This vignette demonstrates
procedures for specifying and validate metadata for the deposits
package. This vignette will use metadata for the two “beaver” datasets
provided with R’s “datasets”
package. Relevant metadata for these datasets are given in the
“Source” listed on that page (or ?beaver1 to see a local
version):
P. S. Reynolds (1994) Time-series analyses of beaver body temperatures. Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry. New York: John Wiley and Sons.
The metadata structure used by deposits follows the specifications of the Dublin Core Metadata Initiative. Users do not need to understand or read any documents on the DCMI structure, as the implementation is explicitly contained within the package’s “dc/schema.json” file. That file should be the only document needed to understand metadata compliance for deposits. It may nevertheless be instructive to examine the DCMI specifications, in order to understand individual terms in a broader context.
Metadata in deposits are validated against JSON schemas, with the schema for the
main “metadata” field contained in the
package’s “dc/schema.json” file. This schema file includes detailed
specifications for every metadata term used in deposits. The list of
terms can also be viewed directly with the
dcmi_terms() function. This validation procedure is
intended to issue instructive errors throughout when metadata do not
conform to the expected format, with this vignette demonstrating several
such error messages.
Let’s start with a minimal version of the metadata list shown above,
and try to validate that using the
deposit_fill_metadata() method:
metadata <- list (
author = "P.S. Reynolds",
title = "Time-series analyses of beaver body temperatures."
)
cli <- depositsClient$new (service = "zenodo", sandbox = TRUE)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword additionalProperty
#> 1 #/additionalProperties additionalProperties author
#> message
#> 1 must NOT have additional properties
#> Error: Stopping because the DCMI metadata terms listed above do not conform with the expected schema.That error tells us that “author” is an additional property, and that
the metadata “must NOT have additional properties.” These “additional
properties” refer to any beyond those specified in the schema. The
schema used to validate deposits metadata is contained in the
package’s dc/schema.json file. A copy of that file is
included with each installation of this package in the location given
by,
system.file (fs::path ("extdata", "dc", "schema.json"), package = "deposits")
#> [1] "/tmp/RtmpRy1rDY/Rinstf3a233b3e62/deposits/extdata/dc/schema.json"Searching for “author” either on the GitHub version or a local file will quickly reveal that author information belongs in a field called “creator”. Renaming that metadata item then gives,
metadata <- list (
creator = "P.S. Reynolds",
title = "Time-series analyses of beaver body temperatures."
)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword type
#> 1 /creator #/properties/creator/anyOf/0/type type array
#> 2 /creator #/properties/creator/anyOf/1/type type array
#> 3 /creator #/properties/creator/anyOf anyOf <NA>
#> message required
#> 1 must be array name
#> 2 must be array name
#> 3 must match a schema in anyOf <NA>
#> Error: Stopping because the DCMI metadata terms listed above do not conform with the expected schema.The first messages say that the “creator” property “must be array”.
Arrays in JSON are list objects in R, so this suggests the
next required modification:
metadata <- list (
creator = list ("P.S. Reynolds"),
title = "Time-series analyses of beaver body temperatures."
)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword type
#> 1 /creator/0 #/properties/creator/anyOf/0/items/type type object
#> 2 /creator/0 #/properties/creator/anyOf/1/items/type type object
#> 3 /creator #/properties/creator/anyOf anyOf <NA>
#> message required
#> 1 must be object name
#> 2 must be object name
#> 3 must match a schema in anyOf <NA>
#> Error: Stopping because the DCMI metadata terms listed above do not conform with the expected schema.The items within the “creator” field must now be of type “object.” R
being the relatively simply language that it is, “objects” are also
lists, leading us to:
metadata <- list (
creator = list (list ("P.S. Reynolds")),
title = "Time-series analyses of beaver body temperatures."
)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword type
#> 1 /creator/0 #/properties/creator/anyOf/0/items/type type object
#> 2 /creator/0 #/properties/creator/anyOf/1/items/type type object
#> 3 /creator #/properties/creator/anyOf anyOf <NA>
#> message required
#> 1 must be object name
#> 2 must be object name
#> 3 must match a schema in anyOf <NA>
#> Error: Stopping because the DCMI metadata terms listed above do not conform with the expected schema.And that generates the same error. Looking a bit further in the error output reveals that the object has a “required” property of “name”. More generally, for any instances in which the error messages themselves are not helpful, it is useful to refer to the actual JSON schema (or a local version). The “creator” field expected for the Zenodo service can then be seen to accept the properties, “name”, “affiliation”, “orcid”, and “gnd”, with the “name” property being required, as indicated by the error message.
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
title = "Time-series analyses of beaver body temperatures."
)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword missingProperty
#> 1 /metadata #/properties/metadata/required required description
#> message
#> 1 must have required property 'description'
#> Error: Stopping because the metadata terms listed above do not conform with the expected schema for the zenodo service.That error seems to indicate that our “creator” field is then valid, yet triggers a further error that that metadata “must have required property ‘description’”. Let’s add that:
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry."
)
cli$deposit_fill_metadata (metadata)That now works, although that does not capture the full metadata
shown above from ?beaver1. We still need information on the
publisher. Examining the JSON schema shows that it includes a
“publisher” field which is expected to be a string.
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons"
)
cli$deposit_fill_metadata (metadata)We may then wish to specify a date on which the resource was created. Searching for “date” in the schema itself reveals that there is a “date” field, but it is intended to describe, “A point or period of time associated with an event in the lifecycle of the resource.” There are various other “date” fields, but the one we want is pretty clearly the “created” field, which is expected to be a string in either “date” or “date-time” format. Let’s try a simple “date”:
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
created = "1994-01-01",
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons"
)
cli$deposit_fill_metadata (metadata)#> instancePath schemaPath keyword format
#> 1 /created #/properties/created/format format date-time
#> message
#> 1 must match format "date-time"
#> Error: Stopping because the metadata terms listed above do not conform with the expected schema for the zenodo service.That then fails because “created” must match the format “date-time”, even though the main JSON schema clearly indicates that either date or date-time strings are acceptable. This error reflects the fact that validation of deposits metadata is a two-stage process. The metadata are first validated against the general JSON schema described above, then converted to formats expected for the nominated deposits service, and the result is then validated again against a service-specific JSON schema. In this case, the Zenodo service itself requires “created” fields to have “date-time”, and not “date”, format.
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
created = "1994-01-01T00:00:00",
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons"
)
cli$deposit_fill_metadata (metadata)That metadata is then finally in a valid format for the Zenodo service. An instructive exercise is to change the service to “figshare”, and use the resultant error messages to tweak the metadata to the expected format for a Figshare deposit.
The schema permits many other fields, importantly including fields intended to be used by the deposits package to document and identify connections between different data resources. These include “hasPart”, “hasVersion”, “isPartOf”, “isReferencedBy”, “isReplacedBy”, “isRequiredBy”, and “isVersionOf”. Specifying these allows one deposit to be connected to others. One of the aims of the deposits package is to facilitate specification of these kinds of metadata, and so to enhance an ability to inter-connect and inter-relate different data depositions, providing insight into a growing ecosystem of inter-connected deposits.
These “is” and “has” metadata fields have complex structures, but
again the JSON schemas can and should be used to understand the expected
format. The isPartOf field for Zenodo is expected to by an
array (in R terms, a list) of objects, each of which must
have an “identifier” and “relation”, and may also have a
“resource_type”.
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
created = "1994-01-01T00:00:00",
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons",
isPartOf = list (list (
identifier = "Case Studies in Biometry",
relation = "isPartOf"
))
)
cli$deposit_fill_metadata (metadata)While those metadata are successfully validated, attempting to create that deposit on Zenodo would trigger an error, because the “identifier” must conform to an expected type. The JSON schema should as always be considered the definitive reference, and that states for “identifier” that:
“Supported identifiers include: DOI, Handle, ARK, PURL, ISSN, ISBN, PubMed ID, PubMed Central ID, ADS Bibliographic Code, arXiv, Life Science Identifiers (LSID), EAN-13, ISTC, URNs and URLs.”
The “Case Studies in Biometry” book has an “ARK” identifier which can be used here,
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
created = "1994-01-01T00:00:00",
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons",
isPartOf = list (list (
identifier = "ark:/13960/t0mt2n370",
relation = "isPartOf"
))
)
cli$deposit_fill_metadata (metadata)Examining the JSON schema also reveals that “isPartOf” allows one additional field of “resource_type”, which has to be an upload, publication, or image type followed by a type specification. These type specifications are included in the second JSON schema used to validate Zenodo-specific metadata. The GitHub version can be seen here, or the location of the locally-installed version found with,
system.file (fs::path ("extdata", "zenodo", "schema.json"), package = "deposits")
#> [1] "/tmp/RtmpRy1rDY/Rinstf3a233b3e62/deposits/extdata/zenodo/schema.json"This schema then reveals the accepted types for “publication” include “book”, so the “resource_type” becomes “publication-book”:
metadata <- list (
creator = list (list (name = "P.S. Reynolds")),
created = "1994-01-01T00:00:00",
title = "Time-series analyses of beaver body temperatures.",
description = "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
publisher = "John Wiley and Sons",
isPartOf = list (list (
identifier = "ark:/13960/t0mt2n370",
relation = "isPartOf",
resource_type = "publication-book"
))
)
cli$deposit_fill_metadata (metadata)Finally we can confirm that those metadata are in a format which will be accepted on our specific Zenodo service by creating a new deposit:
cli$deposit_new ()
#> ID of new deposit : 1186243
print (cli)
#> <deposits client>
#> deposits service : zenodo
#> sandbox: TRUE
#> url_base : https://sandbox.zenodo.org/api/
#> Current deposits : 1 (see 'deposits' element for details)
#>
#> url_service : https://sandbox.zenodo.org/deposit/1186243
#> deposit id : 1186243
#> hostdata : list with 14 elements
#> metadata : 6 terms (see 'metadata' element for details)And that deposit has been successfully created, with the Zenodo record populated with appropriately-translated versions of the metadata.
An alternative way to enter metadata into a deposits client is via a
local JSON metadata file. depostis includes the function,
deposits_metadata_template(),
which generates a local version of a complete template for all allowed
metadata fields. Note that deposits workflows are generally expected to
use metadata templates defined as part of a “frictionless” workflow, as
described in detail in the accompanying frictionless
vignette. The deposits_metadata_template()
is intended more for demonstration purposes, while a full frictionless
template is generally preferred. The format of deposits metadata
nevertheless remains the same in both.
f <- fs::file_temp (ext = ".json")
deposits_metadata_template (filename = f)
#> Edit the file [/tmp/Rtmpf1YHV8/fileff06615b3f8.json] and remove everything except the metadata fields you require.
#> The filename may be then passed as the 'metadata' argument to a 'deposits' client.That command issues an important note, given in even more detail in the first line of the resultant template:
head (readLines (f), 2L) [2]
#> [1] " \"_note\": \"Fields like this starting with underscores are comments. Please delete this field, and all fields in this template except for those you wish to use for your deposit. This template may NOT be used in anything like this default form to construct a 'deposits' client. Many values require editing to comply with expected formats described throughout, such as dates or fields expected to accord with some fixed vocabulary, or modification from text descriptions to JSON objects. Please refer to the main 'dc/schema' file of the 'deposits' package for full details.\","A version of that template modified to reflect the metadata defined above would then look like this:
#> {
#> "created": "1994-01-01T00:00:00",
#> "creator": [
#> {
#> "name": "P.S. Reynolds"
#> }
#> ],
#> "description": "Original source of 'beaver' data, in Chapter 11 of Lange, N., Ryan, L., Billard, L., Brillinger, D., Conquest, L. and Greenhouse, J. eds (1994) Case Studies in Biometry.",
#> "isPartOf": [
#> {
#> "identifier": "ark:/13960/t0mt2n370",
#> "relation": "isPartOf",
#> "resource_type": "publication-book"
#> }
#> ],
#> "publisher": "John Wiley and Sons",
#> "title": "Time-series analyses of beaver body temperatures."
#> }The format of each item within this JSON object then then matches the
specifications of the main
dc/schema.json file. Note that that schema expects both
the “creator” and “isPartOf” fields for Zenodo to be of type “array”.
Arrays in JSON are defined by square brackets,
[ ... array contents ...]. Both of these arrays are then
expected to have items of type “object”, which in JSON are defined by
curly brackets, { ... object contents ...}.
Those are the only two key aspects of JSON specification required to understand and use metadata templates in deposits:
[ ... array ...].{ ... object ...}.Both “array” and “object” items in JSON are represented in R terms as
lists, so an array of objects simply becomes
list(list(...)), as demonstrated in the first second of
this vignette. (While this means that objects composed of arrays could
cause confusion, these are relatively uncommon, and are not used in any
of the JSON schemas within the deposits package.)
The schema for the “creator” field shown above requires (for Zenodo) an “array” of items, each of which is an “object” which must include a “name” field, and may include additional fields for “affiliation”, “orcid”, and “gnd”. An example JSON specification for “creator” would thus be:
{
"creator": [
{
"name": "A. Person",
"orcid": "0000-0001-0002-0003"
},
{
"name": "B. Person"
}
]
}Because “creator” is an “array”, it may contain multiple unnamed items. In contrast, items within an “object” must generally be named, and schemas will generally expect single instances only of each item within an “object.” Switching the square and curly brackets in that definition would invalidate the JSON file, and would trigger an error in deposits.
Errors in the validation of JSON files themselves are, however,
nowhere near as informative as errors arising through comparing JSON
files with schemas. If a JSON file is itself invalid, the errors shown
by deposits will generally be uninformative. It is therefore very
important to ensure that JSON metadata files are formatted in a valid
way. The easiest way to check validity before passing a metadata file to
a deposits client is to use the
validate() function of the jsonlite
package. This function requires a string input, so should be called
as jsonlite::validate(readLines("metadata.json")).
This example demonstrates one important aspect of hand-writing JSON files, which is commas. Commas must be used to separate any sequential fields, and must not be placed at the end of any individual or sequence of fields. The first statement means that valid JSON requires commas like this:
{
"field1": "value1",
"field2": "value2"
}That specification without the comma would not be valid. The second
statement means that placing a comma after the second
"value2" statement would also render that JSON invalid.
Note that these commas are equally important in separating JSON
objects:
{
"object1": {
"field": "value"
},
"object2": {
"field": "value"
}
}That specification requires the single comma separating the two objects. Placing commas anywhere else, such as after the values, or at the end of “object2”, would then invalidate the JSON.
As described in detail in the
“frictionless” vignette, deposits is designed to work seamlessly
with the “frictionless”
workflow, via rOpenSci’s “frictionless” R
package. For metadata, this means that as soon as a data resource is
uploaded to a service (with the
deposit_upload_file() method), a “datapackage.json”
file is automatically created and filled with both descriptions of the
uploaded file, or “resource” in frictionless terms, as well as the
metadata described in this vignette. From that point onward, metadata
can be edited directly in the “datapackage.json” file, and both the
local client and external deposit can always be updated any time those
local data are modified with the
deposit_update() method.
In conclusion: from the moment your deposit has its own “datapackage.json” file, that should be considered the definitive record of all metadata. Any changes you may wish to make to those metadata should be made by directly editing that file, and deposits will update all corresponding local and remote records.
After restarting an R session, a deposits client can be connected to
a local deposit by passing the path to the local directory containing
deposit data and a “datapackage.json” file as the “metadata” parameter
of the new() method:
cli <- depositsClient$new (
service = "<service>",
metadata = "/<local>/<directory>/<or>/<frictionless_file>"
)Equivalently, start an empty deposits client, and fill the metadata
with the
deposit_fill_metadata() method:
cli <- depositsClient$new (service = "<service>")
path <- "/<local>/<directory>/<or>/<frictionless_file>"
cli$deposit_fill_metadata (metadata = path)The resultant client will fill the “metadata” field with the contents of the “datapackage.json” file. If the deposit also exists remotely, any local changes to “datapackage.json” will be reflected in changes on the remote deposits service, including changes within the copy of “datapackage.json” held there.