Passage en version 0.0.0.9010

Introduction lifecycle, correction pour snapshot commentaires. Correction doc. Resolution #31.

DESCRIPTION

 Package: datalibaba
 Title: Interface De Connexion a Une Base Posgres Postgis
-Version: 0.0.0.9009
+Version: 0.0.0.9010
 Authors@R: 
     c(person(given = "Maël",
              family = "Theulière",
@@ -33,11 +33,14 @@ Imports:
     magrittr,
     tibble,
     units,
-    tidyr
+    tidyr,
+    lifecycle
 Suggests: 
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    backports,
+    lubridate
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -25,6 +25,7 @@ export(poster_data)
 export(set_schema_rights)
 export(standard_var_pg)
 export(transferer_table_comments)
+import(lifecycle)
 importFrom(DBI,Id)
 importFrom(DBI,dbConnect)
 importFrom(DBI,dbDisconnect)

NEWS.md

+# datalibaba (development version)
+
 # datalibaba 0.0.0.9009
 - Gestion des tables non géo dans la fonction `importer_data` : Ajout d'une ligne pour définir explicitement `query_sql_limit` dans la fonction importer_data (cas d'une table non géo).
 

R/get_data.R

@@ -91,8 +91,8 @@ importer_data <- function(table = NULL, schema = NULL, db  = "public", server =
 
 
     if ("id_row__" %in% champs$column_name) {
-      data <- dplyr::arrange(.data = data, .data$id_row__) %>%
-        dplyr::select(-.data$id_row__)
+      data <- data %>% dplyr::arrange(id_row__) %>%
+        dplyr::select(-id_row__)
     }
   }
 

R/post_data.R

@@ -274,18 +274,26 @@ post_data <- function(con,
 
 
 #' Chargement d'un dataset sur le serveur en dbi
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' Cette fonction a été dépréciée car non fonctionnelle en l'état
+#' Elle désormais équivalente à post_data et il est conseillé d'utiliser
+#' poster_data
 #'
 #' @param con Le connecteur de classe PosgreSQLConnection.
 #' @param data Un dataframe a importer.
 #' @param schema Le nom du schema sur le serveur de donnees.
 #' @param table Le nom de la table sur le serveur de donnees.
 #' @param overwrite TRUE si on veut ecraser le fichier deja present.
+#' @import lifecycle
 #' @importFrom attempt stop_if stop_if_not
 #' @importFrom DBI dbWriteTable Id
 #' @importFrom glue glue
 #'
 #' @return NULL, la fonction lance le chargement du dataset present dans l'environnement R et son ecriture sur le serveur
 #' @export
+#' @keywords internal
 #'
 
 post_data_dbi <- function(con = NULL,
@@ -293,7 +301,7 @@ post_data_dbi <- function(con = NULL,
                           schema = NULL,
                           table = NULL,
                           overwrite = FALSE) {
-  .Deprecated("poster_data")
+  lifecycle::deprecate_warn("0.0.0.9010", "post_data_dbi()", "poster_data()")
   post_data(con=con, data = data, schema = schema, table = table, overwrite = overwrite)
 
 }

README.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 
 <!-- badges: start -->
-mise_en_place_test: [![pipeline status](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/mise_en_place_test/pipeline.svg)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)[![coverage report](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/mise_en_place_test/coverage.svg?job=coverage)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)
+[![pipeline status](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/master/pipeline.svg)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)[![coverage report](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/master/coverage.svg?job=coverage)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)
 <!-- badges: end -->
 
 {datalibaba} est un ensemble de fonctions visant à faciliter l'alimentation du serveur de données du DREAL <datalab/> Pays de la Loire.

README.md

@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-mise_en_place_test: [![pipeline
-status](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/mise_en_place_test/pipeline.svg)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)[![coverage
-report](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/mise_en_place_test/coverage.svg?job=coverage)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)
+[![pipeline
+status](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/master/pipeline.svg)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)[![coverage
+report](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/badges/master/coverage.svg?job=coverage)](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)
 <!-- badges: end -->
 
 {datalibaba} est un ensemble de fonctions visant à faciliter

datalibaba.Rproj

 Version: 1.0
+ProjectId: 643276e3-9018-4b1c-85b4-c14054b6bc51
 
 RestoreWorkspace: No
 SaveWorkspace: No

dev/0_prepa_env_test.R

@@ -3,12 +3,15 @@ install.packages("odbc")
 
 if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
   con <- DBI::dbConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")
-  if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="test_datalibaba") != TRUE){
+  if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="test_datalibaba") == TRUE){
+    DBI::dbExecute(con, "DROP DATABASE IF EXISTS test_datalibaba;")
+  }
     DBI::dbExecute(con, "CREATE DATABASE test_datalibaba WITH OWNER = runner ENCODING = 'UTF8' CONNECTION LIMIT = -1;")
+    dbDisconnect(con)
     con <- DBI::dbConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="test_datalibaba")
     DBI::dbExecute(con, "CREATE EXTENSION postgis;")
     DBI::dbExecute(con, "CREATE EXTENSION postgis_topology;")
-  }
+
   #autre dbExecute si besoin de plus
   #si on veut lire un script sql mesreq.sql, le mettre dans /dev et executer
   # system(paste0("( echo dev/mesreq.sql ) | psql \"postgresql://runner:",Sys.getenv("BDD_RUNNER_PWD"),"@127.0.0.1:5432/test_datalibaba\""))

man/post_data_dbi.Rd

@@ -27,5 +27,10 @@ post_data_dbi(
 NULL, la fonction lance le chargement du dataset present dans l'environnement R et son ecriture sur le serveur
 }
 \description{
-Chargement d'un dataset sur le serveur en dbi
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
+
+Cette fonction a été dépréciée car non fonctionnelle en l'état
+Elle désormais équivalente à post_data et il est conseillé d'utiliser
+poster_data
 }
+\keyword{internal}

tests/testthat/_snaps/5-get_data.md

-# importer_data works
+# importer_data no geo works
 
     Code
       importer_data(table = "test_iris", schema = "public", db = "test_datalibaba",
@@ -15,14 +15,10 @@
       3 2025-02-27 14:29:32
       4 2025-02-27 14:29:32
 
----
+# importer_data geo works
 
     Code
       importer_data(table = "nc", schema = "public", db = "test_datalibaba", user = "test")
-    Condition
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"id_row__"` instead of `.data$id_row__`
     Output
       Simple feature collection with 100 features and 14 fields
       Geometry type: MULTIPOLYGON
@@ -58,10 +54,6 @@
     Code
       importer_data(table = "nc", schema = "public", db = "test_datalibaba", user = "test",
         limit = 4)
-    Condition
-      Warning:
-      Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
-      i Please use `"id_row__"` instead of `.data$id_row__`
     Output
       Simple feature collection with 4 features and 14 fields
       Geometry type: MULTIPOLYGON

tests/testthat/_snaps/8-commenter_champs.md → tests/testthat/_snaps/7-commenter_champs.md

-# get_table_comment works
-
-    Code
-      get_table_comment(table = "test_iris", schema = "public", db = "test_datalibaba",
-        user = "test", server = Sys.getenv("server"))
-    Output
-        nom_schema nom_table
-      1     public test_iris
-                                                                           commentaire
-      1 la table de test complete\nCommentaire posté le 27/02/2025, par edouard.morin.
-
 # get_cols_comment works
 
     Code
@@ -21,16 +10,23 @@
 # get_table_comments works
 
     Code
-      get_table_comments(table = "test_iris", schema = "public", db = "test_datalibaba",
+      get_table_comments(table = "retest_iris", schema = "public", db = "test_datalibaba",
+        user = "test", server = Sys.getenv("server"))
+    Output
+        nom_schema   nom_table                 commentaire      nom_col
+      1     public retest_iris                        <NA>         <NA>
+      2     public retest_iris libellé de Sepal.Length  cc Sepal.Length
+      3     public retest_iris  libellé de Sepal.Width  cc  Sepal.Width
+      4     public retest_iris libellé de Petal.Length  cc Petal.Length
+      5     public retest_iris  libellé de Petal.Width  cc  Petal.Width
+      6     public retest_iris      libellé de Species  cc      Species
+
+# get_table_comment works
+
+    Code
+      get_table_comment(table = "retest_iris", schema = "public", db = "test_datalibaba",
         user = "test", server = Sys.getenv("server"))
     Output
-        nom_schema nom_table
-      1     public test_iris
-      2     public test_iris
-                                                                           commentaire
-      1 la table de test complete\nCommentaire posté le 27/02/2025, par edouard.morin.
-      2                                                                Commentlibaba !
-        nom_col
-      1    <NA>
-      2 species
+        nom_schema   nom_table commentaire
+      1     public retest_iris        <NA>
 

tests/testthat/test-5-get_data.R

@@ -6,8 +6,9 @@ library(dplyr)
 library(sf)
 library(glue)
 library(backports)
+library(withr)
 
-test_that("importer_data works", {
+test_that("importer_data no geo works", {
   if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
     Sys.setenv(port="5432")
     Sys.setenv(server="localhost")
@@ -40,6 +41,22 @@ test_that("importer_data works", {
         "La table de propri\u00e9t\u00e9s des dataframes R est introuvable, un import standard sera r\u00e9alis\u00e9. ")
     # test basic
     expect_snapshot(importer_data(table = "test_iris", schema = "public", db = "test_datalibaba", user = "test", limit = 4, ecoSQL = FALSE))
+
+  }else{
+    print(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres"))
+    print('warning: connect_to_db - local database postgresql doesnt work !')
+    expect_equal(1,1)
+  }
+})
+
+test_that("importer_data geo works", {
+  withr::local_options(lifecycle_verbosity = "quiet")
+  if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
+    Sys.setenv(port="5432")
+    Sys.setenv(server="localhost")
+    Sys.setenv(user_test="runner")
+    Sys.setenv(pwd_test=Sys.getenv("BDD_RUNNER_PWD"))
+
     # test geometry # pas pris en compte dans le coverage... pourquoi ??
     expect_snapshot(importer_data(table = "nc", schema = "public", db = "test_datalibaba", user = "test"))
     expect_snapshot(importer_data(table = "nc", schema = "public", db = "test_datalibaba", user = "test", limit = 4))

tests/testthat/test-8-commenter_champs.R → tests/testthat/test-7-commenter_champs.R

@@ -66,22 +66,21 @@ test_that("post_dico_attr works", {
   }
 })
 
-test_that("get_table_comment works", {
+test_that("get_cols_comment works", {
   if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
     Sys.setenv(port="5432")
     Sys.setenv(server="localhost")
     Sys.setenv(user_test="runner")
     Sys.setenv(pwd_test=Sys.getenv("BDD_RUNNER_PWD"))
 
-    expect_error(get_table_comment(table = "test_iris", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+    expect_error(get_cols_comment(table = "test_iris", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
                  "L\'argument schema n\'est pas renseign\u00e9. ")
-    expect_error(get_table_comment(schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+    expect_error(get_cols_comment(schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
                  "L\'argument table n\'est pas renseign\u00e9. ")
-    expect_error(get_table_comment(table = "titi_test", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+    expect_error(get_cols_comment(table = "titi_test", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
                  "Il n\'y a pas de table titi_test dans le schema public. ")
 
-    expect_snapshot(get_table_comment(table = "test_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
-
+    expect_snapshot(get_cols_comment(table = "test_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
 
   }else{
     print(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres"))
@@ -90,21 +89,14 @@ test_that("get_table_comment works", {
   }
 })
 
-test_that("get_cols_comment works", {
+test_that("get_table_comments works", {
   if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
     Sys.setenv(port="5432")
     Sys.setenv(server="localhost")
     Sys.setenv(user_test="runner")
     Sys.setenv(pwd_test=Sys.getenv("BDD_RUNNER_PWD"))
 
-    expect_error(get_cols_comment(table = "test_iris", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
-                 "L\'argument schema n\'est pas renseign\u00e9. ")
-    expect_error(get_cols_comment(schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
-                 "L\'argument table n\'est pas renseign\u00e9. ")
-    expect_error(get_cols_comment(table = "titi_test", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
-                 "Il n\'y a pas de table titi_test dans le schema public. ")
-
-    expect_snapshot(get_cols_comment(table = "test_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
+    expect_snapshot(get_table_comments(table = "retest_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
 
   }else{
     print(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres"))
@@ -113,14 +105,22 @@ test_that("get_cols_comment works", {
   }
 })
 
-test_that("get_table_comments works", {
+test_that("get_table_comment works", {
   if(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres")){
     Sys.setenv(port="5432")
     Sys.setenv(server="localhost")
     Sys.setenv(user_test="runner")
     Sys.setenv(pwd_test=Sys.getenv("BDD_RUNNER_PWD"))
 
-    expect_snapshot(get_table_comments(table = "test_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
+    expect_error(get_table_comment(table = "test_iris", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+                 "L\'argument schema n\'est pas renseign\u00e9. ")
+    expect_error(get_table_comment(schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+                 "L\'argument table n\'est pas renseign\u00e9. ")
+    expect_error(get_table_comment(table = "titi_test", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")),
+                 "Il n\'y a pas de table titi_test dans le schema public. ")
+
+    expect_snapshot(get_table_comment(table = "retest_iris", schema = "public", db = "test_datalibaba", user = "test", server = Sys.getenv("server")))
+
 
   }else{
     print(DBI::dbCanConnect(RPostgres::Postgres(), host="localhost", user="runner", password=Sys.getenv("BDD_RUNNER_PWD"), dbname="postgres"))