, cph]
Maintainer:	Carl Boettiger <cboettig@gmail.com>
Repository:	CRAN
Date/Publication:	2020-09-27 10:50:10 UTC

emld: Ecological Metadata as Linked Data

Description

The goal of emld is to provide a way to work with EML metadata in the JSON-LD format. At it's heart, the package is simply a way to translate an EML XML document into JSON-LD and be able to reverse this so that any semantically equivalent JSON-LD file can be serialized into EML-schema valid XML.

Details

The package has only three core functions:

• as_emld() Convert EML's xml files (or the json version created by this package) into a native R object (an S3 class called emld, essentially just a list).

• as_xml() Convert the native R format, emld, back into XML-schema valid EML.

• as_json() Convert the native R format, emld, into json(LD).

Author(s)

Maintainer: Carl Boettiger cboettig@gmail.com (ORCID) [copyright holder]

Authors:

• Matthew B. Jones jones@nceas.ucsb.edu (ORCID) [copyright holder]

• Bryce Mecum mecum@nceas.ucsb.edu (ORCID) [copyright holder]

See Also

Useful links:

• https://docs.ropensci.org/emld/

• https://github.com/ropensci/emld

• Report bugs at https://github.com/ropensci/emld/issues

Coerce an EML file or object into an emld object.

Description

Coerce an EML file or object into an emld object.

Usage

as_emld(x, from = c("guess", "xml", "json", "list"))

Arguments

Value

an emld object

Examples

 hf205 <- system.file("extdata/hf205.xml", package="emld")
 as_emld(hf205)

Coerce an emld object into JSON

Description

Coerce an emld object into JSON

Usage

as_json(x, file = NULL)

Arguments

Details

Note: since emld list object maintains a 1:1 correspondence with JSON, following the conventions of jsonlite, this function is basically trivial. The only purpose is to default to auto_unbox = TRUE in serializing lists to JSON.

Value

a json object. Or if a file path is provided, the metadata is written out in JSON file and the function returns NULL invisibly.

Examples

f <- system.file("extdata/example.xml", package = "emld")
emld <- as_emld(f)
json <- as_json(emld)
## can also write a json file to disk:
json_file <- tempfile()
as_json(emld, json_file)

Coerce an emld object into XML (EML's standard format)

Description

Coerce an emld object into XML (EML's standard format)

Usage

as_xml(x, file = NULL, root = "eml", ns = "eml", schemaLocation = TRUE)

Arguments

Details

Unlike as_json, this function cannot rely on the existing convention of serializing a list to xml, eg, as defined by xml2::as_xml_document() Instead, this relies on a modified version, as_eml_document. In addition further steps must be taken when working with JSON-LD to deal with different possible framings and namespaces from the JSON-LD context element. Thus this as_xml function is particular to EML and emld objects alone.

Value

a xml_document object. Or if a file path is provided, the metadata is written out in XML file and the function returns NULL invisibly.

Examples

f <- system.file("extdata/example.xml", package = "emld")
emld <- as_emld(f)
xml <- as_xml(emld)

## can also write directly to a file:
xml_file <- tempfile()
as_xml(emld, xml_file)

## if you don't want the `xsi:schemaLocation` attribute set
as_xml(emld, schemaLocation = FALSE)

## or if you want to set your own value
as_xml(emld, schemaLocation = "https://eml.ecoinformatics.org/eml-2.2.0
http://example.com/eml-2.2.0/eml.xsd")

Get the XML namespace for a version of EML

Description

Utility function for use when filling in xmlns, schemaLocation, or vocab in various representations of EML. This is a little more future-proof than keeping a dictionary for each version since this won't break on the next release.

Usage

eml_ns(version = eml_version())

Arguments

Value

returns the full XML namespace URI for the specified version of the schema

eml_validate

Description

eml_validate processes an EML document using the XSD schema for the appropriate version of EML and determines if the document is schema-valid as defined by the XSD specification

Usage

eml_validate(eml, encoding = "UTF-8", schema = NULL)

Arguments

Value

Whether the document is valid (logical)

Examples

 f <- system.file("extdata", "example.xml", package = "emld")

 ## validate file directly from disk:
 eml_validate(f)

 ## validate an eml object:
 eml <- as_emld(f)
 eml_validate(eml)

Set or check the EML version default

Description

Set or check the EML version default

Usage

eml_version(version = getOption("emld_db", "eml-2.2.0"))

Arguments

Value

returns the EML version string. As a side-effect, sets the requested version as the default version by setting the emld_db variable in options().

Examples

eml_version()
eml_version("2.1.1")
eml_version("eml-2.1.1")

Get the real QName for the root element, including its prefix

Description

Note that if a default namespace is used, the prefix will be d1.

Usage

find_real_root_name(doc)

Arguments

Value

A list with elements prefix and name. prefix will be NULL if the element has no namespace prefix but name will always be a character.

Find the root schema module and version

Description

Find the root schema module and version

Usage

guess_root_schema(doc)

Arguments

Value

If found, a list with names 'version', 'module', and 'namespace. If not found, throws an error.

Guess an appropriate schemaLocation value for a given version of the schema

Description

This is a simple helper to make filling in the schemaLocation attribute on documents this package creates. Supports EML 2.1.1 and newer.

Usage

guess_schema_location(version = eml_version())

Arguments

Value

Returns a string suitable as a value for schemaLocation or NULL if a value wasn't found.

Examples

## Not run: 
# Get an appropriate schemaLocation value for the current version fo EML
guess_schema_location()

# Get an appropriate value for EML 2.1.1
guess_schema_location("eml-2.1.1")

## End(Not run)

Create a template for an EML object

Description

Create a template for an EML object

Usage

template(object)

Arguments

Details

Note: while this function can be called in recursions, doing so may be a bad idea.

Value

a list with elements named according to the properties of the object. This can be coerced into EML, see vignettes. NULL-valued elements (~) can take a data entry directly, while empty list()-valued elements () indicate properties that take other eml objects as values.

Examples

template("creator")