Merging master into working branch.
This commit is contained in:
Diederik Muylwyk
commit
799848291f
|
|
@ -6,12 +6,10 @@ HAPI FHIR - Java API for HL7 FHIR Clients and Servers
|
|||
[](https://coveralls.io/github/jamesagnew/hapi-fhir?branch=master)
|
||||
[](http://search.maven.org/#search|ga|1|ca.uhn.hapi.fhir)
|
||||
[](http://jamesagnew.github.io/hapi-fhir/license.html)
|
||||
|
||||
* Linux Build: [](https://travis-ci.org/jamesagnew/hapi-fhir)
|
||||
* Windows Build: <a href="https://ci.appveyor.com/project/jamesagnew/hapi-fhir"><img src="https://ci.appveyor.com/api/projects/status/github/jamesagnew/hapi-fhir?branch=master&svg=true"></a>
|
||||
[](https://dev.azure.com/jamesagnew214/jamesagnew214/_build/latest?definitionId=1&branchName=master)
|
||||
|
||||
Complete project documentation is available here:
|
||||
http://jamesagnew.github.io/hapi-fhir/
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||||
http://hapifhir.io
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||||
|
||||
A demonstration of this project is available here:
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||||
http://hapi.fhir.org/
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||||
|
|
@ -19,3 +17,5 @@ http://hapi.fhir.org/
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|||
This project is Open Source, licensed under the Apache Software License 2.0.
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||||
|
||||
Please see [this wiki page](https://github.com/jamesagnew/hapi-fhir/wiki/Getting-Help) for information on where to get help with HAPI FHIR. Please see [Smile CDR](https://smilecdr.com) for information on commercial support.
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||||
|
||||
---
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||||
|
|
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|||
|
|
@ -1,9 +0,0 @@
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|||
version: 1.0.{build}
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||||
image: Visual Studio 2017
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||||
cache:
|
||||
- C:\maven\
|
||||
- C:\Users\appveyor\.m2\repository
|
||||
build_script:
|
||||
- SET JAVA_HOME=C:\Program Files\Java\jdk10
|
||||
- SET PATH=C:\Program Files\Java\jdk10\bin;%PATH%
|
||||
- cmd: mvn -P MINPARALLEL,ALLMODULES,REDUCED_JPA_TESTS clean install
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||||
|
|
@ -0,0 +1,56 @@
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|||
# Starter pipeline
|
||||
# Start with a minimal pipeline that you can customize to build and deploy your code.
|
||||
# Add steps that build, run tests, deploy, and more:
|
||||
# https://aka.ms/yaml
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||||
|
||||
variables:
|
||||
MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
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MAVEN_OPTS: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
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||||
|
||||
trigger:
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||||
- master
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||||
|
||||
pool:
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||||
vmImage: 'ubuntu-latest'
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||||
|
||||
|
||||
jobs:
|
||||
- job: Build
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||||
timeoutInMinutes: 360
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||||
steps:
|
||||
- task: CacheBeta@0
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||||
inputs:
|
||||
key: maven
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||||
path: $(MAVEN_CACHE_FOLDER)
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||||
displayName: Cache Maven local repo
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||||
|
||||
- task: Maven@3
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||||
inputs:
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#mavenPomFile: 'pom.xml'
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goals: 'clean install' # Optional
|
||||
options: ''
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||||
#publishJUnitResults: true
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||||
#testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
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#testRunTitle: # Optional
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||||
#codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
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#codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
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||||
#codeCoverageClassFilesDirectories: # Optional
|
||||
#codeCoverageSourceDirectories: # Optional
|
||||
#codeCoverageFailIfEmpty: false # Optional
|
||||
#javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
|
||||
#jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
|
||||
#jdkDirectory: # Required when javaHomeOption == Path
|
||||
#jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
|
||||
#mavenVersionOption: 'Default' # Options: default, path
|
||||
#mavenDirectory: # Required when mavenVersionOption == Path
|
||||
#mavenSetM2Home: false # Required when mavenVersionOption == Path
|
||||
mavenOptions: '-Xmx2048m $(MAVEN_OPTS)' # Optional
|
||||
#mavenAuthenticateFeed: false
|
||||
#effectivePomSkip: false
|
||||
#sonarQubeRunAnalysis: false
|
||||
#sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
|
||||
#checkStyleRunAnalysis: false # Optional
|
||||
#pmdRunAnalysis: false # Optional
|
||||
#findBugsRunAnalysis: false # Optional
|
||||
|
||||
|
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|
|
@ -19,25 +19,28 @@ package ca.uhn.fhir.rest.param;
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* limitations under the License.
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||||
* #L%
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||||
*/
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||||
import static ca.uhn.fhir.model.primitive.IdDt.isValidLong;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.math.BigDecimal;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.primitive.IdDt;
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||||
import ca.uhn.fhir.parser.DataFormatException;
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||||
import ca.uhn.fhir.util.CoverageIgnore;
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||||
import org.apache.commons.lang3.builder.ToStringBuilder;
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||||
import org.apache.commons.lang3.builder.ToStringStyle;
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||||
import org.hl7.fhir.instance.model.api.IBaseResource;
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||||
|
||||
import ca.uhn.fhir.context.FhirContext;
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||||
import ca.uhn.fhir.model.primitive.IdDt;
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||||
import ca.uhn.fhir.util.CoverageIgnore;
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||||
import java.math.BigDecimal;
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||||
|
||||
import static ca.uhn.fhir.model.primitive.IdDt.isValidLong;
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||||
import static org.apache.commons.lang3.StringUtils.*;
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public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/ {
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private String myChain;
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||||
private String myResourceType;
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||||
private String myBaseUrl;
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||||
private String myValue;
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||||
private String myIdPart;
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||||
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||||
private final IdDt myId = new IdDt();
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||||
/**
|
||||
* Constructor
|
||||
*/
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||||
|
|
@ -64,12 +67,15 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
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|||
* Constructor
|
||||
*/
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||||
public ReferenceParam(String theResourceType, String theChain, String theValue) {
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||||
String qualifier = "";
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||||
if (isNotBlank(theResourceType)) {
|
||||
setValue(theResourceType + "/" + theValue);
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||||
} else {
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||||
setValue(theValue);
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||||
qualifier = ":" + theResourceType;
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||||
}
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||||
setChain(theChain);
|
||||
if (isNotBlank(theChain)) {
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||||
qualifier = qualifier + "." + theChain;
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||||
}
|
||||
|
||||
setValueAsQueryToken(null, null, qualifier, theValue);
|
||||
}
|
||||
|
||||
@Override
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||||
|
|
@ -91,55 +97,61 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
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|||
|
||||
@Override
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||||
String doGetValueAsQueryToken(FhirContext theContext) {
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||||
if (isBlank(myId.getResourceType())) {
|
||||
return myId.getValue(); // e.g. urn:asdjd or 123 or cid:wieiuru or #1
|
||||
if (isBlank(getResourceType())) {
|
||||
return myValue; // e.g. urn:asdjd or 123 or cid:wieiuru or #1
|
||||
} else {
|
||||
if (isBlank(getChain())) {
|
||||
return getResourceType() + "/" + myId.getIdPart();
|
||||
if (isBlank(getChain()) && isNotBlank(getResourceType())) {
|
||||
return getResourceType() + "/" + getIdPart();
|
||||
}
|
||||
return myId.getIdPart();
|
||||
return myValue;
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
|
||||
String q = theQualifier;
|
||||
String resourceType = null;
|
||||
boolean skipSetValue = false;
|
||||
if (isNotBlank(q)) {
|
||||
if (q.startsWith(":")) {
|
||||
int nextIdx = q.indexOf('.');
|
||||
if (nextIdx != -1) {
|
||||
resourceType = q.substring(1, nextIdx);
|
||||
myChain = q.substring(nextIdx + 1);
|
||||
// type is explicitly defined so use it
|
||||
myId.setParts(null, resourceType, theValue, null);
|
||||
skipSetValue = true;
|
||||
myResourceType = q.substring(1, nextIdx);
|
||||
} else {
|
||||
resourceType = q.substring(1);
|
||||
myChain = null;
|
||||
myResourceType = q.substring(1);
|
||||
}
|
||||
|
||||
myValue = theValue;
|
||||
myIdPart = theValue;
|
||||
|
||||
IdDt id = new IdDt(theValue);
|
||||
if (!id.hasBaseUrl() && id.hasIdPart() && id.hasResourceType()) {
|
||||
if (id.getResourceType().equals(myResourceType)) {
|
||||
myIdPart = id.getIdPart();
|
||||
}
|
||||
}
|
||||
|
||||
} else if (q.startsWith(".")) {
|
||||
myChain = q.substring(1);
|
||||
// type not defined but this is a chain, so treat value as opaque
|
||||
myId.setParts(null, null, theValue, null);
|
||||
skipSetValue = true;
|
||||
myResourceType = null;
|
||||
myValue = theValue;
|
||||
myIdPart = theValue;
|
||||
}
|
||||
} else {
|
||||
myChain = null;
|
||||
myValue = theValue;
|
||||
IdDt id = new IdDt(theValue);
|
||||
myResourceType = id.getResourceType();
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||||
myIdPart = id.getIdPart();
|
||||
myBaseUrl = id.getBaseUrl();
|
||||
}
|
||||
|
||||
if (!skipSetValue) {
|
||||
setValue(theValue);
|
||||
|
||||
if (isNotBlank(resourceType) && isBlank(getResourceType())) {
|
||||
setValue(resourceType + '/' + theValue);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
@CoverageIgnore
|
||||
public String getBaseUrl() {
|
||||
return myId.getBaseUrl();
|
||||
return myBaseUrl;
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -147,24 +159,34 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
|
|||
return myChain;
|
||||
}
|
||||
|
||||
public ReferenceParam setChain(String theChain) {
|
||||
myChain = theChain;
|
||||
return this;
|
||||
}
|
||||
|
||||
@CoverageIgnore
|
||||
public String getIdPart() {
|
||||
return myId.getIdPart();
|
||||
return myIdPart;
|
||||
}
|
||||
|
||||
@CoverageIgnore
|
||||
public BigDecimal getIdPartAsBigDecimal() {
|
||||
return myId.getIdPartAsBigDecimal();
|
||||
return new IdDt(myValue).getIdPartAsBigDecimal();
|
||||
}
|
||||
|
||||
|
||||
@CoverageIgnore
|
||||
public Long getIdPartAsLong() {
|
||||
return myId.getIdPartAsLong();
|
||||
return new IdDt(myValue).getIdPartAsLong();
|
||||
}
|
||||
|
||||
public String getResourceType() {
|
||||
return myId.getResourceType();
|
||||
if (isNotBlank(myResourceType)) {
|
||||
return myResourceType;
|
||||
}
|
||||
if (isBlank(myChain)) {
|
||||
return new IdDt(myValue).getResourceType();
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
public Class<? extends IBaseResource> getResourceType(FhirContext theCtx) {
|
||||
|
|
@ -175,11 +197,21 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
|
|||
}
|
||||
|
||||
public String getValue() {
|
||||
return myId.getValue();
|
||||
return myValue;
|
||||
}
|
||||
|
||||
public ReferenceParam setValue(String theValue) {
|
||||
IdDt id = new IdDt(theValue);
|
||||
String qualifier= null;
|
||||
if (id.hasResourceType()) {
|
||||
qualifier = ":" + id.getResourceType();
|
||||
}
|
||||
setValueAsQueryToken(null, null, qualifier, id.getIdPart());
|
||||
return this;
|
||||
}
|
||||
|
||||
public boolean hasResourceType() {
|
||||
return myId.hasResourceType();
|
||||
return isNotBlank(myResourceType);
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -187,16 +219,6 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
|
|||
return true;
|
||||
}
|
||||
|
||||
public ReferenceParam setChain(String theChain) {
|
||||
myChain = theChain;
|
||||
return this;
|
||||
}
|
||||
|
||||
public ReferenceParam setValue(String theValue) {
|
||||
myId.setValue(theValue);
|
||||
return this;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a new param containing the same value as this param, but with the type copnverted
|
||||
* to {@link DateParam}. This is useful if you are using reference parameters and want to handle
|
||||
|
|
|
|||
|
|
@ -78,6 +78,7 @@ public abstract class BaseMigrateDatabaseCommand<T extends Enum> extends BaseCom
|
|||
addRequiredOption(retVal, "t", "to", "Version", "The database schema version to migrate TO");
|
||||
addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")");
|
||||
addOptionalOption(retVal, "x", "flags", "Flags", "A comma-separated list of any specific migration flags (these flags are version specific, see migrator documentation for details)");
|
||||
addOptionalOption(retVal, null, "no-column-shrink", false, "If this flag is set, the system will not attempt to reduce the length of columns. This is useful in environments with a lot of existing data, where shrinking a column can take a very long time.");
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
|
@ -106,6 +107,7 @@ public abstract class BaseMigrateDatabaseCommand<T extends Enum> extends BaseCom
|
|||
validateVersionSupported(to);
|
||||
|
||||
boolean dryRun = theCommandLine.hasOption("r");
|
||||
boolean noColumnShrink = theCommandLine.hasOption("no-column-shrink");
|
||||
|
||||
String flags = theCommandLine.getOptionValue("x");
|
||||
myFlags = Arrays.stream(defaultString(flags).split(","))
|
||||
|
|
@ -119,6 +121,7 @@ public abstract class BaseMigrateDatabaseCommand<T extends Enum> extends BaseCom
|
|||
migrator.setUsername(username);
|
||||
migrator.setPassword(password);
|
||||
migrator.setDryRun(dryRun);
|
||||
migrator.setNoColumnShrink(noColumnShrink);
|
||||
addTasks(migrator, from, to);
|
||||
|
||||
migrator.migrate();
|
||||
|
|
|
|||
|
|
@ -7,3 +7,4 @@ Interceptor classes may "hook into" various points in the processing chain in bo
|
|||
```java
|
||||
{{snippet:classpath:/ca/uhn/hapi/fhir/docs/MyInterceptor.java|sampleClass}}
|
||||
```
|
||||
|
||||
|
|
|
|||
|
|
@ -50,31 +50,26 @@
|
|||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-structures-dstu2</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-structures-dstu2.1</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-structures-dstu3</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-structures-r4</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<optional>true</optional>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
|
|
|
|||
|
|
@ -212,7 +212,6 @@
|
|||
<dependency>
|
||||
<groupId>com.github.dnault</groupId>
|
||||
<artifactId>xml-patch</artifactId>
|
||||
<version>0.3.0</version>
|
||||
</dependency>
|
||||
|
||||
<!-- FHIR RI is pulled in for UCUM support, but we don't want any of its dependencies. -->
|
||||
|
|
|
|||
|
|
@ -47,12 +47,14 @@ import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
|
|||
import ca.uhn.fhir.rest.api.server.IBundleProvider;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
||||
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
|
||||
import ca.uhn.fhir.util.*;
|
||||
import ca.uhn.fhir.util.CoverageIgnore;
|
||||
import ca.uhn.fhir.util.MetaUtil;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import ca.uhn.fhir.util.XmlUtil;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import com.google.common.base.Charsets;
|
||||
import com.google.common.collect.Sets;
|
||||
|
|
@ -86,7 +88,6 @@ import javax.xml.stream.events.XMLEvent;
|
|||
import java.util.*;
|
||||
import java.util.Map.Entry;
|
||||
|
||||
import static ca.uhn.fhir.jpa.model.util.JpaConstants.EXT_EXTERNALIZED_BINARY_ID;
|
||||
import static org.apache.commons.lang3.StringUtils.*;
|
||||
|
||||
/*
|
||||
|
|
@ -974,7 +975,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
|
|||
|
||||
// 6. Handle source (provenance)
|
||||
if (isNotBlank(provenanceRequestId) || isNotBlank(provenanceSourceUri)) {
|
||||
String sourceString = defaultString(provenanceSourceUri)
|
||||
String sourceString = cleanProvenanceSourceUri(provenanceSourceUri)
|
||||
+ (isNotBlank(provenanceRequestId) ? "#" : "")
|
||||
+ defaultString(provenanceRequestId);
|
||||
|
||||
|
|
@ -992,6 +993,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
|
|||
return retVal;
|
||||
}
|
||||
|
||||
static String cleanProvenanceSourceUri(String theProvenanceSourceUri) {
|
||||
if (isNotBlank(theProvenanceSourceUri)) {
|
||||
int hashIndex = theProvenanceSourceUri.indexOf('#');
|
||||
if (hashIndex != -1) {
|
||||
theProvenanceSourceUri = theProvenanceSourceUri.substring(0, hashIndex);
|
||||
}
|
||||
}
|
||||
return defaultString(theProvenanceSourceUri);
|
||||
}
|
||||
|
||||
public String toResourceName(Class<? extends IBaseResource> theResourceType) {
|
||||
return myContext.getResourceDefinition(theResourceType).getName();
|
||||
}
|
||||
|
|
|
|||
|
|
@ -573,7 +573,7 @@ public class SearchBuilder implements ISearchBuilder {
|
|||
private Predicate addPredicateReferenceWithChain(String theResourceName, String theParamName, List<? extends IQueryParameterType> theList, Join<ResourceTable, ResourceLink> theJoin, List<Predicate> theCodePredicates, ReferenceParam theRef, RequestDetails theRequest) {
|
||||
final List<Class<? extends IBaseResource>> resourceTypes;
|
||||
String resourceId;
|
||||
if (!theRef.getValue().matches("[a-zA-Z]+/.*")) {
|
||||
if (!theRef.hasResourceType()) {
|
||||
|
||||
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
|
||||
resourceTypes = new ArrayList<>();
|
||||
|
|
|
|||
|
|
@ -35,10 +35,10 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
|
|||
@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
|
||||
void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
|
||||
|
||||
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
|
||||
List<TermCodeSystemVersion> findByCodeSystemPid(@Param("resource_id") Long theCodeSystemResourcePid);
|
||||
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid")
|
||||
List<TermCodeSystemVersion> findByCodeSystemPid(@Param("codesystem_pid") Long theCodeSystemPid);
|
||||
|
||||
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResource.myId = :resource_id")
|
||||
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myResourcePid = :resource_id")
|
||||
List<TermCodeSystemVersion> findByCodeSystemResourcePid(@Param("resource_id") Long theCodeSystemResourcePid);
|
||||
|
||||
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemHavingThisVersionAsCurrentVersionIfAny.myResource.myId = :resource_id")
|
||||
|
|
|
|||
|
|
@ -58,6 +58,7 @@ public class TermCodeSystemVersion implements Serializable {
|
|||
|
||||
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
|
||||
private String myCodeSystemVersionId;
|
||||
|
||||
/**
|
||||
* This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
|
||||
* issued. It should be made non-nullable at some point.
|
||||
|
|
@ -65,8 +66,11 @@ public class TermCodeSystemVersion implements Serializable {
|
|||
@ManyToOne
|
||||
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
|
||||
private TermCodeSystem myCodeSystem;
|
||||
@SuppressWarnings("unused")
|
||||
|
||||
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
|
||||
private Long myCodeSystemPid;
|
||||
|
||||
@SuppressWarnings("unused")
|
||||
@OneToOne(mappedBy = "myCurrentVersion", optional = true)
|
||||
private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,16 @@
|
|||
package ca.uhn.fhir.jpa.dao;
|
||||
|
||||
import org.junit.Test;
|
||||
|
||||
import static org.junit.Assert.assertEquals;
|
||||
|
||||
public class BaseHapiFhirDaoTest {
|
||||
|
||||
@Test
|
||||
public void cleanProvenanceSourceUri() {
|
||||
assertEquals("", BaseHapiFhirDao.cleanProvenanceSourceUri(null));
|
||||
assertEquals("abc", BaseHapiFhirDao.cleanProvenanceSourceUri("abc"));
|
||||
assertEquals("abc", BaseHapiFhirDao.cleanProvenanceSourceUri("abc#def"));
|
||||
assertEquals("abc", BaseHapiFhirDao.cleanProvenanceSourceUri("abc#def#ghi"));
|
||||
}
|
||||
}
|
||||
|
|
@ -1368,11 +1368,14 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
|
|||
map.setLastUpdated(new DateRangeParam().setUpperBound(new DateParam(ParamPrefixEnum.LESSTHAN, "2022-01-01")));
|
||||
IBundleProvider found = myPatientDao.search(map);
|
||||
Set<String> dates = new HashSet<>();
|
||||
String searchId = found.getUuid();
|
||||
for (int i = 0; i < 9; i++) {
|
||||
List<IBaseResource> resources = found.getResources(i, i + 1);
|
||||
assertThat("Failed to load range " + i + " - " + (i + 1), resources, hasSize(1));
|
||||
assertThat("Failed to load range " + i + " - " + (i + 1) + " - from provider of type: " + found.getClass(), resources, hasSize(1));
|
||||
Patient nextResource = (Patient) resources.get(0);
|
||||
dates.add(nextResource.getBirthDateElement().getValueAsString());
|
||||
|
||||
found = myPagingProvider.retrieveResultList(null, searchId);
|
||||
}
|
||||
|
||||
assertThat(dates, hasItems(
|
||||
|
|
|
|||
|
|
@ -120,7 +120,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
|
||||
myDaoConfig.setSearchPreFetchThresholds(Arrays.asList(20, 50, 190));
|
||||
|
||||
// Seach with count only
|
||||
// Search with count only
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.add(Patient.SP_NAME, new StringParam("FAM"));
|
||||
params.setSummaryMode((SummaryEnum.COUNT));
|
||||
|
|
@ -142,7 +142,9 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
|
|||
assertEquals(201, results.size().intValue());
|
||||
ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
|
||||
assertThat(ids, hasSize(10));
|
||||
assertEquals(201, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
|
||||
IBundleProvider bundleProvider = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid);
|
||||
Integer bundleSize = bundleProvider.size();
|
||||
assertEquals(201, bundleSize.intValue());
|
||||
|
||||
// Search with count only
|
||||
params = new SearchParameterMap();
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.dstu3;
|
|||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
import ca.uhn.fhir.jpa.dao.data.ISearchDao;
|
||||
import ca.uhn.fhir.jpa.entity.Search;
|
||||
import ca.uhn.fhir.jpa.model.util.JpaConstants;
|
||||
import ca.uhn.fhir.jpa.provider.r4.ResourceProviderR4Test;
|
||||
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
|
||||
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
|
||||
|
|
@ -3913,6 +3914,31 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateWithSource() {
|
||||
Patient patient = new Patient();
|
||||
patient.setActive(false);
|
||||
IIdType patientid = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
|
||||
|
||||
{
|
||||
Patient readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getExtensionString(JpaConstants.EXT_META_SOURCE), matchesPattern("#[a-f0-9]+"));
|
||||
}
|
||||
|
||||
patient.setId(patientid);
|
||||
patient.setActive(true);
|
||||
ourClient.update().resource(patient).execute();
|
||||
{
|
||||
Patient readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getExtensionString(JpaConstants.EXT_META_SOURCE), matchesPattern("#[a-f0-9]+"));
|
||||
|
||||
readPatient.addName().setFamily("testUpdateWithSource");
|
||||
ourClient.update().resource(readPatient).execute();
|
||||
readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getExtensionString(JpaConstants.EXT_META_SOURCE), matchesPattern("#[a-f0-9]+"));
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateWithETag() throws Exception {
|
||||
String methodName = "testUpdateWithETag";
|
||||
|
|
|
|||
|
|
@ -167,6 +167,54 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchWithSlashes() {
|
||||
myDaoConfig.setSearchPreFetchThresholds(Lists.newArrayList(10, 50, 10000));
|
||||
|
||||
Procedure procedure = new Procedure();
|
||||
procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
|
||||
String procedureId = ourClient.create().resource(procedure).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
DocumentReference dr = new DocumentReference();
|
||||
dr.addContent().getAttachment().setContentType("application/vnd.mfer");
|
||||
String drId = ourClient.create().resource(dr).execute().getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
for (int i = 0; i < 60; i++) {
|
||||
Observation obs = new Observation();
|
||||
obs.addPartOf().setReference(procedureId);
|
||||
obs.addDerivedFrom().setReference(drId);
|
||||
ourClient.create().resource(obs).execute();
|
||||
}
|
||||
|
||||
ourLog.info("Starting search");
|
||||
|
||||
Bundle response = ourClient
|
||||
.search()
|
||||
.byUrl("Observation?part-of=" + procedureId + "&derived-from:DocumentReference.contenttype=application/vnd.mfer&_total=accurate&_count=2")
|
||||
.returnBundle(Bundle.class)
|
||||
.execute();
|
||||
|
||||
int obsCount = 0;
|
||||
int pageCount = 0;
|
||||
while (response != null) {
|
||||
obsCount += response.getEntry().size();
|
||||
pageCount++;
|
||||
if (response.getLink("next") != null) {
|
||||
response = ourClient.loadPage().next(response).execute();
|
||||
} else {
|
||||
response = null;
|
||||
}
|
||||
|
||||
|
||||
ourLog.info("Have loaded {} pages and {} reources", pageCount, obsCount);
|
||||
}
|
||||
|
||||
assertEquals(60, obsCount);
|
||||
assertEquals(30, pageCount);
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testManualPagingLinkOffsetDoesntReturnBeyondEnd() {
|
||||
myDaoConfig.setSearchPreFetchThresholds(Lists.newArrayList(10, 1000));
|
||||
|
|
@ -5081,6 +5129,31 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateWithSource() {
|
||||
Patient patient = new Patient();
|
||||
patient.setActive(false);
|
||||
IIdType patientid = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
|
||||
|
||||
{
|
||||
Patient readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getSource(), matchesPattern("#[a-f0-9]+"));
|
||||
}
|
||||
|
||||
patient.setId(patientid);
|
||||
patient.setActive(true);
|
||||
ourClient.update().resource(patient).execute();
|
||||
{
|
||||
Patient readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getSource(), matchesPattern("#[a-f0-9]+"));
|
||||
|
||||
readPatient.addName().setFamily("testUpdateWithSource");
|
||||
ourClient.update().resource(readPatient).execute();
|
||||
readPatient = (Patient) ourClient.read().resource("Patient").withId(patientid).execute();
|
||||
assertThat(readPatient.getMeta().getSource(), matchesPattern("#[a-f0-9]+"));
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateWithETag() throws Exception {
|
||||
String methodName = "testUpdateWithETag";
|
||||
|
|
|
|||
|
|
@ -22,6 +22,9 @@ package ca.uhn.fhir.jpa.migrate;
|
|||
|
||||
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import org.apache.commons.lang3.builder.EqualsBuilder;
|
||||
import org.apache.commons.lang3.builder.HashCodeBuilder;
|
||||
import org.apache.commons.lang3.builder.ToStringBuilder;
|
||||
import org.hibernate.boot.model.naming.Identifier;
|
||||
import org.hibernate.dialect.Dialect;
|
||||
import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
|
||||
|
|
@ -48,6 +51,73 @@ import static org.thymeleaf.util.StringUtils.toUpperCase;
|
|||
public class JdbcUtils {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(JdbcUtils.class);
|
||||
|
||||
public static class ColumnType {
|
||||
private final BaseTableColumnTypeTask.ColumnTypeEnum myColumnTypeEnum;
|
||||
private final Long myLength;
|
||||
|
||||
public ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, Long theLength) {
|
||||
myColumnTypeEnum = theColumnType;
|
||||
myLength = theLength;
|
||||
}
|
||||
|
||||
public ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, int theLength) {
|
||||
this(theColumnType, (long) theLength);
|
||||
}
|
||||
|
||||
public ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType) {
|
||||
this(theColumnType, null);
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean equals(Object theO) {
|
||||
if (this == theO) {
|
||||
return true;
|
||||
}
|
||||
|
||||
if (theO == null || getClass() != theO.getClass()) {
|
||||
return false;
|
||||
}
|
||||
|
||||
ColumnType that = (ColumnType) theO;
|
||||
|
||||
return new EqualsBuilder()
|
||||
.append(myColumnTypeEnum, that.myColumnTypeEnum)
|
||||
.append(myLength, that.myLength)
|
||||
.isEquals();
|
||||
}
|
||||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
return new HashCodeBuilder(17, 37)
|
||||
.append(myColumnTypeEnum)
|
||||
.append(myLength)
|
||||
.toHashCode();
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
ToStringBuilder b = new ToStringBuilder(this);
|
||||
b.append("type", myColumnTypeEnum);
|
||||
if (myLength != null) {
|
||||
b.append("length", myLength);
|
||||
}
|
||||
return b.toString();
|
||||
}
|
||||
|
||||
public BaseTableColumnTypeTask.ColumnTypeEnum getColumnTypeEnum() {
|
||||
return myColumnTypeEnum;
|
||||
}
|
||||
|
||||
public Long getLength() {
|
||||
return myLength;
|
||||
}
|
||||
|
||||
public boolean equals(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, Long theColumnLength) {
|
||||
return myColumnTypeEnum == theColumnType && (myLength == null || myLength.equals(theColumnLength));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve all index names
|
||||
*/
|
||||
|
|
@ -127,7 +197,7 @@ public class JdbcUtils {
|
|||
/**
|
||||
* Retrieve all index names
|
||||
*/
|
||||
public static String getColumnType(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theColumnName) throws SQLException {
|
||||
public static ColumnType getColumnType(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theColumnName) throws SQLException {
|
||||
DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
|
||||
try (Connection connection = dataSource.getConnection()) {
|
||||
return theConnectionProperties.getTxTemplate().execute(t -> {
|
||||
|
|
@ -153,18 +223,18 @@ public class JdbcUtils {
|
|||
Long length = indexes.getLong("COLUMN_SIZE");
|
||||
switch (dataType) {
|
||||
case Types.VARCHAR:
|
||||
return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
|
||||
return new ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, length);
|
||||
case Types.NUMERIC:
|
||||
case Types.BIGINT:
|
||||
case Types.DECIMAL:
|
||||
return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(null);
|
||||
return new ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG, length);
|
||||
case Types.INTEGER:
|
||||
return BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null);
|
||||
return new ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.INT, length);
|
||||
case Types.TIMESTAMP:
|
||||
case Types.TIMESTAMP_WITH_TIMEZONE:
|
||||
return BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP.getDescriptor(null);
|
||||
return new ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP, length);
|
||||
case Types.BLOB:
|
||||
return BaseTableColumnTypeTask.ColumnTypeEnum.BLOB.getDescriptor(null);
|
||||
return new ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.BLOB, length);
|
||||
default:
|
||||
throw new IllegalArgumentException("Don't know how to handle datatype " + dataType + " for column " + theColumnName + " on table " + theTableName);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -44,6 +44,7 @@ public class Migrator {
|
|||
private int myChangesCount;
|
||||
private boolean myDryRun;
|
||||
private List<BaseTask.ExecutedStatement> myExecutedStatements = new ArrayList<>();
|
||||
private boolean myNoColumnShrink;
|
||||
|
||||
public int getChangesCount() {
|
||||
return myChangesCount;
|
||||
|
|
@ -82,6 +83,7 @@ public class Migrator {
|
|||
next.setDriverType(myDriverType);
|
||||
next.setConnectionProperties(myConnectionProperties);
|
||||
next.setDryRun(myDryRun);
|
||||
next.setNoColumnShrink(myNoColumnShrink);
|
||||
try {
|
||||
next.execute();
|
||||
} catch (SQLException e) {
|
||||
|
|
@ -126,4 +128,8 @@ public class Migrator {
|
|||
public void addTasks(List<BaseTask<?>> theTasks) {
|
||||
theTasks.forEach(this::addTask);
|
||||
}
|
||||
|
||||
public void setNoColumnShrink(boolean theNoColumnShrink) {
|
||||
myNoColumnShrink = theNoColumnShrink;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
|
|||
}
|
||||
|
||||
for (TableAndColumn next : myConditionalOnExistenceOf) {
|
||||
String columnType = JdbcUtils.getColumnType(getConnectionProperties(), next.getTable(), next.getColumn());
|
||||
JdbcUtils.ColumnType columnType = JdbcUtils.getColumnType(getConnectionProperties(), next.getTable(), next.getColumn());
|
||||
if (columnType == null) {
|
||||
ourLog.info("Table {} does not have column {} - No action performed", next.getTable(), next.getColumn());
|
||||
return;
|
||||
|
|
|
|||
|
|
@ -164,74 +164,23 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
|
|||
return myColumnLength;
|
||||
}
|
||||
|
||||
public BaseTableColumnTypeTask<T> setColumnLength(int theColumnLength) {
|
||||
myColumnLength = (long) theColumnLength;
|
||||
public BaseTableColumnTypeTask<T> setColumnLength(long theColumnLength) {
|
||||
myColumnLength = theColumnLength;
|
||||
return this;
|
||||
}
|
||||
|
||||
|
||||
public enum ColumnTypeEnum {
|
||||
|
||||
LONG {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "bigint";
|
||||
}
|
||||
},
|
||||
STRING {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength != null, "Must supply a column length");
|
||||
return "varchar(" + theColumnLength + ")";
|
||||
}
|
||||
},
|
||||
DATE_TIMESTAMP {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "timestamp";
|
||||
}
|
||||
},
|
||||
BOOLEAN {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "boolean";
|
||||
}
|
||||
},
|
||||
FLOAT {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "float";
|
||||
}
|
||||
},
|
||||
INT {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "int";
|
||||
}
|
||||
},
|
||||
|
||||
BLOB {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "blob";
|
||||
}
|
||||
},
|
||||
|
||||
CLOB {
|
||||
@Override
|
||||
public String getDescriptor(Long theColumnLength) {
|
||||
Assert.isTrue(theColumnLength == null, "Must not supply a column length");
|
||||
return "clob";
|
||||
}
|
||||
};
|
||||
|
||||
public abstract String getDescriptor(Long theColumnLength);
|
||||
LONG,
|
||||
STRING,
|
||||
DATE_TIMESTAMP,
|
||||
BOOLEAN,
|
||||
FLOAT,
|
||||
INT,
|
||||
BLOB,
|
||||
CLOB
|
||||
;
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -42,6 +42,15 @@ public abstract class BaseTask<T extends BaseTask> {
|
|||
private int myChangesCount;
|
||||
private boolean myDryRun;
|
||||
private List<ExecutedStatement> myExecutedStatements = new ArrayList<>();
|
||||
private boolean myNoColumnShrink;
|
||||
|
||||
public boolean isNoColumnShrink() {
|
||||
return myNoColumnShrink;
|
||||
}
|
||||
|
||||
public void setNoColumnShrink(boolean theNoColumnShrink) {
|
||||
myNoColumnShrink = theNoColumnShrink;
|
||||
}
|
||||
|
||||
public boolean isDryRun() {
|
||||
return myDryRun;
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask>
|
|||
@Override
|
||||
public void execute() throws SQLException {
|
||||
|
||||
String existingType;
|
||||
JdbcUtils.ColumnType existingType;
|
||||
boolean nullable;
|
||||
|
||||
Set<String> columnNames = JdbcUtils.getColumnNames(getConnectionProperties(), getTableName());
|
||||
|
|
@ -52,11 +52,17 @@ public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask>
|
|||
throw new InternalErrorException(e);
|
||||
}
|
||||
|
||||
String wantedType = getColumnType().getDescriptor(getColumnLength());
|
||||
boolean alreadyOfCorrectType = existingType.equals(wantedType);
|
||||
if (isNoColumnShrink()) {
|
||||
long existingLength = existingType.getLength() != null ? existingType.getLength() : 0;
|
||||
if (existingLength > getColumnLength()) {
|
||||
setColumnLength(existingLength);
|
||||
}
|
||||
}
|
||||
|
||||
boolean alreadyOfCorrectType = existingType.equals(getColumnType(), getColumnLength());
|
||||
boolean alreadyCorrectNullable = isNullable() == nullable;
|
||||
if (alreadyOfCorrectType && alreadyCorrectNullable) {
|
||||
ourLog.info("Column {} on table {} is already of type {} and has nullable {} - No action performed", getColumnName(), getTableName(), wantedType, nullable);
|
||||
ourLog.info("Column {} on table {} is already of type {} and has nullable {} - No action performed", getColumnName(), getTableName(), existingType, nullable);
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -40,8 +40,8 @@ public class AddColumnTest extends BaseTest {
|
|||
|
||||
getMigrator().migrate();
|
||||
|
||||
String type = JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "newcolint");
|
||||
assertEquals(BaseTableColumnTypeTask.ColumnTypeEnum.INT.getDescriptor(null), type);
|
||||
JdbcUtils.ColumnType type = JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "newcolint");
|
||||
assertEquals(BaseTableColumnTypeTask.ColumnTypeEnum.INT, type.getColumnTypeEnum());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -25,7 +25,32 @@ public class ModifyColumnTest extends BaseTest {
|
|||
|
||||
getMigrator().migrate();
|
||||
|
||||
assertEquals("varchar(300)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 300), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(1, task.getExecutedStatements().size());
|
||||
|
||||
// Make sure additional migrations don't crash
|
||||
getMigrator().migrate();
|
||||
getMigrator().migrate();
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testNoShrink_SameNullable() throws SQLException {
|
||||
executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255), newcol bigint)");
|
||||
|
||||
ModifyColumnTask task = new ModifyColumnTask();
|
||||
task.setTableName("SOMETABLE");
|
||||
task.setColumnName("TEXTCOL");
|
||||
task.setColumnType(AddColumnTask.ColumnTypeEnum.STRING);
|
||||
task.setNullable(true);
|
||||
task.setColumnLength(200);
|
||||
|
||||
getMigrator().setNoColumnShrink(true);
|
||||
getMigrator().addTask(task);
|
||||
getMigrator().migrate();
|
||||
|
||||
assertEquals(0, task.getExecutedStatements().size());
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
|
||||
// Make sure additional migrations don't crash
|
||||
getMigrator().migrate();
|
||||
|
|
@ -38,8 +63,8 @@ public class ModifyColumnTest extends BaseTest {
|
|||
executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255) not null)");
|
||||
assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG, 19), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
|
||||
// PID
|
||||
ModifyColumnTask task = new ModifyColumnTask();
|
||||
|
|
@ -63,8 +88,8 @@ public class ModifyColumnTest extends BaseTest {
|
|||
|
||||
assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG, 19), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
|
||||
// Make sure additional migrations don't crash
|
||||
getMigrator().migrate();
|
||||
|
|
@ -78,8 +103,8 @@ public class ModifyColumnTest extends BaseTest {
|
|||
executeSql("create table SOMETABLE (PID bigint, TEXTCOL varchar(255))");
|
||||
assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG, 19), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
|
||||
// PID
|
||||
ModifyColumnTask task = new ModifyColumnTask();
|
||||
|
|
@ -103,8 +128,8 @@ public class ModifyColumnTest extends BaseTest {
|
|||
|
||||
assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.LONG, 19), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
|
||||
assertEquals(new JdbcUtils.ColumnType(BaseTableColumnTypeTask.ColumnTypeEnum.STRING, 255), JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
|
||||
|
||||
// Make sure additional migrations don't crash
|
||||
getMigrator().migrate();
|
||||
|
|
|
|||
|
|
@ -1,39 +1,60 @@
|
|||
package ca.uhn.fhir.rest.param;
|
||||
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import com.google.common.base.Charsets;
|
||||
import org.apache.commons.lang3.SerializationUtils;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Ignore;
|
||||
import org.junit.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import static org.junit.Assert.assertEquals;
|
||||
|
||||
public class ReferenceParamTest {
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ReferenceParamTest.class);
|
||||
private FhirContext ourCtx = FhirContext.forDstu3();
|
||||
|
||||
@Test
|
||||
public void testValueWithSlashPersistsAcrossSerialization() {
|
||||
ReferenceParam param = new ReferenceParam();
|
||||
param.setValueAsQueryToken(ourCtx, "derived-from", ":DocumentReference.contenttype", "application/vnd.mfer");
|
||||
|
||||
assertEquals("application/vnd.mfer", param.getValueAsQueryToken(ourCtx));
|
||||
assertEquals(":DocumentReference.contenttype", param.getQueryParameterQualifier());
|
||||
|
||||
byte[] serialized = SerializationUtils.serialize(param);
|
||||
ourLog.info("Serialized: {}", new String(serialized, Charsets.US_ASCII));
|
||||
param = SerializationUtils.deserialize(serialized);
|
||||
|
||||
assertEquals("application/vnd.mfer", param.getValueAsQueryToken(ourCtx));
|
||||
assertEquals(":DocumentReference.contenttype", param.getQueryParameterQualifier());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWithResourceType() {
|
||||
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, null, "Location/123");
|
||||
assertEquals("Location", rp.getResourceType());
|
||||
assertEquals("123", rp.getIdPart());
|
||||
assertEquals("Location/123", rp.getValue());
|
||||
assertEquals(null, rp.getQueryParameterQualifier());
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWithResourceType_AbsoluteUrl() {
|
||||
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, null, "http://a.b/c/d/e");
|
||||
assertEquals("d", rp.getResourceType());
|
||||
assertEquals("e", rp.getIdPart());
|
||||
assertEquals("http://a.b/c/d/e", rp.getValue());
|
||||
assertEquals(null, rp.getQueryParameterQualifier());
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -74,24 +95,26 @@ public class ReferenceParamTest {
|
|||
assertEquals("name", rp.getChain());
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testWithResourceTypeAsQualifier() {
|
||||
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, ":Location", "123");
|
||||
assertEquals("Location", rp.getResourceType());
|
||||
assertEquals("123", rp.getIdPart());
|
||||
assertEquals("Location/123", rp.getValue());
|
||||
assertEquals("123", rp.getValue());
|
||||
assertEquals(null, rp.getQueryParameterQualifier());
|
||||
|
||||
}
|
||||
|
||||
// TODO: verify this behavior is correct. If type is explicitly specified (i.e. :Location), should it be
|
||||
// an error if it gets overriden by the resourceType in the url?
|
||||
/**
|
||||
* TODO: is this an error?
|
||||
*/
|
||||
@Test
|
||||
public void testWithResourceTypeAsQualifier_RelativeUrl() {
|
||||
|
||||
@Ignore
|
||||
public void testMismatchedTypeAndValueType() {
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, ":Location", "Patient/123");
|
||||
assertEquals("Patient", rp.getResourceType());
|
||||
|
|
@ -101,14 +124,26 @@ public class ReferenceParamTest {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDuplicatedTypeAndValueType() {
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, ":Patient", "Patient/123");
|
||||
assertEquals("Patient", rp.getResourceType());
|
||||
assertEquals("123", rp.getIdPart());
|
||||
assertEquals("Patient/123", rp.getValue());
|
||||
assertEquals(null, rp.getQueryParameterQualifier());
|
||||
|
||||
}
|
||||
|
||||
// TODO: verify this behavior is correct. Same case as testWithResourceTypeAsQualifier_RelativeUrl()
|
||||
@Test
|
||||
public void testWithResourceTypeAsQualifier_AbsoluteUrl() {
|
||||
|
||||
|
||||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, ":Location", "http://a.b/c/d/e");
|
||||
assertEquals("d", rp.getResourceType());
|
||||
assertEquals("e", rp.getIdPart());
|
||||
assertEquals("Location", rp.getResourceType());
|
||||
assertEquals("http://a.b/c/d/e", rp.getIdPart());
|
||||
assertEquals("http://a.b/c/d/e", rp.getValue());
|
||||
assertEquals(null, rp.getQueryParameterQualifier());
|
||||
|
||||
|
|
@ -122,7 +157,7 @@ public class ReferenceParamTest {
|
|||
rp.setValueAsQueryToken(ourCtx, null, ":Location.name", "FOO");
|
||||
assertEquals("Location", rp.getResourceType());
|
||||
assertEquals("FOO", rp.getIdPart());
|
||||
assertEquals("Location/FOO", rp.getValue());
|
||||
assertEquals("FOO", rp.getValue());
|
||||
assertEquals(":Location.name", rp.getQueryParameterQualifier());
|
||||
assertEquals("name", rp.getChain());
|
||||
|
||||
|
|
@ -135,7 +170,7 @@ public class ReferenceParamTest {
|
|||
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|123");
|
||||
assertEquals("Patient", rp.getResourceType());
|
||||
assertEquals("http://hey.there/a/b|123", rp.getIdPart());
|
||||
assertEquals("Patient/http://hey.there/a/b|123", rp.getValue());
|
||||
assertEquals("http://hey.there/a/b|123", rp.getValue());
|
||||
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
|
||||
assertEquals("identifier", rp.getChain());
|
||||
|
||||
|
|
@ -147,8 +182,8 @@ public class ReferenceParamTest {
|
|||
ReferenceParam rp = new ReferenceParam();
|
||||
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|");
|
||||
assertEquals("Patient", rp.getResourceType());
|
||||
assertEquals("http://hey.there/a/b|", rp.getValue());
|
||||
assertEquals("http://hey.there/a/b|", rp.getIdPart());
|
||||
assertEquals("Patient/http://hey.there/a/b|", rp.getValue());
|
||||
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
|
||||
assertEquals("identifier", rp.getChain());
|
||||
|
||||
|
|
@ -161,7 +196,7 @@ public class ReferenceParamTest {
|
|||
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "|abc");
|
||||
assertEquals("Patient", rp.getResourceType());
|
||||
assertEquals("|abc", rp.getIdPart());
|
||||
assertEquals("Patient/|abc", rp.getValue());
|
||||
assertEquals("|abc", rp.getValue());
|
||||
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
|
||||
assertEquals("identifier", rp.getChain());
|
||||
|
||||
|
|
|
|||
13
pom.xml
13
pom.xml
|
|
@ -45,14 +45,7 @@
|
|||
</scm>
|
||||
|
||||
<repositories>
|
||||
<repository>
|
||||
<snapshots>
|
||||
<enabled>false</enabled>
|
||||
</snapshots>
|
||||
<id>bintray-dnault-maven</id>
|
||||
<name>bintray</name>
|
||||
<url>https://dl.bintray.com/dnault/maven</url>
|
||||
</repository>
|
||||
<!--
|
||||
<repository>
|
||||
<id>jitpack.io</id>
|
||||
<url>https://jitpack.io</url>
|
||||
|
|
@ -60,12 +53,16 @@
|
|||
<enabled>false</enabled>
|
||||
</snapshots>
|
||||
</repository>
|
||||
-->
|
||||
<repository>
|
||||
<id>oss-snapshot</id>
|
||||
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
|
||||
<snapshots>
|
||||
<enabled>true</enabled>
|
||||
</snapshots>
|
||||
<releases>
|
||||
<enabled>false</enabled>
|
||||
</releases>
|
||||
</repository>
|
||||
</repositories>
|
||||
|
||||
|
|
|
|||
|
|
@ -193,10 +193,25 @@
|
|||
resulted in some ValueSets with duplicate codes. This has been corrected by specifying a path with each
|
||||
filename.
|
||||
</action>
|
||||
<action>
|
||||
A corner case bug in the JPA server was solved: When performing a search that contained chained reference searches
|
||||
where the value contained slashes (e.g.
|
||||
<![CDATA[<code>Observation?derived-from:DocumentReference.contenttype=application/vnd.mfer</code>]]>)
|
||||
the server could fail to load later pages in the search results.
|
||||
</action>
|
||||
<action type="add">
|
||||
A new flag has been added to the JPA migrator tool that causes the migrator to not try to reduce the length
|
||||
of existing columns in the schema.
|
||||
</action>
|
||||
<action type="fix" issue="1483">
|
||||
Some resource IDs and URLs for LOINC ValueSets and ConceptMaps were inconsistently populated by the
|
||||
terminology uploader. This has been corrected.
|
||||
</action>
|
||||
<action type="fix">
|
||||
When a resource was updated with a meta.source containing a request id, the meta.source was getting appended
|
||||
with the new request id, resulting in an ever growing source.meta value. E.g. after the first update, it looks
|
||||
like "#9f0a901387128111#5f37835ee38a89e2" when it should only be "#5f37835ee38a89e2". This has been corrected.
|
||||
</action>
|
||||
</release>
|
||||
<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
|
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<action type="fix">
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Reference in New Issue