diff --git a/NAMESPACE b/NAMESPACE index abdc679de..035149570 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -54,12 +54,10 @@ S3method(set_keys,TealDataAbstract) S3method(set_keys,TealDataset) S3method(set_keys,TealDatasetConnector) S3method(to_relational_data,MultiAssayExperiment) -S3method(to_relational_data,TealData) S3method(to_relational_data,TealDataset) S3method(to_relational_data,TealDatasetConnector) S3method(to_relational_data,data.frame) S3method(to_relational_data,list) -S3method(to_relational_data,teal_data) export("col_labels<-") export("data_label<-") export(as_cdisc) diff --git a/man/ddl.Rd b/man/ddl.Rd deleted file mode 100644 index e985cfcb5..000000000 --- a/man/ddl.Rd +++ /dev/null @@ -1,64 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ddl.R -\name{ddl} -\alias{ddl} -\title{DDL object} -\usage{ -ddl( - code, - ui = submit_button_ui, - server = submit_button_server, - offline_args = list(), - postprocess_fun = function(env_list, code, join_keys) { - - do.call(teal.data::teal_data, args = c(env_list, code = code, join_keys = - join_keys)) - }, - join_keys = teal.data::join_keys(), - datanames -) -} -\arguments{ -\item{code}{(\code{character})\cr -Code to be evaluated and returned to the \code{postprocess_fun}} - -\item{ui}{(\code{shiny.tag})\cr -\code{shiny} ui module containing inputs which \code{id} correspond to the -args in the \code{code}.} - -\item{server}{(\verb{function(id, offline_args, code, postprocess_fun)})\cr -\code{shiny} server module returning data. This server suppose to execute -DDL code and return a reactive data containing necessary data. -Package provides universal \code{username_password_server} which -runs \link{ddl_run} function, which returns \code{tdata} object. -Details in the the example} - -\item{offline_args}{(\code{list} named)\cr -arguments to be substituted in the \code{code}. These -argument are going to replace arguments set through -\code{ui} and \code{server}. Example use case is when app user -is asked to input a password and we'd like to skip this -input in the reproducible code. Typically users password -is substituted with \code{askpass::askpass()} call, so the -returned code is still executable but secure.} - -\item{postprocess_fun}{(\verb{function(env, code)})\cr -Function to be run after code is run. This function suppose -has two arguments: -\itemize{ -\item \code{env} (\code{environment}) returned as a result of the code evaluation -\item code (\code{character}) \code{code} provided with resolved (substituted) args. -}} - -\item{join_keys}{(\code{JoinKeys}) or a single (\code{JoinKeySet})\cr -(optional) object with dataset column relationships used for joining. -If empty then no joins between pairs of objects} - -\item{datanames}{(\code{character})\cr -Names of the objects to be created from the code evaluation. -If not specified (\code{character(0)}), all objects will be used to \code{teal_data} function -(via \code{env_list} in \code{postprocess_fun}).} -} -\description{ -Object to execute custom DDL code in the shiny session -} diff --git a/man/ddl_eval_substitute.Rd b/man/ddl_eval_substitute.Rd deleted file mode 100644 index c97786cdc..000000000 --- a/man/ddl_eval_substitute.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ddl.R -\name{ddl_eval_substitute} -\alias{ddl_eval_substitute} -\title{Substitute and evaluate ddl code} -\usage{ -ddl_eval_substitute(code, args) -} -\arguments{ -\item{code}{(\code{character})\cr -Code to be evaluated and returned to the \code{postprocess_fun}} - -\item{args}{(\code{list} named)\cr -Containing elements named after arguments in the code -enclosed in currly brackets ex. \code{{ arg_name }}} -} -\value{ -\code{list} of objects being a result of the code evaluation -} -\description{ -Substitute and evaluate ddl code -} -\examples{ -ddl_eval_substitute("x <- { arg }", list(arg = 1)) -ddl_eval_substitute("x <- { arg }", list(arg = "a")) -ddl_eval_substitute("a <- 1; x <- { arg } + 1", list(arg = quote(a))) -ddl_eval_substitute("a <- b", list(b = 1)) -} diff --git a/man/ddl_run.Rd b/man/ddl_run.Rd deleted file mode 100644 index 1c1f9f887..000000000 --- a/man/ddl_run.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ddl.R -\name{ddl_run} -\alias{ddl_run} -\title{Creates \code{tdata} object} -\usage{ -ddl_run(x, online_args = list()) -} -\arguments{ -\item{online_args}{(\code{list} named)\cr -Arguments to be substituted in the \code{code} and evaluated. Result of the evaluation -is based on the provided (dynamic) arguments.} -} -\value{ -\code{tdata} containing objects created: -\itemize{ -\item \code{env} created by the \code{code} substitution and evaluation using -\code{online_args}, while the \code{code}. -\item \code{code} with substituted `offline_args. -\item \code{join_keys} specified in the \code{ddl} object. -} -} -\description{ -Resolves arguments and executes custom DDL \code{code}. -Custom \code{code} is substituted by \code{online_args} and evaluated. Then obtained code is -substituted again by \code{offline_args} and passed to the \code{postprocess_fun}. -} diff --git a/man/glue_code.Rd b/man/glue_code.Rd deleted file mode 100644 index 65290e2d8..000000000 --- a/man/glue_code.Rd +++ /dev/null @@ -1,36 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ddl.R -\name{glue_code} -\alias{glue_code} -\title{Substitute ddl code args} -\usage{ -glue_code(code, args) -} -\arguments{ -\item{code}{(\code{character})\cr -Code to be evaluated and returned to the \code{postprocess_fun}} - -\item{args}{(\code{list} named)\cr -Containing elements named after arguments in the code -enclosed in currly brackets ex. \code{{ arg_name }}} -} -\value{ -\code{character} -} -\description{ -Substitutes code arguments with \code{args}. Parts of the code -wrapped in curly brackets ex. \code{{ arg_name }} are replaced -with corresponding list elements -} -\examples{ -glue_code("x <- { arg }", list(arg = 1)) -glue_code("x <- { arg }", list(arg = "a")) -glue_code("a <- 1; x <- { arg } + 1", list(arg = quote(a))) -glue_code( - "a <- connect(login = { login }, password = { pass})", - list( - login = quote(askpass::askpass()), - password = quote(askpass::askpass()) - ) -) -} diff --git a/man/new_tdata.Rd b/man/new_tdata.Rd deleted file mode 100644 index 106a6ea84..000000000 --- a/man/new_tdata.Rd +++ /dev/null @@ -1,31 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/tdata.R -\name{new_tdata} -\alias{new_tdata} -\alias{new_tdata,list,expression-method} -\alias{new_tdata,list,language-method} -\alias{new_tdata,list,character-method} -\title{Initialize \code{tdata} object} -\usage{ -new_tdata(env = new.env(), code = expression(), keys = join_keys()) - -\S4method{new_tdata}{list,expression}(env = new.env(), code = expression(), keys = join_keys()) - -\S4method{new_tdata}{list,language}(env = new.env(), code = expression(), keys = join_keys()) - -\S4method{new_tdata}{list,character}(env = new.env(), code = expression(), keys = join_keys()) -} -\arguments{ -\item{env}{(\code{list}) List of data.} - -\item{code}{(\code{character(1)} or \code{language}) code to evaluate. Accepts and stores comments also.} -} -\description{ -Initialize \code{tdata} object. -} -\examples{ -new_tdata(env = list(a = 1), code = quote(a <- 1)) -new_tdata(env = list(a = 1), code = parse(text = "a <- 1")) -new_tdatas(env = list(a = 1), code = "a <- 1") - -}