add debug cql file

input/cql/Debug.cql

@@ -0,0 +1,346 @@
+library Debug version '0.1.0'
+
+using FHIR version '4.0.1'
+
+include FHIRHelpers version '4.0.1'
+include FHIRCommon version '4.0.1' called FC
+include MERConcepts called Cx
+
+// parameter "Measurement Period" Interval<DateTime>
+parameter "Measurement Period" Interval<DateTime> default Interval[@1990-01-01T, @2022-12-31T]
+
+context Patient
+
+
+define "Deceased":
+  Patient.deceased is not null 
+  and (Patient.deceased is true or Patient.deceased before end of "Measurement Period")
+  // and Patient.deceased.value.not()
+  // and Patient.deceased.not()
+  // // alternatively
+  // where P.deceased is false
+  //   or P.deceased before Today()
+
+
+// synthea
+// define "HIV Condition":
+//   exists ["Condition": Cx."HIV Condition Positive"]
+//   // synthea
+//   or exists [Observation: Cx."Acquired immune deficiency syndrome (disorder)"]
+//   or exists [Encounter] E
+//     // where E.reasonCode in Cx."Acquired immune deficiency syndrome (disorder)"
+//     where (Last(E.reasonCode) ~ Cx."Acquired immune deficiency syndrome (disorder)")
+
+
+// define "Is HIV Positive":
+//   "HIV Condition"
+
+
+// define "Is HIV Negative":
+//   not "HIV Condition"
+
+
+// define "HIV Test Results":
+//   case
+//     when "Is HIV Positive" then "HIV Positive Observation"
+//     when "Is HIV Negative" then "HIV Negative Observation"
+//     else null
+//   end
+
+
+define "Pregnant":
+  exists ["Condition": Cx."Pregnancy (finding)"]
+
+
+// define "HIV Test Exists":
+//   exists ([Observation: Cx."HIV 1 and 2 tests - Meaningful Use set"])
+
+
+// define "HIV Positive Observation":
+//   [Observation: Cx."HIV 1 and 2 tests - Meaningful Use set"] Observation
+//     where Observation.value = "Is HIV Positive"
+
+
+// define "HIV Negative Observation":
+//   [Observation: Cx."HIV 1 and 2 tests - Meaningful Use set"] Observation
+//     where Observation.value = "Is HIV Negative"
+
+// this union is a placeholder for implementer or dak valuesets
+// define "Viral Load Test Result":
+//   ["Observation": Cx."HIV 1 RNA NAA+probe (Specimen)"] Obs
+//   union ["Observation": Cx."HIV 1 RNA [#/volume] (viral load) in Serum or Plasma by NAA with probe detection"] Obs
+//     // where Obs.status = 'final'
+//     // and Obs.value is not null
+//   // synthea
+//     // when Obs.effective during "Measurement Period"
+
+
+// define "Living with HIV and on ART with suppressed viral load results (<1000 copies/mL)":
+//   "Viral Load Test Result" Observation
+//     where Observation.value < 1000 '{copies}/mL'
+
+
+// define "Living with HIV and on ART with unsuppressed viral load results (>1000 copies/mL)":
+//   "Viral Load Test Result" Observation
+//     where Observation.value >= 1000 '{copies}/mL'
+
+
+// define "Suppressed":
+//   "Viral Load Test Result" Observation
+//     where Observation.value < 1000 '{copies}/mL'
+
+
+// define "Unsuppressed":
+//   "Viral Load Test Result" Observation
+//     where Observation.value >= 1000 '{copies}/mL'
+
+
+define "Contact date":
+  [Encounter] E
+    return E.period.start
+
+
+// define "HIV Positive but no VL test":
+//   "Is HIV Positive" = true
+
+
+
+// Rest of HIVIndicators
+
+define "on ART PLIR":
+  ["Observation": Cx."Currently taking ARV"] o
+      where o.value.coding[0]= Cx."Coded Answer"
+      or o.value.coding[1]= Cx."Coded Answer"
+      or o.value.coding[2]= Cx."Coded Answer"
+      // and o.status in {'final', 'amended', 'corrected'}
+      // and o.effective in day of "Measurement Period"
+
+
+define "on ART PLIR debug one":
+  ["Observation": Cx."Currently taking ARV"] o
+    with ["Encounter"] E
+    such that E.period during "Measurement Period"
+      // and o.status in {'final', 'amended', 'corrected'}
+
+
+define "on ART PLIR debug two":
+  ["Observation": Cx."Currently taking ARV"] o
+    with [Encounter] E 
+    such that E.period during "Measurement Period"
+
+
+define "on ART PLIR debug three":
+    ( ["Observation": Cx."Currently taking ARV"] ) o
+        where o.value.coding[0]= Cx."Coded Answer"
+        or o.value.coding[1]= Cx."Coded Answer"
+        or o.value.coding[2]= Cx."Coded Answer"
+
+
+define "ART Therapy Observation":
+  ["Observation": Cx."History of antiretroviral therapy (situation)"] O
+    where O.status = 'final'
+
+// to review
+// ART Therapy Observation=[]
+// ART Therapy Condition=[]
+
+define "ART Therapy Condition":
+  ["Condition": Cx."History of antiretroviral therapy (situation)"] C
+    where C.verificationStatus ~ FC."confirmed"
+      and C.clinicalStatus ~ FC."active"
+
+
+// define "ART Therapy Medication":
+//   ["MedicationDispense": Cx."ART Medications"] M
+//     where M.status = 'completed'
+
+// synthea
+define "ART Therapy Medication":
+  ["MedicationRequest": Cx."ART Medications"] M
+    // where M.status = 'active'
+    where M.authoredOn during "Measurement Period"
+
+
+
+define "ART Dates":
+  ("ART Therapy Observation" O return O.effective as dateTime)
+    union ("ART Therapy Condition" C return C.onset as dateTime)
+    union ("ART Therapy Medication" M return M.authoredOn)
+    // union ("ART Therapy Medication" M return M)
+
+
+
+define "Date of First Evidence of ART":
+  Min("ART Dates")
+
+
+// define "PMTCT ART Status":
+//   case
+//     when "Date of First Evidence of ART" before start of "Measurement Period" then Cx."Currently taking ARV"
+//     when "Date of First Evidence of ART" during "Measurement Period" then Cx."New on ART"
+//     else null
+//   end
+
+
+define "On ART":
+  exists ("ART Dates" D where D during "Measurement Period")
+    or exists (
+      "ART Therapy Condition" C
+        where Interval[C.onset, C.abatement] overlaps "Measurement Period"
+    )
+
+
+// define "HIV Test Observation":
+//   [Observation: Cx."HIV 1 and 2 tests - Meaningful Use set"] O
+//     // where O.status = 'final'
+//     //   and O.value is not null
+
+
+// define "Date of First Evidence of HIV Status":
+//   Min("HIV Test Observation" O return O.effective)
+
+
+// define "Date of First Evidence of HIV Positive":
+//   Min("HIV Positive Observation" O return O.effective)
+
+
+// define "Date of First Evidence of HIV Negative":
+//   Min("HIV Negative Observation" O return O.effective)
+
+
+// define "PMTCT HIV Status":
+//   case
+//     when "Date of First Evidence of HIV Positive" before start of "Measurement Period" then 'Known Positive'
+//     when "Date of First Evidence of HIV Positive" during "Measurement Period" then 'Newly Identified Positive'
+//     when "Date of First Evidence of HIV Negative" during "Measurement Period" then 'Newly Identified Negative'
+//     else null
+//   end
+
+
+define "Newly enrolled on antiretroviral therapy (ART) during measurement period":
+  "Date of First Evidence of ART" during "Measurement Period"
+
+
+define "Is Pregnant":
+  exists ([Condition: Cx."Pregnancy status - Reported"] C
+    where C.verificationStatus ~ FC."confirmed"
+      and C.clinicalStatus ~ FC."active"
+      and C.onset during "Measurement Period"
+  )
+
+
+// define "Is Breastfeeding":
+//   exists ([Observation: Cx."Postpartum state (finding)"] O
+//     where O.status = 'final'
+//       and O.effective during "Measurement Period"
+//   )
+
+
+define "Newly enrolled on antiretroviral therapy (ART) during measurement period (pregnant and breastfeeding)":
+  // "Is Pregnant" and "Is Breastfeeding" and "Date of First Evidence of ART" during "Measurement Period"
+  "Is Pregnant" and "Date of First Evidence of ART" during "Measurement Period"
+
+
+define "Receiving antiretroviral therapy (ART) during measurement period":
+  exists ("ART Dates" D where D during "Measurement Period")
+    or exists (
+      "ART Therapy Condition" C
+        where Interval[C.onset, C.abatement] overlaps "Measurement Period"
+    )
+
+
+define "Year Preceding the Measurement Period":
+  Interval[start of "Measurement Period" - 1 year, start of "Measurement Period")
+
+
+define "Month Before the Year Preceding the Measurement Period":
+  Interval[start of "Year Preceding the Measurement Period" - 1 month, start of "Year Preceding the Measurement Period")
+
+
+define "Receiving antiretroviral therapy (ART) at 12 months after initiating":
+  "Date of First Evidence of ART" during "Month Before the Year Preceding the Measurement Period"
+    and "Receiving antiretroviral therapy (ART) during measurement period"
+
+
+define "Receiving antiretroviral therapy (ART) at 12 months after initiating (pregnant and breastfeeding)":
+  "Receiving antiretroviral therapy (ART) at 12 months after initiating"
+    and "Is Pregnant"
+    // and "Is Breastfeeding"
+
+
+define "Initiated antiretroviral therapy (ART) in the 12 months prior to measurement period":
+  "Date of First Evidence of ART" during "Year Preceding the Measurement Period"
+
+
+// define "Antenatal Care Visit":
+//   // [Encounter: Cx."Prenatal initial visit (regime/therapy)"] E
+//   [Encounter: Cx."Prenatal initial visit (regime/therapy)"] E
+//     where E.status = 'finished'
+//       and E.period during Interval[start of "Year Preceding the Measurement Period", end of "Measurement Period"]
+
+
+// define "Live Birth Procedure":
+//   [Procedure: Cx."Livebirth (finding)"] P
+//     where P.status = 'completed'
+
+
+// define "Antenatal Care Visit or Live Birth during the Measurement Period":
+//   ("Is Pregnant" and exists ("Antenatal Care Visit" V where V.period during "Measurement Period"))
+//     or exists ("Live Birth Procedure" P where P.performed during "Measurement Period")
+
+
+// define "Antenatal Care Visit or Live Birth during Measurement Period (HIV Positive)":
+//   "Is HIV Positive"
+//     and "Antenatal Care Visit or Live Birth during the Measurement Period"
+
+
+// define "HIV-positive, pregnant, and receiving antiretroviral therapy (ART) to reduce the risk of mother-to-child-transmission during pregnancy":
+//   "Is HIV Positive"
+//     and "Is Pregnant"
+//     and "Receiving antiretroviral therapy (ART) during measurement period"
+
+
+define "Pregnant and receiving antiretroviral therapy (ART) to reduce the risk of mother-to-child-transmission during pregnancy":
+    "Is Pregnant"
+      and "Receiving antiretroviral therapy (ART) during measurement period"
+
+// define "Viral Load Test Result":
+//   ["Observation": Cx."Viral Load Test"] O
+//     where O.status = 'final'
+//       and O.value is not null
+
+
+// define "Living with HIV and on ART with suppressed viral load results (<1000 copies/mL)":
+//   "Is HIV Positive"
+//     and Cx."Receiving antiretroviral therapy (ART) during measurement period"
+//     and exists (
+//       Cx."Viral Load Test Result" R
+//         where R.effective during "Measurement Period"
+//           and R.value < 1000 '{copies}/mL'
+//       )
+
+
+// define "Received HIV Testing Services (HTS) and Received Test Results":
+//   ["Observation": Cx."HIV Testing Services"] O
+//     where O.status = 'final'
+//       and O.value is not null
+
+
+// define "First antenatal care visit":
+//   First("Antenatal Care Visit" V sort by start of period)
+
+
+// define "Date of First Evidence of HIV Status":
+//   Min("HIV Test Observation" O return O.effective)
+
+
+// define "HIV Status Known at First Antenatal Care Visit":
+//   "Date of First Evidence of HIV Status" on or before start of "First antenatal care visit".period
+
+
+// define "Receiving antiretroviral therapty (ART) and Viral Load Measurement in the past 12 months":
+//   "Receiving antiretroviral therapy (ART) during measurement period"
+//     and exists (
+//       "Viral Load Test Result" R
+//         where R.effective during "Year Preceding the Measurement Period"
+//     )

input/fsh/library.fsh

@@ -37,6 +37,23 @@ Description: "FHIRHelpers"
 * content.id = "ig-loader-FHIRHelpers.cql"
 
 
+// -----------------------------
+
+
+Instance: Debug
+InstanceOf: Library
+Title: "Debug"
+Description: "Debug"
+* insert lib-common
+* name = "Debug"
+* title = "Debug"
+* description = "Debug"
+* version = "0.1.0"
+* url = "https://path-global-health.github.io/MERindicators/Library/Debug"
+// * identifier.value = "Debug"
+* content.id = "ig-loader-Debug.cql"
+
+
 Instance: MERConcepts
 InstanceOf: Library
 Title: "MERConcepts"

input/fsh/measure.fsh

@@ -93,3 +93,19 @@ Description: "MERTXCURR"
 * insert common-numonly
 
 
+Instance: MERDebug
+InstanceOf: Measure
+Title: "MERDebug"
+Description: "MERDebug"
+* id = "MERDebug"
+* insert meas-common
+* name = "MERDebug"
+* title = "MERDebug"
+* description = "MERDebug"
+* url = "https://path-global-health.github.io/MERindicators/Measure/MERDebug"
+* identifier[0].value = "MERDebug"
+// only numerator
+* scoring = $measure-scoring#cohort
+* library[+] = Canonical(Debug)
+* insert common-numonly
+