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Fix cacheing for large valuesets

This commit is contained in:
dotasek 2021-12-09 15:50:03 -05:00
parent e5976307f4
commit 394452b747
4 changed files with 118 additions and 108 deletions
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163
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TerminologyCache.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.context; package org.hl7.fhir.r5.context;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -147,8 +147,13 @@ public class TerminologyCache {
public String extracted(JsonParser json, ValueSet vsc) throws IOException { public String extracted(JsonParser json, ValueSet vsc) throws IOException {
String s = null; String s = null;
if (vsc.getExpansion().getContains().size() > 1000 || vsc.getCompose().getIncludeFirstRep().getConcept().size() > 1000) { if (vsc.getExpansion().getContains().size() > 1000 || vsc.getCompose().getIncludeFirstRep().getConcept().size() > 1000) {
s = Integer.toString(vsc.hashCode()); // turn caching off - hack efficiency optimisation int hashCode = (vsc.getExpansion().getContains().toString() + vsc.getCompose().getIncludeFirstRep().getConcept().toString()).hashCode();
StringBuilder sb = new StringBuilder();
for (ValueSet.ConceptReferenceComponent c : vsc.getCompose().getIncludeFirstRep().getConcept()) {
sb.append(c.getCode());
}
s = Integer.toString((vsc.getExpansion().getContains().toString() + sb.toString()).hashCode()); // turn caching off - hack efficiency optimisation
} else { } else {
s = json.composeString(vsc); s = json.composeString(vsc);
} }
@ -380,56 +385,58 @@ public class TerminologyCache {
} }
private void load() throws FHIRException { private void load() throws FHIRException {
for (String fn : new File(folder).list()) { synchronized (lock) {
if (fn.endsWith(".cache") && !fn.equals("validation.cache")) { for (String fn : new File(folder).list()) {
int c = 0; if (fn.endsWith(".cache") && !fn.equals("validation.cache")) {
try { int c = 0;
String title = fn.substring(0, fn.lastIndexOf(".")); try {
NamedCache nc = new NamedCache(); String title = fn.substring(0, fn.lastIndexOf("."));
nc.name = title; NamedCache nc = new NamedCache();
caches.put(title, nc); nc.name = title;
String src = TextFile.fileToString(Utilities.path(folder, fn)); caches.put(title, nc);
if (src.startsWith("?")) String src = TextFile.fileToString(Utilities.path(folder, fn));
src = src.substring(1); if (src.startsWith("?"))
int i = src.indexOf(ENTRY_MARKER); src = src.substring(1);
while (i > -1) { int i = src.indexOf(ENTRY_MARKER);
c++; while (i > -1) {
String s = src.substring(0, i); c++;
src = src.substring(i+ENTRY_MARKER.length()+1); String s = src.substring(0, i);
i = src.indexOf(ENTRY_MARKER); src = src.substring(i + ENTRY_MARKER.length() + 1);
if (!Utilities.noString(s)) { i = src.indexOf(ENTRY_MARKER);
int j = s.indexOf(BREAK); if (!Utilities.noString(s)) {
String q = s.substring(0, j); int j = s.indexOf(BREAK);
String p = s.substring(j+BREAK.length()+1).trim(); String q = s.substring(0, j);
CacheEntry ce = new CacheEntry(); String p = s.substring(j + BREAK.length() + 1).trim();
ce.persistent = true; CacheEntry ce = new CacheEntry();
ce.request = q; ce.persistent = true;
boolean e = p.charAt(0) == 'e'; ce.request = q;
p = p.substring(3); boolean e = p.charAt(0) == 'e';
JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p); p = p.substring(3);
String error = loadJS(o.get("error")); JsonObject o = (JsonObject) new com.google.gson.JsonParser().parse(p);
if (e) { String error = loadJS(o.get("error"));
if (o.has("valueSet")) if (e) {
ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN); if (o.has("valueSet"))
else ce.e = new ValueSetExpansionOutcome((ValueSet) new JsonParser().parse(o.getAsJsonObject("valueSet")), error, TerminologyServiceErrorClass.UNKNOWN);
ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN); else
} else { ce.e = new ValueSetExpansionOutcome(error, TerminologyServiceErrorClass.UNKNOWN);
String t = loadJS(o.get("severity")); } else {
IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t); String t = loadJS(o.get("severity"));
String display = loadJS(o.get("display")); IssueSeverity severity = t == null ? null : IssueSeverity.fromCode(t);
String code = loadJS(o.get("code")); String display = loadJS(o.get("display"));
String system = loadJS(o.get("system")); String code = loadJS(o.get("code"));
String definition = loadJS(o.get("definition")); String system = loadJS(o.get("system"));
t = loadJS(o.get("class")); String definition = loadJS(o.get("definition"));
TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t) ; t = loadJS(o.get("class"));
ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass); TerminologyServiceErrorClass errorClass = t == null ? null : TerminologyServiceErrorClass.valueOf(t);
ce.v = new ValidationResult(severity, error, system, new ConceptDefinitionComponent().setDisplay(display).setDefinition(definition).setCode(code)).setErrorClass(errorClass);
}
nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
nc.list.add(ce);
} }
nc.map.put(String.valueOf(hashNWS(ce.request)), ce);
nc.list.add(ce);
} }
} } catch (Exception e) {
} catch (Exception e) { throw new FHIRException("Error loading " + fn + ": " + e.getMessage() + " entry " + c, e);
throw new FHIRException("Error loading "+fn+": "+e.getMessage()+" entry "+c, e); }
} }
} }
} }

57
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.terminologies; package org.hl7.fhir.r5.terminologies;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -148,6 +148,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (cs == null) { if (cs == null) {
cs = findSpecialCodeSystem(system); cs = findSpecialCodeSystem(system);
} }
System.out.print("");
if (cs == null) { if (cs == null) {
warningMessage = "Unable to resolve system "+system; warningMessage = "Unable to resolve system "+system;
if (!inExpansion) { if (!inExpansion) {

5
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/TestingUtilities.java
View File

@ -5,15 +5,16 @@ import org.hl7.fhir.validation.ValidationEngine;
public class TestingUtilities { public class TestingUtilities {
public static final ValidationEngine getValidationEngine(java.lang.String src, java.lang.String txsrvr, java.lang.String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, java.lang.String vString, java.lang.String userAgent) throws Exception { public static final ValidationEngine getValidationEngine(java.lang.String src, java.lang.String txsrvr, java.lang.String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, java.lang.String vString, java.lang.String userAgent) throws Exception {
txLog = TestConstants.TX_CACHE + "/tx.log.html";
final ValidationEngine validationEngine = new ValidationEngine(src, txsrvr, txLog, version, canRunWithoutTerminologyServer, vString, userAgent); final ValidationEngine validationEngine = new ValidationEngine(src, txsrvr, txLog, version, canRunWithoutTerminologyServer, vString, userAgent);
validationEngine.getContext().initTS(TestConstants.TX_CACHE); validationEngine.getContext().initTS(TestConstants.TX_CACHE + "/" + version.toString());
validationEngine.getContext().setUserAgent("fhir/test-cases"); validationEngine.getContext().setUserAgent("fhir/test-cases");
return validationEngine; return validationEngine;
} }
public static ValidationEngine getValidationEngine(java.lang.String src, java.lang.String txsrvr, java.lang.String txLog, FhirPublication version, java.lang.String vString, java.lang.String userAgent) throws Exception { public static ValidationEngine getValidationEngine(java.lang.String src, java.lang.String txsrvr, java.lang.String txLog, FhirPublication version, java.lang.String vString, java.lang.String userAgent) throws Exception {
final ValidationEngine validationEngine = new ValidationEngine(src, txsrvr, txLog, version, vString, userAgent); final ValidationEngine validationEngine = new ValidationEngine(src, txsrvr, txLog, version, vString, userAgent);
validationEngine.getContext().initTS(TestConstants.TX_CACHE); validationEngine.getContext().initTS(TestConstants.TX_CACHE + "/" + version.toString());
validationEngine.getContext().setUserAgent("fhir/test-cases"); validationEngine.getContext().setUserAgent("fhir/test-cases");
return validationEngine; return validationEngine;
} }

1
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -101,6 +101,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
List<Object[]> objects = new ArrayList<Object[]>(examples.size()); List<Object[]> objects = new ArrayList<Object[]>(examples.size());
for (String id : names) { for (String id : names) {
//if ("dr-eh".equals(id))
objects.add(new Object[]{id, examples.get(id)}); objects.add(new Object[]{id, examples.get(id)});
} }
return objects; return objects;