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Snowstorm Lite rename.
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kaicode committed Sep 15, 2023
1 parent 6903e7f commit 017d128
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Showing 43 changed files with 124 additions and 128 deletions.
8 changes: 4 additions & 4 deletions pom.xml
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<project xmlns="http:https://maven.apache.org/POM/4.0.0" xmlns:xsi="http:https://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http:https://maven.apache.org/POM/4.0.0 http:https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<name>Snowstorm Micro</name>
<description>SNOMED CT FHIR Terminology Server, with a small memory footprint</description>
<name>Snowstorm Lite</name>
<description>SNOMED-CT FHIR Terminology Server, with a small memory footprint</description>

<artifactId>snowstorm-micro</artifactId>
<artifactId>snowstorm-lite</artifactId>
<version>1.0.0-SNAPSHOT</version>
<parent>
<groupId>org.snomed</groupId>
Expand Down Expand Up @@ -148,7 +148,7 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<mainClass>org.snomed.snowstormmicro.SnowstormMicroApplication</mainClass>
<mainClass>org.snomed.snowstormlite.SnowstormLiteApplication</mainClass>
</configuration>
<executions>
<execution>
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4 changes: 2 additions & 2 deletions readme.md
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@@ -1,5 +1,5 @@
# Snowstorm Micro
A FHIR Terminology server for SNOMED CT with a minimal memory footprint.
# Snowstorm Lite FHIR Terminology Server _(Beta)_
A fast FHIR Terminology Server for SNOMED CT with a small memory footprint.

## Loading SNOMED CT
Start with the `--load` parameter with the path to an RF2 snapshot archive to load
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package org.snomed.snowstormmicro;
package org.snomed.snowstormlite;

import org.hibernate.service.spi.ServiceException;
import org.ihtsdo.otf.snomedboot.ReleaseImportException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.snomed.snowstormmicro.service.AppSetupService;
import org.snomed.snowstormlite.service.AppSetupService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.CommandLineRunner;
import org.springframework.boot.SpringApplication;
Expand All @@ -22,7 +22,7 @@
ThymeleafAutoConfiguration.class
}
)
public class SnowstormMicroApplication implements CommandLineRunner {
public class SnowstormLiteApplication implements CommandLineRunner {

@Autowired
private AppSetupService appSetupService;
Expand All @@ -42,7 +42,7 @@ public void run(String... args) {
}

public static void main(String[] args) {
SpringApplication.run(SnowstormMicroApplication.class, args);
SpringApplication.run(SnowstormLiteApplication.class, args);
}

}
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.config;
package org.snomed.snowstormlite.config;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.EncodingEnum;
Expand All @@ -20,7 +20,7 @@ public ServletRegistrationBean<HapiRestfulServlet> hapi() {
HapiRestfulServlet hapiServlet = new HapiRestfulServlet();

ServletRegistrationBean<HapiRestfulServlet> servletRegistrationBean = new ServletRegistrationBean<>(hapiServlet, "/*");
hapiServlet.setServerName("Snowstorm Micro FHIR Server");
hapiServlet.setServerName("Snowstorm Lite FHIR Server");
hapiServlet.setServerVersion(getClass().getPackage().getImplementationVersion());
hapiServlet.setDefaultResponseEncoding(EncodingEnum.JSON);

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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.config;
package org.snomed.snowstormlite.config;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.LenientErrorHandler;
Expand All @@ -7,9 +7,9 @@
import ca.uhn.fhir.rest.server.RestfulServer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.snomed.snowstormmicro.fhir.CodeSystemProvider;
import org.snomed.snowstormmicro.fhir.FHIRTerminologyCapabilitiesProvider;
import org.snomed.snowstormmicro.fhir.ValueSetProvider;
import org.snomed.snowstormlite.fhir.CodeSystemProvider;
import org.snomed.snowstormlite.fhir.FHIRTerminologyCapabilitiesProvider;
import org.snomed.snowstormlite.fhir.ValueSetProvider;
import org.springframework.web.context.WebApplicationContext;
import org.springframework.web.context.support.WebApplicationContextUtils;

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package org.snomed.snowstormmicro.config;
package org.snomed.snowstormlite.config;

import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
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@@ -1,8 +1,7 @@
package org.snomed.snowstormmicro.domain;
package org.snomed.snowstormlite.domain;

import org.hl7.fhir.r4.model.Enumerations;
import org.jetbrains.annotations.NotNull;
import org.snomed.snowstormmicro.fhir.FHIRConstants;
import org.snomed.snowstormlite.fhir.FHIRConstants;

import java.util.Calendar;
import java.util.GregorianCalendar;
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@@ -1,19 +1,19 @@
package org.snomed.snowstormmicro.domain;
package org.snomed.snowstormlite.domain;

import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.snomed.snowstormmicro.fhir.FHIRConstants;
import org.snomed.snowstormmicro.service.NormalFormBuilder;
import org.snomed.snowstormmicro.service.TermProvider;
import org.snomed.snowstormlite.fhir.FHIRConstants;
import org.snomed.snowstormlite.service.NormalFormBuilder;
import org.snomed.snowstormlite.service.TermProvider;

import java.io.IOException;
import java.util.*;

import static java.lang.String.format;
import static org.snomed.snowstormmicro.fhir.FHIRConstants.PREFERED_FOR_LANGUAGE_CODING;
import static org.snomed.snowstormmicro.fhir.FHIRHelper.createProperty;
import static org.snomed.snowstormlite.fhir.FHIRConstants.PREFERED_FOR_LANGUAGE_CODING;
import static org.snomed.snowstormlite.fhir.FHIRHelper.createProperty;

public class Concept {

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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.domain;
package org.snomed.snowstormlite.domain;

public class Concepts {

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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.domain;
package org.snomed.snowstormlite.domain;

import java.util.HashSet;
import java.util.Objects;
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.domain;
package org.snomed.snowstormlite.domain;

import org.jetbrains.annotations.NotNull;

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@@ -1,10 +1,10 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.server.IResourceProvider;
import org.hl7.fhir.r4.model.*;
import org.snomed.snowstormmicro.service.CodeSystemRepository;
import org.snomed.snowstormmicro.service.CodeSystemService;
import org.snomed.snowstormlite.service.CodeSystemRepository;
import org.snomed.snowstormlite.service.CodeSystemService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

Expand All @@ -15,8 +15,8 @@
import java.util.List;

import static java.lang.String.format;
import static org.snomed.snowstormmicro.fhir.FHIRHelper.*;
import static org.snomed.snowstormmicro.service.Constants.ACCEPT_LANGUAGE_HEADER;
import static org.snomed.snowstormlite.fhir.FHIRHelper.*;
import static org.snomed.snowstormlite.service.Constants.ACCEPT_LANGUAGE_HEADER;

@Component
public class CodeSystemProvider implements IResourceProvider {
Expand All @@ -32,7 +32,7 @@ public List<CodeSystem> findCodeSystems(
@OptionalParam(name="id") String id,
@OptionalParam(name="url") String url) throws IOException {
List<CodeSystem> codeSystems = new ArrayList<>();
org.snomed.snowstormmicro.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
org.snomed.snowstormlite.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
if (codeSystem != null) {
CodeSystem hapi = codeSystem.toHapi();
if ((id == null || hapi.getId().equals(id)) && (url == null || hapi.getUrl().equals(url))) {
Expand All @@ -45,7 +45,7 @@ public List<CodeSystem> findCodeSystems(
@Read()
public CodeSystem getCodeSystem(@IdParam IdType id) throws IOException {
String idPart = id.getIdPart();
org.snomed.snowstormmicro.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
org.snomed.snowstormlite.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
if (codeSystem != null) {
CodeSystem hapi = codeSystem.toHapi();
if (hapi.getId().equals(idPart)) {
Expand All @@ -69,14 +69,14 @@ public Parameters lookupImplicit(

mutuallyExclusive("code", code, "coding", coding);
notSupported("date", date);
org.snomed.snowstormmicro.domain.CodeSystem codeSystem = getCodeSystemVersionOrThrow(system, version, coding);
org.snomed.snowstormlite.domain.CodeSystem codeSystem = getCodeSystemVersionOrThrow(system, version, coding);
return codeSystemService.lookup(codeSystem, recoverCode(code, coding), displayLanguage, request.getHeader(ACCEPT_LANGUAGE_HEADER), propertiesType);
}

private org.snomed.snowstormmicro.domain.CodeSystem getCodeSystemVersionOrThrow(UriType system, StringType version, Coding coding) {
private org.snomed.snowstormlite.domain.CodeSystem getCodeSystemVersionOrThrow(UriType system, StringType version, Coding coding) {
try {
CodeSystemVersionParams codeSystemVersionParams = getCodeSystemVersionParams(system, version, coding);
org.snomed.snowstormmicro.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
org.snomed.snowstormlite.domain.CodeSystem codeSystem = codeSystemRepository.getCodeSystem();
if (codeSystemVersionParams.matchesCodeSystem(codeSystem)) {
return codeSystem;
}
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@@ -1,10 +1,10 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import org.hl7.fhir.r4.model.StringType;
import org.snomed.snowstormmicro.domain.CodeSystem;
import org.snomed.snowstormlite.domain.CodeSystem;

import static org.snomed.snowstormmicro.fhir.FHIRConstants.SNOMED_URI;
import static org.snomed.snowstormmicro.fhir.FHIRConstants.SNOMED_URI_UNVERSIONED;
import static org.snomed.snowstormlite.fhir.FHIRConstants.SNOMED_URI;
import static org.snomed.snowstormlite.fhir.FHIRConstants.SNOMED_URI_UNVERSIONED;

public class CodeSystemVersionParams {

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@@ -1,7 +1,7 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import org.hl7.fhir.r4.model.Coding;
import org.snomed.snowstormmicro.domain.Concepts;
import org.snomed.snowstormlite.domain.Concepts;

public interface FHIRConstants {

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@@ -1,13 +1,13 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import org.hl7.fhir.r4.model.*;

import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static java.lang.String.format;
import static org.snomed.snowstormmicro.fhir.FHIRConstants.SNOMED_URI;
import static org.snomed.snowstormmicro.fhir.FHIRConstants.SNOMED_URI_UNVERSIONED;
import static org.snomed.snowstormlite.fhir.FHIRConstants.SNOMED_URI;
import static org.snomed.snowstormlite.fhir.FHIRConstants.SNOMED_URI_UNVERSIONED;

public class FHIRHelper {

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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import ca.uhn.fhir.model.api.annotation.ChildOrder;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.fhir;
package org.snomed.snowstormlite.fhir;

import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
Expand All @@ -8,15 +8,15 @@
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.snomed.snowstormmicro.service.ValueSetService;
import org.snomed.snowstormlite.service.ValueSetService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

import java.io.IOException;
import java.util.Collections;
import java.util.List;

import static org.snomed.snowstormmicro.fhir.FHIRHelper.exception;
import static org.snomed.snowstormlite.fhir.FHIRHelper.exception;

@Component
public class ValueSetProvider implements IResourceProvider {
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.service;
package org.snomed.snowstormlite.service;

import org.apache.logging.log4j.util.Strings;
import org.apache.lucene.index.DirectoryReader;
Expand All @@ -7,8 +7,8 @@
import org.ihtsdo.otf.snomedboot.ReleaseImportException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.snomed.snowstormmicro.snomedimport.ImportService;
import org.snomed.snowstormmicro.util.TimerUtil;
import org.snomed.snowstormlite.snomedimport.ImportService;
import org.snomed.snowstormlite.util.TimerUtil;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
Expand All @@ -19,7 +19,7 @@
import java.util.Set;
import java.util.stream.Collectors;

import static org.snomed.snowstormmicro.fhir.FHIRHelper.SNOMED_URI_MODULE_AND_VERSION_PATTERN;
import static org.snomed.snowstormlite.fhir.FHIRHelper.SNOMED_URI_MODULE_AND_VERSION_PATTERN;

@Service
public class AppSetupService {
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@@ -1,14 +1,14 @@
package org.snomed.snowstormmicro.service;
package org.snomed.snowstormlite.service;

import org.apache.lucene.document.*;
import org.apache.lucene.index.IndexableField;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.*;
import org.snomed.snowstormmicro.domain.CodeSystem;
import org.snomed.snowstormmicro.domain.Concept;
import org.snomed.snowstormmicro.domain.Description;
import org.snomed.snowstormmicro.domain.Relationship;
import org.snomed.snowstormmicro.fhir.FHIRHelper;
import org.snomed.snowstormlite.domain.CodeSystem;
import org.snomed.snowstormlite.domain.Concept;
import org.snomed.snowstormlite.domain.Description;
import org.snomed.snowstormlite.domain.Relationship;
import org.snomed.snowstormlite.fhir.FHIRHelper;
import org.springframework.stereotype.Service;

import java.io.IOException;
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@@ -1,17 +1,17 @@
package org.snomed.snowstormmicro.service;
package org.snomed.snowstormlite.service;

import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Parameters;
import org.snomed.snowstormmicro.domain.CodeSystem;
import org.snomed.snowstormmicro.domain.Concept;
import org.snomed.snowstormlite.domain.CodeSystem;
import org.snomed.snowstormlite.domain.Concept;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;

import java.io.IOException;
import java.util.List;

import static org.snomed.snowstormmicro.fhir.FHIRHelper.exception;
import static org.snomed.snowstormlite.fhir.FHIRHelper.exception;

@Service
public class CodeSystemService {
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@@ -1,4 +1,4 @@
package org.snomed.snowstormmicro.service;
package org.snomed.snowstormlite.service;

public class Constants {

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@@ -1,7 +1,7 @@
package org.snomed.snowstormmicro.service;
package org.snomed.snowstormlite.service;

import org.snomed.snowstormmicro.domain.Concept;
import org.snomed.snowstormmicro.domain.Relationship;
import org.snomed.snowstormlite.domain.Concept;
import org.snomed.snowstormlite.domain.Relationship;

import java.io.IOException;
import java.util.HashMap;
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