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hapi-fhir
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Merge remote-tracking branch 'upstream/master'

This commit is contained in:
Bill Denton 2016-06-15 18:57:09 -07:00
parent 4e83b59d3c 1683cf8cef
commit 36ed5d8984
50 changed files with 1620 additions and 439 deletions
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4
.travis.yml
View File

@ -19,7 +19,7 @@ before_script:
- export MAVEN_SKIP_RC=true
script:
# - mvn -e -B clean install && cd hapi-fhir-cobertura && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
- mvn -e -B clean install && cd hapi-fhir-cobertura && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID -P COBERTURA clean cobertura:cobertura coveralls:report
# - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
- mvn -e -B clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report

28
hapi-fhir-base/pom.xml
View File

@ -138,6 +138,34 @@
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>

226
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/BaseDateTimeDt.java
View File

@ -7,6 +7,7 @@ import java.util.Date;
import java.util.GregorianCalendar;
import java.util.TimeZone;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.commons.lang3.time.FastDateFormat;
@ -16,14 +17,15 @@ import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.parser.DataFormatException;
public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
static final long NANOS_PER_MILLIS = 1000000L;
static final long NANOS_PER_SECOND = 1000000000L;
private static final FastDateFormat ourHumanDateFormat = FastDateFormat.getDateInstance(FastDateFormat.MEDIUM);
private static final FastDateFormat ourHumanDateTimeFormat = FastDateFormat.getDateTimeInstance(FastDateFormat.MEDIUM, FastDateFormat.MEDIUM);
private String myFractionalSeconds;
private TemporalPrecisionEnum myPrecision = TemporalPrecisionEnum.SECOND;
private TemporalPrecisionEnum myPrecision = null;
private TimeZone myTimeZone;
private boolean myTimeZoneZulu = false;
/**
@ -186,11 +188,13 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
if (getValue() == null) {
return null;
}
GregorianCalendar cal = new GregorianCalendar();
cal.setTime(getValue());
GregorianCalendar cal;
if (getTimeZone() != null) {
cal.setTimeZone(getTimeZone());
cal = new GregorianCalendar(getTimeZone());
} else {
cal = new GregorianCalendar();
}
cal.setTime(getValue());
return cal;
}
@ -199,6 +203,9 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
*/
abstract boolean isPrecisionAllowed(TemporalPrecisionEnum thePrecision);
/**
* Returns true if the timezone is set to GMT-0:00 (Z)
*/
public boolean isTimeZoneZulu() {
return myTimeZoneZulu;
}
@ -213,7 +220,7 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
Validate.notNull(getValue(), getClass().getSimpleName() + " contains null value");
return DateUtils.isSameDay(new Date(), getValue());
}
private void leftPadWithZeros(int theInteger, int theLength, StringBuilder theTarget) {
String string = Integer.toString(theInteger);
for (int i = string.length(); i < theLength; i++) {
@ -228,16 +235,16 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
cal.setTimeZone(TimeZone.getDefault());
String value = theValue;
boolean fractionalSecondsSet = false;
if (value.length() > 0 && (value.charAt(0) == ' ' || value.charAt(value.length()-1) == ' ')) {
if (value.length() > 0 && (value.charAt(0) == ' ' || value.charAt(value.length() - 1) == ' ')) {
value = value.trim();
}
int length = value.length();
if (length == 0) {
return null;
}
if (length < 4) {
throwBadDateFormat(value);
}
@ -325,7 +332,7 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
if (fractionalSecondsSet == false) {
myFractionalSeconds = "";
}
setPrecision(precision);
return cal.getTime();
@ -394,12 +401,12 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
/**
* Sets the value for this type using the given Java Date object as the time, and using the default precision for
* this datatype, as well as the local timezone as determined by the local operating
* this datatype (unless the precision is already set), as well as the local timezone as determined by the local operating
* system. Both of these properties may be modified in subsequent calls if neccesary.
*/
@Override
public BaseDateTimeDt setValue(Date theValue) {
setValue(theValue, getDefaultPrecisionForDatatype());
setValue(theValue, getPrecision());
return this;
}
@ -415,11 +422,14 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
* @throws DataFormatException
*/
public void setValue(Date theValue, TemporalPrecisionEnum thePrecision) throws DataFormatException {
setTimeZone(TimeZone.getDefault());
if (getTimeZone() == null) {
setTimeZone(TimeZone.getDefault());
}
myPrecision = thePrecision;
myFractionalSeconds = "";
if (theValue != null) {
myFractionalSeconds = Integer.toString((int) (theValue.getTime() % 1000));
String fractionalSeconds = Integer.toString((int) (theValue.getTime() % 1000));
myFractionalSeconds = StringUtils.leftPad(fractionalSeconds, 3, '0');
}
super.setValue(theValue);
}
@ -490,11 +500,195 @@ public abstract class BaseDateTimeDt extends BasePrimitive<Date> {
}
}
private void validateLengthIsAtLeast(String theValue, int theLength) {
if (theValue.length() < theLength) {
throwBadDateFormat(theValue);
}
}
/**
* Returns the year, e.g. 2015
*/
public Integer getYear() {
return getFieldValue(Calendar.YEAR);
}
/**
* Returns the month with 0-index, e.g. 0=January
*/
public Integer getMonth() {
return getFieldValue(Calendar.MONTH);
}
/**
* Returns the month with 1-index, e.g. 1=the first day of the month
*/
public Integer getDay() {
return getFieldValue(Calendar.DAY_OF_MONTH);
}
/**
* Returns the hour of the day in a 24h clock, e.g. 13=1pm
*/
public Integer getHour() {
return getFieldValue(Calendar.HOUR_OF_DAY);
}
/**
* Returns the minute of the hour in the range 0-59
*/
public Integer getMinute() {
return getFieldValue(Calendar.MINUTE);
}
/**
* Returns the second of the minute in the range 0-59
*/
public Integer getSecond() {
return getFieldValue(Calendar.SECOND);
}
/**
* Returns the milliseconds within the current second.
* <p>
* Note that this method returns the
* same value as {@link #getNanos()} but with less precision.
* </p>
*/
public Integer getMillis() {
return getFieldValue(Calendar.MILLISECOND);
}
/**
* Returns the nanoseconds within the current second
* <p>
* Note that this method returns the
* same value as {@link #getMillis()} but with more precision.
* </p>
*/
public Long getNanos() {
if (isBlank(myFractionalSeconds)) {
return null;
}
String retVal = StringUtils.rightPad(myFractionalSeconds, 9, '0');
retVal = retVal.substring(0, 9);
return Long.parseLong(retVal);
}
/**
* Sets the year, e.g. 2015
*/
public BaseDateTimeDt setYear(int theYear) {
setFieldValue(Calendar.YEAR, theYear, null, 0, 9999);
return this;
}
/**
* Sets the month with 0-index, e.g. 0=January
*/
public BaseDateTimeDt setMonth(int theMonth) {
setFieldValue(Calendar.MONTH, theMonth, null, 0, 11);
return this;
}
/**
* Sets the month with 1-index, e.g. 1=the first day of the month
*/
public BaseDateTimeDt setDay(int theDay) {
setFieldValue(Calendar.DAY_OF_MONTH, theDay, null, 0, 31);
return this;
}
/**
* Sets the hour of the day in a 24h clock, e.g. 13=1pm
*/
public BaseDateTimeDt setHour(int theHour) {
setFieldValue(Calendar.HOUR_OF_DAY, theHour, null, 0, 23);
return this;
}
/**
* Sets the minute of the hour in the range 0-59
*/
public BaseDateTimeDt setMinute(int theMinute) {
setFieldValue(Calendar.MINUTE, theMinute, null, 0, 59);
return this;
}
/**
* Sets the second of the minute in the range 0-59
*/
public BaseDateTimeDt setSecond(int theSecond) {
setFieldValue(Calendar.SECOND, theSecond, null, 0, 59);
return this;
}
/**
* Sets the milliseconds within the current second.
* <p>
* Note that this method sets the
* same value as {@link #setNanos(long)} but with less precision.
* </p>
*/
public BaseDateTimeDt setMillis(int theMillis) {
setFieldValue(Calendar.MILLISECOND, theMillis, null, 0, 999);
return this;
}
/**
* Sets the nanoseconds within the current second
* <p>
* Note that this method sets the
* same value as {@link #setMillis(int)} but with more precision.
* </p>
*/
public BaseDateTimeDt setNanos(long theNanos) {
validateValueInRange(theNanos, 0, NANOS_PER_SECOND-1);
String fractionalSeconds = StringUtils.leftPad(Long.toString(theNanos), 9, '0');
// Strip trailing 0s
for (int i = fractionalSeconds.length(); i > 0; i--) {
if (fractionalSeconds.charAt(i-1) != '0') {
fractionalSeconds = fractionalSeconds.substring(0, i);
break;
}
}
int millis = (int)(theNanos / NANOS_PER_MILLIS);
setFieldValue(Calendar.MILLISECOND, millis, fractionalSeconds, 0, 999);
return this;
}
private void setFieldValue(int theField, int theValue, String theFractionalSeconds, int theMinimum, int theMaximum) {
validateValueInRange(theValue, theMinimum, theMaximum);
Calendar cal;
if (getValue() == null) {
cal = new GregorianCalendar(0, 0, 0);
} else {
cal = getValueAsCalendar();
}
if (theField != -1) {
cal.set(theField, theValue);
}
if (theFractionalSeconds != null) {
myFractionalSeconds = theFractionalSeconds;
} else if (theField == Calendar.MILLISECOND) {
myFractionalSeconds = StringUtils.leftPad(Integer.toString(theValue), 3, '0');
}
super.setValue(cal.getTime());
}
private void validateValueInRange(long theValue, long theMinimum, long theMaximum) {
if (theValue < theMinimum || theValue > theMaximum) {
throw new IllegalArgumentException("Value " + theValue + " is not between allowable range: " + theMinimum + " - " + theMaximum);
}
}
private Integer getFieldValue(int theField) {
if (getValue() == null) {
return null;
}
Calendar cal = getValueAsCalendar();
return cal.get(theField);
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/DecimalDt.java
View File

@ -78,7 +78,7 @@ public class DecimalDt extends BasePrimitive<BigDecimal> implements Comparable<D
if (getValue() == null && theObj.getValue() == null) {
return 0;
}
if (getValue() != null && theObj.getValue() == null) {
if (getValue() != null && (theObj == null || theObj.getValue() == null)) {
return 1;
}
if (getValue() == null && theObj.getValue() != null) {

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/InstantDt.java
View File

@ -185,5 +185,4 @@ public class InstantDt extends BaseDateTimeDt {
return DEFAULT_PRECISION;
}
}

49
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/UriDt.java
View File

@ -32,22 +32,6 @@ import ca.uhn.fhir.model.api.annotation.SimpleSetter;
@DatatypeDef(name = "uri")
public class UriDt extends BasePrimitive<String> {
/**
* Creates a new UriDt instance which uses the given OID as the content (and prepends "urn:oid:" to the OID string
* in the value of the newly created UriDt, per the FHIR specification).
*
* @param theOid
* The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a
* <code>null</code> value)
* @return A new UriDt instance
*/
public static UriDt fromOid(String theOid) {
if (theOid == null) {
return new UriDt();
}
return new UriDt("urn:oid:" + theOid);
}
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UriDt.class);
/**
@ -119,18 +103,15 @@ public class UriDt extends BasePrimitive<String> {
URI retVal;
try {
retVal = new URI(theValue).normalize();
} catch (URISyntaxException e1) {
ourLog.debug("Failed to normalize URL '{}', message was: {}", theValue, e1.toString());
String urlString = retVal.toString();
if (urlString.endsWith("/") && urlString.length() > 1) {
retVal = new URI(urlString.substring(0, urlString.length() - 1));
}
} catch (URISyntaxException e) {
ourLog.debug("Failed to normalize URL '{}', message was: {}", theValue, e.toString());
return theValue;
}
String urlString = retVal.toString();
if (urlString.endsWith("/") && urlString.length() > 1) {
try {
retVal = new URI(urlString.substring(0, urlString.length() - 1));
} catch (URISyntaxException e) {
ourLog.debug("Failed to normalize URL '{}', message was: {}", urlString, e.toString());
}
}
return retVal.toASCIIString();
}
@ -139,4 +120,20 @@ public class UriDt extends BasePrimitive<String> {
return theValue;
}
/**
* Creates a new UriDt instance which uses the given OID as the content (and prepends "urn:oid:" to the OID string
* in the value of the newly created UriDt, per the FHIR specification).
*
* @param theOid
* The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a
* <code>null</code> value)
* @return A new UriDt instance
*/
public static UriDt fromOid(String theOid) {
if (theOid == null) {
return new UriDt();
}
return new UriDt("urn:oid:" + theOid);
}
}

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/MethodUtil.java
View File

@ -73,7 +73,7 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.client.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.method.OperationParameter.IConverter;
import ca.uhn.fhir.rest.method.OperationParameter.IOperationParamConverter;
import ca.uhn.fhir.rest.param.CollectionBinder;
import ca.uhn.fhir.rest.param.DateAndListParam;
import ca.uhn.fhir.rest.param.NumberAndListParam;
@ -499,7 +499,7 @@ public class MethodUtil {
if (parameterType.equals(ValidationModeEnum.class) == false) {
throw new ConfigurationException("Parameter annotated with @" + Validate.class.getSimpleName() + "." + Validate.Mode.class.getSimpleName() + " must be of type " + ValidationModeEnum.class.getName());
}
param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_MODE, 0, 1).setConverter(new IConverter() {
param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_MODE, 0, 1).setConverter(new IOperationParamConverter() {
@Override
public Object incomingServer(Object theObject) {
if (isNotBlank(theObject.toString())) {
@ -522,7 +522,7 @@ public class MethodUtil {
if (parameterType.equals(String.class) == false) {
throw new ConfigurationException("Parameter annotated with @" + Validate.class.getSimpleName() + "." + Validate.Profile.class.getSimpleName() + " must be of type " + String.class.getName());
}
param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_PROFILE, 0, 1).setConverter(new IConverter() {
param = new OperationParameter(theContext, Constants.EXTOP_VALIDATE, Constants.EXTOP_VALIDATE_PROFILE, 0, 1).setConverter(new IOperationParamConverter() {
@Override
public Object incomingServer(Object theObject) {
return theObject.toString();

273
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationParameter.java
View File

@ -63,6 +63,7 @@ import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.ReflectionUtil;
public class OperationParameter implements IParameter {
@ -74,7 +75,7 @@ public class OperationParameter implements IParameter {
private boolean myAllowGet;
private final FhirContext myContext;
private IConverter myConverter;
private IOperationParamConverter myConverter;
@SuppressWarnings("rawtypes")
private Class<? extends Collection> myInnerCollectionType;
private int myMax;
@ -203,7 +204,7 @@ public class OperationParameter implements IParameter {
mySearchParameterBinding = new SearchParameter(myName, myMin > 0);
mySearchParameterBinding.setCompositeTypes(COMPOSITE_TYPES);
mySearchParameterBinding.setType(myContext, theParameterType, theInnerCollectionType, theOuterCollectionType);
myConverter = new QueryParameterConverter();
myConverter = new OperationParamConverter();
} else {
throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
}
@ -212,7 +213,7 @@ public class OperationParameter implements IParameter {
}
public OperationParameter setConverter(IConverter theConverter) {
public OperationParameter setConverter(IOperationParamConverter theConverter) {
myConverter = theConverter;
return this;
}
@ -242,127 +243,9 @@ public class OperationParameter implements IParameter {
List<Object> matchingParamValues = new ArrayList<Object>();
if (theRequest.getRequestType() == RequestTypeEnum.GET) {
if (mySearchParameterBinding != null) {
List<QualifiedParamList> params = new ArrayList<QualifiedParamList>();
String nameWithQualifierColon = myName + ":";
for (String nextParamName : theRequest.getParameters().keySet()) {
String qualifier;
if (nextParamName.equals(myName)) {
qualifier = null;
} else if (nextParamName.startsWith(nameWithQualifierColon)) {
qualifier = nextParamName.substring(nextParamName.indexOf(':'));
} else {
// This is some other parameter, not the one bound by this instance
continue;
}
String[] values = theRequest.getParameters().get(nextParamName);
if (values != null) {
for (String nextValue : values) {
params.add(QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, nextValue));
}
}
}
if (!params.isEmpty()) {
for (QualifiedParamList next : params) {
Object values = mySearchParameterBinding.parse(myContext, Collections.singletonList(next));
addValueToList(matchingParamValues, values);
}
}
} else {
String[] paramValues = theRequest.getParameters().get(myName);
if (paramValues != null && paramValues.length > 0) {
if (myAllowGet) {
if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
parameters.add(QualifiedParamList.singleton(paramValues[0]));
if (paramValues.length > 1) {
parameters.add(QualifiedParamList.singleton(paramValues[1]));
}
DateRangeParam dateRangeParam = new DateRangeParam();
dateRangeParam.setValuesAsQueryTokens(parameters);
matchingParamValues.add(dateRangeParam);
} else if (String.class.isAssignableFrom(myParameterType)) {
for (String next : paramValues) {
matchingParamValues.add(next);
}
} else if (ValidationModeEnum.class.equals(myParameterType)) {
if (isNotBlank(paramValues[0])) {
ValidationModeEnum validationMode = ValidationModeEnum.forCode(paramValues[0]);
if (validationMode != null) {
matchingParamValues.add(validationMode);
} else {
throwInvalidMode(paramValues[0]);
}
}
} else {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
}
}
} else {
HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
String msg = localizer.getMessage(OperationParameter.class, "urlParamNotPrimitive", myOperationName, myName);
throw new MethodNotAllowedException(msg, RequestTypeEnum.POST);
}
}
}
translateQueryParametersIntoServerArgumentForGet(theRequest, matchingParamValues);
} else {
IBaseResource requestContents = (IBaseResource) theRequest.getUserData().get(REQUEST_CONTENTS_USERDATA_KEY);
RuntimeResourceDefinition def = myContext.getResourceDefinition(requestContents);
if (def.getName().equals("Parameters")) {
BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
IAccessor paramChildAccessor = paramChild.getAccessor();
List<IBase> values = paramChildAccessor.getValues(requestContents);
for (IBase nextParameter : values) {
List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
if (nextNames != null && nextNames.size() > 0) {
IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
if (myName.equals(nextName.getValueAsString())) {
if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
matchingParamValues.add(nextParameter);
} else {
List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
if (paramValues != null && paramValues.size() > 0) {
tryToAddValues(paramValues, matchingParamValues);
} else if (paramResources != null && paramResources.size() > 0) {
tryToAddValues(paramResources, matchingParamValues);
}
}
}
}
}
} else {
if (myParameterType.isAssignableFrom(requestContents.getClass())) {
tryToAddValues(Arrays.asList((IBase) requestContents), matchingParamValues);
}
}
translateQueryParametersIntoServerArgumentForPost(theRequest, matchingParamValues);
}
if (matchingParamValues.isEmpty()) {
@ -373,19 +256,133 @@ public class OperationParameter implements IParameter {
return matchingParamValues.get(0);
}
try {
Collection<Object> retVal = myInnerCollectionType.newInstance();
retVal.addAll(matchingParamValues);
return retVal;
} catch (InstantiationException e) {
throw new InternalErrorException("Failed to instantiate " + myInnerCollectionType, e);
} catch (IllegalAccessException e) {
throw new InternalErrorException("Failed to instantiate " + myInnerCollectionType, e);
Collection<Object> retVal = ReflectionUtil.newInstance(myInnerCollectionType);
retVal.addAll(matchingParamValues);
return retVal;
}
private void translateQueryParametersIntoServerArgumentForGet(RequestDetails theRequest, List<Object> matchingParamValues) {
if (mySearchParameterBinding != null) {
List<QualifiedParamList> params = new ArrayList<QualifiedParamList>();
String nameWithQualifierColon = myName + ":";
for (String nextParamName : theRequest.getParameters().keySet()) {
String qualifier;
if (nextParamName.equals(myName)) {
qualifier = null;
} else if (nextParamName.startsWith(nameWithQualifierColon)) {
qualifier = nextParamName.substring(nextParamName.indexOf(':'));
} else {
// This is some other parameter, not the one bound by this instance
continue;
}
String[] values = theRequest.getParameters().get(nextParamName);
if (values != null) {
for (String nextValue : values) {
params.add(QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, nextValue));
}
}
}
if (!params.isEmpty()) {
for (QualifiedParamList next : params) {
Object values = mySearchParameterBinding.parse(myContext, Collections.singletonList(next));
addValueToList(matchingParamValues, values);
}
}
} else {
String[] paramValues = theRequest.getParameters().get(myName);
if (paramValues != null && paramValues.length > 0) {
if (myAllowGet) {
if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
parameters.add(QualifiedParamList.singleton(paramValues[0]));
if (paramValues.length > 1) {
parameters.add(QualifiedParamList.singleton(paramValues[1]));
}
DateRangeParam dateRangeParam = new DateRangeParam();
dateRangeParam.setValuesAsQueryTokens(parameters);
matchingParamValues.add(dateRangeParam);
} else if (String.class.isAssignableFrom(myParameterType)) {
for (String next : paramValues) {
matchingParamValues.add(next);
}
} else if (ValidationModeEnum.class.equals(myParameterType)) {
if (isNotBlank(paramValues[0])) {
ValidationModeEnum validationMode = ValidationModeEnum.forCode(paramValues[0]);
if (validationMode != null) {
matchingParamValues.add(validationMode);
} else {
throwInvalidMode(paramValues[0]);
}
}
} else {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
}
}
} else {
HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
String msg = localizer.getMessage(OperationParameter.class, "urlParamNotPrimitive", myOperationName, myName);
throw new MethodNotAllowedException(msg, RequestTypeEnum.POST);
}
}
}
}
public static void throwInvalidMode(String paramValues) {
throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
private void translateQueryParametersIntoServerArgumentForPost(RequestDetails theRequest, List<Object> matchingParamValues) {
IBaseResource requestContents = (IBaseResource) theRequest.getUserData().get(REQUEST_CONTENTS_USERDATA_KEY);
RuntimeResourceDefinition def = myContext.getResourceDefinition(requestContents);
if (def.getName().equals("Parameters")) {
BaseRuntimeChildDefinition paramChild = def.getChildByName("parameter");
BaseRuntimeElementCompositeDefinition<?> paramChildElem = (BaseRuntimeElementCompositeDefinition<?>) paramChild.getChildByName("parameter");
RuntimeChildPrimitiveDatatypeDefinition nameChild = (RuntimeChildPrimitiveDatatypeDefinition) paramChildElem.getChildByName("name");
BaseRuntimeChildDefinition valueChild = paramChildElem.getChildByName("value[x]");
BaseRuntimeChildDefinition resourceChild = paramChildElem.getChildByName("resource");
IAccessor paramChildAccessor = paramChild.getAccessor();
List<IBase> values = paramChildAccessor.getValues(requestContents);
for (IBase nextParameter : values) {
List<IBase> nextNames = nameChild.getAccessor().getValues(nextParameter);
if (nextNames != null && nextNames.size() > 0) {
IPrimitiveType<?> nextName = (IPrimitiveType<?>) nextNames.get(0);
if (myName.equals(nextName.getValueAsString())) {
if (myParameterType.isAssignableFrom(nextParameter.getClass())) {
matchingParamValues.add(nextParameter);
} else {
List<IBase> paramValues = valueChild.getAccessor().getValues(nextParameter);
List<IBase> paramResources = resourceChild.getAccessor().getValues(nextParameter);
if (paramValues != null && paramValues.size() > 0) {
tryToAddValues(paramValues, matchingParamValues);
} else if (paramResources != null && paramResources.size() > 0) {
tryToAddValues(paramResources, matchingParamValues);
}
}
}
}
}
} else {
if (myParameterType.isAssignableFrom(requestContents.getClass())) {
tryToAddValues(Arrays.asList((IBase) requestContents), matchingParamValues);
}
}
}
@SuppressWarnings("unchecked")
@ -419,7 +416,11 @@ public class OperationParameter implements IParameter {
}
}
public interface IConverter {
public static void throwInvalidMode(String paramValues) {
throw new InvalidRequestException("Invalid mode value: \"" + paramValues + "\"");
}
interface IOperationParamConverter {
Object incomingServer(Object theObject);
@ -427,9 +428,9 @@ public class OperationParameter implements IParameter {
}
private class QueryParameterConverter implements IConverter {
class OperationParamConverter implements IOperationParamConverter {
public QueryParameterConverter() {
public OperationParamConverter() {
Validate.isTrue(mySearchParameterBinding != null);
}

19
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/DateRangeParam.java
View File

@ -29,7 +29,6 @@ import java.util.List;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.method.QualifiedParamList;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -301,7 +300,9 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
}
/**
* Sets the range from a pair of dates, inclusive on both ends
* Sets the range from a pair of dates, inclusive on both ends. Note that if
* theLowerBound is after theUpperBound, thie method will automatically reverse
* the order of the arguments in order to create an inclusive range.
*
* @param theLowerBound
* A qualified date param representing the lower date bound (optionally may include time), e.g.
@ -313,8 +314,18 @@ public class DateRangeParam implements IQueryParameterAnd<DateParam> {
* theUpperBound may both be populated, or one may be null, but it is not valid for both to be null.
*/
public void setRangeFromDatesInclusive(IPrimitiveType<Date> theLowerBound, IPrimitiveType<Date> theUpperBound) {
myLowerBound = theLowerBound != null ? new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, theLowerBound) : null;
myUpperBound = theUpperBound != null ? new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, theUpperBound) : null;
IPrimitiveType<Date> lowerBound = theLowerBound;
IPrimitiveType<Date> upperBound = theUpperBound;
if (lowerBound != null && lowerBound.getValue() != null && upperBound != null && upperBound.getValue() != null) {
if (lowerBound.getValue().after(upperBound.getValue())) {
IPrimitiveType<Date> temp = lowerBound;
lowerBound = upperBound;
upperBound = temp;
}
}
myLowerBound = lowerBound != null ? new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, lowerBound) : null;
myUpperBound = upperBound != null ? new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, upperBound) : null;
validateAndThrowDataFormatExceptionIfInvalid();
}

22
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/NonPrettyPrintWriterWrapper.java
View File

@ -45,26 +45,31 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
@Override
@CoverageIgnore
public String getPrefix(String theUri) throws XMLStreamException {
return myTarget.getPrefix(theUri);
}
@Override
@CoverageIgnore
public void setPrefix(String thePrefix, String theUri) throws XMLStreamException {
myTarget.setPrefix(thePrefix, theUri);
}
@Override
@CoverageIgnore
public void setDefaultNamespace(String theUri) throws XMLStreamException {
myTarget.setDefaultNamespace(theUri);
}
@Override
@CoverageIgnore
public void setNamespaceContext(NamespaceContext theContext) throws XMLStreamException {
myTarget.setNamespaceContext(theContext);
}
@Override
@CoverageIgnore
public NamespaceContext getNamespaceContext() {
return myTarget.getNamespaceContext();
}
@ -94,16 +99,19 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
@Override
@CoverageIgnore
public void writeEmptyElement(String theNamespaceURI, String theLocalName) throws XMLStreamException {
myTarget.writeEmptyElement(theNamespaceURI, theLocalName);
}
@Override
@CoverageIgnore
public void writeEmptyElement(String thePrefix, String theLocalName, String theNamespaceURI) throws XMLStreamException {
myTarget.writeEmptyElement(thePrefix, theLocalName, theNamespaceURI);
}
@Override
@CoverageIgnore
public void writeEmptyElement(String theLocalName) throws XMLStreamException {
myTarget.writeEmptyElement(theLocalName);
}
@ -127,11 +135,13 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
@Override
@CoverageIgnore
public void writeAttribute(String thePrefix, String theNamespaceURI, String theLocalName, String theValue) throws XMLStreamException {
myTarget.writeAttribute(thePrefix, theNamespaceURI, theLocalName, theValue);
}
@Override
@CoverageIgnore
public void writeAttribute(String theNamespaceURI, String theLocalName, String theValue) throws XMLStreamException {
myTarget.writeAttribute(theNamespaceURI, theLocalName, theValue);
}
@ -152,36 +162,43 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
@Override
@CoverageIgnore
public void writeProcessingInstruction(String theTarget) throws XMLStreamException {
myTarget.writeProcessingInstruction(theTarget);
}
@Override
@CoverageIgnore
public void writeProcessingInstruction(String theTarget, String theData) throws XMLStreamException {
myTarget.writeProcessingInstruction(theTarget, theData);
}
@Override
@CoverageIgnore
public void writeCData(String theData) throws XMLStreamException {
myTarget.writeCData(theData);
}
@Override
@CoverageIgnore
public void writeDTD(String theDtd) throws XMLStreamException {
myTarget.writeDTD(theDtd);
}
@Override
@CoverageIgnore
public void writeEntityRef(String theName) throws XMLStreamException {
myTarget.writeEntityRef(theName);
}
@Override
@CoverageIgnore
public void writeStartDocument() throws XMLStreamException {
myTarget.writeStartDocument();
}
@Override
@CoverageIgnore
public void writeStartDocument(String theVersion) throws XMLStreamException {
myTarget.writeStartDocument(theVersion);
}
@ -206,9 +223,7 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
static void writeCharacters(char[] theText, int theStart, int theLen, XMLStreamWriter target, int insidePre) throws XMLStreamException {
if (theLen == 0) {
return;
} else {
if (theLen > 0) {
if (insidePre > 0) {
target.writeCharacters(theText, theStart, theLen);
} else {
@ -240,6 +255,7 @@ public class NonPrettyPrintWriterWrapper implements XMLStreamWriter {
}
@Override
@CoverageIgnore
public Object getProperty(String theName) throws IllegalArgumentException {
return myTarget.getProperty(theName);
}

41
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/PortUtil.java
View File

@ -1,37 +1,19 @@
package ca.uhn.fhir.util;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2016 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.IOException;
import java.net.ServerSocket;
import java.util.ArrayList;
import java.util.List;
/**
* Provides server ports
*/
@CoverageIgnore
public class PortUtil {
private static List<Integer> ourPorts = new ArrayList<Integer>();
/*
* Non instantiable
*/
private PortUtil() {
// nothing
}
/**
* This is really only used for unit tests but is included in the library so it can be reused across modules. Use with caution.
@ -41,20 +23,13 @@ public class PortUtil {
try {
server = new ServerSocket(0);
int port = server.getLocalPort();
ourPorts.add(port);
server.close();
Thread.sleep(500);
return port;
} catch (IOException e) {
throw new Error(e);
} catch (InterruptedException e) {
} catch (Exception e) {
throw new Error(e);
}
}
public static List<Integer> list() {
return ourPorts;
}
}

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/FhirValidator.java
View File

@ -61,7 +61,7 @@ public class FhirValidator {
myContext = theFhirContext;
if (ourPhlocPresentOnClasspath == null) {
ourPhlocPresentOnClasspath = SchematronProvider.isScematronAvailable(theFhirContext);
ourPhlocPresentOnClasspath = SchematronProvider.isSchematronAvailable(theFhirContext);
}
}

7
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/schematron/SchematronProvider.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.validation.schematron;
import java.lang.reflect.Constructor;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidatorModule;
@ -32,7 +33,8 @@ public class SchematronProvider {
private static final String I18N_KEY_NO_PHLOC_WARNING = FhirValidator.class.getName() + ".noPhlocWarningOnStartup";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirValidator.class);
public static boolean isScematronAvailable(FhirContext theFhirContext) {
@CoverageIgnore
public static boolean isSchematronAvailable(FhirContext theFhirContext) {
try {
Class.forName("com.phloc.schematron.ISchematronResource");
return true;
@ -42,6 +44,8 @@ public class SchematronProvider {
}
}
@SuppressWarnings("unchecked")
@CoverageIgnore
public static Class<? extends IValidatorModule> getSchematronValidatorClass() {
try {
return (Class<? extends IValidatorModule>) Class.forName("ca.uhn.fhir.validation.schematron.SchematronBaseValidator");
@ -50,6 +54,7 @@ public class SchematronProvider {
}
}
@CoverageIgnore
public static IValidatorModule getSchematronValidatorInstance(FhirContext myContext) {
try {
Class<? extends IValidatorModule> cls = getSchematronValidatorClass();

7
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -77,5 +77,10 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully update
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!

358
hapi-fhir-jacoco/pom.xml Normal file
View File

@ -0,0 +1,358 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the site. I don't know why this works...
Need to investigate this. -->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>1.6-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jacoco</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR - JaCoCo Test Coverage</name>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>1.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-schematron</artifactId>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-commons</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</dependency>
<!-- Use an older version of SLF4j just to make sure we compile correctly against old SLF4j - Some people can't upgrade and we have no real need for recent features. -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Test Database -->
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<classifier>jdk15</classifier>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf.json-lib</groupId>
<artifactId>json-lib</artifactId>
<classifier>jdk15-sources</classifier>
<scope>test</scope>
</dependency>
<dependency>
<groupId>directory-naming</groupId>
<artifactId>naming-java</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>xmlunit</groupId>
<artifactId>xmlunit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-server</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<properties>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<configuration>
<skipDeploy>true</skipDeploy>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<executions>
<execution>
<id>jacoco-merge</id>
<goals>
<goal>merge</goal>
</goals>
<phase>install</phase>
<configuration>
<fileSets>
<fileSet implementation="org.apache.maven.shared.model.fileset.FileSet">
<directory>${basedir}/..</directory>
<includes>
<include>hapi-fhir-base/target/jacoco.exec</include>
<include>hapi-fhir-structures-dstu/target/jacoco.exec</include>
<include>hapi-fhir-structures-dstu2/target/jacoco.exec</include>
<include>hapi-fhir-structures-hl7org-dstu2/target/jacoco.exec</include>
<include>hapi-fhir-structures-dstu3/target/jacoco.exec</include>
<include>hapi-fhir-jpaserver-base/target/jacoco.exec</include>
</includes>
</fileSet>
</fileSets>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<configuration>
<sourceEncoding>UTF-8</sourceEncoding>
<serviceName>travis-ci</serviceName>
<serviceJobId>${env.TRAVIS_JOB_ID}</serviceJobId>
<sourceDirectories>
<sourceDirectory>../hapi-fhir-structures-dstu/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-structures-dstu2/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-structures-hl7org-dstu2/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-jpaserver-base/src/test/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-base/src/main/java</sourceDirectory>
<sourceDirectory>../hapi-fhir-jpaserver-base/src/main/java</sourceDirectory>
</sourceDirectories>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>../hapi-fhir-base/src/main/java</source>
<source>../hapi-fhir-jpaserver-base/src/main/java</source>
</sources>
</configuration>
</execution>
<!--
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>../hapi-fhir-structures-dstu/src/test/java</source>
<source>../hapi-fhir-structures-dstu2/src/test/java</source>
<source>../hapi-fhir-structures-hl7org-dstu2/src/test/java</source>
<source>../hapi-fhir-structures-dstu3/src/test/java</source>
<source>../hapi-fhir-jpaserver-base/src/test/java</source>
<source>../hapi-fhir-base/src/test/java</source>
</sources>
</configuration>
</execution>
-->
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
<resources>
</resources>
<testResources>
<testResource>
<directory>../hapi-fhir-base/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-jpaserver-base/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-dstu/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-dstu2/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-hl7org-dstu2/src/test/resources</directory>
</testResource>
<testResource>
<directory>../hapi-fhir-structures-dstu3/src/test/resources</directory>
</testResource>
</testResources>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<reportSets>
<reportSet>
<reports>
<report>cobertura</report>
</reports>
<configuration>
<check>
<haltOnFailure>true</haltOnFailure>
</check>
</configuration>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>${maven_project_info_plugin_version}</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</reporting>
</project>

27
hapi-fhir-jpaserver-base/pom.xml
View File

@ -335,13 +335,36 @@
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
<classFolder>${basedir}../hapi-fhir-base/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<!-- These tests all use a shared database, so it's easier if they run in a predictable order -->
<runOrder>alphabetical</runOrder>
<!--<reuseForks>false</reuseForks>-->
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<forkCount>1</forkCount>
</configuration>
</plugin>
<plugin>

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -28,7 +28,6 @@ import java.util.Collection;
import java.util.List;
import java.util.Set;
import javax.persistence.CascadeType;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
@ -56,12 +55,14 @@ import org.hibernate.search.annotations.Field;
import org.hibernate.search.annotations.Fields;
import org.hibernate.search.annotations.Indexed;
import org.hibernate.search.annotations.Store;
import org.hibernate.search.indexes.interceptor.DontInterceptEntityInterceptor;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
//@formatter:off
@Entity
@Indexed()
@Indexed(interceptor=DeferConceptIndexingInterceptor.class)
@Table(name="TRM_CONCEPT", uniqueConstraints= {
@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
}, indexes= {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -35,8 +35,6 @@ import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@Entity
@Table(name="TRM_CONCEPT_PC_LINK")
public class TermConceptParentChildLink implements Serializable {

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.jpa.provider;
import java.util.Date;
/*
* #%L
* HAPI FHIR JPA Server
@ -28,9 +30,10 @@ import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.jboss.logging.MDC;
import org.springframework.beans.factory.annotation.Autowired;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
public class BaseJpaProvider {
@ -41,6 +44,9 @@ public class BaseJpaProvider {
private FhirContext myContext;
/**
* @param theRequest The servlet request
*/
public void endRequest(HttpServletRequest theRequest) {
MDC.remove(REMOTE_ADDR);
MDC.remove(REMOTE_UA);
@ -54,10 +60,25 @@ public class BaseJpaProvider {
return myContext;
}
protected DateRangeParam processSinceOrAt(Date theSince, DateRangeParam theAt) {
boolean haveAt = theAt != null && (theAt.getLowerBoundAsInstant() != null || theAt.getUpperBoundAsInstant() != null);
if (haveAt && theSince != null) {
String msg = getContext().getLocalizer().getMessage(BaseJpaProvider.class, "cantCombintAtAndSince");
throw new InvalidRequestException(msg);
}
if (haveAt) {
return theAt;
}
return new DateRangeParam(theSince, null);
}
public void setContext(FhirContext theContext) {
myContext = theContext;
}
public void startRequest(HttpServletRequest theRequest) {
if (theRequest == null) {
return;

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProvider.java
View File

@ -65,24 +65,29 @@ public abstract class BaseJpaResourceProvider<T extends IBaseResource> extends B
HttpServletRequest theRequest,
@IdParam IIdType theId,
@Since Date theSince,
// @At DateRangeParam theAt,
@At DateRangeParam theAt,
RequestDetails theRequestDetails) {
//@formatter:on
startRequest(theRequest);
try {
// DateRangeParam sinceOrAt = processSinceOrAt(theSince)
return myDao.history(theId, theSince, null, theRequestDetails);
DateRangeParam sinceOrAt = processSinceOrAt(theSince, theAt);
return myDao.history(theId, sinceOrAt.getLowerBoundAsInstant(), sinceOrAt.getUpperBoundAsInstant(), theRequestDetails);
} finally {
endRequest(theRequest);
}
}
@History
public IBundleProvider getHistoryForResourceType(HttpServletRequest theRequest, @Since Date theDate, RequestDetails theRequestDetails) {
public IBundleProvider getHistoryForResourceType(
HttpServletRequest theRequest,
@Since Date theSince,
@At DateRangeParam theAt,
RequestDetails theRequestDetails) {
startRequest(theRequest);
try {
return myDao.history(theDate, null, theRequestDetails);
DateRangeParam sinceOrAt = processSinceOrAt(theSince, theAt);
return myDao.history(sinceOrAt.getLowerBoundAsInstant(), sinceOrAt.getUpperBoundAsInstant(), theRequestDetails);
} finally {
endRequest(theRequest);
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaSystemProvider.java
View File

@ -28,10 +28,12 @@ import org.springframework.beans.factory.annotation.Required;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.rest.annotation.At;
import ca.uhn.fhir.rest.annotation.GetTags;
import ca.uhn.fhir.rest.annotation.History;
import ca.uhn.fhir.rest.annotation.Since;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider {
@ -48,10 +50,11 @@ public class BaseJpaSystemProvider<T, MT> extends BaseJpaProvider {
}
@History
public IBundleProvider historyServer(HttpServletRequest theRequest, @Since Date theDate, RequestDetails theRequestDetails) {
public IBundleProvider historyServer(HttpServletRequest theRequest, @Since Date theDate, @At DateRangeParam theAt, RequestDetails theRequestDetails) {
startRequest(theRequest);
try {
return myDao.history(theDate, null, theRequestDetails);
DateRangeParam range = super.processSinceOrAt(theDate, theAt);
return myDao.history(range.getLowerBoundAsInstant(), range.getUpperBoundAsInstant(), theRequestDetails);
} finally {
endRequest(theRequest);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -62,7 +62,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
}
if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
throw new InvalidRequestException("$expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
}
startRequest(theServletRequest);

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DeferConceptIndexingInterceptor.java Normal file
View File

@ -0,0 +1,9 @@
package ca.uhn.fhir.jpa.search;
import org.hibernate.search.indexes.interceptor.DontInterceptEntityInterceptor;
public class DeferConceptIndexingInterceptor extends DontInterceptEntityInterceptor
//implements EntityIndexingInterceptor<TermConcept>
{
// nothing for now
}

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -15,7 +15,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseFhirDaoTest.java
View File

@ -40,5 +40,11 @@ public class BaseFhirDaoTest extends BaseJpaTest {
observation.setEffective(period);
}
@Override
protected FhirContext getContext() {
return ourCtx;
}
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -16,6 +16,7 @@ import javax.persistence.EntityManager;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.jpa.Search;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
@ -26,6 +27,7 @@ import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
@ -55,9 +57,10 @@ import ca.uhn.fhir.rest.method.IRequestOperationCallback;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.TestUtil;
public class BaseJpaTest {
public abstract class BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaTest.class);
protected ServletRequestDetails mySrd;
@ -74,6 +77,32 @@ public class BaseJpaTest {
return theSearch.getResources(0, theSearch.size());
}
protected abstract FhirContext getContext();
protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {
List<String> retVal = new ArrayList<String>();
List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
int size = res.size();
ourLog.info("Found {} results", size);
for (IBaseResource next : res) {
retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());
}
return retVal;
}
protected List<String> toUnqualifiedIdValues(IBaseBundle theFound) {
List<String> retVal = new ArrayList<String>();
List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
int size = res.size();
ourLog.info("Found {} results", size);
for (IBaseResource next : res) {
retVal.add(next.getIdElement().toUnqualified().getValue());
}
return retVal;
}
protected List<IIdType> toUnqualifiedVersionlessIds(Bundle theFound) {
List<IIdType> retVal = new ArrayList<IIdType>();
for (Entry next : theFound.getEntry()) {

26
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1Test.java
View File

@ -30,18 +30,22 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
@SuppressWarnings("unused")
public class FhirResourceDaoDstu1Test extends BaseJpaTest {
public class FhirResourceDaoDstu1Test extends BaseJpaTest {
private static AnnotationConfigApplicationContext ourAppCtx;
private static FhirContext ourCtx;
private static IFhirResourceDao<Device> ourDeviceDao;
private static IFhirResourceDao<DiagnosticReport> ourDiagnosticReportDao;
private static IFhirResourceDao<Encounter> ourEncounterDao;
private static AnnotationConfigApplicationContext ourAppCtx;
private static IFhirResourceDao<Location> ourLocationDao;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu1Test.class);
private static IFhirResourceDao<Observation> ourObservationDao;
private static IFhirResourceDao<Organization> ourOrganizationDao;
private static IFhirResourceDao<Patient> ourPatientDao;
private static FhirContext ourCtx;
@Override
protected FhirContext getContext() {
return ourCtx;
}
@Test
public void testCreateDuplicateIdFails() {
@ -64,7 +68,7 @@ public class FhirResourceDaoDstu1Test extends BaseJpaTest {
assertThat(e.getMessage(), containsString("Can not create entity with ID[" + methodName + "], a resource with this ID already exists"));
}
}
@Test
public void testCreateNumericIdFails() {
Patient p = new Patient();
@ -125,6 +129,12 @@ public class FhirResourceDaoDstu1Test extends BaseJpaTest {
}
@AfterClass
public static void afterClassClearContext() {
ourAppCtx.close();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@SuppressWarnings("unchecked")
@BeforeClass
public static void beforeClass() {
@ -139,10 +149,4 @@ public class FhirResourceDaoDstu1Test extends BaseJpaTest {
ourCtx = ourAppCtx.getBean(FhirContext.class);
}
@AfterClass
public static void afterClassClearContext() {
ourAppCtx.close();
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

26
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSystemDaoDstu1Test.java
View File

@ -50,30 +50,28 @@ import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
public class FhirSystemDaoDstu1Test extends BaseJpaTest {
public class FhirSystemDaoDstu1Test extends BaseJpaTest {
private static AnnotationConfigApplicationContext ourCtx;
private static EntityManager ourEntityManager;
private static FhirContext ourFhirContext;
private static IFhirResourceDao<Location> ourLocationDao;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSystemDaoDstu1Test.class);
private static IFhirResourceDao<Observation> ourObservationDao;
private static IFhirResourceDao<Patient> ourPatientDao;
private static IFhirSystemDao<List<IResource>, MetaDt> ourSystemDao;
private static EntityManager ourEntityManager;
private static PlatformTransactionManager ourTxManager;
@AfterClass
public static void afterClassClearContext() {
ourCtx.close();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Before
public void before() {
super.purgeDatabase(ourEntityManager, ourTxManager);
}
@Override
protected FhirContext getContext() {
return ourFhirContext;
}
@Test
public void testGetResourceCounts() {
Observation obs = new Observation();
@ -147,7 +145,7 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest {
assertEquals(1, values.size());
}
@Test
public void testPersistWithSimpleLink() {
Patient patient = new Patient();
@ -378,11 +376,10 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest {
String encodeResourceToString = ourFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response.get(0));
ourLog.info(encodeResourceToString);
assertThat(encodeResourceToString, not(containsString("smsp")));
}
/**
* This is the correct way to do this, not {@link #testTransactionWithCidIds()}
*/
@ -479,6 +476,11 @@ public class FhirSystemDaoDstu1Test extends BaseJpaTest {
}
@AfterClass
public static void afterClassClearContext() {
ourCtx.close();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@SuppressWarnings("unchecked")
@BeforeClass

66
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java
View File

@ -73,31 +73,17 @@ import ca.uhn.fhir.util.TestUtil;
//@formatter:on
public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@AfterClass
public static void afterClassClearContext() throws Exception {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Autowired
protected ApplicationContext myAppCtx;
@Autowired
protected IFulltextSearchSvc mySearchDao;
@Autowired
@Qualifier("myConceptMapDaoDstu2")
protected IFhirResourceDao<ConceptMap> myConceptMapDao;
@Autowired
@Qualifier("myAppointmentDaoDstu2")
protected IFhirResourceDao<Appointment> myAppointmentDao;
@Autowired
@Qualifier("myBundleDaoDstu2")
protected IFhirResourceDao<Bundle> myBundleDao;
@Autowired
@Qualifier("myMedicationDaoDstu2")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationOrderDaoDstu2")
protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
@Qualifier("myConceptMapDaoDstu2")
protected IFhirResourceDao<ConceptMap> myConceptMapDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
@ -112,11 +98,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
@Qualifier("myEncounterDaoDstu2")
protected IFhirResourceDao<Encounter> myEncounterDao;
// @PersistenceContext()
// @PersistenceContext()
@Autowired
protected EntityManager myEntityManager;
@Autowired
@Qualifier("myFhirContextDstu2")
protected FhirContext myFhirCtx;
@ -127,6 +111,17 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
@Qualifier("myLocationDaoDstu2")
protected IFhirResourceDao<Location> myLocationDao;
@Autowired
@Qualifier("myMediaDaoDstu2")
protected IFhirResourceDao<Media> myMediaDao;
@Autowired
@Qualifier("myMedicationDaoDstu2")
protected IFhirResourceDao<Medication> myMedicationDao;
@Autowired
@Qualifier("myMedicationOrderDaoDstu2")
protected IFhirResourceDao<MedicationOrder> myMedicationOrderDao;
@Autowired
@Qualifier("myObservationDaoDstu2")
protected IFhirResourceDao<Observation> myObservationDao;
@ -137,9 +132,6 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Qualifier("myPatientDaoDstu2")
protected IFhirResourceDaoPatient<Patient> myPatientDao;
@Autowired
@Qualifier("myMediaDaoDstu2")
protected IFhirResourceDao<Media> myMediaDao;
@Autowired
@Qualifier("myPractitionerDaoDstu2")
protected IFhirResourceDao<Practitioner> myPractitionerDao;
@Autowired
@ -152,6 +144,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Qualifier("myResourceProvidersDstu2")
protected Object myResourceProviders;
@Autowired
protected IFulltextSearchSvc mySearchDao;
@Autowired
@Qualifier("myStructureDefinitionDaoDstu2")
protected IFhirResourceDao<StructureDefinition> myStructureDefinitionDao;
@Autowired
@ -171,21 +165,11 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
@Qualifier("myValueSetDaoDstu2")
protected IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> myValueSetDao;
@Before
public void beforeCreateInterceptor() {
myInterceptor = mock(IServerInterceptor.class);
myDaoConfig.setInterceptors(myInterceptor);
}
@Before
public void beforeResetConfig() {
myDaoConfig.setHardSearchLimit(1000);
myDaoConfig.setHardTagListLimit(1000);
myDaoConfig.setIncludeLimit(2000);
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Before
@Transactional
public void beforeFlushFT() {
@ -204,6 +188,19 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
purgeDatabase(entityManager, myTxManager);
}
@Before
public void beforeResetConfig() {
myDaoConfig.setHardSearchLimit(1000);
myDaoConfig.setHardTagListLimit(1000);
myDaoConfig.setIncludeLimit(2000);
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
if (stream == null) {
@ -221,4 +218,9 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
return retVal;
}
@AfterClass
public static void afterClassClearContext() throws Exception {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

51
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchFtTest.java
View File

@ -29,11 +29,10 @@ import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchFtTest.class);
@AfterClass
@ -41,7 +40,6 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testSuggestIgnoresBase64Content() {
Patient patient = new Patient();
@ -52,11 +50,11 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
med.getSubject().setReference(ptId);
med.getSubtype().setText("Systolic Blood Pressure");
med.getContent().setContentType("LCws");
med.getContent().setData(new Base64BinaryDt(new byte[] {44,44,44,44,44,44,44,44}));
med.getContent().setData(new Base64BinaryDt(new byte[] { 44, 44, 44, 44, 44, 44, 44, 44 }));
med.getContent().setTitle("bbbb syst");
myMediaDao.create(med, mySrd);
ourLog.info(myFhirCtx.newJsonParser().encodeResourceToString(med));
List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "press");
ourLog.info("Found: " + output);
assertEquals(2, output.size());
@ -76,12 +74,12 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
assertEquals("bbbb syst", output.get(1).getTerm());
assertEquals("Systolic", output.get(2).getTerm());
assertEquals("Systolic Blood Pressure", output.get(3).getTerm());
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "LCws");
ourLog.info("Found: " + output);
assertEquals(0, output.size());
}
@Test
public void testSuggest() {
Patient patient = new Patient();
@ -137,7 +135,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
assertEquals(2, output.size());
assertEquals("HELLO", output.get(0).getTerm());
assertEquals("ZXC HELLO", output.get(1).getTerm());
output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "Z");
ourLog.info("Found: " + output);
assertEquals(0, output.size());
@ -149,8 +147,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
assertEquals("ZXC HELLO", output.get(1).getTerm());
}
@Test
public void testSearchAndReindex() {
Patient patient;
@ -210,7 +207,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
Device dev1 = new Device();
dev1.setManufacturer("Some Manufacturer");
IIdType devId1 = myDeviceDao.create(dev1, mySrd).getId().toUnqualifiedVersionless();
Device dev2 = new Device();
dev2.setManufacturer("Some Manufacturer 2");
myDeviceDao.create(dev2, mySrd).getId().toUnqualifiedVersionless();
@ -234,14 +231,14 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
obs3.getCode().addCoding().setCode("CODE3");
obs3.setValue(new StringDt("obsvalue3"));
IIdType obsId3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
HttpServletRequest request;
List<IIdType> actual;
request = mock(HttpServletRequest.class);
StringAndListParam param;
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] {ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart()});
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] { ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart() });
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIds(myPatientDao.patientInstanceEverything(request, ptId1, null, null, null, param, null, mySrd));
@ -259,7 +256,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
/*
* Add another match
*/
Observation obs4 = new Observation();
obs4.getSubject().setReference(ptId1);
obs4.getCode().addCoding().setCode("CODE1");
@ -275,7 +272,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
/*
* Make one previous match no longer match
*/
obs1 = new Observation();
obs1.setId(obsId1);
obs1.getSubject().setReference(ptId1);
@ -289,7 +286,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
assertThat(actual, containsInAnyOrder(ptId1, obsId4));
}
@Test
public void testEverythingTypeWithContentFilter() {
Patient pt1 = new Patient();
@ -303,7 +300,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
Device dev1 = new Device();
dev1.setManufacturer("Some Manufacturer");
IIdType devId1 = myDeviceDao.create(dev1, mySrd).getId().toUnqualifiedVersionless();
Device dev2 = new Device();
dev2.setManufacturer("Some Manufacturer 2");
IIdType devId2 = myDeviceDao.create(dev2, mySrd).getId().toUnqualifiedVersionless();
@ -326,14 +323,14 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
obs3.getCode().addCoding().setCode("CODE3");
obs3.setValue(new StringDt("obsvalue3"));
IIdType obsId3 = myObservationDao.create(obs3, mySrd).getId().toUnqualifiedVersionless();
HttpServletRequest request;
List<IIdType> actual;
request = mock(HttpServletRequest.class);
StringAndListParam param;
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] {ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart()});
ourLog.info("Pt1:{} Pt2:{} Obs1:{} Obs2:{} Obs3:{}", new Object[] { ptId1.getIdPart(), ptId2.getIdPart(), obsId1.getIdPart(), obsId2.getIdPart(), obsId3.getIdPart() });
param = new StringAndListParam();
param.addAnd(new StringOrListParam().addOr(new StringParam("obsvalue1")));
actual = toUnqualifiedVersionlessIds(myPatientDao.patientTypeEverything(request, null, null, null, param, null, mySrd));
@ -346,7 +343,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
/*
* Add another match
*/
Observation obs4 = new Observation();
obs4.getSubject().setReference(ptId1);
obs4.getCode().addCoding().setCode("CODE1");
@ -362,7 +359,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
/*
* Make one previous match no longer match
*/
obs1 = new Observation();
obs1.setId(obsId1);
obs1.getSubject().setReference(ptId1);
@ -377,10 +374,8 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
}
/**
* When processing transactions, we do two passes. Make sure we don't update the lucene index twice since that would
* be inefficient
* When processing transactions, we do two passes. Make sure we don't update the lucene index twice since that would be inefficient
*/
@Test
public void testSearchDontReindexForUpdateWithIndexDisabled() {

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java
View File

@ -792,19 +792,19 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
{
SearchParameterMap params = new SearchParameterMap();
List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
assertThat(patients, hasItems(id1a, id1b, id2));
assertThat(patients, containsInAnyOrder(id1a, id1b, id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLastUpdated(new DateRangeParam(beforeAny, null));
List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
assertThat(patients, hasItems(id1a, id1b, id2));
assertThat(patients, containsInAnyOrder(id1a, id1b, id2));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLastUpdated(new DateRangeParam(beforeR2, null));
List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
assertThat(patients, hasItems(id2));
assertThat(patients, containsInAnyOrder(id2));
assertThat(patients, not(hasItems(id1a, id1b)));
}
{
@ -812,13 +812,13 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
params.setLastUpdated(new DateRangeParam(beforeAny, beforeR2));
List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
assertThat(patients.toString(), patients, not(hasItems(id2)));
assertThat(patients.toString(), patients, (hasItems(id1a, id1b)));
assertThat(patients.toString(), patients, (containsInAnyOrder(id1a, id1b)));
}
{
SearchParameterMap params = new SearchParameterMap();
params.setLastUpdated(new DateRangeParam(null, beforeR2));
List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
assertThat(patients, (hasItems(id1a, id1b)));
assertThat(patients, (containsInAnyOrder(id1a, id1b)));
assertThat(patients, not(hasItems(id2)));
}
}

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -106,9 +106,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myCarePlanDaoDstu3")
protected IFhirResourceDao<CarePlan> myCarePlanDao;
@Autowired
@Qualifier("myConditionDaoDstu3")
protected IFhirResourceDao<Condition> myConditionDao;
@Autowired
@Qualifier("myCodeSystemDaoDstu3")
protected IFhirResourceDao<CodeSystem> myCodeSystemDao;
@Autowired
@ -118,6 +115,9 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Qualifier("myConceptMapDaoDstu3")
protected IFhirResourceDao<ConceptMap> myConceptMapDao;
@Autowired
@Qualifier("myConditionDaoDstu3")
protected IFhirResourceDao<Condition> myConditionDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
@Qualifier("myDeviceDaoDstu3")
@ -213,7 +213,6 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
@Qualifier("myValueSetDaoDstu3")
protected IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> myValueSetDao;
@After()
public void afterGrabCaches() {
ourValueSetDao = myValueSetDao;
@ -251,6 +250,11 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
myDaoConfig.setIncludeLimit(2000);
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
if (stream == null) {

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -1491,7 +1491,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
List<Date> preDates = Lists.newArrayList();
List<String> ids = Lists.newArrayList();
for (int i = 0; i < 10; i++) {
Thread.sleep(10);
Thread.sleep(100);
preDates.add(new Date());
patient.setId(id);
patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3UpdateTest.java
View File

@ -160,12 +160,13 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
myPatientDao.create(p, mySrd).getId();
InstantDt start = InstantDt.withCurrentTime();
ourLog.info("First time: {}", start.getValueAsString());
Thread.sleep(100);
p = new Patient();
p.addIdentifier().setSystem("urn:system").setValue(methodName);
IIdType id = myPatientDao.create(p, mySrd).getId();
ourLog.info("Created patient, got it: {}", id);
ourLog.info("Created patient, got ID: {}", id);
Thread.sleep(100);
@ -174,7 +175,9 @@ public class FhirResourceDaoDstu3UpdateTest extends BaseJpaDstu3Test {
p.addName().addFamily("Hello");
p.setId("Patient/" + methodName);
myPatientDao.update(p, "Patient?_lastUpdated=gt" + start.getValueAsString(), mySrd);
String matchUrl = "Patient?_lastUpdated=gt" + start.getValueAsString();
ourLog.info("URL is: {}", matchUrl);
myPatientDao.update(p, matchUrl, mySrd);
p = myPatientDao.read(id.toVersionless(), mySrd);
assertThat(p.getIdElement().toVersionless().toString(), not(containsString("test")));

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu1Test.java
View File

@ -63,7 +63,6 @@ import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class ResourceProviderDstu1Test extends BaseJpaTest {
@ -88,6 +87,10 @@ public class ResourceProviderDstu1Test extends BaseJpaTest {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Override
protected FhirContext getContext() {
return ourCtx;
}
// private static JpaConformanceProvider ourConfProvider;
@ -121,11 +124,11 @@ public class ResourceProviderDstu1Test extends BaseJpaTest {
}
ourClient.transaction().withResources(resources).prettyPrint().encodedXml().execute();
Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(10).execute();
Bundle found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).count(10).execute();
assertEquals(100, found.getTotalResults().getValue().intValue());
assertEquals(10, found.getEntries().size());
found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).limitTo(999).execute();
found = ourClient.search().forResource(Organization.class).where(Organization.NAME.matches().value("testCountParam_01")).count(999).execute();
assertEquals(100, found.getTotalResults().getValue().intValue());
assertEquals(50, found.getEntries().size());

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
View File

@ -1559,6 +1559,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
@Test
public void testSearchLastUpdatedParamRp() throws InterruptedException {
String methodName = "testSearchLastUpdatedParamRp";
ourLog.info("Starting " + methodName);
int sleep = 100;
Thread.sleep(sleep);
@ -1668,8 +1669,10 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
@Test
public void testSearchReturnsSearchDate() throws Exception {
ourLog.info("Starting testSearchReturnsSearchDate");
Date before = new Date();
Thread.sleep(1);
Thread.sleep(100);
//@formatter:off
ca.uhn.fhir.model.dstu2.resource.Bundle found = ourClient
@ -1680,7 +1683,7 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
.execute();
//@formatter:on
Thread.sleep(1);
Thread.sleep(100);
Date after = new Date();
InstantDt updated = ResourceMetadataKeyEnum.UPDATED.get(found);

45
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu1Test.java
View File

@ -3,7 +3,8 @@ package ca.uhn.fhir.jpa.provider;
import static org.hamcrest.Matchers.blankOrNullString;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.io.InputStream;
@ -11,13 +12,10 @@ import org.apache.commons.io.IOUtils;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hamcrest.text.IsBlankString;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.TestDstu1Config;
@ -32,19 +30,22 @@ import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.resource.Organization;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu.resource.Questionnaire;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.util.TestUtil;
public class SystemProviderDstu1Test extends BaseJpaTest {
public class SystemProviderDstu1Test extends BaseJpaTest {
private static AnnotationConfigApplicationContext ourAppCtx;
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderDstu1Test.class);
private static Server ourServer;
private static AnnotationConfigApplicationContext ourAppCtx;
private static FhirContext ourCtx;
private static IGenericClient ourClient;
@Override
protected FhirContext getContext() {
return ourCtx;
}
@Test
public void testTransactionFromBundle() throws Exception {
@ -53,7 +54,7 @@ public class SystemProviderDstu1Test extends BaseJpaTest {
String bundle = IOUtils.toString(bundleRes);
String response = ourClient.transaction().withBundle(bundle).prettyPrint().execute();
ourLog.info(response);
ca.uhn.fhir.model.api.Bundle respBundle = ourCtx.newXmlParser().parseBundle(response);
assertEquals(3, respBundle.size());
for (int i = 1; i < 3; i++) {
@ -62,10 +63,15 @@ public class SystemProviderDstu1Test extends BaseJpaTest {
assertThat(nextValue, not(blankOrNullString()));
assertThat(nextValue, not(containsString("cid")));
}
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
ourAppCtx.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@SuppressWarnings("unchecked")
@BeforeClass
@ -108,22 +114,13 @@ public class SystemProviderDstu1Test extends BaseJpaTest {
ourCtx = FhirContext.forDstu1();
restServer.setFhirContext(ourCtx);
ourServer.setHandler(proxyHandler);
ourServer.start();
ourCtx.getRestfulClientFactory().setSocketTimeout(600 * 1000);
ourClient = ourCtx.newRestfulGenericClient(serverBase);
ourClient.setLogRequestAndResponse(true);
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
ourAppCtx.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

157
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -7,6 +7,7 @@ import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.Matchers.stringContainsInOrder;
@ -17,21 +18,17 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.forwardedUrlPattern;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketTimeoutException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -44,6 +41,7 @@ import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hamcrest.Matchers;
import org.hl7.fhir.dstu3.model.BaseResource;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
@ -98,27 +96,23 @@ import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import com.google.common.collect.Lists;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.HasParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
@ -131,21 +125,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {
List<String> retVal = new ArrayList<String>();
List<IBaseResource> res = BundleUtil.toListOfResources(myFhirCtx, theFound);
int size = res.size();
ourLog.info("Found {} results", size);
for (IBaseResource next : res) {
retVal.add(next.getIdElement().toUnqualifiedVersionless().getValue());
}
return retVal;
}
@Test
public void testHasParameter() throws Exception {
IIdType pid0, pid1;
IIdType pid0;
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("001");
@ -156,7 +140,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().addFamily("Tester").addGiven("Joe");
pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
}
{
Observation obs = new Observation();
@ -168,7 +152,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Device device = new Device();
device.addIdentifier().setValue("DEVICEID");
IIdType devId = myDeviceDao.create(device, mySrd).getId().toUnqualifiedVersionless();
Observation obs = new Observation();
obs.addIdentifier().setSystem("urn:system").setValue("NOLINK");
obs.setDevice(new Reference(devId));
@ -176,10 +160,56 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
String uri = ourServerBase + "/Patient?_has:Observation:subject:identifier=" + UrlUtil.escape("urn:system|FOO");
List<String> ids = searchAndReturnUnqualifiedIdValues(uri);
List<String> ids = searchAndReturnUnqualifiedVersionlessIdValues(uri);
assertThat(ids, contains(pid0.getValue()));
}
@Test
public void testHistoryWithAtParameter() throws Exception {
String methodName = "testHistoryWithFromAndTo";
Patient patient = new Patient();
patient.addName().addFamily(methodName);
IIdType id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
List<Date> preDates = Lists.newArrayList();
List<String> ids = Lists.newArrayList();
for (int i = 0; i < 10; i++) {
Thread.sleep(100);
preDates.add(new Date());
patient.setId(id);
patient.getName().get(0).getFamily().get(0).setValue(methodName + "_i");
ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
}
List<String> idValues;
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient/" + id.getIdPart() + "/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/Patient/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt" + toStr(preDates.get(0)) + "&_at=lt" + toStr(preDates.get(3)));
assertThat(idValues, contains(ids.get(2), ids.get(1), ids.get(0)));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt2060");
assertThat(idValues, empty());
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=" + InstantDt.withCurrentTime().getYear());
assertThat(idValues, hasSize(10)); // 10 is the page size
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=ge" + InstantDt.withCurrentTime().getYear());
assertThat(idValues, hasSize(10));
idValues = searchAndReturnUnqualifiedIdValues(ourServerBase + "/_history?_at=gt" + InstantDt.withCurrentTime().getYear());
assertThat(idValues, hasSize(0));
}
private String toStr(Date theDate) {
return new InstantDt(theDate).getValueAsString();
}
@Test
public void testHasParameterNoResults() throws Exception {
@ -194,12 +224,11 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
}
private List<String> searchAndReturnUnqualifiedIdValues(String uri) throws IOException, ClientProtocolException {
private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String uri) throws IOException, ClientProtocolException {
List<String> ids;
HttpGet get = new HttpGet(uri);
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
String resp = IOUtils.toString(response.getEntity().getContent());
@ -212,8 +241,22 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
return ids;
}
private List<String> searchAndReturnUnqualifiedIdValues(String uri) throws IOException, ClientProtocolException {
List<String> ids;
HttpGet get = new HttpGet(uri);
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
String resp = IOUtils.toString(response.getEntity().getContent());
ourLog.info(resp);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, resp);
ids = toUnqualifiedIdValues(bundle);
} finally {
IOUtils.closeQuietly(response);
}
return ids;
}
/**
* Issue submitted by Bryn
*/
@ -224,7 +267,6 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourClient.create().resource(input).execute().getResource();
}
@Test
public void testSearchByExtendedChars() throws Exception {
for (int i = 0; i < 10; i++) {
@ -233,7 +275,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
p.addIdentifier().setValue("ID" + i);
myPatientDao.create(p, mySrd);
}
String uri = ourServerBase + "/Patient?name=" + URLEncoder.encode("Jernelöv", "UTF-8") + "&_count=5&_pretty=true";
ourLog.info("URI: {}", uri);
HttpGet get = new HttpGet(uri);
@ -242,22 +284,20 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(200, resp.getStatusLine().getStatusCode());
String output = IOUtils.toString(resp.getEntity().getContent());
ourLog.info(output);
Bundle b = myFhirCtx.newXmlParser().parseResource(Bundle.class, output);
assertEquals("http://localhost:" + ourPort + "/fhir/context/Patient?_count=5&_pretty=true&name=Jernel%C3%B6v", b.getLink("self").getUrl());
Patient p = (Patient) b.getEntry().get(0).getResource();
assertEquals("Jernelöv", p.getName().get(0).getFamily().get(0).getValue());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
}
@Override
public void before() throws Exception {
super.before();
@ -576,7 +616,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info(responseString);
assertEquals(400, response.getStatusLine().getStatusCode());
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)", oo.getIssue().get(0).getDiagnostics());
assertEquals("Can not create resource with ID \"2\", ID must not be supplied on a create (POST) operation (use an HTTP PUT / update operation if you wish to supply an ID)",
oo.getIssue().get(0).getDiagnostics());
} finally {
response.getEntity().getContent().close();
@ -659,7 +700,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
//@formatter:on
fail();
} catch (PreconditionFailedException e) {
assertEquals("HTTP 412 Precondition Failed: Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources", e.getMessage());
assertEquals("HTTP 412 Precondition Failed: Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources",
e.getMessage());
}
// Not deleted yet..
@ -791,8 +833,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
}
/*
* Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to
* make sure that works too..
* Try it with a raw socket call. The Apache client won't let us use the unescaped "|" in the URL but we want to make sure that works too..
*/
Socket sock = new Socket();
sock.setSoTimeout(3000);
@ -1326,7 +1367,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantType(new Date(time3)).getValueAsString());
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantType(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C"
+ new InstantType(new Date(time3)).getValueAsString());
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
@ -1918,7 +1960,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("testSearchTokenParam001");
patient.addName().addFamily("Tester").addGiven("testSearchTokenParam1");
patient.addCommunication().getLanguage().setText("testSearchTokenParamComText").addCoding().setCode("testSearchTokenParamCode").setSystem("testSearchTokenParamSystem").setDisplay("testSearchTokenParamDisplay");
patient.addCommunication().getLanguage().setText("testSearchTokenParamComText").addCoding().setCode("testSearchTokenParamCode").setSystem("testSearchTokenParamSystem")
.setDisplay("testSearchTokenParamDisplay");
myPatientDao.create(patient, mySrd);
patient = new Patient();
@ -2635,7 +2678,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info(responseString);
assertEquals(400, response.getStatusLine().getStatusCode());
OperationOutcome oo = myFhirCtx.newXmlParser().parseResource(OperationOutcome.class, responseString);
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"2\""));
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString(
"Can not update resource, resource body must contain an ID element which matches the request URL for update (PUT) operation - Resource body ID of \"333\" does not match URL ID of \"2\""));
} finally {
response.close();
}
@ -2659,7 +2703,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
ourLog.info(resp);
assertEquals(412, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, stringContainsInOrder(">ERROR<", "[Patient.contact]", "<pre>SHALL at least contain a contact's details or a reference to an organization", "<issue><severity value=\"error\"/>"));
assertThat(resp,
stringContainsInOrder(">ERROR<", "[Patient.contact]", "<pre>SHALL at least contain a contact's details or a reference to an organization", "<issue><severity value=\"error\"/>"));
} finally {
IOUtils.closeQuietly(response.getEntity().getContent());
response.close();
@ -2785,7 +2830,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<pre>No issues detected during validation</pre>"));
assertThat(resp, stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
assertThat(resp,
stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
} finally {
IOUtils.closeQuietly(response.getEntity().getContent());
response.close();
@ -2810,7 +2856,8 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<pre>No issues detected during validation</pre>"));
assertThat(resp, stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
assertThat(resp,
stringContainsInOrder("<issue>", "<severity value=\"information\"/>", "<code value=\"informational\"/>", "<diagnostics value=\"No issues detected during validation\"/>", "</issue>"));
} finally {
IOUtils.closeQuietly(response.getEntity().getContent());
response.close();
@ -2831,17 +2878,17 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
String resp = IOUtils.toString(response.getEntity().getContent());
ourLog.info(resp);
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<expansion>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"8450-9\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure--expiration\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("<contains>"));
assertThat(resp, containsString("<system value=\"http://acme.org\"/>"));
assertThat(resp, containsString("<code value=\"11378-7\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, containsString("<display value=\"Systolic blood pressure at First encounter\"/>"));
assertThat(resp, containsString("</contains>"));
assertThat(resp, containsString("</expansion>"));
} finally {

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -172,7 +172,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on
@ -188,7 +188,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the type level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
//@formatter:on

30
hapi-fhir-structures-dstu/pom.xml
View File

@ -137,6 +137,36 @@
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>

7
hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/param/DateRangeParamTest.java
View File

@ -46,6 +46,13 @@ public class DateRangeParamTest {
DateRangeParam range = new DateRangeParam(startDateTime, endDateTime);
assertEquals("2009-12-31T19:00:00.000-05:00", range.getValuesAsQueryTokens().get(0).getValueAsString());
assertEquals("2009-12-31T19:00:00.001-05:00", range.getValuesAsQueryTokens().get(1).getValueAsString());
// Now try with arguments reversed (should still create same range)
range = new DateRangeParam(endDateTime, startDateTime);
assertEquals("2009-12-31T19:00:00.000-05:00", range.getValuesAsQueryTokens().get(0).getValueAsString());
assertEquals("2009-12-31T19:00:00.001-05:00", range.getValuesAsQueryTokens().get(1).getValueAsString());
} finally {
TimeZone.setDefault(tz);
}

30
hapi-fhir-structures-dstu2/pom.xml
View File

@ -146,6 +146,36 @@
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>

166
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/BaseDateTimeDtDstu2Test.java
View File

@ -32,10 +32,166 @@ public class BaseDateTimeDtDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2();
private static Locale ourDefaultLocale;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseDateTimeDtDstu2Test.class);
private SimpleDateFormat myDateInstantParser;
private FastDateFormat myDateInstantZoneParser;
@Test
public void testFromTime() {
long millis;
InstantDt dt;
millis = 1466022208001L;
String expected = "2016-06-15T20:23:28.001Z";
validate(millis, expected);
millis = 1466022208123L;
expected = "2016-06-15T20:23:28.123Z";
validate(millis, expected);
millis = 1466022208100L;
expected = "2016-06-15T20:23:28.100Z";
validate(millis, expected);
millis = 1466022208000L;
expected = "2016-06-15T20:23:28.000Z";
validate(millis, expected);
}
private void validate(long millis, String expected) {
InstantDt dt;
dt = new InstantDt(new Date(millis));
dt.setTimeZoneZulu(true);
assertEquals(expected, dt.getValueAsString());
assertEquals(millis % 1000, dt.getMillis().longValue());
assertEquals((millis % 1000) * BaseDateTimeDt.NANOS_PER_MILLIS, dt.getNanos().longValue());
dt = new InstantDt();
dt.setTimeZone(TimeZone.getTimeZone("GMT+0:00"));
dt.setValue(new Date(millis));
assertEquals(expected.replace("Z", "+00:00"), dt.getValueAsString());
}
@Test
public void testSetPartialsYearFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setYear(2016);
assertEquals(2016, dt.getYear().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2016-03-11T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsMonthFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setMonth(3);
assertEquals(3, dt.getMonth().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-04-11T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsDayFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setDay(15);
assertEquals(15, dt.getDay().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-15T15:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsHourFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setHour(23);
assertEquals(23, dt.getHour().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-11T23:44:13.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsMinuteFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setMinute(54);
assertEquals(54, dt.getMinute().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-11T15:54:13.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsSecondFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setSecond(1);
assertEquals(1, dt.getSecond().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-11T15:44:01.27564757855254768473697463986328969635-08:00", valueAsString);
}
@Test
public void testSetPartialsMillisFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setMillis(12);
assertEquals(12, dt.getMillis().intValue());
assertEquals(12 * BaseDateTimeDt.NANOS_PER_MILLIS, dt.getNanos().longValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-11T15:44:13.012-08:00", valueAsString);
}
@Test
public void testSetPartialsNanosFromExisting() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setNanos(100000000L);
assertEquals(100000000L, dt.getNanos().longValue());
assertEquals(100, dt.getMillis().intValue());
String valueAsString = dt.getValueAsString();
ourLog.info(valueAsString);
assertEquals("2011-03-11T15:44:13.100-08:00", valueAsString);
}
@Test
public void testSetPartialsInvalid() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
dt.setNanos(0);
dt.setNanos(BaseDateTimeDt.NANOS_PER_SECOND - 1);
try {
dt.setNanos(BaseDateTimeDt.NANOS_PER_SECOND);
} catch (IllegalArgumentException e) {
assertEquals("Value 1000000000 is not between allowable range: 0 - 999999999", e.getMessage());
}
}
@Test
public void testGetPartials() {
InstantDt dt = new InstantDt("2011-03-11T15:44:13.27564757855254768473697463986328969635-08:00");
assertEquals(2011, dt.getYear().intValue());
assertEquals(2, dt.getMonth().intValue());
assertEquals(11, dt.getDay().intValue());
assertEquals(15, dt.getHour().intValue());
assertEquals(44, dt.getMinute().intValue());
assertEquals(13, dt.getSecond().intValue());
assertEquals(275, dt.getMillis().intValue());
assertEquals(275647578L, dt.getNanos().longValue());
dt = new InstantDt();
assertEquals(null, dt.getYear());
assertEquals(null, dt.getMonth());
assertEquals(null, dt.getDay());
assertEquals(null, dt.getHour());
assertEquals(null, dt.getMinute());
assertEquals(null, dt.getSecond());
assertEquals(null, dt.getMillis());
assertEquals(null, dt.getNanos());
}
@Before
public void before() {
myDateInstantParser = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
@ -49,7 +205,7 @@ public class BaseDateTimeDtDstu2Test {
dt.setTimeZoneZulu(true);
assertEquals("1995-11-15T04:58:08Z", dt.getValueAsString());
}
/**
* Test for #57
*/
@ -194,10 +350,10 @@ public class BaseDateTimeDtDstu2Test {
@Test
public void testGetValueAsCalendar() {
assertNull(new InstantDt().getValueAsCalendar());
InstantDt dt = new InstantDt("2011-01-03T07:11:22.002-08:00");
GregorianCalendar cal = dt.getValueAsCalendar();
assertEquals(2011, cal.get(Calendar.YEAR));
assertEquals(7, cal.get(Calendar.HOUR_OF_DAY));
assertEquals(2, cal.get(Calendar.MILLISECOND));

53
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/DecimalDtTest.java Normal file
View File

@ -0,0 +1,53 @@
package ca.uhn.fhir.model.primitive;
import static org.junit.Assert.*;
import java.math.RoundingMode;
import org.junit.Test;
public class DecimalDtTest {
@Test
public void testRoundWithMode() {
DecimalDt dt = new DecimalDt("1.66666666");
dt.round(3, RoundingMode.FLOOR);
assertEquals("1.66", dt.getValueAsString());
}
@Test
public void testGetValue() {
DecimalDt dt = new DecimalDt("1.66666666");
assertEquals(1, dt.getValueAsInteger());
assertEquals("1.66666666", dt.getValueAsNumber().toString());
assertEquals("1.66666666", dt.getValueAsString());
}
@Test
public void testSetValue() {
DecimalDt dt = new DecimalDt();
dt.setValueAsInteger(123);
assertEquals("123", dt.getValueAsString());
}
@Test
public void testRound() {
DecimalDt dt = new DecimalDt("1.66666666");
dt.round(3);
assertEquals("1.67", dt.getValueAsString());
}
@Test
public void testCompareTo() {
DecimalDt dt = new DecimalDt("1.66666666");
assertEquals(1, dt.compareTo(null));
assertEquals(1, dt.compareTo(new DecimalDt()));
assertEquals(1, dt.compareTo(new DecimalDt("0.1")));
assertEquals(-1, dt.compareTo(new DecimalDt("99")));
assertEquals(0, dt.compareTo(new DecimalDt("1.66666666")));
assertEquals(0, new DecimalDt().compareTo(new DecimalDt()));
assertEquals(-1, new DecimalDt().compareTo(new DecimalDt("1.0")));
}
}

56
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/model/primitive/UriDtTest.java Normal file
View File

@ -0,0 +1,56 @@
package ca.uhn.fhir.model.primitive;
import static org.junit.Assert.*;
import org.junit.Test;
public class UriDtTest {
@Test
public void testFromOid() {
UriDt uri = UriDt.fromOid("0.1.2.3.4");
assertEquals("urn:oid:0.1.2.3.4", uri.getValue());
}
@Test
public void testFromOidNull() {
UriDt uri = UriDt.fromOid(null);
assertEquals(null, uri.getValue());
}
@Test
public void testEqualsObject() {
UriDt dt = new UriDt("http://example.com/foo");
assertTrue(dt.equals(dt));
assertFalse(dt.equals(null));
assertFalse(dt.equals(new UriDt()));
assertTrue(dt.equals(new UriDt("http://example.com/foo")));
assertTrue(dt.equals(new UriDt("http://example.com/foo/")));
assertFalse(dt.equals(new UriDt("http://blah.com/foo/")));
assertFalse(dt.equals(new StringDt("http://example.com/foo")));
}
@Test
public void testEqualsString() {
UriDt dt = new UriDt("http://example.com/foo");
assertTrue(dt.equals("http://example.com/foo"));
}
@Test
public void testHashCode() {
UriDt dt = new UriDt("http://example.com/foo");
assertEquals(-1671329151, dt.hashCode());
dt = new UriDt();
assertEquals(31, dt.hashCode());
}
@Test
public void testSetInvalid() {
UriDt dt = new UriDt();
dt.setValue("blah : // AA");
dt.hashCode();
}
}

27
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java
View File

@ -1040,8 +1040,11 @@ public class XmlParserDstu2Test {
}
/**
* Make sure whitespace is preserved for pre tags
*/
@Test
public void testEncodeDivWithPre() {
public void testEncodeDivWithPrePrettyPrint() {
Patient p = new Patient();
p.getText().setDiv("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3 <b>BOLD</b></pre></p></div>");
@ -1059,6 +1062,28 @@ public class XmlParserDstu2Test {
}
/**
* Make sure whitespace is preserved for pre tags
*/
@Test
public void testEncodeDivWithPreNonPrettyPrint() {
Patient p = new Patient();
p.getText().setDiv("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3 <b>BOLD</b></pre></p></div>");
String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
ourLog.info(output);
//@formatter:off
assertThat(output, stringContainsInOrder(
"<text><div",
"<p>A P TAG</p><p>",
"<pre>line1\nline2\nline3 <b>BOLD</b></pre>"
));
//@formatter:on
}
@Test
public void testEncodeDoesntIncludeUuidId() {
Patient p = new Patient();

27
hapi-fhir-structures-dstu3/pom.xml
View File

@ -175,13 +175,34 @@
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
<classFolder>${basedir}/../hapi-fhir-base/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<!--<redirectTestOutputToFile>false</redirectTestOutputToFile>-->
<runOrder>random</runOrder>
<reuseForks>false</reuseForks>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

25
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -119,8 +119,31 @@ public class XmlParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
/**
* Make sure whitespace is preserved for pre tags
*/
@Test
public void testEncodeDivWithPre() {
public void testEncodeDivWithPreNonPrettyPrint() {
Patient p = new Patient();
p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3 <b>BOLD</b></pre></p></div>");
String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(p);
ourLog.info(output);
//@formatter:off
assertThat(output, stringContainsInOrder(
"<text><div",
"<p>A P TAG</p><p>",
"<pre>line1\nline2\nline3 <b>BOLD</b></pre>"
));
//@formatter:on
}
@Test
public void testEncodeDivWithPrePrettyPrint() {
Patient p = new Patient();
p.getText().setDivAsString("<div>\n\n<p>A P TAG</p><p><pre>line1\nline2\nline3 <b>BOLD</b></pre></p></div>");

30
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -177,6 +177,36 @@
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<configuration>
<classFolders>
<classFolder>${basedir}/target/classes</classFolder>
<classFolder>${basedir}../hapi-fhir-base/target/classes</classFolder>
</classFolders>
<sourceFolders>
<sourceFolder>${basedir}/src/main/java</sourceFolder>
<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
</sourceFolders>
<dumpOnExit>true</dumpOnExit>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>

13
pom.xml
View File

@ -806,7 +806,6 @@
<runOrder>random</runOrder>
<argLine>-Dfile.encoding=UTF-8 -Xmx712m</argLine>
<forkCount>1</forkCount>
<!--<reuseForks>false</reuseForks> -->
</configuration>
</plugin>
<plugin>
@ -860,6 +859,11 @@
</coberturaReports>
</configuration>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.7.201606060606</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
@ -1123,7 +1127,8 @@
<replace dir="target/site" summary="true">
<include name="*.html"/>
<replacetoken>\t</replacetoken>
<replacevalue> </replacevalue>
<replacevalue>
</replacevalue>
</replace>
<replace dir="target/site" summary="true">
<include name="index.html"/>
@ -1376,6 +1381,8 @@
<plugins>
<!-- <plugin> <groupId>org.apache.maven.plugins</groupId> <artifactId>maven-checkstyle-plugin</artifactId> <reportSets> <reportSet> <reports><report>checkstyle-aggregate</report></reports> </reportSet>
</reportSets> <configuration> <configLocation>config/sun_checks.xml</configLocation> <includes> hapi-fhir-base/src/main/java/**/*.java </includes> </configuration> </plugin> -->
<!-- <plugin> <groupId>org.jacoco</groupId> <artifactId>jacoco-maven-plugin</artifactId> <version>0.7.7.201606060606</version> <reportSets> <reportSet> <reports> <report>report</report> </reports> <configuration>
<dataFileIncludes>${baseDir}/hapi-fhir-base/target/jacoco.exec</dataFileIncludes> </configuration> </reportSet> </reportSets> </plugin> -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-changes-plugin</artifactId>
@ -1524,7 +1531,6 @@
<modules>
<module>hapi-deployable-pom</module>
<module>hapi-fhir-base</module>
<!--<module>hapi-fhir-oauth2</module> -->
<module>hapi-fhir-base-test-mindeps-client</module>
<module>hapi-fhir-base-test-mindeps-server</module>
<module>hapi-tinder-plugin</module>
@ -1548,6 +1554,7 @@
<module>hapi-fhir-dist</module>
<module>examples</module>
<module>hapi-fhir-base-example-embedded-ws</module>
<module>hapi-fhir-jacoco</module>
</modules>
</profile>
<profile>