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Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir

This commit is contained in:
lmds1 2014-10-10 15:42:29 -04:00
parent 86b5e4acf9 507ea9bedf
commit 6049df0bfa
28 changed files with 1030 additions and 390 deletions
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37
hapi-fhir-base/src/changes/changes.xml
View File

@ -7,6 +7,12 @@
</properties>
<body>
<release version="0.7" date="TBD">
<action type="add" issue="30">
<![CDATA[<b>API CHANGE:</b>]]> The TagList class previously implemented ArrayList semantics,
but this has been replaced with LinkedHashMap semantics. This means that the list of
tags will no longer accept duplicate tags, but that tag order will still be
preserved. Thanks to Bill de Beaubien for reporting!
</action>
<action type="add" dev="suranga">
Documentation fixes
</action>
@ -55,6 +61,10 @@
entities converted to their equivalent unicode characters when resources are encoded, since FHIR does
not allow extended entities in resource instances.
</action>
<action type="add">
Add a new client interceptor which adds HTTP Authorization Bearer Tokens (for use with OAUTH2 servers)
to client requests.
</action>
<action type="fix">
Add phloc-commons dependency explicitly, which resolves an issue building HAPI from source on
some platforms. Thanks to Odysseas Pentakalos for the patch!
@ -63,6 +73,29 @@
HAPI now logs a single line indicating the StAX implementation being used upon the
first time an XML parser is created.
</action>
<action type="fix">
Update methods on the server did not return a "content-location" header, but
only a "location" header. Both are required according to the FHIR specification.
Thanks to Bill de Beaubien of Systems Made Simple for reporting this!
</action>
<action type="fix" issue="26" dev="akley">
Parser failed to correctly read contained Binary resources. Thanks to Alexander Kley for
the patch!
</action>
<action type="fix" issue="29" dev="akley">
Calling encode multiple times on a resource with contained resources caused the contained
resources to be re-added (and the actual message to grow) with each encode pass. Thanks to
Alexander Kley for the test case!
</action>
<action type="fix">
JSON-encoded contained resources with the incorrect "_id" element (which should be "id", but some
incorrect examples exist on the FHIR specification) now parse correctly.
</action>
<action type="fix">
Several unit tests failed on Windows (or any platform with non UTF-8 default encoding). This may
have also caused resource validation to fail occasionally on these platforms as well.
Thanks to Bill de Beaubien for reporting!
</action>
</release>
<release version="0.6" date="2014-Sep-08" description="This release brings a number of new features and bug fixes!">
<!--
@ -206,7 +239,9 @@
</release>
<release version="0.5" date="2014-Jul-30">
<action type="add">
having multiple ways of accomplishing the same thing. This means that a number of existing classes
HAPI has a number of RESTful method parameter types that have similar but not identical
purposes and confusing names. A cleanup has been undertaken to clean this up.
This means that a number of existing classes
have been deprocated in favour of new naming schemes.
<![CDATA[<br/><br/>]]>
All annotation-based clients and all server search method parameters are now named

55
hapi-fhir-base/src/changes/changes.xml.orig
View File

@ -7,11 +7,23 @@
</properties>
<body>
<release version="0.7" date="TBD">
<action type="add">
Documentation update, thanks to Suranga Nath Kasthurirathne of the OpenMRS project.
<action type="add" dev="suranga">
Documentation fixes
</action>
<action type="add" dev="dougmartin">
Add a collection of new methods on the generic client which support the
<![CDATA[
<b><a href="./apidocs/ca/uhn/fhir/rest/client/IGenericClient.html#read(java.lang.Class,%20ca.uhn.fhir.model.primitive.UriDt)">read</a></b>,
<b><a href="./apidocs/ca/uhn/fhir/rest/client/IGenericClient.html#vread(java.lang.Class,%20ca.uhn.fhir.model.primitive.UriDt)">read</a></b>,
and <b><a href="./apidocs/ca/uhn/fhir/rest/client/IGenericClient.html#search(java.lang.Class,%20ca.uhn.fhir.model.primitive.UriDt)">search</a></b>
]]>
operations using an absolute URL. This allows developers to perform these operations using
URLs they obtained from other sources (or external resource references within resources). In
addition, the existing read/vread operations will now access absolute URL references if
they are passed in. Thanks to Doug Martin of the Regenstrief Center for Biomedical Informatics
for contributing this implementation!
</action>
<action type="fix">
<<<<<<< HEAD
Server implementation was not correctly figuring out its own FHIR Base URL when deployed
on Amazon Web Service server. Thanks to Jeffrey Ting and Bill De Beaubien of
Systems Made Simple for their help in figuring out this issue!
@ -20,15 +32,44 @@
XML Parser failed to encode fields with both a resource reference child and
a primitive type child. Thanks to Jeffrey Ting and Bill De Beaubien of
Systems Made Simple for their help in figuring out this issue!
=======
</action>
<action type="fix">
HAPI now runs successfully on Servlet 2.5 containers (such as Tomcat 6). Thanks to
Bernard Gitaadji for reporting and diagnosing the issue!
</action>
<action type="fix">
Summary (in the bundle entry) is now encoded by the XML and JSON parsers if supplied. Thanks to David Hay of
Orion Health for reporting this!
</action>
<action type="fix" issue="24">
Conformance profiles which are automatically generated by the server were missing a few mandatory elements,
which meant that the profile did not correctly validate. Thanks to Bill de Beaubien of Systems Made Simple
for reporting this!
</action>
<action type="fix">
XHTML (in narratives) containing escapable characters (e.g. &lt; or &quot;) will now always have those characters
escaped properly in encoded messages.
>>>>>>> 83f9c1c6a992266de12f9076b733dffdaaf63203
</action>
<action type="fix">
Resources containing entities which are not valid in basic XML (e.g. &amp;sect;) will have those
entities converted to their equivalent unicode characters when resources are encoded, since FHIR does
not allow extended entities in resource instances.
</action>
<<<<<<< HEAD
<action type="add">
Add a new client interceptor which adds HTTP Authorization Bearer Tokens (for use with OAUTH2 servers)
to client requests.
</action>
=======
<action type="fix">
Add phloc-commons dependency explicitly, which resolves an issue building HAPI from source on
some platforms. Thanks to Odysseas Pentakalos for the patch!
</action>
<action type="add">
HAPI now logs a single line indicating the StAX implementation being used upon the
first time an XML parser is created.
</action>
>>>>>>> 4622af7a822ad80c864516369e1e941660a19194
</release>
<release version="0.6" date="2014-Sep-08" description="This release brings a number of new features and bug fixes!">
<!--
@ -172,7 +213,9 @@
</release>
<release version="0.5" date="2014-Jul-30">
<action type="add">
having multiple ways of accomplishing the same thing. This means that a number of existing classes
HAPI has a number of RESTful method parameter types that have similar but not identical
purposes and confusing names. A cleanup has been undertaken to clean this up.
This means that a number of existing classes
have been deprocated in favour of new naming schemes.
<![CDATA[<br/><br/>]]>
All annotation-based clients and all server search method parameters are now named

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java
View File

@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.*;
import java.io.IOException;
import java.io.InputStream;
import java.lang.reflect.Field;
import java.lang.reflect.Modifier;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.Type;
import java.util.ArrayList;
@ -380,9 +381,14 @@ class ModelScanner {
for (Field next : theClass.getDeclaredFields()) {
if (Modifier.isFinal(next.getModifiers())) {
ourLog.trace("Ignoring constant {} on target type {}", next.getName(), theClass);
continue;
}
Child childAnnotation = next.getAnnotation(Child.class);
if (childAnnotation == null) {
ourLog.debug("Ignoring non-type field '" + next.getName() + "' on target type: " + theClass);
ourLog.trace("Ignoring non @Child field {} on target type {}",next.getName() , theClass);
continue;
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Bundle.java
View File

@ -59,12 +59,20 @@ public class Bundle extends BaseBundle /* implements IElement */{
private IntegerDt myTotalResults;
private InstantDt myUpdated;
/**
* @deprecated Tags wil become immutable in a future release of HAPI, so {@link #addCategory(String, String, String)} should be used instead
*/
public Tag addCategory() {
Tag retVal = new Tag();
getCategories().add(retVal);
return retVal;
}
public void addCategory(String theScheme, String theTerm, String theLabel) {
getCategories().add(new Tag(theScheme, theTerm, theLabel));
}
public void addCategory(Tag theTag) {
getCategories().add(theTag);
}

7
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BundleEntry.java
View File

@ -50,12 +50,19 @@ public class BundleEntry extends BaseBundle {
private StringDt myTitle;
private InstantDt myUpdated;
/**
* @deprecated Tags wil become immutable in a future release of HAPI, so {@link #addCategory(String, String, String)} should be used instead
*/
public Tag addCategory() {
Tag retVal = new Tag();
getCategories().add(retVal);
return retVal;
}
public void addCategory(String theScheme, String theTerm, String theLabel) {
getCategories().add(new Tag(theScheme, theTerm, theLabel));
}
public void addCategory(Tag theTag) {
getCategories().add(theTag);
}

114
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Tag.java
View File

@ -28,38 +28,52 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
/**
* A single tag
* <p>
* Note on equality- When computing hashCode or equals values for this class, only the
* {@link #getScheme() scheme} and
* </p>
*/
public class Tag extends BaseElement implements IElement {
/**
* Convenience constant containing the "http://hl7.org/fhir/tag" scheme
* value
*/
public static final String HL7_ORG_FHIR_TAG = "http://hl7.org/fhir/tag";
public static final String ATTR_LABEL = "label";
public static final String ATTR_SCHEME = "scheme";
public static final String ATTR_TERM = "term";
/**
* Convenience constant containing the "http://hl7.org/fhir/tag/security" scheme
* value
* Convenience constant containing the "http://hl7.org/fhir/tag" scheme value
*/
public static final String HL7_ORG_FHIR_TAG = "http://hl7.org/fhir/tag";
/**
* Convenience constant containing the "http://hl7.org/fhir/tag/profile" scheme value
*/
public static final String HL7_ORG_PROFILE_TAG = "http://hl7.org/fhir/tag/profile";
/**
* Convenience constant containing the "http://hl7.org/fhir/tag/security" scheme value
*/
public static final String HL7_ORG_SECURITY_TAG = "http://hl7.org/fhir/tag/security";
/**
* Convenience constant containing the "http://hl7.org/fhir/tag/profile" scheme
* value
*/
public static final String HL7_ORG_PROFILE_TAG = "http://hl7.org/fhir/tag/profile";
public static final String ATTR_TERM = "term";
public static final String ATTR_LABEL = "label";
public static final String ATTR_SCHEME = "scheme";
private String myLabel;
private String myScheme;
private String myTerm;
/**
* @deprecated Tags will become immutable in a future release, so this constructor should not be used.
*/
public Tag() {
}
/**
* @deprecated There is no reason to create a tag with a term and not a scheme, so this constructor will be removed
*/
public Tag(String theTerm) {
this((String)null, theTerm, null);
this((String) null, theTerm, null);
}
public Tag(String theScheme, String theTerm) {
myScheme = theScheme;
myTerm = theTerm;
}
public Tag(String theScheme, String theTerm, String theLabel) {
@ -78,32 +92,6 @@ public class Tag extends BaseElement implements IElement {
myLabel = theLabel;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Tag other = (Tag) obj;
if (myLabel == null) {
if (other.myLabel != null)
return false;
} else if (!myLabel.equals(other.myLabel))
return false;
if (myScheme == null) {
if (other.myScheme != null)
return false;
} else if (!myScheme.equals(other.myScheme))
return false;
if (myTerm == null) {
if (other.myTerm != null)
return false;
} else if (!myTerm.equals(other.myTerm))
return false;
return true;
}
public String getLabel() {
return myLabel;
@ -117,11 +105,32 @@ public class Tag extends BaseElement implements IElement {
return myTerm;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Tag other = (Tag) obj;
if (myScheme == null) {
if (other.myScheme != null)
return false;
} else if (!myScheme.equals(other.myScheme))
return false;
if (myTerm == null) {
if (other.myTerm != null)
return false;
} else if (!myTerm.equals(other.myTerm))
return false;
return true;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myLabel == null) ? 0 : myLabel.hashCode());
result = prime * result + ((myScheme == null) ? 0 : myScheme.hashCode());
result = prime * result + ((myTerm == null) ? 0 : myTerm.hashCode());
return result;
@ -132,16 +141,31 @@ public class Tag extends BaseElement implements IElement {
return StringUtils.isBlank(myLabel) && StringUtils.isBlank(myScheme) && StringUtils.isBlank(myTerm);
}
/**
* @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
* ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
* tag object
*/
public Tag setLabel(String theLabel) {
myLabel = theLabel;
return this;
}
/**
* @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
* ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
* tag object
*/
public Tag setScheme(String theScheme) {
myScheme = theScheme;
return this;
}
/**
* @deprecated Tags will become immutable in a future release of HAPI in order to facilitate
* ensuring that the TagList acts as an unordered set. Use the constructor to set this field when creating a new
* tag object
*/
public Tag setTerm(String theTerm) {
myTerm = theTerm;
return this;

184
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TagList.java
View File

@ -20,24 +20,146 @@ package ca.uhn.fhir.model.api;
* #L%
*/
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
public class TagList extends ArrayList<Tag> {
/**
* A collection of tags present on a single resource. TagList is backed by a {@link LinkedHashSet}, so the order of added tags will be consistent, but duplicates will not be preserved.
*
* <p>
* <b>Thread safety:</b> This class is not thread safe
* </p>
*/
public class TagList implements Set<Tag>, Serializable {
private static final long serialVersionUID = 1L;
public static final String ATTR_CATEGORY = "category";
public static final String ELEMENT_NAME = "TagList";
public static final String ELEMENT_NAME_LC = ELEMENT_NAME.toLowerCase();
public Tag addTag(String theScheme, String theTerm, String theLabel) {
Tag retVal = new Tag(theScheme, theTerm, theLabel);
public static final String ELEMENT_NAME_LC = ELEMENT_NAME.toLowerCase();
private static final long serialVersionUID = 1L;
private transient List<Tag> myOrderedTags;
private LinkedHashSet<Tag> myTagSet = new LinkedHashSet<Tag>();
/**
* Constructor
*/
public TagList() {
super();
}
@Override
public String toString() {
StringBuilder b = new StringBuilder();
b.append("TagList[").append(size()).append(" tag(s)]");
for (Tag next : this) {
b.append("\n * ").append(next.toString());
}
return b.toString();
}
@Override
public boolean add(Tag theE) {
myOrderedTags = null;
return myTagSet.add(theE);
}
@Override
public boolean addAll(Collection<? extends Tag> theC) {
myOrderedTags = null;
return myTagSet.addAll(theC);
}
/**
* @deprecated Tags wil become immutable in a future release of HAPI, so {@link #addTag(String, String, String)} should be used instead
*/
public Tag addTag() {
myOrderedTags = null;
return addTag(null, null, null);
}
/**
* Add a new tag instance
*
* @param theScheme
* The tag scheme
* @param theTerm
* The tag term
* @return Returns the newly created tag instance. Note that the tag is added to the list by this method, so you generally do not need to interact directly with the added tag.
*/
public Tag addTag(String theScheme, String theTerm) {
Tag retVal = new Tag(theScheme, theTerm);
add(retVal);
myOrderedTags = null;
return retVal;
}
public Tag addTag() {
return addTag(null, null, null);
/**
* Add a new tag instance
*
* @param theScheme
* The tag scheme
* @param theTerm
* The tag term
* @param theLabel
* The tag label
* @return Returns the newly created tag instance. Note that the tag is added to the list by this method, so you generally do not need to interact directly with the added tag.
*/
public Tag addTag(String theScheme, String theTerm, String theLabel) {
Tag retVal = new Tag(theScheme, theTerm, theLabel);
add(retVal);
myOrderedTags = null;
return retVal;
}
@Override
public void clear() {
myOrderedTags = null;
myTagSet.clear();
}
@Override
public boolean contains(Object theO) {
return myTagSet.contains(theO);
}
@Override
public boolean containsAll(Collection<?> theC) {
return myTagSet.containsAll(theC);
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
TagList other = (TagList) obj;
if (myTagSet == null) {
if (other.myTagSet != null)
return false;
} else if (!myTagSet.equals(other.myTagSet))
return false;
return true;
}
/**
* Returns the tag at a given index - Note that the TagList is backed by a {@link LinkedHashSet}, so the order of added tags will be consistent, but duplicates will not be preserved.
*/
public Tag get(int theIndex) {
if (myOrderedTags == null) {
myOrderedTags = new ArrayList<Tag>();
for (Tag next : myTagSet) {
myOrderedTags.add(next);
}
}
return myOrderedTags.get(theIndex);
}
public Tag getTag(String theScheme, String theTerm) {
@ -59,4 +181,52 @@ public class TagList extends ArrayList<Tag> {
return retVal;
}
@Override
public int hashCode() {
return myTagSet.hashCode();
}
@Override
public boolean isEmpty() {
return myTagSet.isEmpty();
}
@Override
public Iterator<Tag> iterator() {
return myTagSet.iterator();
}
@Override
public boolean remove(Object theO) {
myOrderedTags = null;
return myTagSet.remove(theO);
}
@Override
public boolean removeAll(Collection<?> theC) {
myOrderedTags = null;
return myTagSet.removeAll(theC);
}
@Override
public boolean retainAll(Collection<?> theC) {
myOrderedTags = null;
return myTagSet.retainAll(theC);
}
@Override
public int size() {
return myTagSet.size();
}
@Override
public Object[] toArray() {
return myTagSet.toArray();
}
@Override
public <T> T[] toArray(T[] theA) {
return myTagSet.toArray(theA);
}
}

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -29,6 +29,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeDeclaredChildDefinition;
import ca.uhn.fhir.context.ConfigurationException;
@ -130,16 +132,24 @@ public abstract class BaseParser implements IParser {
List<ResourceReferenceDt> allElements = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, ResourceReferenceDt.class);
Set<String> allIds = new HashSet<String>();
for (IResource next : theTarget.getContained().getContainedResources()) {
String nextId = next.getId().getValue();
if (StringUtils.isNotBlank(nextId)) {
allIds.add(nextId);
}
}
for (ResourceReferenceDt next : allElements) {
IResource resource = next.getResource();
if (resource != null) {
if (resource.getId().isEmpty()) {
if (resource.getId().isEmpty()) { // TODO: make this configurable between the two below (and something else?)
resource.setId(new IdDt(myNextContainedId++));
// resource.setId(new IdDt(UUID.randomUUID().toString()));
}
if (!allIds.contains(resource.getId().getValue())) {
String nextResourceId = resource.getId().getValue();
if (!allIds.contains(nextResourceId)) {
theTarget.getContained().getContainedResources().add(resource);
allIds.add(resource.getId().getValue());
}

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -698,6 +698,10 @@ public class JsonParser extends BaseParser implements IParser {
} else if ("id".equals(nextName)) {
elementId = theObject.getString(nextName);
continue;
} else if ("_id".equals(nextName)) {
// _id is incorrect, but some early examples in the FHIR spec used it
elementId = theObject.getString(nextName);
continue;
} else if ("extension".equals(nextName)) {
JsonArray array = theObject.getJsonArray(nextName);
parseExtension(theState, array, false);

71
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -158,8 +158,7 @@ class ParserState<T> {
}
/**
* Invoked after any new XML event is individually processed, containing a copy of the XML event. This is basically
* intended for embedded XHTML content
* Invoked after any new XML event is individually processed, containing a copy of the XML event. This is basically intended for embedded XHTML content
*/
public void xmlEvent(XMLEvent theNextEvent) {
myState.xmlEvent(theNextEvent);
@ -222,35 +221,37 @@ class ParserState<T> {
private static final int STATE_TERM = 1;
private int myCatState = STATE_NONE;
private Tag myInstance;
private TagList myTagList;
private String myTerm;
private String myLabel;
private String myScheme;
public AtomCategoryState(Tag theEntry) {
public AtomCategoryState(TagList theTagList) {
super(null);
myInstance = theEntry;
myTagList = theTagList;
}
@Override
public void attributeValue(String theName, String theValue) throws DataFormatException {
if ("term".equals(theName)) {
myInstance.setTerm(theValue);
myTerm = theValue;
} else if ("label".equals(theName)) {
myInstance.setLabel(theValue);
myLabel = theValue;
} else if ("scheme".equals(theName)) {
myInstance.setScheme(theValue);
myScheme = theValue;
} else if ("value".equals(theName)) {
/*
* This handles XML parsing, which is odd for this quasi-resource type, since the tag has three values
* instead of one like everything else.
* This handles XML parsing, which is odd for this quasi-resource type, since the tag has three values instead of one like everything else.
*/
switch (myCatState) {
case STATE_LABEL:
myInstance.setLabel(theValue);
myLabel = theValue;
break;
case STATE_TERM:
myInstance.setTerm(theValue);
myTerm = theValue;
break;
case STATE_SCHEME:
myInstance.setScheme(theValue);
myScheme = theValue;
break;
default:
super.string(theValue);
@ -265,6 +266,9 @@ class ParserState<T> {
if (myCatState != STATE_NONE) {
myCatState = STATE_NONE;
} else {
if (isNotEmpty(myScheme) || isNotBlank(myTerm) || isNotBlank(myLabel)) {
myTagList.addTag(myScheme, myTerm, myLabel);
}
pop();
}
}
@ -422,7 +426,7 @@ class ParserState<T> {
} else if ("summary".equals(theLocalPart)) {
push(new XhtmlState(getPreResourceState(), myEntry.getSummary(), false));
} else if ("category".equals(theLocalPart)) {
push(new AtomCategoryState(myEntry.addCategory()));
push(new AtomCategoryState(myEntry.getCategories()));
} else if ("deleted".equals(theLocalPart) && myJsonMode) {
// JSON and XML deleted entries are completely different for some reason
myDeleted = true;
@ -629,7 +633,7 @@ class ParserState<T> {
} else if ("author".equals(theLocalPart)) {
push(new AtomAuthorState(myInstance));
} else if ("category".equals(theLocalPart)) {
push(new AtomCategoryState(myInstance.getCategories().addTag()));
push(new AtomCategoryState(myInstance.getCategories()));
} else if ("deleted-entry".equals(theLocalPart) && verifyNamespace(XmlParser.TOMBSTONES_NS, theNamespaceURI)) {
push(new AtomDeletedEntryState(myInstance, myResourceType));
} else {
@ -707,7 +711,8 @@ class ParserState<T> {
}
/**
* @param theData The string value
* @param theData
* The string value
*/
public void string(String theData) {
// ignore by default
@ -718,7 +723,8 @@ class ParserState<T> {
}
/**
* @param theNextEvent The XML event
* @param theNextEvent
* The XML event
*/
public void xmlEvent(XMLEvent theNextEvent) {
// ignore
@ -741,7 +747,13 @@ class ParserState<T> {
@Override
public void attributeValue(String theName, String theValue) throws DataFormatException {
if ("contentType".equals(theName)) {
if ("id".equals(theName)) {
if (myInstance instanceof IIdentifiableElement) {
((IIdentifiableElement) myInstance).setElementSpecificId((theValue));
} else if (myInstance instanceof IResource) {
((IResource) myInstance).setId(new IdDt(theValue));
}
} else if ("contentType".equals(theName)) {
myInstance.setContentType(theValue);
} else if (myJsonMode && "value".equals(theName)) {
string(theValue);
@ -1269,7 +1281,8 @@ class ParserState<T> {
myContext.newTerser().visit(myInstance, new IModelVisitor() {
@Override
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition, ExtensionDt theNextExt) {
public void acceptUndeclaredExtension(ISupportsUndeclaredExtensions theContainingElement, BaseRuntimeChildDefinition theChildDefinition, BaseRuntimeElementDefinition<?> theDefinition,
ExtensionDt theNextExt) {
acceptElement(theNextExt.getValue(), null, null);
}
@ -1502,7 +1515,7 @@ class ParserState<T> {
@Override
public void enteringNewElement(String theNamespaceURI, String theLocalPart) throws DataFormatException {
if (TagList.ATTR_CATEGORY.equals(theLocalPart)) {
push(new TagState(myTagList.addTag()));
push(new TagState(myTagList));
} else {
throw new DataFormatException("Unexpected element: " + theLocalPart);
}
@ -1518,11 +1531,14 @@ class ParserState<T> {
private static final int SCHEME = 3;
private static final int TERM = 1;
private int mySubState = 0;
private Tag myTag;
private TagList myTagList;
private String myTerm;
private String myLabel;
private String myScheme;
public TagState(Tag theTag) {
public TagState(TagList theTagList) {
super(null);
myTag = theTag;
myTagList = theTagList;
}
@Override
@ -1531,13 +1547,13 @@ class ParserState<T> {
switch (mySubState) {
case TERM:
myTag.setTerm(value);
myTerm = (value);
break;
case LABEL:
myTag.setLabel(value);
myLabel = (value);
break;
case SCHEME:
myTag.setScheme(value);
myScheme = (value);
break;
case NONE:
// This handles JSON encoding, which is a bit weird
@ -1553,6 +1569,9 @@ class ParserState<T> {
if (mySubState != NONE) {
mySubState = NONE;
} else {
if (isNotEmpty(myScheme) || isNotBlank(myTerm) || isNotBlank(myLabel)) {
myTagList.addTag(myScheme, myTerm, myLabel);
}
pop();
}
}

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseAddOrDeleteTagsMethodBinding.java
View File

@ -214,10 +214,6 @@ abstract class BaseAddOrDeleteTagsMethodBinding extends BaseMethodBinding<Void>
return false;
}
if ((myVersionIdParamIndex != null) != (theRequest.getId() != null && theRequest.getId().hasVersionIdPart())) {
return false;
}
if (isDelete()) {
if (Constants.PARAM_DELETE.equals(theRequest.getSecondaryOperation()) == false) {
return false;

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseMethodBinding.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.rest.method;
* #L%
*/
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.io.IOException;
import java.io.Reader;
@ -66,7 +66,6 @@ import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.IDynamicSearchResourceProvider;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.SearchParameterMap;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;

59
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/BaseOutcomeReturningMethodBinding.java
View File

@ -61,8 +61,7 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
if (!theMethod.getReturnType().equals(MethodOutcome.class)) {
if (!allowVoidReturnType()) {
throw new ConfigurationException("Method " + theMethod.getName() + " in type " + theMethod.getDeclaringClass().getCanonicalName() + " is a @" + theMethodAnnotation.getSimpleName()
+ " method but it does not return " + MethodOutcome.class);
throw new ConfigurationException("Method " + theMethod.getName() + " in type " + theMethod.getDeclaringClass().getCanonicalName() + " is a @" + theMethodAnnotation.getSimpleName() + " method but it does not return " + MethodOutcome.class);
} else if (theMethod.getReturnType() == void.class) {
myReturnVoid = true;
}
@ -89,8 +88,7 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
}
@Override
public MethodOutcome invokeClient(String theResponseMimeType, Reader theResponseReader, int theResponseStatusCode, Map<String, List<String>> theHeaders) throws IOException,
BaseServerResponseException {
public MethodOutcome invokeClient(String theResponseMimeType, Reader theResponseReader, int theResponseStatusCode, Map<String, List<String>> theHeaders) throws IOException, BaseServerResponseException {
switch (theResponseStatusCode) {
case Constants.STATUS_HTTP_200_OK:
case Constants.STATUS_HTTP_201_CREATED:
@ -147,8 +145,8 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
throw new InternalErrorException("Server method returned invalid resource ID: " + response.getId().getValue());
}
}
OperationOutcome outcome = response != null ? response.getOperationOutcome():null;
OperationOutcome outcome = response != null ? response.getOperationOutcome() : null;
for (int i = theServer.getInterceptors().size() - 1; i >= 0; i--) {
IServerInterceptor next = theServer.getInterceptors().get(i);
boolean continueProcessing = next.outgoingResponse(theRequest, outcome, theRequest.getServletRequest(), theRequest.getServletResponse());
@ -156,19 +154,18 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
return;
}
}
switch (getResourceOperationType()) {
case CREATE:
if (response == null) {
throw new InternalErrorException("Method " + getMethod().getName() + " in type " + getMethod().getDeclaringClass().getCanonicalName()
+ " returned null, which is not allowed for create operation");
throw new InternalErrorException("Method " + getMethod().getName() + " in type " + getMethod().getDeclaringClass().getCanonicalName() + " returned null, which is not allowed for create operation");
}
if (response.getCreated() == null || Boolean.TRUE.equals(response.getCreated())) {
servletResponse.setStatus(Constants.STATUS_HTTP_201_CREATED);
} else {
servletResponse.setStatus(Constants.STATUS_HTTP_200_OK);
}
addLocationHeader(theRequest, servletResponse, response);
addLocationHeader(theRequest, servletResponse, response, Constants.HEADER_LOCATION);
break;
case UPDATE:
@ -178,7 +175,8 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
servletResponse.setStatus(Constants.STATUS_HTTP_201_CREATED);
}
if (response != null && response.getId() != null) {
addLocationHeader(theRequest, servletResponse, response);
addLocationHeader(theRequest, servletResponse, response, Constants.HEADER_LOCATION);
addLocationHeader(theRequest, servletResponse, response, Constants.HEADER_CONTENT_LOCATION);
}
break;
@ -226,7 +224,7 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
return myReturnVoid;
}
private void addLocationHeader(Request theRequest, HttpServletResponse theResponse, MethodOutcome response) {
private void addLocationHeader(Request theRequest, HttpServletResponse theResponse, MethodOutcome response, String headerLocation) {
StringBuilder b = new StringBuilder();
b.append(theRequest.getFhirServerBase());
b.append('/');
@ -240,31 +238,38 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
b.append("/" + Constants.PARAM_HISTORY + "/");
b.append(response.getVersionId().getValue());
}
theResponse.addHeader(Constants.HEADER_LOCATION, b.toString());
theResponse.addHeader(headerLocation, b.toString());
}
/*
* @Override public void invokeServer(RestfulServer theServer, Request theRequest, HttpServletResponse theResponse) throws BaseServerResponseException, IOException { Object[] params = new
* Object[getParameters().size()]; for (int i = 0; i < getParameters().size(); i++) { IParameter param = getParameters().get(i); if (param != null) { params[i] =
* param.translateQueryParametersIntoServerArgument(theRequest, null); } }
* @Override public void invokeServer(RestfulServer theServer, Request theRequest, HttpServletResponse theResponse)
* throws BaseServerResponseException, IOException { Object[] params = new Object[getParameters().size()]; for (int
* i = 0; i < getParameters().size(); i++) { IParameter param = getParameters().get(i); if (param != null) {
* params[i] = param.translateQueryParametersIntoServerArgument(theRequest, null); } }
*
* addParametersForServerRequest(theRequest, params);
*
* MethodOutcome response = (MethodOutcome) invokeServerMethod(getProvider(), params);
*
* if (response == null) { if (myReturnVoid == false) { throw new ConfigurationException("Method " + getMethod().getName() + " in type " + getMethod().getDeclaringClass().getCanonicalName() +
* " returned null"); } else { theResponse.setStatus(Constants.STATUS_HTTP_204_NO_CONTENT); } } else if (!myReturnVoid) { if (response.isCreated()) {
* theResponse.setStatus(Constants.STATUS_HTTP_201_CREATED); StringBuilder b = new StringBuilder(); b.append(theRequest.getFhirServerBase()); b.append('/'); b.append(getResourceName());
* b.append('/'); b.append(response.getId().getValue()); if (response.getVersionId() != null && response.getVersionId().isEmpty() == false) { b.append("/_history/");
* b.append(response.getVersionId().getValue()); } theResponse.addHeader("Location", b.toString()); } else { theResponse.setStatus(Constants.STATUS_HTTP_200_OK); } } else {
* if (response == null) { if (myReturnVoid == false) { throw new ConfigurationException("Method " +
* getMethod().getName() + " in type " + getMethod().getDeclaringClass().getCanonicalName() + " returned null"); }
* else { theResponse.setStatus(Constants.STATUS_HTTP_204_NO_CONTENT); } } else if (!myReturnVoid) { if
* (response.isCreated()) { theResponse.setStatus(Constants.STATUS_HTTP_201_CREATED); StringBuilder b = new
* StringBuilder(); b.append(theRequest.getFhirServerBase()); b.append('/'); b.append(getResourceName());
* b.append('/'); b.append(response.getId().getValue()); if (response.getVersionId() != null &&
* response.getVersionId().isEmpty() == false) { b.append("/_history/");
* b.append(response.getVersionId().getValue()); } theResponse.addHeader("Location", b.toString()); } else {
* theResponse.setStatus(Constants.STATUS_HTTP_200_OK); } } else {
* theResponse.setStatus(Constants.STATUS_HTTP_204_NO_CONTENT); }
*
* theServer.addHeadersToResponse(theResponse);
*
* Writer writer = theResponse.getWriter(); try { if (response != null) { OperationOutcome outcome = new OperationOutcome(); if (response.getOperationOutcome() != null &&
* response.getOperationOutcome().getIssue() != null) { outcome.getIssue().addAll(response.getOperationOutcome().getIssue()); } EncodingUtil encoding =
* BaseMethodBinding.determineResponseEncoding(theRequest .getServletRequest(), theRequest.getParameters()); theResponse.setContentType(encoding.getResourceContentType()); IParser parser =
* encoding.newParser(getContext()); parser.encodeResourceToWriter(outcome, writer); } } finally { writer.close(); } // getMethod().in }
* Writer writer = theResponse.getWriter(); try { if (response != null) { OperationOutcome outcome = new
* OperationOutcome(); if (response.getOperationOutcome() != null && response.getOperationOutcome().getIssue() !=
* null) { outcome.getIssue().addAll(response.getOperationOutcome().getIssue()); } EncodingUtil encoding =
* BaseMethodBinding.determineResponseEncoding(theRequest .getServletRequest(), theRequest.getParameters());
* theResponse.setContentType(encoding.getResourceContentType()); IParser parser = encoding.newParser(getContext());
* parser.encodeResourceToWriter(outcome, writer); } } finally { writer.close(); } // getMethod().in }
*/
protected abstract void addParametersForServerRequest(Request theRequest, Object[] theParams);
@ -279,7 +284,8 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
protected abstract BaseHttpClientInvocation createClientInvocation(Object[] theArgs, IResource resource);
/**
* For servers, this method will match only incoming requests that match the given operation, or which have no operation in the URL if this method returns null.
* For servers, this method will match only incoming requests that match the given operation, or which have no
* operation in the URL if this method returns null.
*/
protected abstract String getMatchingOperation();
@ -352,5 +358,4 @@ abstract class BaseOutcomeReturningMethodBinding extends BaseMethodBinding<Metho
}
}
}

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ObjectUtil.java Normal file
View File

@ -0,0 +1,15 @@
package ca.uhn.fhir.util;
public class ObjectUtil {
public static boolean equals(Object object1, Object object2) {
if (object1 == object2) {
return true;
}
if ((object1 == null) || (object2 == null)) {
return false;
}
return object1.equals(object2);
}
}

51
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java
View File

@ -26,6 +26,7 @@ import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@ -40,6 +41,7 @@ import javax.xml.validation.SchemaFactory;
import javax.xml.validation.Validator;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.w3c.dom.ls.LSInput;
import org.w3c.dom.ls.LSResourceResolver;
import org.xml.sax.SAXException;
@ -50,6 +52,7 @@ import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu.resource.OperationOutcome.Issue;
import ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
class SchemaBaseValidator implements IValidator {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SchemaBaseValidator.class);
@ -77,9 +80,9 @@ class SchemaBaseValidator implements IValidator {
MyErrorHandler handler = new MyErrorHandler(theContext);
validator.setErrorHandler(handler);
String encodedResource = theContext.getXmlEncodedResource();
// ourLog.info(new FhirContext().newXmlParser().setPrettyPrint(true).encodeBundleToString((Bundle) theContext.getResource()));
// ourLog.info(new FhirContext().newXmlParser().setPrettyPrint(true).encodeBundleToString((Bundle) theContext.getResource()));
validator.validate(new StreamSource(new StringReader(encodedResource)));
} catch (SAXException e) {
throw new ConfigurationException("Could not apply schema file", e);
@ -115,11 +118,26 @@ class SchemaBaseValidator implements IValidator {
private Source loadXml(String theVersion, String theSystemId, String theSchemaName) {
String pathToBase = "ca/uhn/fhir/model/" + theVersion + "/schema/" + theSchemaName;
ourLog.debug("Going to load resource: {}", pathToBase);
InputStream baseIs = FhirValidator.class.getClassLoader().getResourceAsStream(pathToBase);
if (baseIs == null) {
throw new ValidationFailureException("No FHIR-BASE schema found");
}
Source baseSource = new StreamSource(baseIs, theSystemId);
baseIs = new BOMInputStream(baseIs, false);
InputStreamReader baseReader = new InputStreamReader(baseIs, Charset.forName("UTF-8"));
Source baseSource = new StreamSource(baseReader, theSystemId);
// String schema;
// try {
// schema = IOUtils.toString(baseIs, Charset.forName("UTF-8"));
// } catch (IOException e) {
// throw new InternalErrorException(e);
// }
//
// ourLog.info("Schema is:\n{}", schema);
//
// Source baseSource = new StreamSource(new StringReader(schema), theSystemId);
// Source baseSource = new StreamSource(baseIs, theSystemId);
return baseSource;
}
@ -180,31 +198,16 @@ class SchemaBaseValidator implements IValidator {
input.setSystemId(theSystemId);
input.setBaseURI(theBaseURI);
String pathToBase = "ca/uhn/fhir/model/" + myVersion + "/schema/" + theSystemId;
ourLog.debug("Loading referenced schema file: " + pathToBase);
InputStream baseIs = FhirValidator.class.getClassLoader().getResourceAsStream(pathToBase);
if (baseIs == null) {
throw new ValidationFailureException("No FHIR-BASE schema found");
}
ourLog.debug("Loading schema: {}", theSystemId);
byte[] schema;
try {
schema = IOUtils.toByteArray(new InputStreamReader(baseIs, "UTF-8"));
} catch (IOException e) {
throw new ValidationFailureException("Failed to load schema " + theSystemId, e);
}
// Account for BOM in UTF-8 text (this seems to choke Java 6's built in XML reader)
int offset = 0;
if (schema[0] == (byte) 0xEF && schema[1] == (byte) 0xBB && schema[2] == (byte) 0xBF) {
offset = 3;
}
try {
input.setCharacterStream(new InputStreamReader(new ByteArrayInputStream(schema, offset, schema.length - offset), "UTF-8"));
} catch (UnsupportedEncodingException e) {
throw new ValidationFailureException("Failed to load schema " + theSystemId, e);
}
input.setByteStream(baseIs);
return input;
}

81
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagListTest.java Normal file
View File

@ -0,0 +1,81 @@
package ca.uhn.fhir.model.api;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.*;
import java.util.Arrays;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu.resource.Patient;
public class TagListTest {
private FhirContext myCtx = new FhirContext();
@Test
public void testEquals() {
TagList tagList1 = new TagList();
tagList1.addTag(null, "Dog", "Puppies");
tagList1.addTag("http://foo", "Cat", "Kittens");
TagList tagList2 = new TagList();
tagList2.addTag(null, "Dog", "Puppies");
tagList2.addTag("http://foo", "Cat", "Kittens");
assertEquals(tagList1,tagList2);
}
@Test
public void testEqualsIgnoresLabel() {
TagList tagList1 = new TagList();
tagList1.addTag(null, "Dog", "AAAA");
tagList1.addTag("http://foo", "Cat", "BBBB");
TagList tagList2 = new TagList();
tagList2.addTag(null, "Dog", "Puppies");
tagList2.addTag("http://foo", "Cat", "Kittens");
assertEquals(tagList1,tagList2);
}
@Test
public void testEqualsIgnoresOrder() {
TagList tagList1 = new TagList();
tagList1.addTag(null, "Dog", "Puppies");
tagList1.addTag("http://foo", "Cat", "Kittens");
TagList tagList2 = new TagList();
tagList2.addTag("http://foo", "Cat", "Kittens");
tagList2.addTag(null, "Dog", "Puppies");
assertEquals(tagList1,tagList2);
}
@Test
public void testPreventDuplication() {
Patient patient = new Patient();
patient.addIdentifier("urn:system", "testTagsWithCreateAndReadAndSearch");
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag(null, "Dog", "Puppies");
// Add this twice
tagList.addTag("http://foo", "Cat", "Kittens");
tagList.addTag("http://foo", "Cat", "Kittens");
patient.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tagList);
Bundle b = new Bundle();
b.addResource(patient, myCtx, "http://foo");
String encoded = myCtx.newXmlParser().encodeBundleToString(b);
assertThat(encoded, stringContainsInOrder(Arrays.asList("Cat", "Kittens")));
assertThat(encoded, not(stringContainsInOrder(Arrays.asList("Cat", "Kittens", "Cat", "Kittens"))));
}
}

159
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/ContainedResourceEncodingTest.java Normal file
View File

@ -0,0 +1,159 @@
package ca.uhn.fhir.parser;
import static org.junit.Assert.*;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu.composite.HumanNameDt;
import ca.uhn.fhir.model.dstu.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu.resource.Composition;
import ca.uhn.fhir.model.dstu.resource.Composition.Section;
import ca.uhn.fhir.model.dstu.resource.Condition;
import ca.uhn.fhir.model.dstu.resource.Patient;
import ca.uhn.fhir.model.dstu.resource.Practitioner;
import ca.uhn.fhir.model.dstu.valueset.AdministrativeGenderCodesEnum;
import ca.uhn.fhir.model.dstu.valueset.ConditionStatusEnum;
import ca.uhn.fhir.model.dstu.valueset.NameUseEnum;
import ca.uhn.fhir.model.dstu.valueset.PractitionerRoleEnum;
import ca.uhn.fhir.model.primitive.IdDt;
/**
* Initially contributed by Alexander Kley for bug #29
*/
public class ContainedResourceEncodingTest {
private static Logger logger = LoggerFactory.getLogger(ContainedResourceEncodingTest.class);
private FhirContext ctx;
private Composition comp;
private Practitioner author;
private Patient patient;
private final String patFamName1 = "FirstFamilyName";
private final String patGivName1 = "FirstGivenName";
@Before
public void initTest() {
logger.info("[initTest]");
initPatient();
initAuthor();
initComposition();
this.ctx = new FhirContext();
}
private void initComposition() {
// new ConditionList
final Condition c = new Condition();
c.setId(UUID.randomUUID().toString());
c.setNotes("This is a note");
c.setSubject(new ResourceReferenceDt(this.patient));
c.setCode(new CodeableConceptDt("mySystem", "theCode"));
c.setStatus(ConditionStatusEnum.CONFIRMED);
// new General Note Section
final Section generalNoteSection = new Section();
generalNoteSection.setElementSpecificId("Note");
generalNoteSection.setTitle("Note");
generalNoteSection.setContent(new ResourceReferenceDt(c));
// new SectionList
final List<Section> sectionList = new ArrayList<Section>();
sectionList.add(generalNoteSection);
// fill composition
this.comp = new Composition();
this.comp.addAuthor().setResource(this.author);
this.comp.setSubject(new ResourceReferenceDt(this.patient));
this.comp.setSection(sectionList);
}
private void initPatient() {
this.patient = new Patient();
this.patient.setId(new IdDt(UUID.randomUUID().toString()));
this.patient.addIdentifier().setSystem("http://example.com/fictitious-mrns").setValue("MRN001");
this.patient.setGender(AdministrativeGenderCodesEnum.M);
this.patient.addName().setUse(NameUseEnum.OFFICIAL).addFamily(this.patFamName1).addGiven(this.patGivName1);
}
private void initAuthor() {
this.author = new Practitioner();
this.author.setId(new IdDt(UUID.randomUUID().toString()));
this.author.addIdentifier().setSystem("DoctorID").setValue("4711");
this.author.addRole(PractitionerRoleEnum.DOCTOR);
this.author.setName(new HumanNameDt().addFamily("Mueller").addGiven("Klaus").addPrefix("Prof. Dr."));
}
@Test
public void testPatient() {
logger.debug("[xmlEncoding] encode resource to xml.");
/**
* This works fine, although patient instance is modifing from encoder
*/
final String expectedPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
logger.debug("[xmlEncoding] first encoding: {}", expectedPatientXml);
final String actualPatientXml = this.ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(this.patient);
// second encoding - xml is corrupt - i.e.: patient content 4 times! should be the same as after first encoding!
logger.debug("[xmlEncoding] second encoding: {}", actualPatientXml);
Assert.assertEquals(expectedPatientXml.length(), actualPatientXml.length());
Assert.assertArrayEquals(expectedPatientXml.getBytes(), actualPatientXml.getBytes());
}
@Test
public void testComposition() {
IParser parser = this.ctx.newXmlParser().setPrettyPrint(true);
assertEquals(0, this.comp.getContained().getContainedResources().size());
/**
* This doesn't works, secund encoding creates corrupt xml
*/
final String expectedCompXml = parser.encodeResourceToString(this.comp);
logger.debug("[xmlEncoding] first encoding: {}", expectedCompXml);
assertEquals(3, this.comp.getContained().getContainedResources().size());
final String actualCompXml = parser.encodeResourceToString(this.comp);
assertEquals(3, this.comp.getContained().getContainedResources().size());
// second encoding - xml could not be parsed back to compositon - i.e.: patient content 4 times! should be the same
// as after first encoding!
logger.debug("[xmlEncoding] second encoding: {}", actualCompXml);
final String thirdCompXml = parser.encodeResourceToString(this.comp);
assertEquals(3, this.comp.getContained().getContainedResources().size());
// third encoding - xml could not be parsed back to compositon i.e.: patient content 4 times! should be the same as
// afterfirst encoding!
logger.debug("[xmlEncoding] third encoding: {}", thirdCompXml);
Assert.assertEquals(expectedCompXml.length(), actualCompXml.length());
Assert.assertArrayEquals(expectedCompXml.getBytes(), actualCompXml.getBytes());
}
}

276
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java
View File

@ -28,6 +28,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.Bundle;
import ca.uhn.fhir.model.api.BundleEntry;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.annotation.Child;
@ -41,6 +42,7 @@ import ca.uhn.fhir.model.dstu.resource.Binary;
import ca.uhn.fhir.model.dstu.resource.Conformance;
import ca.uhn.fhir.model.dstu.resource.Conformance.RestResource;
import ca.uhn.fhir.model.dstu.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu.resource.ListResource;
import ca.uhn.fhir.model.dstu.resource.Observation;
import ca.uhn.fhir.model.dstu.resource.Organization;
import ca.uhn.fhir.model.dstu.resource.Patient;
@ -63,18 +65,17 @@ public class JsonParserTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserTest.class);
private static FhirContext ourCtx;
@Test
public void testEncodeNarrativeBlockInBundle() {
Patient p = new Patient();
p.addIdentifier("foo", "bar");
p.getText().setStatus(NarrativeStatusEnum.GENERATED);
p.getText().setDiv("<div>hello</div>");
Bundle b = new Bundle();
b.getTotalResults().setValue(123);
b.addEntry().setResource(p);
String out = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
ourLog.info(out);
assertThat(out, containsString("<div>hello</div>"));
@ -84,9 +85,30 @@ public class JsonParserTest {
ourLog.info(out);
// Backslashes need to be escaped because they are in a JSON value
assertThat(out, containsString("<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\">hello</xhtml:div>"));
}
@Test
public void testEncodeIds() {
Patient pt =new Patient();
pt.addIdentifier("sys", "val");
ListResource list = new ListResource();
list.setId("listId");
list.addEntry().setItem(new ResourceReferenceDt(pt));
String enc = ourCtx.newJsonParser().encodeResourceToString(list);
ourLog.info(enc);
assertThat(enc, containsString("\"id\":\"1\""));
ListResource parsed = ourCtx.newJsonParser().parseResource(ListResource.class,enc);
assertEquals(Patient.class, parsed.getEntryFirstRep().getItem().getResource().getClass());
enc = enc.replace("\"id\"", "\"_id\"");
parsed = ourCtx.newJsonParser().parseResource(ListResource.class,enc);
assertEquals(Patient.class, parsed.getEntryFirstRep().getItem().getResource().getClass());
}
@Test
public void testEncodingNullExtension() {
@ -94,19 +116,19 @@ public class JsonParserTest {
ExtensionDt extension = new ExtensionDt(false, "http://foo#bar");
p.addUndeclaredExtension(extension);
String str = ourCtx.newJsonParser().encodeResourceToString(p);
assertEquals("{\"resourceType\":\"Patient\"}", str);
extension.setValue(new StringDt());
str = ourCtx.newJsonParser().encodeResourceToString(p);
str = ourCtx.newJsonParser().encodeResourceToString(p);
assertEquals("{\"resourceType\":\"Patient\"}", str);
extension.setValue(new StringDt(""));
str = ourCtx.newJsonParser().encodeResourceToString(p);
str = ourCtx.newJsonParser().encodeResourceToString(p);
assertEquals("{\"resourceType\":\"Patient\"}", str);
}
@Test
@ -119,79 +141,77 @@ public class JsonParserTest {
assertThat(e.getMessage(), containsString("double quote"));
}
}
@Test
public void testEncodeExtensionInCompositeElement() {
Conformance c = new Conformance();
c.addRest().getSecurity().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
ourLog.info(encoded);
encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(c);
ourLog.info(encoded);
assertEquals(encoded, "{\"resourceType\":\"Conformance\",\"rest\":[{\"security\":{\"extension\":[{\"url\":\"http://foo\",\"valueString\":\"AAA\"}]}}]}");
}
@Test
public void testEncodeExtensionInPrimitiveElement() {
Conformance c = new Conformance();
c.getAcceptUnknown().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
ourLog.info(encoded);
encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(c);
ourLog.info(encoded);
assertEquals(encoded, "{\"resourceType\":\"Conformance\",\"_acceptUnknown\":[{\"extension\":[{\"url\":\"http://foo\",\"valueString\":\"AAA\"}]}]}");
// Now with a value
ourLog.info("---------------");
c = new Conformance();
c.getAcceptUnknown().setValue(true);
c.getAcceptUnknown().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
ourLog.info(encoded);
encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(c);
ourLog.info(encoded);
assertEquals(encoded, "{\"resourceType\":\"Conformance\",\"acceptUnknown\":true,\"_acceptUnknown\":[{\"extension\":[{\"url\":\"http://foo\",\"valueString\":\"AAA\"}]}]}");
}
@Test
public void testEncodeExtensionInResourceElement() {
Conformance c = new Conformance();
// c.addRest().getSecurity().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
// c.addRest().getSecurity().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
c.addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
ourLog.info(encoded);
encoded = ourCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(c);
ourLog.info(encoded);
assertEquals(encoded, "{\"resourceType\":\"Conformance\",\"extension\":[{\"url\":\"http://foo\",\"valueString\":\"AAA\"}]}");
}
@Test
public void testEncodeBinaryResource() {
Binary patient = new Binary();
patient.setContentType("foo");
patient.setContent(new byte[] {1,2,3,4});
patient.setContent(new byte[] { 1, 2, 3, 4 });
String val = ourCtx.newJsonParser().encodeResourceToString(patient);
assertEquals("{\"resourceType\":\"Binary\",\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}",val);
assertEquals("{\"resourceType\":\"Binary\",\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}", val);
}
@Test
@ -210,84 +230,69 @@ public class JsonParserTest {
" }" +
"}";
//@formatter:on
Patient res = (Patient) ourCtx.newJsonParser().parseResource(text);
String value = res.getText().getDiv().getValueAsString();
assertNull(value);
}
@Test
public void testNestedContainedResources() {
Observation A = new Observation();
A.getName().setText("A");
Observation B = new Observation();
B.getName().setText("B");
A.addRelated().setTarget(new ResourceReferenceDt(B));
Observation C = new Observation();
C.getName().setText("C");
B.addRelated().setTarget(new ResourceReferenceDt(C));
String str = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(A);
ourLog.info(str);
assertThat(str, stringContainsInOrder(Arrays.asList("\"text\":\"B\"", "\"text\":\"C\"", "\"text\":\"A\"")));
// Only one (outer) contained block
int idx0 = str.indexOf("\"contained\"");
int idx1 = str.indexOf("\"contained\"",idx0+1);
int idx1 = str.indexOf("\"contained\"", idx0 + 1);
assertNotEquals(-1, idx0);
assertEquals(-1, idx1);
Observation obs = ourCtx.newJsonParser().parseResource(Observation.class, str);
assertEquals("A",obs.getName().getText().getValue());
assertEquals("A", obs.getName().getText().getValue());
Observation obsB = (Observation) obs.getRelatedFirstRep().getTarget().getResource();
assertEquals("B",obsB.getName().getText().getValue());
assertEquals("B", obsB.getName().getText().getValue());
Observation obsC = (Observation) obsB.getRelatedFirstRep().getTarget().getResource();
assertEquals("C",obsC.getName().getText().getValue());
assertEquals("C", obsC.getName().getText().getValue());
}
@Test
public void testParseQuery() {
String msg = "{\n" +
" \"resourceType\": \"Query\",\n" +
" \"text\": {\n" +
" \"status\": \"generated\",\n" +
" \"div\": \"<div>[Put rendering here]</div>\"\n" +
" },\n" +
" \"identifier\": \"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\",\n" +
" \"parameter\": [\n" +
" {\n" +
" \"url\": \"http://hl7.org/fhir/query#_query\",\n" +
" \"valueString\": \"example\"\n" +
" }\n" +
" ]\n" +
"}";
String msg = "{\n" + " \"resourceType\": \"Query\",\n" + " \"text\": {\n" + " \"status\": \"generated\",\n" + " \"div\": \"<div>[Put rendering here]</div>\"\n" + " },\n"
+ " \"identifier\": \"urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376\",\n" + " \"parameter\": [\n" + " {\n" + " \"url\": \"http://hl7.org/fhir/query#_query\",\n"
+ " \"valueString\": \"example\"\n" + " }\n" + " ]\n" + "}";
Query query = ourCtx.newJsonParser().parseResource(Query.class, msg);
assertEquals("urn:uuid:42b253f5-fa17-40d0-8da5-44aeb4230376", query.getIdentifier().getValueAsString());
assertEquals("http://hl7.org/fhir/query#_query", query.getParameterFirstRep().getUrlAsString());
assertEquals("example", query.getParameterFirstRep().getValueAsPrimitive().getValueAsString());
}
@Test
public void testEncodeQuery() {
Query q = new Query();
ExtensionDt parameter = q.addParameter();
parameter.setUrl("http://hl7.org/fhir/query#_query").setValue(new StringDt("example"));
String val = new FhirContext().newJsonParser().encodeResourceToString(q);
ourLog.info(val);
@ -307,21 +312,21 @@ public class JsonParserTest {
ourLog.info("Expect: {}", expected);
ourLog.info("Got : {}", val);
assertEquals(expected, val);
}
@Test
public void testParseBinaryResource() {
Binary val = ourCtx.newJsonParser().parseResource(Binary.class, "{\"resourceType\":\"Binary\",\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}");
assertEquals("foo", val.getContentType());
assertArrayEquals(new byte[] {1,2,3,4}, val.getContent());
assertArrayEquals(new byte[] { 1, 2, 3, 4 }, val.getContent());
}
@Test
public void testTagList() {
//@formatter:off
String tagListStr = "{\n" +
" \"resourceType\" : \"TagList\", " +
@ -343,7 +348,7 @@ public class JsonParserTest {
" ] " +
"}";
//@formatter:on
TagList tagList = new FhirContext().newJsonParser().parseTagList(tagListStr);
assertEquals(3, tagList.size());
assertEquals("term0", tagList.get(0).getTerm());
@ -355,7 +360,7 @@ public class JsonParserTest {
assertEquals("term2", tagList.get(2).getTerm());
assertEquals("label2", tagList.get(2).getLabel());
assertEquals(null, tagList.get(2).getScheme());
/*
* Encode
*/
@ -380,28 +385,28 @@ public class JsonParserTest {
"]" +
"}";
//@formatter:on
String encoded = new FhirContext().newJsonParser().encodeTagListToString(tagList);
assertEquals(expected,encoded);
assertEquals(expected, encoded);
}
@Test
public void testEncodeBundleCategory() {
Bundle b = new Bundle();
BundleEntry e = b.addEntry();
e.setResource(new Patient());
b.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
b.addCategory("scheme", "term", "label");
String val = new FhirContext().newJsonParser().setPrettyPrint(false).encodeBundleToString(b);
ourLog.info(val);
assertThat(val, StringContains.containsString("\"category\":[{\"term\":\"term\",\"label\":\"label\",\"scheme\":\"scheme\"}]"));
b = new FhirContext().newJsonParser().parseBundle(val);
assertEquals(1,b.getEntries().size());
assertEquals(1,b.getCategories().size());
assertEquals(1, b.getEntries().size());
assertEquals(1, b.getCategories().size());
assertEquals("term", b.getCategories().get(0).getTerm());
assertEquals("label", b.getCategories().get(0).getLabel());
assertEquals("scheme", b.getCategories().get(0).getScheme());
@ -415,23 +420,23 @@ public class JsonParserTest {
Bundle b = new Bundle();
BundleEntry e = b.addEntry();
e.setResource(new Patient());
e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
String val = new FhirContext().newJsonParser().setPrettyPrint(false).encodeBundleToString(b);
e.addCategory("scheme", "term", "label");
String val = ourCtx.newJsonParser().setPrettyPrint(false).encodeBundleToString(b);
ourLog.info(val);
assertThat(val, StringContains.containsString("\"category\":[{\"term\":\"term\",\"label\":\"label\",\"scheme\":\"scheme\"}]"));
b = new FhirContext().newJsonParser().parseBundle(val);
assertEquals(1,b.getEntries().size());
assertEquals(1,b.getEntries().get(0).getCategories().size());
b = ourCtx.newJsonParser().parseBundle(val);
assertEquals(1, b.getEntries().size());
assertEquals(1, b.getEntries().get(0).getCategories().size());
assertEquals("term", b.getEntries().get(0).getCategories().get(0).getTerm());
assertEquals("label", b.getEntries().get(0).getCategories().get(0).getLabel());
assertEquals("scheme", b.getEntries().get(0).getCategories().get(0).getScheme());
assertNull(b.getEntries().get(0).getResource());
}
@Test
public void testEncodeContainedResources() throws IOException {
@ -450,7 +455,6 @@ public class JsonParserTest {
parseAndEncode("/alert.profile.json");
}
private void parseAndEncode(String name) throws IOException {
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name));
ourLog.info(msg);
@ -465,16 +469,14 @@ public class JsonParserTest {
JSON actual = JSONSerializer.toJSON(encoded.trim());
String exp = expected.toString().replace("\\r\\n", "\\n").replace("&sect;", "§");
String act = actual.toString().replace("\\r\\n","\\n");
String act = actual.toString().replace("\\r\\n", "\\n");
ourLog.info("Expected: {}", exp);
ourLog.info("Actual : {}", act);
assertEquals(exp, act);
}
@Test
public void testEncodeContainedResourcesMore() {
@ -517,8 +519,7 @@ public class JsonParserTest {
assertEquals("line1", ref.getLineFirstRep().getValue());
}
@Test
public void testEncodeDeclaredExtensionWithResourceContent() {
IParser parser = new FhirContext().newJsonParser();
@ -543,20 +544,18 @@ public class JsonParserTest {
ValueSet valueSet = new ValueSet();
valueSet.addTelecom().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
String encoded = ourCtx.newJsonParser().encodeResourceToString(valueSet);
assertThat(encoded, containsString("\"telecom\":[{\"extension\":[{\"url\":\"http://foo\",\"valueString\":\"AAA\"}]}"));
}
@Test
public void testEncodeExt() throws Exception {
ValueSet valueSet = new ValueSet();
valueSet.setId("123456");
Define define = valueSet.getDefine();
DefineConcept code = define.addConcept();
code.setCode("someCode");
@ -567,11 +566,12 @@ public class JsonParserTest {
ourLog.info(encoded);
assertThat(encoded, not(containsString("123456")));
assertEquals("{\"resourceType\":\"ValueSet\",\"define\":{\"concept\":[{\"extension\":[{\"url\":\"urn:alt\",\"valueString\":\"alt name\"}],\"code\":\"someCode\",\"display\":\"someDisplay\"}]}}", encoded);
assertEquals(
"{\"resourceType\":\"ValueSet\",\"define\":{\"concept\":[{\"extension\":[{\"url\":\"urn:alt\",\"valueString\":\"alt name\"}],\"code\":\"someCode\",\"display\":\"someDisplay\"}]}}",
encoded);
}
@Test
public void testEncodeExtensionWithResourceContent() {
IParser parser = new FhirContext().newJsonParser();
@ -593,7 +593,6 @@ public class JsonParserTest {
}
@Test
public void testEncodeInvalidChildGoodException() {
Observation obs = new Observation();
@ -607,7 +606,7 @@ public class JsonParserTest {
assertThat(e.getMessage(), StringContains.containsString("DecimalDt"));
}
}
@Test
public void testEncodeResourceRef() throws DataFormatException {
@ -662,7 +661,7 @@ public class JsonParserTest {
String enc = new FhirContext().newJsonParser().encodeResourceToString(patient);
ourLog.info(enc);
assertEquals("{\"resourceType\":\"Patient\",\"name\":[{\"extension\":[{\"url\":\"http://examples.com#givenext\",\"valueString\":\"Hello\"}],\"family\":[\"Shmoe\"],\"given\":[\"Joe\"]}]}", enc);
IParser newJsonParser = new FhirContext().newJsonParser();
StringReader reader = new StringReader(enc);
Patient parsed = newJsonParser.parseResource(Patient.class, reader);
@ -753,7 +752,7 @@ public class JsonParserTest {
assertEquals("http://scheme", bundle.getCategories().get(0).getScheme());
assertEquals("http://term", bundle.getCategories().get(0).getTerm());
assertEquals("label", bundle.getCategories().get(0).getLabel());
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(bundle);
ourLog.info(encoded);
@ -768,9 +767,9 @@ public class JsonParserTest {
DiagnosticReport res = (DiagnosticReport) entry.getResource();
assertEquals("Complete Blood Count", res.getName().getText().getValue());
assertThat(entry.getSummary().getValueAsString(), containsString("CBC Report for Wile"));
}
@Test
@ -790,10 +789,9 @@ public class JsonParserTest {
BundleEntry deletedEntry = bundle.getEntries().get(3);
assertEquals("2014-06-20T20:15:49Z", deletedEntry.getDeletedAt().getValueAsString());
}
/**
* This sample has extra elements in <searchParam> that are not actually a part of the spec any more..
*/
@ -828,10 +826,10 @@ public class JsonParserTest {
public static void beforeClass() {
ourCtx = new FhirContext();
}
@Test
public void testParseBundleDeletedEntry() {
//@formatter:off
String bundleString =
"{" +
@ -851,7 +849,7 @@ public class JsonParserTest {
"]" +
"}";
//@formatter:on
Bundle bundle = ourCtx.newJsonParser().parseBundle(bundleString);
BundleEntry entry = bundle.getEntries().get(0);
assertEquals("2012-05-29T23:45:32+00:00", entry.getDeletedAt().getValueAsString());
@ -859,19 +857,19 @@ public class JsonParserTest {
assertEquals("1", entry.getResource().getId().getIdPart());
assertEquals("2", entry.getResource().getId().getVersionIdPart());
assertEquals(new InstantDt("2012-05-29T23:45:32+00:00"), entry.getResource().getResourceMetadata().get(ResourceMetadataKeyEnum.DELETED_AT));
// Now encode
ourLog.info(ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(bundle));
String encoded = ourCtx.newJsonParser().encodeBundleToString(bundle);
assertEquals(bundleString,encoded);
assertEquals(bundleString, encoded);
}
@Test
public void testEncodeBundle() throws InterruptedException {
Bundle b= new Bundle();
Bundle b = new Bundle();
InstantDt pub = InstantDt.withCurrentTime();
b.setPublished(pub);
Thread.sleep(2);
@ -882,35 +880,34 @@ public class JsonParserTest {
entry.getId().setValue("1");
entry.setResource(p1);
entry.getSummary().setValueAsString("this is the summary");
Patient p2 = new Patient();
p2.addName().addFamily("Family2");
entry = b.addEntry();
entry.getId().setValue("2");
entry.setLinkAlternate(new StringDt("http://foo/bar"));
entry.setResource(p2);
BundleEntry deletedEntry = b.addEntry();
deletedEntry.setId(new IdDt("Patient/3"));
InstantDt nowDt = InstantDt.withCurrentTime();
deletedEntry.setDeleted(nowDt);
String bundleString = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
ourLog.info(bundleString);
List<String> strings = new ArrayList<String>();
strings.addAll(Arrays.asList("\"published\":\""+pub.getValueAsString()+"\""));
strings.addAll(Arrays.asList("\"published\":\"" + pub.getValueAsString() + "\""));
strings.addAll(Arrays.asList("\"id\":\"1\""));
strings.addAll(Arrays.asList("this is the summary"));
strings.addAll(Arrays.asList("\"id\":\"2\"", "\"rel\":\"alternate\"", "\"href\":\"http://foo/bar\""));
strings.addAll(Arrays.asList("\"deleted\":\""+nowDt.getValueAsString()+"\"", "\"id\":\"Patient/3\""));
strings.addAll(Arrays.asList("\"deleted\":\"" + nowDt.getValueAsString() + "\"", "\"id\":\"Patient/3\""));
assertThat(bundleString, StringContainsInOrder.stringContainsInOrder(strings));
b.getEntries().remove(2);
bundleString = ourCtx.newJsonParser().setPrettyPrint(true).encodeBundleToString(b);
assertThat(bundleString, not(containsString("deleted")));
}
@Test
@ -956,7 +953,7 @@ public class JsonParserTest {
String encoded = jsonParser.encodeResourceToString(obs);
ourLog.info(encoded);
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.json"));
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.json"), Charset.forName("UTF-8"));
JSON expected = JSONSerializer.toJSON(jsonString);
JSON actual = JSONSerializer.toJSON(encoded.trim());
@ -964,7 +961,7 @@ public class JsonParserTest {
// The encoded escapes quote marks using XML escaping instead of JSON escaping, which is probably nicer anyhow...
String exp = expected.toString().replace("\\\"Jim\\\"", "&quot;Jim&quot;");
String act = actual.toString();
ourLog.info("Expected: {}", exp);
ourLog.info("Actual : {}", act);
assertEquals(exp, act);
@ -978,11 +975,10 @@ public class JsonParserTest {
public void testParseWithIncorrectReference() throws IOException {
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.json"));
jsonString = jsonString.replace("\"reference\"", "\"resource\"");
Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class,jsonString);
Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, jsonString);
assertEquals("Organization/1", parsed.getManagingOrganization().getReference().getValue());
}
@Test
public void testSimpleResourceEncodeWithCustomType() throws IOException {
@ -1003,7 +999,7 @@ public class JsonParserTest {
String encoded = jsonParser.encodeResourceToString(obs);
ourLog.info(encoded);
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.json"));
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.json"), Charset.forName("UTF-8"));
JSON expected = JSONSerializer.toJSON(jsonString);
JSON actual = JSONSerializer.toJSON(encoded.trim());
@ -1011,7 +1007,7 @@ public class JsonParserTest {
// The encoded escapes quote marks using XML escaping instead of JSON escaping, which is probably nicer anyhow...
String exp = expected.toString().replace("\\\"Jim\\\"", "&quot;Jim&quot;");
String act = actual.toString();
ourLog.info("Expected: {}", exp);
ourLog.info("Actual : {}", act);
assertEquals(exp, act);

23
hapi-fhir-base/src/test/java/ca/uhn/fhir/parser/XmlParserTest.java
View File

@ -73,10 +73,15 @@ public class XmlParserTest {
private static FhirContext ourCtx;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserTest.class);
@BeforeClass
public static void beforeClass2() {
System.setProperty("file.encoding", "ISO-8859-1");
}
/**
* Thanks to Alexander Kley!
*/
// @Test
@Test
public void testParseContainedBinaryResource() {
byte[] bin = new byte[] {0,1,2,3,4};
final Binary binary = new Binary("PatientConsent", bin);
@ -199,7 +204,7 @@ public class XmlParserTest {
Bundle b = new Bundle();
BundleEntry e = b.addEntry();
e.setResource(new Patient());
e.addCategory().setLabel("label").setTerm("term").setScheme("scheme");
e.addCategory("scheme", "term", "label");
String val = ourCtx.newXmlParser().setPrettyPrint(true).encodeBundleToString(b);
ourLog.info(val);
@ -696,7 +701,7 @@ public class XmlParserTest {
IParser p = ourCtx.newXmlParser();
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/observation-example-eeg.xml"));
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/observation-example-eeg.xml"), Charset.forName("UTF-8"));
IResource resource = p.parseResource(string);
String result = p.encodeResourceToString(resource);
@ -709,7 +714,7 @@ public class XmlParserTest {
// Use new context here to ensure List isn't already loaded
IParser p = new FhirContext().newXmlParser();
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/feed-with-list.xml"));
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/feed-with-list.xml"), Charset.forName("UTF-8"));
Bundle bundle = p.parseBundle(string);
ListResource res = (ListResource) bundle.toListOfResources().get(2);
@ -722,7 +727,7 @@ public class XmlParserTest {
IParser p = ourCtx.newXmlParser();
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/patient-example-dicom.xml"));
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/patient-example-dicom.xml"), Charset.forName("UTF-8"));
IResource resource = p.parseResource(string);
String result = p.encodeResourceToString(resource);
@ -730,7 +735,7 @@ public class XmlParserTest {
// Nothing
string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/patient-example-us-extensions.xml"));
string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/patient-example-us-extensions.xml"), Charset.forName("UTF-8"));
resource = p.parseResource(string);
result = p.encodeResourceToString(resource);
@ -743,7 +748,7 @@ public class XmlParserTest {
IParser p = ourCtx.newXmlParser();
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/questionnaire-example.xml"));
String string = IOUtils.toString(XmlParserTest.class.getResourceAsStream("/questionnaire-example.xml"), Charset.forName("UTF-8"));
IResource resource = p.parseResource(string);
String result = p.encodeResourceToString(resource);
@ -1188,7 +1193,7 @@ public class XmlParserTest {
String encoded = jsonParser.encodeResourceToString(obs);
ourLog.info(encoded);
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.xml"));
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.xml"), Charset.forName("UTF-8"));
String expected = (jsonString);
String actual = (encoded.trim());
@ -1220,7 +1225,7 @@ public class XmlParserTest {
String encoded = jsonParser.encodeResourceToString(obs);
ourLog.info(encoded);
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.xml"));
String jsonString = IOUtils.toString(JsonParser.class.getResourceAsStream("/example-patient-general.xml"), Charset.forName("UTF-8"));
String expected = (jsonString);
String actual = (encoded.trim());

12
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/client/ClientTest.java
View File

@ -521,7 +521,9 @@ public class ClientTest {
ITestClient client = ctx.newRestfulClient(ITestClient.class, "http://foo");
client.getHistoryPatientInstance(new IdDt("111"), new InstantDt("2012-01-02T00:01:02"), new IntegerDt(12));
assertEquals("http://foo/Patient/111/_history?_since=2012-01-02T00%3A01%3A02&_count=12", capt.getAllValues().get(0).getURI().toString());
assertThat(capt.getAllValues().get(0).getURI().toString(), containsString("http://foo/Patient/111/_history?"));
assertThat(capt.getAllValues().get(0).getURI().toString(), containsString("_since=2012-01-02T00%3A01%3A02"));
assertThat(capt.getAllValues().get(0).getURI().toString(), containsString("_count=12"));
String expectedDateString = new InstantDt(new InstantDt("2012-01-02T00:01:02").getValue()).getValueAsString(); // ensures
// the
@ -529,7 +531,9 @@ public class ClientTest {
// timezone
expectedDateString = expectedDateString.replace(":", "%3A");
client.getHistoryPatientInstance(new IdDt("111"), new InstantDt("2012-01-02T00:01:02").getValue(), new IntegerDt(12).getValue());
assertEquals("http://foo/Patient/111/_history?_since=" + expectedDateString + "&_count=12", capt.getAllValues().get(1).getURI().toString());
assertThat(capt.getAllValues().get(1).getURI().toString(), containsString("http://foo/Patient/111/_history?"));
assertThat(capt.getAllValues().get(1).getURI().toString(), containsString("_since="+expectedDateString));
assertThat(capt.getAllValues().get(1).getURI().toString(), containsString("_count=12"));
client.getHistoryPatientInstance(new IdDt("111"), null, new IntegerDt(12));
assertEquals("http://foo/Patient/111/_history?_count=12", capt.getAllValues().get(2).getURI().toString());
@ -538,10 +542,10 @@ public class ClientTest {
assertEquals("http://foo/Patient/111/_history?_since=2012-01-02T00%3A01%3A02", capt.getAllValues().get(3).getURI().toString());
client.getHistoryPatientInstance(new IdDt("111"), new InstantDt(), new IntegerDt(12));
assertEquals("http://foo/Patient/111/_history?_count=12", capt.getAllValues().get(2).getURI().toString());
assertEquals("http://foo/Patient/111/_history?_count=12", capt.getAllValues().get(4).getURI().toString());
client.getHistoryPatientInstance(new IdDt("111"), new InstantDt("2012-01-02T00:01:02"), new IntegerDt());
assertEquals("http://foo/Patient/111/_history?_since=2012-01-02T00%3A01%3A02", capt.getAllValues().get(3).getURI().toString());
assertEquals("http://foo/Patient/111/_history?_since=2012-01-02T00%3A01%3A02", capt.getAllValues().get(5).getURI().toString());
}

3
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/DynamicSearchTest.java
View File

@ -1,7 +1,6 @@
package ca.uhn.fhir.rest.server;
import static org.apache.commons.lang.StringUtils.*;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import java.util.ArrayList;
import java.util.List;

10
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/IncludeTest.java
View File

@ -1,9 +1,11 @@
package ca.uhn.fhir.rest.server;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.concurrent.TimeUnit;
@ -205,8 +207,12 @@ public class IncludeTest {
Patient p = bundle.getResources(Patient.class).get(0);
assertEquals(2, p.getName().size());
assertEquals("Hello", p.getId().getIdPart());
assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
assertEquals("bar", p.getName().get(1).getFamilyFirstRep().getValue());
Set<String> values = new HashSet<String>();
values.add( p.getName().get(0).getFamilyFirstRep().getValue());
values.add( p.getName().get(1).getFamilyFirstRep().getValue());
assertThat(values, containsInAnyOrder("foo", "bar"));
}
@Test

73
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/TagsServerTest.java
View File

@ -1,11 +1,12 @@
package ca.uhn.fhir.rest.server;
import static org.apache.commons.lang.StringUtils.*;
import static org.junit.Assert.*;
import static org.apache.commons.lang.StringUtils.defaultString;
import static org.junit.Assert.assertEquals;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
@ -33,7 +34,6 @@ import ca.uhn.fhir.rest.annotation.DeleteTags;
import ca.uhn.fhir.rest.annotation.GetTags;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.TagListParam;
import ca.uhn.fhir.rest.annotation.VersionIdParam;
import ca.uhn.fhir.util.PortUtil;
/**
@ -94,17 +94,6 @@ public class TagsServerTest {
assertEquals(tagList, ourLastTagList);
}
@Test
public void testEquals() {
TagList list1 = ourProvider.getAllTagsPatient();
TagList list2 = ourProvider.getAllTagsPatient();
assertEquals(list1, list2);
list1 = ourProvider.getAllTagsPatient();
list2 = ourProvider.getAllTagsPatient();
list2.get(0).setTerm("!!!!!");
assertNotEquals(list1, list2);
}
@Test
public void testGetAllTags() throws Exception {
@ -134,8 +123,10 @@ public class TagsServerTest {
assertEquals(200, status.getStatusLine().getStatusCode());
TagList actual = ourCtx.newXmlParser().parseTagList(responseContent);
TagList expected = ourProvider.getAllTags();
expected.get(0).setTerm("Patient");
TagList expected = new TagList();
expected.addTag(null, "Patient", "DogLabel");
expected.addTag("http://cats", "AllCat", "CatLabel");
assertEquals(expected, actual);
}
@ -152,8 +143,10 @@ public class TagsServerTest {
assertEquals(200, status.getStatusLine().getStatusCode());
TagList actual = ourCtx.newXmlParser().parseTagList(responseContent);
TagList expected = ourProvider.getAllTags();
expected.get(0).setTerm("Patient111");
TagList expected = new TagList();
expected.addTag(null, "Patient111", "DogLabel");
expected.addTag("http://cats", "AllCat", "CatLabel");
assertEquals(expected, actual);
}
@ -170,8 +163,9 @@ public class TagsServerTest {
assertEquals(200, status.getStatusLine().getStatusCode());
TagList actual = ourCtx.newXmlParser().parseTagList(responseContent);
TagList expected = ourProvider.getAllTags();
expected.get(0).setTerm("Patient111222");
TagList expected = new TagList();
expected.addTag(null, "Patient111222", "DogLabel");
expected.addTag("http://cats", "AllCat", "CatLabel");
assertEquals(expected, actual);
}
@ -188,8 +182,9 @@ public class TagsServerTest {
assertEquals(200, status.getStatusLine().getStatusCode());
TagList actual = ourCtx.newXmlParser().parseTagList(responseContent);
TagList expected = ourProvider.getAllTags();
expected.get(0).setTerm("Patient111222");
TagList expected = new TagList();
expected.addTag(null, "Patient111222", "DogLabel");
expected.addTag("http://cats", "AllCat", "CatLabel");
assertEquals(expected, actual);
}
@ -261,15 +256,9 @@ public class TagsServerTest {
public static class DummyProvider {
@AddTags(type = Patient.class)
public void addTagsPatient(@IdParam IdDt theId, @VersionIdParam IdDt theVersion, @TagListParam TagList theTagList) {
ourLastOutcome = "add" + theId.getIdPart() + theVersion.getVersionIdPart();
ourLastTagList=theTagList;
}
@AddTags(type = Patient.class)
public void addTagsPatient(@IdParam IdDt theId, @TagListParam TagList theTagList) {
ourLastOutcome = "add" + theId.getIdPart();
ourLastOutcome = "add" + theId.getIdPart() + StringUtils.defaultString(theId.getVersionIdPart());
ourLastTagList=theTagList;
}
@ -297,13 +286,13 @@ public class TagsServerTest {
return tagList;
}
@GetTags(type = Patient.class)
public TagList getAllTagsPatientIdVersion(@IdParam IdDt theId, @VersionIdParam IdDt theVersion) {
TagList tagList = new TagList();
tagList.add(new Tag((String) null, "Patient" + theId.getIdPart() + theVersion.getVersionIdPart(), "DogLabel"));
tagList.add(new Tag("http://cats", "AllCat", "CatLabel"));
return tagList;
}
// @GetTags(type = Patient.class)
// public TagList getAllTagsPatientIdVersion(@IdParam IdDt theId, @VersionIdParam IdDt theVersion) {
// TagList tagList = new TagList();
// tagList.add(new Tag((String) null, "Patient" + theId.getIdPart() + theVersion.getVersionIdPart(), "DogLabel"));
// tagList.add(new Tag("http://cats", "AllCat", "CatLabel"));
// return tagList;
// }
@GetTags(type = Observation.class)
public TagList getAllTagsObservationIdVersion(@IdParam IdDt theId) {
@ -313,15 +302,15 @@ public class TagsServerTest {
return tagList;
}
@DeleteTags(type = Patient.class)
public void RemoveTagsPatient(@IdParam IdDt theId, @VersionIdParam IdDt theVersion, @TagListParam TagList theTagList) {
ourLastOutcome = "Remove" + theId.getIdPart() + theVersion.getVersionIdPart();
ourLastTagList=theTagList;
}
// @DeleteTags(type = Patient.class)
// public void RemoveTagsPatient(@IdParam IdDt theId, @VersionIdParam IdDt theVersion, @TagListParam TagList theTagList) {
// ourLastOutcome = "Remove" + theId.getIdPart() + theVersion.getVersionIdPart();
// ourLastTagList=theTagList;
// }
@DeleteTags(type = Patient.class)
public void RemoveTagsPatient(@IdParam IdDt theId, @TagListParam TagList theTagList) {
ourLastOutcome = "Remove" + theId.getIdPart();
ourLastOutcome = "Remove" + theId.getIdPart()+StringUtils.defaultString(theId.getVersionIdPart());
ourLastTagList=theTagList;
}

51
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/server/UpdateTest.java
View File

@ -69,6 +69,7 @@ public class UpdateTest {
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals("http://localhost:" + ourPort + "/Patient/001/_history/002", status.getFirstHeader("location").getValue());
assertEquals("http://localhost:" + ourPort + "/Patient/001/_history/002", status.getFirstHeader("content-location").getValue());
}
@ -141,23 +142,25 @@ public class UpdateTest {
dr.addCodedDiagnosis().addCoding().setCode("AAA");
HttpPut httpPost = new HttpPut("http://localhost:" + ourPort + "/DiagnosticReport/001");
httpPost.addHeader("Category", "Dog, Cat");
httpPost.addHeader("Category", "Dog; scheme=\"urn:animals\", Cat; scheme=\"urn:animals\"");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse status = ourClient.execute(httpPost);
assertEquals(2, ourReportProvider.getLastTags().size());
assertEquals(new Tag("Dog"), ourReportProvider.getLastTags().get(0));
assertEquals(new Tag("Cat"), ourReportProvider.getLastTags().get(1));
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(2, ourReportProvider.getLastTags().size());
assertEquals(new Tag("urn:animals", "Dog"), ourReportProvider.getLastTags().get(0));
assertEquals(new Tag("urn:animals", "Cat"), ourReportProvider.getLastTags().get(1));
httpPost = new HttpPut("http://localhost:" + ourPort + "/DiagnosticReport/001");
httpPost.addHeader("Category", "Dog; label=\"aa\", Cat; label=\"bb\"");
httpPost.addHeader("Category", "Dog; label=\"aa\"; scheme=\"urn:animals\", Cat; label=\"bb\"; scheme=\"urn:animals\"");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
status = ourClient.execute(httpPost);
assertEquals(2, ourReportProvider.getLastTags().size());
assertEquals(new Tag((String) null, "Dog", "aa"), ourReportProvider.getLastTags().get(0));
assertEquals(new Tag((String) null, "Cat", "bb"), ourReportProvider.getLastTags().get(1));
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(2, ourReportProvider.getLastTags().size());
assertEquals(new Tag("urn:animals", "Dog", "aa"), ourReportProvider.getLastTags().get(0));
assertEquals(new Tag("urn:animals", "Cat", "bb"), ourReportProvider.getLastTags().get(1));
}
@Test
@ -167,13 +170,14 @@ public class UpdateTest {
dr.addCodedDiagnosis().addCoding().setCode("AAA");
HttpPut httpPost = new HttpPut("http://localhost:" + ourPort + "/DiagnosticReport/001");
httpPost.addHeader("Category", "Dog");
httpPost.addHeader("Category", "Dog; scheme=\"animals\"");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse status = ourClient.execute(httpPost);
assertEquals(1, ourReportProvider.getLastTags().size());
assertEquals(new Tag("Dog"), ourReportProvider.getLastTags().get(0));
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(1, ourReportProvider.getLastTags().size());
assertEquals(new Tag("animals", "Dog"), ourReportProvider.getLastTags().get(0));
}
@Test
@ -186,17 +190,19 @@ public class UpdateTest {
httpPost.addHeader("Category", "Dog; scheme=\"http://foo\"");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse status = ourClient.execute(httpPost);
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(1, ourReportProvider.getLastTags().size());
assertEquals(new Tag("http://foo", "Dog", null), ourReportProvider.getLastTags().get(0));
IOUtils.closeQuietly(status.getEntity().getContent());
httpPost = new HttpPut("http://localhost:" + ourPort + "/DiagnosticReport/001");
httpPost.addHeader("Category", "Dog; scheme=\"http://foo\";");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
ourClient.execute(httpPost);
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(1, ourReportProvider.getLastTags().size());
assertEquals(new Tag("http://foo", "Dog", null), ourReportProvider.getLastTags().get(0));
IOUtils.closeQuietly(status.getEntity().getContent());
}
@ -218,9 +224,10 @@ public class UpdateTest {
httpPost.addHeader("Category", "Dog; scheme=\"http://foo\"; label=\"aaaa\"; ");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(dr), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
status=ourClient.execute(httpPost);
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(1, ourReportProvider.getLastTags().size());
assertEquals(new Tag("http://foo", "Dog", "aaaa"), ourReportProvider.getLastTags().get(0));
IOUtils.closeQuietly(status.getEntity().getContent());
}
@ -235,6 +242,7 @@ public class UpdateTest {
httpPut.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
HttpResponse status = ourClient.execute(httpPut);
IOUtils.closeQuietly(status.getEntity().getContent());
// String responseContent =
// IOUtils.toString(status.getEntity().getContent());
@ -242,7 +250,6 @@ public class UpdateTest {
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals("http://localhost:" + ourPort + "/DiagnosticReport/001/_history/002", status.getFirstHeader("Location").getValue());
IOUtils.closeQuietly(status.getEntity().getContent());
}
@ -257,10 +264,11 @@ public class UpdateTest {
httpPut.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse status = ourClient.execute(httpPut);
assertEquals(400, status.getStatusLine().getStatusCode());
String responseContent = IOUtils.toString(status.getEntity().getContent());
ourLog.info("Response was:\n{}", responseContent);
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(400, status.getStatusLine().getStatusCode());
ourLog.info("Response was:\n{}", responseContent);
}
@ -289,9 +297,11 @@ public class UpdateTest {
HttpPut httpPost = new HttpPut("http://localhost:" + ourPort + "/Organization/001");
httpPost.setEntity(new StringEntity(new FhirContext().newXmlParser().encodeResourceToString(patient), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse response = ourClient.execute(httpPost);
assertEquals(200, response.getStatusLine().getStatusCode());
response.close();
CloseableHttpResponse status = ourClient.execute(httpPost);
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
status.close();
}
@ -376,6 +386,7 @@ public class UpdateTest {
return Observation.class;
}
@SuppressWarnings("unused")
@Update()
public MethodOutcome updateDiagnosticReportWithVersion(@IdParam IdDt theId, @ResourceParam DiagnosticOrder thePatient) {
/*

52
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDao.java
View File

@ -92,6 +92,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ObjectUtil;
@Transactional(propagation = Propagation.REQUIRED)
public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements IFhirResourceDao<T> {
@ -117,7 +118,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
if (next.getTag().getScheme().equals(theScheme) && next.getTag().getTerm().equals(theTerm)) {
if (ObjectUtil.equals(next.getTag().getScheme(), theScheme) && ObjectUtil.equals(next.getTag().getTerm(), theTerm)) {
return;
}
}
@ -141,7 +142,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
if (theResource.getId().isEmpty() == false) {
if (isValidPid(theResource.getId())) {
throw new UnprocessableEntityException("This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
throw new UnprocessableEntityException(
"This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
}
createForcedIdIfNeeded(entity, theResource.getId());
@ -229,7 +231,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
final T current = currentTmp;
String querySring = "SELECT count(h) FROM ResourceHistoryTable h " + "WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE" + " AND h.myUpdated < :END" + (theSince != null ? " AND h.myUpdated >= :SINCE" : "");
String querySring = "SELECT count(h) FROM ResourceHistoryTable h " + "WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE" + " AND h.myUpdated < :END"
+ (theSince != null ? " AND h.myUpdated >= :SINCE" : "");
TypedQuery<Long> countQuery = myEntityManager.createQuery(querySring, Long.class);
countQuery.setParameter("PID", translateForcedIdToPid(theId));
countQuery.setParameter("RESTYPE", resourceType);
@ -267,8 +270,9 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
retVal.add(current);
}
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery("SELECT h FROM ResourceHistoryTable h WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE AND h.myUpdated < :END " + (theSince != null ? " AND h.myUpdated >= :SINCE" : "")
+ " ORDER BY h.myUpdated ASC", ResourceHistoryTable.class);
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(
"SELECT h FROM ResourceHistoryTable h WHERE h.myResourceId = :PID AND h.myResourceType = :RESTYPE AND h.myUpdated < :END "
+ (theSince != null ? " AND h.myUpdated >= :SINCE" : "") + " ORDER BY h.myUpdated ASC", ResourceHistoryTable.class);
q.setParameter("PID", translateForcedIdToPid(theId));
q.setParameter("RESTYPE", resourceType);
q.setParameter("END", end.getValue(), TemporalType.TIMESTAMP);
@ -317,7 +321,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
throw new ConfigurationException("Unknown search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "]");
}
if (sp.getParamType() != SearchParamTypeEnum.TOKEN) {
throw new ConfigurationException("Search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "] is not a token type, only token is supported");
throw new ConfigurationException("Search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName
+ "] is not a token type, only token is supported");
}
}
@ -353,10 +358,11 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
entity = null;
}
}
if (entity == null) {
if (theId.hasVersionIdPart()) {
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery("SELECT t from ResourceHistoryTable t WHERE t.myResourceId = :RID AND t.myResourceType = :RTYP AND t.myResourceVersion = :RVER", ResourceHistoryTable.class);
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(
"SELECT t from ResourceHistoryTable t WHERE t.myResourceId = :RID AND t.myResourceType = :RTYP AND t.myResourceVersion = :RVER", ResourceHistoryTable.class);
q.setParameter("RID", pid);
q.setParameter("RTYP", myResourceName);
q.setParameter("RVER", theId.getVersionIdPartAsLong());
@ -365,10 +371,10 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
if (entity == null) {
throw new ResourceNotFoundException(theId);
}
}
}
validateGivenIdIsAppropriateToRetrieveResource(theId, entity);
validateResourceType(entity);
return entity;
@ -532,7 +538,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
if (previouslyLoadedPids.size() >= getConfig().getIncludeLimit()) {
OperationOutcome oo = new OperationOutcome();
oo.addIssue().setSeverity(IssueSeverityEnum.WARNING).setDetails("Not all _include resources were actually included as the request surpassed the limit of " + getConfig().getIncludeLimit() + " resources");
oo.addIssue().setSeverity(IssueSeverityEnum.WARNING)
.setDetails("Not all _include resources were actually included as the request surpassed the limit of " + getConfig().getIncludeLimit() + " resources");
retVal.add(0, oo);
}
}
@ -704,8 +711,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
/**
* If set, the given param will be treated as a secondary primary key, and multiple resources will not be able to
* share the same value.
* If set, the given param will be treated as a secondary primary key, and multiple resources will not be able to share the same value.
*/
public void setSecondaryPrimaryKeyParamName(String theSecondaryPrimaryKeyParamName) {
mySecondaryPrimaryKeyParamName = theSecondaryPrimaryKeyParamName;
@ -728,7 +734,7 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
if (theId.hasVersionIdPart() && theId.getVersionIdPartAsLong().longValue() != entity.getVersion()) {
throw new InvalidRequestException("Trying to update " + theId + " but this is not the current version");
}
ResourceTable savedEntity = updateEntity(theResource, entity, true, false);
notifyWriteCompleted();
@ -1294,7 +1300,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
return p;
}
private Predicate createPredicateString(IQueryParameterType theParameter, String theParamName, CriteriaBuilder theBuilder, From<ResourceIndexedSearchParamString, ResourceIndexedSearchParamString> theFrom) {
private Predicate createPredicateString(IQueryParameterType theParameter, String theParamName, CriteriaBuilder theBuilder,
From<ResourceIndexedSearchParamString, ResourceIndexedSearchParamString> theFrom) {
String rawSearchTerm;
if (theParameter instanceof TokenParam) {
TokenParam id = (TokenParam) theParameter;
@ -1313,7 +1320,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
if (rawSearchTerm.length() > ResourceIndexedSearchParamString.MAX_LENGTH) {
throw new InvalidRequestException("Parameter[" + theParamName + "] has length (" + rawSearchTerm.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamString.MAX_LENGTH + "): " + rawSearchTerm);
throw new InvalidRequestException("Parameter[" + theParamName + "] has length (" + rawSearchTerm.length() + ") that is longer than maximum allowed ("
+ ResourceIndexedSearchParamString.MAX_LENGTH + "): " + rawSearchTerm);
}
String likeExpression = normalizeString(rawSearchTerm);
@ -1327,7 +1335,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
return singleCode;
}
private Predicate createPredicateToken(IQueryParameterType theParameter, String theParamName, CriteriaBuilder theBuilder, From<ResourceIndexedSearchParamToken, ResourceIndexedSearchParamToken> theFrom) {
private Predicate createPredicateToken(IQueryParameterType theParameter, String theParamName, CriteriaBuilder theBuilder,
From<ResourceIndexedSearchParamToken, ResourceIndexedSearchParamToken> theFrom) {
String code;
String system;
if (theParameter instanceof TokenParam) {
@ -1347,10 +1356,12 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
}
if (system != null && system.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
throw new InvalidRequestException("Parameter[" + theParamName + "] has system (" + system.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH + "): " + system);
throw new InvalidRequestException("Parameter[" + theParamName + "] has system (" + system.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH
+ "): " + system);
}
if (code != null && code.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) {
throw new InvalidRequestException("Parameter[" + theParamName + "] has code (" + code.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH + "): " + code);
throw new InvalidRequestException("Parameter[" + theParamName + "] has code (" + code.length() + ") that is longer than maximum allowed (" + ResourceIndexedSearchParamToken.MAX_LENGTH
+ "): " + code);
}
ArrayList<Predicate> singleCodePredicates = (new ArrayList<Predicate>());
@ -1499,7 +1510,8 @@ public class FhirResourceDao<T extends IResource> extends BaseFhirDao implements
private void validateResourceType(BaseHasResource entity) {
if (!myResourceName.equals(entity.getResourceType())) {
throw new ResourceNotFoundException("Resource with ID " + entity.getIdDt().getIdPart() + " exists but it is not of type " + myResourceName + ", found resource of type " + entity.getResourceType());
throw new ResourceNotFoundException("Resource with ID " + entity.getIdDt().getIdPart() + " exists but it is not of type " + myResourceName + ", found resource of type "
+ entity.getResourceType());
}
}

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

@ -1189,14 +1189,17 @@ public class FhirResourceDaoTest {
patient.addName().addFamily("Tester").addGiven("Joe");
TagList tagList = new TagList();
tagList.addTag(null, "Dog", "Puppies");
// Add this twice
tagList.addTag("http://foo", "Cat", "Kittens");
tagList.addTag("http://foo", "Cat", "Kittens");
patient.getResourceMetadata().put(ResourceMetadataKeyEnum.TAG_LIST, tagList);
MethodOutcome outcome = ourPatientDao.create(patient);
assertNotNull(outcome.getId());
assertFalse(outcome.getId().isEmpty());
IdDt patientId = outcome.getId();
assertNotNull(patientId);
assertFalse(patientId.isEmpty());
Patient retrieved = ourPatientDao.read(outcome.getId());
Patient retrieved = ourPatientDao.read(patientId);
TagList published = (TagList) retrieved.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
assertEquals(2, published.size());
assertEquals("Dog", published.get(0).getTerm());
@ -1217,6 +1220,23 @@ public class FhirResourceDaoTest {
assertEquals("Kittens", published.get(1).getLabel());
assertEquals("http://foo", published.get(1).getScheme());
ourPatientDao.addTag(patientId, "http://foo", "Cat", "Kittens");
ourPatientDao.addTag(patientId, "http://foo", "Cow", "Calves");
retrieved = ourPatientDao.read(patientId);
published = (TagList) retrieved.getResourceMetadata().get(ResourceMetadataKeyEnum.TAG_LIST);
assertEquals(3, published.size());
assertEquals("Dog", published.get(0).getTerm());
assertEquals("Puppies", published.get(0).getLabel());
assertEquals(null, published.get(0).getScheme());
assertEquals("Cat", published.get(1).getTerm());
assertEquals("Kittens", published.get(1).getLabel());
assertEquals("http://foo", published.get(1).getScheme());
assertEquals("Cow", published.get(2).getTerm());
assertEquals("Calves", published.get(2).getLabel());
assertEquals("http://foo", published.get(2).getScheme());
}
@Test

16
pom.xml
View File

@ -46,13 +46,17 @@
<developers>
<developer>
<id>jamesagnew</id>
<name>James Agnew</name>
<organization>University Health Network</organization>
</developer>
<developer>
<name>Dmitri Sotnikov</name>
<organization>University Health Network</organization>
</developer>
<developer>
<name>Lisa Wong</name>
<organization>University Health Network</organization>
</developer>
<developer>
<name>Josh Mandel</name>
@ -60,6 +64,11 @@
</developer>
<developer>
<name>Laura MacDougall Sookraj</name>
<organization>University Health Network</organization>
</developer>
<developer>
<name>Neal Acharya</name>
<organization>University Health Network</organization>
</developer>
<developer>
<name>David Hay</name>
@ -68,13 +77,17 @@
<developer>
<id>suranga</id>
<name>Suranga Nath Kasthurirathne</name>
<organization>OpenMRS</organization>
<organization>OpenMRS / Regenstrief Center for Biomedical Informatics</organization>
</developer>
<developer>
<id>dougmartin</id>
<name>Doug Martin</name>
<organization>Regenstrief Center for Biomedical Informatics</organization>
</developer>
<developer>
<id>akley</id>
<name>Alexander Kley</name>
</developer>
</developers>
<licenses>
@ -150,6 +163,7 @@
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
<runOrder>random</runOrder>
<!--<argLine>-Dfile.encoding=ISO-8859-1</argLine>-->
</configuration>
</plugin>
<plugin>

2
restful-server-example/pom.xml
View File

@ -13,7 +13,7 @@
<groupId>ca.uhn.hapi.example</groupId>
<artifactId>restful-server-example</artifactId>
<version>0.7-SNAPSHOT</version>
<version>0.8-SNAPSHOT</version>
<packaging>war</packaging>
<name>HAPI FHIR Sample RESTful Server</name>