Decouple ANC logic from tclose #1027

marghe-molaro · 2023-07-14T11:30:01Z

This PR seeks to decouple the logic implemented in PR New t-close dates for maternal HSIs to allow for prioritisation logic #984 from tclose;
Required changes have been implemented on the first three HSIs listed below;
Inside the HSI, a check is enforced whereby if more than 2 days have passed, the footprint is unchanged but no action is taken. This is consistent with the “tclose= +2days” logic we had previously enforced, although ideally use of consumables should be logged (HSI should still be performed, but wouldn’t be effective at all).

As a separate note: in some of these HSIs, upon checking whether the person is no longer alive, the returned footprint should be blank, rather than unchanged.

HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement
“t open” – abortion_onset (mni dictionary)
HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour
“t open” – la_due_date_current_pregnancy
HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare
“t open” – la_due_date_current_pregnancy (check)
Some changes needed:
HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare
“t open” – Complication onset which needs to be added.
HSI_Labour_ReceivesPostnatalCheck
Depends on if its ‘early’ or ‘late’ PNC…
HSI_NewbornOutcomes_ReceivesPostnatalCheck
Depends on if its ‘early’ or ‘late’ PNC…
HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy
Depends if pre or post rupture…

…nancy_PostAbortionCaseManagement, HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour, HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare

…patientCare including for seeking care from the population and being admitted

…opicPregnancy

…ur_ReceivesComprehensiveEmergencyObstetricCare

joehcollins · 2023-07-20T10:23:43Z

To do:

Fixes for failing maternal health tests
Add logic to reset any of the new 'topen' dates if the event cant run due to constraints
Add logic for 'late' PNC issue (newborns and mothers)
Also adding in some more error logging
Might be good to do a big population run to check if errors are being thrown up

… doesnt run do to constraints determined by the healthsystem model

joehcollins

@marghe-molaro - I think this is done now. If I had more time i'd re-run all the calibrations etc but I think the logic makes sense now. Would you be able to have a look and see what you think? would be good to simplify when we have more time

marghe-molaro · 2023-08-03T08:28:56Z

Thank you so much @joehcollins !! Just one last thing - it seems that there are still some errors in test_newborn_outcomes.py? Just wanted to check if you had spotted that?

joehcollins · 2023-08-03T08:30:16Z

Ahh annoying!! i blindly submitted and hoped for the best!! I'll have a look

(also latest master isnt merged in yet)

joehcollins · 2023-08-03T09:05:14Z

Ok fixed - just waiting for confirmation on github

marghe-molaro · 2023-08-03T10:57:24Z

Great, seems to be passing all tests now! Will review later today and give you any feedback asap!

src/tlo/methods/care_of_women_during_pregnancy.py

tbhallett · 2023-08-04T10:17:23Z

src/tlo/methods/labour.py

    def not_available(self):
        self.module.run_if_receives_skilled_birth_attendance_cant_run(self)


don't see how not_available is ever called.

tbhallett · 2023-08-04T10:18:34Z

src/tlo/methods/care_of_women_during_pregnancy.py

    def not_available(self):
        self.module.ectopic_pregnancy_treatment_doesnt_run(self)


never called not_available `: delete?

tbhallett · 2023-08-04T10:31:45Z

Thanks @joehcollins and @marghe-molaro for this.

It seems fine to me.

I noticed that there were these definitions of not_available throughout the HSI, but I don't think they were ever being called by anything. Let me know if you think I missed something though (and revert that commit if it was planned to be used for something in the future and you'd like to keep them in.)

joehcollins · 2023-08-04T10:33:04Z

hi @tbhallett - thanks for reviewing. I can't remember any reason for those functions being used so fine to be removed!!

This reverts commit bbf33e2 **** & subsequent changes

* Revert "Decouple ANC logic from tclose (#1027)" This reverts commit bbf33e2 **** & subsequent changes * removed old logic relating to pnc_date that should have been rolled back --------- Co-authored-by: joehcollins <joseph.h.collins@ucl.ac.uk>

* Revert "Decouple ANC logic from tclose (#1027)" This reverts commit bbf33e2 **** & subsequent changes * Enforce expeption for anc modules during tclose overwriting * removed old logic relating to pnc_date that should have been rolled back * Style fixes * Create scenario file to test if error in anc modules has been solved when overwriting tclose to 10 days * Increase population size * Correct CareOfWomenDuringPregnancy * check module name against a tuple of name of modules * factorize for DEFAULT_DAYS_OFFSET_VALUE_FOR_TCLOSE_IF_NONE_SPECIFIED --------- Co-authored-by: Tim Hallett <39991060+tbhallett@users.noreply.github.com> Co-authored-by: joehcollins <joseph.h.collins@ucl.ac.uk>

Implement no effect of care after 2 days in HSI_CareOfWomenDuringPreg…

79535db

…nancy_PostAbortionCaseManagement, HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour, HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare

marghe-molaro requested a review from joehcollins July 14, 2023 11:30

marghe-molaro mentioned this pull request Jul 19, 2023

Version 1.0 (End July 2023) #1017

Open

10 tasks

joehcollins added 4 commits July 20, 2023 10:22

adding topen logic for HSI_CareOfWomenDuringPregnancy_AntenatalWardIn…

9759fa3

…patientCare including for seeking care from the population and being admitted

adding topen logic for HSI_CareOfWomenDuringPregnancy_TreatmentForEct…

40e3fe6

…opicPregnancy

adding topen logic for HSI_NewbornOutcomes_ReceivesPostnatalCheck

1027d8f

adding topen logic for HSI_Labour_ReceivesPostnatalCheck and HSI_Labo…

fe86f5e

…ur_ReceivesComprehensiveEmergencyObstetricCare

joehcollins added 9 commits July 23, 2023 12:04

fix to failing ANC tests

1039f2f

fix error which was caught by the labour test

629011a

fix for flake8

2148bae

Add logic to makesure new topen date variables are reset if the event…

67418ab

… doesnt run do to constraints determined by the healthsystem model

adding new error logging to check new topen dates are present

a795833

fixes to errors in an inpatient care caught by test

ab6d0eb

fix error logging

da44caf

flake8

1d1c789

fix for 'late' postnatal scheduling

5b00c1a

joehcollins approved these changes Aug 3, 2023

View reviewed changes

fixes to failed tests

28a38d3

remove unneeded logic from did_not_run functions

2faff5e

marghe-molaro requested a review from tbhallett August 3, 2023 15:51

tbhallett marked this pull request as ready for review August 3, 2023 16:09

tbhallett reviewed Aug 4, 2023

View reviewed changes

Update src/tlo/methods/care_of_women_during_pregnancy.py

f5091ee

remove definitions of not_available for which no calls found.

15b04f7

tbhallett approved these changes Aug 4, 2023

View reviewed changes

tbhallett merged commit bbf33e2 into master Aug 15, 2023

BinglingICL mentioned this pull request Aug 24, 2023

Figures for Bingling's paper on Healthcare Workforce #436

Draft

marghe-molaro mentioned this pull request Sep 7, 2023

Issue with enforcing two-day limit on delay of care in ANC modules #1102

Open

tbhallett added a commit that referenced this pull request Sep 28, 2023

Revert "Decouple ANC logic from tclose (#1027)"

1265781

This reverts commit bbf33e2 **** & subsequent changes

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Decouple ANC logic from tclose #1027

Decouple ANC logic from tclose #1027

marghe-molaro commented Jul 14, 2023

joehcollins commented Jul 20, 2023 •

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marghe-molaro commented Aug 3, 2023

tbhallett Aug 4, 2023

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tbhallett commented Aug 4, 2023

joehcollins commented Aug 4, 2023

		def not_available(self):
		self.module.run_if_receives_skilled_birth_attendance_cant_run(self)

		def not_available(self):
		self.module.ectopic_pregnancy_treatment_doesnt_run(self)

Decouple ANC logic from tclose #1027

Decouple ANC logic from tclose #1027

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