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bryantaustin13c-schuler
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Add race and ethnicity bindings to bindings collection (#531)
* added extension bindings * added org.reflections to pom * changes for PR --------- Co-authored-by: c-schuler <hoofschu@gmail.com>
1 parent 7a04aaf commit 6dd2f5c

4 files changed

Lines changed: 112 additions & 20 deletions

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‎tooling/pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -397,4 +397,4 @@
397397
</dependencyManagement>
398398

399399

400-
</project>
400+
</project>

‎tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/StructureDefinitionElementBindingVisitor.java‎

Lines changed: 95 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,8 @@ public Map<String, StructureDefinitionBindingObject> visitStructureDefinition(St
4343
getBindings(sdName, eds, sdURL, sdVersion, bindingObjects);
4444
}
4545
if (sd.hasBaseDefinition()) {
46-
bindingObjects.putAll(visitStructureDefinition(this.canonicalResourceDependenciesAtlas.getStructureDefinitions().getByCanonicalUrlWithVersion(sd.getBaseDefinition()), snapshotOnly)); }
46+
bindingObjects.putAll(visitStructureDefinition(this.canonicalResourceDependenciesAtlas.getStructureDefinitions().getByCanonicalUrlWithVersion(sd.getBaseDefinition()), snapshotOnly));
47+
}
4748
}
4849
return bindingObjects;
4950
}
@@ -71,7 +72,7 @@ private void getBindings(String sdName, List<ElementDefinition> eds, String sdUR
7172
sdbo.setSdURL(sdURL);
7273
sdbo.setSdVersion(sdVersion);
7374
sdbo.setBindingStrength(ed.getBinding().getStrength().toString().toLowerCase());
74-
if(ed.hasMin() && ed.hasMax()){
75+
if (ed.hasMin() && ed.hasMax()) {
7576
String edCardinality = ed.getMin() + "..." + ed.getMax();
7677
sdbo.setCardinality(edCardinality);
7778
}
@@ -97,16 +98,16 @@ private void getBindings(String sdName, List<ElementDefinition> eds, String sdUR
9798
valueSetVersion = pipeVersion;
9899
}
99100
if (null != elementValueSet) {
100-
StringBuilder codeSystemURLs = new StringBuilder();;
101+
StringBuilder codeSystemURLs = new StringBuilder();
101102
Map<String, String> codeSystemsMap = new HashMap<>();
102103
getValueSetCodeSystems(elementValueSet, codeSystemsMap);
103-
if(null != codeSystemsMap && !codeSystemsMap.isEmpty()) {
104-
AtomicReference <Integer> valueCount = new AtomicReference<>(0);
105-
codeSystemsMap.values().forEach((url)->{
104+
if (null != codeSystemsMap && !codeSystemsMap.isEmpty()) {
105+
AtomicReference<Integer> valueCount = new AtomicReference<>(0);
106+
codeSystemsMap.values().forEach((url) -> {
106107
codeSystemURLs.append(url);
107108
valueCount.set(valueCount.get() + 1);
108-
if(valueCount.get() > 0 &&
109-
valueCount.get() < codeSystemsMap.size()) {
109+
if (valueCount.get() > 0 &&
110+
valueCount.get() < codeSystemsMap.size()) {
110111
codeSystemURLs.append(";");
111112
}
112113
});
@@ -121,15 +122,100 @@ private void getBindings(String sdName, List<ElementDefinition> eds, String sdUR
121122
sdbo.setBindingValueSetVersion(valueSetVersion);
122123
bindingObjects.put(sdName + "." + sdbo.getElementId(), sdbo);
123124
}
125+
else if (ed.hasExtension()) {
126+
visitExtensions(ed, bindingObjects, sdName, sdURL, sdVersion);
127+
}
124128
index.set(index.get() + 1);
125129
}
126130
}
127131

132+
private void visitExtensions(ElementDefinition ed, Map<String, StructureDefinitionBindingObject> bindingObjects, String sdName, String sdURL, String sdVersion) {
133+
StructureDefinitionBindingObject sdbo = new StructureDefinitionBindingObject();
134+
sdbo.setSdName(sdName);
135+
sdbo.setSdURL(sdURL);
136+
sdbo.setSdVersion(sdVersion);
137+
sdbo.setElementId(ed.getId());
138+
if (ed.getMustSupport()) {
139+
sdbo.setMustSupport("Y");
140+
} else {
141+
sdbo.setMustSupport("N");
142+
}
143+
if (ed.hasMin()) {
144+
String edCardinality = ed.getMin() + "..." + ed.getMax();
145+
sdbo.setCardinality(edCardinality);
146+
}
147+
CanonicalType canonicalType = new CanonicalType();
148+
Iterable<StructureDefinition> sdList = null;
149+
try {
150+
if (ed.getType().get(0).getProfile().size() != 0) {
151+
canonicalType.setValue(String.valueOf(ed.getType().get(0).getProfile().get(0)));
152+
sdList = this.canonicalResourceDependenciesAtlas.getStructureDefinitions().getByCanonicalUrl(ed.getType().get(0).getProfile().get(0).getValueAsString());
153+
} else if (ed.getType().get(0).getTargetProfile().size() != 0) {
154+
canonicalType.setValue(String.valueOf(ed.getType().get(0).getTargetProfile()));
155+
sdList = this.canonicalResourceDependenciesAtlas.getStructureDefinitions().getByCanonicalUrl(ed.getType().get(0).getTargetProfile().get(0).getValueAsString());
156+
}
157+
else{
158+
return;
159+
}
160+
} catch (Exception ex) {
161+
return;
162+
}
163+
if (sdList != null) {
164+
sdList.forEach((structDef) -> {
165+
List<ElementDefinition> edsds = structDef.getDifferential().getElement();
166+
edsds.forEach(edsd -> {
167+
if (edsd.hasBinding()) {
168+
sdbo.setBindingStrength(edsd.getBinding().getStrength().toString().toLowerCase());
169+
String bindingValueSet = edsd.getBinding().getValueSet();
170+
String pipeVersion = "";
171+
if (bindingValueSet.contains("|")) {
172+
pipeVersion = bindingValueSet.substring(bindingValueSet.indexOf("|") + 1);
173+
bindingValueSet = bindingValueSet.substring(0, bindingValueSet.indexOf("|"));
174+
}
175+
sdbo.setBindingValueSetURL(bindingValueSet);
176+
String valueSetVersion = "";
177+
ValueSet elementValueSet = null;
178+
if (null != this.canonicalResourceAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL())) {
179+
valueSetVersion = this.canonicalResourceAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL()).getVersion();
180+
sdbo.setBindingValueSetName(this.canonicalResourceAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL()).getName());
181+
elementValueSet = this.canonicalResourceAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL());
182+
} else if (null != this.canonicalResourceDependenciesAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL())) {
183+
valueSetVersion = this.canonicalResourceDependenciesAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL()).getVersion();
184+
sdbo.setBindingValueSetName(this.canonicalResourceDependenciesAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL()).getName());
185+
elementValueSet = this.canonicalResourceDependenciesAtlas.getValueSets().getByCanonicalUrlWithVersion(sdbo.getBindingValueSetURL());
186+
} else if (valueSetVersion.isEmpty() && bindingValueSet.contains("|")) {
187+
valueSetVersion = pipeVersion;
188+
}
189+
sdbo.setBindingValueSetVersion(valueSetVersion);
190+
if (null != elementValueSet) {
191+
StringBuilder codeSystemURLs = new StringBuilder();
192+
Map<String, String> codeSystemsMap = new HashMap<>();
193+
getValueSetCodeSystems(elementValueSet, codeSystemsMap);
194+
if (!codeSystemsMap.isEmpty()) {
195+
AtomicReference<Integer> valueCount = new AtomicReference<>(0);
196+
codeSystemsMap.values().forEach((url) -> {
197+
codeSystemURLs.append(url);
198+
valueCount.set(valueCount.get() + 1);
199+
if (valueCount.get() > 0 &&
200+
valueCount.get() < codeSystemsMap.size()) {
201+
codeSystemURLs.append(";");
202+
}
203+
});
204+
sdbo.setCodeSystemsURLs(codeSystemURLs.toString());
205+
}
206+
}
207+
}
208+
});
209+
});
210+
}
211+
bindingObjects.put(sdName + "." + sdbo.getElementId(), sdbo);
212+
}
213+
128214
private void getValueSetCodeSystems(ValueSet elementValueSet, Map<String, String> codeSystemsMap) {
129215
ValueSet.ValueSetComposeComponent compose = elementValueSet.getCompose();
130216
if (null != compose) {
131217
for (ValueSet.ConceptSetComponent include : compose.getInclude()) {
132-
if(include.hasSystem()){
218+
if (include.hasSystem()) {
133219
codeSystemsMap.put(include.getSystem(), include.getSystem());
134220
}
135221
for (CanonicalType r : include.getValueSet()) {

‎tooling/src/main/java/org/opencds/cqf/tooling/operation/ProfilesToSpreadsheet.java‎

Lines changed: 14 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -82,10 +82,14 @@ private void createOutput(List<StructureDefinitionBindingObject> bindingObjects)
8282
XSSFRow currentRow = firstSheet.createRow(rowCount.getAndAccumulate(1, ibo));
8383
SpreadsheetCreatorHelper.createHeaderRow(workBook, createHeaderNameList(), currentRow);
8484
bindingObjects.forEach((bindingObject) -> {
85-
addBindingObjectRowDataToCurrentSheet(firstSheet, rowCount.getAndAccumulate(1, ibo), bindingObject);
85+
try {
86+
addBindingObjectRowDataToCurrentSheet(firstSheet, rowCount.getAndAccumulate(1, ibo), bindingObject);
87+
}catch(Exception ex){
88+
ex.printStackTrace();
89+
}
8690
});
8791
SpreadsheetCreatorHelper.writeSpreadSheet(workBook,
88-
IOUtils.concatFilePath(getOutputPath(), modelName + modelVersion + ".xlsx"));
92+
IOUtils.concatFilePath(getOutputPath(), modelName + " " + modelVersion + " Profile Elements.xlsx"));
8993
}
9094

9195
private List<String> createHeaderNameList() {
@@ -95,7 +99,7 @@ private List<String> createHeaderNameList() {
9599
add("Conformance");
96100
add("ValueSet");
97101
add("ValueSetURL");
98-
add("Version");
102+
add("Binding ValueSet Version");
99103
add("Code System URLs");
100104
add("Must Support Y/N");
101105
add("Cardinality");
@@ -129,11 +133,13 @@ private void addBindingObjectRowDataToCurrentSheet(XSSFSheet currentSheet, int r
129133
currentCell.setCellValue(bo.getBindingValueSetName());
130134

131135
currentCell = currentRow.createCell(cellCount++);
132-
currentCell.setCellValue(bo.getBindingValueSetURL());
133-
link = (XSSFHyperlink)helper.createHyperlink(HyperlinkType.URL);
134-
link.setAddress(bo.getBindingValueSetURL());
135-
currentCell.setHyperlink(link);
136-
currentCell.setCellStyle(linkStyle);
136+
if(bo.getBindingValueSetURL() != null) {
137+
currentCell.setCellValue(bo.getBindingValueSetURL());
138+
link = (XSSFHyperlink) helper.createHyperlink(HyperlinkType.URL);
139+
link.setAddress(bo.getBindingValueSetURL());
140+
currentCell.setHyperlink(link);
141+
currentCell.setCellStyle(linkStyle);
142+
}
137143

138144
currentCell = currentRow.createCell(cellCount++);
139145
currentCell.setCellValue(bo.getBindingValueSetVersion());

‎tooling/src/main/java/org/opencds/cqf/tooling/operation/QICoreElementsToSpreadsheet.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,7 +24,7 @@ public class QICoreElementsToSpreadsheet extends StructureDefinitionToSpreadshee
2424
private int ConstraintColumn = 7;
2525
private int ConstraintColumnWidth = 85 * 256;
2626

27-
// example call: -ProfilesToSpreadsheet -ip=/Users/bryantaustin/Projects/FHIR-Spec -op=output -rp="4.0.1;US-Core/3.1.0;QI-Core/4.1.0" -sp=true -mn=QICore -mv=4.1.0
27+
// example call: -QICoreElementsToSpreadsheet -ip=/Users/bryantaustin/Projects/FHIR-Spec -op=output -rp="4.0.1;US-Core/3.1.0;QI-Core/4.1.0" -sp=true -mn=QICore -mv=4.1.0
2828
@Override
2929
public void execute(String[] args) {
3030
for (String arg : args) {
@@ -93,7 +93,7 @@ private void createOutput(List<StructureDefinitionElementObject> elementObjects)
9393
firstSheet.setColumnWidth(ConstraintColumn, ConstraintColumnWidth);
9494
// firstSheet.autoSizeColumn(ConstraintColumn);
9595
SpreadsheetCreatorHelper.writeSpreadSheet(workBook,
96-
IOUtils.concatFilePath(getOutputPath(), modelName + modelVersion + ".xlsx"));
96+
IOUtils.concatFilePath(getOutputPath(), modelName + modelVersion + " Data Elements" + ".xlsx"));
9797
}
9898

9999
private List<String> createHeaderNameList() {

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