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Re-enable errorprone on standard hapi fhir build. woohoo!

This commit is contained in:
James Agnew 2017-10-15 11:27:30 -04:00
parent 2b230d3d9c
commit 9ca85b4cf3
26 changed files with 11002 additions and 11164 deletions
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2
.travis.yml
View File

@ -22,4 +22,4 @@ before_script:
script:
# - mvn -e -B clean install && cd hapi-fhir-ra && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID clean test jacoco:report coveralls:report
# - mvn -Dci=true -e -B -P ALLMODULES,NOPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report
- mvn -Dci=true -e -B -P ALLMODULES,MINPARALLEL clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report
- mvn -Dci=true -e -B -P ALLMODULES,MINPARALLEL,ERRORPRONE clean install && cd hapi-fhir-jacoco && mvn -e -B -DTRAVIS_JOB_ID=$TRAVIS_JOB_ID jacoco:report coveralls:report

54
hapi-deployable-pom/pom.xml
View File

@ -63,6 +63,60 @@
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<executions>
<execution>
<id>default</id>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
<inherited>true</inherited>
</execution>
</executions>
<configuration>
<printEqualFiles>false</printEqualFiles>
<failBuildInCaseOfDifferentContentConflict>true</failBuildInCaseOfDifferentContentConflict>
<failBuildInCaseOfEqualContentConflict>true</failBuildInCaseOfEqualContentConflict>
<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
<checkCompileClasspath>true</checkCompileClasspath>
<checkRuntimeClasspath>false</checkRuntimeClasspath>
<checkTestClasspath>false</checkTestClasspath>
<skip>false</skip>
<quiet>false</quiet>
<preferLocal>true</preferLocal>
<useResultFile>true</useResultFile>
<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
<resultFile>${project.build.directory}/duplicate-finder-result.xml</resultFile>
<ignoredDependencies>
<dependency>
<groupId>javax.el</groupId>
<artifactId>javax.el-api</artifactId>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-commons</artifactId>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</dependency>
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
</dependency>
</ignoredDependencies>
<ignoredResources>
<ignoredResource>changelog.txt</ignoredResource>
</ignoredResources>
</configuration>
</plugin>
</plugins>
</build>

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java
View File

@ -152,7 +152,8 @@ public class RuntimeSearchParam {
public enum RuntimeSearchParamStatusEnum {
ACTIVE,
DRAFT,
RETIRED
RETIRED,
UNKNOWN
}
}

15026
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_40.java
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File diff suppressed because it is too large Load Diff

2
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_40.java
View File

@ -1346,7 +1346,7 @@ public class VersionConvertor_14_40 {
org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingComponent tgt = new org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionSlicingComponent();
copyElement(src, tgt);
for (org.hl7.fhir.dstu2016may.model.StringType t : src.getDiscriminator())
tgt.addDiscriminator(ProfileUtilities.interpretR2Discriminator(t.getValue()));
tgt.addDiscriminator(ProfileUtilities.interpretR2Discriminator(t.getValue(), true));
if (src.hasDescription())
tgt.setDescription(src.getDescription());
if (src.hasOrdered())

83
hapi-fhir-converter/src/main/java/org/hl7/fhir/utilities/OIDUtils.java
View File

@ -1,83 +0,0 @@
package org.hl7.fhir.utilities;
/*
* #%L
* HAPI FHIR - Converter
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class OIDUtils {
/*
2.16.840.1.113883.3.72.5.2 - NIST owns this
2.16.840.1.113883.4.6 - National Provider Identifier
2.16.840.1.113883.6.21 - UB92
2.16.840.1.113883.6.69 - NDC
*/
public static String getUriForOid(String r) {
if (r.equals("2.16.840.1.113883.6.96"))
return "http://snomed.info/sct";
if (r.equals("2.16.840.1.113883.6.1"))
return "http://loinc.org";
if (r.equals("2.16.840.1.113883.6.8"))
return "http://unitsofmeasure.org";
if (r.equals("2.16.840.1.113883.6.3"))
return "http://hl7.org/fhir/sid/icd-10";
if (r.equals("2.16.840.1.113883.6.42"))
return "http://hl7.org/fhir/sid/icd-9";
if (r.equals("2.16.840.1.113883.6.104"))
return "http://hl7.org/fhir/sid/icd-9";
if (r.equals("2.16.840.1.113883.6.103"))
return "http://hl7.org/fhir/sid/icd-9"; //todo: confirm this
if (r.equals("2.16.840.1.113883.6.73"))
return "http://hl7.org/fhir/sid/atc";
if (r.equals("2.16.840.1.113883.3.26.1.1"))
return "http://ncimeta.nci.nih.gov";
if (r.equals("2.16.840.1.113883.3.26.1.1.1"))
return "http://ncimeta.nci.nih.gov";
if (r.equals("2.16.840.1.113883.6.88"))
return "http://www.nlm.nih.gov/research/umls/rxnorm"; // todo: confirm this
if (r.equals("2.16.840.1.113883.5.1008"))
return "http://hl7.org/fhir/v3/NullFlavor";
if (r.equals("2.16.840.1.113883.5.111"))
return "http://hl7.org/fhir/v3/RoleCode";
if (r.equals("2.16.840.1.113883.5.4"))
return "http://hl7.org/fhir/v3/ActCode";
if (r.equals("2.16.840.1.113883.5.8"))
return "http://hl7.org/fhir/v3/ActReason";
if (r.equals("2.16.840.1.113883.5.83"))
return "http://hl7.org/fhir/v3/ObservationInterpretation";
if (r.equals("2.16.840.1.113883.6.238"))
return "http://hl7.org/fhir/v3/Race";
if (r.equals("2.16.840.1.113883.6.59"))
return "http://hl7.org/fhir/sid/cvx";
if (r.equals("2.16.840.1.113883.12.292"))
return "http://hl7.org/fhir/sid/cvx";
if (r.equals("2.16.840.1.113883.6.12"))
return "http://www.ama-assn.org/go/cpt";
if (r.startsWith("2.16.840.1.113883.12."))
return "http://hl7.org/fhir/sid/v2-"+r.substring(21);
return null;
}
}

193
hapi-fhir-converter/src/main/java/org/hl7/fhir/utilities/ucum/UcumService.java
View File

@ -1,193 +0,0 @@
package org.hl7.fhir.utilities.ucum;
/*
* #%L
* HAPI FHIR - Converter
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
/*******************************************************************************
* Crown Copyright (c) 2006+, Copyright (c) 2006 - 2014 Kestral Computing & Health Intersections.
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contributors:
* Kestral Computing P/L - initial implementation
* Health Intersections - ongoing maintenance
*******************************************************************************/
import java.util.Date;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.exceptions.UcumException;
/**
* General Ucum Service
*
* UCUM functionality that is useful for applications that make use of UCUM codes
*
* This is a tightly bound interface - consumers use the internal model classes
*
* @author Grahame Grieve
*
*/
public interface UcumService {
public class UcumVersionDetails {
private Date releaseDate;
private String version;
/**
* @param releaseDate
* @param version
*/
public UcumVersionDetails(Date releaseDate, String version) {
super();
this.releaseDate = releaseDate;
this.version = version;
}
/**
* @return the releaseDate
*/
public Date getReleaseDate() {
return releaseDate;
}
/**
* @return the version
*/
public String getVersion() {
return version;
}
}
/**
* return Ucum Identification details for the version in use
*/
public abstract UcumVersionDetails ucumIdentification();
/**
* Check UCUM. Note that this stands as a test of the service
* more than UCUM itself (for version 1.7, there are no known
* semantic errors in UCUM). But you should always run this test at least
* once with the version of UCUM you are using to ensure that
* the service implementation correctly understands the UCUM data
* to which it is bound
*
* @return a list of internal errors in the UCUM spec.
*
*/
public abstract List<String> validateUCUM();
/**
* return a list of the defined types of units in this UCUM version
*
* @return
*/
public abstract Set<String> getProperties();
/**
* validate whether a unit code are valid UCUM units
*
* @param units - the unit code to check
* @return nil if valid, or an error message describing the problem
*/
public abstract String validate(String unit);
/**
* given a unit, return a formal description of what the units stand for using
* full names
* @param units the unit code
* @return formal description
* @throws UcumException
* @throws OHFException
*/
public String analyse(String unit) throws UcumException ;
/**
* validate whether a units are valid UCUM units and additionally require that the
* units from a particular property
*
* @param units - the unit code to check
* @return nil if valid, or an error message describing the problem
*/
public abstract String validateInProperty(String unit, String property);
/**
* validate whether a units are valid UCUM units and additionally require that the
* units match a particular base canonical unit
*
* @param units - the unit code to check
* @return nil if valid, or an error message describing the problem
*/
public abstract String validateCanonicalUnits(String unit, String canonical);
/**
* given a set of units, return their canonical form
* @param unit
* @return the canonical form
* @throws UcumException
* @throws OHFException
*/
public abstract String getCanonicalUnits(String unit) throws UcumException ;
/**
* given two pairs of units, return true if they sahre the same canonical base
*
* @param units1
* @param units2
* @return
* @throws UcumException
* @
*/
public abstract boolean isComparable(String units1, String units2) throws UcumException ;
/**
* given a value and source unit, return the value in the given dest unit
* an exception is thrown if the conversion is not possible
*
* @param value
* @param sourceUnit
* @param destUnit
* @return the value if a conversion is possible
* @throws UcumException
* @throws OHFException
*/
public abstract Decimal convert(Decimal value, String sourceUnit, String destUnit) throws UcumException ;
/**
* given a set of UCUM units, return a likely preferred human dense form
*
* SI units - as is.
* Other units - improved by manual fixes, or the removal of []
*
* @param code
* @return the preferred human display form
*/
public abstract String getCommonDisplay(String code);
}

20
hapi-fhir-jacoco/pom.xml
View File

@ -1,8 +1,13 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the site. I don't know why this works...
Need to investigate this. -->
<!--
The parent of this project is the deployable POM. This project isn't
deployable, but this keeps it before the root pom in the reactor
order when building the site. I don't know why this works...
Need to investigate this.
-->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
@ -253,6 +258,13 @@
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
@ -296,8 +308,6 @@
<outputDirectory>${project.reporting.outputDirectory}/jacoco-report</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>

5
hapi-fhir-jpaserver-base/pom.xml
View File

@ -163,7 +163,7 @@
<artifactId>thymeleaf-spring4</artifactId>
</dependency>
<!-- For UCUM -->
<!-- For UCUM: TODO we should replace this with org.fhir UCUM -->
<dependency>
<groupId>org.jscience</groupId>
<artifactId>jscience</artifactId>
@ -233,10 +233,12 @@
<!-- <dependency> <groupId>org.hsqldb</groupId> <artifactId>hsqldb</artifactId> <version>2.3.2</version> </dependency> -->
<!-- Spring -->
<!--
<dependency>
<groupId>aopalliance</groupId>
<artifactId>aopalliance</artifactId>
</dependency>
-->
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
@ -358,6 +360,7 @@
<dependency>
<groupId>javax.mail</groupId>
<artifactId>javax.mail-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java
View File

@ -215,6 +215,9 @@ public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
case RETIRED:
status = RuntimeSearchParamStatusEnum.RETIRED;
break;
case UNKNOWN:
status = RuntimeSearchParamStatusEnum.UNKNOWN;
break;
case NULL:
break;
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/SearchParamRegistryR4.java
View File

@ -216,6 +216,9 @@ public class SearchParamRegistryR4 extends BaseSearchParamRegistry {
case RETIRED:
status = RuntimeSearchParamStatusEnum.RETIRED;
break;
case UNKNOWN:
status = RuntimeSearchParamStatusEnum.UNKNOWN;
break;
case NULL:
break;
}

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

@ -115,6 +115,8 @@ public class JpaStorageServices extends BaseHapiFhirDao<IBaseResource> implement
break;
case URI:
break;
case HAS:
break;
}
params.add(nextArgument.getName(), param);

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

@ -103,6 +103,8 @@ public class SubscriptionActivatingSubscriber {
}
activateAndRegisterSubscriptionIfRequired(theSubscription);
break;
default:
break;
}
}

0
hapi-fhir-jpaserver-base/src/main/resources/.keep
View File

0
hapi-fhir-structures-dstu2.1/src/main/resources/.keep
View File

0
hapi-fhir-structures-dstu2/src/main/resources/.keep
View File

29
hapi-fhir-structures-dstu3/pom.xml
View File

@ -77,35 +77,6 @@
<fork>true</fork>
</configuration>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<id>default</id>
<phase>verify</phase>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
<configuration>
<printEqualFiles>false</printEqualFiles>
<failBuildInCaseOfDifferentContentConflict>true</failBuildInCaseOfDifferentContentConflict>
<failBuildInCaseOfEqualContentConflict>true</failBuildInCaseOfEqualContentConflict>
<failBuildInCaseOfConflict>true</failBuildInCaseOfConflict>
<checkCompileClasspath>true</checkCompileClasspath>
<checkRuntimeClasspath>false</checkRuntimeClasspath>
<checkTestClasspath>false</checkTestClasspath>
<skip>false</skip>
<quiet>false</quiet>
<preferLocal>true</preferLocal>
<useResultFile>true</useResultFile>
<resultFileMinClasspathCount>2</resultFileMinClasspathCount>
<resultFile>${project.build.directory}/duplicate-finder-result.xml</resultFile>
</configuration>
</plugin>
</plugins>
</build>

23
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileUtilities.java
View File

@ -1532,7 +1532,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private boolean hasBindableType(ElementDefinition ed) {
for (TypeRefComponent tr : ed.getType()) {
if (Utilities.existsInList(tr.getCode(), "Coding", "CodeableConcept", "Quantity", "url", "string", "code"))
if (Utilities.existsInList(tr.getCode(), "Coding", "CodeableConcept", "Quantity", "uri", "string", "code"))
return true;
}
return false;
@ -1918,8 +1918,8 @@ public class ProfileUtilities extends TranslatingUtilities {
case BUNDLED : return "b";
case CONTAINED : return "c";
case REFERENCED: return "r";
default: return "?";
}
return "?";
}
@ -2366,7 +2366,7 @@ public class ProfileUtilities extends TranslatingUtilities {
if (definition != null && definition.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(definition.getShortElement(), gen.new Piece(null, gt(definition.getShortElement()), null)));
} else if (fallback != null && fallback != null && fallback.hasShort()) {
} else if (fallback != null && fallback.hasShort()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.addPiece(checkForNoChange(fallback.getShortElement(), gen.new Piece(null, gt(fallback.getShortElement()), null)));
}
@ -2604,6 +2604,13 @@ public class ProfileUtilities extends TranslatingUtilities {
}
}
}
if (definition.hasDefinition()) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.getPieces().add(gen.new Piece(null, "Definition: ", null).addStyle("font-weight:bold"));
c.addPiece(gen.new Piece("br"));
c.addMarkdown(definition.getDefinition());
// c.getPieces().add(checkForNoChange(definition.getCommentElement(), gen.new Piece(null, definition.getComment(), null)));
}
if (definition.getComment()!=null) {
if (!c.getPieces().isEmpty()) c.addPiece(gen.new Piece("br"));
c.getPieces().add(gen.new Piece(null, "Comments: ", null).addStyle("font-weight:bold"));
@ -3734,17 +3741,21 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public static ElementDefinitionSlicingDiscriminatorComponent interpretR2Discriminator(String discriminator) {
public static ElementDefinitionSlicingDiscriminatorComponent interpretR2Discriminator(String discriminator, boolean isExists) {
if (discriminator.endsWith("@profile"))
return makeDiscriminator(DiscriminatorType.PROFILE, discriminator.length() == 8 ? "" : discriminator.substring(discriminator.length()-9));
if (discriminator.endsWith("@type"))
return makeDiscriminator(DiscriminatorType.TYPE, discriminator.length() == 5 ? "" : discriminator.substring(discriminator.length()-6));
if (discriminator.endsWith("@exists"))
return makeDiscriminator(DiscriminatorType.EXISTS, discriminator.length() == 7 ? "" : discriminator.substring(discriminator.length()-8));
if (isExists)
return makeDiscriminator(DiscriminatorType.EXISTS, discriminator);
return new ElementDefinitionSlicingDiscriminatorComponent().setType(DiscriminatorType.VALUE).setPath(discriminator);
}
private static ElementDefinitionSlicingDiscriminatorComponent makeDiscriminator(DiscriminatorType profile, String str) {
return new ElementDefinitionSlicingDiscriminatorComponent().setType(DiscriminatorType.VALUE).setPath(Utilities.noString(str)? "$this" : str);
private static ElementDefinitionSlicingDiscriminatorComponent makeDiscriminator(DiscriminatorType dType, String str) {
return new ElementDefinitionSlicingDiscriminatorComponent().setType(dType).setPath(Utilities.noString(str)? "$this" : str);
}

222
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/model/BaseDateTimeType.java
View File

@ -208,14 +208,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.DAY_OF_MONTH);
}
/**
* Sets the month with 1-index, e.g. 1=the first day of the month
*/
public BaseDateTimeType setDay(int theDay) {
setFieldValue(Calendar.DAY_OF_MONTH, theDay, null, 0, 31);
return this;
}
/**
* Returns the default precision for the given datatype
*/
@ -236,14 +228,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.HOUR_OF_DAY);
}
/**
* Sets the hour of the day in a 24h clock, e.g. 13=1pm
*/
public BaseDateTimeType setHour(int theHour) {
setFieldValue(Calendar.HOUR_OF_DAY, theHour, null, 0, 23);
return this;
}
/**
* Returns the milliseconds within the current second.
* <p>
@ -255,18 +239,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.MILLISECOND);
}
/**
* Sets the milliseconds within the current second.
* <p>
* Note that this method sets the
* same value as {@link #setNanos(long)} but with less precision.
* </p>
*/
public BaseDateTimeType setMillis(int theMillis) {
setFieldValue(Calendar.MILLISECOND, theMillis, null, 0, 999);
return this;
}
/**
* Returns the minute of the hour in the range 0-59
*/
@ -274,14 +246,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.MINUTE);
}
/**
* Sets the minute of the hour in the range 0-59
*/
public BaseDateTimeType setMinute(int theMinute) {
setFieldValue(Calendar.MINUTE, theMinute, null, 0, 59);
return this;
}
/**
* Returns the month with 0-index, e.g. 0=January
*/
@ -289,14 +253,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.MONTH);
}
/**
* Sets the month with 0-index, e.g. 0=January
*/
public BaseDateTimeType setMonth(int theMonth) {
setFieldValue(Calendar.MONTH, theMonth, null, 0, 11);
return this;
}
/**
* Returns the nanoseconds within the current second
* <p>
@ -313,29 +269,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return Long.parseLong(retVal);
}
/**
* Sets the nanoseconds within the current second
* <p>
* Note that this method sets the
* same value as {@link #setMillis(int)} but with more precision.
* </p>
*/
public BaseDateTimeType setNanos(long theNanos) {
validateValueInRange(theNanos, 0, NANOS_PER_SECOND - 1);
String fractionalSeconds = StringUtils.leftPad(Long.toString(theNanos), 9, '0');
// Strip trailing 0s
for (int i = fractionalSeconds.length(); i > 0; i--) {
if (fractionalSeconds.charAt(i - 1) != '0') {
fractionalSeconds = fractionalSeconds.substring(0, i);
break;
}
}
int millis = (int) (theNanos / NANOS_PER_MILLIS);
setFieldValue(Calendar.MILLISECOND, millis, fractionalSeconds, 0, 999);
return this;
}
private int getOffsetIndex(String theValueString) {
int plusIndex = theValueString.indexOf('+', 16);
int minusIndex = theValueString.indexOf('-', 16);
@ -362,19 +295,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return myPrecision;
}
/**
* Sets the precision for this datatype
*
* @throws DataFormatException
*/
public void setPrecision(TemporalPrecisionEnum thePrecision) throws DataFormatException {
if (thePrecision == null) {
throw new NullPointerException("Precision may not be null");
}
myPrecision = thePrecision;
updateStringValue();
}
/**
* Returns the second of the minute in the range 0-59
*/
@ -382,32 +302,17 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.SECOND);
}
/**
* Sets the second of the minute in the range 0-59
*/
public BaseDateTimeType setSecond(int theSecond) {
setFieldValue(Calendar.SECOND, theSecond, null, 0, 59);
return this;
}
/**
* Returns the TimeZone associated with this dateTime's value. May return <code>null</code> if no timezone was
* supplied.
*/
public TimeZone getTimeZone() {
if (myTimeZoneZulu) {
return TimeZone.getTimeZone("Z");
return TimeZone.getTimeZone("GMT");
}
return myTimeZone;
}
public BaseDateTimeType setTimeZone(TimeZone theTimeZone) {
myTimeZone = theTimeZone;
myTimeZoneZulu = false;
updateStringValue();
return this;
}
/**
* Returns the value of this object as a {@link GregorianCalendar}
*/
@ -432,14 +337,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return getFieldValue(Calendar.YEAR);
}
/**
* Sets the year, e.g. 2015
*/
public BaseDateTimeType setYear(int theYear) {
setFieldValue(Calendar.YEAR, theYear, null, 0, 9999);
return this;
}
/**
* To be implemented by subclasses to indicate whether the given precision is allowed by this type
*/
@ -452,13 +349,6 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return myTimeZoneZulu;
}
public BaseDateTimeType setTimeZoneZulu(boolean theTimeZoneZulu) {
myTimeZoneZulu = theTimeZoneZulu;
myTimeZone = null;
updateStringValue();
return this;
}
/**
* Returns <code>true</code> if this object represents a date that is today's date
*
@ -602,6 +492,14 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return retVal;
}
/**
* Sets the month with 1-index, e.g. 1=the first day of the month
*/
public BaseDateTimeType setDay(int theDay) {
setFieldValue(Calendar.DAY_OF_MONTH, theDay, null, 0, 31);
return this;
}
private void setFieldValue(int theField, int theValue, String theFractionalSeconds, int theMinimum, int theMaximum) {
validateValueInRange(theValue, theMinimum, theMaximum);
Calendar cal;
@ -621,6 +519,86 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
super.setValue(cal.getTime());
}
/**
* Sets the hour of the day in a 24h clock, e.g. 13=1pm
*/
public BaseDateTimeType setHour(int theHour) {
setFieldValue(Calendar.HOUR_OF_DAY, theHour, null, 0, 23);
return this;
}
/**
* Sets the milliseconds within the current second.
* <p>
* Note that this method sets the
* same value as {@link #setNanos(long)} but with less precision.
* </p>
*/
public BaseDateTimeType setMillis(int theMillis) {
setFieldValue(Calendar.MILLISECOND, theMillis, null, 0, 999);
return this;
}
/**
* Sets the minute of the hour in the range 0-59
*/
public BaseDateTimeType setMinute(int theMinute) {
setFieldValue(Calendar.MINUTE, theMinute, null, 0, 59);
return this;
}
/**
* Sets the month with 0-index, e.g. 0=January
*/
public BaseDateTimeType setMonth(int theMonth) {
setFieldValue(Calendar.MONTH, theMonth, null, 0, 11);
return this;
}
/**
* Sets the nanoseconds within the current second
* <p>
* Note that this method sets the
* same value as {@link #setMillis(int)} but with more precision.
* </p>
*/
public BaseDateTimeType setNanos(long theNanos) {
validateValueInRange(theNanos, 0, NANOS_PER_SECOND - 1);
String fractionalSeconds = StringUtils.leftPad(Long.toString(theNanos), 9, '0');
// Strip trailing 0s
for (int i = fractionalSeconds.length(); i > 0; i--) {
if (fractionalSeconds.charAt(i - 1) != '0') {
fractionalSeconds = fractionalSeconds.substring(0, i);
break;
}
}
int millis = (int) (theNanos / NANOS_PER_MILLIS);
setFieldValue(Calendar.MILLISECOND, millis, fractionalSeconds, 0, 999);
return this;
}
/**
* Sets the precision for this datatype
*
* @throws DataFormatException
*/
public void setPrecision(TemporalPrecisionEnum thePrecision) throws DataFormatException {
if (thePrecision == null) {
throw new NullPointerException("Precision may not be null");
}
myPrecision = thePrecision;
updateStringValue();
}
/**
* Sets the second of the minute in the range 0-59
*/
public BaseDateTimeType setSecond(int theSecond) {
setFieldValue(Calendar.SECOND, theSecond, null, 0, 59);
return this;
}
private BaseDateTimeType setTimeZone(String theWholeValue, String theValue) {
if (isBlank(theValue)) {
@ -642,6 +620,20 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
return this;
}
public BaseDateTimeType setTimeZone(TimeZone theTimeZone) {
myTimeZone = theTimeZone;
myTimeZoneZulu = false;
updateStringValue();
return this;
}
public BaseDateTimeType setTimeZoneZulu(boolean theTimeZoneZulu) {
myTimeZoneZulu = theTimeZoneZulu;
myTimeZone = null;
updateStringValue();
return this;
}
/**
* Sets the value for this type using the given Java Date object as the time, and using the default precision for
* this datatype (unless the precision is already set), as well as the local timezone as determined by the local operating
@ -729,6 +721,14 @@ public abstract class BaseDateTimeType extends PrimitiveType<Date> {
}
}
/**
* Sets the year, e.g. 2015
*/
public BaseDateTimeType setYear(int theYear) {
setFieldValue(Calendar.YEAR, theYear, null, 0, 9999);
return this;
}
private void throwBadDateFormat(String theValue) {
throw new DataFormatException("Invalid date/time format: \"" + theValue + "\"");
}

2
hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/utils/client/ResourceAddress.java
View File

@ -383,7 +383,7 @@ public class ResourceAddress {
}
public static String getCalendarDateInIsoTimeFormat(Calendar calendar) {
SimpleDateFormat format = new SimpleDateFormat("YYYY-MM-dd'T'hh:mm:ss");//TODO Move out
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss");//TODO Move out
format.setTimeZone(TimeZone.getTimeZone("GMT"));
return format.format(calendar.getTime());
}

0
hapi-fhir-testpage-overlay/src/main/resources/.keep
View File

0
hapi-fhir-validation-resources-dstu3/src/main/java/.keep
View File

12
hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/validation/InstanceValidator.java
View File

@ -339,10 +339,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
switch (bpWarnings) {
case Error:
rule(errors, invalid, line, col, literalPath, test, message);
break;
case Warning:
warning(errors, invalid, line, col, literalPath, test, message);
break;
case Hint:
hint(errors, invalid, line, col, literalPath, test, message);
break;
default: // do nothing
}
}
@ -2452,6 +2455,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer");
else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string", true);
break;
case QUESTION:
case NULL:
break;
}
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, answer, stack, inProgress);
}
@ -3050,11 +3056,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (ei.path.endsWith(".extension"))
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ei.definition != null, "Element is unknown or does not match any slice (url=\"" + ei.element.getNamedChildValue("url") + "\")" + (profile==null ? "" : " for profile " + profile.getUrl()));
else if (!unsupportedSlicing)
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
hint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.path, (ei.definition != null),
"Element " + ei.element.getName() + " is unknown or does not match any slice " + sliceInfo + (profile==null ? "" : " for profile " + profile.getUrl()));
else
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, (ei.definition != null),
"Element " + ei.element.getName() + " is unknown or does not match any slice " + sliceInfo + (profile==null ? "" : " for profile " + profile.getUrl()));
else
@ -3230,7 +3236,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
goodProfiles.put(typeProfile, profileErrors);
}
if (goodProfiles.size()==1) {
errors.addAll(goodProfiles.get(0));
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size()==0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles));
for (List<ValidationMessage> messages : badProfiles) {

3
hapi-fhir-validation/src/main/java/org/hl7/fhir/instance/validation/InstanceValidator.java
View File

@ -333,10 +333,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
switch (bpWarnings) {
case Error:
rule(errors, invalid, line, col, literalPath, test, message);
break;
case Warning:
warning(errors, invalid, line, col, literalPath, test, message);
break;
case Hint:
hint(errors, invalid, line, col, literalPath, test, message);
break;
default: // do nothing
}
}

17
hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/validation/InstanceValidator.java
View File

@ -379,10 +379,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
switch (bpWarnings) {
case Error:
rule(errors, invalid, line, col, literalPath, test, message);
break;
case Warning:
warning(errors, invalid, line, col, literalPath, test, message);
break;
case Hint:
hint(errors, invalid, line, col, literalPath, test, message);
break;
default: // do nothing
}
}
@ -2419,6 +2422,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer");
else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string", true);
break;
case QUESTION:
// TODO: how to validate this???
break;
case NULL:
// Should not happen
break;
}
validateQuestionannaireResponseItems(qsrc, qItem.getItem(), errors, answer, stack, inProgress);
}
@ -3019,11 +3028,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (ei.path.endsWith(".extension"))
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ei.definition != null, "Element is unknown or does not match any slice (url=\"" + ei.element.getNamedChildValue("url") + "\")" + (profile==null ? "" : " for profile " + profile.getUrl()));
else if (!unsupportedSlicing)
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
hint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.path, (ei.definition != null),
"Element " + ei.element.getName() + " is unknown or does not match any slice " + sliceInfo + (profile==null ? "" : " for profile " + profile.getUrl()));
else
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
if (ei.slice!=null && (ei.slice.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN)))
rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, (ei.definition != null),
"Element " + ei.element.getName() + " is unknown or does not match any slice " + sliceInfo + (profile==null ? "" : " for profile " + profile.getUrl()));
else
@ -3220,7 +3229,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
goodProfiles.put(typeProfile, profileErrors);
}
if (goodProfiles.size()==1) {
errors.addAll(goodProfiles.get(0));
/* TODO: this was goodProfiless.get(0) which will always
* return null - Is the first value what was wanted? */
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size()==0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles));
for (List<ValidationMessage> messages : badProfiles) {

8
pom.xml
View File

@ -994,6 +994,11 @@
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
<version>1.2.1</version>
</plugin>
<plugin>
<groupId>de.juplo</groupId>
<artifactId>hibernate-maven-plugin</artifactId>
@ -1908,6 +1913,9 @@
</profile>
<profile>
<id>ERRORPRONE</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>