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Integration and cleanup of profiling work (#61)
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* Profiling integration

* Additional integration, fixes, and updates

* Additional integration, fixes, and updates

* Post-discussion fixes

* Build fixes

* Small fix

* CQL fixes

* Profiling

* Additional profiling work

* Fixes

* Fixes

* Fixes

* Fixes

* Fixes

* Fixes

* Froze dependency versions
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@pmanko
pmanko authored Dec 6, 2024
1 parent 3f9bca1 commit b6eb9b9
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Showing 72 changed files with 669 additions and 435 deletions.
5 changes: 3 additions & 2 deletions input/cql/HIVConcepts.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -388,7 +388,7 @@ code "Prevention services offered and referrals - HIV.B.DE149": 'HIV.B.DE149' fr
code "Offer male and female condoms and condom-compatible lubricants - HIV.B.DE150": 'HIV.B.DE150' from "HIVConcepts" display 'Offer male and female condoms and condom-compatible lubricants'
code "Offer pre-exposure prophylaxis PrEP for people at elevated risk for HIV acquisition": 'HIV.B.DE151' from "HIVConcepts" display 'Offer pre-exposure prophylaxis PrEP for people at elevated risk for HIV acquisition'
code "Offer post-exposure prophylaxis PEP following suspected exposure": 'HIV.B.DE152' from "HIVConcepts" display 'Offer post-exposure prophylaxis PEP following suspected exposure'
code "Voluntary medical male circumcision VMMC": 'HIV.B.DE153' from "HIVConcepts" display 'Voluntary medical male circumcision VMMC'
code "Voluntary medical male circumcision VMMC referral": 'HIV.B.DE153' from "HIVConcepts" display 'Voluntary medical male circumcision VMMC referral offered'
code "Harm reduction for people who inject drugs - HIV.B.DE154": 'HIV.B.DE154' from "HIVConcepts" display 'Harm reduction for people who inject drugs'
code "Behavioural interventions to support risk reduction, particularly for people with HIV and members of key populations": 'HIV.B.DE155' from "HIVConcepts" display 'Behavioural interventions to support risk reduction, particularly for people with HIV and members of key populations'
code "HIV testing for partners and biological children - HIV.B.DE156": 'HIV.B.DE156' from "HIVConcepts" display 'HIV testing for partners and biological children'
Expand Down Expand Up @@ -417,6 +417,7 @@ code "Type of follow-up appointment - HIV.B.DE191": 'HIV.B.DE191' from "HIVConce
code "Retesting for HIV - HIV.B.DE192": 'HIV.B.DE192' from "HIVConcepts" display 'Retesting for HIV'
code "Other - HIV.B.DE193": 'HIV.B.DE193' from "HIVConcepts" display 'Other'
code "Date/time of follow-up appointment - HIV.B.DE195": 'HIV.B.DE195' from "HIVConcepts" display 'Date/time of follow-up appointment'
code "VMMC procedure": 'HIV.B.DE197' from "HIVConcepts" display 'VMMC procedure performed'
code "VMMC procedure date": 'HIV.B.DE198' from "HIVConcepts" display 'VMMC procedure date'
code "Adverse event severity": 'HIV.B.DE201' from "HIVConcepts" display 'Adverse event severity'
code "Moderate": 'HIV.B.DE202' from "HIVConcepts" display 'Moderate'
Expand Down Expand Up @@ -560,7 +561,7 @@ code "Follow-up appointment for PrEP": 'HIV.C.DE127' from "HIVConcepts" display
code "Other - HIV.C.DE128": 'HIV.C.DE128' from "HIVConcepts" display 'Other'
code "Prevention services offered and referrals - HIV.C.DE131": 'HIV.C.DE131' from "HIVConcepts" display 'Prevention services offered and referrals'
code "Male and female condoms and condom-compatible lubricants offered": 'HIV.C.DE132' from "HIVConcepts" display 'Male and female condoms and condom-compatible lubricants offered'
code "Voluntary medical male circumcision VMMC referral": 'HIV.C.DE133' from "HIVConcepts" display 'Voluntary medical male circumcision VMMC referral'
code "Voluntary medical male circumcision VMMC referral - HIV.C.DE133": 'HIV.C.DE133' from "HIVConcepts" display 'Voluntary medical male circumcision VMMC referral'
code "Harm reduction for people who inject drugs - HIV.C.DE134": 'HIV.C.DE134' from "HIVConcepts" display 'Harm reduction for people who inject drugs'
code "Behavioural interventions to support risk reduction - HIV.C.DE135": 'HIV.C.DE135' from "HIVConcepts" display 'Behavioural interventions to support risk reduction'
code "Condom type": 'HIV.C.DE138' from "HIVConcepts" display 'Condom type'
Expand Down
84 changes: 38 additions & 46 deletions input/cql/HIVElements.cql
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Original file line number Diff line number Diff line change
Expand Up @@ -138,13 +138,10 @@ define "Viral load tests received after ART intitiation":
@activity: HIV.A2 Gather client details
@description: The date and time of the client's visit
*/
// TODO: Replace placeholder with relevant CQL logic
define "Visit date A.DE3":
[Observation: Concepts."Visit date - HIV.A.DE3"] O
where O.status in { 'final', 'amended', 'corrected' }
define "Visit date A.DE3 Value":
"Visit date A.DE3" O
return O.value
[Encounter] E
where E.type.coding.code contains Concepts."HIV testing services visit".code

/* End of Visit date A.DE3 */

/*
Expand Down Expand Up @@ -289,17 +286,17 @@ define "Other A.DE23 Observation":
@activity: HIV.B1 Determine reason for visit
@description: Encounter for HIV testing services visit
*/
define "HTS Visit Encounter":
define "HTS Visit":
[Encounter] E
where E.type.coding.code contains ConceptsCustom."HTS Visit".code

/*
@dataElement: HIV.B.DE1 - Reason for visit
@activity: HIV.B1 Determine reason for visit
@description: Reason for HIV testing services visit
*/
define "Reason for visit B.DE1":
"HTS Visit Encounter" E
"HTS Visit" E
return E.reasonCode
/* End of Reason for visit B.DE1 */

Expand All @@ -309,7 +306,7 @@ define "Reason for visit B.DE1":
@description: First encounter for screening for human immunodeficiency virus
*/
define "First-time HIV test Encounter":
"HTS Visit Encounter" E
"HTS Visit" E
where E.reasonCode.coding.code contains Concepts."First-time HIV test".code
/* End of First-time HIV test */

Expand All @@ -320,7 +317,7 @@ define "First-time HIV test Encounter":
*/
// TODO: Replace placeholder with relevant CQL logic
define "Retesting for HIV B.DE3 Encounter":
"HTS Visit Encounter" E
"HTS Visit" E
where E.reasonCode.coding.code contains Concepts."Retesting for HIV - HIV.B.DE3".code
/* End of Retesting for HIV B.DE3 */

Expand All @@ -331,7 +328,7 @@ define "Retesting for HIV B.DE3 Encounter":
*/
// TODO: Replace placeholder with relevant CQL logic
define "HIV testing services visit Encounter":
"HTS Visit Encounter" E
"HTS Visit" E
where E.reasonCode.coding.code contains Concepts."HIV testing services visit".code
/* End of HIV testing services visit */

Expand Down Expand Up @@ -1720,11 +1717,11 @@ define "Voluntary medical male circumcision VMMC":
exists "Voluntary medical male circumcision VMMC Condition"
or exists "Voluntary medical male circumcision VMMC Observation"
define "Voluntary medical male circumcision VMMC Condition":
[Condition: Concepts."Voluntary medical male circumcision VMMC"]
[Condition: Concepts."Voluntary medical male circumcision VMMC referral"]
define "Voluntary medical male circumcision VMMC Observation":
"Prevention services offered and referrals B.DE149 Observation" O
where O.status in { 'final', 'amended', 'corrected' }
and O.value ~ Concepts."Voluntary medical male circumcision VMMC"
and O.value ~ Concepts."Voluntary medical male circumcision VMMC referral"
/* End of Voluntary medical male circumcision VMMC */

/*
Expand Down Expand Up @@ -6261,10 +6258,8 @@ define "HBV treatment TDF start date":
*/

define "HCV test date D.DE169":
[Procedure] P
where P.status = 'completed'
and P.code ~ ConceptsCustom."HCV test"

"HCV test result D.DE170" O
return O.effective.toInterval().low
/* End of HCV test date D.DE169 */


Expand Down Expand Up @@ -9511,8 +9506,8 @@ define "Other medications Observation":
*/

define "Date of cervical cancer screening test":
"Cervical cancer primary screening test type" P
sort by start of performed.toInterval()
"Cervical cancer primary screening test" O
return O.effective.toInterval().low
/* End of Date of cervical cancer screening test */

/*
Expand All @@ -9536,10 +9531,12 @@ define "Lifetime screening test number Value":
@description: Type of cervical cancer screening test used in primary screening
*/

define "Cervical cancer primary screening test type":
[Procedure] P
where P.status = 'completed'
and P.category ~ ConceptsCustom."cervical cancer screening test"
define "Cervical cancer primary screening test":
[Observation] O
where O.status in { 'final', 'amended', 'corrected' }
and O.code in Concepts."Cervical cancer primary screening test type Choices"

// and P.category ~ Concepts."Procedure" we could
/* End of Cervical cancer primary screening test type */

/*
Expand All @@ -9549,7 +9546,7 @@ define "Cervical cancer primary screening test type":
*/

define "HPV-DNA":
"Cervical cancer primary screening test type" P
"Cervical cancer primary screening test" P
where P.code ~ Concepts."HPV-DNA"
/* End of HPV-DNA */

Expand All @@ -9560,7 +9557,7 @@ define "HPV-DNA":
*/

define "VIA":
"Cervical cancer primary screening test type" P
"Cervical cancer primary screening test" P
where P.code ~ Concepts."VIA"
/* End of VIA */

Expand All @@ -9571,7 +9568,7 @@ define "VIA":
*/

define "Cervical cytology":
"Cervical cancer primary screening test type" P
"Cervical cancer primary screening test" P
where P.code ~ Concepts."Cervical cytology"
/* End of Cervical cytology */

Expand All @@ -9582,7 +9579,7 @@ define "Cervical cytology":
*/

define "Other D.DE662":
"Cervical cancer primary screening test type" P
"Cervical cancer primary screening test" P
where P.code ~ Concepts."Other - HIV.D.DE662"
/* End of Other D.DE662 */

Expand All @@ -9591,13 +9588,7 @@ define "Other D.DE662":
@activity: HIV.D28 Offer other services
@description: Date of diagnosis of cervical precancer lesions or invasive cervical cancer
*/
// TODO: Replace placeholder with relevant CQL logic
define "Date of diagnosis of cervical precancer lesions or invasive cervical cancer":
[Observation: Concepts."Date of diagnosis of cervical precancer lesions or invasive cervical cancer"] O
where O.status in { 'final', 'amended', 'corrected' }
define "Date of diagnosis of cervical precancer lesions or invasive cervical cancer Value":
"Date of diagnosis of cervical precancer lesions or invasive cervical cancer" O
return O.value

/* End of Date of diagnosis of cervical precancer lesions or invasive cervical cancer */

/*
Expand Down Expand Up @@ -9673,7 +9664,8 @@ define "Cervical precancer lesions":
*/

define "Invasive cervical cancer":
[Condition: Concepts."Invasive cervical cancer"]
[Condition: Concepts."Invasive cervical cancer"] C
where exists (C.clinicalStatus.coding CStatus where CStatus.code in { 'active', 'recurrence', 'relapse' })

/* End of Invasive cervical cancer */

Expand Down Expand Up @@ -9752,7 +9744,7 @@ define "Stage IV":
define "Date of treatment for cervical precancer lesions":
[Procedure] P
where P.status = 'completed'
and P.category ~ ConceptsCustom."cervical precancer lesion treatment"
and P.code in Concepts."Invasive cervical cancer treatment method Choices"
/* End of Date of treatment for cervical precancer lesions */

/*
Expand All @@ -9778,8 +9770,8 @@ define "Invasive cervical cancer treatment episode Value":

define "Invasive cervical cancer treatment method":
[Procedure] P
where P.status = 'completed'
and P.category ~ ConceptsCustom."Invasive cervical cancer treatment"
where P.status in { 'completed', 'in-progress' }
and P.code in Concepts."Invasive cervical cancer treatment method Choices"

/* End of Invasive cervical cancer treatment method */

Expand Down Expand Up @@ -14275,12 +14267,10 @@ define "STI services date":
define "VMMC":
[Procedure] P
where P.status = 'completed'
and P.code ~ Concepts."Voluntary medical male circumcision VMMC"
and P.code ~ Concepts."VMMC procedure"

define "VMMC date":
[Procedure] P
where P.status = 'completed'
and P.code ~ Concepts."Voluntary medical male circumcision VMMC"
"VMMC" P
return start of P.performed.toInterval()
/* End of VMMC */

Expand Down Expand Up @@ -14344,8 +14334,7 @@ define "HIV-positive PRV.DE12 Condition":
[Condition: Concepts."HIV-positive - HIV.PRV.DE12"]
define "HIV-positive PRV.DE12 Observation":
"HIV status of contact Observation" O
where O.status in { 'final', 'amended', 'corrected' }
and O.value ~ Concepts."HIV-positive - HIV.PRV.DE12"
where O.value ~ Concepts."HIV-positive - HIV.PRV.DE12"
/* End of HIV-positive PRV.DE12 */

/*
Expand Down Expand Up @@ -14374,8 +14363,10 @@ define "HIV-negative PRV.DE13 Observation":
define "Unknown PRV.DE14":
exists "Unknown PRV.DE14 Condition"
or exists "Unknown PRV.DE14 Observation"

define "Unknown PRV.DE14 Condition":
[Condition: Concepts."Unknown - HIV.PRV.DE14"]

define "Unknown PRV.DE14 Observation":
"HIV status of contact Observation" O
where O.status in { 'final', 'amended', 'corrected' }
Expand Down Expand Up @@ -14618,9 +14609,10 @@ define "Viral load test result SRV.DE13 Value":
@activity: HIV.A2 Gather client details
@description: The date and time of the client's visit
*/

// TODO: MARK as visit?
define "Visit date SRV.DE15":
[Encounter] E
return E.period
/* End of Visit date SRV.DE15 */

/*
Expand Down
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