├── _pkgdown.yml ├── LICENSE ├── R ├── sysdata.rda ├── emld-package.R ├── emld-methods.R ├── emld.R ├── as_json.R ├── template.R └── validate_units.R ├── docs ├── favicon.ico ├── pkgdown.yml ├── link.svg └── docsearch.js ├── notebook ├── ex1.png ├── ex2.png ├── jq_maps.Rmd ├── big_solr_query.R ├── get_all_eml.R ├── XSD-to-RDFS.R ├── jq_maps.md └── solr_functions.R ├── Dockerfile ├── inst ├── examples │ ├── hf205-methods.docx │ ├── hf205-abstract.docx │ └── hf205-abstract.md ├── WORDLIST ├── context │ ├── eml-2.1.1 │ │ └── eml-context.json │ └── eml-2.2.0 │ │ └── eml-context.json ├── frame │ ├── eml-2.1.1 │ │ └── eml-frame.json │ └── eml-2.2.0 │ │ └── eml-frame.json ├── jq │ ├── eml_to_schema.jq │ └── schema_to_eml.jq ├── tests │ ├── eml-2.1.1 │ │ ├── eml-offline.xml │ │ ├── eml-units.xml │ │ ├── eml-party.xml │ │ ├── eml-access.xml │ │ ├── eml-method.xml │ │ ├── eml-project.xml │ │ ├── eml-physical-inline.xml │ │ ├── stmml_dictionaryWithDefintion.xml │ │ ├── eml-literatureInPress.xml │ │ ├── eml-datasetWhitespacePatterns.xml │ │ ├── eml-literature.xml │ │ ├── citation-sbclter-bibliography.233.xml │ │ ├── eml-physical-inline-cdatasection.xml │ │ ├── citation-sbclter-bibliography.231.xml │ │ ├── citation-sbclter-bibliography.280.xml │ │ ├── eml-entity.xml │ │ ├── eml-physical.xml │ │ ├── eml-view.xml │ │ ├── citation-sbclter-bibliography.232.xml │ │ ├── eml-protocol.xml │ │ ├── eml-dataTable.xml │ │ ├── eml-text.xml │ │ ├── eml-spatialVector.xml │ │ ├── citation-sbclter-bibliography.279.xml │ │ ├── citation-sbclter-bibliography.51.xml │ │ ├── citation-sbclter-bibliography.201.xml │ │ ├── invalid │ │ │ └── eml-2.1.1-invalidunit.xml │ │ ├── eml-inline.xml │ │ ├── eml-storedProcedure.xml │ │ ├── eml-software.xml │ │ ├── citation-sbclter-bibliography.297.xml │ │ ├── citation-sbclter-bibliography.203.xml │ │ ├── citation-sbclter-bibliography.202.xml │ │ ├── citation-sbclter-bibliography.50.xml │ │ ├── eml-citationWithContactReference.xml │ │ ├── eml-citationWithContact.xml │ │ ├── eml.xml │ │ ├── identical-repeated-key-bibliography.289.xml │ │ ├── eml-dataset.xml │ │ ├── eml-softwareWithAcessDistribution.xml │ │ ├── eml-datasetMultipleDistribution.xml │ │ └── eml-datasetWithAccess.xml │ └── eml-2.2.0 │ │ ├── eml-offline.xml │ │ ├── eml-access.xml │ │ ├── eml-party.xml │ │ ├── eml-method.xml │ │ ├── eml-project.xml │ │ ├── eml-physical-inline.xml │ │ ├── stmml_dictionaryWithDefintion.xml │ │ ├── eml-literatureInPress.xml │ │ ├── eml-datasetWhitespacePatterns.xml │ │ ├── eml-literature.xml │ │ ├── citation-sbclter-bibliography.233.xml │ │ ├── eml-physical-inline-cdatasection.xml │ │ ├── citation-sbclter-bibliography.231.xml │ │ ├── citation-sbclter-bibliography.280.xml │ │ ├── eml-entity.xml │ │ ├── eml-physical.xml │ │ ├── eml-view.xml │ │ ├── citation-sbclter-bibliography.232.xml │ │ ├── eml-protocol.xml │ │ ├── eml-dataTable.xml │ │ ├── eml-text.xml │ │ ├── eml-2.2.0-milligramPerLiter.xml │ │ ├── eml-spatialVector.xml │ │ ├── citation-sbclter-bibliography.279.xml │ │ ├── citation-sbclter-bibliography.51.xml │ │ ├── citation-sbclter-bibliography.201.xml │ │ ├── eml-inline.xml │ │ ├── eml-storedProcedure.xml │ │ ├── eml-datasetGRing.xml │ │ ├── eml-software.xml │ │ ├── citation-sbclter-bibliography.297.xml │ │ ├── citation-sbclter-bibliography.203.xml │ │ ├── citation-sbclter-bibliography.202.xml │ │ ├── citation-sbclter-bibliography.50.xml │ │ ├── eml-citationWithContactReference.xml │ │ ├── eml-citationWithContact.xml │ │ ├── eml-semantics.xml │ │ ├── eml.xml │ │ ├── eml-datasetNoSchemaLocationInvalid.xml │ │ ├── eml-datasetGringpoint.xml │ │ ├── skiptest-sbclter-bibliography.289.xml │ │ ├── citation-sbclter-bibliography.289.xml │ │ ├── eml-datasetNoSchemaLocation.xml │ │ ├── eml-dataset.xml │ │ ├── eml-software-dependency.xml │ │ ├── eml-softwareWithAcessDistribution.xml │ │ ├── eml-datasetMultipleDistribution.xml │ │ └── eml-datasetWithAccess.xml ├── xsd │ ├── eml-2.2.0 │ │ └── xml.xsd │ └── eml-2.1.0 │ │ └── eml-documentation.xsd ├── CITATION ├── extdata │ ├── example.xml │ └── schema-org-dataset.json └── notebook │ └── emld_spec.Rmd ├── tests ├── testthat.R ├── spelling.R └── testthat │ ├── test-group_repeated_key.R │ ├── test-template.R │ ├── test-validator.R │ ├── test-base.R │ ├── test-version.R │ └── test-rdf-roundtrip.R ├── .gitignore ├── data-raw ├── stmml_classes.txt └── eml_db.R ├── CRAN-RELEASE ├── cran-comments.md ├── codecov.yml ├── test.sh ├── emld.Rproj ├── .travis.yml ├── .Rbuildignore ├── man ├── guess_root_schema.Rd ├── find_real_root_name.Rd ├── eml_ns.Rd ├── eml_version.Rd ├── template.Rd ├── as_emld.Rd ├── eml_validate.Rd ├── as_json.Rd ├── guess_schema_location.Rd ├── as_xml.Rd └── emld-package.Rd ├── appveyor.yml ├── LICENSE.md ├── NAMESPACE ├── CODE_OF_CONDUCT.md └── DESCRIPTION /_pkgdown.yml: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2018 2 | COPYRIGHT HOLDER: Carl Boettiger 3 | -------------------------------------------------------------------------------- /R/sysdata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/R/sysdata.rda -------------------------------------------------------------------------------- /docs/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/docs/favicon.ico -------------------------------------------------------------------------------- /notebook/ex1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/notebook/ex1.png -------------------------------------------------------------------------------- /notebook/ex2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/notebook/ex2.png -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | from rocker/verse 2 | 3 | RUN apt-get update \ 4 | && apt-get install -y libjq-dev 5 | -------------------------------------------------------------------------------- /inst/examples/hf205-methods.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/inst/examples/hf205-methods.docx -------------------------------------------------------------------------------- /inst/examples/hf205-abstract.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ropensci/emld/HEAD/inst/examples/hf205-abstract.docx -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- 1 | pandoc: 2.7.3 2 | pkgdown: 1.4.1 3 | pkgdown_sha: ~ 4 | articles: 5 | tutorial: tutorial.html 6 | 7 | -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- 1 | library(testthat) 2 | library(emld) 3 | 4 | options("emld_db" = "eml-2.2.0") 5 | test_check("emld") 6 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | inst/doc 6 | .DS_Store 7 | onboarding-submission.md 8 | test.R 9 | -------------------------------------------------------------------------------- /R/emld-package.R: -------------------------------------------------------------------------------- 1 | #' @keywords internal 2 | "_PACKAGE" 3 | 4 | ## usethis namespace: start 5 | ## usethis namespace: end 6 | NULL 7 | -------------------------------------------------------------------------------- /data-raw/stmml_classes.txt: -------------------------------------------------------------------------------- 1 | appinfo 2 | documentation 3 | annotation 4 | description 5 | dimension 6 | unitList 7 | unitType 8 | unit 9 | -------------------------------------------------------------------------------- /CRAN-RELEASE: -------------------------------------------------------------------------------- 1 | This package was submitted to CRAN on 2020-09-27. 2 | Once it is accepted, delete this file and tag the release (commit ab6ccf7). 3 | -------------------------------------------------------------------------------- /tests/spelling.R: -------------------------------------------------------------------------------- 1 | if(requireNamespace('spelling', quietly=TRUE)) 2 | spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE) 3 | -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- 1 | Dear CRAN, 2 | 3 | This release provides the requested fix to use `xml2` 1.5.0, and addresses several 4 | unrelated bugs, as documented in NEWS. 5 | 6 | Cheers, 7 | 8 | Carl Boettiger 9 | 10 | 11 | -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- 1 | comment: false 2 | 3 | coverage: 4 | precision: 2 5 | round: down 6 | range: "65...100" 7 | 8 | status: 9 | project: 10 | default: 11 | threshold: 2% 12 | patch: 13 | default: 14 | target: auto 15 | threshold: 2% 16 | only_pulls: true 17 | -------------------------------------------------------------------------------- /inst/WORDLIST: -------------------------------------------------------------------------------- 1 | AppVeyor 2 | EML 3 | EML's 4 | EML’s 5 | JQ 6 | LD 7 | ORCID 8 | RDF 9 | README 10 | Roundtrip 11 | SPARQL 12 | XPATH 13 | XPath 14 | XSD 15 | additionalMetadata 16 | bibentry 17 | eg 18 | eml 19 | framings 20 | github 21 | json 22 | jsonlite 23 | lifecycle 24 | packageId 25 | rOpenSci 26 | ropensci 27 | roundtrip 28 | roundtripped 29 | -------------------------------------------------------------------------------- /test.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | 4 | echo 'devtools::install(dep=TRUE) 5 | status <- devtools::check() 6 | testthat::expect_length(status[["errors"]],0) 7 | testthat::expect_length(status[["warnings"]],0) 8 | status[["notes"]]' > test.R 9 | 10 | docker build . -t emld-tests 11 | docker run -ti \ 12 | -v $(pwd):/home/rstudio/repo \ 13 | -w /home/rstudio/repo \ 14 | emld-tests \ 15 | R -f test.R 16 | -------------------------------------------------------------------------------- /inst/context/eml-2.1.1/eml-context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@vocab": "eml://ecoinformatics.org/eml-2.1.1/", 4 | "eml": "eml://ecoinformatics.org/eml-2.1.1/", 5 | "xsi": "http://www.w3.org/2001/XMLSchema-instance/", 6 | "xml": "http://www.w3.org/XML/1998/namespace", 7 | "stmml": "http://www.xml-cml.org/schema/stmml-1.1/", 8 | "id": "@id", 9 | "@base": "eml://" 10 | } 11 | } 12 | -------------------------------------------------------------------------------- /inst/context/eml-2.2.0/eml-context.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@vocab": "https://eml.ecoinformatics.org/eml-2.2.0/", 4 | "eml": "https://eml.ecoinformatics.org/eml-2.2.0/", 5 | "xsi": "http://www.w3.org/2001/XMLSchema-instance/", 6 | "xml": "http://www.w3.org/XML/1998/namespace", 7 | "stmml": "http://www.xml-cml.org/schema/stmml-1.2/", 8 | "id": "@id", 9 | "@base": "eml://" 10 | } 11 | } 12 | -------------------------------------------------------------------------------- /inst/frame/eml-2.1.1/eml-frame.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@vocab": "eml://ecoinformatics.org/eml-2.1.1/", 4 | "eml": "eml://ecoinformatics.org/eml-2.1.1/", 5 | "xsi": "http://www.w3.org/2001/XMLSchema-instance/", 6 | "xml": "http://www.w3.org/XML/1998/namespace", 7 | "stmml": "http://www.xml-cml.org/schema/stmml-1.1/", 8 | "id": "@id" 9 | }, 10 | "@type": "EML", 11 | "@embed": "@always" 12 | } 13 | -------------------------------------------------------------------------------- /inst/frame/eml-2.2.0/eml-frame.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context": { 3 | "@vocab": "https://eml.ecoinformatics.org/eml-2.2.0/", 4 | "eml": "https://eml.ecoinformatics.org/eml-2.2.0/", 5 | "xsi": "http://www.w3.org/2001/XMLSchema-instance/", 6 | "xml": "http://www.w3.org/XML/1998/namespace", 7 | "stmml": "http://www.xml-cml.org/schema/stmml-1.2/", 8 | "id": "@id" 9 | }, 10 | "@type": "EML", 11 | "@embed": "@always" 12 | } 13 | -------------------------------------------------------------------------------- /R/emld-methods.R: -------------------------------------------------------------------------------- 1 | 2 | #' @importFrom yaml as.yaml 3 | #' @importFrom jsonlite toJSON 4 | #' @export 5 | print.emld <- function(x, ...){ 6 | x[["@context"]] <- NULL # context just adds clutter to display 7 | x[["@type"]] <- NULL 8 | style <- getOption("emld_print", "yaml") 9 | #cat("EML as an emld object:\n\n\n") 10 | switch(style, 11 | "yaml" = cat(yaml::as.yaml(x)), 12 | "json" = cat(jsonlite::toJSON(x, auto_unbox = TRUE, pretty = TRUE)) 13 | ) 14 | } 15 | -------------------------------------------------------------------------------- /emld.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: No 4 | SaveWorkspace: No 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Package 19 | PackageUseDevtools: Yes 20 | PackageInstallArgs: --no-multiarch --with-keep.source 21 | PackageRoxygenize: rd,collate,namespace 22 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r 2 | language: R 3 | cache: packages 4 | latex: false 5 | 6 | matrix: 7 | include: 8 | - os: linux 9 | r: devel 10 | - os: linux 11 | r: release 12 | 13 | addons: 14 | apt: 15 | sources: 16 | - sourceline: 'ppa:opencpu/jq' 17 | packages: 18 | - librdf0-dev 19 | - libv8-dev 20 | - libjq-dev 21 | after_success: 22 | - Rscript -e 'covr::codecov()' 23 | -------------------------------------------------------------------------------- /data-raw/eml_db.R: -------------------------------------------------------------------------------- 1 | ## 2018-11-28 2 | ## 3 | ## Creates the `eml_db` reference list objects as internal data 4 | ## (in R/sysdata.rda) used by many core EML functions. 5 | ## 6 | ## The JSON files are currently created by XSD parsing scripts in 7 | ## data-raw/eml_schema_parser.R 8 | 9 | 10 | eml_db <- list("eml-2.1.1" = jsonlite::read_json("data-raw/eml-2.1.1.json"), 11 | "eml-2.2.0" = jsonlite::read_json("data-raw/eml-2.2.0.json")) 12 | usethis::use_data(eml_db, overwrite = TRUE, internal = TRUE) 13 | -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^CRAN-RELEASE$ 2 | ^cran-comments\.md$ 3 | ^codemeta\.json$ 4 | ^CODE_OF_CONDUCT\.md$ 5 | ^docs$ 6 | ^_pkgdown\.yml$ 7 | ^appveyor\.yml$ 8 | ^.*\.Rproj$ 9 | ^\.Rproj\.user$ 10 | ^data-raw$ 11 | ^notebook/ 12 | ^README\.Rmd$ 13 | ^README-.*\.png$ 14 | ^\.travis\.yml$ 15 | ^codecov\.yml$ 16 | ^test\.sh$ 17 | ^paper\.Rmd$ 18 | ^paper\.md$ 19 | ^paper\.bib$ 20 | ^onboarding-submission\.md$ 21 | LICENSE.md 22 | ^CONDUCT\.md$ 23 | ^CONTRIBUTING\.md$ 24 | ^\.github$ 25 | .*-review.md$ 26 | Dockerfile 27 | test.R 28 | -------------------------------------------------------------------------------- /man/guess_root_schema.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_validate.R 3 | \name{guess_root_schema} 4 | \alias{guess_root_schema} 5 | \title{Find the root schema module and version} 6 | \usage{ 7 | guess_root_schema(doc) 8 | } 9 | \arguments{ 10 | \item{doc}{An \code{xml_document}} 11 | } 12 | \value{ 13 | If found, a list with names 'version', 'module', and `namespace. If 14 | not found, throws an error. 15 | } 16 | \description{ 17 | Find the root schema module and version 18 | } 19 | -------------------------------------------------------------------------------- /inst/jq/eml_to_schema.jq: -------------------------------------------------------------------------------- 1 | .dataset | 2 | { 3 | id: .["@id"], 4 | type: .["@type"], 5 | temporalCoverage: .coverage.temporalCoverage.rangeOfDates | 6 | [.beginDate.calendarDate, .endDate.calendarDate] | join("/"), 7 | spatialCoverage: .coverage.geographicCoverage | { 8 | description: .geographicDescription, 9 | geo: { 10 | box: .boundingCoordinates | 11 | [.southBoundingCoordinate, 12 | .westBoundingCoordinate, 13 | .northBoundingCoordinate, 14 | .eastBoundingCoordinate] | join(" ") 15 | } 16 | } 17 | } 18 | -------------------------------------------------------------------------------- /tests/testthat/test-group_repeated_key.R: -------------------------------------------------------------------------------- 1 | testthat::context("group repeated key") 2 | 3 | test_that("we can group repeated xml keys into json", { 4 | input <- 5 | ' 6 | value1 7 | value2 8 | value3 9 | stuff 10 | ' 11 | 12 | output <- 13 | '{ 14 | "key" = ["value", "value2","value3"], 15 | "other" = "stuff" 16 | }' 17 | 18 | ## tests 19 | in_list <- xml2::as_list(xml2::read_xml(input)) 20 | json <- jsonlite::toJSON(emld:::group_repeated_key(in_list), auto_unbox = TRUE) 21 | expect_is(json, "json") 22 | 23 | }) 24 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-offline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | offline_data 8 | 9 | 10 | 11 | myFormat 12 | 13 | 14 | 15 | 16 | 17 | my medium 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /inst/xsd/eml-2.2.0/xml.xsd: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-offline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | offline_data 8 | 9 | 10 | 11 | myFormat 12 | 13 | 14 | 15 | 16 | 17 | my medium 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-units.xml: -------------------------------------------------------------------------------- 1 | 2 | 5 | 7 | 9 | 10 | -------------------------------------------------------------------------------- /man/find_real_root_name.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_validate.R 3 | \name{find_real_root_name} 4 | \alias{find_real_root_name} 5 | \title{Get the real \code{QName} for the root element, including its prefix} 6 | \usage{ 7 | find_real_root_name(doc) 8 | } 9 | \arguments{ 10 | \item{doc}{An \code{xml_document}} 11 | } 12 | \value{ 13 | A \code{list} with elements \code{prefix} and \code{name}. \code{prefix} will be \code{NULL} 14 | if the element has no namespace prefix but \code{name} will always be a 15 | \code{character}. 16 | } 17 | \description{ 18 | Note that if a default namespace is used, the prefix will be \code{d1}. 19 | } 20 | -------------------------------------------------------------------------------- /inst/jq/schema_to_eml.jq: -------------------------------------------------------------------------------- 1 | . | 2 | { 3 | "@id": .["@id"], 4 | "@type": .["@type"], 5 | coverage: { 6 | temporalCoverage: { 7 | rangeOfDates: { 8 | beginDate : .temporalCoverage | split("/") |.[0], 9 | endDate : .temporalCoverage | split("/") |.[1] 10 | } 11 | }, 12 | geographicCoverage: .spatialCoverage | { 13 | geographicDescription: .description, 14 | boundingCoordinates: { 15 | westBoundingCoordinate: .geo.box | split(" ") | .[1], 16 | eastBoundingCoordinate: .geo.box | split(" ") | .[3], 17 | northBoundingCoordinate: .geo.box | split(" ") | .[2], 18 | southBoundingCoordinate: .geo.box | split(" ") | .[0] 19 | } 20 | } 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /man/eml_ns.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_version.R 3 | \name{eml_ns} 4 | \alias{eml_ns} 5 | \title{Get the XML namespace for a version of EML} 6 | \usage{ 7 | eml_ns(version = eml_version()) 8 | } 9 | \arguments{ 10 | \item{version}{EML version, currently either eml-2.2.0 (current version) or 11 | eml-2.1.1. Defaults to current version.} 12 | } 13 | \value{ 14 | returns the full XML namespace URI for the specified version of the 15 | schema 16 | } 17 | \description{ 18 | Utility function for use when filling in \code{xmlns}, \code{schemaLocation}, or 19 | \code{vocab} in various representations of EML. This is a little more future-proof 20 | than keeping a dictionary for each version since this won't break on the next 21 | release. 22 | } 23 | -------------------------------------------------------------------------------- /tests/testthat/test-template.R: -------------------------------------------------------------------------------- 1 | testthat::context("template print method") 2 | 3 | 4 | test_that("We can show slots for the creator object", { 5 | expect_output(print(template("creator")), "individualName: \\{\\}") 6 | expect_output(print(template("creator")), "phone: ~") 7 | 8 | }) 9 | 10 | test_that("template knows about internal classes too", { 11 | skip("internal class template deprecated") 12 | ## Only true in emld_db 2.1.1 right now... Probably deprecating this 13 | expect_output(print(template("ResponsibleParty")), "individualName: \\{\\}") 14 | }) 15 | 16 | test_that("template knows about internal classes too", { 17 | options(emld_print = "json") 18 | expect_output(print(template("creator")), '"individualName": \\{\\}') 19 | options(emld_print = "yaml") 20 | 21 | }) 22 | 23 | 24 | -------------------------------------------------------------------------------- /man/eml_version.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_version.R 3 | \name{eml_version} 4 | \alias{eml_version} 5 | \title{Set or check the EML version default} 6 | \usage{ 7 | eml_version(version = getOption("emld_db", "eml-2.2.0")) 8 | } 9 | \arguments{ 10 | \item{version}{EML version, currently either eml-2.2.0 (current version), or 11 | eml-2.1.1. The 'eml-' prefix can be omitted.} 12 | } 13 | \value{ 14 | returns the EML version string. As a side-effect, sets the 15 | requested version as the default version by setting the \code{emld_db} 16 | variable in \code{\link[=options]{options()}}. 17 | } 18 | \description{ 19 | Set or check the EML version default 20 | } 21 | \examples{ 22 | eml_version() 23 | eml_version("2.1.1") 24 | eml_version("eml-2.1.1") 25 | 26 | } 27 | -------------------------------------------------------------------------------- /tests/testthat/test-validator.R: -------------------------------------------------------------------------------- 1 | 2 | 3 | testthat::test_that("we can use emld validator", { 4 | f <- system.file("extdata", "example.xml", package = "emld") 5 | testthat::expect_true(eml_validate(f)) 6 | testthat::expect_true(eml_validate(xml2::read_xml(f))) 7 | my_eml <- as_emld(f) 8 | testthat::expect_true(eml_validate(my_eml)) 9 | 10 | testthat::expect_error(eml_validate(f, schema = "notafile")) 11 | 12 | 13 | }) 14 | 15 | 16 | testthat::test_that("validation uses the right unitDictionary", { 17 | f <- system.file("tests", "eml-2.1.1", "invalid", "eml-2.1.1-invalidunit.xml", package = "emld") 18 | testthat::expect_warning(eml_validate(f), "not recognized") 19 | 20 | f <- system.file("tests", "eml-2.2.0", "eml-2.2.0-milligramPerLiter.xml", package = "emld") 21 | testthat::expect_true(eml_validate(f)) 22 | }) 23 | -------------------------------------------------------------------------------- /R/emld.R: -------------------------------------------------------------------------------- 1 | #' emld: Ecological Metadata as Linked Data 2 | #' 3 | #' The goal of emld is to provide a way to work with EML metadata 4 | #' in the JSON-LD format. At it's heart, the package is simply a 5 | #' way to translate an EML XML document into JSON-LD and be able 6 | #' to reverse this so that any semantically equivalent JSON-LD 7 | #' file can be serialized into EML-schema valid XML. 8 | #' 9 | #' The package has only three core functions: 10 | #' 11 | #' - [as_emld()] Convert EML's `xml` files (or the `json` version created 12 | #' by this package) into a native R object (an S3 class called `emld`, 13 | #' essentially just a `list`). 14 | #' - [as_xml()] Convert the native R format, `emld`, back into 15 | #' XML-schema valid EML. 16 | #' - [as_json()] Convert the native R format, `emld`, into `json`(LD). 17 | #' 18 | "_PACKAGE" 19 | -------------------------------------------------------------------------------- /man/template.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/template.R 3 | \name{template} 4 | \alias{template} 5 | \title{Create a template for an EML object} 6 | \usage{ 7 | template(object) 8 | } 9 | \arguments{ 10 | \item{object}{the name of an eml object to create} 11 | } 12 | \value{ 13 | a list with elements named according to the properties of the object. 14 | This can be coerced into EML, see vignettes. NULL-valued elements (~) 15 | can take a data entry directly, while empty list()-valued elements ({}) 16 | indicate properties that take other eml objects as values. 17 | } 18 | \description{ 19 | Create a template for an EML object 20 | } 21 | \details{ 22 | Note: while this function can be called in recursions, doing so may be a bad idea. 23 | } 24 | \examples{ 25 | template("creator") 26 | } 27 | -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- 1 | 2 | bibentry( 3 | bibtype = 'article', 4 | title = 'Ecological Metadata as Linked Data. Journal of Open Source Software', 5 | author = c( 6 | person( "Carl", 7 | "Boettiger", 8 | role = c("cre", "aut"), 9 | email = "cboettig@gmail.com", 10 | comment = c(ORCID = "http://orcid.org/0000-0002-1642-628X") 11 | )), 12 | month = 'feb', 13 | year = '2019', 14 | publisher = 'The Open Journals', 15 | journal = 'The Journal of Open Source Software', 16 | number = 34, 17 | volume = 4, 18 | pages = 1276, 19 | doi = '10.21105/joss.01276', 20 | url = 'https://doi.org/10.21105/joss.01276', 21 | textVersion = paste('Boettiger, (2019). Ecological Metadata as Linked Data.', 22 | 'Journal of Open Source Software, 4(34), 1276, https://doi.org/10.21105/joss.01276') 23 | ) 24 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-party.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | University of California 9 | 10 |
11 | 123 Campus Dr. 12 | Santa Barbara 13 | CA 14 | 93101 15 | USA 16 |
17 | 18 | 805-123-1234 19 | 20 | joe@something.org 21 | www.something.org/~joe 22 | joe 23 | 24 | -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 5 | 8 | 12 | 13 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-access.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | uid=brooke,o=NCEAS,dc=ecoinformatics,dc=org 10 | all 11 | 12 | 13 | public 14 | read 15 | 16 | 17 | uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org 18 | read 19 | write 20 | all 21 | 22 | 23 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-access.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | uid=brooke,o=NCEAS,dc=ecoinformatics,dc=org 9 | all 10 | 11 | 12 | public 13 | read 14 | 15 | 16 | uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org 17 | read 18 | write 19 | all 20 | 21 | 22 | -------------------------------------------------------------------------------- /man/as_emld.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/as_emld.R 3 | \name{as_emld} 4 | \alias{as_emld} 5 | \title{Coerce an EML file or object into an emld object.} 6 | \usage{ 7 | as_emld(x, from = c("guess", "xml", "json", "list")) 8 | } 9 | \arguments{ 10 | \item{x}{path to an EML file} 11 | 12 | \item{from}{explicit type for the input format. By default, will 13 | attempt to guess the format, but it always safer to specify the 14 | input format. This is essential for literal text strings or raw 15 | vectors where the type cannot be guessed by the R object class 16 | or file extension of the input.} 17 | } 18 | \value{ 19 | an emld object 20 | } 21 | \description{ 22 | Coerce an EML file or object into an emld object. 23 | } 24 | \examples{ 25 | hf205 <- system.file("extdata/hf205.xml", package="emld") 26 | as_emld(hf205) 27 | } 28 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-party.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | University of California 9 | 10 |
11 | 123 Campus Dr. 12 | Santa Barbara 13 | CA 14 | 93101 15 | USA 16 |
17 | 18 | 805-123-1234 19 | 20 | joe@something.org 21 | http://www.something.org/~joe 22 | https://orcid.org/0000-0002-1825-0097 23 | 24 | -------------------------------------------------------------------------------- /tests/testthat/test-base.R: -------------------------------------------------------------------------------- 1 | testthat::context("base methods") 2 | 3 | ## These tests show round trips with base jsonld and xml2 methods 4 | ## independent of the methods built into this package. The tests show 5 | ## that even these require a little care to work successfully 6 | 7 | library(jsonld) 8 | library(jsonlite) 9 | library(magrittr) 10 | library(xml2) 11 | 12 | 13 | test_that("we can roundtrip JSON-LD expansion and compaction", { 14 | 15 | 16 | ex <- system.file("extdata/hf205.json", package = "emld") 17 | 18 | x <- jsonlite::read_json(ex) 19 | json_context <- toJSON(x[["@context"]], auto_unbox = TRUE) 20 | roundtrip <- 21 | jsonld_expand(ex) %>% 22 | jsonld_compact(json_context) 23 | 24 | A <- unlist(read_json(ex)) 25 | B <- unlist(fromJSON(roundtrip,simplifyVector = FALSE)) 26 | testthat::expect_equivalent(length(A), 27 | length(B)) 28 | 29 | }) 30 | 31 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-method.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | some method 9 | stethescope 10 | 11 | 12 | some method 13 | stethescope 14 | 15 | 16 | 17 | 18 | some description 19 | 20 | 21 | 22 | we sampled some fishes 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /tests/testthat/test-version.R: -------------------------------------------------------------------------------- 1 | testthat::context("version") 2 | 3 | test_that("we can get the namespace for different EML versions", { 4 | expect_equal(eml_ns("eml-2.0.0"), "eml://eml.ecoinformatics.org/eml-2.0.0") 5 | expect_equal(eml_ns("eml-2.1.1"), "eml://eml.ecoinformatics.org/eml-2.1.1") 6 | expect_equal(eml_ns("eml-2.2.0"), "https://eml.ecoinformatics.org/eml-2.2.0") 7 | expect_equal(eml_ns("eml-2.2.1"), "https://eml.ecoinformatics.org/eml-2.2.1") 8 | }) 9 | 10 | test_that("we can set the EML version", { 11 | expect_equal(eml_version("eml-2.1.1"), "eml-2.1.1") 12 | expect_equal(eml_version("eml-2.2.0"), "eml-2.2.0") 13 | expect_equal(eml_version("2.1.1"), "eml-2.1.1") 14 | expect_equal(eml_version("2.2.0"), "eml-2.2.0") 15 | }) 16 | 17 | test_that("we throw a warning when a user specifies an invalid version", { 18 | expect_warning(eml_version("a")) 19 | expect_warning(eml_version("eml2.1.1")) 20 | }) 21 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-method.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | some method 9 | stethescope 10 | 11 | 12 | some method 13 | stethescope 14 | 15 | 16 | 17 | 18 | some description 19 | 20 | 21 | 22 | we sampled some fishes 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-project.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | fish counting project 8 | 9 | 10 | University of California 11 | 12 |
13 | 123 Campus Dr. 14 | Santa Barbara 15 | CA 16 | 93101 17 | USA 18 |
19 | 20 | 805-123-1234 21 | 22 | joe@something.org 23 | www.something.org/~joe 24 | fish counter 25 | 26 | 27 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-project.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | fish counting project 8 | 9 | 10 | University of California 11 | 12 |
13 | 123 Campus Dr. 14 | Santa Barbara 15 | CA 16 | 93101 17 | USA 18 |
19 | 20 | 805-123-1234 21 | 22 | joe@something.org 23 | www.something.org/~joe 24 | fish counter 25 | 26 | 27 | -------------------------------------------------------------------------------- /notebook/jq_maps.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: github_document 3 | --- 4 | 5 | # Mapping between Schema.Org and EML via JQ 6 | 7 | 8 | 9 | We will use J-Query as XSLT-like stylesheets. These two examples shipping in this package are currently a work in progress: 10 | 11 | ```{r} 12 | library(jqr) 13 | ``` 14 | 15 | 16 | ```{r} 17 | eml_to_schema <- readr::read_file(system.file("jq/eml_to_schema.jq", package="emld")) 18 | schema_to_eml <- readr::read_file(system.file("jq/schema_to_eml.jq", package="emld")) 19 | 20 | ``` 21 | 22 | 23 | Let's map a more complete EML document into schema.org: 24 | 25 | ```{r} 26 | eml <- readr::read_file("https://raw.githubusercontent.com/cboettig/emld/master/inst/extdata/hf205.json") 27 | jq(eml, eml_to_schema) 28 | ``` 29 | 30 | 31 | 32 | Convert a dataset marked up in terms into EML 33 | 34 | ```{r} 35 | schema <- readr::read_file("../inst/extdata/schema-org-dataset.json") 36 | 37 | jq(schema, schema_to_eml) 38 | ``` 39 | 40 | 41 | -------------------------------------------------------------------------------- /man/eml_validate.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_validate.R 3 | \name{eml_validate} 4 | \alias{eml_validate} 5 | \title{eml_validate} 6 | \usage{ 7 | eml_validate(eml, encoding = "UTF-8", schema = NULL) 8 | } 9 | \arguments{ 10 | \item{eml}{file path, xml_document,} 11 | 12 | \item{encoding}{optional encoding for files, default UTF-8.} 13 | 14 | \item{schema}{path to schema} 15 | } 16 | \value{ 17 | Whether the document is valid (logical) 18 | } 19 | \description{ 20 | eml_validate processes an EML document using the XSD schema for the 21 | appropriate version of EML and determines if the document is schema-valid 22 | as defined by the XSD specification 23 | } 24 | \examples{ 25 | \donttest{ 26 | 27 | f <- system.file("extdata", "example.xml", package = "emld") 28 | 29 | ## validate file directly from disk: 30 | eml_validate(f) 31 | 32 | ## validate an eml object: 33 | eml <- as_emld(f) 34 | eml_validate(eml) 35 | 36 | } 37 | 38 | } 39 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-physical-inline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 4096 9 | 10 | 11 | 12 | 1 13 | \n 14 | 6 15 | column 16 | 17 | , 18 | " 19 | \ 20 | 21 | 22 | 23 | 24 | 25 | x,y,z 26 | 1,2,3 27 | 4,5,6 28 | 7,8,9 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-physical-inline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 4096 9 | 10 | 11 | 12 | 1 13 | \n 14 | 6 15 | column 16 | 17 | , 18 | " 19 | \ 20 | 21 | 22 | 23 | 24 | 25 | x,y,z 26 | 1,2,3 27 | 4,5,6 28 | 7,8,9 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/stmml_dictionaryWithDefintion.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 9 | 10 | a definition of my term 11 | myterm1 12 | description of myterm 13 | related entry for my term 14 | 15 | 16 | description of my other term 17 | another description, but a defintion is not allowed 18 | 19 | any text here. 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/stmml_dictionaryWithDefintion.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 9 | 10 | a definition of my term 11 | myterm1 12 | description of myterm 13 | related entry for my term 14 | 15 | 16 | description of my other term 17 | another description, but a defintion is not allowed 18 | 19 | any text here. 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /inst/examples/hf205-abstract.md: -------------------------------------------------------------------------------- 1 | The primary goal of this project is to determine 2 | experimentally the amount of lead time required to prevent a state 3 | change. To achieve this goal, we will (1) experimentally induce state 4 | changes in a natural aquatic ecosystem - the Sarracenia microecosystem; 5 | (2) use proteomic analysis to identify potential indicators of states 6 | and state changes; and (3) test whether we can forestall state changes 7 | by experimentally intervening in the system. This work uses state-of-the 8 | art molecular tools to identify early warning indicators in the field 9 | of aerobic to anaerobic state changes driven by nutrient enrichment 10 | in an aquatic ecosystem. The study tests two general hypotheses: (1) 11 | proteomic biomarkers can function as reliable indicators of impending 12 | state changes and may give early warning before increasing variances 13 | and statistical flickering of monitored variables; and (2) well-timed 14 | intervention based on proteomic biomarkers can avert future state changes 15 | in ecological systems. -------------------------------------------------------------------------------- /inst/extdata/example.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 10 | Data from Cedar Creek LTER on productivity and species richness 11 | for use in a workshop titled "An Analysis of the Relationship between 12 | Productivity and Diversity using Experimental Results from the Long-Term 13 | Ecological Research Network" held at NCEAS in September 1996. 14 | 15 | 16 | Mr. 17 | Clarence 18 | MiddleName 19 | Lehman 20 | 21 | 22 | 23 | clarence.lehman 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /notebook/big_solr_query.R: -------------------------------------------------------------------------------- 1 | library("httr") 2 | library("jsonlite") 3 | library("jsonld") 4 | library("tidyverse") 5 | source(system.file("examples/solr_functions.R", package="emld")) 6 | 7 | ## See: https://cn.dataone.org/cn/v2/query/solr 8 | 9 | numFound <- 10 | GET(paste0("https://knb.ecoinformatics.org/knb/d1/mn/v2/query/solr", 11 | "?q=-obsoletedBy:*&fl=identifier&rows=1")) %>% 12 | content() %>% 13 | xml2::xml_find_first("//result") %>% 14 | xml2::xml_attr("numFound") %>% 15 | as.integer() 16 | message(paste(numFound, "records found")) 17 | rows <- 1000 18 | n_calls <- numFound %/% rows 19 | 20 | query <- 21 | paste0( 22 | "https://knb.ecoinformatics.org/knb/d1/mn/v2/query/solr?", 23 | "q=*:*&fl=identifier,", 24 | "northBoundCoord,eastBoundCoord,southBoundCoord,westBoundCoord,", 25 | "namedLocation,geohash_9", 26 | "scientificName,kingdom,phylum,class,order,family,genus,species,", 27 | "beginDate,endDate,originator", 28 | "&wt=json", 29 | "&-obsoletedBy:*", 30 | "&start=", rows*(0:n_calls), "&rows=", rows) 31 | 32 | df <- map_df(query, solr_df) 33 | 34 | -------------------------------------------------------------------------------- /man/as_json.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/as_json.R 3 | \name{as_json} 4 | \alias{as_json} 5 | \title{Coerce an emld object into JSON} 6 | \usage{ 7 | as_json(x, file = NULL) 8 | } 9 | \arguments{ 10 | \item{x}{an emld object} 11 | 12 | \item{file}{optional path to write out to file. 13 | Otherwise, defaults to NULL and will return a json object.} 14 | } 15 | \value{ 16 | a json object. Or if a file path is provided, the metadata 17 | is written out in JSON file and the function returns \code{NULL} invisibly. 18 | } 19 | \description{ 20 | Coerce an emld object into JSON 21 | } 22 | \details{ 23 | Note: since emld list object maintains a 1:1 correspondence with JSON, 24 | following the conventions of jsonlite, this function is basically trivial. The 25 | only purpose is to default to auto_unbox = TRUE in serializing lists to JSON. 26 | } 27 | \examples{ 28 | f <- system.file("extdata/example.xml", package = "emld") 29 | emld <- as_emld(f) 30 | json <- as_json(emld) 31 | ## can also write a json file to disk: 32 | json_file <- tempfile() 33 | as_json(emld, json_file) 34 | } 35 | -------------------------------------------------------------------------------- /appveyor.yml: -------------------------------------------------------------------------------- 1 | # DO NOT CHANGE the "init" and "install" sections below 2 | environment: 3 | global: 4 | USE_RTOOLS: true 5 | 6 | # Download script file from GitHub 7 | init: 8 | - ps: | 9 | $ErrorActionPreference = "Stop" 10 | Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" 11 | Import-Module '..\appveyor-tool.ps1' 12 | 13 | 14 | install: 15 | - ps: Bootstrap 16 | 17 | cache: 18 | - C:\RLibrary 19 | 20 | # Adapt as necessary starting from here 21 | 22 | build_script: 23 | - travis-tool.sh install_deps 24 | 25 | test_script: 26 | - travis-tool.sh run_tests 27 | 28 | on_failure: 29 | - 7z a failure.zip *.Rcheck\* 30 | - appveyor PushArtifact failure.zip 31 | 32 | artifacts: 33 | - path: '*.Rcheck\**\*.log' 34 | name: Logs 35 | 36 | - path: '*.Rcheck\**\*.out' 37 | name: Logs 38 | 39 | - path: '*.Rcheck\**\*.fail' 40 | name: Logs 41 | 42 | - path: '*.Rcheck\**\*.Rout' 43 | name: Logs 44 | 45 | - path: '\*_*.tar.gz' 46 | name: Bits 47 | 48 | - path: '\*_*.zip' 49 | name: Bits 50 | -------------------------------------------------------------------------------- /man/guess_schema_location.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/eml_version.R 3 | \name{guess_schema_location} 4 | \alias{guess_schema_location} 5 | \title{Guess an appropriate \code{schemaLocation} value for a given version of the schema} 6 | \usage{ 7 | guess_schema_location(version = eml_version()) 8 | } 9 | \arguments{ 10 | \item{version}{Optional. Override the version of the schema. Defaults to the 11 | current version returned by \code{eml_version}. See \code{eml_version} for information 12 | on how to change the current version.} 13 | } 14 | \value{ 15 | Returns a string suitable as a value for \code{schemaLocation} or \code{NULL} 16 | if a value wasn't found. 17 | } 18 | \description{ 19 | This is a simple helper to make filling in the \code{schemaLocation} attribute 20 | on documents this package creates. Supports EML 2.1.1 and newer. 21 | } 22 | \examples{ 23 | \dontrun{ 24 | # Get an appropriate schemaLocation value for the current version fo EML 25 | guess_schema_location() 26 | 27 | # Get an appropriate value for EML 2.1.1 28 | guess_schema_location("eml-2.1.1") 29 | } 30 | } 31 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | # MIT License 2 | 3 | Copyright (c) 2018 Carl Boettiger 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-literatureInPress.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Measuring the effectiveness of EML in the field. 8 | 9 | 10 | Matthew 11 | B. 12 | Jones 13 | 14 | 15 | 2002 16 | this is the abstract without TextType elements. 17 | This is the abstract's first paragraph. 18 | This is the abstract's second paragraph. With 19 | emphasis. 20 | 21 |
22 | Journal of Irreproducible Results 23 | 24 |
25 | 26 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-datasetWhitespacePatterns.xml: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | A title: 7 | with 8 | carriage returns 9 | and newlines 10 | 11 | 12 | this surname-is-hyphenated 13 | 14 | 15 | keyword with leading whitespaces 16 | 17 | 18 | organization has leading whitespace and and trailing newline 19 | 20 | 21 | 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-literatureInPress.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Measuring the effectiveness of EML in the field. 8 | 9 | 10 | Matthew 11 | B. 12 | Jones 13 | 14 | 15 | 2002 16 | this is the abstract without TextType elements. 17 | This is the abstract's first paragraph. 18 | This is the abstract's second paragraph. With 19 | emphasis. 20 | 21 |
22 | Journal of Irreproducible Results 23 | 24 |
25 | 26 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-literature.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Measuring the effectiveness of EML in the field. 8 | 9 | 10 | Matthew 11 | B. 12 | Jones 13 | 14 | 15 | 2002 16 | this is the abstract without TextType elements. 17 | This is the abstract's first paragraph. 18 | This is the abstract's second paragraph. With 19 | emphasis. 20 | 21 |
22 | Journal of Irreproducible Results 23 | 23 24 | 5 25 | 44-63 26 |
27 | 28 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetWhitespacePatterns.xml: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | A title: 7 | with 8 | carriage returns 9 | and newlines 10 | 11 | 12 | this surname-is-hyphenated 13 | 14 | 15 | keyword with leading whitespaces 16 | 17 | 18 | organization has leading whitespace and and trailing newline 19 | 20 | 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-literature.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Measuring the effectiveness of EML in the field. 8 | 9 | 10 | Matthew 11 | B. 12 | Jones 13 | 14 | 15 | 2002 16 | this is the abstract without TextType elements. 17 | This is the abstract's first paragraph. 18 | This is the abstract's second paragraph. With 19 | emphasis. 20 | 21 |
22 | Journal of Irreproducible Results 23 | 23 24 | 5 25 | 44-63 26 |
27 | 28 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.233.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 233 10 | Charting the course of human waste migration from watersheds through coastal waters 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 2004 19 | 20 | 2004 ASLO Ocean Sciences 21 | 22 | Honolulu 23 | HI 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.233.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 233 10 | Charting the course of human waste migration from watersheds through coastal waters 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 2004 19 | 20 | 2004 ASLO Ocean Sciences 21 | 22 | Honolulu 23 | HI 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-physical-inline-cdatasection.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 4096 9 | 10 | 11 | 12 | 1 13 | \n 14 | 6 15 | column 16 | 17 | , 18 | " 19 | \ 20 | 21 | 22 | 23 | 24 | 25 | 26 | 41 | 42 | 43 | 44 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-physical-inline-cdatasection.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 4096 9 | 10 | 11 | 12 | 1 13 | \n 14 | 6 15 | column 16 | 17 | , 18 | " 19 | \ 20 | 21 | 22 | 23 | 24 | 25 | 26 | 41 | 42 | 43 | 44 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | S3method(as_emld,character) 4 | S3method(as_emld,json) 5 | S3method(as_emld,list) 6 | S3method(as_emld,raw) 7 | S3method(as_emld,xml_document) 8 | S3method(as_json,emld) 9 | S3method(as_json,list) 10 | S3method(as_jsonlist,xml_node) 11 | S3method(as_jsonlist,xml_nodeset) 12 | S3method(as_xml,emld) 13 | S3method(as_xml,list) 14 | S3method(print,emld) 15 | export(as_emld) 16 | export(as_json) 17 | export(as_xml) 18 | export(eml_validate) 19 | export(eml_version) 20 | export(template) 21 | importFrom(jsonld,jsonld_compact) 22 | importFrom(jsonld,jsonld_frame) 23 | importFrom(jsonlite,toJSON) 24 | importFrom(methods,is) 25 | importFrom(stats,setNames) 26 | importFrom(xml2,read_xml) 27 | importFrom(xml2,xml_add_child) 28 | importFrom(xml2,xml_attr) 29 | importFrom(xml2,xml_attrs) 30 | importFrom(xml2,xml_contents) 31 | importFrom(xml2,xml_find_all) 32 | importFrom(xml2,xml_find_first) 33 | importFrom(xml2,xml_name) 34 | importFrom(xml2,xml_new_document) 35 | importFrom(xml2,xml_ns) 36 | importFrom(xml2,xml_remove) 37 | importFrom(xml2,xml_root) 38 | importFrom(xml2,xml_set_attr) 39 | importFrom(xml2,xml_set_namespace) 40 | importFrom(xml2,xml_text) 41 | importFrom(xml2,xml_type) 42 | importFrom(xml2,xml_validate) 43 | importFrom(yaml,as.yaml) 44 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.231.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 231 10 | Water interfaces and environmental complexity at the microscale (Plenary talk) 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 2004 19 | 20 | Water: Challenges at the Intersection of Human and Natural Systems Workshop, a PNL sponsored NSF/DOE Workshop 21 | September 16-17, 2004 22 | 23 | Richland 24 | WA 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /R/as_json.R: -------------------------------------------------------------------------------- 1 | #' Coerce an emld object into JSON 2 | #' 3 | #' @param x an emld object 4 | #' @param file optional path to write out to file. 5 | #' Otherwise, defaults to NULL and will return a json object. 6 | #' @export 7 | #' @details Note: since emld list object maintains a 1:1 correspondence with JSON, 8 | #' following the conventions of jsonlite, this function is basically trivial. The 9 | #' only purpose is to default to auto_unbox = TRUE in serializing lists to JSON. 10 | #' @examples 11 | #' f <- system.file("extdata/example.xml", package = "emld") 12 | #' emld <- as_emld(f) 13 | #' json <- as_json(emld) 14 | #' ## can also write a json file to disk: 15 | #' json_file <- tempfile() 16 | #' as_json(emld, json_file) 17 | #' @return a json object. Or if a file path is provided, the metadata 18 | #' is written out in JSON file and the function returns `NULL` invisibly. 19 | as_json <- function(x, file=NULL){ UseMethod("as_json") } 20 | 21 | #' @export 22 | as_json.emld <- function(x, file=NULL){ 23 | # x <- drop_nulls(x) # recursion sometimes infinite / beyond stack limit 24 | if(is.null(file)){ 25 | jsonlite::toJSON(x, pretty = TRUE, auto_unbox = TRUE) 26 | } else { 27 | jsonlite::write_json(x, file, pretty = TRUE, auto_unbox = TRUE) 28 | } 29 | } 30 | 31 | #' @export 32 | as_json.list <- function(x, file=NULL){ 33 | class(x) <- c("emld", "list") 34 | as_json(x) 35 | } 36 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.231.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 231 10 | Water interfaces and environmental complexity at the microscale (Plenary talk) 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 2004 19 | 20 | Water: Challenges at the Intersection of Human and Natural Systems Workshop, a PNL sponsored NSF/DOE Workshop 21 | September 16-17, 2004 22 | 23 | Richland 24 | WA 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.280.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 280 10 | Catchment and Sub-catchment Scale Linkages between Land Use and Nutrient Concentrations and Fluxes in Coastal California Streams 11 | 12 | 13 | T 14 | H 15 | Robinson 16 | 17 | 18 | 2006 19 | 20 | Ph.D. 21 | 22 | Bren School of Environmental Science and Management 23 |
24 | University of California 25 | Santa Barbara 26 |
27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.280.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 280 10 | Catchment and Sub-catchment Scale Linkages between Land Use and Nutrient Concentrations and Fluxes in Coastal California Streams 11 | 12 | 13 | T 14 | H 15 | Robinson 16 | 17 | 18 | 2006 19 | 20 | Ph.D. 21 | 22 | Bren School of Environmental Science and Management 23 |
24 | University of California 25 | Santa Barbara 26 |
27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-entity.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | 11 | 12 | rain 13 | Surface Rainfall 14 | The amount of rainfall on the sampling unit. 15 | 16 | float 17 | double 18 | 19 | 20 | millimeter 21 | 0.5 22 | 23 | real 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 32 | some other entity 33 | 34 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-physical.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 22 9 | 10 | 11 | 12 | 1 13 | \n 14 | 10 15 | column 16 | 17 | 18 | , 19 | " 20 | \ 21 | 22 | 23 | 7 24 | 25 | 26 | 4 27 | 28 | 29 | , 30 | " 31 | \ 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | http://www.somewhere.org/data.txt 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-view.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | 11 | 12 | rain 13 | Surface Rainfall 14 | The amount of rainfall on the sampling unit. 15 | 16 | float 17 | double 18 | 19 | 20 | millimeter 21 | 0.5 22 | 23 | real 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | select * from xml_documents; 35 | 36 | 37 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-entity.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | 11 | 12 | rain 13 | Surface Rainfall 14 | The amount of rainfall on the sampling unit. 15 | 16 | float 17 | double 18 | 19 | 20 | millimeter 21 | 0.5 22 | 23 | real 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 32 | some other entity 33 | 34 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-physical.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | data.txt 8 | 22 9 | 10 | 11 | 12 | 1 13 | \n 14 | 10 15 | column 16 | 17 | 18 | , 19 | " 20 | \ 21 | 22 | 23 | 7 24 | 25 | 26 | 4 27 | 28 | 29 | , 30 | " 31 | \ 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | http://www.somewhere.org/data.txt 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-view.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | 11 | 12 | rain 13 | Surface Rainfall 14 | The amount of rainfall on the sampling unit. 15 | 16 | float 17 | double 18 | 19 | 20 | millimeter 21 | 0.5 22 | 23 | real 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | select * from xml_documents; 35 | 36 | 37 | -------------------------------------------------------------------------------- /notebook/get_all_eml.R: -------------------------------------------------------------------------------- 1 | library("httr") 2 | library("jsonlite") 3 | library("jsonld") 4 | library("tidyverse") 5 | library("xml2") 6 | source(system.file("examples/solr_functions.R", package="emld")) 7 | 8 | ## See: https://cn.dataone.org/cn/v2/query/solr/ 9 | 10 | eml_solr_query <- 11 | "http://cn.dataone.org/cn/v2/query/solr/?q=formatId:eml*+AND+-obsoletedBy:*" 12 | 13 | numFound <- 14 | GET(eml_solr_query) %>% 15 | content() %>% 16 | xml2::xml_find_first("//result") %>% 17 | xml2::xml_attr("numFound") %>% 18 | as.integer() 19 | message(paste(numFound, "records found")) 20 | rows <- 1000 21 | n_calls <- numFound %/% rows 22 | 23 | 24 | 25 | query <- 26 | paste0(eml_solr_query, 27 | "&fl=identifier,formatId,dataUrl,fileName", 28 | "&wt=json", 29 | "&start=", rows*(0:n_calls), "&rows=", rows) 30 | 31 | solr_df <- function(q){ 32 | message(paste(q)) 33 | resp <- GET(q) 34 | if(!grepl("json", headers(resp)$`content-type`)) 35 | return(tibble()) 36 | json <- jsonlite::fromJSON(content(resp, as = "text")) 37 | json$response$docs 38 | } 39 | 40 | df <- map_dfr(query, solr_df) 41 | 42 | eml <- df %>% 43 | mutate(name = paste0("emls/", gsub("[\\/\\.]", "_", identifier), ".xml")) 44 | 45 | readr::write_csv(eml, "eml-solrs.csv.bz2") 46 | 47 | 48 | safe_down <- safely(function(url, dest){ 49 | if(!file.exists(dest)) 50 | download.file(url, dest) 51 | }) 52 | 53 | dir.create("emls", FALSE) 54 | map2(eml$name, eml$dataUrl, ~safe_down(.y, .x)) 55 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Code of Conduct 2 | 3 | As contributors and maintainers of this project, we pledge to respect all people who 4 | contribute through reporting issues, posting feature requests, updating documentation, 5 | submitting pull requests or patches, and other activities. 6 | 7 | We are committed to making participation in this project a harassment-free experience for 8 | everyone, regardless of level of experience, gender, gender identity and expression, 9 | sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion. 10 | 11 | Examples of unacceptable behavior by participants include the use of sexual language or 12 | imagery, derogatory comments or personal attacks, trolling, public or private harassment, 13 | insults, or other unprofessional conduct. 14 | 15 | Project maintainers have the right and responsibility to remove, edit, or reject comments, 16 | commits, code, wiki edits, issues, and other contributions that are not aligned to this 17 | Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 18 | from the project team. 19 | 20 | Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 21 | opening an issue or contacting one or more of the project maintainers. 22 | 23 | This Code of Conduct is adapted from the Contributor Covenant 24 | (http://contributor-covenant.org), version 1.0.0, available at 25 | http://contributor-covenant.org/version/1/0/0/ 26 | -------------------------------------------------------------------------------- /R/template.R: -------------------------------------------------------------------------------- 1 | 2 | ## Warning: do not attempt to request `recursive` on high-level objects 3 | 4 | 5 | #' Create a template for an EML object 6 | #' 7 | #' @param object the name of an eml object to create 8 | #' 9 | #' @return a list with elements named according to the properties of the object. 10 | #' This can be coerced into EML, see vignettes. NULL-valued elements (~) 11 | #' can take a data entry directly, while empty list()-valued elements ({}) 12 | #' indicate properties that take other eml objects as values. 13 | #' @details Note: while this function can be called in recursions, doing so may be a bad idea. 14 | #' @export 15 | #' 16 | #' @examples 17 | #' template("creator") 18 | template <- function(object){ 19 | properties <- gsub("^(@|#)", "", eml_db[[eml_version()]][[object]]) 20 | 21 | output <- vector("list", length(properties)) 22 | names(output) <- properties 23 | 24 | 25 | ## Recursive call is trouble, just single depth 26 | names(properties) <- properties 27 | children <- 28 | vapply(properties, 29 | function(x){ 30 | properties <- eml_db[[eml_version()]][[x]] 31 | drop <- grep("^(@|#)\\w+", properties) 32 | if(length(drop) > 0 ) properties <- properties[-drop] 33 | length(properties) 34 | }, 35 | integer(1)) 36 | 37 | 38 | for(n in names(which(children > 0))) 39 | output[[n]] <- setNames(list(), character(0)) 40 | class(output) <- c("emld", "list") 41 | output 42 | } 43 | 44 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.232.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 232 10 | Molecular community analysis in environmental monitoring 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 19 | 20 | M 21 | G 22 | LaMontagne 23 | 24 | 25 | 2004 26 | 27 | Association of Environmental Health Sciences (AEHS) 28 | March 16, 2004 29 | 30 | San Diego 31 | CA 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-protocol.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | fish counting 9 | 10 | 11 | 12 | University of California 13 | 14 |
15 | 123 Campus Dr. 16 | Santa Barbara 17 | CA 18 | 93101 19 | USA 20 |
21 | 22 | 805-123-1234 23 | 24 | joe@something.org 25 | www.something.org/~joe 26 | 27 | 1999 28 | English 29 | 30 | fish 31 | lake 32 | jim's thesaurus 33 | 34 | 35 | This is some other fake info. 36 | 37 | 38 | 39 | 40 | 41 | catch a fish, make a hash mark, weigh it, 42 | enter the data in the spreadsheet 43 | 44 | 45 | scale 46 | 47 | 48 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.232.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 232 10 | Molecular community analysis in environmental monitoring 11 | 12 | 13 | P 14 | A 15 | Holden 16 | 17 | 18 | 19 | 20 | M 21 | G 22 | LaMontagne 23 | 24 | 25 | 2004 26 | 27 | Association of Environmental Health Sciences (AEHS) 28 | March 16, 2004 29 | 30 | San Diego 31 | CA 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-protocol.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | fish counting 9 | 10 | 11 | 12 | University of California 13 | 14 |
15 | 123 Campus Dr. 16 | Santa Barbara 17 | CA 18 | 93101 19 | USA 20 |
21 | 22 | 805-123-1234 23 | 24 | joe@something.org 25 | www.something.org/~joe 26 | 27 | 1999 28 | English 29 | 30 | fish 31 | lake 32 | jim's thesaurus 33 | 34 | 35 | This is some other fake info. 36 | 37 | 38 | 39 | 40 | 41 | catch a fish, make a hash mark, weigh it, 42 | enter the data in the spreadsheet 43 | 44 | 45 | scale 46 | 47 | 48 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-dataTable.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | TEMPID234 9 | Test Data 10 | This is a test entity that is fake. 11 | This is test data 12 | 13 | 14 | rain 15 | Surface Rainfall 16 | The amount of rainfall on the sampling unit. 17 | 18 | float 19 | double 20 | 21 | 22 | millimeter 23 | 0.5 24 | 25 | real 26 | 27 | 0 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-text.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 |
7 | This is some text. 8 |
9 | Subsection title 10 | Some text in the subsection 11 |
12 |
13 |
14 | Start with some text, and then mix in some elements: 15 | 16 | Item numero uno 17 | Item numero dos 18 | Item three contains a list itself: 19 | 20 | Oranges 21 | Apples 22 | 23 | 24 | 25 | And then some text with emphasis 26 | following the list of items. 27 | 28 |
29 |
30 | Test of sub and super scripts 31 | Subscript: H2O 32 | Superscript: y=x3 33 | Nested superscript: 34 | y=x34 35 | Nested subscript: 36 | x34 37 |
38 | 39 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-dataTable.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | TEMPID234 9 | Test Data 10 | This is a test entity that is fake. 11 | This is test data 12 | 13 | 14 | rain 15 | Surface Rainfall 16 | The amount of rainfall on the sampling unit. 17 | 18 | float 19 | double 20 | 21 | 22 | millimeter 23 | 0.5 24 | 25 | real 26 | 27 | 0 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-text.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 |
7 | This is some text. 8 |
9 | Subsection title 10 | Some text in the subsection 11 |
12 |
13 |
14 | Start with some text, and then mix in some elements: 15 | 16 | Item numero uno 17 | Item numero dos 18 | Item three contains a list itself: 19 | 20 | Oranges 21 | Apples 22 | 23 | 24 | 25 | And then some text with emphasis 26 | following the list of items. 27 | 28 |
29 |
30 | Test of sub and super scripts 31 | Subscript: H2O 32 | Superscript: y=x3 33 | Nested superscript: 34 | y=x34 35 | Nested subscript: 36 | x34 37 |
38 | 39 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-spatialVector.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | Test Data 10 | This is a test entity that is fake. 11 | 12 | 13 | rain 14 | Surface Rainfall 15 | The amount of rainfall on the sampling unit. 16 | 17 | float 18 | double 19 | 20 | 21 | millimeter 22 | 0.5 23 | 24 | real 25 | 26 | 0 27 | 28 | 29 | 30 | 31 | 32 | 33 | Point 34 | 1 35 | 36 | GCS_Accra 37 | 38 | 39 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.279.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 279 10 | Species Invasions: Insights into Ecology, Evolution, and Biogeography 11 | 12 | 13 | Dov 14 | F 15 | Sax 16 | 17 | 18 | 19 | 20 | John 21 | J 22 | Stachowicz 23 | 24 | 25 | 26 | 27 | Steven 28 | D 29 | Gaines 30 | 31 | 32 | 2005 33 | 34 | 35 | Sinauer Associates 36 | 37 | 480 38 | 39 | 40 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-2.2.0-milligramPerLiter.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | EML 2.2.0 milligramPerLiter test 5 | 6 | 7 | Example 8 | User 9 | 10 | 11 | 12 | example.user 13 | 14 | 15 | entity 16 | entity description 17 | 18 | 19 | attribute1 20 | attribute1definition 21 | float 22 | 23 | 24 | 25 | milligramPerLiter 26 | 27 | 0.1 28 | 29 | real 30 | 31 | 0 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-spatialVector.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | Test Data 10 | This is a test entity that is fake. 11 | 12 | 13 | rain 14 | Surface Rainfall 15 | The amount of rainfall on the sampling unit. 16 | 17 | float 18 | double 19 | 20 | 21 | millimeter 22 | 0.5 23 | 24 | real 25 | 26 | 0 27 | 28 | 29 | 30 | 31 | 32 | 33 | Point 34 | 1 35 | 36 | GCS_Accra 37 | 38 | 39 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.279.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 279 10 | Species Invasions: Insights into Ecology, Evolution, and Biogeography 11 | 12 | 13 | Dov 14 | F 15 | Sax 16 | 17 | 18 | 19 | 20 | John 21 | J 22 | Stachowicz 23 | 24 | 25 | 26 | 27 | Steven 28 | D 29 | Gaines 30 | 31 | 32 | 2005 33 | 34 | 35 | Sinauer Associates 36 | 37 | 480 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.51.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 51 10 | Hopping with Life: The Ecology of Kelp on the Beach 11 | 12 | 13 | Jenifer 14 | Dugan 15 | 16 | 17 | 2002 18 | 19 | This 4 minute video describes the ecology of kelp wrack on the sandy beaches of Southern California, USA. The kelp wrack provides an important food source and habitat for kelp flies, maggots and small crustaceans on which several species of shore birds, starlings, common crows, black phoebes and warblers feed. 20 | 21 | 22 | 23 | http://www.ocean.com 24 | 25 | 26 | 27 | 28 | The Ocean Channel (for Ty Warner Sea Center) 29 | 30 | Carpinteria, CA 31 | 32 | 33 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.201.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 201 10 | A conceptual model for river water and sediment dispersal in the Santa Barbara Channel, California 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | D 29 | A 30 | Siegel 31 | 32 | 33 | 2004 34 |
35 | Continental-Shelf Research 36 | 24 37 | 2029-2043 38 |
39 | 40 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.51.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 51 10 | Hopping with Life: The Ecology of Kelp on the Beach 11 | 12 | 13 | Jenifer 14 | Dugan 15 | 16 | 17 | 2002 18 | 19 | This 4 minute video describes the ecology of kelp wrack on the sandy beaches of Southern California, USA. The kelp wrack provides an important food source and habitat for kelp flies, maggots and small crustaceans on which several species of shore birds, starlings, common crows, black phoebes and warblers feed. 20 | 21 | 22 | 23 | http://www.ocean.com 24 | 25 | 26 | 27 | 28 | The Ocean Channel (for Ty Warner Sea Center) 29 | 30 | Carpinteria, CA 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.201.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 201 10 | A conceptual model for river water and sediment dispersal in the Santa Barbara Channel, California 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | D 29 | A 30 | Siegel 31 | 32 | 33 | 2004 34 |
35 | Continental-Shelf Research 36 | 24 37 | 2029-2043 38 |
39 | 40 | 41 | -------------------------------------------------------------------------------- /notebook/XSD-to-RDFS.R: -------------------------------------------------------------------------------- 1 | ## EXPERIMENTAL ONLY 2 | 3 | library(xml2) 4 | library(purrr) 5 | 6 | ## List all Classes 7 | 8 | ## class, description, inherits, inherits2, inherits3, 9 | 10 | ## class, property, type, description, accepted_types 11 | # 12 | ## Define properties of every class 13 | ## property definitions 14 | 15 | 16 | 17 | ### Get all xs:complexType 18 | 19 | xsd <- "inst/xsd/eml-2.2.0/eml-attribute.xsd" 20 | 21 | xml <- xml2::read_xml(xsd) 22 | 23 | ## Types. Just get the docs and stick stuff back together later?? 24 | complex <- xml_find_all(xml, "//xs:complexType[@name]") %>% xml_attr("name") 25 | simple <- xml_find_all(xml, "//xs:simpleType[@name]") %>% xml_attr("name") 26 | groups <- xml_find_all(xml, "//xs:group[@name]") %>% xml_attr("name") 27 | 28 | 29 | xml_find_all(xml, "//xs:complexType[@name]/xs:annotation") %>% xml_children() %>% xml_children() %>% xml_text(TRUE) 30 | 31 | 32 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']//xs:element[@name]") %>% xml_attr("name") 33 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']/child::*/xs:element[@name]") %>% xml_attr("name") 34 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']/child::*/child::*/xs:element[@name]") %>% xml_attr("name") 35 | 36 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']/child::*/(xs:choice | xs:sequence)") 37 | 38 | 39 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']") %>% xml_children() %>% xml_children() 40 | 41 | xml_find_all(xml, "//xs:complexType[@name='NonNumericDomainType']/child::*/child::*/child::*") 42 | 43 | 44 | named_elements <- xml_find_all(xml, "//xs:element[@name]") %>% xml_attr("name") 45 | 46 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/invalid/eml-2.1.1-invalidunit.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | EML 2.1.1 invalid units test 5 | 6 | 7 | Example 8 | User 9 | 10 | 11 | 12 | example.user 13 | 14 | 15 | entity 16 | entity description 17 | 18 | 19 | attribute1 20 | attribute1definition 21 | float 22 | 23 | 24 | 25 | milligramPerLiter 26 | 27 | 0.1 28 | 29 | real 30 | 31 | 0 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-inline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | inline_xml_data 8 | 9 | 10 | 11 | XML 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | Some Peptide 20 | 21 | Operator 22 | PSI 23 | EBI-EMBL 24 | 25 | 26 | somepeptide.raw 27 | xcalibur 1.3 28 | 29 | 30 | 31 | LCQ 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | PSI-MS 40 | 1.1 41 | PSI-MS Converter 42 | 43 | 44 | 45 | centroid 46 | 47 | 48 | 49 | 50 | 51 | 52 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-inline.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | inline_xml_data 8 | 9 | 10 | 11 | XML 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | Some Peptide 20 | 21 | Operator 22 | PSI 23 | EBI-EMBL 24 | 25 | 26 | somepeptide.raw 27 | xcalibur 1.3 28 | 29 | 30 | 31 | LCQ 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | PSI-MS 40 | 1.1 41 | PSI-MS Converter 42 | 43 | 44 | 45 | centroid 46 | 47 | 48 | 49 | 50 | 51 | 52 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-storedProcedure.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | 11 | 12 | rain 13 | Surface Rainfall 14 | The amount of rainfall on the sampling unit. 15 | 16 | float 17 | double 18 | 19 | 20 | millimeter 21 | 0.5 22 | 23 | real 24 | 25 | 0 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | x 35 | This is an integer between 0 and 10,003, which can 36 | be represented using the xs:integer type from XML Schema datatypes. 37 | 38 | true 39 | false 40 | 41 | 42 | -------------------------------------------------------------------------------- /inst/notebook/emld_spec.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "emld Spec" 3 | author: "Carl Boettiger" 4 | date: "1/13/2018" 5 | output: github_document 6 | --- 7 | 8 | This document outlines the conventions used in mapping EML XML into JSON-LD. 9 | 10 | - XML node names become JSON keys 11 | - XML node contents (either text/data or node names) become the corresponding JSON value to the key 12 | - Repeated elements become list-valued: 13 | 14 | ```xml 15 | http://example.com/1 16 | http://example.com/2 17 | http://example.com/3 18 | ``` 19 | 20 | becomes: 21 | 22 | ```json 23 | "url": ["http://example.com/1", "http://example.com/2", "http://example.com/3"] 24 | ``` 25 | 26 | - XML node attribute names are converted into JSON keys prefixed with `#`, unless the attribute name is `id`, in which case it uses the special JSON-LD prefix, `@`. For instance: 27 | 28 | 29 | ```xml 30 | The Title<title></dataset> 31 | ``` 32 | 33 | becomes 34 | 35 | ```json 36 | "dataset": { 37 | "@id": "abc123", 38 | "#system": "knb", 39 | "title": "The Title" 40 | } 41 | 42 | ``` 43 | 44 | 45 | - If a node contains text/data and an attribute, the node name is repeated to denote the value as well: 46 | 47 | ```xml 48 | <url function="download">http://example.com</url> 49 | ``` 50 | 51 | becomes: 52 | 53 | ```json 54 | "url": { 55 | "#function"="download" 56 | "url": "http://example.com" 57 | } 58 | ``` 59 | 60 | - Contents of `para` and `section` (the two choices for components of any `TextType` content) are encoded as literal character strings and not parsed. 61 | 62 | - references are expanded: 63 | 64 | - Semantic annotations (EML 2.2) are expanded into native JSON-LD 65 | 66 | 67 | 68 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-storedProcedure.xml: -------------------------------------------------------------------------------- 1 | <?xml version="1.0"?> 2 | <sp:storedProcedure 3 | xmlns:sp="https://eml.ecoinformatics.org/storedProcedure-2.2.0" 4 | xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 5 | xsi:schemaLocation="https://eml.ecoinformatics.org/storedProcedure-2.2.0 eml-storedProcedure.xsd"> 6 | 7 | <alternateIdentifier>TEMPID234</alternateIdentifier> 8 | <entityName>Test Data</entityName> 9 | <entityDescription>This is a test entity that is fake.</entityDescription> 10 | <attributeList> 11 | <attribute> 12 | <attributeName>rain</attributeName> 13 | <attributeLabel>Surface Rainfall</attributeLabel> 14 | <attributeDefinition>The amount of rainfall on the sampling unit. 15 | </attributeDefinition> 16 | <storageType>float</storageType> 17 | <storageType typeSystem="http://java.sun.com/docs/books/jls/second_edition/html">double</storageType> 18 | <measurementScale> 19 | <interval> 20 | <unit><standardUnit>millimeter</standardUnit></unit> 21 | <precision>0.5</precision> 22 | <numericDomain id="nd.1"> 23 | <numberType>real</numberType> 24 | <bounds> 25 | <minimum exclusive="false">0</minimum> 26 | </bounds> 27 | </numericDomain> 28 | </interval> 29 | </measurementScale> 30 | </attribute> 31 | </attributeList> 32 | 33 | <parameter> 34 | <name>x</name> 35 | <domainDescription>This is an integer between 0 and 10,003, which can 36 | be represented using the xs:integer type from XML Schema datatypes. 37 | </domainDescription> 38 | <required>true</required> 39 | <repeats>false</repeats> 40 | </parameter> 41 | </sp:storedProcedure> 42 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetGRing.xml: -------------------------------------------------------------------------------- 1 | <?xml version="1.0" encoding="UTF-8"?> 2 | <eml:eml xmlns:eml="https://eml.ecoinformatics.org/eml-2.2.0" xmlns:acc="https://eml.ecoinformatics.org/access-2.2.0" xmlns:ds="https://eml.ecoinformatics.org/dataset-2.2.0" xmlns:doc="https://eml.ecoinformatics.org/documentation-2.2.0" xmlns:cit="eml://ecoinformatics.org/literature-2.2.0" xmlns:prot="https://eml.ecoinformatics.org/protocol-2.2.0" xmlns:res="https://eml.ecoinformatics.org/resource-2.2.0" xmlns:sw="https://eml.ecoinformatics.org/software-2.2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://eml.ecoinformatics.org/eml-2.2.0 3 | eml.xsd" packageId="" system=""> 4 | <dataset> 5 | <title>A title dataset with bad gringpoints. 6 | 7 | 8 | 9 | surname-is-hyphenated 10 | 11 | 12 | 13 | 14 | this coverage tree has invalid gring points 15 | 16 | 23 17 | 23 18 | 23 19 | 23 20 | 21 | 22 | 23 | 12,34 13,34 34,34 24 | 25 | 26 | 27 | 28 | 29 | my org 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-software.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | fish counting 9 | 10 | 11 | 12 | University of California 13 | 14 |
15 | 123 Campus Dr. 16 | Santa Barbara 17 | CA 18 | 93101 19 | USA 20 |
21 | 22 | 805-123-1234 23 | 24 | joe@something.org 25 | www.something.org/~joe 26 | 27 | 1999 28 | English 29 | 30 | fish 31 | lake 32 | jim's thesaurus 33 | 34 | 35 | This is some other fake info. 36 | 37 | 38 | 39 | 40 | 41 | http://www.something.org 42 | 43 | 44 | 45 | 123 MB 46 | 47 | Linux 48 | JVM 49 | 123 MB 50 | Java 51 | 52 | 53 | GPL 54 | 55 | 56 | 1.0 57 | 58 | 59 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-software.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | fish counting 9 | 10 | 11 | 12 | University of California 13 | 14 |
15 | 123 Campus Dr. 16 | Santa Barbara 17 | CA 18 | 93101 19 | USA 20 |
21 | 22 | 805-123-1234 23 | 24 | joe@something.org 25 | www.something.org/~joe 26 | 27 | 1999 28 | English 29 | 30 | fish 31 | lake 32 | jim's thesaurus 33 | 34 | 35 | This is some other fake info. 36 | 37 | 38 | 39 | 40 | 41 | http://www.something.org 42 | 43 | 44 | 45 | 123 MB 46 | 47 | Linux 48 | JVM 49 | 123 MB 50 | Java 51 | 52 | 53 | GPL 54 | 55 | 56 | 1.0 57 | 58 | 59 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.297.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 297 10 | An experimental investigation of the use of artificial reefs to mitigate the loss of giant kelp forest habitat. A case study of the San Onofre Nuclear Generating Station's artificial reef project 11 | 12 | 13 | D 14 | C 15 | Reed 16 | 17 | 18 | 19 | 20 | Steve 21 | C 22 | Schroeter 23 | 24 | 25 | 26 | 27 | D 28 | Huang 29 | 30 | 31 | 2006 32 | 33 | T-058 34 | 35 | California Sea Grant College Program, University of California, San Diego, CA 36 | 37 | 143 38 | 39 | 40 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.297.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 297 10 | An experimental investigation of the use of artificial reefs to mitigate the loss of giant kelp forest habitat. A case study of the San Onofre Nuclear Generating Station's artificial reef project 11 | 12 | 13 | D 14 | C 15 | Reed 16 | 17 | 18 | 19 | 20 | Steve 21 | C 22 | Schroeter 23 | 24 | 25 | 26 | 27 | D 28 | Huang 29 | 30 | 31 | 2006 32 | 33 | T-058 34 | 35 | California Sea Grant College Program, University of California, San Diego, CA 36 | 37 | 143 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.203.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 203 10 | Dispersal forcing of southern California river plumes based on field and remote sensing observations 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | L 29 | Washburn 30 | 31 | 32 | 33 | 34 | D 35 | A 36 | Siegel 37 | 38 | 39 | 2004 40 |
41 | Geo-Marine Letters 42 | 24 43 | 46-52 44 |
45 | 46 | -------------------------------------------------------------------------------- /tests/testthat/test-rdf-roundtrip.R: -------------------------------------------------------------------------------- 1 | testthat::context("test rdf roundtrips") 2 | 3 | library(rdflib) 4 | library(jsonlite) 5 | library(jsonld) 6 | library(magrittr) 7 | library(testthat) 8 | 9 | f <- system.file(file.path("tests", 10 | eml_version(), 11 | "eml.xml"), package="emld") 12 | 13 | test_that("We can roundtrip into rdf and validate", { 14 | 15 | eml.json <- tempfile("eml", fileext = ".json") 16 | eml.xml <- tempfile("eml", fileext = ".xml") 17 | 18 | f %>% 19 | as_emld() %>% 20 | as_json() %>% 21 | rdf_parse("jsonld") %>% 22 | rdf_serialize(eml.json, "jsonld") 23 | 24 | ## frame & compact explicitly, even though as_emld should now do this on json input 25 | frame <- system.file(paste0("frame/", 26 | eml_version(), 27 | "/eml-frame.json"), package = "emld") 28 | context <- system.file(paste0("context/", 29 | eml_version(), 30 | "/eml-context.json"), package = "emld") 31 | jsonld_frame(eml.json, frame) %>% 32 | jsonld_compact(context) %>% 33 | as_emld() %>% 34 | as_xml(eml.xml) 35 | expect_true(eml_validate(eml.xml)) 36 | }) 37 | 38 | test_that("We can roundtrip out to rdf-xml", { 39 | eml.rdf <- tempfile("eml", fileext = ".rdf") 40 | eml.json <- tempfile("eml", fileext = ".json") 41 | eml.xml <- tempfile("eml", fileext = ".xml") 42 | 43 | ## Into RDF-XML 44 | f %>% 45 | as_emld() %>% 46 | as_json() %>% 47 | rdf_parse("jsonld") %>% 48 | rdf_serialize(eml.rdf, "rdfxml") 49 | 50 | ## Back into jsonld (via rdflib) 51 | rdf_parse(eml.rdf, "rdfxml") %>% 52 | rdf_serialize(eml.json, "jsonld") 53 | 54 | 55 | ## Prove that as_emld frames and compacts automatically: 56 | as_emld(eml.json) %>% 57 | as_xml(eml.xml) 58 | expect_true(eml_validate(eml.xml)) 59 | 60 | }) 61 | 62 | 63 | -------------------------------------------------------------------------------- /inst/extdata/schema-org-dataset.json: -------------------------------------------------------------------------------- 1 | { 2 | "@context":"http://schema.org/", 3 | "@type":"Dataset", 4 | "name":"NCDC Storm Events Database", 5 | "description":"Storm Data is provided by the National Weather Service (NWS) and contain statistics on...", 6 | "url":"https://catalog.data.gov/dataset/ncdc-storm-events-database", 7 | "sameAs":"https://gis.ncdc.noaa.gov/geoportal/catalog/search/resource/details.page?id=gov.noaa.ncdc:C00510", 8 | "keywords":[ 9 | "ATMOSPHERE > ATMOSPHERIC PHENOMENA > CYCLONES", 10 | "ATMOSPHERE > ATMOSPHERIC PHENOMENA > DROUGHT", 11 | "ATMOSPHERE > ATMOSPHERIC PHENOMENA > FOG", 12 | "ATMOSPHERE > ATMOSPHERIC PHENOMENA > FREEZE" 13 | ], 14 | "creator":{ 15 | "@type":"Organization", 16 | "url": "https://www.ncei.noaa.gov/", 17 | "name":"OC/NOAA/NESDIS/NCEI > National Centers for Environmental Information, NESDIS, NOAA, U.S. Department of Commerce", 18 | "contactPoint":{ 19 | "@type":"ContactPoint", 20 | "contactType": "customer service", 21 | "telephone":"+1-828-271-4800", 22 | "email":"ncei.orders@noaa.gov" 23 | } 24 | }, 25 | "includedInDataCatalog":{ 26 | "@type":"DataCatalog", 27 | "name":"data.gov" 28 | }, 29 | "distribution":[ 30 | { 31 | "@type":"DataDownload", 32 | "encodingFormat":"CSV", 33 | "contentUrl":"http://www.ncdc.noaa.gov/stormevents/ftp.jsp" 34 | }, 35 | { 36 | "@type":"DataDownload", 37 | "encodingFormat":"XML", 38 | "contentUrl":"http://gis.ncdc.noaa.gov/all-records/catalog/search/resource/details.page?id=gov.noaa.ncdc:C00510" 39 | } 40 | ], 41 | "temporalCoverage":"1950-01-01/2013-12-18", 42 | "spatialCoverage":{ 43 | "@type":"Place", 44 | "geo":{ 45 | "@type":"GeoShape", 46 | "box":"18.0 -65.0 72.0 172.0" 47 | } 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.202.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 202 10 | Estimating suspended sediment concentrations in turbid coastal waters with SeaWiFS 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | D 29 | A 30 | Siegel 31 | 32 | 33 | 34 | 35 | C 36 | MacKenzie 37 | 38 | 39 | 2004 40 |
41 | International Journal of Remote Sensing 42 | 25 43 | 1995-2002 44 |
45 | 46 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.203.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 203 10 | Dispersal forcing of southern California river plumes based on field and remote sensing observations 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | L 29 | Washburn 30 | 31 | 32 | 33 | 34 | D 35 | A 36 | Siegel 37 | 38 | 39 | 2004 40 |
41 | Geo-Marine Letters 42 | 24 43 | 46-52 44 |
45 | 46 | 47 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.202.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 202 10 | Estimating suspended sediment concentrations in turbid coastal waters with SeaWiFS 11 | 12 | 13 | J 14 | A 15 | Warrick 16 | 17 | 18 | 19 | 20 | L 21 | A 22 | K 23 | Mertes 24 | 25 | 26 | 27 | 28 | D 29 | A 30 | Siegel 31 | 32 | 33 | 34 | 35 | C 36 | MacKenzie 37 | 38 | 39 | 2004 40 |
41 | International Journal of Remote Sensing 42 | 25 43 | 1995-2002 44 |
45 | 46 | 47 | -------------------------------------------------------------------------------- /R/validate_units.R: -------------------------------------------------------------------------------- 1 | # Validate that every `standardUnit` is a standardUnit 2 | # Validate that any `customUnit` is defined in the customUnits 3 | validate_units <- function(eml, 4 | encoding = "UTF-8") { 5 | 6 | doc <- generalized_parser(eml, encoding = encoding) 7 | ns <- xml_ns(doc) 8 | standard_units <- unique(xml2::xml_text( 9 | xml2::xml_find_all(doc, "//standardUnit", ns = ns), 10 | trim = TRUE)) 11 | custom_units <- unique(xml2::xml_text( 12 | xml2::xml_find_all(doc, "//customUnit", ns = ns), 13 | trim = TRUE)) 14 | 15 | # Read in the version of eml-unitDictionary.xml to match this document's 16 | # schema version 17 | root_schema <- guess_root_schema(eml) 18 | 19 | standard <- xml2::read_xml(system.file("tests", 20 | paste(root_schema$module, root_schema$version, sep = "-"), 21 | "eml-unitDictionary.xml", 22 | package = "emld" 23 | )) 24 | 25 | standard_defs <- xml_attr( 26 | xml2::xml_find_all(standard, 27 | "//*[local-name()='unitList']/*[local-name()='unit']"), 28 | "id" 29 | ) 30 | 31 | custom_defs <- xml2::xml_attr(xml2::xml_find_all( 32 | doc, 33 | "//*[local-name()='unitList']/*[local-name()='unit']" 34 | ), "id") 35 | 36 | error_log <- character() 37 | if(!all(standard_units %in% standard_defs)) 38 | error_log <- c(error_log, "some standardUnit elements are not recognized.") 39 | 40 | if(!all(custom_units %in% custom_defs)) 41 | error_log <- c(error_log, "not all 'custom units are defined.") 42 | 43 | # If no validity errors are found above or by the parser, then the document is valid 44 | if(length(error_log) == 0) 45 | result <- TRUE 46 | else { 47 | warning(paste("Document is invalid. Found the following errors:\n", 48 | paste(error_log, collapse = "\n"))) 49 | result <- FALSE 50 | } 51 | attr(result, "errors") <- error_log 52 | result 53 | } 54 | 55 | 56 | 57 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/citation-sbclter-bibliography.50.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 50 10 | Satellite Views of Plumes and Blooms in the Santa Barbara Channel (in) Channel Islands I: Introduction to Channel Islands National Marine Sanctuary 11 | 12 | 13 | S 14 | Fangman 15 | 16 | 17 | 18 | 19 | D 20 | A 21 | Siegel 22 | 23 | 24 | 2002 25 | 26 | This 30 min video is an introduction to the Channel Islands National Marine Sanctuary designed for a nation-wide audience of middle school aged students. It includes six minutes on satellite views of sediment plumes and phytoplankton blooms in the Santa Barbara Channel. 27 | 28 | 29 | 30 | http://www.marine.usf.edu/pjocean/video/index.html 31 | 32 | 33 | 34 | 35 | Project Oceanography, University of South Florida 36 | 37 | Tampa, FL 38 | 39 | 40 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-citationWithContactReference.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 289 5 | 10.1029/2005GL023017 6 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 7 | 8 | 9 | Corinne 10 | J 11 | Bassin 12 | 13 | 14 | 15 | 16 | Libe 17 | Washburn 18 | 19 | washburn@icess.ucsb.edu 20 | 21 | 22 | 23 | M 24 | A 25 | Brzezinski 26 | 27 | 28 | 29 | washburn 30 | 31 | 2005 32 | 33 | 34 | Libe 35 | Washburn 36 | 37 | washburn@icess.ucsb.edu 38 | 39 |
40 | Geophysical Research Letters 41 | 32 42 | LI2604 43 |
44 | 45 | 46 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.50.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 50 10 | Satellite Views of Plumes and Blooms in the Santa Barbara Channel (in) Channel Islands I: Introduction to Channel Islands National Marine Sanctuary 11 | 12 | 13 | S 14 | Fangman 15 | 16 | 17 | 18 | 19 | D 20 | A 21 | Siegel 22 | 23 | 24 | 2002 25 | 26 | This 30 min video is an introduction to the Channel Islands National Marine Sanctuary designed for a nation-wide audience of middle school aged students. It includes six minutes on satellite views of sediment plumes and phytoplankton blooms in the Santa Barbara Channel. 27 | 28 | 29 | 30 | http://www.marine.usf.edu/pjocean/video/index.html 31 | 32 | 33 | 34 | 35 | Project Oceanography, University of South Florida 36 | 37 | Tampa, FL 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-citationWithContactReference.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 289 5 | 10.1029/2005GL023017 6 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 7 | 8 | 9 | Corinne 10 | J 11 | Bassin 12 | 13 | 14 | 15 | 16 | Libe 17 | Washburn 18 | 19 | washburn@icess.ucsb.edu 20 | 21 | 22 | 23 | M 24 | A 25 | Brzezinski 26 | 27 | 28 | 29 | washburn 30 | 31 | 2005 32 | 33 | 34 | Libe 35 | Washburn 36 | 37 | washburn@icess.ucsb.edu 38 | 39 |
40 | Geophysical Research Letters 41 | 32 42 | LI2604 43 |
44 | 45 | 46 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-citationWithContact.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 289 5 | 10.1029/2005GL023017 6 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 7 | 8 | 9 | Corinne 10 | J 11 | Bassin 12 | 13 | 14 | 15 | 16 | Libe 17 | Washburn 18 | 19 | washburn@icess.ucsb.edu 20 | 21 | 22 | 23 | M 24 | A 25 | Brzezinski 26 | 27 | 28 | 29 | 30 | E 31 | B 32 | McPhee-Shaw 33 | 34 | 35 | 2005 36 | 37 | 38 | Libe 39 | Washburn 40 | 41 | washburn@icess.ucsb.edu 42 | 43 |
44 | Geophysical Research Letters 45 | 32 46 | LI2604 47 |
48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-citationWithContact.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 289 5 | 10.1029/2005GL023017 6 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 7 | 8 | 9 | Corinne 10 | J 11 | Bassin 12 | 13 | 14 | 15 | 16 | Libe 17 | Washburn 18 | 19 | washburn@icess.ucsb.edu 20 | 21 | 22 | 23 | M 24 | A 25 | Brzezinski 26 | 27 | 28 | 29 | 30 | E 31 | E 32 | McPhee-Shaw 33 | 34 | 35 | 2005 36 | 37 | 38 | Libe 39 | Washburn 40 | 41 | washburn@icess.ucsb.edu 42 | 43 |
44 | Geophysical Research Letters 45 | 32 46 | LI2604 47 |
48 | 49 | 50 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-semantics.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | TEMPID234 8 | Test Data 9 | This is a test entity that is fake. 10 | This is test data 11 | 12 | 13 | tmpair 14 | Air Temperature 15 | Air temperature at 1m from ground. 16 | float 17 | 18 | 19 | celsius 20 | 0.5 21 | 22 | real 23 | 24 | 25 | 26 | 27 | http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#ofCharacteristic 28 | http://ecoinformatics.org/oboe/oboe.1.2/oboe-characteristics.owl#Temperature 29 | 30 | 31 | http://ecoinformatics.org/oboe/oboe.1.2/oboe-core.owl#ofEntity 32 | http://purl.obolibrary.org/obo/ENVO_00002005 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | Sample dataset Description 11 | 12 | 13 | Smith 14 | 15 | 16 | 17 | 18 | Smith 19 | 20 | 21 | My comments go here. 22 |
Anyone can use it.
23 | 24 | 25 | 26 | 27 | 28 | sde 29 | The SDE scheme used at CAP LTER 30 | 31 | hostname 32 | The host 33 | mohave.asu.edu 34 | 35 | 36 | databaseName 37 | The name of the database or catalog 38 | 39 | 40 | owner 41 | The owner catalog 42 | dbo 43 | 44 | 45 | 46 | 47 | 48 | Provide data to the whole world. 49 | 50 | 51 | Johnson 52 | 53 | 54 | 55 | 23445 56 | 57 | 58 | 59 | 60 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | Sample dataset Description 11 | 12 | 13 | Smith 14 | 15 | 16 | 17 | 18 | Smith 19 | 20 | 21 | My comments go here. 22 |
Anyone can use it.
23 | 24 | 25 | 26 | 27 | 28 | sde 29 | The SDE scheme used at CAP LTER 30 | 31 | hostname 32 | The host 33 | mohave.asu.edu 34 | 35 | 36 | databaseName 37 | The name of the database or catalog 38 | 39 | 40 | owner 41 | The owner catalog 42 | dbo 43 | 44 | 45 | 46 | 47 | 48 | Provide data to the whole world. 49 | 50 | 51 | Johnson 52 | 53 | 54 | 55 | 23445 56 | 57 | 58 | 59 | -------------------------------------------------------------------------------- /notebook/jq_maps.md: -------------------------------------------------------------------------------- 1 | 2 | Mapping between Schema.Org and EML via JQ 3 | ========================================= 4 | 5 | We will use J-Query as XSLT-like stylesheets. These two examples shipping in this package are currently a work in progress: 6 | 7 | ``` r 8 | library(jqr) 9 | ``` 10 | 11 | ``` r 12 | eml_to_schema <- readr::read_file(system.file("jq/eml_to_schema.jq", package="emld")) 13 | schema_to_eml <- readr::read_file(system.file("jq/schema_to_eml.jq", package="emld")) 14 | ``` 15 | 16 | Let's map a more complete EML document into schema.org: 17 | 18 | ``` r 19 | eml <- readr::read_file("https://raw.githubusercontent.com/cboettig/emld/master/inst/extdata/hf205.json") 20 | jq(eml, eml_to_schema) 21 | ``` 22 | 23 | ## { 24 | ## "id": "HF205", 25 | ## "type": null, 26 | ## "temporalCoverage": "2012-06-01/2013-12-31", 27 | ## "spatialCoverage": { 28 | ## "description": "Harvard Forest Greenhouse, Tom Swamp Tract (Harvard Forest)", 29 | ## "geo": { 30 | ## "box": "+42.42 -72.29 +42.55 -72.10" 31 | ## } 32 | ## } 33 | ## } 34 | 35 | Convert a dataset marked up in terms into EML 36 | 37 | ``` r 38 | schema <- readr::read_file("../inst/extdata/schema-org-dataset.json") 39 | 40 | jq(schema, schema_to_eml) 41 | ``` 42 | 43 | ## { 44 | ## "@id": null, 45 | ## "@type": "Dataset", 46 | ## "coverage": { 47 | ## "temporalCoverage": { 48 | ## "rangeOfDates": { 49 | ## "beginDate": "1950-01-01", 50 | ## "endDate": "2013-12-18" 51 | ## } 52 | ## }, 53 | ## "geographicCoverage": { 54 | ## "geographicDescription": null, 55 | ## "boundingCoordinates": { 56 | ## "westBoundingCoordinate": "-65.0", 57 | ## "eastBoundingCoordinate": "172.0", 58 | ## "northBoundingCoordinate": "72.0", 59 | ## "southBoundingCoordinate": "18.0" 60 | ## } 61 | ## } 62 | ## } 63 | ## } 64 | -------------------------------------------------------------------------------- /man/as_xml.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/as_xml.R 3 | \name{as_xml} 4 | \alias{as_xml} 5 | \title{Coerce an emld object into XML (EML's standard format)} 6 | \usage{ 7 | as_xml(x, file = NULL, root = "eml", ns = "eml", schemaLocation = TRUE) 8 | } 9 | \arguments{ 10 | \item{x}{an emld object} 11 | 12 | \item{file}{optional path to write out to file. 13 | Otherwise, defaults to NULL and will return an xml_document object.} 14 | 15 | \item{root}{name for the root node; default to 'eml'} 16 | 17 | \item{ns}{namespace abbreviation on root node, default 'eml'} 18 | 19 | \item{schemaLocation}{If not explicitly set on \code{x}, automatically set 20 | \code{xsi:schemaLocation} based upon the root namespace (\code{TRUE}, default), do not 21 | set a \code{xsi:schemaLocation} (\code{FALSE}), or set a specific \code{xsi:schemaLocation} 22 | value (\code{"Your value here..."}). See Examples.} 23 | } 24 | \value{ 25 | a xml_document object. Or if a file path is provided, the metadata 26 | is written out in XML file and the function returns \code{NULL} invisibly. 27 | } 28 | \description{ 29 | Coerce an emld object into XML (EML's standard format) 30 | } 31 | \details{ 32 | Unlike as_json, this function cannot rely on the existing 33 | convention of serializing a list to xml, eg, as defined by xml2::as_xml_document() 34 | Instead, this relies on a modified version, as_eml_document. In addition 35 | further steps must be taken when working with JSON-LD to deal with 36 | different possible framings and namespaces from the JSON-LD context 37 | element. Thus this \code{as_xml} function is particular to EML and \code{emld} 38 | objects alone. 39 | } 40 | \examples{ 41 | f <- system.file("extdata/example.xml", package = "emld") 42 | emld <- as_emld(f) 43 | xml <- as_xml(emld) 44 | 45 | ## can also write directly to a file: 46 | xml_file <- tempfile() 47 | as_xml(emld, xml_file) 48 | 49 | ## if you don't want the `xsi:schemaLocation` attribute set 50 | as_xml(emld, schemaLocation = FALSE) 51 | 52 | ## or if you want to set your own value 53 | as_xml(emld, schemaLocation = "https://eml.ecoinformatics.org/eml-2.2.0 54 | http://example.com/eml-2.2.0/eml.xsd") 55 | 56 | } 57 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetNoSchemaLocationInvalid.xml: -------------------------------------------------------------------------------- 1 | 2 | 5 | Sample datset Description 6 | 7 | My comments go here. 8 |
Anyone can use it.
9 | 10 | 11 | 12 | 13 | 14 | sde 15 | The SDE scheme used at CAP LTER 16 | 17 | hostname 18 | The host 19 | mohave.asu.edu 20 | 21 | 22 | databaseName 23 | The name of the database or catalog 24 | 25 | 26 | owner 27 | The owner catalog 28 | dbo 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | def.1 37 | 38 | 39 | databaseName 40 | landuse95 41 | 42 | 43 | owner 44 | sde 45 | 46 | 47 | 48 | 49 | Provide data to the whole world. 50 | 51 | 52 | Johnson 53 | 54 | 55 | 56 | 23445 57 | 58 | 59 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetGringpoint.xml: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | A title dataset with bad gringpoints. 6 | 7 | 8 | 9 | surname-is-hyphenated 10 | 11 | 12 | 13 | 14 | this coverage tree has invalid gring points 15 | 16 | 23 17 | 23 18 | 23 19 | 23 20 | 21 | 22 | 23 | 24 | 12 25 | 123 26 | 27 | 28 | 12.7 29 | 123 30 | 31 | 32 | 13 33 | 120.5555555 34 | 35 | 36 | 37 | 38 | 39 | 40 | my org 41 | 42 | 43 | 44 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/skiptest-sbclter-bibliography.289.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 289 10 | 10.1029/2005GL023017 11 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 12 | 13 | 14 | C 15 | J 16 | Bassin 17 | 18 | 19 | 20 | 21 | L 22 | Washburn 23 | 24 | 25 | 26 | 27 | M 28 | A 29 | Brzezinski 30 | 31 | 32 | 33 | 34 | E 35 | E 36 | McPhee-Shaw 37 | 38 | 39 | 2005 40 | 41 | 42 | Libe 43 | Washburn 44 | 45 | washburn@icess.ucsb.edu 46 | 47 |
48 | Geophysical Research Letters 49 | 32 50 | LI2604 51 |
52 | 53 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/identical-repeated-key-bibliography.289.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 289 10 | 10.1029/2005GL023017 11 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 12 | 13 | 14 | C 15 | J 16 | Bassin 17 | 18 | 19 | 20 | 21 | L 22 | Washburn 23 | 24 | 25 | 26 | 27 | M 28 | A 29 | Brzezinski 30 | 31 | 32 | 33 | 34 | E 35 | E 36 | McPhee-Shaw 37 | 38 | 39 | 2005 40 | 41 | 42 | Libe 43 | Washburn 44 | 45 | washburn@icess.ucsb.edu 46 | 47 |
48 | Geophysical Research Letters 49 | 32 50 | LI2604 51 |
52 | 53 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/citation-sbclter-bibliography.289.xml: -------------------------------------------------------------------------------- 1 | 2 | 8 | 9 | 289 10 | 10.1029/2005GL023017 11 | Sub-mesoscale coastal eddies observed by high frequency radar: A new mechanism for delivering nutrients to kelp forests in the Southern California Bight 12 | 13 | 14 | C 15 | J 16 | Bassin 17 | 18 | 19 | 20 | 21 | L 22 | Washburn 23 | 24 | 25 | 26 | 27 | M 28 | A 29 | Brzezinski 30 | 31 | 32 | 33 | 34 | E 35 | E 36 | McPhee-Shaw 37 | 38 | 39 | 2005 40 | 41 | 42 | Libe 43 | Washburn 44 | 45 | washburn@icess.ucsb.edu 46 | 47 |
48 | Geophysical Research Letters 49 | 32 50 | LI2604 51 |
52 | 53 | 54 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: emld 2 | Title: Ecological Metadata as Linked Data 3 | Version: 0.5.2 4 | Authors@R: c( 5 | person("Carl", "Boettiger", 6 | email = "cboettig@gmail.com", 7 | role = c("aut", "cre", "cph"), 8 | comment=c(ORCID = "0000-0002-1642-628X")), 9 | person("Matthew B.", "Jones", 10 | email = "jones@nceas.ucsb.edu", 11 | role = c("aut", "cph"), 12 | comment=c(ORCID = "0000-0003-0077-4738")), 13 | person("Bryce", "Mecum", 14 | email = "mecum@nceas.ucsb.edu", 15 | role = c("aut", "cph"), 16 | comment=c(ORCID = "0000-0002-0381-3766")) 17 | ) 18 | Description: This is a utility for transforming Ecological Metadata Language 19 | ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a 20 | list-based representation of 'EML' in R, so that 'EML' data can easily 21 | be manipulated using standard 'R' tools. This makes this package an 22 | effective backend for other 'R'-based tools working with 'EML.' By 23 | abstracting away the complexity of 'XML' Schema, developers can 24 | build around native 'R' list objects and not have to worry about satisfying 25 | many of the additional constraints of set by the schema (such as element 26 | ordering, which is handled automatically). Additionally, the 'JSON-LD' 27 | representation enables the use of developer-friendly 'JSON' parsing and 28 | serialization that may facilitate the use of 'EML' in contexts outside of 'R,' 29 | as well as the informatics-friendly serializations such as 'RDF' and 30 | 'SPARQL' queries. 31 | URL: https://docs.ropensci.org/emld/, https://github.com/ropensci/emld 32 | BugReports: https://github.com/ropensci/emld/issues 33 | Depends: R (>= 3.1.0) 34 | License: MIT + file LICENSE 35 | Encoding: UTF-8 36 | RoxygenNote: 7.3.3 37 | Roxygen: list(markdown = TRUE) 38 | Suggests: 39 | spelling, 40 | testthat, 41 | magrittr, 42 | rmarkdown, 43 | covr, 44 | knitr, 45 | rdflib, 46 | jqr 47 | Imports: 48 | xml2, 49 | jsonlite, 50 | jsonld, 51 | methods, 52 | yaml 53 | VignetteBuilder: knitr 54 | Language: en-US 55 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetNoSchemaLocation.xml: -------------------------------------------------------------------------------- 1 | 2 | 5 | Sample datset Description 6 | 7 | 8 | Smith 9 | 10 | 11 | My comments go here. 12 |
Anyone can use it.
13 | 14 | 15 | 16 | 17 | 18 | sde 19 | The SDE scheme used at CAP LTER 20 | 21 | hostname 22 | The host 23 | mohave.asu.edu 24 | 25 | 26 | databaseName 27 | The name of the database or catalog 28 | 29 | 30 | owner 31 | The owner catalog 32 | dbo 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | def.1 41 | 42 | 43 | databaseName 44 | landuse95 45 | 46 | 47 | owner 48 | sde 49 | 50 | 51 | 52 | 53 | Provide data to the whole world. 54 | 55 | 56 | Johnson 57 | 58 | 59 | 60 | 23445 61 | 62 | 63 | -------------------------------------------------------------------------------- /notebook/solr_functions.R: -------------------------------------------------------------------------------- 1 | 2 | ## get JSON! 3 | # json_queries <- paste0(query, "&wt=json") 4 | 5 | q = "https://knb.ecoinformatics.org/knb/d1/mn/v2/query/solr?q=genus:*&fl=identifier,northBoundCoord,eastBoundCoord,southBoundCoord,westBoundCoord,namedLocation,scientificName,kingdom,phylum,class,order,family,genus,species,beginDate,endDate&-obsoletedBy:*&start=0&rows=1000&wt=json" 6 | # solr_df(q) 7 | 8 | solr_df <- function(q){ 9 | message(paste(q)) 10 | resp <- GET(q) 11 | if(!grepl("json", headers(resp)$`content-type`)) 12 | return(tibble()) 13 | json <- content(resp, as = "parsed", type = "application/json") 14 | docs_to_nquads(json$response$docs, append = TRUE) 15 | } 16 | 17 | docs_to_nquads <- function(docs, f = tempfile(), ...){ 18 | list("@context" = list("@vocab"="http://ecoinformatics.org/eml-2.1.1/", 19 | "identifier" = "@id"), 20 | "@graph" = docs) %>% 21 | toJSON(pretty=TRUE, auto_unbox = TRUE) %>% 22 | jsonld_to_rdf() %>% 23 | write_lines(path = f, ...) 24 | tabularize(f) 25 | } 26 | 27 | 28 | tabularize <- function(file){ 29 | 30 | ## Express type string inside "" so we can parse 31 | read_lines(file) %>% str_replace("\"\\^\\^(.*)>", "\\^\\^\\1\"") %>% write_lines(file) 32 | 33 | df <- readr::read_delim(file, delim = " ", col_names = FALSE, col_types = "cccc") 34 | names(df) <- c("id", "property", "value", "about") 35 | df %>% 36 | mutate(property = gsub("", "\\1", property)) %>% 37 | separate(value, c("value", "type"), sep="\\^\\^<", fill="right") 38 | 39 | } 40 | 41 | spread_nquads <- function(file){ 42 | 43 | tabularize(file) %>% 44 | select(id, property, value) %>% 45 | group_by(id, property) %>% 46 | mutate(key = row_number()) %>% 47 | spread(property, value) %>% 48 | select(-key) %>% 49 | fill(-id) %>% ## Fill in NA based on known properties for id, needs group_by id 50 | ungroup() %>% 51 | select(-identifier) %>% View() 52 | } 53 | 54 | 55 | 56 | 57 | 58 | ## Attempt a json & unnest strategy 59 | pure_json <- function(docs){ 60 | toJSON(auto_unbox = TRUE) %>% 61 | fromJSON() %>% as_tibble() -> df 62 | 63 | ## cannot unnest appropriately across multiple areas 64 | df$scientificName[[1]] <- "" 65 | df$species[[1]] <- "" 66 | unnest(df, scientificName) %>% distinct() %>% View() 67 | } 68 | 69 | 70 | -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- 1 | $(function() { 2 | 3 | // register a handler to move the focus to the search bar 4 | // upon pressing shift + "/" (i.e. "?") 5 | $(document).on('keydown', function(e) { 6 | if (e.shiftKey && e.keyCode == 191) { 7 | e.preventDefault(); 8 | $("#search-input").focus(); 9 | } 10 | }); 11 | 12 | $(document).ready(function() { 13 | // do keyword highlighting 14 | /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ 15 | var mark = function() { 16 | 17 | var referrer = document.URL ; 18 | var paramKey = "q" ; 19 | 20 | if (referrer.indexOf("?") !== -1) { 21 | var qs = referrer.substr(referrer.indexOf('?') + 1); 22 | var qs_noanchor = qs.split('#')[0]; 23 | var qsa = qs_noanchor.split('&'); 24 | var keyword = ""; 25 | 26 | for (var i = 0; i < qsa.length; i++) { 27 | var currentParam = qsa[i].split('='); 28 | 29 | if (currentParam.length !== 2) { 30 | continue; 31 | } 32 | 33 | if (currentParam[0] == paramKey) { 34 | keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); 35 | } 36 | } 37 | 38 | if (keyword !== "") { 39 | $(".contents").unmark({ 40 | done: function() { 41 | $(".contents").mark(keyword); 42 | } 43 | }); 44 | } 45 | } 46 | }; 47 | 48 | mark(); 49 | }); 50 | }); 51 | 52 | /* Search term highlighting ------------------------------*/ 53 | 54 | function matchedWords(hit) { 55 | var words = []; 56 | 57 | var hierarchy = hit._highlightResult.hierarchy; 58 | // loop to fetch from lvl0, lvl1, etc. 59 | for (var idx in hierarchy) { 60 | words = words.concat(hierarchy[idx].matchedWords); 61 | } 62 | 63 | var content = hit._highlightResult.content; 64 | if (content) { 65 | words = words.concat(content.matchedWords); 66 | } 67 | 68 | // return unique words 69 | var words_uniq = [...new Set(words)]; 70 | return words_uniq; 71 | } 72 | 73 | function updateHitURL(hit) { 74 | 75 | var words = matchedWords(hit); 76 | var url = ""; 77 | 78 | if (hit.anchor) { 79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; 80 | } else { 81 | url = hit.url + '?q=' + escape(words.join(" ")); 82 | } 83 | 84 | return url; 85 | } 86 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-dataset.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Sample datset Description 8 | 9 | 10 | Smith 11 | 12 | 13 | My comments go here. 14 |
Anyone can use it.
15 | 16 | 17 | 18 | 19 | 20 | sde 21 | The SDE scheme used at CAP LTER 22 | 23 | hostname 24 | The host 25 | mohave.asu.edu 26 | 27 | 28 | databaseName 29 | The name of the database or catalog 30 | 31 | 32 | owner 33 | The owner catalog 34 | dbo 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | def.1 43 | 44 | 45 | databaseName 46 | landuse95 47 | 48 | 49 | owner 50 | sde 51 | 52 | 53 | 54 | 55 | Provide data to the whole world. 56 | 57 | 58 | Johnson 59 | 60 | 61 | 62 | 23445 63 | 64 | 65 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-dataset.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | Sample datset Description 8 | 9 | 10 | Smith 11 | 12 | 13 | My comments go here. 14 |
Anyone can use it.
15 | 16 | 17 | 18 | 19 | 20 | sde 21 | The SDE scheme used at CAP LTER 22 | 23 | hostname 24 | The host 25 | mohave.asu.edu 26 | 27 | 28 | databaseName 29 | The name of the database or catalog 30 | 31 | 32 | owner 33 | The owner catalog 34 | dbo 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | def.1 43 | 44 | 45 | databaseName 46 | landuse95 47 | 48 | 49 | owner 50 | sde 51 | 52 | 53 | 54 | 55 | Provide data to the whole world. 56 | 57 | 58 | Johnson 59 | 60 | 61 | 62 | 23445 63 | 64 | 65 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-softwareWithAcessDistribution.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | uid=joe,o=lter,dc=ecoinformatics,dc=org 6 | all 7 | 8 | 9 | public 10 | read 11 | 12 | 13 | 14 | 15 | fish counting 16 | 17 | 18 | 19 | University of California 20 | 21 |
22 | 123 Campus Dr. 23 | Santa Barbara 24 | CA 25 | 93101 26 | USA 27 |
28 | 29 | 805-123-1234 30 | 31 | joe@something.org 32 | www.something.org/~joe 33 | 34 | 1999 35 | English 36 | 37 | fish 38 | lake 39 | jim's thesaurus 40 | 41 | 42 | This is some other fake info. 43 | 44 | 45 | 46 | you gotta buy the cd 47 | 48 | 49 | 50 | 51 | 52 | http://www.something.org 53 | 54 | 55 | 56 | uid=joe,o=lter,dc=ecoinformatics,dc=org 57 | all 58 | 59 | 60 | public 61 | read 62 | 63 | 64 | 65 | 66 | 123 MB 67 | 68 | Linux 69 | JVM 70 | 123 MB 71 | Java 72 | 73 | 74 | GPL 75 | 76 | 77 | 1.0 78 | 79 | 80 | 81 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-software-dependency.xml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | eml2 8 | eml2: Create and Manipulate Data using the Ecological Metadata Language 9 | 10 | 11 | Carl 12 | Boettiger 13 | 14 |
15 | cboettig@gmail.com 16 | 17 | A successor to the 'EML' R package which provides the same high level 18 | functions for creating and extracting data from 'EML' files, while 19 | providing a simpler and more user friendly lower level interface. 20 | 21 | 22 | 23 | 24 | https://github.com/cboettig/eml2 25 | 26 | 27 | 466.612KB 28 | R 3.5.0 29 | 30 | 31 | install 32 | 33 | xml2 34 | xml2 35 | 36 | http://orcid.org/0000-0002-1642-628X 37 | 38 | 39 | 40 | 41 | https://github.com/cboettig/eml2 42 | 43 | 44 | 466.612KB 45 | R 3.5.0 46 | 47 | https://spdx.org/licenses/MIT 48 | 1.4 49 | 50 | 51 | https://spdx.org/licenses/MIT 52 | xxx 53 | 54 | 55 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-softwareWithAcessDistribution.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | uid=joe,o=lter,dc=ecoinformatics,dc=org 6 | all 7 | 8 | 9 | public 10 | read 11 | 12 | 13 | 14 | 15 | fish counting 16 | 17 | 18 | 19 | University of California 20 | 21 |
22 | 123 Campus Dr. 23 | Santa Barbara 24 | CA 25 | 93101 26 | USA 27 |
28 | 29 | 805-123-1234 30 | 31 | joe@something.org 32 | www.something.org/~joe 33 | 34 | 1999 35 | English 36 | 37 | fish 38 | lake 39 | jim's thesaurus 40 | 41 | 42 | This is some other fake info. 43 | 44 | 45 | 46 | you gotta buy the cd 47 | 48 | 49 | 50 | 51 | 52 | http://www.something.org 53 | 54 | 55 | 56 | uid=joe,o=lter,dc=ecoinformatics,dc=org 57 | all 58 | 59 | 60 | public 61 | read 62 | 63 | 64 | 65 | 66 | 123 MB 67 | 68 | Linux 69 | JVM 70 | 123 MB 71 | Java 72 | 73 | 74 | GPL 75 | 76 | 77 | 1.0 78 | 79 | 80 | 81 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-datasetMultipleDistribution.xml: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | Sample datset Description 6 | 7 | 8 | Smith 9 | 10 | 11 | 12 | My comments go here. 13 | 14 | 15 |
16 | Anyone can use it. 17 |
18 | 19 | 20 | 21 | 22 | sde 23 | 24 | The SDE scheme used at CAP LTER 25 | 26 | 27 | hostname 28 | The host 29 | mohave.asu.edu 30 | 31 | 32 | databaseName 33 | The name of the database or catalog 34 | 35 | 36 | owner 37 | The owner catalog 38 | dbo 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | def.1 48 | 49 | 50 | databaseName 51 | landuse95 52 | 53 | 54 | owner 55 | sde 56 | 57 | 58 | 59 | 60 | 61 | 62 | http://my.url.edu 63 | 64 | 65 | 66 | 23445 67 | 68 | 69 | Provide data to the whole world. 70 | 71 | 72 | 73 | Johnson 74 | 75 | 76 | 77 | 23445 78 | 79 | 80 | 81 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetMultipleDistribution.xml: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | Sample datset Description 6 | 7 | 8 | Smith 9 | 10 | 11 | 12 | My comments go here. 13 | 14 | 15 |
16 | Anyone can use it. 17 |
18 | 19 | 20 | 21 | 22 | sde 23 | 24 | The SDE scheme used at CAP LTER 25 | 26 | 27 | hostname 28 | The host 29 | mohave.asu.edu 30 | 31 | 32 | databaseName 33 | The name of the database or catalog 34 | 35 | 36 | owner 37 | The owner catalog 38 | dbo 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | def.1 48 | 49 | 50 | databaseName 51 | landuse95 52 | 53 | 54 | owner 55 | sde 56 | 57 | 58 | 59 | 60 | 61 | 62 | http://my.url.edu 63 | 64 | 65 | 66 | 23445 67 | 68 | 69 | Provide data to the whole world. 70 | 71 | 72 | 73 | Johnson 74 | 75 | 76 | 77 | 23445 78 | 79 | 80 | 81 | -------------------------------------------------------------------------------- /man/emld-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/emld-package.R, R/emld.R 3 | \docType{package} 4 | \name{emld-package} 5 | \alias{emld-package} 6 | \title{emld: Ecological Metadata as Linked Data} 7 | \description{ 8 | 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. 9 | 10 | The goal of emld is to provide a way to work with EML metadata 11 | in the JSON-LD format. At it's heart, the package is simply a 12 | way to translate an EML XML document into JSON-LD and be able 13 | to reverse this so that any semantically equivalent JSON-LD 14 | file can be serialized into EML-schema valid XML. 15 | } 16 | \details{ 17 | The package has only three core functions: 18 | \itemize{ 19 | \item \code{\link[=as_emld]{as_emld()}} Convert EML's \code{xml} files (or the \code{json} version created 20 | by this package) into a native R object (an S3 class called \code{emld}, 21 | essentially just a \code{list}). 22 | \item \code{\link[=as_xml]{as_xml()}} Convert the native R format, \code{emld}, back into 23 | XML-schema valid EML. 24 | \item \code{\link[=as_json]{as_json()}} Convert the native R format, \code{emld}, into \code{json}(LD). 25 | } 26 | } 27 | \seealso{ 28 | Useful links: 29 | \itemize{ 30 | \item \url{https://docs.ropensci.org/emld/} 31 | \item \url{https://github.com/ropensci/emld} 32 | \item Report bugs at \url{https://github.com/ropensci/emld/issues} 33 | } 34 | 35 | 36 | Useful links: 37 | \itemize{ 38 | \item \url{https://docs.ropensci.org/emld/} 39 | \item \url{https://github.com/ropensci/emld} 40 | \item Report bugs at \url{https://github.com/ropensci/emld/issues} 41 | } 42 | 43 | } 44 | \author{ 45 | \strong{Maintainer}: Carl Boettiger \email{cboettig@gmail.com} (\href{https://orcid.org/0000-0002-1642-628X}{ORCID}) [copyright holder] 46 | 47 | Authors: 48 | \itemize{ 49 | \item Matthew B. Jones \email{jones@nceas.ucsb.edu} (\href{https://orcid.org/0000-0003-0077-4738}{ORCID}) [copyright holder] 50 | \item Bryce Mecum \email{mecum@nceas.ucsb.edu} (\href{https://orcid.org/0000-0002-0381-3766}{ORCID}) [copyright holder] 51 | } 52 | 53 | } 54 | \keyword{internal} 55 | -------------------------------------------------------------------------------- /inst/tests/eml-2.2.0/eml-datasetWithAccess.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | uid=brooke,o=NCEAS,dc=ecoinformatics,dc=org 11 | all 12 | 13 | 14 | public 15 | read 16 | 17 | 18 | uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org 19 | read 20 | write 21 | all 22 | 23 | 24 | 25 | 26 | Sample datset Description 27 | 28 | 29 | Smith 30 | 31 | 32 | My comments go here. 33 |
Anyone can use it.
34 | 35 | 36 | 37 | 38 | 39 | sde 40 | The SDE scheme used at CAP LTER 41 | 42 | hostname 43 | The host 44 | mohave.asu.edu 45 | 46 | 47 | databaseName 48 | The name of the database or catalog 49 | 50 | 51 | owner 52 | The owner catalog 53 | dbo 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | def.1 62 | 63 | 64 | databaseName 65 | landuse95 66 | 67 | 68 | owner 69 | sde 70 | 71 | 72 | 73 | 74 | Provide data to the whole world. 75 | 76 | 77 | Johnson 78 | 79 | 80 | 81 | 23445 82 | 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /inst/tests/eml-2.1.1/eml-datasetWithAccess.xml: -------------------------------------------------------------------------------- 1 | 2 | 7 | 8 | 9 | 10 | uid=brooke,o=NCEAS,dc=ecoinformatics,dc=org 11 | all 12 | 13 | 14 | public 15 | read 16 | 17 | 18 | uid=berkley,o=NCEAS,dc=ecoinformatics,dc=org 19 | read 20 | write 21 | all 22 | 23 | 24 | 25 | 26 | Sample datset Description 27 | 28 | 29 | Smith 30 | 31 | 32 | My comments go here. 33 |
Anyone can use it.
34 | 35 | 36 | 37 | 38 | 39 | sde 40 | The SDE scheme used at CAP LTER 41 | 42 | hostname 43 | The host 44 | mohave.asu.edu 45 | 46 | 47 | databaseName 48 | The name of the database or catalog 49 | 50 | 51 | owner 52 | The owner catalog 53 | dbo 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | def.1 62 | 63 | 64 | databaseName 65 | landuse95 66 | 67 | 68 | owner 69 | sde 70 | 71 | 72 | 73 | 74 | Provide data to the whole world. 75 | 76 | 77 | Johnson 78 | 79 | 80 | 81 | 23445 82 | 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /inst/xsd/eml-2.1.0/eml-documentation.xsd: -------------------------------------------------------------------------------- 1 | 2 | 8 | 10 | 11 | 12 | '$RCSfile: eml-documentation.xsd,v $' 13 | Copyright: 1997-2002 Regents of the University of California, 14 | University of New Mexico, and 15 | Arizona State University 16 | Sponsors: National Center for Ecological Analysis and Synthesis and 17 | Partnership for Interdisciplinary Studies of Coastal Oceans, 18 | University of California Santa Barbara 19 | Long-Term Ecological Research Network Office, 20 | University of New Mexico 21 | Center for Environmental Studies, Arizona State University 22 | Other funding: National Science Foundation (see README for details) 23 | The David and Lucile Packard Foundation 24 | For Details: http://knb.ecoinformatics.org/ 25 | 26 | '$Author: obrien $' 27 | '$Date: 2008-08-27 21:30:04 $' 28 | '$Revision: 1.27 $' 29 | 30 | This program is free software; you can redistribute it and/or modify 31 | it under the terms of the GNU General Public License as published by 32 | the Free Software Foundation; either version 2 of the License, or 33 | (at your option) any later version. 34 | 35 | This program is distributed in the hope that it will be useful, 36 | but WITHOUT ANY WARRANTY; without even the implied warranty of 37 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 38 | GNU General Public License for more details. 39 | 40 | You should have received a copy of the GNU General Public License 41 | along with this program; if not, write to the Free Software 42 | Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | --------------------------------------------------------------------------------