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Feature/petasos version 1.5 #472

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d55b0b2
Added ADT_A60 support and partial IAM segment support
Dec 2, 2021
b2125d8
Added mapping for allergy categories used by cbord
Dec 2, 2021
9821af1
Enabled support for ADT_A04, ADT_A05 and ADT_A31 (minor changes only)
Dec 2, 2021
7e4f653
configuration changes specific to pegacorn
Dec 2, 2021
e71b61a
Added FHIR Location tree creation under Encounter from input PV1 segment
Dec 6, 2021
de9e6d9
Created pom.xml for ease of building in maven
Dec 7, 2021
cd2e10e
Added fallback processing for any Trigger Event type to try to handle…
Dec 8, 2021
41827ab
Updated artifact id to match changes to pegacorn-ponos
Jan 4, 2022
689b40c
Updated pom file
akinboj Jan 7, 2022
12fe0a1
Altered pom to have parent of pegacorn-ponos and include relative path
Jan 10, 2022
07c3666
Support for Patient Identifier
mhunter0407 Mar 12, 2022
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3 changes: 2 additions & 1 deletion build.gradle
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Expand Up @@ -13,7 +13,8 @@ plugins {
id 'signing'
}

group = 'io.github.linuxforhealth'
// group = 'io.github.linuxforhealth'
group = 'net.fhirfactory.pegacorn'
version = (findProperty('version') == 'unspecified') ? '1.0.1-SNAPSHOT' : version
ext.isReleaseVersion = !version.endsWith("SNAPSHOT")

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2 changes: 1 addition & 1 deletion gradle/wrapper/gradle-wrapper.properties
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@@ -1,5 +1,5 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-6.6.1-bin.zip
distributionUrl=https\://downloads.gradle-dn.com/distributions/gradle-6.6.1-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
263 changes: 263 additions & 0 deletions pom.xml
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@@ -0,0 +1,263 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

<!--***********************************************************************************-->
<!-- WARNING: -->
<!-- This pom file has been created for Pegacorn for ease of deployment. It is based -->
<!-- off of the pom generated by gradle and manually altered. It does not run tests -->
<!-- correctly. Any merging of upstream development (from linuxforhealth) may require -->
<!-- manual changes to this pom. Alternatively the install can be created directly -->
<!-- from gradle using 'gradle publishToMavenLocal' and then generating as normal. -->
<!-- Note that there is option to call gradle publish from maven using a plugin but -->
<!-- this option has not been looked into in detail -->
<!--***********************************************************************************-->

<modelVersion>4.0.0</modelVersion>

<!--***********************************************************************************-->
<!-- -->
<!-- Project Metadata -->
<!-- -->
<!--***********************************************************************************-->

<parent>
<groupId>net.fhirfactory.pegacorn</groupId>
<artifactId>pegacorn</artifactId>
<version>1.5.0-SNAPSHOT</version>
<relativePath>../pegacorn</relativePath>
</parent>

<artifactId>pegacorn-hl7v2-fhir-converter</artifactId>
<packaging>jar</packaging>
<version>1.0.1-SNAPSHOT</version>

<name>Pegacorn :: HL7-FHIR-Converter</name>
<description>Converter of HL7 to FHIR JSON</description>

<!--***********************************************************************************-->
<!-- -->
<!-- Project Dependencies -->
<!-- -->
<!--***********************************************************************************-->

<!-- TODO: change from explicit versions to properties -->

<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.9</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>23.0</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-base</artifactId>
<version>2.3</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi</groupId>
<artifactId>hapi-structures-v26</artifactId>
<version>2.3</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jsr310</artifactId>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-jdk8</artifactId>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>2.10.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.8</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation</artifactId>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jexl3</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-configuration2</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>4.4</version>
</dependency>
<dependency>
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-registry</artifactId>
<version>4.9.0</version>
</dependency>
<dependency>
<groupId>com.ibm.fhir</groupId>
<artifactId>fhir-term</artifactId>
<version>4.9.0</version>
</dependency>
<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.9.4</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.assertj</groupId>
<artifactId>assertj-core</artifactId>
<version>3.9.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>jakarta.json</groupId>
<artifactId>jakarta.json-api</artifactId>
<version>2.0.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.7.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<version>5.7.2</version>
<scope>test</scope>
</dependency>

<!--*******************************************************************************-->
<!-- Logging (SLF4J) Libraries -->
<!--*******************************************************************************-->

<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${version-ch.qos.logback-classic}</version>
<scope>compile</scope>
</dependency>

<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${version-ch.qos.logback-classic}</version>
<scope>compile</scope>
</dependency>

</dependencies>

<!--***********************************************************************************-->
<!-- -->
<!-- Project Build -->
<!-- -->
<!--***********************************************************************************-->

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${version-org.apache.maven-compiler-plugin}</version>
<configuration>
<source>${maven.compiler.source}</source>
<target>${maven.compiler.target}</target>
</configuration>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${version-org.apache.maven-surefire-plugin}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${version-org.apache.maven-failsafe-plugin}</version>
</plugin>

</plugins>
</build>

<!--***********************************************************************************-->
<!-- -->
<!-- Project Profiles -->
<!-- -->
<!--***********************************************************************************-->

<profiles>
<profile>
<!-- The default profile skips all tests as this pom does not yet run tests correctly -->
<id>default</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${version-org.apache.maven-surefire-plugin}</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>

</project>
11 changes: 10 additions & 1 deletion src/main/java/io/github/linuxforhealth/hl7/HL7ToFHIRConverter.java
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Expand Up @@ -40,6 +40,7 @@
public class HL7ToFHIRConverter {
private static HL7HapiParser hparser = new HL7HapiParser();
private static final Logger LOGGER = LoggerFactory.getLogger(HL7ToFHIRConverter.class);
private static final String FALLBACK_BASE = "Fallback_Base"; // fallback configuration file to use when Trigger Event does not match anything (only used if enabled in supported.hl7.messages)
private Map<String, HL7MessageModel> messagetemplates = new HashMap<>();

/**
Expand Down Expand Up @@ -130,7 +131,15 @@ public String convert(String hl7MessageData, ConverterOptions options) {
if (hl7MessageTemplateModel != null) {
return hl7MessageTemplateModel.convert(hl7message, engine);
} else {
throw new UnsupportedOperationException("Message type not yet supported " + messageType);
// try to get the our fallback template
hl7MessageTemplateModel = messagetemplates.get(FALLBACK_BASE);
if (hl7MessageTemplateModel != null) {
// fallback template is enabled so use it just like a normal message template model
return hl7MessageTemplateModel.convert(hl7message, engine);
} else {
// it is not enabled by being in the supported.hl7.messages
throw new UnsupportedOperationException("Message type not yet supported " + messageType);
}
}
} else {
throw new IllegalArgumentException("Parsed HL7 message was null.");
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1 change: 1 addition & 0 deletions src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataTypeMapper.java
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Expand Up @@ -44,6 +44,7 @@ public enum SimpleDataTypeMapper {
ALLERGY_INTOLERANCE_CATEGORY(SimpleDataValueResolver.ALLERGY_INTOLERANCE_CATEGORY_CODE_FHIR),
ALLERGY_INTOLERANCE_CRITICALITY(
SimpleDataValueResolver.ALLERGY_INTOLERANCE_CRITICALITY_CODE_FHIR),
ALLERGY_INTOLERANCE_TYPE(SimpleDataValueResolver.ALLERGY_INTOLERANCE_TYPE_CODE_FHIR),
ADMINISTRATIVE_GENDER(SimpleDataValueResolver.ADMINISTRATIVE_GENDER_CODE_FHIR),
CONDITION_CATEGORY_CODES(SimpleDataValueResolver.CONDITION_CATEGORY_CODES),
DIAGNOSTIC_REPORT_STATUS(SimpleDataValueResolver.DIAGNOSTIC_REPORT_STATUS_CODES),
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6 changes: 6 additions & 0 deletions src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataValueResolver.java
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Expand Up @@ -32,6 +32,7 @@
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCriticality;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceType;
import org.hl7.fhir.r4.model.DiagnosticReport.DiagnosticReportStatus;
import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.Immunization.ImmunizationStatus;
Expand Down Expand Up @@ -577,6 +578,11 @@ private static final SimpleCode commonCodingSystemV2 (String table, String code,
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, AllergyIntoleranceCategory.class);
};

public static final ValueExtractor<Object, String> ALLERGY_INTOLERANCE_TYPE_CODE_FHIR = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
return getFHIRCode(val, AllergyIntoleranceType.class);
};

public static final ValueExtractor<Object, String> DOSE_SYSTEM = (Object value) -> {
String val = Hl7DataHandlerUtil.getStringValue(value);
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4 changes: 2 additions & 2 deletions src/main/resources/config.properties
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@@ -1,4 +1,4 @@
base.path.resource=
supported.hl7.messages=ADT_A01, ADT_A08, ADT_A34, ADT_A40, MDM_T02, MDM_T06, ORM_O01, OMP_O09, ORU_R01, PPR_PC1, RDE_O11, RDE_O25, VXU_V04
default.zoneid=+08:00
supported.hl7.messages=Fallback_Base, ADT_A01, ADT_A04, ADT_A05, ADT_A08, ADT_A31, ADT_A34, ADT_A40, ADT_A60, MDM_T02, MDM_T06, ORM_O01, OMP_O09, ORU_R01, PPR_PC1, RDE_O11, RDE_O25, VXU_V04
default.zoneid=+11:00
additional.conceptmap.file=
1 change: 1 addition & 0 deletions src/main/resources/fhir/resourcemapping.yml
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Expand Up @@ -12,6 +12,7 @@ Condition: org.hl7.fhir.r4.model.Condition
Practitioner: org.hl7.fhir.r4.model.Practitioner
DiagnosticReport: org.hl7.fhir.r4.model.DiagnosticReport
Immunization: org.hl7.fhir.r4.model.Immunization
Location: org.hl7.fhir.r4.model.Location
Organization: org.hl7.fhir.r4.model.Organization
MessageHeader: org.hl7.fhir.r4.model.MessageHeader
Medication: org.hl7.fhir.r4.model.Medication
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5 changes: 5 additions & 0 deletions src/main/resources/hl7/codesystem/v2ToFhirMapping.yml
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Expand Up @@ -7,14 +7,19 @@
AllergyIntoleranceCategory:
AA: environment
DA: medication
DRUG: medication
EA: environment
FA: food
FOOD: food
LA: environment
PA: environment
AllergyIntoleranceCriticality:
MI: low
SV: high
U: unable-to-assess
AllergyIntoleranceType:
AL: allergy
IN: intolerance
ObservationStatus:
C: corrected
D: cancelled
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