Package 'virionData'

Description

This is download_deposit_version wrapped in a purr::map call.

Usage

batch_download_deposit_versions(zenodo_ids = "all", dir_path, ...)

Arguments

Value

List of download locations.

Examples

## Not run: 
# get all deposit versions
batch_download_deposit_versions(dir_path = "outputs")

# get select versions
batch_download_deposit_versions(zenodo_ids = c("15677137", "15643004"), dir_path = "outputs")

## End(Not run)

Description

An R6 client for getting virion data and metadata.

Value

A deposit class (R6 class)

invisibly returns self

dataframe of remote csv file.

String. Path to download location.

data.frame from readr::read_csv()

String. cleaned zenodo id

metadata in the specificed format (invisible)

List. Named list of data frames with the following fields:

• name = field name

• type = field type

• description = characterization of the field

parent_id String. Identifier for a Zenodo deposit with multiple versions.

all_versions Character. All zenodo ids for versions of the deposit.

summary_df Data frame. A table of all zenodo ids for versions of the deposit.

latest_version String. Identifier for the latest version of the zenodo deposit.

working_version String. Identifier for the version of the zenodo deposit you are working with

working_bibtex String. Bibtex for the version of the zenodo deposit you are working with.

working_citation String. Citation for the version of the zenodo deposit you are working with.

working_files Data frame. Working files consist of key (file name) and url (url to file on zenodo)

working_json list. Metadata for the working version.

Methods

Public methods

• deposit$new()

• deposit$set_working_version()

• deposit$load_remote_csv_file()

• deposit$download_versioned_data()

• deposit$load_local_csv_file()

• deposit$check_zenodo_id()

• deposit$export_metadata()

• deposit$get_data_dictionary()

• deposit$get_parent_id()

• deposit$get_all_versions()

• deposit$get_summary_df()

• deposit$get_latest_version()

• deposit$get_working_version()

• deposit$get_working_bibtex()

• deposit$get_working_citation()

• deposit$get_working_files()

• deposit$get_working_json()

• deposit$clone()

Method new()

Create a new deposit object, as an R6 client. This object is connected to the zenodo deposit for virion and is the gateway for accessing different versions of the data.

Usage

deposit$new(parent_id = "15643003")

Arguments

Returns

A new deposit object

Examples

\dontrun{
virion_deposit <- deposit$new()
}

Method set_working_version()

Set the version of the data you would like to work with. Note that the structure of Virion data may change through time.

Usage

deposit$set_working_version(
  zenodo_id = "latest",
  style = "apa",
  print_bibtex = TRUE,
  print_citation = TRUE
)

Arguments

Examples

\dontrun{
# set the working version to the latest version of the deposit
virion_deposit$set_working_version("latest")

# set the working versino to an arbitrary deposit
virion_deposit$get_all_versions()
virion_deposit$set_working_version("19502921")
}

Method load_remote_csv_file()

Load a remote csv listed in the working files field directly into the environment.

Can handle either csv or csv.gz files. This function downloads a temporary file to your machine, reads it, then returns a dataframe.

The local file cache is removed when your R session restarts.

Consider using the download_versioned_data to save a persistent version of the virion dataset on your machine.

Usage

deposit$load_remote_csv_file(file_key, refresh = FALSE, ...)

Arguments

Examples

\dontrun{
## see the working files
working_files <- virion$get_working_files()
working_files$file_key
virion_data <- virion_deposit$load_remote_csv_file("virion.csv.gz")

}

Method download_versioned_data()

Download versioned data

Downloads all the files for a particular version of Virion to dir/zenodo_id.

This function does not change the working version!

Usage

deposit$download_versioned_data(
  zenodo_id = "working",
  dir = "outputs",
  refresh = FALSE
)

Arguments

Examples

\dontrun{
# download files for the working version
virion_deposit$download_versioned_data()

# download files for the latest version
virion_deposit$download_versioned_data("latest")

# download files for some zenodo id
virion_deposit$download_versioned_data("19502921")
}

Method load_local_csv_file()

Load a local version of the csv.

Assumes you would like to load the file from the current working version.

If the csv file is not present, a persistent version of the file will be downloaded to your machine.

Usage

deposit$load_local_csv_file(file_key, refresh, ...)

Arguments

Examples

\dontrun{

virion <- deposit$new()
virion$set_working_version()
working_files <- virion$get_working_files()
working_files$file_key
virion$load_local_csv_file("virion.csv.gz")
}

Method check_zenodo_id()

Check the zenodo ID

Look for key words like working or latest and convert them to integer ids OR pass the zenodo id directly to sanitize_id()

Usage

deposit$check_zenodo_id(zenodo_id)

Arguments

Examples

\dontrun{
virion_deposit$check_zenodo_id("latest")
}

Method export_metadata()

Export metadata for a version of the deposit.

Usage

deposit$export_metadata(zenodo_id, format, verbose)

Arguments

Examples

\dontrun{
 virion_deposit$export_metadata("working")
}

Method get_data_dictionary()

Create a list of data dictionaries.

Usage

deposit$get_data_dictionary(
  file_key = "datapackage.json",
  dir = tempdir(),
  refresh
)

Arguments

Examples

\dontrun{
virion <- deposit$new()
virion$set_working_version()
virion$get_data_dictionary()

}

Method get_parent_id()

Get a property of the object that is private

• all_versions Character. All zenodo ids for versions of the deposit.

• summary_df Data frame. A table of all zenodo ids for versions of the deposit.

• latest_version String. Identifier for the latest version of the zenodo deposit.

• working_version String. Identifier for the version of the zenodo deposit you are working with.

• working_bibtex String. Bibtex for the version of the zenodo deposit you are working with.,

• working_citation String. Citation for the version of the zenodo deposit you are working with.

• working_files Data frame. Working files consist of key (file name) and url (url to file on zenodo)

• working_json list. Metadata for the working version.

Usage

deposit$get_parent_id()

Method get_all_versions()

Get a property of the object that is private

Usage

deposit$get_all_versions()

Method get_summary_df()

Get a property of the object that is private

• latest_version String. Identifier for the latest version of the zenodo deposit.

• working_version String. Identifier for the version of the zenodo deposit you are working with.

• working_bibtex String. Bibtex for the version of the zenodo deposit you are working with.,

• working_citation String. Citation for the version of the zenodo deposit you are working with.

• working_files Data frame. Working files consist of key (file name) and url (url to file on zenodo)

• working_json list. Metadata for the working version.

Usage

deposit$get_summary_df()

Method get_latest_version()

Get a property of the object that is private

Usage

deposit$get_latest_version()

Method get_working_version()

Get a property of the object that is private

Usage

deposit$get_working_version()

Method get_working_bibtex()

Get a property of the object that is private

Usage

deposit$get_working_bibtex()

Method get_working_citation()

Get a property of the object that is private

Usage

deposit$get_working_citation()

Method get_working_files()

Get a property of the object that is private

Usage

deposit$get_working_files()

Method get_working_json()

Get a property of the object that is private

Usage

deposit$get_working_json()

Method clone()

The objects of this class are cloneable with this method.

Usage

deposit$clone(deep = FALSE)

Arguments

Examples

## Not run: 
# make a client
virion_deposit <- deposit$new()

# methods
virion_deposit$set_working_version("latest")
virion_deposit$get_working_files()

# load remote data directly into your session
virion_data  <- virion_deposit$load_remote_csv_file(file_key = "virion.csv.gz")

# download remote data to disk - defaults to working version
virion_deposit$download_versioned_data()


## End(Not run)

## ------------------------------------------------
## Method `deposit$new`
## ------------------------------------------------

## Not run: 
virion_deposit <- deposit$new()

## End(Not run)

## ------------------------------------------------
## Method `deposit$set_working_version`
## ------------------------------------------------


## Not run: 
# set the working version to the latest version of the deposit
virion_deposit$set_working_version("latest")

# set the working versino to an arbitrary deposit
virion_deposit$get_all_versions()
virion_deposit$set_working_version("19502921")

## End(Not run)


## ------------------------------------------------
## Method `deposit$load_remote_csv_file`
## ------------------------------------------------

## Not run: 
## see the working files
working_files <- virion$get_working_files()
working_files$file_key
virion_data <- virion_deposit$load_remote_csv_file("virion.csv.gz")


## End(Not run)

## ------------------------------------------------
## Method `deposit$download_versioned_data`
## ------------------------------------------------

## Not run: 
# download files for the working version
virion_deposit$download_versioned_data()

# download files for the latest version
virion_deposit$download_versioned_data("latest")

# download files for some zenodo id
virion_deposit$download_versioned_data("19502921")

## End(Not run)


## ------------------------------------------------
## Method `deposit$load_local_csv_file`
## ------------------------------------------------

## Not run: 

virion <- deposit$new()
virion$set_working_version()
working_files <- virion$get_working_files()
working_files$file_key
virion$load_local_csv_file("virion.csv.gz")

## End(Not run)


## ------------------------------------------------
## Method `deposit$check_zenodo_id`
## ------------------------------------------------


## Not run: 
virion_deposit$check_zenodo_id("latest")

## End(Not run)

## ------------------------------------------------
## Method `deposit$export_metadata`
## ------------------------------------------------


## Not run: 
 virion_deposit$export_metadata("working")

## End(Not run)


## ------------------------------------------------
## Method `deposit$get_data_dictionary`
## ------------------------------------------------

## Not run: 
virion <- deposit$new()
virion$set_working_version()
virion$get_data_dictionary()


## End(Not run)

Description

Simple summary data frame for the deposit

Usage

deposit_summary()

Value

data frame. Simplified deposit metadata with the following fields:

• id = zenodo id

• latest_version = True or False indicating if that record is the latest version of the dataset.

• publication_date = YMD the item was published to zenodo

• doi_url = digital object identifier for that version of the record.

Examples

deposit_summary()

Description

Downloads and extracts some version of the deposit.

Usage

download_deposit_version(
  zenodo_id,
  deposit_versions = list_deposit_versions(),
  dir_path,
  datapackage_only = FALSE
)

Arguments

Value

String. Path to downloaded version.

Description

Downloads a file or re-downloads a file to refresh the cached files.

Usage

download_refresh(file_url, local, refresh)

Arguments

Value

String. Local File path

Description

Apparently a known issue in R6 as the class is not created until install.

Usage

dummy_imports()

Value

Character string explaining why this function exists.

Description

Bibtex specific wrapper for export_deposit_metadata

Usage

export_deposit_bibtex(zenodo_id = the$working_version, verbose = TRUE)

Arguments

Value

Character. bibtex formatted entry

Examples

## Not run: 
export_deposit_bibtex(zenodo_id = "15692263" ) |>
  writeLines(con = "outputs/citation.bib")

## End(Not run)

Description

Export Deposit Metadata in various formats

Usage

export_deposit_metadata(
  zenodo_id = the$working_version,
  format,
  verbose = TRUE
)

Arguments

Value

Character. Returns text in selected format.

Examples

## Not run: 
export_deposit_metadata(zenodo_id = "15692263","json-ld" ) |>
  writeLines(con = "outputs/citation.jsonld")

## End(Not run)

Description

Recursively traverse a deposit link to get all versions of a deposit.

Usage

get_all_versions(url)

Arguments

Value

Data.frame. Metadata for all deposit version

Examples

## Not run: 

self_link <- "https://zenodo.org/api/records/21232661/versions?page=1&size=25&sort=version"
get_all_versions(self_link)

## End(Not run)

Description

Creates a list of data frames that constitutes the data dictionary.

Usage

get_data_dictionary(datapackage_json)

Arguments

Value

List. Named list of data frames with the following fields:

• name = field name

• type = field type

• description = characterization of the field

Examples

## Not run: 
get_data_dictionary(datapackage_json = "data/1235600/datapackage.json")

## End(Not run)

Description

Get the dictionary for a single resource

Usage

get_individual_dictionary(x)

Arguments

Value

dataframe with three fields.

Description

jsonlite::fromJSON() wrapped in rlang::try_fetch() to make calls smoother.

Usage

get_json(url)

Arguments

Value

List. JSON as a list

Examples

## Not run: 
get_json("https://www.example.com/example.json")

## End(Not run)

Description

Get the name of a resource

Usage

get_resource_name(x)

Arguments

Value

character. Name of resources

Description

Get Version Citation

Usage

get_version_citation(
  zenodo_id = the$working_version,
  style = c("havard-cite-them-right", "apa", "modern-language-association", "vancouver",
    "chicago-fullnote-bibliography", "ieee"),
  verbose = TRUE
)

Arguments

Value

Character. Text for a citation

Examples

## Not run: 
get_version_citation(zenodo_id = "15692263",
                    style = "apa")

## End(Not run)

Description

This is a convenience function that downloads a specific version of the data and returns attribution information.

Usage

get_versioned_data(
  version = "latest",
  style = "apa",
  dir_path,
  refresh_deposits_versions = TRUE,
  verbose = TRUE,
  ...
)

Arguments

Details

If you would like to download a bibtex entry use export_deposit_bibtex. For other metadata types (CSL, CFF, JSON-LD, etcetera) use export_deposit_metadata.

Value

Character. path to versioned data.

Description

This function gets the metadata for all the versions of a deposit associated with a parent id. The parent id is used to identify a set of works that are different versions of the same work. The parent id is provided by the Zenodo API. To find the parent ID, download a JSON representation of the deposit (export to json on the webpage or use export_deposit_metadata), there will be an attribute called parent that looks like "https://zenodo.org/api/records/15020049". The 8 digit string at the end of the url is the parent id.

Usage

list_deposit_versions(parent_id = "15643003")

Arguments

Details

This function also sets package variables

Value

Data frame. Invisible. The data frame contains the Zenodo id for each version of the deposit, as well as the version name, and logical field called latest that indicates if this is the latest version.

Description

Appends a zenodo id to the zenodo api url.

Usage

make_url(base_url = "https://zenodo.org/api/records/%s", id)

Arguments

Value

String. URL for zenodo api.

Examples

make_url(id = "1235600")

Description

Remove any white space and check that it conforms to the zenodo id pattern.

Usage

sanitize_id(zenodo_id)

Arguments

Value

String. A cleaned zenodo id.

Examples

sanitize_id(" 2948598")

Description

Checks that version ids are properly formatted. IDs should either be integers ("15643003") OR "latest"

Usage

sanitize_version(version)

Arguments

Value

Character. Version identifier from Zenodo.

Examples

sanitize_version("latest")
sanitize_version(" 15643003")