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Mars receipt exception #96

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Mars receipt exception #96

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f3e7f59
Filling MARS receipt error in case of exception occuring instead of t…
Pedram-A-Keyvani Nov 12, 2024
2d72fcb
MarsReceiptException (RuntimeException)
Pedram-A-Keyvani Nov 12, 2024
72aa346
MarsReceiptServiceInterceptorConfig for isajson-biosamples
Pedram-A-Keyvani Nov 12, 2024
62597cd
Mars receipt, null pointer exception handling
Pedram-A-Keyvani Nov 12, 2024
c2b3b1e
More clear naming for ReceiptAccessionMap fields
Pedram-A-Keyvani Nov 19, 2024
87db6d6
MarsReceiptException with MarsPath
Pedram-A-Keyvani Nov 19, 2024
e166fb8
isajson-ena, filter invalid alias-accession pairs and set MARS errors…
Pedram-A-Keyvani Nov 19, 2024
d9aa6ab
isajson-ena, Java 11 in gradle config
Pedram-A-Keyvani Nov 19, 2024
225f4dc
EnaReceiptToMarsTest, validInput & invalidInput
Pedram-A-Keyvani Nov 19, 2024
f6b97a0
MARS receipt with exception handling for isajson-biosamples
Pedram-A-Keyvani Dec 4, 2024
f39f198
isajson-biosamples test is updated to be synced with the new changes …
Pedram-A-Keyvani Dec 4, 2024
6317c9b
:spotlessApply for isajson-ena
Pedram-A-Keyvani Dec 4, 2024
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58 changes: 34 additions & 24 deletions .../com/elixir/biohackaton/ISAToSRA/biosamples/controller/BioSampleSubmissionController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,21 +4,27 @@
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
import static org.springframework.http.MediaType.APPLICATION_XML_VALUE;

import java.util.List;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.CrossOrigin;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.biosamples.service.BioSamplesSubmitter;
import com.elixir.biohackaton.ISAToSRA.biosamples.service.MarsReceiptService;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsReceipt;
import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.databind.ObjectMapper;

import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.responses.ApiResponses;

import java.util.List;

import lombok.extern.slf4j.Slf4j;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.*;

@Slf4j
@RestController
Expand All @@ -42,33 +48,37 @@ public class BioSampleSubmissionController {
consumes = { APPLICATION_JSON_VALUE, APPLICATION_XML_VALUE })
public String performSubmissionToBioSamplesAndEna(
@RequestBody final String submissionPayload,
@RequestParam(value = "webinjwt") String webinJwt)
throws Exception {
String webinToken;
if (webinJwt != null) {
webinToken = webinJwt;
} else {
throw new RuntimeException("Webin Authentication Token is not provided");
}
@RequestParam(value = "webinjwt") String webinJwt) {
try {
if (webinJwt == null || webinJwt.isEmpty()) {
throw new RuntimeException("Webin Authentication Token is not provided");
}

objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
objectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);

final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
final List<Study> studies = getStudies(isaJson);
final IsaJson isaJson = this.objectMapper.readValue(submissionPayload, IsaJson.class);
final List<Study> studies = getStudies(isaJson);

final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinToken);
final MarsReceipt marsReceipt = marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);
final BiosampleAccessionsMap accessionsMap = this.bioSamplesSubmitter.createBioSamples(studies, webinJwt);
marsReceiptService.convertReceiptToMars(accessionsMap, isaJson);

return marsReceiptService.convertMarsReceiptToJson(marsReceipt);
return marsReceiptService.convertMarsReceiptToJson();
} catch (final MarsReceiptException e) {
log.error("Mars receipt excption", e);
marsReceiptService.setMarsReceiptErrors(e.getError());
return marsReceiptService.convertMarsReceiptToJson();
} catch (final Exception e) {
log.error("Internal server error", e);
marsReceiptService.setMarsReceiptErrors(e.getMessage());
return marsReceiptService.convertMarsReceiptToJson();
}
}

public List<Study> getStudies(final IsaJson isaJson) {
try {
return isaJson.getInvestigation().getStudies();
} catch (final Exception e) {
log.info("Failed to parse ISA JSON and get studies", e);
throw new MarsReceiptException(e, "Failed to parse ISA JSON and get studies");
}

return null;
}
}
103 changes: 63 additions & 40 deletions ...src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java
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Original file line number Diff line number Diff line change
@@ -1,17 +1,14 @@
/** Elixir BioHackathon 2022 */
package com.elixir.biohackaton.ISAToSRA.biosamples.service;

import com.elixir.biohackaton.ISAToSRA.biosamples.model.Attribute;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.Relationship;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample;
import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;

import java.time.Instant;
import java.util.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.concurrent.atomic.AtomicReference;
import lombok.extern.slf4j.Slf4j;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.hateoas.EntityModel;
import org.springframework.http.HttpEntity;
Expand All @@ -21,10 +18,28 @@
import org.springframework.stereotype.Service;
import org.springframework.web.client.RestTemplate;

import com.elixir.biohackaton.ISAToSRA.biosamples.model.Attribute;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.BioSample;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.biosamples.model.Relationship;
import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptException;
import com.elixir.biohackaton.ISAToSRA.receipt.ReceiptAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Category;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Characteristic;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Sample;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Source;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Study;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.Value;

import lombok.extern.slf4j.Slf4j;

@Service
@Slf4j
public class BioSamplesSubmitter {

@Autowired
private MarsReceiptService marsReceiptService;

public BiosampleAccessionsMap createBioSamples(final List<Study> studies, final String webinToken) {
final BiosampleAccessionsMap typeToBioSamplesAccessionMap = new BiosampleAccessionsMap();

Expand All @@ -38,7 +53,7 @@ public BiosampleAccessionsMap createBioSamples(final List<Study> studies, final
}
}

typeToBioSamplesAccessionMap.sourceAccessionsMap.keyName = Source.Fields.name;
typeToBioSamplesAccessionMap.sourceAccessionsMap.isaItemName = Source.Fields.name;
typeToBioSamplesAccessionMap.sourceAccessionsMap.accessionMap.put(
sourceBioSample.getName(),
sourceBioSample.getAccession());
Expand All @@ -51,36 +66,44 @@ public BiosampleAccessionsMap createBioSamples(final List<Study> studies, final
typeToBioSamplesAccessionMap.studyAccessionsMap = new ReceiptAccessionsMap(
Study.Fields.title,
study.getTitle());

study
.getMaterials()
.getSamples()
.forEach(
sample -> {
final BioSample persistedChildSample = this.createAndUpdateChildSampleWithRelationship(
sample,
sourceBioSample.getAccession(),
finalSourceBioSampleOrganismAttribute.getValue(),
webinToken);

if (persistedChildSample != null) {
final Characteristic biosampleAccessionCharacteristic = getBioSampleAccessionCharacteristic(
new AtomicReference<>(persistedChildSample));
final ArrayList<Characteristic> sampleCharacteristics = sample.getCharacteristics() != null
? sample.getCharacteristics()
: new ArrayList<>();
sampleCharacteristics.add(biosampleAccessionCharacteristic);

typeToBioSamplesAccessionMap.sampleAccessionsMap.keyName = Sample.Fields.name;
typeToBioSamplesAccessionMap.sampleAccessionsMap.accessionMap.put(
persistedChildSample.getName(),
persistedChildSample.getAccession());
try {
final BioSample persistedChildSample = this.createAndUpdateChildSampleWithRelationship(
sample,
sourceBioSample.getAccession(),
finalSourceBioSampleOrganismAttribute.getValue(),
webinToken);

if (persistedChildSample != null) {
final Characteristic biosampleAccessionCharacteristic = getBioSampleAccessionCharacteristic(
new AtomicReference<>(persistedChildSample));
final ArrayList<Characteristic> sampleCharacteristics = sample
.getCharacteristics() != null
? sample.getCharacteristics()
: new ArrayList<>();
sampleCharacteristics.add(biosampleAccessionCharacteristic);

typeToBioSamplesAccessionMap.sampleAccessionsMap.isaItemName = Sample.Fields.name;
typeToBioSamplesAccessionMap.sampleAccessionsMap.accessionMap.put(
persistedChildSample.getName(),
persistedChildSample.getAccession());
}
} catch (Exception e) {
throw new MarsReceiptException(e,
"Failed to parse ISA Json and create samples in BioSamples (SAMPLE)",
marsReceiptService.getSampleMarsPath(
Map.entry(Study.Fields.title, study.title),
Map.entry(Sample.Fields.id, sample.id)));
}
});
});
}
} catch (final Exception e) {
throw new RuntimeException("Failed to parse ISA Json and create samples in BioSamples", e);
throw new MarsReceiptException(e, "Failed to parse ISA Json and create samples in BioSamples");
}

return typeToBioSamplesAccessionMap;
Expand All @@ -95,8 +118,8 @@ private BioSample createAndUpdateChildSampleWithRelationship(
.withRelease(Instant.now())
.withAttributes(
List.of(Attribute.build("organism", parentSampleOrganism),
Attribute.build("collection date", "not provided"),
Attribute.build("geographic location (country and/or sea)", "not provided")))
Attribute.build("collection date", "not provided"),
Attribute.build("geographic location (country and/or sea)", "not provided")))
.build();
try {
final EntityModel<BioSample> persistedSampleEntity = this.createSampleInBioSamples(bioSample, webinToken);
Expand All @@ -122,7 +145,7 @@ private BioSample createAndUpdateChildSampleWithRelationship(
return null;
}
} catch (final Exception e) {
throw new RuntimeException("Failed to handle child samples", e);
throw new MarsReceiptException(e, "Failed to handle child samples");
}
}

Expand Down Expand Up @@ -150,8 +173,8 @@ private BioSample createSourceBioSample(final List<Study> studies, final String
final BioSample sourceSample = new BioSample.Builder(source.getName())
.withRelease(Instant.now())
.withAttributes(List.of(organismAttribute.get(),
Attribute.build("collection date", "not provided"),
Attribute.build("geographic location (country and/or sea)", "not provided")))
Attribute.build("collection date", "not provided"),
Attribute.build("geographic location (country and/or sea)", "not provided")))
.build();
final EntityModel<BioSample> persistedParentSampleEntity = this.createSampleInBioSamples(sourceSample,
webinToken);
Expand All @@ -165,7 +188,7 @@ private BioSample createSourceBioSample(final List<Study> studies, final String
sourceCharacteristics.add(biosampleAccessionCharacteristic);
source.setCharacteristics(sourceCharacteristics);
} else {
throw new RuntimeException("Failed to store source sample to BioSamples");
throw new MarsReceiptException("Failed to store source sample to BioSamples");
}
}));

Expand Down Expand Up @@ -204,8 +227,8 @@ private BioSample updateSampleWithRelationshipsToBioSamples(
new ParameterizedTypeReference<>() {
});
return biosamplesResponse.getBody().getContent();
} catch (final Exception ex) {
throw new RuntimeException("Failed to add relationships to child samples", ex);
} catch (final Exception e) {
throw new MarsReceiptException(e, "Failed to add relationships to child samples");
}
}

Expand All @@ -226,8 +249,8 @@ private EntityModel<BioSample> createSampleInBioSamples(
});

return biosamplesResponse.getBody();
} catch (final Exception ex) {
throw new RuntimeException("Failed to create samples in BioSamples", ex);
} catch (final Exception e) {
throw new MarsReceiptException(e, "Failed to create samples in BioSamples");
}
}

Expand Down
49 changes: 35 additions & 14 deletions .../src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptService.java
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Original file line number Diff line number Diff line change
@@ -1,17 +1,23 @@
/** Elixir BioHackathon 2022 */
package com.elixir.biohackaton.ISAToSRA.biosamples.service;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;

import org.springframework.stereotype.Service;
import org.springframework.web.servlet.HandlerInterceptor;

import com.elixir.biohackaton.ISAToSRA.biosamples.model.BiosampleAccessionsMap;
import com.elixir.biohackaton.ISAToSRA.receipt.MarsReceiptProvider;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.*;
import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.*;
import com.elixir.biohackaton.ISAToSRA.receipt.isamodel.IsaJson;
import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsError;
import com.elixir.biohackaton.ISAToSRA.receipt.marsmodel.MarsErrorType;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import org.springframework.stereotype.Service;

@Service
public class MarsReceiptService extends MarsReceiptProvider {
public class MarsReceiptService extends MarsReceiptProvider implements HandlerInterceptor {
private final ObjectMapper jsonMapper = new ObjectMapper();

private void setupJsonMapper() {
Expand All @@ -21,29 +27,44 @@ private void setupJsonMapper() {
}

public MarsReceiptService() {
super("biosamples"); // TODO decide whether to use instead
// https://registry.identifiers.org/registry/biosample
setupJsonMapper();
}

public String convertMarsReceiptToJson(final MarsReceipt marsReceipt) {
// Reset MARS receipt per request
@Override
public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler)
throws Exception {
resetMarsReceipt();
return HandlerInterceptor.super.preHandle(request, response, handler);
}

public String convertMarsReceiptToJson() {
try {
return jsonMapper.writeValueAsString(marsReceipt);
return jsonMapper.writeValueAsString(getMarsReceipt());
} catch (Exception ex) {
throw new RuntimeException("receipt", ex);
throw new RuntimeException("Receipt", ex);
}
}

public void setMarsReceiptErrors(String... errors) {
super.setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors);
}

public void setMarsReceiptErrors(MarsError... errors) {
super.setMarsReceiptErrors(MarsErrorType.INVALID_METADATA, errors);
}

/**
* Converting BioSample receipt to Mars data format
*
* @see
* https://github.com/elixir-europe/MARS/blob/refactor/repository-services/repository-api.md#response
* @see <a href='https://github.com/elixir-europe/MARS/blob/main/repository-services/repository-api.md#response'>Repository API Specification</a>
* @param biosampleAccessionsMap {@link BiosampleAccessionsMap} Receipt from Biosample
* @param isaJson {@link IsaJson} Requested ISA-Json
* @return {@link MarsReceipt} Mars response data
* @param isaJson {@link IsaJson} Requested ISA-Json
*/
public MarsReceipt convertReceiptToMars(final BiosampleAccessionsMap biosampleAccessionsMap, final IsaJson isaJson) {
return buildMarsReceipt(
"biosamples", // https://registry.identifiers.org/registry/biosample
public void convertReceiptToMars(final BiosampleAccessionsMap biosampleAccessionsMap, final IsaJson isaJson) {
buildMarsReceipt(
biosampleAccessionsMap.studyAccessionsMap,
biosampleAccessionsMap.sampleAccessionsMap,
biosampleAccessionsMap.sourceAccessionsMap,
Expand Down
18 changes: 18 additions & 0 deletions ...m/elixir/biohackaton/ISAToSRA/biosamples/service/MarsReceiptServiceInterceptorConfig.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
/** Elixir BioHackathon 2022 */
package com.elixir.biohackaton.ISAToSRA.biosamples.service;

import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Configuration;
import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;

@Configuration
public class MarsReceiptServiceInterceptorConfig implements WebMvcConfigurer {

@Autowired private MarsReceiptService marsReceiptService;

@Override
public void addInterceptors(InterceptorRegistry registry) {
registry.addInterceptor(marsReceiptService);
}
}
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