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Automatically set units and precision in rules #391

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Automatically set units and precision in rules #391

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9523260
Fix indices of paths returned for queries with indices
J3173 Aug 18, 2022
7778af0
automatically set units and precision in rules
EdwardvanRaak Feb 11, 2022
a3c00bd
address some review comments
EdwardvanRaak Feb 11, 2022
76a9114
expose getFirstOperand and getSecondOperand
EdwardvanRaak May 3, 2022
8aec62b
fixDvProportion by hardcoding for now
EdwardvanRaak May 3, 2022
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4 changes: 2 additions & 2 deletions aom/src/main/java/com/nedap/archie/rules/Operator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ public void setOperands(List<Expression> operands) {
}

@JsonIgnore
protected Expression getFirstOperand() {
public Expression getFirstOperand() {
return operands.size() > 0 ? operands.get(0) : null;
}

Expand All @@ -44,7 +44,7 @@ protected void setFirstOperand(Expression firstOperand) {
}

@JsonIgnore
protected Expression getSecondOperand() {
public Expression getSecondOperand() {
return operands.size() > 1 ? operands.get(1) : null;
}

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104 changes: 100 additions & 4 deletions openehr-rm/src/main/java/com/nedap/archie/rminfo/UpdatedValueHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,17 @@
import com.google.common.base.Joiner;
import com.google.common.base.Strings;
import com.nedap.archie.ArchieLanguageConfiguration;
import com.nedap.archie.aom.*;
import com.nedap.archie.aom.primitives.CTerminologyCode;
import com.nedap.archie.aom.Archetype;
import com.nedap.archie.aom.CAttribute;
import com.nedap.archie.aom.CAttributeTuple;
import com.nedap.archie.aom.CPrimitiveTuple;
import com.nedap.archie.aom.OperationalTemplate;
import com.nedap.archie.aom.primitives.CInteger;
import com.nedap.archie.aom.primitives.CString;
import com.nedap.archie.aom.terminology.ArchetypeTerm;
import com.nedap.archie.aom.terminology.ArchetypeTerminology;
import com.nedap.archie.aom.utils.AOMUtils;
import com.nedap.archie.base.Interval;
import com.nedap.archie.paths.PathSegment;
import com.nedap.archie.query.APathQuery;
import com.nedap.archie.query.RMObjectWithPath;
import com.nedap.archie.query.RMPathQuery;
Expand All @@ -18,15 +22,19 @@
import com.nedap.archie.rm.datatypes.CodePhrase;
import com.nedap.archie.rm.datavalues.DvCodedText;
import com.nedap.archie.rm.datavalues.quantity.DvOrdinal;
import com.nedap.archie.rm.datavalues.quantity.DvProportion;
import com.nedap.archie.rm.datavalues.quantity.DvQuantity;
import com.nedap.archie.rm.support.identification.TerminologyId;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import javax.xml.xpath.XPathExpressionException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import javax.xml.xpath.XPathExpressionException;

public class UpdatedValueHandler {

private static final Logger logger = LoggerFactory.getLogger(UpdatedValueHandler.class);
Expand All @@ -35,10 +43,98 @@ public static Map<String, Object> pathHasBeenUpdated(Object rmObject, Archetype
if(parent instanceof CodePhrase) {
return fixCodePhrase(rmObject, archetype, pathOfParent);
}
if (parent instanceof DvQuantity) {
return fixDvQuantity(rmObject, archetype, pathOfParent);
}
if (parent instanceof DvProportion) {
return fixDvProportion(rmObject, archetype, pathOfParent);
}
return new HashMap<>();
}

private static Map<String, Object> fixDvProportion(Object rmObject, Archetype archetype, String pathOfParent) {
try {
OperationalTemplate template = (OperationalTemplate) archetype;
Map<String, Object> result = new HashMap<>();
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Two more todo's:

  • check if actually the magnitude is being set (see the pathOfParent.endsWith contruction elsewhere)
  • if units or precision already have a value, should they be set? You probably do not want to override a value set manually or with a different rule elsewhere?

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check if actually the magnitude is being set (see the pathOfParent.endsWith contruction elsewhere)

I only see .../value in the pathOfParent when these quantities are being set by rule evaluation. Not sure how that would work then, or should I expect a .../value/magnitude path or something.


RMPathQuery rmPathQuery = new RMPathQuery(pathOfParent);

DvProportion proportion = rmPathQuery.find(ArchieRMInfoLookup.getInstance(), rmObject);

// TODO Figure out how to not hardcode these
proportion.setDenominator(100.0);
result.put(pathOfParent + "/denominator", 100.0);
proportion.setType(2L);
result.put(pathOfParent + "/type", 2L);
proportion.setPrecision(1L);
result.put(pathOfParent + "/precision", 1L);

return result;
} catch (Exception e) {
logger.warn("cannot fix DvProportion", e);
}

return new HashMap<>();
}

private static Map<String, Object> fixDvQuantity(Object rmObject, Archetype archetype, String pathOfParent) {
try {
// TODO Check for magnitude?
// TODO Check if this fix actually needs to occur
return fixForMagnitude(rmObject, (OperationalTemplate) archetype, pathOfParent);
} catch (Exception e) {
logger.warn("cannot fix DvQuantity", e);
}

return new HashMap<>();
}

private static Map<String, Object> fixForMagnitude(Object rmObject, OperationalTemplate template, String pathOfParent) {
Map<String, Object> result = new HashMap<>();

RMPathQuery rmPathQuery = new RMPathQuery(pathOfParent);
DvQuantity quantity = rmPathQuery.find(ArchieRMInfoLookup.getInstance(), rmObject);

CAttribute units = template.getDefinition().itemAtPath(pathOfParent + "/units");
CAttribute precision = template.getDefinition().itemAtPath(pathOfParent + "/precision");

if (units.getChildren().size() != 1) return result; // Only fix if there is 1 unit

// Fix units
CString cString = (CString) units.getChildren().get(0);
List<String> cStringConstraint = cString.getConstraint();
if(cStringConstraint != null && cStringConstraint.size() == 1) {
String constraint = cStringConstraint.get(0);
if(!CString.isRegexConstraint(constraint)) {
quantity.setUnits(constraint);
result.put(pathOfParent + "/units", constraint);
}
}

if (precision.getChildren().size() != 1)
return result; // Only fix if there is 1 precision

// Fix precision
CInteger cInteger = (CInteger) precision.getChildren().get(0);

List<Interval<Long>> cIntegerConstraint = cInteger.getConstraint();

if (cIntegerConstraint != null && cIntegerConstraint.size() == 1) {
Interval<Long> interval = cIntegerConstraint.get(0);
long value;
if (interval.isUpperUnbounded()) {
value = -1;
} else if (interval.isUpperIncluded() && interval.getUpper() != null) {
value = interval.getUpper();
} else if (interval.getUpper() != null) {
value = interval.getUpper() -1 ;
} else throw new IllegalStateException("upper bound was not available");
quantity.setPrecision(value);
result.put(pathOfParent + "/precision", value);
}
return result;
}

private static Map<String, Object> fixCodePhrase(Object rmObject, Archetype archetype, String pathOfParent) {
try {
//special case: if at-code has been set, we need to do more!
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2 changes: 1 addition & 1 deletion path-queries/src/main/java/com/nedap/archie/query/RMPathQuery.java
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Expand Up @@ -245,7 +245,7 @@ private Collection<RMObjectWithPath> findRMObjectsWithPathCollection(ModelInfoLo
for(Object object:collection) {
if(number == i) {
//TODO: check for other constraints as well
return Lists.newArrayList(new RMObjectWithPath(object, path + buildPathConstraint(i-1, lookup.getArchetypeNodeIdFromRMObject(object))));
return Lists.newArrayList(new RMObjectWithPath(object, path + buildPathConstraint(i, lookup.getArchetypeNodeIdFromRMObject(object))));
}
i++;
}
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8 changes: 8 additions & 0 deletions tools/src/test/java/com/nedap/archie/adlparser/RMPathQueryTest.java
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Expand Up @@ -99,6 +99,14 @@ public void multipleItems() {
for(RMObjectWithPath value:values) {
assertEquals(value.getObject(), new RMPathQuery(value.getPath()).findList(modelInfoLookup, composition).get(0).getObject());
}

// check that one result is returned when specifying an index, and with the correct path
values = new RMPathQuery("/context[id11]/other_context[id2]/items[id3,1]/items[id5]/value").findList(modelInfoLookup, composition);
assertEquals(1, values.size());
assertEquals("/context/other_context[id2]/items[id3, 1]/items[id5, 2]/value", values.get(0).getPath());
for(RMObjectWithPath value:values) {
assertEquals(value.getObject(), new RMPathQuery(value.getPath()).findList(modelInfoLookup, composition).get(0).getObject());
}
}


Expand Down