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Merge remote-tracking branch
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'origin/issues/53_timestamp_encoding_in_search_bundle' into develop
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@hhund
hhund committed Jun 7, 2022
2 parents 636fee3 + 86b53a7 commit 9c015fd
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Showing 4 changed files with 290 additions and 34 deletions.
10 changes: 10 additions & 0 deletions codex-process-data-transfer/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,11 @@
<artifactId>hapi-fhir-client</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>de.hs-heilbronn.mi</groupId>
Expand All @@ -37,6 +42,11 @@
<artifactId>dsf-fhir-validation</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

<build>
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135 changes: 102 additions & 33 deletions ...rk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,20 @@
import java.nio.file.Files;
import java.nio.file.Path;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import java.util.stream.Stream;

import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
Expand All @@ -31,6 +35,9 @@
import org.hl7.fhir.r4.model.Patient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.web.util.UriComponents;
import org.springframework.web.util.UriComponents.UriTemplateVariables;
import org.springframework.web.util.UriComponentsBuilder;

import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.Constants;
Expand Down Expand Up @@ -91,6 +98,63 @@ public abstract class AbstractFhirClient implements GeccoFhirClient
private static final SimpleDateFormat DAY_FORMAT = new SimpleDateFormat("yyyy-MM-dd");
private static final SimpleDateFormat TIME_FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSXXX");

private static final class QueryParameters implements UriTemplateVariables
{
final List<QuerParameter> parameters = new ArrayList<>();

@Override
public Object getValue(String name)
{
return parameters.stream().filter(p -> p.getValue(name) != null).findFirst().map(p -> p.getValue(name))
.orElseThrow(() -> new IllegalArgumentException("No value for '" + name + "'"));
}

boolean add(QuerParameter param)
{
if (param != null)
return parameters.add(param);
else
return false;
}

void replace(UriComponentsBuilder urlBuilder)
{
parameters.forEach(p -> p.replace(urlBuilder));
}
}

private static final class QuerParameter
{
final String name;
final Map<String, String> valuesByTemplateParameter = new HashMap<>();

QuerParameter(String templateParameter, String name, String... values)
{
Objects.requireNonNull(templateParameter, "templateParameter");
Objects.requireNonNull(name, "name");
Objects.requireNonNull(values, "values");

this.name = name;
IntStream.range(0, values.length).forEach(i ->
{
if (values[i] != null)
valuesByTemplateParameter.put(templateParameter + "_" + i, values[i]);
});
}

void replace(UriComponentsBuilder builder)
{
builder.replaceQueryParam(name);
valuesByTemplateParameter.keySet()
.forEach(templateParam -> builder.queryParam(name, "{" + templateParam + "}"));
}

String getValue(String templateParameter)
{
return valuesByTemplateParameter.get(templateParameter);
}
}

protected final GeccoClient geccoClient;

/**
Expand Down Expand Up @@ -343,71 +407,78 @@ private Function<BundleEntryComponent, BundleEntryComponent> modifySearchUrl(Str
}

String resource = queryPatternMatcher.group("resource");
String query = queryPatternMatcher.group("query");
UriComponentsBuilder urlBuilder = UriComponentsBuilder.fromUriString(entry.getRequest().getUrl());
QueryParameters queryParameters = new QueryParameters();

if (RESOURCES_WITH_PATIENT_REF.contains(resource))
{
if (patientId != null)
query += createPatIdSearchUrlPart(patientId);
queryParameters.add(createPatIdSearchUrlPart(patientId));
else
query += createPatPrefixPseudonymSearchUrlPart(pseudonym);
queryParameters.add(createPatPrefixPseudonymSearchUrlPart(pseudonym));

if (includePatient)
query += createIncludeSearchUrlPart(resource);
queryParameters.add(createIncludeSearchUrlPart(resource));
}
else if ("Patient".equals(resource))
{
// filtering search for patient if patient id known
if (patientId != null)
return null;

query += createPseudonymSearchUrlPart(pseudonym);
else
queryParameters.add(createPseudonymSearchUrlPart(pseudonym));
}
else
{
logger.warn(
"Search-Bundle contains entry with invalid serach query {}, target resource {} not supported",
resource + query, resource);
entry.getRequest().getUrl(), resource);
throw new RuntimeException("Search-Bundle contains entry with invalid serach query, target resource "
+ resource + " not supported");
}

query += createExportFromSearchUrlPart(exportFrom);
query += createExportToSearchUrlPart(exportTo);
queryParameters.add(new QuerParameter("from_to", "_lastUpdated", createExportFromSearchUrlPart(exportFrom),
createExportToSearchUrlPart(exportTo)));

entry.getRequest().setUrl(resource + query);
queryParameters.replace(urlBuilder);
UriComponents url = urlBuilder.encode().build().expand(queryParameters);

entry.getRequest().setUrl(url.toString());
return entry;
};
}

private String createPseudonymSearchUrlPart(String pseudonym)
private QuerParameter createPseudonymSearchUrlPart(String pseudonym)
{
if (pseudonym != null && !pseudonym.isBlank())
return "&identifier=" + NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM + "|" + pseudonym;
if (pseudonym == null || pseudonym.isBlank())
return null;
else
return "";
return new QuerParameter("pseudonym", "identifier",
NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM + "|" + pseudonym);
}

private String createPatIdSearchUrlPart(String patientId)
private QuerParameter createPatIdSearchUrlPart(String patientId)
{
if (patientId != null && !patientId.isBlank())
return "&patient=" + patientId;
if (patientId == null || patientId.isBlank())
return null;
else
return "";
return new QuerParameter("patientId", "patient", patientId);
}

private String createPatPrefixPseudonymSearchUrlPart(String pseudonym)
private QuerParameter createPatPrefixPseudonymSearchUrlPart(String pseudonym)
{
if (pseudonym != null && !pseudonym.isBlank())
return "&patient:identifier=" + NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM + "|" + pseudonym;
if (pseudonym == null || pseudonym.isBlank())
return null;
else
return "";
return new QuerParameter("pseudonym", "patient:identifier",
NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM + "|" + pseudonym);
}

private String createExportFromSearchUrlPart(DateWithPrecision exportFrom)
{
if (exportFrom != null)
if (exportFrom == null)
return null;
else
{
String dateTime = null;
switch (exportFrom.getPrecision())
Expand All @@ -432,26 +503,24 @@ private String createExportFromSearchUrlPart(DateWithPrecision exportFrom)
"TemporalPrecisionEnum value " + exportFrom.getPrecision() + " not supported");
}

return "&_lastUpdated=ge" + dateTime;
return "ge" + dateTime;
}
else
return "";
}

private String createExportToSearchUrlPart(Date exportTo)
{
if (exportTo != null)
return "&_lastUpdated=lt" + TIME_FORMAT.format(exportTo);
if (exportTo == null)
return null;
else
return "";
return "lt" + TIME_FORMAT.format(exportTo);
}

private String createIncludeSearchUrlPart(String resource)
private QuerParameter createIncludeSearchUrlPart(String resource)
{
if (resource != null)
return "&_include=" + resource + ":patient";
if (resource == null)
return null;
else
return "";
return new QuerParameter("include_resource", "_include", resource + ":patient");
}

protected Stream<DomainResource> getDomainResources(Bundle bundle)
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