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Feature/multiple mandates #136

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merged 10 commits into from
Oct 15, 2024
Merged

Feature/multiple mandates #136

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f1ba103
work on docker compose file
mafasva Jul 17, 2024
8529fdf
make docker compose runnable
mafasva Jul 25, 2024
2ce54c5
Add client config map into receive process
mafasva Jul 30, 2024
14b5b3b
Add assumption for study ID to task; !only dummy, revert bevor PR!
mafasva Jul 30, 2024
744de2a
client config as map, with test property file
mafasva Jul 31, 2024
92a20d3
receive: multiple client first try
mafasva Jul 31, 2024
2f57b43
cleanup and renaming
mafasva Aug 1, 2024
aa3ebe2
add tests and cleanups
mafasva Aug 5, 2024
24d84a2
revert assumption task with study ID
mafasva Aug 5, 2024
39d54a4
update error log massage, add target store key
mafasva Aug 7, 2024
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15 changes: 13 additions & 2 deletions codex-process-data-transfer/pom.xml
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Expand Up @@ -65,6 +65,17 @@
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
<version>6.0.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
Expand Down Expand Up @@ -102,7 +113,7 @@
<createDependencyReducedPom>false</createDependencyReducedPom>
<artifactSet>
<excludes>

</excludes>
</artifactSet>
</configuration>
Expand Down Expand Up @@ -263,4 +274,4 @@
</plugin>
</plugins>
</build>
</project>
</project>
1 change: 1 addition & 0 deletions ...de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java
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Expand Up @@ -43,6 +43,7 @@ public interface ConstantsDataTransfer
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_EXPORT_TO = "export-to";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE = "data-reference";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DRY_RUN = "dry-run";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_STUDY_ID = "study-id";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_ENCRYPTED_BUNDLE_SIZE = "encrypted-bundle-size";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_LOCAL_VALIDATION_SUCCESSFUL = "local-validation-successful";
String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_ENCRYPTED_BUNDLE_RESOURCES_COUNT = "encrypted-bundle-resources-count";
Expand Down
11 changes: 2 additions & 9 deletions ...iversitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java
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Expand Up @@ -5,14 +5,7 @@
import java.util.List;
import java.util.Map;

import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ProcessPluginDeploymentConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ReceiveConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.SendConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.TransferDataConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.TransferDataSerializerConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.TranslateConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.TriggerConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ValidationConfig;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.*;
import dev.dsf.bpe.v1.ProcessPluginDefinition;

public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition
Expand Down Expand Up @@ -49,7 +42,7 @@ public List<Class<?>> getSpringConfigurations()
{
return List.of(TransferDataConfig.class, TransferDataSerializerConfig.class, ValidationConfig.class,
TriggerConfig.class, SendConfig.class, TranslateConfig.class, ReceiveConfig.class,
ProcessPluginDeploymentConfig.class);
ReceiveDataStoreConfig.class, ProcessPluginDeploymentConfig.class);
}

@Override
Expand Down
67 changes: 43 additions & 24 deletions ...erk_universitaetsmedizin/codex/processes/data_transfer/client/DataStoreClientFactory.java
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Expand Up @@ -9,6 +9,7 @@
import java.security.cert.Certificate;
import java.security.cert.CertificateException;
import java.security.cert.X509Certificate;
import java.util.Map;
import java.util.UUID;

import org.bouncycastle.pkcs.PKCSException;
Expand All @@ -20,13 +21,15 @@
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.DataStoreFhirClient;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.DataStoreFhirClientStub;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ReceiveDataStoreConfig;
import de.rwh.utils.crypto.CertificateHelper;
import de.rwh.utils.crypto.io.CertificateReader;
import de.rwh.utils.crypto.io.PemIo;

public class DataStoreClientFactory
{
private static final Logger logger = LoggerFactory.getLogger(DataStoreClientFactory.class);
private static final String DEFAULT_DATA_STORE = "default";

private static final class DataStoreClientStub implements DataStoreClient
{
Expand Down Expand Up @@ -91,10 +94,7 @@ public boolean shouldUseChainedParameterNotLogicalReference()
private final int socketTimeout;
private final int connectionRequestTimeout;

private final String dataStoreServerBase;
private final String dataStoreServerBasicAuthUsername;
private final String dataStoreServerBasicAuthPassword;
private final String dataStoreServerBearerToken;
private final Map<String, ReceiveDataStoreConfig.DataStoreConnectionValues> dataStoreConnectionMap;

private final String proxyUrl;
private final String proxyUsername;
Expand All @@ -112,7 +112,8 @@ public boolean shouldUseChainedParameterNotLogicalReference()
public DataStoreClientFactory(Path trustStorePath, Path certificatePath, Path privateKeyPath,
char[] privateKeyPassword, int connectTimeout, int socketTimeout, int connectionRequestTimeout,
String dataStoreServerBase, String dataStoreServerBasicAuthUsername,
String dataStoreServerBasicAuthPassword, String dataStoreServerBearerToken, String proxyUrl,
String dataStoreServerBasicAuthPassword, String dataStoreServerBearerToken,
Map<String, ReceiveDataStoreConfig.DataStoreConnectionValues> dataStoreConnectionMap, String proxyUrl,
String proxyUsername, String proxyPassword, boolean hapiClientVerbose, FhirContext fhirContext,
Path searchBundleOverride, Class<DataStoreFhirClient> dataStoreFhirClientClass,
boolean useChainedParameterNotLogicalReference, DataLogger dataLogger)
Expand All @@ -126,10 +127,11 @@ public DataStoreClientFactory(Path trustStorePath, Path certificatePath, Path pr
this.socketTimeout = socketTimeout;
this.connectionRequestTimeout = connectionRequestTimeout;

this.dataStoreServerBase = dataStoreServerBase;
this.dataStoreServerBasicAuthUsername = dataStoreServerBasicAuthUsername;
this.dataStoreServerBasicAuthPassword = dataStoreServerBasicAuthPassword;
this.dataStoreServerBearerToken = dataStoreServerBearerToken;
this.dataStoreConnectionMap = dataStoreConnectionMap;
this.dataStoreConnectionMap.put(DEFAULT_DATA_STORE,
new ReceiveDataStoreConfig.DataStoreConnectionValues(dataStoreServerBase,
dataStoreServerBasicAuthUsername, dataStoreServerBasicAuthPassword,
dataStoreServerBearerToken));

this.proxyUrl = proxyUrl;
this.proxyUsername = proxyUsername;
Expand All @@ -146,21 +148,25 @@ public DataStoreClientFactory(Path trustStorePath, Path certificatePath, Path pr

public String getServerBase()
{
return dataStoreServerBase;
return dataStoreConnectionMap.get(DEFAULT_DATA_STORE).getBaseUrl();
}

public void testConnection()
{
try
{
logger.info(
"Testing connection to Data Store FHIR server with {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {},"
+ " basicAuthUsername: {}, basicAuthPassword: {}, bearerToken: {}, serverBase: {}, proxy: values from 'DEV_DSF_PROXY'... config}",
trustStorePath, certificatePath, privateKeyPath, privateKeyPassword != null ? "***" : "null",
dataStoreServerBasicAuthUsername, dataStoreServerBasicAuthPassword != null ? "***" : "null",
dataStoreServerBearerToken != null ? "***" : "null", dataStoreServerBase);

getDataStoreClient().testConnection();
for (String client : dataStoreConnectionMap.keySet())
{
final ReceiveDataStoreConfig.DataStoreConnectionValues value = dataStoreConnectionMap.get(client);
logger.info(
"Testing connection to Data Store FHIR server with {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {},"
+ " basicAuthUsername: {}, basicAuthPassword: {}, bearerToken: {}, serverBase: {}, proxy: values from 'DEV_DSF_PROXY'... config}",
trustStorePath, certificatePath, privateKeyPath, privateKeyPassword != null ? "***" : "null",
value.getBaseUrl(), value.getPassword() != null ? "***" : "null",
value.getBearerToken() != null ? "***" : "null", value.getUsername());

getDataStoreClient(client).testConnection();
}
}
catch (Exception e)
{
Expand All @@ -170,18 +176,29 @@ public void testConnection()

public DataStoreClient getDataStoreClient()
{
if (configured())
return createDataStoreClient();
return getDataStoreClient(DEFAULT_DATA_STORE);
}

public DataStoreClient getDataStoreClient(String client)
{
if (configured(client))
return createDataStoreClient(client);
else
return new DataStoreClientStub(fhirContext, dataLogger);
}

private boolean configured()
private boolean configured(String client)
{
return dataStoreServerBase != null && !dataStoreServerBase.isBlank();
return dataStoreConnectionMap.get(client).getBaseUrl() != null
&& !dataStoreConnectionMap.get(client).getBaseUrl().isBlank();
}

protected DataStoreClient createDataStoreClient()
{
return createDataStoreClient(DEFAULT_DATA_STORE);
}

protected DataStoreClient createDataStoreClient(String dataStore)
{
KeyStore trustStore = null;
char[] keyStorePassword = null;
Expand All @@ -200,9 +217,11 @@ protected DataStoreClient createDataStoreClient()
keyStore = readKeyStore(certificatePath, privateKeyPath, privateKeyPassword, keyStorePassword);
}

final ReceiveDataStoreConfig.DataStoreConnectionValues dataStoreConfig = dataStoreConnectionMap.get(dataStore);

return new DataStoreClientImpl(trustStore, keyStore, keyStorePassword, connectTimeout, socketTimeout,
connectionRequestTimeout, dataStoreServerBasicAuthUsername, dataStoreServerBasicAuthPassword,
dataStoreServerBearerToken, dataStoreServerBase, proxyUrl, proxyUsername, proxyPassword,
connectionRequestTimeout, dataStoreConfig.getUsername(), dataStoreConfig.getPassword(),
dataStoreConfig.getBearerToken(), dataStoreConfig.getBaseUrl(), proxyUrl, proxyUsername, proxyPassword,
hapiClientVerbose, fhirContext, searchBundleOverride, dataStoreFhirClientClass,
useChainedParameterNotLogicalReference, dataLogger);
}
Expand Down
31 changes: 24 additions & 7 deletions ...iversitaetsmedizin/codex/processes/data_transfer/service/receive/InsertDataIntoCodex.java
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@@ -1,14 +1,14 @@
package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive;

import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_BUNDLE;
import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_CONTINUE_STATUS;
import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_INSERT_INTO_CRR_FHIR_REPOSITORY_FAILED;
import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.*;

import java.util.Objects;
import java.util.Optional;

import org.camunda.bpm.engine.delegate.BpmnError;
import org.camunda.bpm.engine.delegate.DelegateExecution;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Task;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand All @@ -18,6 +18,7 @@
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.ContinueStatus;
import dev.dsf.bpe.v1.ProcessPluginApi;
import dev.dsf.bpe.v1.activity.AbstractServiceDelegate;
import dev.dsf.bpe.v1.service.TaskHelper;
import dev.dsf.bpe.v1.variables.Variables;

public class InsertDataIntoCodex extends AbstractServiceDelegate
Expand Down Expand Up @@ -49,14 +50,21 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
{
Bundle bundle = variables.getResource(BPMN_EXECUTION_VARIABLE_BUNDLE);

String studyId = getStudyId(variables.getStartTask());
if (studyId == null || studyId.isEmpty())
{
logger.error("Unable to receive, {} is empty", CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_STUDY_ID);
throw new IllegalArgumentException(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_STUDY_ID + " is empty");
}

try
{
try
{
logger.info("Executing bundle against FHIR store ...");
logger.info("Executing bundle against FHIR store '{}'", studyId);
dataLogger.logData("Received bundle", bundle);

dataClientFactory.getDataStoreClient().getFhirClient().storeBundle(bundle);
dataClientFactory.getDataStoreClient(studyId).getFhirClient().storeBundle(bundle);

execution.setVariable(BPMN_EXECUTION_VARIABLE_CONTINUE_STATUS, ContinueStatus.SUCCESS);
}
Expand All @@ -69,9 +77,18 @@ protected void doExecute(DelegateExecution execution, Variables variables) throw
}
catch (Exception e)
{
logger.warn("Unable to insert data into CRR: {} - {}", e.getClass().getName(), e.getMessage());
logger.warn("Unable to insert data into '{}': {} - {}", studyId, e.getClass().getName(), e.getMessage());
throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_INSERT_INTO_CRR_FHIR_REPOSITORY_FAILED,
"Unable to insert data into CRR");
"Unable to insert data into '" + studyId + "'");
}
}

private String getStudyId(Task task)
{
TaskHelper taskHelper = this.api.getTaskHelper();
Optional<String> studyId = taskHelper.getFirstInputParameterStringValue(task,
CODESYSTEM_NUM_CODEX_DATA_TRANSFER, CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_STUDY_ID);

return studyId.orElse("");
}
}
10 changes: 1 addition & 9 deletions ...zwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ReceiveConfig.java
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Expand Up @@ -9,15 +9,7 @@
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.message.ContinueTranslateProcess;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.message.ContinueTranslateProcessWithError;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.message.ContinueTranslateProcessWithValidationError;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.DecryptData;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.DeleteValidationErrorForDts;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.DownloadDataFromDts;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.EncryptValidationError;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.InsertDataIntoCodex;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.LogError;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.LogSuccess;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.LogValidationError;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.StoreValidationErrorForDts;
import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.receive.*;
import dev.dsf.bpe.v1.ProcessPluginApi;

@Configuration
Expand Down
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