} else if ("body_side_class".equals(annotation.type)) {
BodySide attribute = new BodySide(jCas);
attribute.setValue(stringSlots.remove("body_side_normalization"));
attribute.addToIndexes();
BodySideModifier modifier = new BodySideModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("course_class".equals(annotation.type)) {
Course attribute = new Course(jCas);
attribute.setValue(stringSlots.remove("course_normalization"));
attribute.addToIndexes();
CourseModifier modifier = new CourseModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setTypeID(CONST.MODIFIER_TYPE_ID_COURSE_CLASS);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("estimated_flag_indicator".equals(annotation.type)) {
boolean value = booleanSlots.remove("estimated_normalization");
LabEstimatedModifier modifier = new LabEstimatedModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setIndicated(value);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("lab_interpretation_indicator".equals(annotation.type)) {
String value = stringSlots.remove("lab_interpretation_normalization");
LabInterpretationModifier modifier = new LabInterpretationModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setTypeID(CONST.MODIFIER_TYPE_ID_LAB_INTERPRETATION_INDICATOR);
modifier.setValue(value);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("reference_range".equals(annotation.type)) {
LabReferenceRangeModifier modifier = new LabReferenceRangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
LabReferenceRange attribute = new LabReferenceRange(jCas);
attribute.setValue(modifier.getCoveredText());
attribute.addToIndexes();
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Value".equals(annotation.type)) {
KnowtatorAnnotation unit = annotationSlots.remove("value_unit");
KnowtatorAnnotation number = annotationSlots.remove("value_number");
LabValue attribute = new LabValue(jCas);
if (unit != null) {
KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
String unitString = text.substring(unitSpan.begin, unitSpan.end);
attribute.setUnit(unitString);
}
if (number != null) {
KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
String numberString = text.substring(numberSpan.begin, numberSpan.end);
attribute.setNumber(numberString);
}
attribute.addToIndexes();
LabValueModifier modifier = new LabValueModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Value number".equals(annotation.type)) {
// already handled in "Value" above
} else if ("Value unit".equals(annotation.type)) {
// already handled in "Value" above
} else if ("allergy_indicator_class".equals(annotation.type)) {
String value = stringSlots.remove("allergy_indicator_normalization");
MedicationAllergyModifier modifier = new MedicationAllergyModifier(jCas, coveringSpan.begin, coveringSpan.end);
if (null == value) {
modifier.setIndicated(false);
} else if ("indicator_present".equals(value)) {
modifier.setIndicated(true);
} else if ("indicator_absent".equals(value)) {
modifier.setIndicated(false);
} else {
LOGGER.error(String.format(
"unrecognized allergy-indicator value \"%s\" on annotation with id \"%s\"",
value,
annotation.id));
}
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Dosage".equals(annotation.type)) {
String value = stringSlots.remove("dosage_values");
MedicationDosage attribute = new MedicationDosage(jCas);
attribute.setValue(value);
attribute.addToIndexes();
MedicationDosageModifier modifier = new MedicationDosageModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Duration".equals(annotation.type)) {
String value = stringSlots.remove("duration_values");
MedicationDuration attribute = new MedicationDuration(jCas);
attribute.setValue(value);
attribute.addToIndexes();
MedicationDurationModifier modifier = new MedicationDurationModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Form".equals(annotation.type)) {
String value = stringSlots.remove("form_values");
MedicationForm attribute = new MedicationForm(jCas);
attribute.setValue(value);
attribute.addToIndexes();
MedicationFormModifier modifier = new MedicationFormModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Frequency".equals(annotation.type)) {
KnowtatorAnnotation unit = annotationSlots.remove("frequency_unit");
KnowtatorAnnotation number = annotationSlots.remove("frequency_number");
MedicationFrequency attribute = new MedicationFrequency(jCas);
if (unit != null) {
String unitString = unit.stringSlots.get("frequency_unit_values");
attribute.setUnit(unitString);
}
if (number != null) {
String numberString = number.stringSlots.get("frequency_number_normalization");
attribute.setNumber(numberString);
}
attribute.addToIndexes();
MedicationFrequencyModifier modifier = new MedicationFrequencyModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Frequency number".equals(annotation.type)) {
// already handled in "Frequency" above
stringSlots.remove("frequency_number_normalization");
} else if ("Frequency unit".equals(annotation.type)) {
// already handled in "Frequency" above
stringSlots.remove("frequency_unit_values");
} else if ("Route".equals(annotation.type)) {
String value = stringSlots.remove("route_values");
MedicationRoute attribute = new MedicationRoute(jCas);
attribute.setValue(value);
attribute.addToIndexes();
MedicationRouteModifier modifier = new MedicationRouteModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Status change".equals(annotation.type)) {
String value = stringSlots.remove("change_status_value");
MedicationStatusChange attribute = new MedicationStatusChange(jCas);
attribute.setValue(value);
attribute.addToIndexes();
MedicationStatusChangeModifier modifier = new MedicationStatusChangeModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Strength".equals(annotation.type)) {
KnowtatorAnnotation unit = annotationSlots.remove("strength_unit");
KnowtatorAnnotation number = annotationSlots.remove("strength_number");
MedicationStrength attribute = new MedicationStrength(jCas);
if (unit != null) {
KnowtatorAnnotation.Span unitSpan = unit.getCoveringSpan();
String unitString = text.substring(unitSpan.begin, unitSpan.end);
attribute.setUnit(unitString);
}
if (number != null) {
KnowtatorAnnotation.Span numberSpan = number.getCoveringSpan();
String numberString = text.substring(numberSpan.begin, numberSpan.end);
attribute.setNumber(numberString);
}
attribute.addToIndexes();
MedicationStrengthModifier modifier = new MedicationStrengthModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Strength number".equals(annotation.type)) {
// already handled in "Strength" above
} else if ("Strength unit".equals(annotation.type)) {
// already handled in "Strength" above
} else if ("device_class".equals(annotation.type)) {
String code = stringSlots.remove("associatedCode");
ProcedureDevice attribute = new ProcedureDevice(jCas);
attribute.setValue(code);
ProcedureDeviceModifier modifier = new ProcedureDeviceModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("method_class".equals(annotation.type)) {
String code = stringSlots.remove("associatedCode");
ProcedureMethod attribute = new ProcedureMethod(jCas);
attribute.setValue(code);
ProcedureMethodModifier modifier = new ProcedureMethodModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("severity_class".equals(annotation.type)) {
Severity attribute = new Severity(jCas);
attribute.setValue(stringSlots.remove("severity_normalization"));
attribute.addToIndexes();
SeverityModifier modifier = new SeverityModifier(jCas, coveringSpan.begin, coveringSpan.end);
modifier.setTypeID(CONST.MODIFIER_TYPE_ID_SEVERITY_CLASS);
modifier.setNormalizedForm(attribute);
modifier.addToIndexes();
idAnnotationMap.put(annotation.id, modifier);
} else if ("Date".equals(annotation.type)) {
String month = stringSlots.remove("month");
String day = stringSlots.remove("day");