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Fix medium/low tests#19

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pipliggins:fix-tests
Open

Fix medium/low tests#19
pipliggins wants to merge 7 commits into
ISARICResearch:mainfrom
pipliggins:fix-tests

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@pipliggins pipliggins commented Mar 23, 2026

This PR reviews the test suite written by Tom and classed as medium/low priority. Ideally we want to be running these as well as the critical/high priority tests, as they are designed as a useful tool to reduce mistakes creeping into ARC, so it would be good to get to the point where these are all passing via edits either to ARC or the tests themselves.

So far the 'breaking' change has been to add in the skip-logic fields which were missing from various presets, summarised below.

These are almost exclusively 'housekeeping' variables. If there's a reason some were not included in certain presets (e.g. if there's only 1 or 2 fields you don't want to bother with adding the housekeeping variables to the survey, and BRIDGE can cope with the skip-logic fields being missing) lets discuss here, so we can edit the tests & docs accordingly.

Preset Fields Added
preset_ARChetype Disease CRF_Covid sympt_dailydata, treat_dailydata, imagi_dailydata, imagi_ultrasound, imagi_ultrasound_findi, inter_ivfluid
preset_ARChetype Disease CRF_Dengue sympt_vomit, sign_dailydata, imagi_ctchest_result
preset_ARChetype Disease CRF_H5Nx medi_treat
preset_ARChetype Disease CRF_Mpox expo14_ancon
preset_ARChetype Syndromic CRF_ARI treat_other
preset_ARChetype Syndromic CRF_Arbovirus demog_calcage_days, sympt_dailydata
preset_Populations_Paediatric demog_calcage_days, demog_sex, expo14_yn, preg_pregnant, preg_postpartum, sympt_dailydata, sign_dailydata
preset_Populations_Pregnancy demog_calcage_days, demog_sex
preset_Recommended Outcomes_Dengue demog_calcage_days, adsym_vomit, vital_dailydata, vital_o2supp, sympt_dailydata, sympt_vomit, sign_dailydata, treat_dailydata, treat_o2supp, critd_critcare, labs_dailydata, imagi_dailydata, imagi_xray, imagi_xray_result, imagi_ctchest, imagi_ctchest_result, imagi_ultrasound, imagi_ultrasound_findi, test_labtestmethod
preset_Score_mSOFA vital_dailydata, vital_o2supp, sign_dailydata, critd_critcare, labs_dailydata
preset_Score_mSOFA_Dengue vital_dailydata, vital_o2supp, labs_dailydata

Other changes

  1. Converting all the float '1.0' selection values in the List/* files to and integer '1' value
  2. Stripped trailing whitespace from entries in the List/* files and ARC

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pipliggins commented Mar 23, 2026

Some questions

  1. In the Lists/drugs/Antibiotics.csv file, there are some '2' options in the Selected column. What is that supposed to signify?
  2. Is the preset_ARChetype Disease CRF_Mpox Pregnancy and Paediatric in ARC supposed to be the same as preset_ARChetype Disease CRF_Mpox-Pregnancy&Paediatrics in e.g. Lists/followup/outcome.csv? If so, which is the preferred name?
  3. Three are some presets in the List files not in ARC, e.g. preset_Syndrome_VHF, preset_Respiratory. Are these supposed to be reflected in ARC, or remain only in certain files? Is there any guidance around where these presets should be specified?
  4. In many of the List files, there are options with the same SNOMED (or other) code. I assume in many cases this is either because in subsequent versions of ARC an option was renamed for clarity/to correct typos (e.g. HSV -> Herpes simplex virus infection (HSV)) or where multiple options map to the same code. I think the purpose of this test was to check that duplicate items aren't being added to the list accidentally when ARC is updated, but if the current contents are thought to be correct then this test will need to be re-written/removed.
  5. How are ARC Definitions used within BRIDGE/redcap? Are they actually required, or just for internal use (i.e. is the failing test arc_definition_exists actually important)?

@pipliggins pipliggins requested a review from saraduque March 24, 2026 12:26
@pipliggins pipliggins marked this pull request as ready for review March 24, 2026 12:26
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