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feat(openchallenges): model input data types of challenges with EDAM #2557

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merged 17 commits into from
Mar 16, 2024
Merged

feat(openchallenges): model input data types of challenges with EDAM #2557

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7ed164d
add EDAM Data API schema
tschaffter Mar 8, 2024
a958ac6
switch to EDAM Data concept for input data types
tschaffter Mar 8, 2024
c3cdc7f
remove API files related to input data types
tschaffter Mar 8, 2024
5c57ccd
update db files in challenge service
tschaffter Mar 8, 2024
3ed3557
remove reference to challenge_data_edam
tschaffter Mar 8, 2024
d23de09
update db filename
tschaffter Mar 8, 2024
ff4a545
generate challenge service
tschaffter Mar 8, 2024
65c2e40
first pass at adapting the service implementation
tschaffter Mar 8, 2024
1ec48ca
finalize implementation
tschaffter Mar 9, 2024
8154fb6
merge main
tschaffter Mar 12, 2024
02b6473
use distinct ES indices for EDAM data and operation
tschaffter Mar 12, 2024
ce0e509
update API client for angular
tschaffter Mar 12, 2024
3e6866e
fix web app
tschaffter Mar 12, 2024
a52e413
set IDs to NULL in EDAM CSV file
tschaffter Mar 12, 2024
4a4a7ac
Merge branch 'main' into input-data-type-edam
tschaffter Mar 13, 2024
461944b
add README.md
tschaffter Mar 13, 2024
40f0e79
add call to dump EDAM input data
vpchung Mar 15, 2024
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10 changes: 1 addition & 9 deletions apps/openchallenges/challenge-service/.openapi-generator/FILES
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Expand Up @@ -10,9 +10,6 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/Challenge
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeContributionApi.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeContributionApiController.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeContributionApiDelegate.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApi.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApiController.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApiDelegate.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApi.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApiController.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengePlatformApiDelegate.java
Expand All @@ -27,11 +24,6 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/Cha
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeDirectionDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeIncentiveDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypeDirectionDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypeDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypeSearchQueryDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypeSortDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypesPageDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengePlatformDirectionDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengePlatformDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengePlatformSearchQueryDto.java
Expand All @@ -43,8 +35,8 @@ src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/Cha
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeSubmissionTypeDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengesPageDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengesPerYearDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamDataDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/EdamOperationDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/PageMetadataDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/SimpleChallengeInputDataTypeDto.java
src/main/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/SimpleChallengePlatformDto.java
src/main/resources/openapi.yaml
2 changes: 1 addition & 1 deletion ...n/java/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeApiDelegate.java
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Expand Up @@ -36,7 +36,7 @@ default ResponseEntity<ChallengeDto> getChallenge(Long challengeId) {
for (MediaType mediaType : MediaType.parseMediaTypes(request.getHeader("Accept"))) {
if (mediaType.isCompatibleWith(MediaType.valueOf("application/json"))) {
String exampleString =
"{ \"avatarUrl\" : \"https://openchallenges.io\", \"endDate\" : \"2017-07-21T00:00:00.000+00:00\", \"description\" : \"This is an example description of the challenge.\", \"platform\" : { \"name\" : \"name\", \"id\" : 1, \"slug\" : \"example-challenge-platform\" }, \"starredCount\" : 100, \"createdAt\" : \"2022-07-04T22:19:11Z\", \"incentives\" : [ \"publication\", \"publication\" ], \"submissionTypes\" : [ \"container_image\", \"container_image\" ], \"websiteUrl\" : \"https://openchallenges.io\", \"name\" : \"name\", \"id\" : 1, \"categories\" : [ \"featured\", \"featured\" ], \"headline\" : \"Example challenge headline\", \"operation\" : { \"classId\" : \"http://edamontology.org/operation_0230\", \"preferredLabel\" : \"Sequence generation\" }, \"slug\" : \"awesome-challenge\", \"startDate\" : \"2017-07-21T00:00:00.000+00:00\", \"doi\" : \"https://doi.org/123/abc\", \"status\" : \"active\", \"inputDataTypes\" : [ { \"name\" : \"gene expression\", \"id\" : 1, \"slug\" : \"gene-expression\" }, { \"name\" : \"gene expression\", \"id\" : 1, \"slug\" : \"gene-expression\" } ], \"updatedAt\" : \"2022-07-04T22:19:11Z\" }";
"{ \"avatarUrl\" : \"https://openchallenges.io\", \"endDate\" : \"2017-07-21T00:00:00.000+00:00\", \"description\" : \"This is an example description of the challenge.\", \"platform\" : { \"name\" : \"name\", \"id\" : 1, \"slug\" : \"example-challenge-platform\" }, \"starredCount\" : 100, \"createdAt\" : \"2022-07-04T22:19:11Z\", \"incentives\" : [ \"publication\", \"publication\" ], \"submissionTypes\" : [ \"container_image\", \"container_image\" ], \"websiteUrl\" : \"https://openchallenges.io\", \"name\" : \"name\", \"id\" : 1, \"categories\" : [ \"featured\", \"featured\" ], \"headline\" : \"Example challenge headline\", \"operation\" : { \"classId\" : \"http://edamontology.org/operation_0230\", \"preferredLabel\" : \"Sequence generation\" }, \"slug\" : \"awesome-challenge\", \"startDate\" : \"2017-07-21T00:00:00.000+00:00\", \"doi\" : \"https://doi.org/123/abc\", \"status\" : \"active\", \"inputDataTypes\" : [ { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\" }, { \"classId\" : \"http://edamontology.org/data_0850\", \"preferredLabel\" : \"Sequence set\" } ], \"updatedAt\" : \"2022-07-04T22:19:11Z\" }";
ApiUtil.setExampleResponse(request, "application/json", exampleString);
break;
}
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91 changes: 0 additions & 91 deletions ...a/org/sagebionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApi.java
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27 changes: 0 additions & 27 deletions ...bionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApiController.java
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53 changes: 0 additions & 53 deletions ...gebionetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApiDelegate.java
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24 changes: 0 additions & 24 deletions ...onetworks/openchallenges/challenge/service/api/ChallengeInputDataTypeApiDelegateImpl.java
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22 changes: 0 additions & 22 deletions ...ionetworks/openchallenges/challenge/service/configuration/EnumConverterConfiguration.java
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Expand Up @@ -4,8 +4,6 @@
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeContributionRoleDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeDirectionDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeIncentiveDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeInputDataTypeDirectionDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeInputDataTypeSortDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengePlatformDirectionDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengePlatformSortDto;
import org.sagebionetworks.openchallenges.challenge.service.model.dto.ChallengeSortDto;
Expand Down Expand Up @@ -58,26 +56,6 @@ public ChallengeIncentiveDto convert(String source) {
};
}

@Bean
Converter<String, ChallengeInputDataTypeDirectionDto> challengeInputDataTypeDirectionConverter() {
return new Converter<String, ChallengeInputDataTypeDirectionDto>() {
@Override
public ChallengeInputDataTypeDirectionDto convert(String source) {
return ChallengeInputDataTypeDirectionDto.fromValue(source);
}
};
}

@Bean
Converter<String, ChallengeInputDataTypeSortDto> challengeInputDataTypeSortConverter() {
return new Converter<String, ChallengeInputDataTypeSortDto>() {
@Override
public ChallengeInputDataTypeSortDto convert(String source) {
return ChallengeInputDataTypeSortDto.fromValue(source);
}
};
}

@Bean
Converter<String, ChallengePlatformDirectionDto> challengePlatformDirectionConverter() {
return new Converter<String, ChallengePlatformDirectionDto>() {
Expand Down
10 changes: 5 additions & 5 deletions ...ain/java/org/sagebionetworks/openchallenges/challenge/service/model/dto/ChallengeDto.java
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Expand Up @@ -61,7 +61,7 @@ public class ChallengeDto {

@JsonProperty("inputDataTypes")
@Valid
private List<SimpleChallengeInputDataTypeDto> inputDataTypes = null;
private List<EdamDataDto> inputDataTypes = null;

@JsonProperty("categories")
@Valid
Expand Down Expand Up @@ -380,12 +380,12 @@ public void setSubmissionTypes(List<ChallengeSubmissionTypeDto> submissionTypes)
this.submissionTypes = submissionTypes;
}

public ChallengeDto inputDataTypes(List<SimpleChallengeInputDataTypeDto> inputDataTypes) {
public ChallengeDto inputDataTypes(List<EdamDataDto> inputDataTypes) {
this.inputDataTypes = inputDataTypes;
return this;
}

public ChallengeDto addInputDataTypesItem(SimpleChallengeInputDataTypeDto inputDataTypesItem) {
public ChallengeDto addInputDataTypesItem(EdamDataDto inputDataTypesItem) {
if (this.inputDataTypes == null) {
this.inputDataTypes = new ArrayList<>();
}
Expand All @@ -400,11 +400,11 @@ public ChallengeDto addInputDataTypesItem(SimpleChallengeInputDataTypeDto inputD
*/
@Valid
@Schema(name = "inputDataTypes", required = false)
public List<SimpleChallengeInputDataTypeDto> getInputDataTypes() {
public List<EdamDataDto> getInputDataTypes() {
return inputDataTypes;
}

public void setInputDataTypes(List<SimpleChallengeInputDataTypeDto> inputDataTypes) {
public void setInputDataTypes(List<EdamDataDto> inputDataTypes) {
this.inputDataTypes = inputDataTypes;
}

Expand Down
41 changes: 0 additions & 41 deletions ...tworks/openchallenges/challenge/service/model/dto/ChallengeInputDataTypeDirectionDto.java
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