Merge pull request #58 from NorwegianVeterinaryInstitute/dev

NVIdb v0.11.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Tools to facilitate the use of NVI's databases
-Version: 0.11.1
-Date: 2024-02-05
+Version: 0.11.2
+Date: 2024-04-05
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -63,7 +63,7 @@ LazyData: true
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = FALSE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: 
     knitr,
     R.rsp

NEWS

@@ -1,3 +1,22 @@
+NVIdb 0.11.2 - (2024-04-05)
+----------------------------------------
+
+Bug fixes:
+
+- `retrieve_PJSdata` now accepts input for `selection_parameters` that includes `FUN` and `selection_statement`.
+
+- `set_disease_parameters` now accepts input for `selection_parameters` that includes `FUN`. 
+
+
+BREAKING CHANGES:
+
+- For `retrieve_PJSdata`, the arguments `FUN` and `select_statement` are deprecated. These should instead be included in the list input to `selection_parameters`. See NVIdb-deprecated (help("NVIdb-deprecated")).
+
+- The wrapper functions `login_EOS`, `login_by_input_EOS`, and `login_by_credentials_EOS` are deprecated. Use the corresponding login-functions with the argument `dbservice` = "EOS" instead. See NVIdb-deprecated (help("NVIdb-deprecated")).
+
+- The wrapper function `set_credentials_EOS` is deprecated. Use `set_credentials("EOS")` instead. See NVIdb-deprecated (help("NVIdb-deprecated")).
+
+
 NVIdb 0.11.1 - (2024-02-05)
 ----------------------------------------
 
@@ -41,9 +60,9 @@ Other changes:
 
 BREAKING CHANGES:
 
-- In `set_disease_parameters` the arguments `missing_art` and `file` is deprecated. These are replaced by `include_missing_art` and `selection_parameters`, respectively. If using the old arguments, the input will be transferred to the new arguments. 
+- In `set_disease_parameters` the arguments `missing_art` and `file` is deprecated. These are replaced by `include_missing_art` and `selection_parameters`, respectively. If using the old arguments, the input will be transferred to the new arguments. See NVIdb-deprecated (help("NVIdb-deprecated")).
 
-- `set_PAT`, `get_PAT`, and `remove_PAT` was deprecated.These should be replaced by corresponding functions in package `gitcreds`.
+- `set_PAT`, `get_PAT`, and `remove_PAT` was deprecated.These should be replaced by corresponding functions in package `gitcreds`. See NVIdb-deprecated (help("NVIdb-deprecated")).
 
 
 NVIdb 0.10.1 - (2023-05-31)

R/NVIdb-deprecated.R

@@ -6,16 +6,39 @@
 #' @details \code{add_produsent} was deprecated from v0.8.0 released 2022-08-25
 #'     as other properties
 #'     than 'gjeldende_prodnr8' could not be included without breaking backward
-#'     compatibility. Use \code{add_produsent_properties} instead and ensure
+#'     compatibility. Use \code{\link{add_produsent_properties}} instead and ensure
 #'     to set the parameter \code{impute_old_when_missing = TRUE} when translating
 #'     from "prodnr8" to "gjeldende_prodnr8" and set the parameter
 #'     \code{impute_old_when_missing = FALSE} when translating from "prodnr8" to
 #'     other properties.
 #'
 #' \code{set_PAT}, \code{get_PAT}, and \code{remove_PAT} was deprecated from
-#'     v0.11.0 released 2023-09-22. The functions were never taken into use.
+#'     v0.11.0 released 2024-01-24. The functions were never taken into use.
 #'     Functions from the much better package \code{gitcreds} should be used instead.
 #'
+#' The arguments \code{missing_art} and \code{file} in \code{set_disease_parameters}
+#'     was deprecated from v0.11.0 released 2024-01-24. These arguments are 
+#'     replaced by the more meaningful \code{include_missing_art} and 
+#'     \code{selection_parameters}, respectively. If using the old arguments, 
+#'     the input will be transferred to the new arguments. 
+#'     
+#' \code{login_EOS}, \code{login_by_input_EOS}, and \code{login_by_credentials_EOS}
+#'     was deprecated from v0.##.# released 2024-##-##. The functions were rarely
+#'     used and are unnecessary wrappers around the login-functions. The
+#'     login-functions with the argument \code{dbservice} = "EOS" should be used
+#'     instead, see \code{\link{login}}.
+#'
+#' \code{set_credentials_EOS} was deprecated from v0.##.# released 2024-##-##.
+#'     The function was rarely used and is an unnecessary wrapper around
+#'      \code{set_credentials}. \code{\link{set_credentials}} with the argument
+#'      \code{dbservice} = "EOS" should be used instead.
+#'
+#' The arguments \code{FUN} and \code{selection_statement} in \code{retrieve_PJSdata}
+#'     was deprecated from v0.##.# released 2024-##-##. These arguments should 
+#'     instead be included in the list input to \code{selection_parameters}. If
+#'     using the old arguments, the input will be transferred to 
+#'     \code{selection_parameters}. 
+#'     
 #' @param \dots (arguments)
 #' @return (results)
 #' @name NVIdb-deprecated
@@ -25,9 +48,13 @@
 #'
 #' @examples
 #' \dontrun{
-#' add_produsent(...) ### -- use \code{\link{add_produsent_properties}} instead.
-#' set_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_set}} instead.
-#' get_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_get}} instead.
-#' remove_PAT(...) ### -- use \code{\link{gitcreds::gitcreds_delete}} instead.
+#' add_produsent(...) ### -- use add_produsent_properties() instead.
+#' set_PAT(...) ### -- use gitcreds::gitcreds_set() instead.
+#' get_PAT(...) ### -- use gitcreds::gitcreds_get() instead.
+#' remove_PAT(...) ### -- use gitcreds::gitcreds_delete() instead.
+#' login_EOS(...) ### -- use login("EOS") instead.
+#' login_by_input_EOS(...) ### -- use login_by_input("EOS") instead.
+#' login_by_credentials_EOS(...) ### -- use login_by_credentials("EOS") instead.
+#' set_credentials_EOS(...) ### -- use set_credentials("EOS") instead.
 #' }
 NULL

R/login.R

@@ -1,52 +1,53 @@
 #' @title Log in to data base services
-#' @description  Log in to NVI's data base services, in particular journal_rapp/PJS and EOS.
+#' @description  Log in to NVI's data base services, in particular journal_rapp/PJS.
 #' @details The NVI has access to several database services. These functions log
 #'     in to such services. The functions provides methods to either log in using
 #'     credentials set in the user profile by \code{\link{set_credentials}} or use
 #'     input windows for username and password. Thereby the hard coding of
 #'     username and password can be avoided.
 #'
-#'     \code{login} is general functions where all necessary specifications like
-#'     server name and database name of the database must be input. The database
-#'     provider can give information on what specifications that has to be used.
-#'     This can be used to log in to many different databases. In the case that
-#'     one login to a database service for which the connection parameters have
-#'     been predefined (i.e. PJS, EOS, sea_sites and Fallvilt), it will be sufficient
-#'     to provide the parameter \code{dbservice =}.
+#'     \code{login} is a general function for connecting to databases, where all
+#'     necessary connection parameters like server name and database name of the
+#'     database must be input. The database provider can inform you on the
+#'     connection parameters for their database. In the case that one login to
+#'     a database service for which the connection parameters have been predefined
+#'     (i.e. PJS, EOS, sea_sites, Fallvilt and Dataflex), it will be sufficient
+#'     to provide the parameter \code{dbservice}, for example \code{dbservice} =
+#'     "EOS".
 #'
 #'     Depending on whether username and password have been saved in the users
 #'     profile at the current computer or not, the user is asked to input credentials.
 #'
-#'     \code{login_by_input} is general functions where all necessary
-#'     specifications like server name and database name of the database must be
-#'     input. In the case that one login to a database service for which the
-#'     connection parameters have been predefined (i.e. PJS, EOS, sea_sites and
-#'     Fallvilt), it will be sufficient to provide the parameter \code{dbservice =}.
-#'     The user is always asked to input username and password.
+#'     \code{login_by_input} is a general function for connecting to databases,
+#'     where all necessary connection parameters like server name and database name
+#'     of the database must be input. The database provider can inform you on the
+#'     connection parameters for their database. In the case that one login to
+#'     a database service for which the connection parameters have been predefined
+#'     (i.e. PJS, EOS, sea_sites, Fallvilt and Dataflex), it will be sufficient
+#'     to provide the parameter \code{dbservice}. The user is always asked to input
+#'     username and password.
 #'
-#'     \code{login_by_credentials} is general functions where all necessary
-#'     specifications like server name and database name of the database must be
-#'     input. In the case that one login to a database service for which the
-#'     connection parameters have been predefined (i.e. PJS, EOS, sea_sites and
-#'     Fallvilt), it will be sufficient to provide the parameter \code{dbservice =}.
-#'     The user is never asked for username and password, and the function can
-#'     only be used when the credentials previously have been set in the user's
-#'     profile at the current computer.
+#'     \code{login_by_credentials} is a general function for connecting to databases,
+#'     where all necessary connection parameters like server name and database name
+#'     of the database must be input. The database provider can inform you on the
+#'     connection parameters for their database. In the case that one login to
+#'     a database service for which the connection parameters have been predefined
+#'     (i.e. PJS, EOS, sea_sites, Fallvilt and Dataflex), it will be sufficient
+#'     to provide the parameter \code{dbservice}. The user is never asked for username
+#'     and password, and the function can only be used when the credentials previously
+#'     have been set in the user's profile at the current computer.
 #'
 #'     \code{login_PJS}, \code{login_by_input_PJS}, and \code{login_by_credentials_PJS}
 #'     are wrappers for the functions above where the specifications for the
-#'     database journal_rapp/PJS have been preset. The user only need to input
+#'     database journal_rapp/PJS have been pre set. The user only need to input
 #'     username and password. In the case that the username and password for
 #'     journal_rapp/PJS have been stored in the user profile at the current
 #'     computer, the user is automatically logged in to journal_rapp. If the
 #'     password is no longer valid, an error occur. If so, the user must update
 #'     the username and password by \code{\link{set_credentials_PJS}}.
 #'
-#'     \code{login_EOS}, \code{login_by_input_EOS}, and \code{login_by_credentials_EOS}
-#'     are wrappers for the functions above where the specifications for the
-#'     database EOS have been preset. The user only need to input username and
-#'     password or if the credentials are saved in the users profile by
-#'     \code{\link{set_credentials_EOS}}, no input is needed.
+#'     The wrapper functions \code{login_EOS}, \code{login_by_input_EOS}, and
+#'     \code{login_by_credentials_EOS} have been deprecated.
 #'
 #'     The login functions returns an open ODBC-channel to the database service.
 #'     The database can then be queried by using functions in the package used for
@@ -55,31 +56,39 @@
 #'     \code{RODBC} for "SQL server" and \code{RPostgreSQL} for "PostgreSQL".
 #'
 #'     When the session is finished, the script shall close the ODBC-channel by
-#'     \code{odbcClose("myodbcchannel")} or \code{odbcCloseAll}.
+#'     \code{odbcClose("myodbcchannel")} or \code{odbcCloseAll} when using RODBC.
 #'
-#' @param dbservice Name of the database service, for example "PJS" or "EOS".
+#' @param dbservice [\code{character(1)}]\cr
+#' Name of the database service, for example "PJS" or "EOS".
 #'     For database services where one don't use the premade wrappers, the name
 #'     can be chosen freely, but must be the same as used in \code{\link{set_credentials}}.
-#' @param dbdriver Name of database engine.
-#' @param db Name of database.
-#' @param dbserver Name of database server.
-#' @param dbport Port.
-#' @param dbprotocol Protocol to be used.
-#' @param dbinterface The R-package that is used for interface towards the data
-#'     base.
-#' @param dbtext used in login with input. Gives the possibility of showing
-#'     another name than the dbservice in the windows asking for username and
-#'     password.
+#' @param dbdriver [\code{character(1)}]\cr
+#' Name of database engine. Defaults to \code{NULL}.
+#' @param db [\code{character(1)}]\cr
+#' Name of database. Defaults to \code{NULL}.
+#' @param dbserver [\code{character(1)}]\cr
+#' Name of database server. Defaults to \code{NULL}.
+#' @param dbport [\code{character(1)}]\cr
+#' Port. Defaults to \code{NULL}.
+#' @param dbprotocol [\code{character(1)}]\cr
+#' Protocol to be used. Defaults to \code{NULL}.
+#' @param dbinterface [\code{character(1)}]\cr
+#' The R-package that is used for interface towards the data
+#'     base. Defaults to \code{NULL}.
+#' @param dbtext [\code{character(1)}]\cr
+#' Gives the possibility of showing another name than the dbservice
+#'     in the windows asking for username and password when using
+#'     \code{login_by_input}. Defaults to \code{NULL}.
 #' @param \dots Other arguments to be passed from the wrappers to
-#'     login_by_credentials or login_by_input
+#'     \code{login_by_credentials} or \code{login_by_input}.
 #' @return An open ODBC-channel to the database service.
 #' @family Log in functions
 #' @seealso  \code{\link{set_credentials}}
 #' @author Petter Hopp Petter.Hopp@@vetinst.no
 #' @export
 #' @examples
 #' \dontrun{
-#' require(RODBC)
+#' library(RODBC)
 #' journal_rapp <- login_PJS()
 #' # Reads hensiktregistret from PJS
 #' hensikter <- sqlQuery(journal_rapp,
@@ -240,32 +249,3 @@ login_PJS <- function(dbinterface = NULL, ...) {
     login_by_input(dbservice, dbinterface = dbinterface, ...)
   }
 }
-
-
-#' @export
-#' @rdname login
-
-login_EOS <- function(dbinterface = NULL, ...) {
-
-  # ARGUMENT CHECKING ----
-  # Object to store check-results
-  checks <- checkmate::makeAssertCollection()
-
-  # dbinterface
-  checkmate::assert_choice(dbinterface, choices = c("odbc", "RPostgreSQL", "RODBC"), null.ok = TRUE, add = checks)
-
-  # Report check-results
-  checkmate::reportAssertions(checks)
-
-  # Set service to EOS
-  dbservice <- "EOS"
-
-  # Use check for saved credentials to chose between login_by_input and login_by_credentials
-  if (isTRUE(NVIcheckmate::check_credentials(dbservice))) {
-    # If credentials are saved for the user profile
-    login_by_credentials(dbservice, dbinterface = dbinterface, ...)
-  } else {
-    # If credentials are missing from the user profile
-    login_by_input(dbservice, dbinterface = dbinterface, ...)
-  }
-}