WIP - Merge Development to master (or other) #766

Moohan · 2023-07-28T11:21:07Z

Just opening this Draft PR to make clear the changes that have been added to development.

The new version is needed to read the SLFs now. We use this in `get_existing_data_for_tests()`

* remove unnecessary code from `get_anon_chi` `get_anon_chi` was updated in slfhelper v0.10 * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5669528966/attempts/1 Accepted in #759 (comment) Signed-off-by: check-spelling-bot <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: Megan McNicol <[email protected]>

These take a very long time to run, so were skipped at the last update. They need to be revisited.

* Correct some documentation This resolves a build warning. * Style code --------- Co-authored-by: Moohan <[email protected]>

Lots of layout changes, as well as lots of implicit to explicit integer / double changes.

* Format postcode into `pc7` format * Style code * Style code * Update documentation * Update comment in R/process_extract_ae.R * Implement catch-all for PC7 format --------- Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]>

* Remove some obsolete code Renaming and removing some functions. * Style code --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Zihao Li <[email protected]>

* Simplify `create_hscp_test_flags` * Update documentation * Style code * simplify `create_hb_test_flags` * implement hscp test flags into tests * Simplify `create_demog_test_flags` --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]>

* updated code from case_when to case_match as it's a bit easier to read * Style code * changed some more `case_when` to `case_match` * Style code * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5752014211/attempts/1 Accepted in #780 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Add tests for `convert_sending_location_to_lca` --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: marjom02 <[email protected]> Co-authored-by: SwiftySalmon <[email protected]> Co-authored-by: James McMahon <[email protected]>

Co-authored-by: Jennit07 <[email protected]>

In processed extract variable is called hscp, and in final SLF it's called hscp2018. Fixed with nested if statement Co-authored-by: marjom02 <[email protected]>

Tiny error and a simple fix. Co-authored-by: Jennit07 <[email protected]>

* fix duplicated matches in chi in sc data. * Update R/create_individual_file.R * update on join_sc_client * Create a test checking if individual files have duplicated chi * add duplicated chi number to the tests in process_tests_individual_file --------- Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: James McMahon <[email protected]>

Update `check_year_valid` for NSUs

…785) * Update `get_boxi_extract_path` for DN/CMH data * Remove extra function * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5856792420/attempts/1 Accepted in #785 (comment) Signed-off-by: check-spelling-bot <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]>

* further obsolete code change * fix the preventable_beddays Co-authored-by: James McMahon <[email protected]> --------- Co-authored-by: James McMahon <[email protected]> Co-authored-by: Jennit07 <[email protected]>

github-actions · 2023-08-14T14:27:24Z

@check-spelling-bot Report

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Unrecognized words (25)

atrialfib
chd
consulations
copd
cvd
dotdash
Drugsand
dvprod
gls
hefailure
hhg
hiw
knitr
linetype
lintr
nrs
parkinsons
Physicaland
PLICS
rdname
refailure
SCTASK
sourcedev
sparra
telecare

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Dictionary	Entries	Covers
cspell:swift/src/swift.txt	205	1
cspell:sql/src/tsql.txt	455	1
cspell:python/src/python/python.txt	453	1
cspell:python/src/python/python-lib.txt	3873	1
cspell:npm/npm.txt	288	1
cspell:lorem-ipsum/dictionary.txt	240	1
cspell:latex/latex.txt	424	1
cspell:html/html.txt	1863	1
cspell:fullstack/fullstack.txt	390	1
cspell:filetypes/filetypes.txt	264	1

Consider adding them using (in .github/workflows/spelling.yml):

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          cspell:sql/src/tsql.txt
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          cspell:python/src/python/python-lib.txt
          cspell:npm/npm.txt
          cspell:lorem-ipsum/dictionary.txt
          cspell:latex/latex.txt
          cspell:html/html.txt
          cspell:fullstack/fullstack.txt
          cspell:filetypes/filetypes.txt

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Jennit07 · 2023-08-15T09:28:28Z

This can be deleted and a new one open for merging sept update into master

Moohan and others added 2 commits July 28, 2023 11:44

Bump {slfhelper} version

d9ac7ca

The new version is needed to read the SLFs now. We use this in `get_existing_data_for_tests()`