From 304fb0e7327a56309ecf99daa73294c2c20bfa87 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Wed, 1 Nov 2023 12:14:35 -0700 Subject: [PATCH] Add missing works_lab fields (#198) --- isaric/parsers/ccp-cameroon.toml | 4 ++-- isaric/parsers/ccp-drc.toml | 5 +++++ isaric/parsers/ccp-ghana.toml | 4 ++++ isaric/parsers/ccp-guinea.toml | 5 +++++ isaric/parsers/ccp-netherlands.toml | 3 +++ isaric/parsers/ccp-senegal.toml | 6 ++++++ isaric/parsers/ccp-spain.toml | 4 ++-- isaric/parsers/ccp-uganda-v2.toml | 3 ++- isaric/parsers/datcov-southafrica.toml | 4 ++-- isaric/parsers/idor-brazil.toml | 6 ++++++ isaric/parsers/isaric-ccpuk.toml | 5 +++++ isaric/parsers/isaric-rapid.toml | 4 ++-- isaric/parsers/lmic.toml | 2 +- isaric/parsers/ncov-malaysia.toml | 5 +++++ isaric/parsers/sprintsari-australia.toml | 5 +++++ isaric/parsers/uganda-vri-v1.toml | 2 +- isaric/parsers/western-australia.toml | 3 +-- 17 files changed, 57 insertions(+), 13 deletions(-) diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml index aa098d0f..1fbb5e82 100644 --- a/isaric/parsers/ccp-cameroon.toml +++ b/isaric/parsers/ccp-cameroon.toml @@ -114,9 +114,9 @@ description = "7) Employed as a health care worker / Employé en tant que travailleur de la santé ? " ref = "Y/N" - [subject.works_microbiology_lab] + [subject.works_lab] field = "q8_demographics" - description = "8) If health professional, specify / Si professionnel de santé" + description = "Laboratory professional" values = { 1 = false, 2 = false, 3 = false, 4 = false, 5 = true, 6 = false, 7 = false } [subject.has_asthma] diff --git a/isaric/parsers/ccp-drc.toml b/isaric/parsers/ccp-drc.toml index 5b00c0ad..efcb5cbb 100644 --- a/isaric/parsers/ccp-drc.toml +++ b/isaric/parsers/ccp-drc.toml @@ -298,6 +298,11 @@ description = "Health worker?" ref = "Y/N/NK" +[subject.works_lab] + field = "microb" + description = "Employee of a microbiology laboratory" + values = { 1 = true } + [subject.works_microbiology_lab] field = "microb" description = "Employee of a microbiology laboratory" diff --git a/isaric/parsers/ccp-ghana.toml b/isaric/parsers/ccp-ghana.toml index efb747f0..d6b4abb7 100644 --- a/isaric/parsers/ccp-ghana.toml +++ b/isaric/parsers/ccp-ghana.toml @@ -332,6 +332,10 @@ field = "dob" apply = { function = "splitDate", params = ["day", 2022, "%d/%m/%Y"] } + [subject.works_lab] + field = "microb" + values = { 1 = true } + [subject.works_microbiology_lab] field = "microb" ref = "Y/N/NK" diff --git a/isaric/parsers/ccp-guinea.toml b/isaric/parsers/ccp-guinea.toml index cbec05a1..c99fe59f 100644 --- a/isaric/parsers/ccp-guinea.toml +++ b/isaric/parsers/ccp-guinea.toml @@ -459,6 +459,11 @@ description = "Employed as a health worker?" values = { 1 = true, 0 = false } +[subject.works_lab] + field = "microb" + description = "Employee of a microbiology laboratory" + values = { 1 = true } + [subject.works_microbiology_lab] field = "microb" description = "Employee of a microbiology laboratory" diff --git a/isaric/parsers/ccp-netherlands.toml b/isaric/parsers/ccp-netherlands.toml index 31ca3b1d..92e07e38 100644 --- a/isaric/parsers/ccp-netherlands.toml +++ b/isaric/parsers/ccp-netherlands.toml @@ -96,6 +96,9 @@ { field = "ethnic_group#Unknown", values = { "1.0" = "Unknown" } }, ] +[subject.works_lab] + field = "microbiology_worker" + values = { 1 = true } [subject.works_microbiology_lab] field = "microbiology_worker" diff --git a/isaric/parsers/ccp-senegal.toml b/isaric/parsers/ccp-senegal.toml index 3a22ef60..e1696800 100644 --- a/isaric/parsers/ccp-senegal.toml +++ b/isaric/parsers/ccp-senegal.toml @@ -244,8 +244,14 @@ field = "healthwork_erterm" ref = "Y/N/NK" +[subject.works_lab] + field = "labwork_erterm" + description = "employed in a biological analysis laboratory?" + values = { 1 = true } + [subject.works_microbiology_lab] field = "labwork_erterm" + description = "employed in a biological analysis laboratory?" ref = "Y/N/NK" [subject.has_comorbidity_other] diff --git a/isaric/parsers/ccp-spain.toml b/isaric/parsers/ccp-spain.toml index 8daff287..f9726c56 100644 --- a/isaric/parsers/ccp-spain.toml +++ b/isaric/parsers/ccp-spain.toml @@ -62,9 +62,9 @@ { field = "raza", values = { 1 = "White", 2 = "Black", 3 = "Hispanic", 4 = "Asian", 5 = "Arab", 6 = "Other" } }, ] - [subject.works_microbiology_lab] + [subject.works_lab] field = "infhospi" - description = "Employed in a microbiology laboratory?" + description = "laboratory staff" values = { 2 = true } [subject.works_healthcare] diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml index f47f0fc1..d32e175f 100644 --- a/isaric/parsers/ccp-uganda-v2.toml +++ b/isaric/parsers/ccp-uganda-v2.toml @@ -111,8 +111,9 @@ description = "Gender" values = { 0 = "female", 1 = "male" } - [subject.works_microbiology_lab] + [subject.works_lab] field = "occupation" + description = "Lab worker" values = { 1 = false, 2 = false, 3 = false, 4 = false, 5 = false, 6 = true, 7 = false, 8 = false, 9 = false, 10 = false, 11 = false, 12 = false } [subject.works_healthcare] diff --git a/isaric/parsers/datcov-southafrica.toml b/isaric/parsers/datcov-southafrica.toml index af633be8..b448b113 100644 --- a/isaric/parsers/datcov-southafrica.toml +++ b/isaric/parsers/datcov-southafrica.toml @@ -122,10 +122,10 @@ ] description = "Is the patient a healthcare worker?" - [subject.works_microbiology_lab] + [subject.works_lab] field = "healthwork_type" values = { 1 = false, 2 = false, 3 = false, 4 = true, 5 = false, 6 = false, 7 = false, 8 = false, 9 = false, 10 = false } - description = "Is the patient a healthcare worker?" + description = "laboratory worker" [subject.pregnancy] # pregnancy fields not in the data? field = "PregnancyStatus" diff --git a/isaric/parsers/idor-brazil.toml b/isaric/parsers/idor-brazil.toml index 317e878f..47bd6773 100644 --- a/isaric/parsers/idor-brazil.toml +++ b/isaric/parsers/idor-brazil.toml @@ -267,8 +267,14 @@ field = "healthwork_erterm" ref = "Y/N/NK" +[subject.works_lab] + field = "labwork_erterm" + description = "employed in a microbiology lab?" + values = { 1 = true } + [subject.works_microbiology_lab] field = "labwork_erterm" + description = "employed in a microbiology lab?" ref = "Y/N/NK" [subject.has_comorbidity_other] diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml index 8de1b54c..a497637d 100644 --- a/isaric/parsers/isaric-ccpuk.toml +++ b/isaric/parsers/isaric-ccpuk.toml @@ -69,6 +69,11 @@ { field = "ethnic___10", values = { 1 = "Unknown" } }, ] + [subject.works_lab] + field = "labwork_erterm" + values = { 1 = true } + description = "Employed in a microbiology laboratory?" + [subject.works_microbiology_lab] field = "labwork_erterm" ref = "Y/N/NK" diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml index e1371723..c62cd6bf 100644 --- a/isaric/parsers/isaric-rapid.toml +++ b/isaric/parsers/isaric-rapid.toml @@ -284,10 +284,10 @@ { field = "flw2_ethnicity_oth", description = "Other ethnicity" }, ] - [subject.works_microbiology_lab] + [subject.works_lab] field = "labwork_erterm" ref = "Y/N/NK" - description = "Employed in a microbiology laboratory?" + description = "laboratory worker" [subject.works_healthcare] field = "healthwork_erterm" diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index 82e99757..fffc4d72 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -145,7 +145,7 @@ description = "Healthcare Worker?" ref = "Y/N/NK" - [subject.works_microbiology_lab] # This doesn't specify microB lab, but the syntax is the same as other isaric studies + [subject.works_lab] field = "labwork_erterm" description = "Laboratory Worker?" ref = "Y/N/NK" diff --git a/isaric/parsers/ncov-malaysia.toml b/isaric/parsers/ncov-malaysia.toml index 5fa4114d..e508ccf8 100644 --- a/isaric/parsers/ncov-malaysia.toml +++ b/isaric/parsers/ncov-malaysia.toml @@ -126,6 +126,11 @@ description = "Employed as a Healthcare Worker?" ref = "Y/N" +[subject.works_lab] + field = "lab_worker" + description = "Employed in a microbiology laboratory?" + values = { 1 = true } + [subject.works_microbiology_lab] field = "lab_worker" description = "Employed in a microbiology laboratory?" diff --git a/isaric/parsers/sprintsari-australia.toml b/isaric/parsers/sprintsari-australia.toml index bf34bf2d..40ecee16 100644 --- a/isaric/parsers/sprintsari-australia.toml +++ b/isaric/parsers/sprintsari-australia.toml @@ -109,6 +109,11 @@ # 8 = "aged care worker" # 9 = "disability worker" + [subject.works_lab] + field = "healthwork_erterm" + description = "Employed a a healthcare worker or any of following professions?" + values = { 1 = false, 2 = false, 3 = false, 4 = true, 5 = false, 7 = false, 8 = false, 9 = false, 10 = false, 11 = false } + [subject.works_microbiology_lab] field = "healthwork_erterm" description = "Employed a a healthcare worker or any of following professions?" diff --git a/isaric/parsers/uganda-vri-v1.toml b/isaric/parsers/uganda-vri-v1.toml index 29349916..eabae4b9 100644 --- a/isaric/parsers/uganda-vri-v1.toml +++ b/isaric/parsers/uganda-vri-v1.toml @@ -87,7 +87,7 @@ field = "sex" values = { 1 = "male", 0 = "female" } - [subject.works_microbiology_lab] + [subject.works_lab] field = "occupation" values = { 1 = false, 2 = false, 3 = false, 4 = false, 5 = false, 6 = true, 7 = false, 8 = false, 9 = false, 10 = false, 11 = false, 12 = false } diff --git a/isaric/parsers/western-australia.toml b/isaric/parsers/western-australia.toml index 8d6154d5..92c9341c 100644 --- a/isaric/parsers/western-australia.toml +++ b/isaric/parsers/western-australia.toml @@ -90,13 +90,12 @@ "%d/%m/%Y", ] } - [subject.works_healthcare] field = "healthwork_erterm" description = "Healthcare Worker?" ref = "Y/N/NK" - [subject.works_microbiology_lab] + [subject.works_lab] field = "labwork_erterm" description = "Laboratory worker?" ref = "Y/N/NK"