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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Grahame Grieve 2020-03-03 21:25:41 +11:00
parent c86fc8bbb5 c923cba4e2
commit 690f983177
10 changed files with 34 additions and 30 deletions
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28
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/BaseWorkerContext.java
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@ -45,17 +45,21 @@ import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r4.terminologies.ValueSetExpanderSimple; import org.hl7.fhir.r4.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r4.utils.ToolingExtensions; import org.hl7.fhir.r4.utils.ToolingExtensions;
import org.hl7.fhir.utilities.OIDUtils; import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices; import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.IOException; import java.io.IOException;
import java.util.*; import java.util.ArrayList;
import java.util.Date;
import static org.apache.commons.lang3.StringUtils.isNotBlank; import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
public abstract class BaseWorkerContext implements IWorkerContext { public abstract class BaseWorkerContext implements IWorkerContext {
@ -438,25 +442,25 @@ public abstract class BaseWorkerContext implements IWorkerContext {
// --- validate code ------------------------------------------------------------------------------- // --- validate code -------------------------------------------------------------------------------
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display) { public ValidationResult validateCode(ValidationOptions options, String system, String code, String display) {
Coding c = new Coding(system, code, display); Coding c = new Coding(system, code, display);
return validateCode(options, c, null); return validateCode(options, c, null);
} }
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display, ValueSet vs) { public ValidationResult validateCode(ValidationOptions options, String system, String code, String display, ValueSet vs) {
Coding c = new Coding(system, code, display); Coding c = new Coding(system, code, display);
return validateCode(options, c, vs); return validateCode(options, c, vs);
} }
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, String code, ValueSet vs) { public ValidationResult validateCode(ValidationOptions options, String code, ValueSet vs) {
Coding c = new Coding(null, code, null); Coding c = new Coding(null, code, null);
return doValidateCode(options, c, vs, true); return doValidateCode(options, c, vs, true);
} }
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display, ConceptSetComponent vsi) { public ValidationResult validateCode(ValidationOptions options, String system, String code, String display, ConceptSetComponent vsi) {
Coding c = new Coding(system, code, display); Coding c = new Coding(system, code, display);
ValueSet vs = new ValueSet(); ValueSet vs = new ValueSet();
vs.setUrl(Utilities.makeUuidUrn()); vs.setUrl(Utilities.makeUuidUrn());
@ -465,11 +469,11 @@ public abstract class BaseWorkerContext implements IWorkerContext {
} }
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, Coding code, ValueSet vs) { public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
return doValidateCode(options, code, vs, false); return doValidateCode(options, code, vs, false);
} }
public ValidationResult doValidateCode(TerminologyServiceOptions options, Coding code, ValueSet vs, boolean implySystem) { public ValidationResult doValidateCode(ValidationOptions options, Coding code, ValueSet vs, boolean implySystem) {
CacheToken cacheToken = txCache != null ? txCache.generateValidationToken(options, code, vs) : null; CacheToken cacheToken = txCache != null ? txCache.generateValidationToken(options, code, vs) : null;
ValidationResult res = null; ValidationResult res = null;
if (txCache != null) if (txCache != null)
@ -511,7 +515,7 @@ public abstract class BaseWorkerContext implements IWorkerContext {
return res; return res;
} }
private void setTerminologyOptions(TerminologyServiceOptions options, Parameters pIn) { private void setTerminologyOptions(ValidationOptions options, Parameters pIn) {
if (options != null) { if (options != null) {
if (!Utilities.noString(options.getLanguage())) if (!Utilities.noString(options.getLanguage()))
pIn.addParameter("displayLanguage", options.getLanguage()); pIn.addParameter("displayLanguage", options.getLanguage());
@ -519,7 +523,7 @@ public abstract class BaseWorkerContext implements IWorkerContext {
} }
@Override @Override
public ValidationResult validateCode(TerminologyServiceOptions options, CodeableConcept code, ValueSet vs) { public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs) {
CacheToken cacheToken = txCache.generateValidationToken(options, code, vs); CacheToken cacheToken = txCache.generateValidationToken(options, code, vs);
ValidationResult res = txCache.getValidation(cacheToken); ValidationResult res = txCache.getValidation(cacheToken);
if (res != null) if (res != null)

13
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/IWorkerContext.java
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@ -51,6 +51,7 @@ import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.utilities.TerminologyServiceOptions; import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices; import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
/** /**
@ -376,7 +377,7 @@ public interface IWorkerContext {
* @param display * @param display
* @return * @return
*/ */
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display); public ValidationResult validateCode(ValidationOptions options, String system, String code, String display);
/** /**
* Validation of a code - consult the terminology service * Validation of a code - consult the terminology service
@ -392,10 +393,10 @@ public interface IWorkerContext {
* @param display * @param display
* @return * @return
*/ */
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display, ValueSet vs); public ValidationResult validateCode(ValidationOptions options, String system, String code, String display, ValueSet vs);
public ValidationResult validateCode(TerminologyServiceOptions options, String code, ValueSet vs); public ValidationResult validateCode(ValidationOptions options, String code, ValueSet vs);
public ValidationResult validateCode(TerminologyServiceOptions options, Coding code, ValueSet vs); public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs);
public ValidationResult validateCode(TerminologyServiceOptions options, CodeableConcept code, ValueSet vs); public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs);
/** /**
* Validation of a code - consult the terminology service * Validation of a code - consult the terminology service
@ -411,7 +412,7 @@ public interface IWorkerContext {
* @param display * @param display
* @return * @return
*/ */
public ValidationResult validateCode(TerminologyServiceOptions options, String system, String code, String display, ConceptSetComponent vsi); public ValidationResult validateCode(ValidationOptions options, String system, String code, String display, ConceptSetComponent vsi);
/** /**
* returns the recommended tla for the type * returns the recommended tla for the type

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/TerminologyCache.java
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@ -46,7 +46,6 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.TerminologyServiceErrorClass; import org.hl7.fhir.r4.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome; import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TextFile; import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@ -55,6 +54,7 @@ import com.google.gson.JsonElement;
import com.google.gson.JsonNull; import com.google.gson.JsonNull;
import com.google.gson.JsonObject; import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive; import com.google.gson.JsonPrimitive;
import org.hl7.fhir.utilities.validation.ValidationOptions;
/** /**
* This implements a two level cache. * This implements a two level cache.
@ -112,7 +112,7 @@ public class TerminologyCache {
load(); load();
} }
public CacheToken generateValidationToken(TerminologyServiceOptions options, Coding code, ValueSet vs) { public CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
CacheToken ct = new CacheToken(); CacheToken ct = new CacheToken();
if (code.hasSystem()) if (code.hasSystem())
ct.name = getNameForSystem(code.getSystem()); ct.name = getNameForSystem(code.getSystem());
@ -130,7 +130,7 @@ public class TerminologyCache {
return ct; return ct;
} }
public CacheToken generateValidationToken(TerminologyServiceOptions options, CodeableConcept code, ValueSet vs) { public CacheToken generateValidationToken(ValidationOptions options, CodeableConcept code, ValueSet vs) {
CacheToken ct = new CacheToken(); CacheToken ct = new CacheToken();
for (Coding c : code.getCoding()) { for (Coding c : code.getCoding()) {
if (c.hasSystem()) if (c.hasSystem())

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/ValueSetCheckerSimple.java
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@ -30,8 +30,8 @@ import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionDesignationComponent; import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionDesignationComponent;
import org.hl7.fhir.r4.model.ValueSet.*; import org.hl7.fhir.r4.model.ValueSet.*;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
@ -43,9 +43,9 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
private ValueSet valueset; private ValueSet valueset;
private IWorkerContext context; private IWorkerContext context;
private Map<String, ValueSetCheckerSimple> inner = new HashMap<>(); private Map<String, ValueSetCheckerSimple> inner = new HashMap<>();
private TerminologyServiceOptions options; private ValidationOptions options;
public ValueSetCheckerSimple(TerminologyServiceOptions options, ValueSet source, IWorkerContext context) { public ValueSetCheckerSimple(ValidationOptions options, ValueSet source, IWorkerContext context) {
this.valueset = source; this.valueset = source;
this.context = context; this.context = context;
this.options = options; this.options = options;

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -83,7 +83,6 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple;
import org.hl7.fhir.r5.utils.ToolingExtensions; import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.client.ToolingClientLogger; import org.hl7.fhir.r5.utils.client.ToolingClientLogger;
import org.hl7.fhir.utilities.OIDUtils; import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices; import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities; import org.hl7.fhir.utilities.VersionUtilities;

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
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@ -51,7 +51,6 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorCla
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome; import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.utils.INarrativeGenerator; import org.hl7.fhir.r5.utils.INarrativeGenerator;
import org.hl7.fhir.r5.utils.IResourceValidator; import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.TranslationServices; import org.hl7.fhir.utilities.TranslationServices;
import org.hl7.fhir.utilities.validation.ValidationOptions; import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
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@ -45,7 +45,6 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent; import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent; import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TerminologyServiceOptions;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationOptions; import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode; import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode;

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/OIDUtils.java
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@ -49,7 +49,7 @@ public class OIDUtils {
if (r.equals("2.16.840.1.113883.6.103")) if (r.equals("2.16.840.1.113883.6.103"))
return "http://hl7.org/fhir/sid/icd-9"; //todo: confirm this return "http://hl7.org/fhir/sid/icd-9"; //todo: confirm this
if (r.equals("2.16.840.1.113883.6.73")) if (r.equals("2.16.840.1.113883.6.73"))
return "http://hl7.org/fhir/sid/atc"; return "http://www.whocc.no/atc";
if (r.equals("2.16.840.1.113883.3.26.1.1")) if (r.equals("2.16.840.1.113883.3.26.1.1"))
return "http://ncimeta.nci.nih.gov"; return "http://ncimeta.nci.nih.gov";
if (r.equals("2.16.840.1.113883.3.26.1.1.1")) if (r.equals("2.16.840.1.113883.3.26.1.1.1"))

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
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@ -171,7 +171,8 @@ public class BaseValidator {
*/ */
protected boolean hint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg) { protected boolean hint(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg) {
if (!thePass) { if (!thePass) {
addValidationMessage(errors, type, line, col, path, msg, IssueSeverity.INFORMATION); String message = formatMessage(msg);
addValidationMessage(errors, type, line, col, path, message, IssueSeverity.INFORMATION);
} }
return thePass; return thePass;
} }

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -2018,7 +2018,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
long t = System.nanoTime(); long t = System.nanoTime();
ValidationResult vr = null; ValidationResult vr = null;
if (binding.getStrength() != BindingStrength.EXAMPLE) { if (binding.getStrength() != BindingStrength.EXAMPLE) {
vr = context.validateCode(new ValidationOptions(stack.workingLang), value, vs); ValidationOptions options = new ValidationOptions(stack.workingLang).guessSystem();
vr = context.validateCode(options, value, vs);
} }
txTime = txTime + (System.nanoTime() - t); txTime = txTime + (System.nanoTime() - t);
if (vr != null && !vr.isOk()) { if (vr != null && !vr.isOk()) {