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Parse domain specific types, add conversion config to archie-utils
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Lines changed: 277 additions & 140 deletions

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‎README.md‎

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@@ -453,7 +453,8 @@ The following features are experimental. This means its working or API will like
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Starting from version 0.7, Archie can import ADL 1.4 files, and convert them to ADL 2. To do so, do the following:
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```java
456-
ADL14ConversionConfiguration conversionConfiguration = new ADL14ConversionConfiguration();
456+
//this is the default configuration. You can implement your own if you want to
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ADL14ConversionConfiguration conversionConfiguration = OpenEHRADL14ConversionConfiguration.getConfig();
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ADL14Converter converter = new ADL14Converter(BuiltinReferenceModels.getMetaModels(), conversionConfiguration);
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List<Archetype> archetypes = new ArrayList<>();
@@ -498,7 +499,7 @@ The conversion log can be serialized to a file for storage using Jackson, so it
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### Conversion Configuration
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You may have noticed an instance of `ADL14ConversionConfiguration` in the previous example. In this configuration the mapping from term codes as used in ADL 1.4 to term URIs as used in ADL 2 can be specified. See the `ConversionConfigForTest.java` file for an example on how this works, and how this can be serialized to a file, and the file `/tools/src/test/java/com/nedap/archie/adl14/configuration.json` for an example of a simple serialized configuration that contains sane defaults for snomed, loinc and openehr URIs.
502+
You may have noticed an instance of `ADL14ConversionConfiguration` in the previous example. In this configuration the mapping from term codes as used in ADL 1.4 to term URIs as used in ADL 2 can be specified. The archie-utils package provides a default configuration in the class `OpenEHRADL14ConversionConfiguration`. It is possible to supply your own, see the default implementation on how this works, and how this can be serialized to a file, and the file `/archie-utils/src/main/resources/adl14conversionconfiguration.json` for an example of a simple serialized configuration that contains sane defaults for snomed, loinc and openehr URIs.
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If you leave the configuration empty, the converter will fall back to a default URI conversion.
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‎aom/src/main/java/com/nedap/archie/adl14/treewalkers/Adl14CComplexObjectParser.java‎

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‎archie-utils/build.gradle‎

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@@ -1,4 +1,4 @@
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description = "Utils for the Archie OpenEHR library"
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description = "OpenEHR-RM specific utils for the Archie OpenEHR library"
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dependencies {
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compile project(':base')

tools/src/test/java/com/nedap/archie/adl14/ConversionConfigForTest.java renamed to archie-utils/src/main/java/com/nedap/archie/adl14/OpenEHRADL14ConversionConfiguration.java

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@@ -1,18 +1,17 @@
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package com.nedap.archie.adl14;
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3+
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import com.nedap.archie.json.JacksonUtil;
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import java.io.IOException;
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import java.io.InputStream;
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8-
public class ConversionConfigForTest {
9-
9+
public class OpenEHRADL14ConversionConfiguration {
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public static ADL14ConversionConfiguration getConfig() throws IOException {
12-
13-
try(InputStream stream = ConversionConfigForTest.class.getResourceAsStream("configuration.json")) {
12+
try(InputStream stream = OpenEHRADL14ConversionConfiguration.class.getResourceAsStream("/adl14conversionconfiguration.json")) {
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return JacksonUtil.getObjectMapper().readValue(stream, ADL14ConversionConfiguration.class);
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}
16-
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}
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}

‎archie-utils/src/main/resources/adl14conversionconfiguration.json‎

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@@ -0,0 +1,25 @@
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{
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"terminology_conversion_templates": [
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{
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"terminology_id": "snomedct",
5+
"template": "http://snomed.info/id/$code_string"
6+
},
7+
{
8+
"terminology_id": "snomed-ct",
9+
"template": "http://snomed.info/id/$code_string"
10+
},
11+
{
12+
"terminology_id": "snomed",
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"template": "http://snomed.info/id/$code_string"
14+
},
15+
{
16+
"terminology_id": "openehr",
17+
"template": "http://openehr.org/id/$code_string"
18+
},
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{
20+
"terminology_id": "loinc",
21+
"template": "http://loinc.org/id/$code_string"
22+
}
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24+
]
25+
}

opt14/src/main/java/com/nedap/archie/opt14/IntervalConverter.java renamed to opt14/src/main/java/com/nedap/archie/opt14/BaseTypesConverter.java

Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,9 @@
33
import com.nedap.archie.base.Cardinality;
44
import com.nedap.archie.base.Interval;
55
import com.nedap.archie.base.MultiplicityInterval;
6+
import com.nedap.archie.base.terminology.TerminologyCode;
67

7-
public class IntervalConverter {
8+
public class BaseTypesConverter {
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910
public static Cardinality convertCardinality(CARDINALITY cardinality14) {
1011
if(cardinality14 == null) {
@@ -52,4 +53,11 @@ public static com.nedap.archie.base.Interval<Double> convertInterval(IntervalOfR
5253
range.isUpperIncluded() == null ? true : range.isUpperIncluded());
5354
}
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56+
public static TerminologyCode convert(CODEPHRASE definingCode) {
57+
if(definingCode == null) {
58+
return null;
59+
}
60+
return TerminologyCode.createFromString(definingCode.getTerminologyId().getValue(), null, definingCode.getCodeString());
61+
}
62+
5563
}

‎opt14/src/main/java/com/nedap/archie/opt14/DefinitionConverter.java‎

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@@ -9,8 +9,8 @@
99
import com.nedap.archie.aom.Template;
1010
import com.nedap.archie.aom.TemplateOverlay;
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12-
import static com.nedap.archie.opt14.IntervalConverter.convertCardinality;
13-
import static com.nedap.archie.opt14.IntervalConverter.convertMultiplicity;
12+
import static com.nedap.archie.opt14.BaseTypesConverter.convertCardinality;
13+
import static com.nedap.archie.opt14.BaseTypesConverter.convertMultiplicity;
1414
import static com.nedap.archie.opt14.PrimitiveConverter.convertPrimitive;
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public class DefinitionConverter {
@@ -30,7 +30,7 @@ private CComplexObject convert(CCOMPLEXOBJECT cComplexObject14) {
3030
CComplexObject cComplexObject = new CComplexObject();
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cComplexObject.setNodeId(cComplexObject14.getNodeId());
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cComplexObject.setRmTypeName(cComplexObject14.getRmTypeName());
33-
cComplexObject.setOccurrences(IntervalConverter.convertMultiplicity(cComplexObject14.getOccurrences()));
33+
cComplexObject.setOccurrences(BaseTypesConverter.convertMultiplicity(cComplexObject14.getOccurrences()));
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for (CATTRIBUTE attribute14 : cComplexObject14.getAttributes()) {
3636
cComplexObject.addAttribute(convert(attribute14));
@@ -81,7 +81,7 @@ private CObject convertSlot(ARCHETYPESLOT cobject14) {
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archetypeSlot.setNodeId(cobject14.getNodeId());
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archetypeSlot.setRmTypeName(cobject14.getRmTypeName());
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84-
archetypeSlot.setOccurrences(IntervalConverter.convertMultiplicity(cobject14.getOccurrences()));
84+
archetypeSlot.setOccurrences(BaseTypesConverter.convertMultiplicity(cobject14.getOccurrences()));
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//TODO: assertions for include/exclude, should be straightforward
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return archetypeSlot;
8787
}
@@ -99,7 +99,7 @@ private CObject convertRoot(CARCHETYPEROOT cRoot14) {
9999
CArchetypeRoot root = new CArchetypeRoot();
100100
root.setArchetypeRef(overlay.getArchetypeId().getFullId());
101101
root.setNodeId(cRoot14.getNodeId());
102-
root.setOccurrences(IntervalConverter.convertMultiplicity(cRoot14.getOccurrences()));
102+
root.setOccurrences(BaseTypesConverter.convertMultiplicity(cRoot14.getOccurrences()));
103103
root.setRmTypeName(cRoot14.getRmTypeName());
104104
return root;
105105
}

‎opt14/src/main/java/com/nedap/archie/opt14/DescriptionConverter.java‎

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Original file line numberDiff line numberDiff line change
@@ -19,14 +19,18 @@ public static void convert(Template template, OPERATIONALTEMPLATE opt14) {
1919
author.put(item.getId(), item.getValue());
2020
}
2121
}
22+
if(description14.getOtherDetails() != null) {
23+
for(StringDictionaryItem item:description14.getOtherDetails()) {
24+
description.getOtherDetails().put(item.getId(), item.getValue());
25+
}
26+
}
27+
28+
description.setOtherContributors(description14.getOtherContributors());
29+
2230
description.setOriginalAuthor(author);
2331
template.setDescription(description);
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25-
template.setOriginalLanguage(
26-
TerminologyCode.createFromString(
27-
opt14.getLanguage().getTerminologyId().getValue(),
28-
null,
29-
opt14.getLanguage().getCodeString()));
33+
template.setOriginalLanguage(BaseTypesConverter.convert(opt14.getLanguage()));
3034
//TODO: implement me further
3135
}
3236
}

‎opt14/src/main/java/com/nedap/archie/opt14/DomainTypeConverter.java‎

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@@ -1,9 +1,82 @@
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package com.nedap.archie.opt14;
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3+
import com.nedap.archie.adl14.aom14.CDVOrdinal;
4+
import com.nedap.archie.adl14.aom14.CDVOrdinalItem;
5+
import com.nedap.archie.adl14.aom14.CDVQuantity;
6+
7+
import com.nedap.archie.adl14.aom14.CDVQuantityAssumedValue;
8+
import com.nedap.archie.adl14.aom14.CDVQuantityItem;
9+
import com.nedap.archie.adl14.treewalkers.Adl14CComplexObjectParser;
310
import com.nedap.archie.aom.CObject;
11+
import com.nedap.archie.base.terminology.TerminologyCode;
12+
13+
import java.util.LinkedHashMap;
14+
import java.util.Map;
15+
16+
import static com.nedap.archie.opt14.BaseTypesConverter.convert;
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518
public class DomainTypeConverter {
619
public static CObject convertDomainType(CDOMAINTYPE cobject14) {
20+
if(cobject14 instanceof CDVORDINAL) {
21+
return convertCDVOrdinal((CDVORDINAL) cobject14);
22+
} else if (cobject14 instanceof CDVQUANTITY) {
23+
return convertCDVQuantity((CDVQUANTITY) cobject14);
24+
} else if (cobject14 instanceof CDVSTATE) {
25+
26+
} else if (cobject14 instanceof CCODEPHRASE) {
27+
28+
}
729
return null;
830
}
31+
32+
private static CObject convertCDVOrdinal(CDVORDINAL ordinal14) {
33+
CDVOrdinal ordinal = new CDVOrdinal();
34+
Map<String, CDVOrdinalItem> items = new LinkedHashMap<>();
35+
if(ordinal14.getList() != null) {
36+
Integer i = 0;
37+
for(DVORDINAL dvordinal14:ordinal14.getList()) {
38+
CDVOrdinalItem item = new CDVOrdinalItem();
39+
item.setValue(dvordinal14.getValue());
40+
if(dvordinal14.getSymbol() != null) {
41+
item.setSymbol(convert(dvordinal14.getSymbol().getDefiningCode()));
42+
}
43+
items.put(i.toString(), item);
44+
i++;
45+
}
46+
}
47+
//TODO: no assumed value in our own model, but there is in the OPT form.
48+
49+
return Adl14CComplexObjectParser.convertCDVOrdinal(ordinal);
50+
}
51+
52+
private static CObject convertCDVQuantity(CDVQUANTITY cobject14) {
53+
CDVQUANTITY quantity14 = cobject14;
54+
CDVQuantity quantity = new CDVQuantity();
55+
Map<String, CDVQuantityItem> items = new LinkedHashMap<>();
56+
57+
if(quantity14.getList() != null) {
58+
Integer i = 0;
59+
for(CQUANTITYITEM item14:quantity14.getList()) {
60+
CDVQuantityItem item = new CDVQuantityItem();
61+
item.setMagnitude(BaseTypesConverter.convertInterval(item14.getMagnitude()));
62+
item.setPrecision(BaseTypesConverter.convertInterval(item14.getPrecision()));
63+
item.setUnits(item14.getUnits());
64+
items.put(i.toString(), item);
65+
i++;
66+
}
67+
}
68+
quantity.setList(items);
69+
70+
quantity.setProperty(convert(quantity14.getProperty()));
71+
72+
DVQUANTITY assumedValue14 = quantity14.getAssumedValue();
73+
if(assumedValue14 != null) {
74+
CDVQuantityAssumedValue assumedValue = new CDVQuantityAssumedValue();
75+
assumedValue.setMagnitude(assumedValue14.getMagnitude());
76+
assumedValue.setPrecision(assumedValue14.getPrecision() == null ? null : assumedValue14.getPrecision().longValue());
77+
assumedValue.setUnits(assumedValue14.getUnits());
78+
quantity.setAssumedValue(assumedValue);
79+
}
80+
return Adl14CComplexObjectParser.convertCDvQuantity(quantity);
81+
}
982
}

‎opt14/src/main/java/com/nedap/archie/opt14/Opt14Converter.java‎

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Original file line numberDiff line numberDiff line change
@@ -9,6 +9,9 @@ public Template convert(OPERATIONALTEMPLATE opt14) {
99
Template template = new Template();
1010
template.setArchetypeId(new ArchetypeHRID("openEHR-EHR-" + opt14.getDefinition().getRmTypeName() + "." + opt14.getTemplateId().getValue() + "v1.0.0"));
1111
template.setParentArchetypeId(opt14.getDefinition().getArchetypeId().getValue());
12+
if(opt14.getUid() != null) {
13+
template.setUid(opt14.getUid().getValue());
14+
}
1215
DescriptionConverter.convert(template, opt14);
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1417
new DefinitionConverter().convert(template, opt14);

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