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fixed the medication scripts to pull additional data from mappings #95

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merged 1 commit into from
Nov 7, 2024
Merged

fixed the medication scripts to pull additional data from mappings #95

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29 changes: 15 additions & 14 deletions src/main/groovy/projects/patientfinder/medication.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,12 @@ final String CONCENTRATION_STRENGTH = "concentration_strength"
final String CONCENTRATION_STRENGTH_UNIT = "concentration_strength_unit"

final Map PROFILE_TYPES = [
DOSAGE_SITE : LaborFindingLaborValue.STRING_VALUE,
DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT: LaborFindingLaborValue.STRING_VALUE,
VOLUMEINFUSED : LaborFindingLaborValue.NUMERIC_VALUE,
VOLUMEINFUSED_UOM : LaborFindingLaborValue.STRING_VALUE,
CONCENTRATION_STRENGTH : LaborFindingLaborValue.NUMERIC_VALUE,
CONCENTRATION_STRENGTH_UNIT : LaborFindingLaborValue.STRING_VALUE
(DOSAGE_SITE) : LaborFindingLaborValue.STRING_VALUE,
(DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT): LaborFindingLaborValue.STRING_VALUE,
(VOLUMEINFUSED) : LaborFindingLaborValue.NUMERIC_VALUE,
(VOLUMEINFUSED_UOM) : LaborFindingLaborValue.STRING_VALUE,
(CONCENTRATION_STRENGTH) : LaborFindingLaborValue.NUMERIC_VALUE,
(CONCENTRATION_STRENGTH_UNIT) : LaborFindingLaborValue.STRING_VALUE
]


Expand All @@ -43,7 +43,7 @@ medication {

final def mapping = getLaborMapping(context)

final Map<String, Map> lflvMap = getLflvMap(mapping, PROFILE_TYPES)
final Map<String, Object> lflvMap = getLflvMap(mapping, PROFILE_TYPES)

code {
coding {
Expand Down Expand Up @@ -80,8 +80,8 @@ medication {
strength {
if (lflvMap.containsKey(CONCENTRATION_STRENGTH)) {
numerator {
value = lflvMap[CONCENTRATION_STRENGTH][LaborFindingLaborValue.NUMERIC_VALUE]
unit = lflvMap[CONCENTRATION_STRENGTH_UNIT][LaborFindingLaborValue.STRING_VALUE]
value = lflvMap[CONCENTRATION_STRENGTH]
unit = lflvMap[CONCENTRATION_STRENGTH_UNIT]
}
}
}
Expand Down Expand Up @@ -110,18 +110,19 @@ static boolean isFakeEpisode(final def episode) {
return fakeId != null
}

static Map<String, Map> getLflvMap(final def mapping, final Map<String, String> types) {
final Map<String, Map> lflvMap = [:]
static Map<String, Object> getLflvMap(final def mapping, final Map<String, String> types) {
final Map<String, Object> lflvMap = [:]
if (!mapping) {
return lflvMap
}

types.each { final String lvCode, final String lvType ->
final def lflv = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find { final def lflv ->
final def lflvForLv = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find { final def lflv ->
lflv[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][LaborValue.CODE] == lvCode
}
if (lflv && lflv[lvType]) {
lflvMap[lvCode] = [key: lflv[lvType]]

if (lflvForLv && lflvForLv[lvType]) {
lflvMap[(lvCode)] = lflvForLv[lvType]
}
}
return lflvMap
Expand Down
49 changes: 17 additions & 32 deletions src/main/groovy/projects/patientfinder/medicationAdministration.groovy
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package projects.patientfinder

import ca.uhn.fhir.model.api.TemporalPrecisionEnum
import de.kairos.centraxx.fhir.r4.utils.FhirUrls
import de.kairos.fhir.centraxx.metamodel.CrfTemplateField
import de.kairos.fhir.centraxx.metamodel.Episode
Expand All @@ -10,7 +9,6 @@ import de.kairos.fhir.centraxx.metamodel.LaborMapping
import de.kairos.fhir.centraxx.metamodel.LaborMethod
import de.kairos.fhir.centraxx.metamodel.LaborValue
import de.kairos.fhir.centraxx.metamodel.Unity
import de.kairos.fhir.centraxx.metamodel.enums.DatePrecision
import de.kairos.fhir.centraxx.metamodel.enums.MedicationServiceType
import org.apache.commons.lang3.StringUtils
import org.hl7.fhir.r4.model.MedicationAdministration
Expand All @@ -26,12 +24,12 @@ final String CONCENTRATION_STRENGTH = "concentration_strength"
final String CONCENTRATION_STRENGTH_UNIT = "concentration_strength_unit"

final Map PROFILE_TYPES = [
DOSAGE_SITE : LaborFindingLaborValue.STRING_VALUE,
DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT : LaborFindingLaborValue.STRING_VALUE,
VOLUMEINFUSED : LaborFindingLaborValue.NUMERIC_VALUE,
VOLUMEINFUSED_UOM : LaborFindingLaborValue.STRING_VALUE,
CONCENTRATION_STRENGTH : LaborFindingLaborValue.NUMERIC_VALUE,
CONCENTRATION_STRENGTH_UNIT : LaborFindingLaborValue.STRING_VALUE
(DOSAGE_SITE) : LaborFindingLaborValue.STRING_VALUE,
(DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT): LaborFindingLaborValue.STRING_VALUE,
(VOLUMEINFUSED) : LaborFindingLaborValue.NUMERIC_VALUE,
(VOLUMEINFUSED_UOM) : LaborFindingLaborValue.STRING_VALUE,
(CONCENTRATION_STRENGTH) : LaborFindingLaborValue.NUMERIC_VALUE,
(CONCENTRATION_STRENGTH_UNIT) : LaborFindingLaborValue.STRING_VALUE
]


Expand All @@ -43,17 +41,17 @@ final Map PROFILE_TYPES = [
*/
medicationAdministration {

id = "MedicationAdministration/" + context.source[medication().id()]

if (context.source[medication().serviceType()] != MedicationServiceType.GAB.name()) {
return
}

id = "MedicationAdministration/" + context.source[medication().id()]

final def mapping = context.source[medication().laborMappings()].find { final def lm ->
lm[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_METHOD][LaborMethod.CODE] == "MedicationAdministration_profile"
}

final Map<String, Map> lflvMap = getLflvMap(mapping, PROFILE_TYPES)
final Map<String, Object> lflvMap = getLflvMap(mapping, PROFILE_TYPES)

status = MedicationAdministration.MedicationAdministrationStatus.COMPLETED

Expand Down Expand Up @@ -99,7 +97,7 @@ medicationAdministration {

if (lflvMap.containsKey(DOSAGE_SITE)){
site {
text = lflvMap.get(DOSAGE_SITE) as String
text = lflvMap[DOSAGE_SITE] as String
}
}

Expand All @@ -118,7 +116,7 @@ medicationAdministration {
rateQuantity {
value = sanitizeScale(context.source[medication().quantity()] as String)
if (lflvMap.containsKey(DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT)){
unit = lflvMap.get(DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT) as String
unit = lflvMap[DOSAGE_DOSEANDRATE_RATEQUANTITY_UNIT] as String
}
}
}
Expand All @@ -138,20 +136,6 @@ static String normalizeDate(final String dateTimeString) {
return dateTimeString != null ? dateTimeString.substring(0, 19) : null
}

static String convertPrecision(final String cxxPrecision) {
if (DatePrecision.EXACT.name() == cxxPrecision) {
return TemporalPrecisionEnum.MILLI.name()
} else if (DatePrecision.DAY.name() == cxxPrecision) {
return TemporalPrecisionEnum.DAY.name()
} else if (DatePrecision.MONTH.name() == cxxPrecision) {
return TemporalPrecisionEnum.MONTH.name()
} else if (DatePrecision.YEAR.name() == cxxPrecision) {
return TemporalPrecisionEnum.YEAR.name()
} else {
return DatePrecision.DAY
}
}

static BigDecimal sanitizeScale(final String numeric) {
return numeric == null || !StringUtils.isNumeric(numeric) ? null : new BigDecimal(numeric).stripTrailingZeros()
}
Expand All @@ -169,18 +153,19 @@ static boolean isFakeEpisode(final def episode) {
return fakeId != null
}

static Map<String, Map> getLflvMap(final def mapping, final Map<String, String> types){
final Map<String, Map> lflvMap = [:]
static Map<String, Object> getLflvMap(final def mapping, final Map<String, String> types) {
final Map<String, Object> lflvMap = [:]
if (!mapping) {
return lflvMap
}

types.each { final String lvCode, final String lvType ->
final def lflv = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find { final def lflv ->
final def lflvForLv = mapping[LaborMapping.LABOR_FINDING][LaborFinding.LABOR_FINDING_LABOR_VALUES].find { final def lflv ->
lflv[LaborFindingLaborValue.CRF_TEMPLATE_FIELD][CrfTemplateField.LABOR_VALUE][LaborValue.CODE] == lvCode
}
if (lflv && lflv[lvType]) {
lflvMap[lvCode] = [key: lflv[lvType]]

if (lflvForLv && lflvForLv[lvType]) {
lflvMap[(lvCode)] = lflvForLv[lvType]
}
}
return lflvMap
Expand Down
1 change: 1 addition & 0 deletions src/main/groovy/projects/patientfinder/medicationRequest.groovy
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Expand Up @@ -25,6 +25,7 @@ import static de.kairos.fhir.centraxx.metamodel.RootEntities.medication
* @since v.1.41.0, CXX.v.2024.2.0
*/
medicationRequest {

if (context.source[medication().serviceType()] != MedicationServiceType.VER.name()) {
return
}
Expand Down