HandlrClient: HandlrClient

Description Details Public fields Methods Note Examples

Description

handlr client, read and write to and from all citation formats

Details

The various inputs to the x parameter are handled in different ways:

Public fields

path

(character) non-empty if file path passed to initialize

string

(character) non-empty if string (non-file) passed to initialize

parsed

after read() is run, the parsed content

file

(logical) TRUE if a file passed to initialize, else FALSE

ext

(character) the file extension

format_guessed

(character) the guessed file format

doi

(character) the DOI, if any found

Methods

Public methods


Method print()

print method for HandlrClient objects

Usage
HandlrClient$print(x, ...)
Arguments
x

self

...

ignored


Method new()

Create a new HandlrClient object

Usage
HandlrClient$new(x, format = NULL, ...)
Arguments
x

(character) a file path (the file must exist), a string containing contents of the citation, a DOI, or a DOI as a URL. See Details.

format

(character) one of citeproc, ris, bibtex, codemeta, cff, or NULL. If NULL, we attempt to guess the format, and error if we can not guess

...

curl options passed on to crul::verb-GET

Returns

A new HandlrClient object


Method read()

read input

Usage
HandlrClient$read(format = NULL, ...)
Arguments
format

(character) one of citeproc, ris, bibtex, codemeta, cff, or NULL. If NULL, we attempt to guess the format, and error if we can not guess

...

further args to the writer fxn, if any


Method write()

write to std out or file

Usage
HandlrClient$write(format, file = NULL, ...)
Arguments
format

(character) one of citeproc, ris, bibtex, schema_org, rdfxml, codemeta, or cff

file

a file path, if NULL to stdout. for format=ris, number of files must equal number of ris citations

...

further args to the writer fxn, if any


Method as_df()

convert data to a data.frame using handl_to_df()

Usage
HandlrClient$as_df()
Returns

a data.frame


Method clone()

The objects of this class are cloneable with this method.

Usage
HandlrClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

If $parsed is NULL then it's likely $read() has not been run - in which case we attempt to run $read() to populate $parsed

Examples

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# read() can be run with format specified or not
# if format not given, we attempt to guess the format and then read
z <- system.file('extdata/citeproc.json', package = "handlr")
(x <- HandlrClient$new(x = z))
x$read()
x$read("citeproc")
x$parsed

# you can run read() then write()
# or just run write(), and read() will be run for you if possible
z <- system.file('extdata/citeproc.json', package = "handlr")
(x <- HandlrClient$new(x = z))
cat(x$write("ris"))

# read from a DOI as a url
if (interactive()) {
  (x <- HandlrClient$new('https://doi.org/10.7554/elife.01567'))
  x$parsed
  x$read()
  x$parsed
  x$write('bibtex')
}

# read from a DOI
if (interactive()) {
  (x <- HandlrClient$new('10.7554/elife.01567'))
  x$parsed
  x$read()
  x$write('bibtex')
}

# read in citeproc, write out bibtex
z <- system.file('extdata/citeproc.json', package = "handlr")
(x <- HandlrClient$new(x = z))
x$path
x$ext
x$read("citeproc")
x$parsed
x$write("bibtex")
f <- tempfile(fileext = ".bib")
x$write("bibtex", file = f)
readLines(f)
unlink(f)

# read in ris, write out ris
z <- system.file('extdata/peerj.ris', package = "handlr")
(x <- HandlrClient$new(x = z))
x$path
x$format_guessed
x$read("ris")
x$parsed
x$write("ris")
cat(x$write("ris"))

# read in bibtex, write out ris
(z <- system.file('extdata/bibtex.bib', package = "handlr"))
(x <- HandlrClient$new(x = z))
x$path
x$format_guessed
if (requireNamespace("bibtex", quietly = TRUE)) {
x$read("bibtex")
x$parsed
x$write("ris")
cat(x$write("ris"))
}

# read in bibtex, write out RDF XML
if (requireNamespace("bibtex", quietly = TRUE) && interactive()) {
  (z <- system.file('extdata/bibtex.bib', package = "handlr"))
  (x <- HandlrClient$new(x = z))
  x$path
  x$format_guessed
  x$read("bibtex")
  x$parsed
  x$write("rdfxml")
  cat(x$write("rdfxml"))
}

# codemeta
(z <- system.file('extdata/codemeta.json', package = "handlr"))
(x <- HandlrClient$new(x = z))
x$path
x$format_guessed
x$read("codemeta")
x$parsed
x$write("codemeta")

# cff: Citation File Format
(z <- system.file('extdata/citation.cff', package = "handlr"))
(x <- HandlrClient$new(x = z))
x$path
x$format_guessed
x$read("cff")
x$parsed
x$write("codemeta")

# > 1 citation
z <- system.file('extdata/citeproc-many.json', package = "handlr")
(x <- HandlrClient$new(x = z))
x$parsed
x$read()
x$parsed
## schmea org
x$write("schema_org")
## bibtex
x$write("bibtex")
## bibtex to file
f <- tempfile(fileext=".bib")
x$write("bibtex", f)
readLines(f)
unlink(f)
## to RIS
x$write("ris")
### only one per file, so not combined
files <- replicate(2, tempfile(fileext=".ris"))
x$write("ris", files)
lapply(files, readLines)

# handle strings instead of files
z <- system.file('extdata/citeproc-crossref.json', package = "handlr")
(x <- HandlrClient$new(x = readLines(z)))
x$read("citeproc")
x$parsed
cat(x$write("bibtex"), sep = "\n")

handlr documentation built on Jan. 13, 2021, 7:27 a.m.