Merge pull request #71 from sidora-tools/new-columns-apr24-site-extract

New columns since Apri 2023
sidora-tools · May 2, 2024 · 4146a51 · 4146a51
2 parents 8d4603f + 6abf721
commit 4146a51
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Showing 14 changed files with 29 additions and 12 deletions.
diff --git a/.github/workflows/check-release.yaml b/.github/workflows/check-release.yaml
@@ -35,7 +35,6 @@ jobs:
         with:
           extra-packages: |
             rcmdcheck
-            covr
 
       - name: Check
         env:
@@ -45,7 +44,3 @@ jobs:
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sidora.core
-Title: Basic Interface for PANDORA (MPI-SHH DAG)
-Version: 2.4.0
+Title: Basic Interface for PANDORA (MPI-EVA DAG)
+Version: 2.4.1
 Authors@R: 
     c(person(given = "Clemens",
            family = "Schmid",
@@ -42,4 +42,4 @@ Imports:
   utils
 Suggests: 
   testthat (>= 3.0.0)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# sidora 2.4.1 - 2024-05-02
+
+## Changes in columns/tables
+
+TAB_Site: +Master_Site_Id
+TAB_Individual: +Main_Individual_Id, +Publication, +Exclude
+TAB_Sample: +Exclude
+TAB_Extract: +CoreDB_Subsample_Id, +Exclude
+TAB_Library: +Concentration_Post_Plateau_Indexing, +Exclude
+TAB_Capture: +Exclude
+TAB_Sequencing: +Exclude
+
 # sidora 2.4.0 - 2023-04-21
 
 ## New features

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.md b/README.md
@@ -1,5 +1,4 @@
 [![R-CMD-check](https://github.com/sidora-tools/sidora.core/actions/workflows/check-release.yaml/badge.svg?style=for-the-badge&logo=appveyor)](https://github.com/sidora-tools/sidora.core/actions/workflows/check-release.yaml)
-[![Coverage Status](https://img.shields.io/codecov/c/github/sidora-tools/sidora.core/master.svg?style=for-the-badge&logo=appveyor)](https://codecov.io/github/sidora-tools/sidora.core?branch=master)
 ![GitHub R package version](https://img.shields.io/github/r-package/v/sidora-tools/sidora.core)
 
 # sidora.core

diff --git a/data-raw/pandora_column_types.tsv b/data-raw/pandora_column_types.tsv
@@ -78,6 +78,7 @@ TAB_Index_Set_P7	index_p7	Index	character	NA	NA	NA
 TAB_Index_Set_P7	index_p7	Sequence	character	NA	NA	NA
 TAB_Site	site	Id	integer	NA	NA	NA
 TAB_Site	site	Site_Id	character	NA	NA	mandatory
+TAB_Site	site	Master_Site_Id	integer	NA	NA	optional
 TAB_Site	site	Full_Site_Id	character	NA	NA	NA
 TAB_Site	site	Name	character	NA	NA	mandatory
 TAB_Site	site	Worker	integer	TAB_User	Name	mandatory
@@ -100,9 +101,11 @@ TAB_Individual	individual	Id	integer	NA	NA	NA
 TAB_Individual	individual	Site	integer	NA	NA	NA
 TAB_Individual	individual	Individual_Id	integer	NA	NA	mandatory
 TAB_Individual	individual	Full_Individual_Id	character	NA	NA	NA
+TAB_Individual	individual	Main_Individual_Id	integer	NA	NA	NA	optional
 TAB_Individual	individual	Institution_of_Origin	integer	TAB_Owner	Name	mandatory
 TAB_Individual	individual	Contact_Person	character	NA	NA	optional
 TAB_Individual	individual	Provenience	character	NA	NA	optional
+TAB_Individual	individual	Publication	character	NA	NA	optional
 TAB_Individual	individual	Worker	integer	TAB_User	Name	mandatory
 TAB_Individual	individual	Creation_Date	datetime	NA	NA	optional
 TAB_Individual	individual	Organism	integer	TAB_Organism	Name	mandatory
@@ -139,6 +142,7 @@ TAB_Individual	individual	Files	integer	NA	NA	optional
 TAB_Individual	individual	Notes	character	NA	NA	optional
 TAB_Individual	individual	Tags	character	NA	NA	optional
 TAB_Individual	individual	Projects	character	NA	NA	optional
+TAB_Individual	individual	Exclude	yesno_logical	NA	NA	NA	optional
 TAB_Individual	individual	Deleted	logical	NA	NA	NA
 TAB_Individual	individual	Deleted_Date	datetime	NA	NA	NA
 TAB_Sample	sample	Id	integer	NA	NA	NA
@@ -169,6 +173,7 @@ TAB_Sample	sample	Deleted	logical	NA	NA	NA
 TAB_Sample	sample	Deleted_Date	datetime	NA	NA	NA
 TAB_Sample	sample	CoreDB_Id	character	NA	NA	optional
 TAB_Sample	sample	CT_scanned	yesno_logical	NA	NA	optional
+TAB_Sample	sample	Exclude	yesno_logical	NA	NA	NA	optional
 TAB_Extract	extract	Id	integer	NA	NA	NA
 TAB_Extract	extract	Sample	integer	NA	NA	NA
 TAB_Extract	extract	Extract_Id	character	NA	NA	mandatory
@@ -195,6 +200,8 @@ TAB_Extract	extract	Deleted	logical	NA	NA	NA
 TAB_Extract	extract	Deleted_Date	datetime	NA	NA	NA
 TAB_Extract	extract	CoreDB_Id	character	NA	NA	optional
 TAB_Extract	extract	CoreDB_Lysate_Id	character	NA	NA	optional
+TAB_Extract	extract	CoreDB_Subsample_Id	character	NA	NA	optional
+TAB_Extract	extract	Exclude	yesno_logical	NA	NA	NA	optional
 TAB_Library	library	Id	integer	NA	NA	NA
 TAB_Library	library	Extract	integer	NA	NA	NA
 TAB_Library	library	Library_Id	integer	NA	NA	mandatory
@@ -218,6 +225,7 @@ TAB_Library	library	Quantification_pre-Indexing_total	big_integer	NA	NA	optional
 TAB_Library	library	Quantification_post-Indexing_total	big_integer	NA	NA	optional
 TAB_Library	library	Efficiency_Factor	double	NA	NA	optional
 TAB_Library	library	Post-Indexing_elution_volume	integer	NA	NA	optional
+TAB_Library	library	Concentration_Post_Plateau_Indexing	double	NA	NA	optional
 TAB_Library	library	External_Library_Id	character	NA	NA	optional
 TAB_Library	library	Position_on_Plate	character	NA	NA	optional
 TAB_Library	library	Location_Room	integer	TAB_Location_Room	Name	optional
@@ -230,6 +238,7 @@ TAB_Library	library	Projects	character	NA	NA	optional
 TAB_Library	library	Deleted	logical	NA	NA	NA
 TAB_Library	library	Deleted_Date	datetime	NA	NA	NA
 TAB_Library	library	CoreDB_Id	character	NA	NA	optional
+TAB_Library	library	Exclude	yesno_logical	NA	NA	optional
 TAB_Capture	capture	Id	integer	NA	NA	NA
 TAB_Capture	capture	Library	integer	NA	NA	NA
 TAB_Capture	capture	Capture_Id	character	NA	NA	mandatory
@@ -254,6 +263,7 @@ TAB_Capture	capture	Deleted	logical	NA	NA	NA
 TAB_Capture	capture	Deleted_Date	datetime	NA	NA	NA
 TAB_Capture	capture	CoreDB_Id	character	NA	NA	optional
 TAB_Capture	capture	CoreDB_Pool_Id	character	NA	NA	optional
+TAB_Capture	capture	Exclude	yesno_logical	NA	NA	optional
 TAB_Sequencing	sequencing	Id	integer	NA	NA	NA
 TAB_Sequencing	sequencing	Capture	integer	NA	NA	NA
 TAB_Sequencing	sequencing	Sequencing_Id	integer	NA	NA	mandatory
@@ -284,6 +294,7 @@ TAB_Sequencing	sequencing	Tags	character	NA	NA	optional
 TAB_Sequencing	sequencing	Projects	character	NA	NA	optional
 TAB_Sequencing	sequencing	Deleted	logical	NA	NA	NA
 TAB_Sequencing	sequencing	Deleted_Date	datetime	NA	NA	NA
+TAB_Sequencing	sequencing	Exclude	yesno_logical	NA	NA	optional
 TAB_Analysis	analysis	Id	integer	NA	NA	NA
 TAB_Analysis	analysis	Raw_Data	integer	NA	NA	NA
 TAB_Analysis	analysis	Analysis_Id	character	NA	NA	NA

diff --git a/data/pandora_column_types.rda b/data/pandora_column_types.rda
diff --git a/data/pandora_table_elements.rda b/data/pandora_table_elements.rda
diff --git a/data/pandora_tables.rda b/data/pandora_tables.rda
diff --git a/data/pandora_tables_all.rda b/data/pandora_tables_all.rda
diff --git a/data/pandora_tables_prejoin.rda b/data/pandora_tables_prejoin.rda
diff --git a/data/pandora_tables_restricted.rda b/data/pandora_tables_restricted.rda
diff --git a/man/sidora.core-package.Rd b/man/sidora.core-package.Rd
diff --git a/tests/testthat/test-get_data.R b/tests/testthat/test-get_data.R
@@ -5,7 +5,7 @@ test_that("get_con() behaves as expected", {
   expect_error(get_con("Wurstbrot", con))
   ind_table_con <- get_con("TAB_Site", con)
   expect_s3_class(ind_table_con, c("tbl_MariaDBConnection", "tbl_dbi", "tbl_sql", "tbl_lazy", "tbl"), exact = T)
-  expect_equal(ncol(ind_table_con), 20)
+  expect_equal(ncol(ind_table_con), 21)
 })
 
 test_that("get_con_list() behaves as expected", {
@@ -23,7 +23,7 @@ test_that("get_df() behaves as expected", {
   skip_on_ci()
   ind_table_df <- get_df("TAB_Site", con)
   expect_s3_class(ind_table_df, c("tbl_df", "tbl", "data.frame"), exact = T)
-  expect_equal(ncol(ind_table_df), 20)
+  expect_equal(ncol(ind_table_df), 21)
   expect_gt(nrow(ind_table_df), 1000)
   expect_false(as.logical(unique(ind_table_df$site.Deleted)))
 })