From 1e811c46af59bebe6b883e1d87e3eed1a36cc3cd Mon Sep 17 00:00:00 2001
From: MORIN Edouard <edouard.morin@developpement-durable.gouv.fr>
Date: Fri, 28 Feb 2025 16:49:54 +0100
Subject: [PATCH] Passage en version 0.0.0.9010 Introduction lifecycle,
correction pour snapshot commentaires. Correction doc. Resolution #31.
---
DESCRIPTION | 9 +++--
NAMESPACE | 1 +
NEWS.md | 2 ++
R/get_data.R | 4 +--
R/post_data.R | 10 +++++-
README.Rmd | 2 +-
README.md | 6 ++--
datalibaba.Rproj | 1 +
dev/0_prepa_env_test.R | 7 ++--
man/post_data_dbi.Rd | 7 +++-
tests/testthat/_snaps/5-get_data.md | 12 ++-----
tests/testthat/_snaps/7-commenter_champs.md | 32 +++++++++++++++++
tests/testthat/_snaps/8-commenter_champs.md | 36 -------------------
tests/testthat/test-5-get_data.R | 19 +++++++++-
...ter_champs.R => test-7-commenter_champs.R} | 34 +++++++++---------
...enter_table.R => test-8-commenter_table.R} | 0
16 files changed, 105 insertions(+), 77 deletions(-)
create mode 100644 tests/testthat/_snaps/7-commenter_champs.md
delete mode 100644 tests/testthat/_snaps/8-commenter_champs.md
rename tests/testthat/{test-8-commenter_champs.R => test-7-commenter_champs.R} (96%)
rename tests/testthat/{test-7-commenter_table.R => test-8-commenter_table.R} (100%)
diff --git a/DESCRIPTION b/DESCRIPTION
index d1391f6..b247759 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
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)
diff --git a/NAMESPACE b/NAMESPACE
index 322fcd2..545021e 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/NEWS.md b/NEWS.md
index 6b7029f..f6861a7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# 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).
diff --git a/R/get_data.R b/R/get_data.R
index 4393608..d24924a 100644
--- a/R/get_data.R
+++ b/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$id_row__)
+ data <- data %>% dplyr::arrange(id_row__) %>%
+ dplyr::select(-id_row__)
}
}
diff --git a/R/post_data.R b/R/post_data.R
index ea70036..fd10ece 100644
--- a/R/post_data.R
+++ b/R/post_data.R
@@ -274,18 +274,26 @@ post_data <- function(con,
#' Chargement d'un dataset sur le serveur en dbi
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' Cette fonction a été dépréciée car non fonctionnelle en l'état
+#' Elle désormais équivalente à post_data et il est conseillé d'utiliser
+#' poster_data
#'
#' @param con Le connecteur de classe PosgreSQLConnection.
#' @param data Un dataframe a importer.
#' @param schema Le nom du schema sur le serveur de donnees.
#' @param table Le nom de la table sur le serveur de donnees.
#' @param overwrite TRUE si on veut ecraser le fichier deja present.
+#' @import lifecycle
#' @importFrom attempt stop_if stop_if_not
#' @importFrom DBI dbWriteTable Id
#' @importFrom glue glue
#'
#' @return NULL, la fonction lance le chargement du dataset present dans l'environnement R et son ecriture sur le serveur
#' @export
+#' @keywords internal
#'
post_data_dbi <- function(con = NULL,
@@ -293,7 +301,7 @@ post_data_dbi <- function(con = NULL,
schema = NULL,
table = NULL,
overwrite = FALSE) {
- .Deprecated("poster_data")
+ lifecycle::deprecate_warn("0.0.0.9010", "post_data_dbi()", "poster_data()")
post_data(con=con, data = data, schema = schema, table = table, overwrite = overwrite)
}
diff --git a/README.Rmd b/README.Rmd
index 2d87b99..f768b77 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
<!-- badges: start -->
-mise_en_place_test: [](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)[](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.
diff --git a/README.md b/README.md
index 9e1c294..e30c7ab 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,9 @@
<!-- badges: start -->
-mise_en_place_test: [](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/mise_en_place_test)
+[](https://gitlab-forge.din.developpement-durable.gouv.fr/dreal-pdl/csd/datalibaba/-/commits/master)[](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
diff --git a/datalibaba.Rproj b/datalibaba.Rproj
index 69fafd4..8a479e3 100644
--- a/datalibaba.Rproj
+++ b/datalibaba.Rproj
@@ -1,4 +1,5 @@
Version: 1.0
+ProjectId: 643276e3-9018-4b1c-85b4-c14054b6bc51
RestoreWorkspace: No
SaveWorkspace: No
diff --git a/dev/0_prepa_env_test.R b/dev/0_prepa_env_test.R
index c62f82d..b0523ac 100644
--- a/dev/0_prepa_env_test.R
+++ b/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\""))
diff --git a/man/post_data_dbi.Rd b/man/post_data_dbi.Rd
index 41cdd26..b703afe 100644
--- a/man/post_data_dbi.Rd
+++ b/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}
diff --git a/tests/testthat/_snaps/5-get_data.md b/tests/testthat/_snaps/5-get_data.md
index 78ea15e..329e3d1 100644
--- a/tests/testthat/_snaps/5-get_data.md
+++ b/tests/testthat/_snaps/5-get_data.md
@@ -1,4 +1,4 @@
-# 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
diff --git a/tests/testthat/_snaps/7-commenter_champs.md b/tests/testthat/_snaps/7-commenter_champs.md
new file mode 100644
index 0000000..c84818e
--- /dev/null
+++ b/tests/testthat/_snaps/7-commenter_champs.md
@@ -0,0 +1,32 @@
+# get_cols_comment works
+
+ Code
+ get_cols_comment(table = "test_iris", schema = "public", db = "test_datalibaba",
+ user = "test", server = Sys.getenv("server"))
+ Output
+ nom_schema nom_table nom_col commentaire
+ 1 public test_iris species Commentlibaba !
+
+# get_table_comments works
+
+ Code
+ 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 commentaire
+ 1 public retest_iris <NA>
+
diff --git a/tests/testthat/_snaps/8-commenter_champs.md b/tests/testthat/_snaps/8-commenter_champs.md
deleted file mode 100644
index 46dc530..0000000
--- a/tests/testthat/_snaps/8-commenter_champs.md
+++ /dev/null
@@ -1,36 +0,0 @@
-# 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
- get_cols_comment(table = "test_iris", schema = "public", db = "test_datalibaba",
- user = "test", server = Sys.getenv("server"))
- Output
- nom_schema nom_table nom_col commentaire
- 1 public test_iris species Commentlibaba !
-
-# get_table_comments works
-
- Code
- get_table_comments(table = "test_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
-
diff --git a/tests/testthat/test-5-get_data.R b/tests/testthat/test-5-get_data.R
index a833384..3b1f138 100644
--- a/tests/testthat/test-5-get_data.R
+++ b/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))
diff --git a/tests/testthat/test-8-commenter_champs.R b/tests/testthat/test-7-commenter_champs.R
similarity index 96%
rename from tests/testthat/test-8-commenter_champs.R
rename to tests/testthat/test-7-commenter_champs.R
index adc6e4c..ca40328 100644
--- a/tests/testthat/test-8-commenter_champs.R
+++ b/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"))
diff --git a/tests/testthat/test-7-commenter_table.R b/tests/testthat/test-8-commenter_table.R
similarity index 100%
rename from tests/testthat/test-7-commenter_table.R
rename to tests/testthat/test-8-commenter_table.R
--
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