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Merge pull request #972 from hapifhir/do-terminology-cache-filewpipechar 

Fix pipes in terminologyCache files
This commit is contained in:
Grahame Grieve 2022-11-06 07:04:58 +11:00 committed by GitHub
parent c01d434b33 14fdb713d9
commit d19ff2e1f6
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
9 changed files with 494 additions and 161 deletions
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114
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/TerminologyCache.java
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@ -84,16 +84,88 @@ public class TerminologyCache {
private static final String ENTRY_MARKER = "-------------------------------------------------------------------------------------";
private static final String BREAK = "####";
private SystemNameKeyGenerator systemNameKeyGenerator = new SystemNameKeyGenerator();
protected SystemNameKeyGenerator getSystemNameKeyGenerator() {
return systemNameKeyGenerator;
}
public class SystemNameKeyGenerator {
public static final String SNOMED_SCT_CODESYSTEM_URL = "http://snomed.info/sct";
public static final String RXNORM_CODESYSTEM_URL = "http://www.nlm.nih.gov/research/umls/rxnorm";
public static final String LOINC_CODESYSTEM_URL = "http://loinc.org";
public static final String UCUM_CODESYSTEM_URL = "http://unitsofmeasure.org";
public static final String HL7_TERMINOLOGY_CODESYSTEM_BASE_URL = "http://terminology.hl7.org/CodeSystem/";
public static final String HL7_SID_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/sid/";
public static final String HL7_FHIR_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/";
public static final String ISO_CODESYSTEM_URN = "urn:iso:std:iso:";
public static final String LANG_CODESYSTEM_URN = "urn:ietf:bcp:47";
public static final String MIMETYPES_CODESYSTEM_URN = "urn:ietf:bcp:13";
public static final String _11073_CODESYSTEM_URN = "urn:iso:std:iso:11073:10101";
public static final String DICOM_CODESYSTEM_URL = "http://dicom.nema.org/resources/ontology/DCM";
public String getNameForSystem(String system) {
final int lastPipe = system.lastIndexOf('|');
final String systemBaseName = lastPipe == -1 ? system : system.substring(0,lastPipe);
final String systemVersion = lastPipe == -1 ? null : system.substring(lastPipe + 1);
if (systemBaseName.equals(SNOMED_SCT_CODESYSTEM_URL))
return getVersionedSystem("snomed", systemVersion);
if (systemBaseName.equals(RXNORM_CODESYSTEM_URL))
return getVersionedSystem("rxnorm", systemVersion);
if (systemBaseName.equals(LOINC_CODESYSTEM_URL))
return getVersionedSystem("loinc", systemVersion);
if (systemBaseName.equals(UCUM_CODESYSTEM_URL))
return getVersionedSystem("ucum", systemVersion);
if (systemBaseName.startsWith(HL7_SID_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_SID_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(_11073_CODESYSTEM_URN))
return getVersionedSystem("11073", systemVersion);
if (systemBaseName.startsWith(ISO_CODESYSTEM_URN))
return getVersionedSystem("iso"+systemBaseName.substring(ISO_CODESYSTEM_URN.length()).replace(":", ""), systemVersion);
if (systemBaseName.startsWith(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.startsWith(HL7_FHIR_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_FHIR_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(LANG_CODESYSTEM_URN))
return getVersionedSystem("lang", systemVersion);
if (systemBaseName.equals(MIMETYPES_CODESYSTEM_URN))
return getVersionedSystem("mimetypes", systemVersion);
if (systemBaseName.equals(DICOM_CODESYSTEM_URL))
return getVersionedSystem("dicom", systemVersion);
return getVersionedSystem(systemBaseName.replace("/", "_").replace(":", "_").replace("?", "X").replace("#", "X"), systemVersion);
}
public String normalizeBaseURL(String baseUrl, String fullUrl) {
return fullUrl.substring(baseUrl.length()).replace("/", "");
}
public String getVersionedSystem(String baseSystem, String version) {
if (version != null) {
return baseSystem + "_" + version;
}
return baseSystem;
}
}
public class CacheToken {
private String name;
private String key;
private String request;
public void setName(String n) {
String systemName = getSystemNameKeyGenerator().getNameForSystem(n);
if (name == null)
name = n;
else if (!n.equals(name))
name = systemName;
else if (!systemName.equals(name))
name = NAME_FOR_NO_SYSTEM;
}
public String getName() {
return name;
}
}
private class CacheEntry {
@ -126,7 +198,7 @@ public class TerminologyCache {
public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
CacheToken ct = new CacheToken();
if (code.hasSystem())
ct.name = getNameForSystem(code.getSystem());
ct.name = getSystemNameKeyGenerator().getNameForSystem(code.getSystem());
else
ct.name = NAME_FOR_NO_SYSTEM;
JsonParser json = new JsonParser();
@ -145,7 +217,7 @@ public class TerminologyCache {
CacheToken ct = new CacheToken();
for (Coding c : code.getCoding()) {
if (c.hasSystem())
ct.setName(getNameForSystem(c.getSystem()));
ct.setName(c.getSystem());
}
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
@ -176,13 +248,13 @@ public class TerminologyCache {
ValueSet vsc = getVSEssense(vs);
for (ConceptSetComponent inc : vs.getCompose().getInclude())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
for (ConceptSetComponent inc : vs.getCompose().getExclude())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
for (ValueSetExpansionContainsComponent inc : vs.getExpansion().getContains())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
try {
@ -194,34 +266,6 @@ public class TerminologyCache {
return ct;
}
private String getNameForSystem(String system) {
if (system.equals("http://snomed.info/sct"))
return "snomed";
if (system.equals("http://www.nlm.nih.gov/research/umls/rxnorm"))
return "rxnorm";
if (system.equals("http://loinc.org"))
return "loinc";
if (system.equals("http://unitsofmeasure.org"))
return "ucum";
if (system.startsWith("http://hl7.org/fhir/sid/"))
return system.substring(24).replace("/", "");
if (system.startsWith("urn:iso:std:iso:"))
return "iso"+system.substring(16).replace(":", "");
if (system.startsWith("http://terminology.hl7.org/CodeSystem/"))
return system.substring(38).replace("/", "");
if (system.startsWith("http://hl7.org/fhir/"))
return system.substring(20).replace("/", "");
if (system.equals("urn:ietf:bcp:47"))
return "lang";
if (system.equals("urn:ietf:bcp:13"))
return "mimetypes";
if (system.equals("urn:iso:std:iso:11073:10101"))
return "11073";
if (system.equals("http://dicom.nema.org/resources/ontology/DCM"))
return "dicom";
return system.replace("/", "_").replace(":", "_");
}
public NamedCache getNamedCache(CacheToken cacheToken) {
NamedCache nc = caches.get(cacheToken.name);
if (nc == null) {

8
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/context/CacheTestUtils.java Normal file
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@ -0,0 +1,8 @@
package org.hl7.fhir.r4.context;
import org.hl7.fhir.utilities.validation.ValidationOptions;
public class CacheTestUtils {
public static final ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
}

61
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/context/TerminologyCacheTests.java Normal file
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@ -0,0 +1,61 @@
package org.hl7.fhir.r4.context;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.utilities.tests.ResourceLoaderTests;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import java.io.IOException;
import java.net.URISyntaxException;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class TerminologyCacheTests implements ResourceLoaderTests {
private TerminologyCache createTerminologyCache() throws IOException {
Object lock = new Object();
TerminologyCache terminologyCache = new TerminologyCache(lock, null);
return terminologyCache;
}
@ParameterizedTest
@CsvSource({
"http://terminology.hl7.org/CodeSystem/id,id",
"http://hl7.org/fhir/id,id",
"http://hl7.org/fhir/sid/id,id",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://snomed.info/sct,snomed",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://loinc.org,loinc",
"http://unitsofmeasure.org,ucum",
"urn:iso:std:iso:id,isoid",
"urn:ietf:bcp:47,lang",
"urn:ietf:bcp:13,mimetypes",
"urn:iso:std:iso:11073:10101,11073",
"my://random/system?with#chars,my___random_systemXwithXchars",
"http://dicom.nema.org/resources/ontology/DCM,dicom"
})
public void testCacheTokenGeneration(String system, String expectedName) throws IOException, URISyntaxException {
TerminologyCache terminologyCache = createTerminologyCache();
ValueSet valueSet = new ValueSet();
{
Coding coding = new Coding();
coding.setSystem(system);
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName, cacheToken.getName());
}
{
Coding coding = new Coding();
coding.setSystem(system + "|dummyVersion");
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName + "_dummyVersion", cacheToken.getName());
}
}
}

116
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/context/TerminologyCache.java
View File

@ -84,16 +84,88 @@ public class TerminologyCache {
private static final String ENTRY_MARKER = "-------------------------------------------------------------------------------------";
private static final String BREAK = "####";
private SystemNameKeyGenerator systemNameKeyGenerator = new SystemNameKeyGenerator();
protected SystemNameKeyGenerator getSystemNameKeyGenerator() {
return systemNameKeyGenerator;
}
public class SystemNameKeyGenerator {
public static final String SNOMED_SCT_CODESYSTEM_URL = "http://snomed.info/sct";
public static final String RXNORM_CODESYSTEM_URL = "http://www.nlm.nih.gov/research/umls/rxnorm";
public static final String LOINC_CODESYSTEM_URL = "http://loinc.org";
public static final String UCUM_CODESYSTEM_URL = "http://unitsofmeasure.org";
public static final String HL7_TERMINOLOGY_CODESYSTEM_BASE_URL = "http://terminology.hl7.org/CodeSystem/";
public static final String HL7_SID_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/sid/";
public static final String HL7_FHIR_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/";
public static final String ISO_CODESYSTEM_URN = "urn:iso:std:iso:";
public static final String LANG_CODESYSTEM_URN = "urn:ietf:bcp:47";
public static final String MIMETYPES_CODESYSTEM_URN = "urn:ietf:bcp:13";
public static final String _11073_CODESYSTEM_URN = "urn:iso:std:iso:11073:10101";
public static final String DICOM_CODESYSTEM_URL = "http://dicom.nema.org/resources/ontology/DCM";
public String getNameForSystem(String system) {
final int lastPipe = system.lastIndexOf('|');
final String systemBaseName = lastPipe == -1 ? system : system.substring(0,lastPipe);
final String systemVersion = lastPipe == -1 ? null : system.substring(lastPipe + 1);
if (systemBaseName.equals(SNOMED_SCT_CODESYSTEM_URL))
return getVersionedSystem("snomed", systemVersion);
if (systemBaseName.equals(RXNORM_CODESYSTEM_URL))
return getVersionedSystem("rxnorm", systemVersion);
if (systemBaseName.equals(LOINC_CODESYSTEM_URL))
return getVersionedSystem("loinc", systemVersion);
if (systemBaseName.equals(UCUM_CODESYSTEM_URL))
return getVersionedSystem("ucum", systemVersion);
if (systemBaseName.startsWith(HL7_SID_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_SID_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(_11073_CODESYSTEM_URN))
return getVersionedSystem("11073", systemVersion);
if (systemBaseName.startsWith(ISO_CODESYSTEM_URN))
return getVersionedSystem("iso"+systemBaseName.substring(ISO_CODESYSTEM_URN.length()).replace(":", ""), systemVersion);
if (systemBaseName.startsWith(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.startsWith(HL7_FHIR_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_FHIR_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(LANG_CODESYSTEM_URN))
return getVersionedSystem("lang", systemVersion);
if (systemBaseName.equals(MIMETYPES_CODESYSTEM_URN))
return getVersionedSystem("mimetypes", systemVersion);
if (systemBaseName.equals(DICOM_CODESYSTEM_URL))
return getVersionedSystem("dicom", systemVersion);
return getVersionedSystem(systemBaseName.replace("/", "_").replace(":", "_").replace("?", "X").replace("#", "X"), systemVersion);
}
public String normalizeBaseURL(String baseUrl, String fullUrl) {
return fullUrl.substring(baseUrl.length()).replace("/", "");
}
public String getVersionedSystem(String baseSystem, String version) {
if (version != null) {
return baseSystem + "_" + version;
}
return baseSystem;
}
}
public class CacheToken {
private String name;
private String key;
private String request;
public void setName(String n) {
String systemName = getSystemNameKeyGenerator().getNameForSystem(n);
if (name == null)
name = n;
else if (!n.equals(name))
name = systemName;
else if (!systemName.equals(name))
name = NAME_FOR_NO_SYSTEM;
}
public String getName() {
return name;
}
}
private class CacheEntry {
@ -130,7 +202,7 @@ public class TerminologyCache {
public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
CacheToken ct = new CacheToken();
if (code.hasSystem())
ct.name = getNameForSystem(code.getSystem());
ct.name = getSystemNameKeyGenerator().getNameForSystem(code.getSystem());
else
ct.name = NAME_FOR_NO_SYSTEM;
JsonParser json = new JsonParser();
@ -159,7 +231,7 @@ public class TerminologyCache {
CacheToken ct = new CacheToken();
for (Coding c : code.getCoding()) {
if (c.hasSystem())
ct.setName(getNameForSystem(c.getSystem()));
ct.setName(c.getSystem());
}
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
@ -190,13 +262,13 @@ public class TerminologyCache {
ValueSet vsc = getVSEssense(vs);
for (ConceptSetComponent inc : vs.getCompose().getInclude())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
for (ConceptSetComponent inc : vs.getCompose().getExclude())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
for (ValueSetExpansionContainsComponent inc : vs.getExpansion().getContains())
if (inc.hasSystem())
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY);
try {
@ -208,33 +280,7 @@ public class TerminologyCache {
return ct;
}
private String getNameForSystem(String system) {
if (system.equals("http://snomed.info/sct"))
return "snomed";
if (system.equals("http://www.nlm.nih.gov/research/umls/rxnorm"))
return "rxnorm";
if (system.equals("http://loinc.org"))
return "loinc";
if (system.equals("http://unitsofmeasure.org"))
return "ucum";
if (system.startsWith("http://hl7.org/fhir/sid/"))
return system.substring(24).replace("/", "");
if (system.startsWith("urn:iso:std:iso:"))
return "iso"+system.substring(16).replace(":", "");
if (system.startsWith("http://terminology.hl7.org/CodeSystem/"))
return system.substring(38).replace("/", "");
if (system.startsWith("http://hl7.org/fhir/"))
return system.substring(20).replace("/", "");
if (system.equals("urn:ietf:bcp:47"))
return "lang";
if (system.equals("urn:ietf:bcp:13"))
return "mimetypes";
if (system.equals("urn:iso:std:iso:11073:10101"))
return "11073";
if (system.equals("http://dicom.nema.org/resources/ontology/DCM"))
return "dicom";
return system.replace("/", "_").replace(":", "_").replace("?", "X").replace("#", "X");
}
public NamedCache getNamedCache(CacheToken cacheToken) {
NamedCache nc = caches.get(cacheToken.name);
@ -520,7 +566,7 @@ public class TerminologyCache {
public void removeCS(String url) {
synchronized (lock) {
String name = getNameForSystem(url);
String name = getSystemNameKeyGenerator().getNameForSystem(url);
if (caches.containsKey(name)) {
caches.remove(name);
}

8
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/context/CacheTestUtils.java Normal file
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@ -0,0 +1,8 @@
package org.hl7.fhir.r4b.context;
import org.hl7.fhir.utilities.validation.ValidationOptions;
public class CacheTestUtils {
public static final ValidationOptions validationOptions = new ValidationOptions().guessSystem().setVersionFlexible(false);
}

68
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/context/TerminologyCacheTests.java Normal file
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@ -0,0 +1,68 @@
package org.hl7.fhir.r4b.context;
import org.hl7.fhir.r4b.model.Coding;
import org.hl7.fhir.r4b.model.ValueSet;
import org.hl7.fhir.utilities.tests.ResourceLoaderTests;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
import java.io.IOException;
import java.net.URISyntaxException;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class TerminologyCacheTests implements ResourceLoaderTests {
private TerminologyCache createTerminologyCache() throws IOException {
Object lock = new Object();
TerminologyCache terminologyCache = new TerminologyCache(lock, null);
return terminologyCache;
}
@ParameterizedTest
@CsvSource({
"http://terminology.hl7.org/CodeSystem/id,id",
"http://hl7.org/fhir/id,id",
"http://hl7.org/fhir/sid/id,id",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://snomed.info/sct,snomed",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://loinc.org,loinc",
"http://unitsofmeasure.org,ucum",
"urn:iso:std:iso:id,isoid",
"urn:ietf:bcp:47,lang",
"urn:ietf:bcp:13,mimetypes",
"urn:iso:std:iso:11073:10101,11073",
"my://random/system?with#chars,my___random_systemXwithXchars",
"http://dicom.nema.org/resources/ontology/DCM,dicom"
})
public void testCacheTokenGeneration(String system, String expectedName) throws IOException, URISyntaxException {
TerminologyCache terminologyCache = createTerminologyCache();
ValueSet valueSet = new ValueSet();
{
Coding coding = new Coding();
coding.setSystem(system);
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName, cacheToken.getName());
}
{
Coding coding = new Coding();
coding.setSystem(system + "|dummyVersion");
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName + "_dummyVersion", cacheToken.getName());
}
}
}

116
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TerminologyCache.java
View File

@ -38,7 +38,6 @@ import java.io.IOException;
import java.io.OutputStreamWriter;
import java.util.*;
import lombok.AccessLevel;
import lombok.Getter;
import lombok.Setter;
import lombok.experimental.Accessors;
@ -85,6 +84,9 @@ public class TerminologyCache {
private static final String CAPABILITY_STATEMENT_TITLE = ".capabilityStatement";
private static final String TERMINOLOGY_CAPABILITIES_TITLE = ".terminologyCapabilities";
private SystemNameKeyGenerator systemNameKeyGenerator = new SystemNameKeyGenerator();
public class CacheToken {
@Getter
private String name;
@ -96,13 +98,79 @@ public class TerminologyCache {
private boolean hasVersion;
public void setName(String n) {
String systemName = getSystemNameKeyGenerator().getNameForSystem(n);
if (name == null)
name = n;
else if (!n.equals(name))
name = systemName;
else if (!systemName.equals(name))
name = NAME_FOR_NO_SYSTEM;
}
}
protected SystemNameKeyGenerator getSystemNameKeyGenerator() {
return systemNameKeyGenerator;
}
public class SystemNameKeyGenerator {
public static final String SNOMED_SCT_CODESYSTEM_URL = "http://snomed.info/sct";
public static final String RXNORM_CODESYSTEM_URL = "http://www.nlm.nih.gov/research/umls/rxnorm";
public static final String LOINC_CODESYSTEM_URL = "http://loinc.org";
public static final String UCUM_CODESYSTEM_URL = "http://unitsofmeasure.org";
public static final String HL7_TERMINOLOGY_CODESYSTEM_BASE_URL = "http://terminology.hl7.org/CodeSystem/";
public static final String HL7_SID_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/sid/";
public static final String HL7_FHIR_CODESYSTEM_BASE_URL = "http://hl7.org/fhir/";
public static final String ISO_CODESYSTEM_URN = "urn:iso:std:iso:";
public static final String LANG_CODESYSTEM_URN = "urn:ietf:bcp:47";
public static final String MIMETYPES_CODESYSTEM_URN = "urn:ietf:bcp:13";
public static final String _11073_CODESYSTEM_URN = "urn:iso:std:iso:11073:10101";
public static final String DICOM_CODESYSTEM_URL = "http://dicom.nema.org/resources/ontology/DCM";
public String getNameForSystem(String system) {
final int lastPipe = system.lastIndexOf('|');
final String systemBaseName = lastPipe == -1 ? system : system.substring(0,lastPipe);
final String systemVersion = lastPipe == -1 ? null : system.substring(lastPipe + 1);
if (systemBaseName.equals(SNOMED_SCT_CODESYSTEM_URL))
return getVersionedSystem("snomed", systemVersion);
if (systemBaseName.equals(RXNORM_CODESYSTEM_URL))
return getVersionedSystem("rxnorm", systemVersion);
if (systemBaseName.equals(LOINC_CODESYSTEM_URL))
return getVersionedSystem("loinc", systemVersion);
if (systemBaseName.equals(UCUM_CODESYSTEM_URL))
return getVersionedSystem("ucum", systemVersion);
if (systemBaseName.startsWith(HL7_SID_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_SID_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(_11073_CODESYSTEM_URN))
return getVersionedSystem("11073", systemVersion);
if (systemBaseName.startsWith(ISO_CODESYSTEM_URN))
return getVersionedSystem("iso"+systemBaseName.substring(ISO_CODESYSTEM_URN.length()).replace(":", ""), systemVersion);
if (systemBaseName.startsWith(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_TERMINOLOGY_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.startsWith(HL7_FHIR_CODESYSTEM_BASE_URL))
return getVersionedSystem(normalizeBaseURL(HL7_FHIR_CODESYSTEM_BASE_URL, systemBaseName), systemVersion);
if (systemBaseName.equals(LANG_CODESYSTEM_URN))
return getVersionedSystem("lang", systemVersion);
if (systemBaseName.equals(MIMETYPES_CODESYSTEM_URN))
return getVersionedSystem("mimetypes", systemVersion);
if (systemBaseName.equals(DICOM_CODESYSTEM_URL))
return getVersionedSystem("dicom", systemVersion);
return getVersionedSystem(systemBaseName.replace("/", "_").replace(":", "_").replace("?", "X").replace("#", "X"), systemVersion);
}
public String normalizeBaseURL(String baseUrl, String fullUrl) {
return fullUrl.substring(baseUrl.length()).replace("/", "");
}
public String getVersionedSystem(String baseSystem, String version) {
if (version != null) {
return baseSystem + "_" + version;
}
return baseSystem;
}
}
private class CacheEntry {
private String request;
private boolean persistent;
@ -185,7 +253,7 @@ public class TerminologyCache {
public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
CacheToken ct = new CacheToken();
if (code.hasSystem()) {
ct.name = getNameForSystem(code.getSystem());
ct.setName(code.getSystem());
ct.hasVersion = code.hasVersion();
}
else
@ -226,7 +294,7 @@ public class TerminologyCache {
CacheToken ct = new CacheToken();
for (Coding c : code.getCoding()) {
if (c.hasSystem()) {
ct.setName(getNameForSystem(c.getSystem()));
ct.setName(c.getSystem());
ct.hasVersion = c.hasVersion();
}
}
@ -287,53 +355,31 @@ public class TerminologyCache {
if (vs != null) {
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
if (inc.hasSystem()) {
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
ct.hasVersion = inc.hasVersion();
}
}
for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
if (inc.hasSystem()) {
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
ct.hasVersion = inc.hasVersion();
}
}
for (ValueSetExpansionContainsComponent inc : vs.getExpansion().getContains()) {
if (inc.hasSystem()) {
ct.setName(getNameForSystem(inc.getSystem()));
ct.setName(inc.getSystem());
ct.hasVersion = inc.hasVersion();
}
}
}
}
private String getNameForSystem(String system) {
if (system.equals("http://snomed.info/sct"))
return "snomed";
if (system.equals("http://www.nlm.nih.gov/research/umls/rxnorm"))
return "rxnorm";
if (system.equals("http://loinc.org"))
return "loinc";
if (system.equals("http://unitsofmeasure.org"))
return "ucum";
if (system.startsWith("http://hl7.org/fhir/sid/"))
return system.substring(24).replace("/", "");
if (system.startsWith("urn:iso:std:iso:"))
return "iso"+system.substring(16).replace(":", "");
if (system.startsWith("http://terminology.hl7.org/CodeSystem/"))
return system.substring(38).replace("/", "");
if (system.startsWith("http://hl7.org/fhir/"))
return system.substring(20).replace("/", "");
if (system.equals("urn:ietf:bcp:47"))
return "lang";
if (system.equals("urn:ietf:bcp:13"))
return "mimetypes";
if (system.equals("urn:iso:std:iso:11073:10101"))
return "11073";
if (system.equals("http://dicom.nema.org/resources/ontology/DCM"))
return "dicom";
return system.replace("/", "_").replace(":", "_").replace("?", "X").replace("#", "X");
private String normalizeSystemPath(String path) {
return path.replace("/", "").replace('|','X');
}
public NamedCache getNamedCache(CacheToken cacheToken) {
final String cacheName = cacheToken.name == null ? "null" : cacheToken.name;
@ -687,7 +733,7 @@ public class TerminologyCache {
public void removeCS(String url) {
synchronized (lock) {
String name = getNameForSystem(url);
String name = getSystemNameKeyGenerator().getNameForSystem(url);
if (caches.containsKey(name)) {
caches.remove(name);
}

40
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/context/TerminologyCacheTests.java
View File

@ -33,6 +33,7 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.CsvSource;
import org.junit.jupiter.params.provider.MethodSource;
import com.google.gson.JsonElement;
@ -238,6 +239,8 @@ public class TerminologyCacheTests implements ResourceLoaderTests {
assertTrue(cacheToken.hasVersion());
}
@Test
public void testCodableConceptCacheTokenGeneration() throws IOException, URISyntaxException {
@ -453,4 +456,41 @@ public class TerminologyCacheTests implements ResourceLoaderTests {
assertEquals("http://dummy.org", extracted);
}
@ParameterizedTest
@CsvSource({
"http://terminology.hl7.org/CodeSystem/id,id",
"http://hl7.org/fhir/id,id",
"http://hl7.org/fhir/sid/id,id",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://snomed.info/sct,snomed",
"http://www.nlm.nih.gov/research/umls/rxnorm,rxnorm",
"http://loinc.org,loinc",
"http://unitsofmeasure.org,ucum",
"urn:iso:std:iso:id,isoid",
"urn:ietf:bcp:47,lang",
"urn:ietf:bcp:13,mimetypes",
"urn:iso:std:iso:11073:10101,11073",
"my://random/system?with#chars,my___random_systemXwithXchars",
"http://dicom.nema.org/resources/ontology/DCM,dicom"
})
public void testCacheTokenGeneration(String system, String expectedName) throws IOException, URISyntaxException {
TerminologyCache terminologyCache = createTerminologyCache();
ValueSet valueSet = new ValueSet();
{
Coding coding = new Coding();
coding.setSystem(system);
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName, cacheToken.getName());
}
{
Coding coding = new Coding();
coding.setSystem(system + "|dummyVersion");
TerminologyCache.CacheToken cacheToken = terminologyCache.generateValidationToken(CacheTestUtils.validationOptions,
coding, valueSet);
assertEquals(expectedName + "_dummyVersion", cacheToken.getName());
}
}
}

12
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/v2-0360_2.7.cache Normal file
View File

@ -0,0 +1,12 @@
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://terminology.hl7.org/CodeSystem/v2-0360|2.7",
"code" : "BS",
"display" : "Bachelor of Science"
}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"true"}####
v: {
"display" : "Bachelor of Science",
"code" : "BS",
"system" : "http://terminology.hl7.org/CodeSystem/v2-0360|2.7"
}
-------------------------------------------------------------------------------------