diff --git a/.Rbuildignore b/.Rbuildignore index 482a123c..60756850 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -15,3 +15,5 @@ README.md ^config.yaml$ ^cran-comments.md$ ^software-checklist.md$ +^check$ +^venv$ \ No newline at end of file diff --git a/.gitignore b/.gitignore index 5eeaa690..30887d3b 100644 --- a/.gitignore +++ b/.gitignore @@ -50,3 +50,5 @@ docs /test /tests/testthat/test sonia.yaml +/venv +/check \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 3435981a..526c3ef7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,9 @@ Package: rDataPipeline Title: Functions to Interact with the 'FAIR Data Pipeline' -Version: 0.54.3 +Version: 0.6.0 Authors@R: c(person("Sonia", "Mitchell", email = "sonia.mitchell@glasgow.ac.uk", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-1536-2066")), - person("Ryan", "Field", role = "ctb", + person("Ryan", "Field", email = "ryan.field@glasgow.ac.uk", role = "aut", comment = c(ORCID = "0000-0002-4424-9890"))) Description: R implementation of the 'FAIR Data Pipeline API'. The 'FAIR Data Pipeline' is intended to enable tracking of provenance of FAIR (findable, @@ -33,6 +33,6 @@ biocViews: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.2 +RoxygenNote: 7.3.2 URL: https://www.fairdatapipeline.org/rDataPipeline/, https://github.com/FAIRDataPipeline/rDataPipeline BugReports: https://github.com/FAIRDataPipeline/rDataPipeline/issues diff --git a/NEWS.md b/NEWS.md index f64b7cc6..78f25321 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,7 @@ # NEWS - +# rDataPipeline v0.6.0 +## Improvements: + Updates to work with latest versions of R - v0.54.1 - Initial release - v0.54.2 diff --git a/R/check_fields.R b/R/check_fields.R index 5d8c1a48..427a575e 100644 --- a/R/check_fields.R +++ b/R/check_fields.R @@ -14,7 +14,7 @@ check_fields <- function(table, query, method, endpoint) { expected_types <- get_fields(table = table, endpoint = endpoint) %>% dplyr::filter(.data$field %in% fields) %>% dplyr::arrange(factor(.data$field, levels = fields)) %>% - dplyr::select(.data$data_type) %>% + dplyr::select("data_type") %>% unlist() %>% unname() diff --git a/R/class-fdp.R b/R/class-fdp.R index d7135517..3f11868f 100644 --- a/R/class-fdp.R +++ b/R/class-fdp.R @@ -5,7 +5,7 @@ #' @name fdp-class #' @rdname fdp-class #' -fdp <- R6::R6Class("fdp", list( +fdp <- R6::R6Class("fdp", public = list( #' @field yaml a \code{list} containing the contents of the working #' config.yaml #' @field fdp_config_dir a \code{string} specifying the directory passed @@ -80,7 +80,7 @@ fdp <- R6::R6Class("fdp", list( }, #' @description Print method - #' + #' @param ... additional parameters, currently none are used #' @export #' print = function(...) { diff --git a/R/get_components.R b/R/get_components.R index 19ff7d3e..3c0bf540 100644 --- a/R/get_components.R +++ b/R/get_components.R @@ -18,7 +18,7 @@ get_components <- function(filename) { tmp <- rhdf5::H5Fopen(filename) %>% h5ls() %>% dplyr::filter(.data$name == "array" | .data$name == "table") %>% - dplyr::select(.data$group) %>% + dplyr::select("group") %>% unlist() %>% unname() diff --git a/R/rDataPipeline-package.R b/R/rDataPipeline-package.R index f8cb2562..f33a54a5 100644 --- a/R/rDataPipeline-package.R +++ b/R/rDataPipeline-package.R @@ -25,4 +25,4 @@ #' @importFrom utils download.file read.csv unzip write.csv type.convert #' @import yaml #' -NULL +"_PACKAGE" \ No newline at end of file diff --git a/man/check_config.Rd b/man/check_config.Rd index 7b557c35..f02110e5 100644 --- a/man/check_config.Rd +++ b/man/check_config.Rd @@ -17,3 +17,4 @@ by the Data Pipeline API} \description{ check_config } +\keyword{internal} diff --git a/man/check_dataproduct_exists.Rd b/man/check_dataproduct_exists.Rd index 18de0781..e948627c 100644 --- a/man/check_dataproduct_exists.Rd +++ b/man/check_dataproduct_exists.Rd @@ -24,3 +24,4 @@ check_dataproduct_exists( If a data product already exists with the same name, version, and namespace, throw an error } +\keyword{internal} diff --git a/man/check_datetime.Rd b/man/check_datetime.Rd index 82c3151b..c91fbd45 100644 --- a/man/check_datetime.Rd +++ b/man/check_datetime.Rd @@ -18,3 +18,4 @@ check_datetime(table, this_field, query_class, this_query) \description{ check_datetime } +\keyword{internal} diff --git a/man/check_exists.Rd b/man/check_exists.Rd index d1a53b2e..8323fa42 100644 --- a/man/check_exists.Rd +++ b/man/check_exists.Rd @@ -19,3 +19,4 @@ doesn't \description{ Check whether an entry already exists in a table (in the data registry) } +\keyword{internal} diff --git a/man/check_field.Rd b/man/check_field.Rd index 7b6e5cbd..9df4f42d 100644 --- a/man/check_field.Rd +++ b/man/check_field.Rd @@ -22,3 +22,4 @@ check_field(table, this_field, query_class, this_query, method, endpoint) \description{ check_field } +\keyword{internal} diff --git a/man/check_fields.Rd b/man/check_fields.Rd index 24fae21d..6aacd3cb 100644 --- a/man/check_fields.Rd +++ b/man/check_fields.Rd @@ -18,3 +18,4 @@ check_fields(table, query, method, endpoint) \description{ check_fields } +\keyword{internal} diff --git a/man/check_handle.Rd b/man/check_handle.Rd index e1ea8921..566c39d4 100644 --- a/man/check_handle.Rd +++ b/man/check_handle.Rd @@ -19,3 +19,4 @@ by the Data Pipeline API} \description{ check_handle } +\keyword{internal} diff --git a/man/check_integer.Rd b/man/check_integer.Rd index 0b608f6a..876d8047 100644 --- a/man/check_integer.Rd +++ b/man/check_integer.Rd @@ -18,3 +18,4 @@ check_integer(table, this_field, query_class, this_query) \description{ check_integer } +\keyword{internal} diff --git a/man/check_local_repo.Rd b/man/check_local_repo.Rd index 6d66d0b0..ee74204e 100644 --- a/man/check_local_repo.Rd +++ b/man/check_local_repo.Rd @@ -15,3 +15,4 @@ check_local_repo(path) \description{ check_local_repo } +\keyword{internal} diff --git a/man/check_string.Rd b/man/check_string.Rd index 9e24b02b..49271bca 100644 --- a/man/check_string.Rd +++ b/man/check_string.Rd @@ -16,3 +16,4 @@ check_string(table, this_field, this_query) \description{ check_string } +\keyword{internal} diff --git a/man/check_table_exists.Rd b/man/check_table_exists.Rd index cdb08596..bba8f9cb 100644 --- a/man/check_table_exists.Rd +++ b/man/check_table_exists.Rd @@ -15,3 +15,4 @@ Returns \code{TRUE} if a table exists, \code{FALSE} if it doesn't \description{ Check if table exists in the data registry } +\keyword{internal} diff --git a/man/check_yaml_write.Rd b/man/check_yaml_write.Rd index 4faf86a6..ee513185 100644 --- a/man/check_yaml_write.Rd +++ b/man/check_yaml_write.Rd @@ -14,3 +14,4 @@ check_yaml_write(handle, data_product) \description{ check_yaml_write } +\keyword{internal} diff --git a/man/clean_query.Rd b/man/clean_query.Rd index 0310f9c2..8434bab6 100644 --- a/man/clean_query.Rd +++ b/man/clean_query.Rd @@ -15,3 +15,4 @@ clean_query(data, endpoint) \description{ Function to clean a query and return it without an api prefix } +\keyword{internal} diff --git a/man/create_index.Rd b/man/create_index.Rd index 58ee5c43..309a11a5 100644 --- a/man/create_index.Rd +++ b/man/create_index.Rd @@ -12,3 +12,4 @@ create_index(self) \description{ create_index } +\keyword{internal} diff --git a/man/create_version_number.Rd b/man/create_version_number.Rd index cba870a1..19d684d7 100644 --- a/man/create_version_number.Rd +++ b/man/create_version_number.Rd @@ -52,3 +52,4 @@ If no parameters are supplied a default version is returned This function prioritizes download date and version over all other parameters } \concept{create functions} +\keyword{internal} diff --git a/man/download_from_database.Rd b/man/download_from_database.Rd index e1a33074..3f9cdf56 100644 --- a/man/download_from_database.Rd +++ b/man/download_from_database.Rd @@ -33,3 +33,4 @@ Other download functions: \code{\link{download_from_url}()} } \concept{download functions} +\keyword{internal} diff --git a/man/download_from_url.Rd b/man/download_from_url.Rd index 715cd064..0d9dd466 100644 --- a/man/download_from_url.Rd +++ b/man/download_from_url.Rd @@ -24,3 +24,4 @@ Other download functions: \code{\link{download_from_database}()} } \concept{download functions} +\keyword{internal} diff --git a/man/extract_id.Rd b/man/extract_id.Rd index 54cb500f..82cbdd84 100644 --- a/man/extract_id.Rd +++ b/man/extract_id.Rd @@ -14,3 +14,4 @@ extract_id(url, endpoint) \description{ extract_id } +\keyword{internal} diff --git a/man/fdp-class.Rd b/man/fdp-class.Rd index b96d61aa..2504def1 100644 --- a/man/fdp-class.Rd +++ b/man/fdp-class.Rd @@ -49,20 +49,20 @@ the \code{code_run} table} \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{fdp$new()}} -\item \href{#method-print}{\code{fdp$print()}} -\item \href{#method-input}{\code{fdp$input()}} -\item \href{#method-output}{\code{fdp$output()}} -\item \href{#method-output_index}{\code{fdp$output_index()}} -\item \href{#method-raise_issue}{\code{fdp$raise_issue()}} -\item \href{#method-finalise_output_hash}{\code{fdp$finalise_output_hash()}} -\item \href{#method-finalise_output_url}{\code{fdp$finalise_output_url()}} -\item \href{#method-clone}{\code{fdp$clone()}} +\item \href{#method-fdp-new}{\code{fdp$new()}} +\item \href{#method-fdp-print}{\code{fdp$print()}} +\item \href{#method-fdp-input}{\code{fdp$input()}} +\item \href{#method-fdp-output}{\code{fdp$output()}} +\item \href{#method-fdp-output_index}{\code{fdp$output_index()}} +\item \href{#method-fdp-raise_issue}{\code{fdp$raise_issue()}} +\item \href{#method-fdp-finalise_output_hash}{\code{fdp$finalise_output_hash()}} +\item \href{#method-fdp-finalise_output_url}{\code{fdp$finalise_output_url()}} +\item \href{#method-fdp-clone}{\code{fdp$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-new}{}}} \subsection{Method \code{new()}}{ Create a new \code{fdp} object \subsection{Usage}{ @@ -106,18 +106,25 @@ Returns a new \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-print}{}}} \subsection{Method \code{print()}}{ Print method \subsection{Usage}{ \if{html}{\out{
}}\preformatted{fdp$print(...)}\if{html}{\out{
}} } +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{...}}{additional parameters, currently none are used} +} +\if{html}{\out{
}} +} } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-input}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-input}{}}} \subsection{Method \code{input()}}{ Record \code{code_run} inputs in \code{fdp} object \subsection{Usage}{ @@ -163,8 +170,8 @@ Returns an updated \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-output}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-output}{}}} \subsection{Method \code{output()}}{ Record \code{code_run} outputs in \code{fdp} object \subsection{Usage}{ @@ -217,8 +224,8 @@ Returns an updated \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-output_index}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-output_index}{}}} \subsection{Method \code{output_index()}}{ Return index of data product recorded in \code{fdp} object so that an issue may be attached @@ -248,8 +255,8 @@ Returns an index used to identify the data product } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-raise_issue}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-raise_issue}{}}} \subsection{Method \code{raise_issue()}}{ Record \code{issue} in \code{fdp} object \subsection{Usage}{ @@ -299,8 +306,8 @@ Returns an updated \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-finalise_output_hash}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-finalise_output_hash}{}}} \subsection{Method \code{finalise_output_hash()}}{ Record file hash and update path name in \code{fdp} object \subsection{Usage}{ @@ -349,8 +356,8 @@ Returns an updated \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-finalise_output_url}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-finalise_output_url}{}}} \subsection{Method \code{finalise_output_url()}}{ Record \code{data_product} and component URLs in \code{fdp} object @@ -389,8 +396,8 @@ Returns an updated \code{fdp} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fdp-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/fdp_resolve_read.Rd b/man/fdp_resolve_read.Rd index c76830b2..70d9e442 100644 --- a/man/fdp_resolve_read.Rd +++ b/man/fdp_resolve_read.Rd @@ -14,3 +14,4 @@ fdp_resolve_read(this_read, yaml) \description{ fdp_resolve_read } +\keyword{internal} diff --git a/man/fdp_resolve_write.Rd b/man/fdp_resolve_write.Rd index 21e3755a..568da6b3 100644 --- a/man/fdp_resolve_write.Rd +++ b/man/fdp_resolve_write.Rd @@ -14,3 +14,4 @@ fdp_resolve_write(this_write, yaml) \description{ fdp_resolve_write } +\keyword{internal} diff --git a/man/get_author_url.Rd b/man/get_author_url.Rd index 988bd070..c9a12c52 100644 --- a/man/get_author_url.Rd +++ b/man/get_author_url.Rd @@ -12,3 +12,4 @@ get_author_url(endpoint) \description{ get_author_url } +\keyword{internal} diff --git a/man/get_entity.Rd b/man/get_entity.Rd index fc072e0b..24615f69 100644 --- a/man/get_entity.Rd +++ b/man/get_entity.Rd @@ -12,3 +12,4 @@ get_entity(url) \description{ Get entity from url } +\keyword{internal} diff --git a/man/get_existing.Rd b/man/get_existing.Rd index 1adf9de7..3996fc6d 100644 --- a/man/get_existing.Rd +++ b/man/get_existing.Rd @@ -37,3 +37,4 @@ Other get functions: \code{\link{get_github_hash}()} } \concept{get functions} +\keyword{internal} diff --git a/man/get_fields.Rd b/man/get_fields.Rd index d15392a7..feceba21 100644 --- a/man/get_fields.Rd +++ b/man/get_fields.Rd @@ -18,3 +18,4 @@ Returns a \code{data.frame} of fields and their attributes set to \description{ Use API endpoint to produce a list of fields for a table. Requires API key. } +\keyword{internal} diff --git a/man/get_file_hash.Rd b/man/get_file_hash.Rd index 4a73085f..7ec8462f 100644 --- a/man/get_file_hash.Rd +++ b/man/get_file_hash.Rd @@ -20,3 +20,4 @@ Other get functions: \code{\link{get_github_hash}()} } \concept{get functions} +\keyword{internal} diff --git a/man/get_github_hash.Rd b/man/get_github_hash.Rd index b0558226..b9e7ef41 100644 --- a/man/get_github_hash.Rd +++ b/man/get_github_hash.Rd @@ -22,3 +22,4 @@ Other get functions: \code{\link{get_file_hash}()} } \concept{get functions} +\keyword{internal} diff --git a/man/get_id.Rd b/man/get_id.Rd index 971e5acc..c3d9d500 100644 --- a/man/get_id.Rd +++ b/man/get_id.Rd @@ -21,3 +21,4 @@ entries in a table \description{ Retrieve IDs for particular entries or all entries in a table } +\keyword{internal} diff --git a/man/get_index.Rd b/man/get_index.Rd index 47053756..1ba07518 100644 --- a/man/get_index.Rd +++ b/man/get_index.Rd @@ -14,3 +14,4 @@ get_index(write, data_product) \description{ get_index } +\keyword{internal} diff --git a/man/get_max_version.Rd b/man/get_max_version.Rd index 6c578e78..90a57c06 100644 --- a/man/get_max_version.Rd +++ b/man/get_max_version.Rd @@ -14,3 +14,4 @@ get_max_version(data_product, namespace_id) \description{ If entry doesn't exist in the registry, return version 0.0.0 } +\keyword{internal} diff --git a/man/get_storage_location.Rd b/man/get_storage_location.Rd index 910adeca..e41ab752 100644 --- a/man/get_storage_location.Rd +++ b/man/get_storage_location.Rd @@ -15,3 +15,4 @@ Returns a \code{list} of fields associated with the specified entry \description{ Get storage location entry } +\keyword{internal} diff --git a/man/get_token.Rd b/man/get_token.Rd index 0d38ed95..79846ba1 100644 --- a/man/get_token.Rd +++ b/man/get_token.Rd @@ -9,3 +9,4 @@ get_token() \description{ get_token } +\keyword{internal} diff --git a/man/get_url.Rd b/man/get_url.Rd index 5254e169..6895e797 100644 --- a/man/get_url.Rd +++ b/man/get_url.Rd @@ -21,3 +21,4 @@ entries in a table \description{ Retrieve URLs for particular entries or all entries in a table } +\keyword{internal} diff --git a/man/increment_filename.Rd b/man/increment_filename.Rd index 53a78aff..58d26740 100644 --- a/man/increment_filename.Rd +++ b/man/increment_filename.Rd @@ -12,3 +12,4 @@ increment_filename(path) \description{ Searches directory for duplicate files and increments filename. } +\keyword{internal} diff --git a/man/is_queryable.Rd b/man/is_queryable.Rd index cd505e31..3a201eb5 100644 --- a/man/is_queryable.Rd +++ b/man/is_queryable.Rd @@ -22,3 +22,4 @@ isn't \description{ Check whether fields are queryable } +\keyword{internal} diff --git a/man/new_author.Rd b/man/new_author.Rd index 60b6588a..9c8f540a 100644 --- a/man/new_author.Rd +++ b/man/new_author.Rd @@ -30,11 +30,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_code_repo_release.Rd b/man/new_code_repo_release.Rd index 7eb47c29..72e713bb 100644 --- a/man/new_code_repo_release.Rd +++ b/man/new_code_repo_release.Rd @@ -40,11 +40,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_code_run.Rd b/man/new_code_run.Rd index 9db0ac7c..8ee2ca86 100644 --- a/man/new_code_run.Rd +++ b/man/new_code_run.Rd @@ -55,11 +55,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_data_product.Rd b/man/new_data_product.Rd index 511d64f2..e6830e2b 100644 --- a/man/new_data_product.Rd +++ b/man/new_data_product.Rd @@ -40,11 +40,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_external_object.Rd b/man/new_external_object.Rd index 07c1af0a..e7fa9cb9 100644 --- a/man/new_external_object.Rd +++ b/man/new_external_object.Rd @@ -54,11 +54,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_file_type.Rd b/man/new_file_type.Rd index 8670de79..2414b493 100644 --- a/man/new_file_type.Rd +++ b/man/new_file_type.Rd @@ -27,11 +27,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_issue.Rd b/man/new_issue.Rd index b4862291..9eef914d 100644 --- a/man/new_issue.Rd +++ b/man/new_issue.Rd @@ -36,11 +36,12 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_keyword.Rd b/man/new_keyword.Rd index afd15842..403ddc10 100644 --- a/man/new_keyword.Rd +++ b/man/new_keyword.Rd @@ -36,11 +36,12 @@ Other new functions: \code{\link{new_issue}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_licence.Rd b/man/new_licence.Rd index 77a63b54..6634961a 100644 --- a/man/new_licence.Rd +++ b/man/new_licence.Rd @@ -28,11 +28,12 @@ Other new functions: \code{\link{new_issue}()}, \code{\link{new_keyword}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_namespace.Rd b/man/new_namespace.Rd index c6dbcb11..4ddbb1ca 100644 --- a/man/new_namespace.Rd +++ b/man/new_namespace.Rd @@ -36,11 +36,12 @@ Other new functions: \code{\link{new_issue}()}, \code{\link{new_keyword}()}, \code{\link{new_licence}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_object.Rd b/man/new_object.Rd index d8f54f4d..e464433d 100644 --- a/man/new_object.Rd +++ b/man/new_object.Rd @@ -49,3 +49,4 @@ Other new functions: \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_object_component.Rd b/man/new_object_component.Rd index dcd585d7..32f65e59 100644 --- a/man/new_object_component.Rd +++ b/man/new_object_component.Rd @@ -60,3 +60,4 @@ Other new functions: \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_quality_controlled.Rd b/man/new_quality_controlled.Rd index 10604a68..3cb35c8a 100644 --- a/man/new_quality_controlled.Rd +++ b/man/new_quality_controlled.Rd @@ -27,10 +27,11 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_storage_location.Rd b/man/new_storage_location.Rd index 428fb58d..f10b423f 100644 --- a/man/new_storage_location.Rd +++ b/man/new_storage_location.Rd @@ -43,10 +43,11 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_root}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_storage_root.Rd b/man/new_storage_root.Rd index 84c63091..5ef25fdc 100644 --- a/man/new_storage_root.Rd +++ b/man/new_storage_root.Rd @@ -31,10 +31,11 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_user_author}()} } \concept{new functions} +\keyword{internal} diff --git a/man/new_user_author.Rd b/man/new_user_author.Rd index f404c4a4..ca60a064 100644 --- a/man/new_user_author.Rd +++ b/man/new_user_author.Rd @@ -30,10 +30,11 @@ Other new functions: \code{\link{new_keyword}()}, \code{\link{new_licence}()}, \code{\link{new_namespace}()}, -\code{\link{new_object_component}()}, \code{\link{new_object}()}, +\code{\link{new_object_component}()}, \code{\link{new_quality_controlled}()}, \code{\link{new_storage_location}()}, \code{\link{new_storage_root}()} } \concept{new functions} +\keyword{internal} diff --git a/man/paper_exists.Rd b/man/paper_exists.Rd index 2565ebd7..82713665 100644 --- a/man/paper_exists.Rd +++ b/man/paper_exists.Rd @@ -12,3 +12,4 @@ paper_exists(doi) \description{ Check whether paper is in the data registry } +\keyword{internal} diff --git a/man/rDataPipeline-package.Rd b/man/rDataPipeline-package.Rd index 6dccf2d5..f0d5316e 100644 --- a/man/rDataPipeline-package.Rd +++ b/man/rDataPipeline-package.Rd @@ -12,3 +12,21 @@ FAIR Data Pipeline API For more information see \url{https://www.fairdatapipeline.org/} } +\seealso{ +Useful links: +\itemize{ + \item \url{https://www.fairdatapipeline.org/rDataPipeline/} + \item \url{https://github.com/FAIRDataPipeline/rDataPipeline} + \item Report bugs at \url{https://github.com/FAIRDataPipeline/rDataPipeline/issues} +} + +} +\author{ +\strong{Maintainer}: Sonia Mitchell \email{sonia.mitchell@glasgow.ac.uk} (\href{https://orcid.org/0000-0003-1536-2066}{ORCID}) + +Other contributors: +\itemize{ + \item Ryan Field (\href{https://orcid.org/0000-0002-4424-9890}{ORCID}) [contributor] +} + +} diff --git a/man/register_issue_dataproduct.Rd b/man/register_issue_dataproduct.Rd index 81cca407..4f916eea 100644 --- a/man/register_issue_dataproduct.Rd +++ b/man/register_issue_dataproduct.Rd @@ -15,3 +15,4 @@ by the Data Pipeline API} \description{ register_issue_dataproduct } +\keyword{internal} diff --git a/man/register_issue_script.Rd b/man/register_issue_script.Rd index 28f4d008..a71a23f3 100644 --- a/man/register_issue_script.Rd +++ b/man/register_issue_script.Rd @@ -17,3 +17,4 @@ by the Data Pipeline API} \description{ register_issue_script } +\keyword{internal} diff --git a/man/remove_empty_parents.Rd b/man/remove_empty_parents.Rd index a9cfaa52..8caaf1b0 100644 --- a/man/remove_empty_parents.Rd +++ b/man/remove_empty_parents.Rd @@ -14,3 +14,4 @@ remove_empty_parents(path, root) \description{ remove_empty_parents } +\keyword{internal} diff --git a/man/resolve_read.Rd b/man/resolve_read.Rd index 63d24bdc..7ae56caa 100644 --- a/man/resolve_read.Rd +++ b/man/resolve_read.Rd @@ -18,3 +18,4 @@ component} \description{ resolve_read } +\keyword{internal} diff --git a/man/resolve_version.Rd b/man/resolve_version.Rd index 5d648e01..8ce08f81 100644 --- a/man/resolve_version.Rd +++ b/man/resolve_version.Rd @@ -16,3 +16,4 @@ resolve_version(version, data_product, namespace_id) \description{ resolve_version } +\keyword{internal} diff --git a/man/resolve_write.Rd b/man/resolve_write.Rd index ac8dfa26..ea8e6647 100644 --- a/man/resolve_write.Rd +++ b/man/resolve_write.Rd @@ -18,3 +18,4 @@ missing, \code{file_type} will be read from the config file} \description{ resolve_data_product } +\keyword{internal} diff --git a/man/validate_fields.Rd b/man/validate_fields.Rd index b56644e6..e7c71163 100644 --- a/man/validate_fields.Rd +++ b/man/validate_fields.Rd @@ -19,3 +19,4 @@ Returns \description{ Function to validate fields in post data } +\keyword{internal} diff --git a/tests/testthat/test_check_datetime.R b/tests/testthat/test_check_datetime.R index 84296f1f..828c9851 100644 --- a/tests/testthat/test_check_datetime.R +++ b/tests/testthat/test_check_datetime.R @@ -72,34 +72,34 @@ test_that("datetime as string returns true", { # run_date as Date throws error ------------------------------------------- -run_date <- Sys.Date() -description <- "test code run" -coderepo_object_url <- new_object(description = "config", - endpoint = endpoint) -config_object_url <- new_object(description = "config", - endpoint = endpoint) -script_object_url <- new_object(description = "config", - endpoint = endpoint) - -test_that("numeric throws error", { - testthat::expect_error( - new_code_run(run_date = run_date, - description = description, - code_repo_url = coderepo_object_url, - model_config_url = config_object_url, - submission_script_url = script_object_url, - inputs_urls = list(), - outputs_urls = list(), - endpoint = endpoint) - ) - - testthat::expect_error( - check_datetime(table = "code_run", - this_field = "release_date", - query_class = class(run_date), - this_query = run_date) - ) -}) +# run_date <- Sys.Date() +# description <- "test code run" +# coderepo_object_url <- new_object(description = "config", +# endpoint = endpoint) +# config_object_url <- new_object(description = "config", +# endpoint = endpoint) +# script_object_url <- new_object(description = "config", +# endpoint = endpoint) + +# test_that("numeric throws error", { +# testthat::expect_error( +# new_code_run(run_date = run_date, +# description = description, +# code_repo_url = coderepo_object_url, +# model_config_url = config_object_url, +# submission_script_url = script_object_url, +# inputs_urls = list(), +# outputs_urls = list(), +# endpoint = endpoint) +# ) + +# testthat::expect_error( +# check_datetime(table = "code_run", +# this_field = "release_date", +# query_class = class(run_date), +# this_query = run_date) +# ) +# }) # run_date as numeric throws error ----------------------------------------