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Include checks for data version, branch, sha and data hash in template script #129

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Include checks for data version, branch, sha and data hash in template script #129

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fa6d0d1
Updated skeleton.RMD with data checks for data_version,branch_name, s…
Sal4321 Feb 28, 2024
0d53b21
add data hash and datapackage branch name to reproducibility table
valduran18 Feb 28, 2024
e5e79a0
Merge branch 'develop' into sha
slager Feb 29, 2024
ce380af
Merge branch 'develop' into sha
slager Apr 29, 2024
b9e0d3c
Merge branch 'develop' into sha
slager Aug 8, 2024
410aacc
fix merge commit in one more place
slager Aug 8, 2024
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26 changes: 23 additions & 3 deletions inst/rmarkdown/templates/visc_report/skeleton/skeleton.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -117,10 +117,20 @@ remotes::install_git(file.path('cavd', 'Studies', 'cvdNNN', 'pdata', 'VDCNNN.git
lib = my_data_package_lib)
```

```{r check_data_version}
DataPackageR::assert_data_version("VDCNNNAnalysis",version_string = "data_version")
testthat::expect_equal(packageDescription("VDCNNNAnalysis")$RemoteSha,"commit_sha")
testthat::expect_equal(packageDescription("VDCNNNAnalysis")$RemoteRef,"branch_name")

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I'm wondering if: instead of having a spot where the SRA manually includes the commit_sha and branch_name (which would still not be visible from the knitted PDF) it would make more sense to assign these values and add them in the reproducibility table at the end (next to the data_hash). i.e. lines 106-107 would be replaced with:

commit_sha <- packageDescription("VDCNNNAnalysis")$RemoteSha
branch_name <- packageDescription("VDCNNNAnalysis")$RemoteRef

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Editing this further... shouldn't this be for the datapackage not for the analysis folder (since the analysis folder is not a package):

commit_sha <- packageDescription("VDCNNN")$RemoteSha
branch_name <- packageDescription("VDCNNN")$RemoteRef

```


```{r data-processing}
# For this template use VISCfunction example data
data('exampleData_ICS', package = 'VISCfunctions', envir = environment())

testthat::expect_equal(digest::digest(exampleData_ICS),"data_hash")
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Same here. We can replace lines 114-116 with:

exampleData_ICS <- visc_load_pdata(exampleData_ICS, proj_or_datapackage = "datapackage", criteria = "SRA_enter_data_hash")
data_hash <- digest::digest(exampleData_ICS)

In case the data object (exampleData_ICS) is modified without being assigned a new name before the reproducibility table at the end, I would create the data_hash object immediately after loading in the data and call that in the reproducibility table.


ICS_adata <- exampleData_ICS %>%
filter(Population == "IFNg" & Group != 3)
```
Expand Down Expand Up @@ -369,8 +379,9 @@ if (any(installed.packages()[,1] == 'rmarkdown')) suppressWarnings(library(rmark

my_session_info <- VISCfunctions::get_session_info()

kable(
my_session_info$platform_table,
my_session_info$platform_table %>%
add_row(name = "data hash", value = digest::digest(exampleData_ICS), .before = nrow(.)) %>%
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replace 366 with lines:

add_row(name = "data hash", value = data_hash, .before = nrow(.)) %>%
add_row(name = "branch", value = branch_name, .before = nrow(.)) %>%
add_row(name = "commit", value = commit_sha, .before = nrow(.)) %>%

kable(
format = output_type,
booktabs = TRUE,
linesep = "",
Expand All @@ -380,8 +391,17 @@ kable(
```

```{r Software-Package-Version-Information, results="asis", warning=kable_warnings}
my_session_info$packages_table %>%
left_join(
sessioninfo::package_info() %>% filter(str_detect(source, pattern = "git2r")) %>%
pull(package) %>%
packageDescription() %>%
.[c("Package","RemoteRef")] %>%
as_tibble() %>%
rename("package" = "Package",
"branch" = "RemoteRef"),
by = "package") %>%
kable(
my_session_info$packages_table,
format = output_type,
booktabs = TRUE,
linesep = "",
Expand Down
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