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Fixes PR #601 Add override code with a another valid code feature (in…
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…stead of arbitary pick) feature to CodesUpdater tool
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Bhaskarla authored and Bhaskarla committed May 30, 2024
1 parent 62499b7 commit cf69956
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Showing 17 changed files with 190 additions and 85 deletions.
162 changes: 129 additions & 33 deletions test-engine/src/main/java/gov/nist/toolkit/testengine/scripts/CodesUpdater.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,12 +53,67 @@ public class CodesUpdater {
private String out=new String();
private boolean error;

private List<Code> overrideCodes;
/**
* Reset the class variable to their initial state before the algorithm is run again.
* goes by the index of overrideCodes. If index value is null or empty, all files are affected.
*/
private List<String> targetFileByOverrideCodeIndex;
private boolean backupReplacedFiles = true;
private boolean dryRun = false;

/**
* Normal mode to be used with the run method (replaces bad a Code by picking a new Code by an arbitrary index)
*/
public CodesUpdater() {
}

/**
* Alternate mode to replacing Code with a supplied replacement
* @param overrideCodes
* @param replacementMap
* @param backupReplacedFiles
*/
public CodesUpdater(List<String> targetFileByOverrideCodeIndex, List<Code> overrideCodes, Map<String, Code> replacementMap, boolean backupReplacedFiles, boolean dryRun) {
this.targetFileByOverrideCodeIndex = targetFileByOverrideCodeIndex;
this.overrideCodes = overrideCodes;
this.replacementMap = replacementMap;
this.backupReplacedFiles = backupReplacedFiles;
this.dryRun = dryRun;
}

public static void main(String[] args) {

// "C:\\Users\\skb1\\myprojects\\iheos-toolkit2\\xdstools2\\src\\main\\webapp\\toolkitx\\environment\\default";
String codesXmlFileParent = "c:\\temp\\xdscodesupdatertool\\toolkitx\\environment\\default";
String testkitSourceLocation = "C:\\Users\\skb1\\myprojects\\iheos-toolkit2\\xdstools2\\src\\main\\webapp\\toolkitx\\testkit";
TestSession testSession = TestSession.DEFAULT_TEST_SESSION;

List<Code> overrideCodes = Arrays.asList(
new Code("urn:connectathon:bppc:foundational:policy", "1.3.6.1.4.1.21367.2017.3", "Foundational Connectathon Read-Access Policy")
);
List<String> targetFileByOverrideCodeIndex = Arrays.asList(
"\\idc_init\\XDS-I-idc-a"
);

CodesUpdater tool = new CodesUpdater(
targetFileByOverrideCodeIndex,
overrideCodes,
new HashMap<String, Code>() {{
/* key Is code + "^" + display + "^" + scheme; */
put(overrideCodes.get(0).toString(), new Code("CT", "1.2.840.10008.2.16.4", "Computed Tomography"));
}},
false, // false=no bak files
false); // false=perform update, true=does not update update files
tool.run(codesXmlFileParent, testkitSourceLocation, testSession);
}

/**
* Reset the class variable to their initial state before the algorithm is run again.
*/
void reset(){
filesTreated=new ArrayList<String>();
replacementMap=new HashMap<String,Code>();
overrideCodes = null;
}

/**
Expand Down Expand Up @@ -195,18 +250,25 @@ private void processQueryFile(File folderPath, String fileName) {
if (!badCodes.isEmpty()) {
LOGGER.info(badCodes.size() + " codes to update in query file: " + filePath);
out += badCodes.size() + " codes to update in query file: " + filePath + "\n";
File backupFile = new File(file.toString() + ".bak");
if (!backupFile.exists()) {
// backup the unmodified file before updating
FileUtils.copyFile(file, backupFile);
if (!dryRun && backupReplacedFiles) {
File backupFile = new File(file.toString() + ".bak");
if (!backupFile.exists()) {
// backup the unmodified file before updating
FileUtils.copyFile(file, backupFile);
}
}

// update bad codes
updateCode(badCodes);
// update the file itself
String returnType = queryElement.getFirstElement().getAttributeValue(new QName("returnType"));
Io.stringToFile(file, new OMFormatter(StoredQueryGenerator.generateQueryFile(returnType, params)).toString());

if (! dryRun) {
// update the file itself
String returnType = queryElement.getFirstElement().getAttributeValue(new QName("returnType"));
Io.stringToFile(file, new OMFormatter(StoredQueryGenerator.generateQueryFile(returnType, params)).toString());
}
} else {
out += "No codes to update in query file: " + filePath + "\n";
if (! dryRun && overrideCodes == null)
out += "No codes to update in query file: " + filePath + "\n";
}
}
} else {
Expand Down Expand Up @@ -243,21 +305,31 @@ private void processMetadataFile(File folderPath, String fileName) {
if (file.exists()) {
// read the file
OMElement metadataElement = Util.parse_xml(file);
List<OMElement> badCodes = findNonConformingCodes(metadataElement);
// if (file.toString().contains("IDCDEPT012-a")) {
// out += "found the target file.\n";
// }
List<OMElement> badCodes = findNonConformingCodes(file.toString(), metadataElement);
if (!badCodes.isEmpty()) {
LOGGER.info(badCodes.size() + " codes to update in " + filePath);
out += badCodes.size() + " codes to update in " + filePath + '\n';
File backupFile = new File(file.toString() + ".bak");
if (!backupFile.exists()) {
// backup the unmodified file before updating
FileUtils.copyFile(file, backupFile);
if (!dryRun && backupReplacedFiles) {
File backupFile = new File(file.toString() + ".bak");
if (!backupFile.exists()) {
// backup the unmodified file before updating
FileUtils.copyFile(file, backupFile);
}
}

// update bad codes
updateCodes(badCodes);
// update the file itself
Io.stringToFile(file, new OMFormatter(metadataElement).toString());

if (! dryRun) {
// update the file itself
Io.stringToFile(file, new OMFormatter(metadataElement).toString());
}
} else {
out += "No codes to update in " + filePath + '\n';
if (! dryRun && overrideCodes == null)
out += "No codes to update in " + filePath + '\n';
}
} else {
LOGGER.warning("WARNING: " + filePath + " file referenced in test does not exist.");
Expand Down Expand Up @@ -375,7 +447,7 @@ void updateCodes(List<OMElement> badCodes) throws XdsInternalException, FactoryC
OMElement localizedStringElement = MetadataSupport.firstChildWithLocalName(nameElement, "LocalizedString");
if (localizedStringElement == null) return;
OMAttribute nameToReplace = localizedStringElement.getAttribute(MetadataSupport.value_qname);
Code oldCode=new Code(codeToReplace.getAttributeValue(),valueToReplace.getText(),""/*nameToReplace.getAttributeValue()*/);
Code oldCode = asCode(codeToReplace.getAttributeValue(), valueToReplace.getText(), nameToReplace.getAttributeValue());
// check if the code to be replaced as already been changed before.
Code replacementCode=replacementMap.get(oldCode.toString());
if (replacementCode==null){
Expand All @@ -387,6 +459,13 @@ void updateCodes(List<OMElement> badCodes) throws XdsInternalException, FactoryC
replacementMap.put(oldCode.toString(),replacementCode);
out += "New mapping: " + oldCode + " --> " + replacementCode + "\n";
} else {
if (overrideCodes != null && ! overrideCodes.isEmpty()) {
String classificationScheme = classification.getAttributeValue(MetadataSupport.classificationscheme_qname);
Uuid classificationUuid = new Uuid(classificationScheme);
if (! allCodes.exists(classificationUuid, replacementCode)) {
throw new RuntimeException("Override replacement code does not exist in the loaded code map: " + replacementCode.toString());
}
}
out += "Old mapping: " + oldCode + " --> " + replacementCode + "\n";
}
// replace the code
Expand All @@ -396,13 +475,20 @@ void updateCodes(List<OMElement> badCodes) throws XdsInternalException, FactoryC
}
}

private Code asCode(String attributeValue, String text, String display) {
if (overrideCodes != null && ! overrideCodes.isEmpty()) {
return new Code(attributeValue, text, display);
}
return new Code(attributeValue, text, "");
}


/**
* This method explore a parsed document and looks for non-conforming codes with codes.xml file.
* @param metadataElement parsed document to analyze
* @return list of non-confirming code elements
*/
private List<OMElement> findNonConformingCodes(OMElement metadataElement) {
private List<OMElement> findNonConformingCodes(String file, OMElement metadataElement) {
List<OMElement> badCodes = new ArrayList<OMElement>();
List<OMElement> classifications = MetadataSupport.decendentsWithLocalName(metadataElement, "Classification");
for (OMElement classification : classifications) {
Expand All @@ -414,8 +500,15 @@ private List<OMElement> findNonConformingCodes(OMElement metadataElement) {
// Check if the type of code exists.
if (allCodes.isKnownClassification(classificationUuid)) {
Code code = getCode(classification);
if (overrideCodes != null && ! overrideCodes.isEmpty()) {
int oCodeIndex = overrideCodes.indexOf(code);
if (oCodeIndex > -1 && file.contains(targetFileByOverrideCodeIndex.get(oCodeIndex))) {
out += "Overriding code: " + code.getCode() + ". ";
badCodes.add(classification);
}
}
// check if the code exists in the environment codes.xml file
if (!allCodes.exists(classificationUuid, code)) {
else if (!allCodes.exists(classificationUuid, code)) {
// if it does not add the code to the list of bad codes.
badCodes.add(classification);
}
Expand Down Expand Up @@ -491,19 +584,22 @@ public void run(String pathToEnvironment, String pathToTestkit, TestSession test
String to = replacementMap.get(from).toString();
out += (from + " ===> " + to + "\n");
}
reset();
out += outputSeparator + "\n";
out += "Pass 2\n\n";
execute();
if (error) return;
out = outputSeparator + outputSeparator + "\n" + " SUCCESS on generating testkit in environment in " +
pathToEnvironment.split("/")[pathToEnvironment.split("/").length - 1] + "\n" +
outputSeparator + outputSeparator + "\n\n" + out;
out += outputSeparator + "\n";
out += "Mappings\n\n";
for (String from : replacementMap.keySet()) {
String to = replacementMap.get(from).toString();
out += (from + " ===> " + to + "\n");
if (! dryRun) {
// Check own work
reset();
out += outputSeparator + "\n";
out += "Pass 2\n\n";
execute();
if (error) return;
out = outputSeparator + outputSeparator + "\n" + " SUCCESS on generating testkit in environment in " +
pathToEnvironment.split("/")[pathToEnvironment.split("/").length - 1] + "\n" +
outputSeparator + outputSeparator + "\n\n" + out;
out += outputSeparator + "\n";
out += "Mappings\n\n";
for (String from : replacementMap.keySet()) {
String to = replacementMap.get(from).toString();
out += (from + " ===> " + to + "\n");
}
}
try {
SimpleDateFormat dateFormatter = new SimpleDateFormat("yyyyMMddHHmmss");
Expand Down
23 changes: 16 additions & 7 deletions validators-registry-metadata/src/main/java/gov/nist/toolkit/valregmetadata/coding/Code.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
package gov.nist.toolkit.valregmetadata.coding;

import java.util.Objects;

public class Code {
private String code;
private String scheme;
Expand All @@ -22,14 +24,21 @@ public String getScheme() {
public String getDisplay() {
return display;
}

public boolean equals(Code c) {
if (c == null) return false;
if (!c.getCode().equals(code)) return false;
if (!c.getScheme().equals(scheme)) return false;
return true;

@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
Code code1 = (Code) o;
return code.equals(code1.code) &&
scheme.equals(code1.scheme);
}


@Override
public int hashCode() {
return Objects.hash(code, scheme);
}

public String toString() {
return code + "^" + display + "^" + scheme;
}
Expand Down
6 changes: 3 additions & 3 deletions ...ls2/src/main/webapp/toolkitx/testkit/tests/idc_init/XDS-I-idc-a/metadata-IDCDEPT001-a.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,16 @@
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
classifiedObject="Document01" nodeRepresentation="urn:connectathon:bppc:foundational:policy"
classifiedObject="Document01" nodeRepresentation="CT"
objectType="urn:oasis:names:tc:ebxml-regrep:ObjectType:RegistryObject:Classification"
id="id_8">
<rim:Slot name="codingScheme">
<rim:ValueList>
<rim:Value>1.3.6.1.4.1.21367.2017.3</rim:Value>
<rim:Value>1.2.840.10008.2.16.4</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Name>
<rim:LocalizedString value="Foundational Connectathon Read-Access Policy"/>
<rim:LocalizedString value="Computed Tomography"/>
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
Expand Down
6 changes: 3 additions & 3 deletions ...ls2/src/main/webapp/toolkitx/testkit/tests/idc_init/XDS-I-idc-a/metadata-IDCDEPT011-a.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,16 @@
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
classifiedObject="Document01" nodeRepresentation="urn:connectathon:bppc:foundational:policy"
classifiedObject="Document01" nodeRepresentation="CT"
objectType="urn:oasis:names:tc:ebxml-regrep:ObjectType:RegistryObject:Classification"
id="id_8">
<rim:Slot name="codingScheme">
<rim:ValueList>
<rim:Value>1.3.6.1.4.1.21367.2017.3</rim:Value>
<rim:Value>1.2.840.10008.2.16.4</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Name>
<rim:LocalizedString value="Foundational Connectathon Read-Access Policy"/>
<rim:LocalizedString value="Computed Tomography"/>
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
Expand Down
6 changes: 3 additions & 3 deletions ...ls2/src/main/webapp/toolkitx/testkit/tests/idc_init/XDS-I-idc-a/metadata-IDCDEPT012-a.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,16 @@
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
classifiedObject="Document01" nodeRepresentation="urn:connectathon:bppc:foundational:policy"
classifiedObject="Document01" nodeRepresentation="CT"
objectType="urn:oasis:names:tc:ebxml-regrep:ObjectType:RegistryObject:Classification"
id="id_8">
<rim:Slot name="codingScheme">
<rim:ValueList>
<rim:Value>1.3.6.1.4.1.21367.2017.3</rim:Value>
<rim:Value>1.2.840.10008.2.16.4</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Name>
<rim:LocalizedString value="Foundational Connectathon Read-Access Policy"/>
<rim:LocalizedString value="Computed Tomography"/>
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
Expand Down
6 changes: 3 additions & 3 deletions ...ls2/src/main/webapp/toolkitx/testkit/tests/idc_init/XDS-I-idc-a/metadata-IDCDEPT013-a.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,16 @@
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
classifiedObject="Document01" nodeRepresentation="urn:connectathon:bppc:foundational:policy"
classifiedObject="Document01" nodeRepresentation="CT"
objectType="urn:oasis:names:tc:ebxml-regrep:ObjectType:RegistryObject:Classification"
id="id_8">
<rim:Slot name="codingScheme">
<rim:ValueList>
<rim:Value>1.3.6.1.4.1.21367.2017.3</rim:Value>
<rim:Value>1.2.840.10008.2.16.4</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Name>
<rim:LocalizedString value="Foundational Connectathon Read-Access Policy"/>
<rim:LocalizedString value="Computed Tomography"/>
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
Expand Down
6 changes: 3 additions & 3 deletions ...ls2/src/main/webapp/toolkitx/testkit/tests/idc_init/XDS-I-idc-a/metadata-IDCDEPT021-a.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -159,16 +159,16 @@
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
classifiedObject="Document01" nodeRepresentation="urn:connectathon:bppc:foundational:policy"
classifiedObject="Document01" nodeRepresentation="CT"
objectType="urn:oasis:names:tc:ebxml-regrep:ObjectType:RegistryObject:Classification"
id="id_8">
<rim:Slot name="codingScheme">
<rim:ValueList>
<rim:Value>1.3.6.1.4.1.21367.2017.3</rim:Value>
<rim:Value>1.2.840.10008.2.16.4</rim:Value>
</rim:ValueList>
</rim:Slot>
<rim:Name>
<rim:LocalizedString value="Foundational Connectathon Read-Access Policy"/>
<rim:LocalizedString value="Computed Tomography"/>
</rim:Name>
</rim:Classification>
<rim:Classification classificationScheme="urn:uuid:2c6b8cb7-8b2a-4051-b291-b1ae6a575ef4"
Expand Down
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