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Merge Sept update 23 into master #838

Merged
merged 129 commits into from
Sep 28, 2023
Merged

Merge Sept update 23 into master #838

merged 129 commits into from
Sep 28, 2023

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Jennit07
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September 23 update is now complete and we are ready to bring the code into master

Moohan and others added 30 commits July 28, 2023 11:44
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]>
Also, use `dplyr::last_col()` to more generically specify the range.
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
Moohan and others added 21 commits September 25, 2023 14:57
* Remove incorrect references to rds

Since we (mostly) don't use rds anymore these references are incorrect and potentially confusing.

I've updated lots of documentation to remove the reference to rds.

I've also updated many comments that mentioned rds (these were probably the most confusing).

* Update documentation

---------

Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
* Update `read_file` to return an empty tibble if passed the dummy path

This is needed for some other bits, notably NSUs

* Update SPARRA and HHG paths to return dummy if the year is invalid

* Extract all data as a parameter

* Style code

* Update documentation

* Style code

* Update documentation

* rename `run` to `create_episode_file`

* Update documentation

---------

Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Add additional tests for `check_it_reference()`

* Make the check on the IT reference stricter

* Update documentation

---------

Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* Make test-coverage.yaml run against development

* Make lint-changed-files.yaml run against development

---------

Co-authored-by: Jennit07 <[email protected]>
Addresses #672 

I've updated the code for social care client lookup. This used to live
in each year folder, however i have changed this so that the lookups
live next to the demographic lookup in `/hscdiip/social_care` and supply
the update month. This is so that we can have a comparison of the sc
client lookup data at the current quarter vs the previous update.
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github-actions bot commented Sep 28, 2023

@check-spelling-bot Report

🔴 Please review

See the 📂 files view or the 📜action log for details.

Unrecognized words (55)
ACa
anu
atrialfib
CAK
chd
consulations
copd
costinc
CPN
cvd
discondition
DMe
dotdash
Drugsand
dvprod
Fhelper
fnc
gls
glsrecord
hbp
hefailure
hhg
hiw
hri
incdn
incdnas
JXz
knitr
lcap
linetype
Lizihao
MIU
nrs
overcounting
parkinsons
Physicaland
PLICS
prac
rdname
refailure
reftype
ROBERM
scotp
SCTASK
slf
sourcedev
sparra
spss
starwars
sysmis
telecare
tidyverse
totalnodncontacts
unrecognised
URx
To accept ✔️ these unrecognized words as correct and remove the previously acknowledged and now absent words, run the following commands

... in a clone of the [email protected]:Public-Health-Scotland/source-linkage-files.git repository
on the sept-update-23 branch (ℹ️ how do I use this?):

curl -s -S -L 'https://raw.githubusercontent.com/check-spelling/check-spelling/main/apply.pl' |
perl - 'https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/6337086641/attempts/1'

To have the bot do this for you, reply quoting the following line:
@check-spelling-bot apply updates.

Available 📚 dictionaries could cover words not in the 📘 dictionary

This includes both expected items (235) from .github/actions/spelling/expect.txt and unrecognized words (55)

Dictionary Entries Covers
cspell:npm/npm.txt 288 2
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:python/src/common/extra.txt 741 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

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

      with:
        extra_dictionaries:
          cspell:npm/npm.txt
          cspell:swift/src/swift.txt
          cspell:sql/src/tsql.txt
          cspell:python/src/python/python.txt
          cspell:python/src/python/python-lib.txt
          cspell:python/src/common/extra.txt
          cspell:lorem-ipsum/dictionary.txt
          cspell:latex/latex.txt
          cspell:html/html.txt
          cspell:fullstack/fullstack.txt

To stop checking additional dictionaries, add:

      with:
        check_extra_dictionaries: ''
If the flagged items are 🤯 false positives

If items relate to a ...

  • binary file (or some other file you wouldn't want to check at all).

    Please add a file path to the excludes.txt file matching the containing file.

    File paths are Perl 5 Regular Expressions - you can test yours before committing to verify it will match your files.

    ^ refers to the file's path from the root of the repository, so ^README\.md$ would exclude README.md (on whichever branch you're using).

  • well-formed pattern.

    If you can write a pattern that would match it,
    try adding it to the patterns.txt file.

    Patterns are Perl 5 Regular Expressions - you can test yours before committing to verify it will match your lines.

    Note that patterns can't match multiline strings.

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All looks fine

@Jennit07 Jennit07 added this pull request to the merge queue Sep 28, 2023
Merged via the queue into master with commit 91bb468 Sep 28, 2023
9 of 15 checks passed
@Jennit07 Jennit07 deleted the sept-update-23 branch March 26, 2024 14:37
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5 participants