Parsing Codemeta Data

Here we illustrate some example use cases that involve parsing codemeta data.

library(jsonld)
library(jsonlite)
library(magrittr)
library(codemetar)
library(purrr)
library(dplyr)
library(printr)
library(tibble)

We then digest this input using a JSON-LD “frame.” While not strictly necessary, this helps ensure the data matches the format we expect, even if the original file had errors or missing data. See the vignette “Validating in JSON-LD” in this package and the official JSON-LD docs for details). The codemetar package includes a reasonably explicit frame to get us started:

frame <- system.file("schema/frame_schema.json", package="codemetar")
codemeta <- system.file("codemeta.json", package="codemetar")
meta <- 
  jsonld_frame(codemeta, frame) %>%
  fromJSON(FALSE) %>% getElement("@graph") %>% getElement(1)

Construct a citation

authors <- 
lapply(meta$author, 
       function(author) 
         person(given = author$given, 
                family = author$family, 
                email = author$email,
                role = "aut"))
year <- meta$datePublished
if(is.null(year)) 
  year <- format(Sys.Date(), "%Y")
bibitem <- 
 bibentry(
     bibtype = "Manual",
     title = meta$name,
     author = authors,
     year = year,
     note = paste0("R package version ", meta$version),
     url = meta$URL,
     key = meta$identifier
   )

cat(format(bibitem, "bibtex"))

@Manual{,
  title = {codemetar: Generate 'CodeMeta' Metadata for R Packages},
  year = {2024},
  note = {R package version 0.3.3},
}

bibitem

(2024). _codemetar: Generate 'CodeMeta' Metadata for R Packages_. R
package version 0.3.3.

Parsing the ropensci corpus

The ropensci corpus consists of a list of codemeta files for all packages provided by the rOpenSci project, <ropensci.org>. This provides a good test-case for how a large collection of codemeta files can be manipulated to help us get a better picture of the corpus.

download.file("https://github.com/codemeta/codemetar/raw/main/inst/notebook/ropensci.json",
              "ropensci.json")

As before, it is helpful, though not essential, to start off by framing the input data.

frame <- system.file("schema/frame_schema.json", package="codemetar")

corpus <- 
    jsonld_frame("ropensci.json", frame) %>%
    fromJSON(simplifyVector = FALSE) %>%
    getElement("@graph")

We’re now ready to start exploring. As usual, functions from purrr prove very useful for iterating through large JSON files. First, we look at some basic summary data:

## deal with nulls explicitly by starting with map
pkgs <- map(corpus, "name") %>% compact() %>% as.character()

# keep only those with package identifiers (names)
keep <- map_lgl(corpus, ~ length(.x$identifier) > 0)
corpus <- corpus[keep]

## now we can just do
all_pkgs <- map_chr(corpus, "name")
head(all_pkgs)

[1] "AntWeb: programmatic interface to the AntWeb"                                
[2] "aRxiv: Interface to the arXiv API"                                           
[3] "chromer: Interface to Chromosome Counts Database API"                        
[4] "ckanr: Client for the Comprehensive Knowledge Archive Network ('CKAN') 'API'"
[5] "dashboard: A package status dashboard"                                       
[6] "ggit: Git Graphics"

## 60 unique maintainers
map_chr(corpus, c("maintainer", "familyName")) %>% unique() %>% length()

[1] 61

## Mostly Scott
map_chr(corpus, c("maintainer", "familyName")) %>% 
  as_tibble() %>%
  group_by(value) %>%
  tally(sort=TRUE)

value	n
Chamberlain	105
Ooms	12
Mullen	8
Ram	8
Boettiger	6
Salmon	5
FitzJohn	4
Hart	2
Leeper	2
Marwick	2
Müller	2
Padgham	2
South	2
Varela	2
Vitolo	2
Arnold	1
Attali	1
Banbury	1
Becker	1
Bengtsson	1
Braginsky	1
Broman	1
Bryan	1
Dallas	1
Drost	1
Fischetti	1
Ghahraman	1
Goring	1
Harrison	1
Hughes	1
Jahn	1
Jones	1
Keyes	1
Krah	1
Lehtomaki	1
Lovelace	1
Lundstrom	1
McGlinn	1
McVey	1
Meissner	1
Michonneau	1
Moroz	1
Otegui	1
Pardo	1
Pennell	1
Poelen	1
Robinson	1
Ross	1
Rowlingson	1
Scott	1
Seers	1
Shotwell	1
Sievert	1
Sparks	1
Stachelek	1
Szöcs	1
Widgren	1
Wiggin	1
Winter	1
de Queiroz	1
hackathoners	1

## number of co-authors ... 
map_int(corpus, function(r) length(r$author)) %>% 
  as_tibble() %>%
  group_by(value) %>%
  tally(sort=TRUE)

value	n
1	146
2	30
3	17
4	8
5	5
7	3
13	1

## Contributors isn't used as much...
map_int(corpus, function(r) length(r$contributor)) %>% 
  as_tibble() %>%
  group_by(value) %>%
  tally(sort=TRUE)

value	n
0	178
2	13
3	12
4	5
6	1
8	1

Numbers (n) of packages with a total of (value) dependencies:

map_int(corpus, function(r) length(r$softwareRequirements))  %>% 
  as_tibble() %>%
  group_by(value) %>%
  tally(sort=TRUE)

value	n
3	37
4	31
5	31
2	25
7	19
6	16
8	13
9	8
12	7
10	6
11	6
13	3
0	2
14	1
17	1
18	1
21	1
22	1
23	1

which dependencies are used most frequently?

corpus %>%
map_df(function(x){
  ## single, unboxed dep
  if("name" %in% names(x$softwareRequirements))
    dep <- x$name
  else if("name" %in% names(x$softwareRequirements[[1]]))
    dep <- map_chr(x$softwareRequirements, "name")
  else { ## No requirementsß
    dep <- NA
  }
  
  tibble(identifier = x$identifier, dep = dep)
}) -> dep_df


dep_df %>%
group_by(dep) %>% 
  tally(sort = TRUE)

dep	n
jsonlite	99
httr	92
R	66
tibble	46
dplyr	43
methods	37
xml2	37
data.table	35
utils	35
crul	31
plyr	29
XML	25
magrittr	24
sp	22
stringr	21
curl	18
ggplot2	18
lazyeval	17
stats	17
R6	14
lubridate	14
rappdirs	13
RCurl	12
assertthat	12
digest	12
readr	11
rgdal	10
whisker	10
scales	9
ape	8
raster	8
tidyr	8
Rcpp	7
reshape2	7
rvest	7
V8	6
rgeos	6
hoardr	5
rjson	5
taxize	5
tools	5
R(>=3.2.1)	4
git2r	4
maps	4
oai	4
openssl	4
solrium	4
urltools	4
RColorBrewer	3
foreach	3
knitr	3
leaflet	3
maptools	3
memoise	3
mime	3
pdftools	3
purrr	3
rgbif	3
rmarkdown	3
shiny	3
spocc	3
stringi	3
uuid	3
wicket	3
yaml	3
Biostrings	2
MASS	2
R.cache	2
R.utils	2
base64enc	2
bibtex	2
crayon	2
devtools	2
downloader	2
fauxpas	2
gdata	2
gistr	2
graphics	2
grid	2
htmltools	2
htmlwidgets	2
httpcode	2
igraph	2
jqr	2
miniUI	2
ncdf4	2
png	2
rcrossref	2
rentrez	2
reshape	2
rmapshaper	2
rplos	2
rvertnet	2
shinyjs	2
storr	2
tm	2
NA	2
Biobase	1
BiocGenerics	1
DBI	1
DT(>=0.1)	1
EML	1
GenomeInfoDb	1
GenomicFeatures	1
GenomicRanges(>=1.23.24)	1
Hmisc	1
IRanges	1
Matrix	1
RApiSerialize	1
RJSONIO	1
RMySQL	1
RPostgreSQL	1
RSQLite	1
Rmpfr	1
S4Vectors	1
SSOAP	1
SnowballC	1
USAboundariesData: Datasets for the ‘USAboundaries’ package	1
VariantAnnotation	1
WikidataR	1
aRxiv	1
analogue	1
antiword: Extract Text from Microsoft Word Documents	1
apipkgen: Package Generator for HTTP API Wrapper Packages	1
appl: Approximate POMDP Planning Software	1
binman	1
biomaRt	1
bold	1
caTools	1
ckanr	1
cld2: Google’s Compact Language Detector 2	1
countrycode	1
cranlogs	1
crminer	1
crosstalk	1
dirdf: Extracts Metadata from Directory and File Names	1
doParallel	1
elastic	1
fastmatch	1
foreign	1
functionMap	1
genderdata: Historical Datasets for Predicting Gender from Names	1
geoaxe	1
geojson	1
geojsonrewind: Fix ‘GeoJSON’ Winding Direction	1
geonames	1
geoops: ‘GeoJSON’ Manipulation Operations	1
geosphere	1
getPass	1
ggm	1
ggmap	1
ggthemes	1
grDevices	1
graphql	1
gridExtra	1
gtools	1
hash	1
hexbin	1
historydata: Data Sets for Historians	1
httpuv	1
isdparser	1
jsonvalidate	1
jsonvalidate: Validate ‘JSON’	1
leafletR	1
loggr	1
mapproj	1
markdown	1
memisc	1
miniUI(>=0.1.1)	1
nabor	1
natserv	1
openxlsx	1
osmar	1
outliers	1
pdftools: Text Extraction and Rendering of PDF Documents	1
phytools	1
plotly	1
plumber	1
progress	1
protolite	1
qlcMatrix	1
rJava	1
rapport	1
rbhl	1
rbison	1
rebird	1
redland	1
redux	1
remotes	1
ridigbio	1
ritis	1
rlist	1
rncl	1
rnoaa	1
rnrfa	1
rotl	1
rowr	1
rredis	1
rredlist	1
rstudioapi(>=0.5)	1
rtracklayer	1
rworldmap	1
rzmq: R Bindings for ZeroMQ	1
scrapeR	1
selectr	1
sf	1
shiny(>=0.13.2)	1
snow	1
spatstat	1
stringdist	1
sys	1
tabulizerjars	1
testthat	1
tif: Text Interchange Format	1
viridisLite	1
wdman(>=0.2.2)	1
wellknown	1
wicket: Utilities to Handle WKT Spatial Data	1
wikitaxa	1
withr	1
worrms	1
xslt: XSLT 1.0 Transformations	1
zoo	1

Alternate approach using a frame instead of purrr functions for subsetting the data. Note that this gets all Depends and suggests (really all SoftwareApplication types mentioned)

dep_frame <- '{
  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
  "@explicit": "true",
  "name": {}
}'
jsonld_frame("ropensci.json", dep_frame) %>% 
  fromJSON() %>% 
  getElement("@graph") %>%
  filter(type == "SoftwareApplication") %>%
  group_by(name) %>% 
  tally(sort = TRUE)

name	n
testthat	168
knitr	122
jsonlite	105
httr	96
roxygen2	92
R	72
rmarkdown	68
covr	52
dplyr	49
tibble	48
xml2	41
methods	38
utils	37
data.table	36
ggplot2	36
crul	33
plyr	32
magrittr	28
sp	26
XML	25
curl	21
stringr	21
lazyeval	18
stats	18
lubridate	16
R6	14
readr	14
rgdal	14
rappdirs	13
RCurl	12
assertthat	12
devtools	12
digest	12
raster	12
scales	12
Rcpp	11
whisker	11
leaflet	10
rgeos	10
taxize	10
tidyr	10
reshape2	9
V8	8
ape	8
maps	8
maptools	7
purrr	7
rvest	7
pdftools	6
rgbif	6
shiny	6
ggmap	5
git2r	5
hoardr	5
ncdf4	5
png	5
rjson	5
tools	5
R(>=3.2.1)	4
RSQLite	4
oai	4
openssl	4
rcrossref	4
sf	4
solrium	4
urltools	4
uuid	4
yaml	4
DBI	3
MASS	3
R.utils	3
RColorBrewer	3
fauxpas	3
foreach	3
gdata	3
gistr	3
graphics	3
lintr	3
memoise	3
mime	3
miniUI	3
rentrez	3
rmapshaper	3
rvertnet	3
rworldmap	3
spocc	3
stringi	3
wicket	3
Biostrings	2
GGally	2
Matrix	2
R.cache	2
RcppRedis	2
base64enc	2
bibtex	2
broom	2
crayon	2
downloader	2
elastic	2
geiger	2
getPass	2
ggthemes	2
grDevices	2
grid	2
gridExtra	2
htmltools	2
htmlwidgets	2
httpcode	2
igraph	2
jqr	2
jsonvalidate	2
listviewer	2
mapproj	2
phylobase	2
phytools	2
readxl	2
remotes	2
reshape	2
rplos	2
shinyjs	2
storr	2
sys	2
tm	2
viridis	2
webp	2
zoo	2
Biobase	1
BiocGenerics	1
Cairo	1
DT(>=0.1)	1
EML	1
GSODR	1
GenomeInfoDb	1
GenomicFeatures	1
GenomicRanges(>=1.23.24)	1
Hmisc	1
IRanges	1
IRdisplay	1
MCMCglmm	1
RApiSerialize	1
RJSONIO	1
RMySQL	1
RNeXML	1
RPostgreSQL	1
RSclient	1
RSelenium	1
RUnit	1
Rcompression	1
RedisAPI	1
Rmpfr	1
Rserve	1
S4Vectors	1
SSOAP	1
SnowballC	1
Suggests:testthat	1
Sxslt	1
USAboundaries	1
USAboundariesData	1
VariantAnnotation	1
WikidataR	1
XMLSchema	1
aRxiv	1
akima	1
analogue	1
binman	1
biomaRt	1
bold	1
caTools	1
ckanr	1
corrplot	1
countrycode	1
cranlogs	1
crminer	1
crosstalk	1
dendextend	1
doParallel	1
dplyr(>=0.3.0.2)	1
etseed	1
fastmatch	1
fields	1
forecast	1
foreign	1
fulltext	1
functionMap	1
genderdata	1
geoaxe	1
geojson	1
geojsonio	1
geojsonlint	1
geonames	1
geosphere	1
ggalt	1
ggm	1
graphql	1
gtools	1
hash	1
hexbin	1
historydata	1
httpuv	1
isdparser	1
janeaustenr	1
jpeg	1
knitcitations	1
leafletR	1
loggr	1
magick	1
mapdata	1
markdown	1
memisc	1
miniUI(>=0.1.1)	1
mongolite	1
nabor	1
natserv	1
openair	1
openxlsx	1
osmar	1
outliers	1
pander	1
parallel	1
plot3D	1
plotKML	1
plotly	1
plumber	1
progress	1
protolite	1
purrrlyr	1
qlcMatrix	1
rJava	1
rapport	1
rbhl	1
rbison	1
rcdk	1
readtext	1
rebird	1
redland	1
redux	1
reeack	1
rfigshare	1
ridigbio	1
rinat	1
ritis	1
rlist	1
rnaturalearthdata	1
rnaturalearthhires	1
rncl	1
rnoaa	1
rnrfa	1
ropenaq	1
rotl	1
rowr	1
rrdf	1
rredis	1
rredlist	1
rrlite	1
rstudioapi(>=0.5)	1
rsvg	1
rtracklayer	1
sangerseqR	1
scrapeR	1
selectr	1
seqinr	1
shiny(>=0.13.2)	1
snow	1
sofa	1
spacetime	1
spatstat	1
stringdist	1
tabulizerjars	1
testthat(>=0.7)	1
tidytext	1
tidyverse	1
tiff	1
tmap	1
vegan	1
viridisLite	1
wdman(>=0.2.2)	1
weathermetrics	1
webmockr	1
webshot	1
wellknown	1
wikitaxa	1
withr	1
wordcloud2	1
worrms	1
xtable	1
xts	1

#  summarise(count(name))

Illustrate the kind of information we can discover by parsing collections of codemeta documents programmatically

Carl Boettiger

2024-11-27

Parsing the ropensci corpus

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