From ce4d4c7a908453c196a47c5747553bd8dd6c093c Mon Sep 17 00:00:00 2001 From: everlyn kamau Date: Tue, 31 Oct 2023 18:25:33 -0400 Subject: [PATCH 1/7] add covid19 vaccination info --- isaric/parsers/brazil-followup.toml | 10 ++++++++++ isaric/parsers/ccp-cameroon.toml | 12 ++++++++++++ isaric/parsers/ccp-uganda-v2.toml | 10 ++++++++++ isaric/parsers/isaric-ccpuk.toml | 10 ++++++++++ isaric/parsers/isaric-core.toml | 13 +++++++++++++ isaric/parsers/isaric-ecmo.toml | 13 +++++++++++++ isaric/parsers/isaric-followup-fr.toml | 11 +++++++++++ isaric/parsers/isaric-rapid.toml | 13 +++++++++++++ isaric/parsers/isaric-tier1.toml | 12 ++++++++++++ isaric/parsers/ncov-gambia.toml | 10 ++++++++++ isaric/parsers/predicovid.toml | 10 ++++++++++ isaric/parsers/recover-eu.toml | 11 +++++++++++ isaric/parsers/uganda-vri-v1.toml | 5 +++++ 13 files changed, 140 insertions(+) diff --git a/isaric/parsers/brazil-followup.toml b/isaric/parsers/brazil-followup.toml index b086b9e6..155983ba 100644 --- a/isaric/parsers/brazil-followup.toml +++ b/isaric/parsers/brazil-followup.toml @@ -211,6 +211,16 @@ description = "Admission to an Intensive Care Unit (ICU / CTI)" ref = "Y/N" +[subject.vaccinated_covid19] + field = "flw_cov_vacc" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "flw_vacc_last_dose" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml index aa098d0f..0623c9ad 100644 --- a/isaric/parsers/ccp-cameroon.toml +++ b/isaric/parsers/ccp-cameroon.toml @@ -272,6 +272,18 @@ { field = "q14_treatment_outcome", if = { q1_treatment_outcome = 5 } }, ] +[subject.vaccinated_covid19] + field = "q1_vaccination" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "q5_vaccination" }, + { field = "q6_vaccination" }, + { field = "q7_vaccination" }, + ] + [visit] country_iso3 = "CMR" diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml index f47f0fc1..b306d1d4 100644 --- a/isaric/parsers/ccp-uganda-v2.toml +++ b/isaric/parsers/ccp-uganda-v2.toml @@ -243,6 +243,16 @@ { field = "icu_date", apply = { function = "isNotNull" } }, ] + [subject.vaccinated_covid19] + field = "vaccin_covid" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "vaccin_date" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml index 8de1b54c..09be4e18 100644 --- a/isaric/parsers/isaric-ccpuk.toml +++ b/isaric/parsers/isaric-ccpuk.toml @@ -343,6 +343,16 @@ description = "Admitted to ICU?" apply = { function = "isNotNull" } +[subject.vaccinated_covid19] + field = "covid19_vaccine" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "covid19_vaccined" }, + { field = "covid19_vaccine2d" }, + ] ## VISITS diff --git a/isaric/parsers/isaric-core.toml b/isaric/parsers/isaric-core.toml index c607a96b..debbedf3 100644 --- a/isaric/parsers/isaric-core.toml +++ b/isaric/parsers/isaric-core.toml @@ -550,6 +550,19 @@ { field = "flw2_date_death", description = "If known, date of death" }, ] +[subject.vaccinated_covid19] + field = "vacc_cov19_cmyn" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "vacc_cov19_1_cmdat" }, + { field = "vacc_cov19_2_cmdat" }, + { field = "vacc_cov19_3_cmdat" }, + { field = "vacc_cov19_4_cmdat" }, + ] + [visit] country_iso3 = { field = "country", ref = "countryMap" } diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml index 4e995179..96b299c7 100644 --- a/isaric/parsers/isaric-ecmo.toml +++ b/isaric/parsers/isaric-ecmo.toml @@ -550,6 +550,19 @@ description = "Admitted to ICU?" apply = { function = "isNotNull" } +[subject.vaccinated_covid19] + field = "vacc_cov19_cmyn" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "vacc_cov19_1_cmdat" }, + { field = "vacc_cov19_2_cmdat" }, + { field = "vacc_cov19_3_cmdat" }, + { field = "vacc_cov19_cmdat" }, + ] + [visit] country_iso3 = { field = "country", ref = "countryMap" } diff --git a/isaric/parsers/isaric-followup-fr.toml b/isaric/parsers/isaric-followup-fr.toml index b79ecbbc..52a83293 100644 --- a/isaric/parsers/isaric-followup-fr.toml +++ b/isaric/parsers/isaric-followup-fr.toml @@ -60,6 +60,17 @@ [subject.date_death] field = "ca_death_date" + [subject.vaccinated_covid19] + field = "flw_cov_vaccine" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "flw_vacc_first_dose" }, + { field = "flw_vacc_2nd_dose" }, + { field = "flw_vacc_3rd_dose" }, + ] # No visit table as data is followup only diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml index e1371723..a6700c9c 100644 --- a/isaric/parsers/isaric-rapid.toml +++ b/isaric/parsers/isaric-rapid.toml @@ -482,6 +482,19 @@ { field = "icu_hoterm", description = "first day of admission", values = { 1 = true, 2 = false } }, ] +[subject.vaccinated_covid19] + field = "vacc_cov19_cmyn" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "vacc_cov19_1_cmdat" }, + { field = "vacc_cov19_2_cmdat" }, + { field = "vacc_cov19_3_cmdat" }, + { field = "vacc_cov19_4_cmdat" }, + ] + ## VISIT [visit] diff --git a/isaric/parsers/isaric-tier1.toml b/isaric/parsers/isaric-tier1.toml index 38d3a698..9bdddfc9 100644 --- a/isaric/parsers/isaric-tier1.toml +++ b/isaric/parsers/isaric-tier1.toml @@ -198,6 +198,18 @@ ref = "Y/N" can_skip = true + [subject.vaccinated_covid19] + field = "flw_vacc_cov19_cmyn" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "flw_vacc_cov19_1_cmdat" }, + { field = "flw_vacc_cov19_2_cmdat" }, + { field = "flw_vacc_cov19_3_cmdat" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ncov-gambia.toml b/isaric/parsers/ncov-gambia.toml index 8d6dd46d..90661777 100644 --- a/isaric/parsers/ncov-gambia.toml +++ b/isaric/parsers/ncov-gambia.toml @@ -292,6 +292,16 @@ ] }, # followup field at day 90 ] +[subject.vaccinated_covid19] + field = "q_68" + ref = "Y/N" + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "q_68a_i" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index a63dd8f1..699ce992 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -138,6 +138,16 @@ field = "questionaire" # added into merged data to distinguish between questionaires values = { month_12 = false } + [subject.vaccinated_covid19] + field = "covid_vaccine" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "covax_dat" }, + ] + # VISIT [visit] diff --git a/isaric/parsers/recover-eu.toml b/isaric/parsers/recover-eu.toml index 18b32d12..ab20e9aa 100644 --- a/isaric/parsers/recover-eu.toml +++ b/isaric/parsers/recover-eu.toml @@ -210,6 +210,17 @@ description = "Did episode included ICU/High Care Unit admission?" ref = "Y/N" +[subject.vaccinated_covid19] + field = "VACC_REC" + ref = "Y/N" + +[subject.vaccinated_covid19_dates] + combinedType = "list" + fields = [ + { field = "DOSE1_DT" }, + { field = "DOSE2_DT" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/uganda-vri-v1.toml b/isaric/parsers/uganda-vri-v1.toml index 29349916..6ce24d6a 100644 --- a/isaric/parsers/uganda-vri-v1.toml +++ b/isaric/parsers/uganda-vri-v1.toml @@ -155,6 +155,11 @@ field = "outcome_date" if = { outcome = 2 } +[subject.vaccinated_covid19] + field = "vcard" + values = { 1 = true, 0 = false } + + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" From 30518d375dede7bbc6ac0a030e8266518912bc6b Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Tue, 31 Oct 2023 16:24:31 -0700 Subject: [PATCH 2/7] Add vaccinated options to parser schema --- schemas/dev/parser.schema.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/schemas/dev/parser.schema.json b/schemas/dev/parser.schema.json index a543380c..26f2c631 100644 --- a/schemas/dev/parser.schema.json +++ b/schemas/dev/parser.schema.json @@ -525,6 +525,14 @@ "icu_admitted": { "description": "Admitted to ICU", "$ref": "#/definitions/mapping" + }, + "vaccinated_covid19": { + "description": "Received a COVID19 vaccination", + "$ref": "#/definitions/mapping" + }, + "vaccinated_covid19_dates": { + "description": "Date(s) of covid vaccination", + "$ref": "#/definitions/mapping" } } }, From cf81babf6882b3a3969e01a290c8e879e08a64d8 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Tue, 31 Oct 2023 20:19:49 -0700 Subject: [PATCH 3/7] Edits --- isaric/parsers/brazil-followup.toml | 5 ++--- isaric/parsers/ccp-cameroon.toml | 1 + isaric/parsers/ccp-uganda-v2.toml | 5 ++--- isaric/parsers/isaric-ccpuk.toml | 10 ++++------ isaric/parsers/isaric-core.toml | 23 +++++++++++++---------- isaric/parsers/isaric-ecmo.toml | 5 +++-- isaric/parsers/isaric-followup-fr.toml | 12 ------------ isaric/parsers/isaric-rapid.toml | 5 +++-- isaric/parsers/isaric-tier1.toml | 16 ++++++++++------ isaric/parsers/ncov-gambia.toml | 5 ++--- isaric/parsers/predicovid.toml | 6 ------ isaric/parsers/recover-eu.toml | 6 ++---- 12 files changed, 42 insertions(+), 57 deletions(-) diff --git a/isaric/parsers/brazil-followup.toml b/isaric/parsers/brazil-followup.toml index 155983ba..5de25ac6 100644 --- a/isaric/parsers/brazil-followup.toml +++ b/isaric/parsers/brazil-followup.toml @@ -217,9 +217,8 @@ [subject.vaccinated_covid19_dates] combinedType = "list" - fields = [ - { field = "flw_vacc_last_dose" }, - ] + excludeWhen = "none" + fields = [{ field = "flw_vacc_last_dose" }] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml index 0623c9ad..5c09c884 100644 --- a/isaric/parsers/ccp-cameroon.toml +++ b/isaric/parsers/ccp-cameroon.toml @@ -278,6 +278,7 @@ [subject.vaccinated_covid19_dates] combinedType = "list" + excludeWhen = "none" fields = [ { field = "q5_vaccination" }, { field = "q6_vaccination" }, diff --git a/isaric/parsers/ccp-uganda-v2.toml b/isaric/parsers/ccp-uganda-v2.toml index b306d1d4..81939bc5 100644 --- a/isaric/parsers/ccp-uganda-v2.toml +++ b/isaric/parsers/ccp-uganda-v2.toml @@ -249,9 +249,8 @@ [subject.vaccinated_covid19_dates] combinedType = "list" - fields = [ - { field = "vaccin_date" }, - ] + excludeWhen = "none" + fields = [{ field = "vaccin_date" }] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/isaric-ccpuk.toml b/isaric/parsers/isaric-ccpuk.toml index 09be4e18..b7dff47f 100644 --- a/isaric/parsers/isaric-ccpuk.toml +++ b/isaric/parsers/isaric-ccpuk.toml @@ -344,15 +344,13 @@ apply = { function = "isNotNull" } [subject.vaccinated_covid19] - field = "covid19_vaccine" - values = { 1 = true, 0 = false } + field = "covid19_vaccine" + values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] combinedType = "list" - fields = [ - { field = "covid19_vaccined" }, - { field = "covid19_vaccine2d" }, - ] + excludeWhen = "none" + fields = [{ field = "covid19_vaccined" }, { field = "covid19_vaccine2d" }] ## VISITS diff --git a/isaric/parsers/isaric-core.toml b/isaric/parsers/isaric-core.toml index debbedf3..fa00bd9f 100644 --- a/isaric/parsers/isaric-core.toml +++ b/isaric/parsers/isaric-core.toml @@ -430,7 +430,7 @@ description = "Smoking at least one cigarette, cigar, pipe or equivalent per day before the onset of the current illness." [subject.has_smoking.values] - 1 = "yes" + 1 = "current" 2 = "never" 3 = "former" @@ -551,16 +551,18 @@ ] [subject.vaccinated_covid19] - field = "vacc_cov19_cmyn" - values = { 1 = true, 0 = false } + field = "vacc_cov19_cmyn" + can_skip = true + values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] - combinedType = "list" + combinedType = "set" + excludeWhen = "none" fields = [ - { field = "vacc_cov19_1_cmdat" }, - { field = "vacc_cov19_2_cmdat" }, - { field = "vacc_cov19_3_cmdat" }, - { field = "vacc_cov19_4_cmdat" }, + { field = "vacc_cov19_1_cmdat", can_skip = true }, + { field = "vacc_cov19_2_cmdat", can_skip = true }, + { field = "vacc_cov19_3_cmdat", can_skip = true }, + { field = "vacc_cov19_4_cmdat", can_skip = true }, ] [visit] @@ -749,6 +751,7 @@ [[visit.treatment_corticosteroid_type.fields]] field = "corticost_cmtrt" + can_skip = true apply.function = "wordSubstituteSet" apply.params = [ ["D[e,é][x,s]a?m[e,é]th?a[s,z]one?", "Dexamethasone"], @@ -1449,14 +1452,14 @@ [[observation]] name = "inability_to_walk_scale" phase = "admission" - date = { field = "admissionDateHierarchy" } + date = { ref = "admissionDateHierarchy" } value = { field = "flw_walking_pre_c19", values = { 1 = 1, 2 = 2, 3 = 3, 4 = 4 } } context = ["Ability to walk or climb steps prior to COVID-19 illness"] [[observation]] name = "inability_to_walk_scale" phase = "admission" - date = { field = "admissionDateHierarchy" } + date = { ref = "admissionDateHierarchy" } value = { field = "flw_eq5d_mb_5l_uk_eng", values = { 1 = 1, 2 = 2, 3 = 2, 4 = 3, 5 = 4 } } context = ["Ability to walk prior to COVID-19 illness"] diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml index 96b299c7..a0e9a744 100644 --- a/isaric/parsers/isaric-ecmo.toml +++ b/isaric/parsers/isaric-ecmo.toml @@ -551,11 +551,12 @@ apply = { function = "isNotNull" } [subject.vaccinated_covid19] - field = "vacc_cov19_cmyn" - values = { 1 = true, 0 = false } + field = "vacc_cov19_cmyn" + values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] combinedType = "list" + excludeWhen = "none" fields = [ { field = "vacc_cov19_1_cmdat" }, { field = "vacc_cov19_2_cmdat" }, diff --git a/isaric/parsers/isaric-followup-fr.toml b/isaric/parsers/isaric-followup-fr.toml index 52a83293..0e7ffc53 100644 --- a/isaric/parsers/isaric-followup-fr.toml +++ b/isaric/parsers/isaric-followup-fr.toml @@ -60,18 +60,6 @@ [subject.date_death] field = "ca_death_date" - [subject.vaccinated_covid19] - field = "flw_cov_vaccine" - values = { 1 = true, 0 = false } - - [subject.vaccinated_covid19_dates] - combinedType = "list" - fields = [ - { field = "flw_vacc_first_dose" }, - { field = "flw_vacc_2nd_dose" }, - { field = "flw_vacc_3rd_dose" }, - ] - # No visit table as data is followup only [visit] diff --git a/isaric/parsers/isaric-rapid.toml b/isaric/parsers/isaric-rapid.toml index a6700c9c..75a7da32 100644 --- a/isaric/parsers/isaric-rapid.toml +++ b/isaric/parsers/isaric-rapid.toml @@ -483,11 +483,12 @@ ] [subject.vaccinated_covid19] - field = "vacc_cov19_cmyn" - values = { 1 = true, 0 = false } + field = "vacc_cov19_cmyn" + values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] combinedType = "list" + excludeWhen = "none" fields = [ { field = "vacc_cov19_1_cmdat" }, { field = "vacc_cov19_2_cmdat" }, diff --git a/isaric/parsers/isaric-tier1.toml b/isaric/parsers/isaric-tier1.toml index 9bdddfc9..26b6cd06 100644 --- a/isaric/parsers/isaric-tier1.toml +++ b/isaric/parsers/isaric-tier1.toml @@ -199,15 +199,19 @@ can_skip = true [subject.vaccinated_covid19] - field = "flw_vacc_cov19_cmyn" - values = { 1 = true, 0 = false } + combinedType = "firstNonNull" + fields = [ + { fieldPattern = 'flw\d*_vacc_cov19_cmyn', values = { 1 = true, 0 = false } }, + ] + [subject.vaccinated_covid19_dates] - combinedType = "list" + combinedType = "set" + excludeWhen = "none" fields = [ - { field = "flw_vacc_cov19_1_cmdat" }, - { field = "flw_vacc_cov19_2_cmdat" }, - { field = "flw_vacc_cov19_3_cmdat" }, + { fieldPattern = 'flw\d*_vacc_cov19_1_cmdat' }, + { fieldPattern = 'flw\d*_vacc_cov19_2_cmdat' }, + { fieldPattern = 'flw\d*_vacc_cov19_3_cmdat', source_date = "%d/%m/%Y" }, ] # VISIT diff --git a/isaric/parsers/ncov-gambia.toml b/isaric/parsers/ncov-gambia.toml index 90661777..25a570f5 100644 --- a/isaric/parsers/ncov-gambia.toml +++ b/isaric/parsers/ncov-gambia.toml @@ -298,9 +298,8 @@ [subject.vaccinated_covid19_dates] combinedType = "list" - fields = [ - { field = "q_68a_i" }, - ] + excludeWhen = "none" + fields = [{ field = "q_68a_i", source_date = "%Y-%m-%d" }] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index 699ce992..c4ce5cc1 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -142,12 +142,6 @@ field = "covid_vaccine" values = { 1 = true, 0 = false } - [subject.vaccinated_covid19_dates] - combinedType = "list" - fields = [ - { field = "covax_dat" }, - ] - # VISIT [visit] diff --git a/isaric/parsers/recover-eu.toml b/isaric/parsers/recover-eu.toml index ab20e9aa..5726c3ec 100644 --- a/isaric/parsers/recover-eu.toml +++ b/isaric/parsers/recover-eu.toml @@ -216,10 +216,8 @@ [subject.vaccinated_covid19_dates] combinedType = "list" - fields = [ - { field = "DOSE1_DT" }, - { field = "DOSE2_DT" }, - ] + excludeWhen = "none" + fields = [{ field = "DOSE1_DT" }, { field = "DOSE2_DT" }] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" From 82ec91b22e8289baff8c157db2fa5d922f342b3d Mon Sep 17 00:00:00 2001 From: everlyn kamau Date: Sun, 5 Nov 2023 15:03:06 -0800 Subject: [PATCH 4/7] edits & revisions to parsers --- isaric/parsers/brazil-followup.toml | 1 + isaric/parsers/datcov-southafrica.toml | 13 +++++++++++++ isaric/parsers/isaric-ecmo.toml | 1 + isaric/parsers/isaric-tier1.toml | 13 +++++-------- isaric/parsers/lmic.toml | 9 +++++++++ isaric/parsers/ncov-gambia.toml | 1 + isaric/parsers/ncov-phosp.toml | 12 ++++++++++++ isaric/parsers/predicovid.toml | 4 ++++ isaric/parsers/uganda-vri-v1.toml | 4 ---- 9 files changed, 46 insertions(+), 12 deletions(-) diff --git a/isaric/parsers/brazil-followup.toml b/isaric/parsers/brazil-followup.toml index 5de25ac6..aec8ca19 100644 --- a/isaric/parsers/brazil-followup.toml +++ b/isaric/parsers/brazil-followup.toml @@ -219,6 +219,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "flw_vacc_last_dose" }] + context = ["Date of most recent dose"] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/datcov-southafrica.toml b/isaric/parsers/datcov-southafrica.toml index af633be8..7d03b1c7 100644 --- a/isaric/parsers/datcov-southafrica.toml +++ b/isaric/parsers/datcov-southafrica.toml @@ -291,6 +291,19 @@ { field = "flw_icu", description = "If ever admitted to hospital, were you admitted to intensive care (ICU/ITU)?", values = { 0 = false, 1 = true } }, ] + [subject.vaccinated_covid19] + field = "Vaccinated" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + combinedType = "set" + excludeWhen = "none" + fields = [ + { field = "First Dose Date" }, + { field = "Second Dose Date" }, + { field = "Booster Dose Date" }, + ] + [visit] country_iso3 = "ZAF" diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml index a0e9a744..416723e2 100644 --- a/isaric/parsers/isaric-ecmo.toml +++ b/isaric/parsers/isaric-ecmo.toml @@ -563,6 +563,7 @@ { field = "vacc_cov19_3_cmdat" }, { field = "vacc_cov19_cmdat" }, ] + context = ["Date of most recent dose"] [visit] country_iso3 = { field = "country", ref = "countryMap" } diff --git a/isaric/parsers/isaric-tier1.toml b/isaric/parsers/isaric-tier1.toml index 26b6cd06..32d9b079 100644 --- a/isaric/parsers/isaric-tier1.toml +++ b/isaric/parsers/isaric-tier1.toml @@ -199,19 +199,16 @@ can_skip = true [subject.vaccinated_covid19] - combinedType = "firstNonNull" - fields = [ - { fieldPattern = 'flw\d*_vacc_cov19_cmyn', values = { 1 = true, 0 = false } }, - ] - + field = "flw_vacc_cov19_cmyn" + values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] combinedType = "set" excludeWhen = "none" fields = [ - { fieldPattern = 'flw\d*_vacc_cov19_1_cmdat' }, - { fieldPattern = 'flw\d*_vacc_cov19_2_cmdat' }, - { fieldPattern = 'flw\d*_vacc_cov19_3_cmdat', source_date = "%d/%m/%Y" }, + { field = "flw_vacc_cov19_1_cmdat" }, + { field = "flw_vacc_cov19_2_cmdat" }, + { field = "flw_vacc_cov19_3_cmdat", source_date = "%d/%m/%Y" }, ] # VISIT diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index 82e99757..bf070faa 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -176,6 +176,15 @@ description = "Intensive Care Unit admission" ref = "Y/N/NK" + [subject.vaccinated_covid19] + field = "c19_vacc" + values = { 1 = true, 0 = false } + + [subject.vaccinated_covid19_dates] + field = "dose_date" + context = ["Date of the most recent dose"] + + [visit] country_iso3 = "MWI" diff --git a/isaric/parsers/ncov-gambia.toml b/isaric/parsers/ncov-gambia.toml index 25a570f5..31e21378 100644 --- a/isaric/parsers/ncov-gambia.toml +++ b/isaric/parsers/ncov-gambia.toml @@ -300,6 +300,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "q_68a_i", source_date = "%Y-%m-%d" }] + context = ["Date of last dose"] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/ncov-phosp.toml b/isaric/parsers/ncov-phosp.toml index ce27e536..9f58235f 100644 --- a/isaric/parsers/ncov-phosp.toml +++ b/isaric/parsers/ncov-phosp.toml @@ -257,6 +257,18 @@ field = "crf2a_reason_not_done" values = { Language = false, Declined = false, Died = true, Other = false } +[subject.vaccinated_covid19] + field = "psq_vac_first_yn" + values = { 1 = true, 0 = false } + +[subject.vaccinated_covid19_dates] + combinedType = "set" + excludeWhen = "none" + fields = [ + { field = "psq_vac_first_date" }, + { field = "psq_vac_sec_date" }, + ] + # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index c4ce5cc1..1baa6e41 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -142,6 +142,10 @@ field = "covid_vaccine" values = { 1 = true, 0 = false } + [subject.vaccinated_covid19_dates] + field = "covax_dat" + context = ["Date of last dose"] + # VISIT [visit] diff --git a/isaric/parsers/uganda-vri-v1.toml b/isaric/parsers/uganda-vri-v1.toml index 6ce24d6a..2c1bc948 100644 --- a/isaric/parsers/uganda-vri-v1.toml +++ b/isaric/parsers/uganda-vri-v1.toml @@ -155,10 +155,6 @@ field = "outcome_date" if = { outcome = 2 } -[subject.vaccinated_covid19] - field = "vcard" - values = { 1 = true, 0 = false } - # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" From 493e6b67e69bed081f6788df12067ef0b743f4ab Mon Sep 17 00:00:00 2001 From: everlyn kamau Date: Sun, 5 Nov 2023 15:10:28 -0800 Subject: [PATCH 5/7] edits to parsers --- isaric/parsers/lmic.toml | 4 +++- isaric/parsers/predicovid.toml | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index bf070faa..c4e18f6f 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -181,7 +181,9 @@ values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] - field = "dose_date" + combinedType = "list" + excludeWhen = "none" + fields = [{ "dose_date" }] context = ["Date of the most recent dose"] diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index 1baa6e41..36b112fa 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -143,7 +143,9 @@ values = { 1 = true, 0 = false } [subject.vaccinated_covid19_dates] - field = "covax_dat" + combinedType = "list" + excludeWhen = "none" + fields = [{ field = "covax_dat" }] context = ["Date of last dose"] # VISIT From 1404bc7f7ab9d1bbf24e5e6a5dc43a3ec37e8479 Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 6 Nov 2023 18:00:25 -0800 Subject: [PATCH 6/7] Remove context from subject table --- isaric/parsers/brazil-followup.toml | 2 +- isaric/parsers/isaric-ecmo.toml | 2 +- isaric/parsers/isaric-followup-fr.toml | 1 + isaric/parsers/lmic.toml | 16 ++++++++-------- isaric/parsers/ncov-gambia.toml | 2 +- isaric/parsers/predicovid.toml | 2 +- 6 files changed, 13 insertions(+), 12 deletions(-) diff --git a/isaric/parsers/brazil-followup.toml b/isaric/parsers/brazil-followup.toml index aec8ca19..85821c3a 100644 --- a/isaric/parsers/brazil-followup.toml +++ b/isaric/parsers/brazil-followup.toml @@ -219,7 +219,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "flw_vacc_last_dose" }] - context = ["Date of most recent dose"] + # context = ["Date of most recent dose"] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/isaric-ecmo.toml b/isaric/parsers/isaric-ecmo.toml index 416723e2..5faa3460 100644 --- a/isaric/parsers/isaric-ecmo.toml +++ b/isaric/parsers/isaric-ecmo.toml @@ -563,7 +563,7 @@ { field = "vacc_cov19_3_cmdat" }, { field = "vacc_cov19_cmdat" }, ] - context = ["Date of most recent dose"] + # context = ["Date of most recent dose"] [visit] country_iso3 = { field = "country", ref = "countryMap" } diff --git a/isaric/parsers/isaric-followup-fr.toml b/isaric/parsers/isaric-followup-fr.toml index 0e7ffc53..b79ecbbc 100644 --- a/isaric/parsers/isaric-followup-fr.toml +++ b/isaric/parsers/isaric-followup-fr.toml @@ -60,6 +60,7 @@ [subject.date_death] field = "ca_death_date" + # No visit table as data is followup only [visit] diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index c4e18f6f..24ef7520 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -176,15 +176,15 @@ description = "Intensive Care Unit admission" ref = "Y/N/NK" - [subject.vaccinated_covid19] - field = "c19_vacc" - values = { 1 = true, 0 = false } +[subject.vaccinated_covid19] + field = "c19_vacc" + values = { 1 = true, 0 = false } - [subject.vaccinated_covid19_dates] - combinedType = "list" - excludeWhen = "none" - fields = [{ "dose_date" }] - context = ["Date of the most recent dose"] +[subject.vaccinated_covid19_dates] + combinedType = "list" + excludeWhen = "none" + fields = [{ field = "dose_date" }] + context = ["Date of the most recent dose"] [visit] diff --git a/isaric/parsers/ncov-gambia.toml b/isaric/parsers/ncov-gambia.toml index 31e21378..66138a7f 100644 --- a/isaric/parsers/ncov-gambia.toml +++ b/isaric/parsers/ncov-gambia.toml @@ -300,7 +300,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "q_68a_i", source_date = "%Y-%m-%d" }] - context = ["Date of last dose"] + # context = ["Date of last dose"] # VISIT # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome" diff --git a/isaric/parsers/predicovid.toml b/isaric/parsers/predicovid.toml index 36b112fa..53f04052 100644 --- a/isaric/parsers/predicovid.toml +++ b/isaric/parsers/predicovid.toml @@ -146,7 +146,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "covax_dat" }] - context = ["Date of last dose"] + # context = ["Date of last dose"] # VISIT From c94f4936ad19dfc1f99cb9150d4bcc5375730c4a Mon Sep 17 00:00:00 2001 From: Pip Liggins Date: Mon, 6 Nov 2023 18:07:42 -0800 Subject: [PATCH 7/7] Missed LMIC context --- isaric/parsers/lmic.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/isaric/parsers/lmic.toml b/isaric/parsers/lmic.toml index 24ef7520..a248b3bb 100644 --- a/isaric/parsers/lmic.toml +++ b/isaric/parsers/lmic.toml @@ -184,7 +184,7 @@ combinedType = "list" excludeWhen = "none" fields = [{ field = "dose_date" }] - context = ["Date of the most recent dose"] + # context = ["Date of the most recent dose"] [visit]