update generate_consumables_item_codes_and_packages script

[EvaJanouskova]

In past, we merged manual changes in ResourceFile_Consumables_Items_and_Packages.csv, however this supposed to be generated by script generate_consumables_item_codes_and_packages. The script need to be updated to generate the version including the manual changes.

[EvaJanouskova]

We add here (within the commit generate_cons_item_pkgs: new consumables added to be included in RF_C…) new consumables into the RF_Consumables_Items_and_Pkgs by the generate_consumables_item_codes_and_packages script. In the PR #1124, it will need to be done manually for now as the script is not updated to generate the current version of the RF, see issue #1274.

[EvaJanouskova]

Hi @sakshimohan, as we discussed on slack. Once you have time for this, please update the generate_consumables_item_codes_and_packages script to generate the current master version of ResourceFile_Consumables_Items_and_Packages. Feel free to reach to me with any question.

Here, ResourceFile_Consumables_Items_and_Packages_generated.csv,
is what I think is now generated via generate_consumables_item_codes_and_packages script (only showing the part related to contraception methods as I think that's the only difference):

Intervention_Cat	Intervention_Pkg	Intervention_Pkg_Code	Items	Item_Code	Expected_Units_Per_Case	Unit_Cost
Maternal/Newborn and Reproductive Health	Pill	0	Levonorgestrel 0.0375 mg, cycle	0	7.5	48.25212
Maternal/Newborn and Reproductive Health	Pill	0	Levonorgestrel 0.15 mg + Ethinyl estradiol 30 mcg (Microgynon), cycle	1	7.5	53.35008
Maternal/Newborn and Reproductive Health	Male condom	1	Condom, male	2	120	20.97018
Maternal/Newborn and Reproductive Health	Injectable	2	Depot-Medroxyprogesterone Acetate 150 mg - 3 monthly	3	4	50.9439
Maternal/Newborn and Reproductive Health	Injectable	2	Gloves, exam, latex, disposable, pair	4	4	31.90866
Maternal/Newborn and Reproductive Health	Injectable	2	Povidone iodine, solution, 10 %, 5 ml per injection	5	4	2.00634
Maternal/Newborn and Reproductive Health	Injectable	2	Syringe, Autodisable SoloShot IX	6	4	5.4264
Maternal/Newborn and Reproductive Health	IUD	3	Gloves, exam, latex, disposable, pair	4	3	31.90866
Maternal/Newborn and Reproductive Health	IUD	3	IUD, Copper T-380A	7	1	19.39224
Maternal/Newborn and Reproductive Health	Implant	4	Gloves, exam, latex, disposable, pair	4	2	31.90866
Maternal/Newborn and Reproductive Health	Implant	4	Lidocaine HCl (in dextrose 7.5%), ampoule 2 ml	8	2	52.00062
Maternal/Newborn and Reproductive Health	Implant	4	Povidone iodine, solution, 10 %, 5 ml per injection	5	2	2.00634
Maternal/Newborn and Reproductive Health	Implant	4	Syringe, needle + swab	9	2	7.7469
Maternal/Newborn and Reproductive Health	Implant	4	Trocar	10	0.1	1203.99678
Maternal/Newborn and Reproductive Health	Implant	4	Needle suture intestinal round bodied ½ circle trocar_6_CMST	11	0.2	115.99644
Maternal/Newborn and Reproductive Health	Implant	4	Jadelle (implant), box of 2_CMST	12	0.5	447.22104
Maternal/Newborn and Reproductive Health	Implant	4	Implanon (Etonogestrel 68 mg)	13	0.5	484.97022
Maternal/Newborn and Reproductive Health	Female sterilization	5	Atropine sulphate, injection, 1 mg in 1 ml ampoule	14	1	17.99994
Maternal/Newborn and Reproductive Health	Female sterilization	5	Diazepam, injection, 5 mg/ml, in 2 ml ampoule	15	1	130.47636
Maternal/Newborn and Reproductive Health	Female sterilization	5	Lidocaine, injection, 1 % in 20 ml vial	16	1	149.99712
Maternal/Newborn and Reproductive Health	Female sterilization	5	Lidocaine, spray, 10%, 500 ml bottle	17	0.02	1244.0022
Maternal/Newborn and Reproductive Health	Female sterilization	5	Syringe, needle + swab	9	3	7.7469
Maternal/Newborn and Reproductive Health	Female sterilization	5	Gauze pad, 10 x 10 cm, sterile	18	2	14.72268
Maternal/Newborn and Reproductive Health	Female sterilization	5	Needle, suture, assorted sizes, round body	19	3	600.00276
Maternal/Newborn and Reproductive Health	Female sterilization	5	Suture, catgut, chromic, 0, 150 cm	20	3	3744.0018
Maternal/Newborn and Reproductive Health	Female sterilization	5	Tape, adhesive, 2.5 cm wide, zinc oxide, 5 m roll	21	1	426.10092
Maternal/Newborn and Reproductive Health	Female sterilization	5	Gloves, surgeon’s, latex, disposable, sterile, pair	22	2	137.45928
Maternal/Newborn and Reproductive Health	Female sterilization	5	Paracetamol, tablet, 500 mg	23	8	4.3554
Maternal/Newborn and Reproductive Health	Female sterilization	5	Povidone iodine, solution, 10 %, 5 ml per injection	5	2	2.00634
Maternal/Newborn and Reproductive Health	Female sterilization	5	Cotton swab	24	2	1.9992
Maternal/Newborn and Reproductive Health	Male sterilization	6	Gauze pad, 10 x 10 cm, sterile	18	1	14.72268
Maternal/Newborn and Reproductive Health	Male sterilization	6	Gloves, surgeon’s, latex, disposable, sterile, pair	22	1	137.45928
Maternal/Newborn and Reproductive Health	Male sterilization	6	Lidocaine, injection, 1 % in 20 ml vial	16	1	149.99712
Maternal/Newborn and Reproductive Health	Male sterilization	6	Needle, suture, assorted sizes, round body	19	1	600.00276
Maternal/Newborn and Reproductive Health	Male sterilization	6	Povidone iodine, solution, 10 %, 5 ml per injection	5	1	2.00634
Maternal/Newborn and Reproductive Health	Male sterilization	6	Suture, catgut, chromic, 0, 150 cm	20	1	3744.0018
Maternal/Newborn and Reproductive Health	Male sterilization	6	Syringe, needle + swab	9	1	7.7469
Maternal/Newborn and Reproductive Health	Male sterilization	6	Tape, adhesive, 2.5 cm wide, zinc oxide, 5 m roll	21	1	426.10092
Maternal/Newborn and Reproductive Health	Female Condom	7	Female Condom_Each_CMST	25	120	33.72222

And here, ResourceFile_Consumables_Items_and_Packages_2024-05-15_master.csv, is what we have on the master branch:

Intervention_Cat	Intervention_Pkg	Intervention_Pkg_Code	Items	Item_Code	Item_Code_Avail	Expected_Units_Per_Case	Unit_Cost	Source_Cost_Item	Source_ExpectedUnits
Maternal/Newborn and Reproductive Health	Contraception initiation	164	Pregnancy Slide Test Kit (Human - Chorionic Gonadotrophin (Hcg))_100_MM192300_CMST, strip	2019	2019	1	32.164	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Pill	0	Ethinylestradiol 0.03mg + levonorgestrel 0.15mg_Each_FP000800_CMST, cycle //80% patients//; or Microlut (Levonorgestrel 0.03mg)_Each_FP004200_CMST, cycle //20% patients//	1	1	3.75	492.9423273778	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male condom	1	Condom, male	2	2	30	20.97	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Injectable	2	Medroxyprogesterone acetate injection 150mg/mL, 1mL vial with 2ml syringe with 22g 0.7 X 25mm needle_Each_BB049500_CMST, ampule	3	3	1	481.2	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Injectable	2	Glove disposable powdered latex medium_100_HH077700_CMST, pair	1933	135	1	37.1336	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Injectable	2	Water for injections, 10ml_Each_BB077100_CMST	98	98	1	31.63	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Injectable	2	Povidone iodine 10% solution_200ml_DN004470_CMST, 5 ml sachet	5	5	1	84.78	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Injectable	2	Gauze, swabs 8-ply 10cm x 10cm_100_FF010800_CMST	75	101	1	15.6377	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	IUD	3	Glove disposable powdered latex medium_100_HH077700_CMST, pair	1933	135	2	37.1336	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	IUD	3	IUD, Copper T-380A	7	7	1	26.42	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Glove disposable powdered latex medium_100_HH077700_CMST, pair	1933	135	3	37.1336	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Lidocaine HCl (in dextrose 7.5%), ampoule 2 ml	8	8	2	309.69	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Povidone iodine 10% solution_200ml_DN004470_CMST, 5 ml sachet	5	5	1	84.78	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Syringe, needle + swab	9	6	2	200	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Trocar	10	10	0.1	312	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Needle suture intestinal round bodied ½ circle trocar_6_CMST	11	11	1	178.75	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Implant	4	Jadelle(implant)_Each_FP003700_CMST, 2 rods //50% patients//; or Implanon (Etonogestrel 68mg)_Each_FP004100_CMST, 1 rod //50% patients//	12	12	1	760.11	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Implant	4	Gauze, swabs 8-ply 10cm x 10cm_100_FF010800_CMST	75	101	1	15.6377	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Lidocaine HCl (in dextrose 7.5%), ampoule 2 ml	8	8	1	309.69	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Atropine sulphate 600 micrograms/ml, 1ml_Each_BB006600_CMST //1 unit 50% patients → 0.5 units per case//	307	14	0.5	121.25	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Diazepam 5mg/ml, 2ml_Each_BB024000_CMST	15	15	1	130.36	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Syringe, autodestruct, 5ml, disposable, hypoluer with 21g needle_Each_HH150000_CMST + Alcohol swabs/wipes 70% isopropyl alcohol 100 pieces_100_FF000300_CMST	1960	6	3	153.5155	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Gauze, swabs 8-ply 10cm x 10cm_100_FF010800_CMST	75	101	2	15.6377	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Polyamide monofilament suture sterile 1, on 40mm 3/8 circle reverse cutting needle_12_GG005100_CMST	2676	11	3	178.765	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Catgut chromic suture sterile 0, 75cm, round bodied ½ circle 40mm needle_12_GG000600_CMST	2677	11	3	306.8841667	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Tape, adhesive, 2.5 cm wide, zinc oxide, 5 m roll	21	21	0.25	1558	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Female sterilization	5	Glove surgeons size 7 sterile_Pair_HH080400_CMST	112	135	2	302.24	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Paracetamol 500mg, tablets_1000_AA049500_CMST, tablet	23	23	8	4.38683	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Povidone iodine 10% solution_200ml_DN004470_CMST, 5 ml sachet	5	5	2	84.78	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Female sterilization	5	Cotton wool, 500g_Each_FF007800_CMST	49	24	0.2	2689.81	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Male sterilization	6	Gauze, swabs 8-ply 10cm x 10cm_100_FF010800_CMST	75	101	1	15.6377	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Glove surgeons size 7 sterile_Pair_HH080400_CMST	112	135	1	302.24	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Lidocaine, injection, 1 % in 20 ml vial	16	16	1	260	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Polyamide monofilament suture sterile 1, on 40mm 3/8 circle reverse cutting needle_12_GG005100_CMST	2676	11	1	178.765	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Povidone iodine 10% solution_200ml_DN004470_CMST, 5 ml sachet	5	5	1	84.78	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Catgut chromic suture sterile 0, 75cm, round bodied ½ circle 40mm needle_12_GG000600_CMST	2677	11	1	306.8841667	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Syringe, autodestruct, 5ml, disposable, hypoluer with 21g needle_Each_HH150000_CMST + Alcohol swabs/wipes 70% isopropyl alcohol 100 pieces_100_FF000300_CMST	1960	6	1	153.5155	Malawi EHP 2021	OHT 2016
Maternal/Newborn and Reproductive Health	Male sterilization	6	Tape, adhesive, 2.5 cm wide, zinc oxide, 5 m roll	21	21	0.125	1158	Malawi EHP 2021	Malawi EHP 2021
Maternal/Newborn and Reproductive Health	Female Condom	7	Female Condom_Each_FP003500_CMST	25	25	30	22.16	Malawi EHP 2021	OHT 2016

[EvaJanouskova]

The columns, Item_Code_Avail, Source_Cost_Item, and Source_ExpectedUnits are only filled in for contraception related items, but now with what you have done and are doing right now, these may not be needed anymore.

The purpose of Item_Code_Avail was to use an alternative item code for availability as these items were not included in the availability RF. But if I remember correctly, you fixed this already and the availability for these is now approximated with availability of similar items automatically, isn't it? If so, I will remove this in separate PR.

If I understand your current work, the unit costs in the RF_..Items_and_Pkgs will be soon updated with the Final_price_per_chosen_unit (MWK, year of original cost), is that so? There you have covered the sources of costs, could be then information about the source of that cost generated into the column Source_Cost_Item? This is where the modellers look up the information on items, so I think it would be helpful to know that too, especially the year of the cost estimate.

And I would still vote on having the Expected_Units_Per_Case, not necessarily filled for all items, but it's essential to be able to use the get_item_codes_from_package_name() fnc. Ideally if expected units coming also from the RF_Costing/consumables if also other information will be generated from there. I used two sources for the Expected units per case OHT 2016, and where not possible Malawi EHP 2021 (as suggested by Emi because the excepted units in EHP where mostly suspiciously weird). So we could add these into RF_Costing, and then only generate the final used source to appear in RF_...Items_and_Pkgs.

[EvaJanouskova]

@matt-graham, @tamuri, @tbhallett, Could we have a test for Resource Files like this (ie, not created manually, but generated by a script) to assure no one has manually made a change in that RF?

I had no idea it was generated by a script, so I made all the changes manually, but if it caused the test to fail, I might have known.

[EvaJanouskova]

@sakshimohan, For some reason, which I can't remember exactly, we chose different gloves for some methods than what was originally there. If you want, I think we could return it, because I don't think it's necessary. (This may have been because we wanted to have them all from the same source (EHP 2021).)

[EvaJanouskova]

@sakshimohan
We added two new items for female sterilisation which are not in the version of RF_Items&Pkgs in the #1298:

• 'Polyamide monofilament suture sterile 1, on 40mm 3/8 circle reverse cutting needle_12_GG005100_CMST'
• 'Catgut chromic suture sterile 0, 75cm, round bodied ½ circle 40mm needle_12_GG000600_CMST'

Hence I use what used to be there before in #1298 when re-coding the consumables for contraception:

• 'Needle, suture, assorted sizes, round body'
• 'Suture, catgut, chromic, 0, 150 cm'

Would you know if there is difference between these, or should we just go back to the original items? It doesn't seem to me to be the same, but maybe it is close enough?

[tbhallett]

@sakshimohan We added two new items for female sterilisation which are not in the version of RF_Items&Pkgs in the #1298:

• 'Polyamide monofilament suture sterile 1, on 40mm 3/8 circle reverse cutting needle_12_GG005100_CMST'
• 'Catgut chromic suture sterile 0, 75cm, round bodied ½ circle 40mm needle_12_GG000600_CMST'

Hence I use what used to be there before in #1298 when re-coding the consumables for contraception:

• 'Needle, suture, assorted sizes, round body'
• 'Suture, catgut, chromic, 0, 150 cm'

Would you know if there is difference between these, or should we just go back to the original items? It doesn't seem to me to be the same, but maybe it is close enough?

Those things look very close to one another to me. If at all possible, I would certainly say to use the items that were defined originally in the ResourceFile without resorting to adding additional items.

[EvaJanouskova]

@matt-graham, @tamuri, @tbhallett, Could we have a test for Resource Files like this (ie, not created manually, but generated by a script) to assure no one has manually made a change in that RF?

I had no idea it was generated by a script, so I made all the changes manually, but if it caused the test to fail, I might have known.

I opened an issue for this: #1385.

[EvaJanouskova]

@sakshimohan, I think we can close this PR as we do all differently now, ie we are not using the packages to get the consumable item codes in contraception module anymore and all was re-coded to use the existing names from ResourceFile_Consumables_Items_and_Packages.csv , do you agree?

[tbhallett]

@sakshimohan, I think we can close this PR as we do all differently now, ie we are not using the packages to get the consumable item codes in contraception module anymore and all was re-coded to use the existing names from ResourceFile_Consumables_Items_and_Packages.csv , do you agree?

That being the case, I think we need a PR to roll back the manual changes that were made (but now no longer used) so that we're back to the situation of the ResourceFile being regenerable from the processing scripts.