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Add support for adding Markdown descriptions to models in OpenAPI spec
1 parent 281c92c commit a982a01

19 files changed

+227
-197
lines changed

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/AnalysisResultSetsWebService.java

+3
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@@ -21,6 +21,8 @@
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.Parameter;
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import io.swagger.v3.oas.annotations.enums.Explode;
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import io.swagger.v3.oas.annotations.extensions.Extension;
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import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
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import io.swagger.v3.oas.annotations.media.Content;
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import io.swagger.v3.oas.annotations.media.ExampleObject;
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import io.swagger.v3.oas.annotations.media.Schema;
@@ -86,6 +88,7 @@ public class AnalysisResultSetsWebService {
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public PaginatedResponseDataObject<DifferentialExpressionAnalysisResultSetValueObject> getResultSets(
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@Parameter(schema = @Schema(implementation = DatasetArrayArg.class), explode = Explode.FALSE) @QueryParam("datasets") DatasetArrayArg datasets,
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@Parameter(schema = @Schema(implementation = DatabaseEntryArrayArg.class), explode = Explode.FALSE) @QueryParam("databaseEntries") DatabaseEntryArrayArg databaseEntries,
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionAnalysisResultSetService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filters,
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset,
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@QueryParam("limit") @DefaultValue("20") LimitArg limit,

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/AnnotationsWebService.java

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@@ -22,6 +22,8 @@
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.Parameter;
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import io.swagger.v3.oas.annotations.enums.Explode;
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import io.swagger.v3.oas.annotations.extensions.Extension;
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import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
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import io.swagger.v3.oas.annotations.media.Content;
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import io.swagger.v3.oas.annotations.media.Schema;
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import io.swagger.v3.oas.annotations.responses.ApiResponse;
@@ -155,6 +157,7 @@ public ResponseDataObject<List<AnnotationSearchResultValueObject>> searchAnnotat
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})
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatasets( // Params:
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@Parameter(schema = @Schema(implementation = StringArrayArg.class), explode = Explode.FALSE) @QueryParam("query") @DefaultValue("") StringArrayArg query,
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filterArg, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
@@ -206,6 +209,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatase
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}, deprecated = true)
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatasetsByQueryInPath( // Params:
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@PathParam("query") @DefaultValue("") StringArrayArg query, // Required
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filterArg, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
@@ -228,6 +232,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatase
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonDatasets( // Params:
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@PathParam("taxon") TaxonArg<?> taxonArg, // Required
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@Parameter(schema = @Schema(implementation = StringArrayArg.class), explode = Explode.FALSE) @QueryParam("query") @DefaultValue("") StringArrayArg query,
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
@@ -273,6 +278,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonD
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonDatasetsByQueryInPath( // Params:
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@PathParam("taxon") TaxonArg<?> taxonArg, // Required
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@PathParam("query") @DefaultValue("") StringArrayArg query, // Required
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/DatasetsWebService.java

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@@ -15,6 +15,8 @@
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package ubic.gemma.web.services.rest;
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.extensions.Extension;
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import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
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import io.swagger.v3.oas.annotations.media.Content;
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import io.swagger.v3.oas.annotations.media.Schema;
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import io.swagger.v3.oas.annotations.responses.ApiResponse;
@@ -128,6 +130,7 @@ public DatasetsWebService( ExpressionExperimentService expressionExperimentServi
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@Produces(MediaType.APPLICATION_JSON)
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@Operation(summary = "Retrieve all datasets")
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasets( // Params:
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
@@ -159,6 +162,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasets(
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@Operation(summary = "Retrieve datasets by their identifiers")
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasetsByIds( // Params:
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@PathParam("dataset") DatasetArrayArg datasetsArg, // Optional
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/PlatformsWebService.java

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@@ -15,6 +15,8 @@
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package ubic.gemma.web.services.rest;
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.extensions.Extension;
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import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
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import io.swagger.v3.oas.annotations.media.Content;
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import io.swagger.v3.oas.annotations.media.Schema;
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import io.swagger.v3.oas.annotations.responses.ApiResponse;
@@ -88,6 +90,7 @@ public PlatformsWebService( GeneService geneService, ArrayDesignService arrayDes
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@Produces(MediaType.APPLICATION_JSON)
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@Operation(summary = "Retrieve all platforms")
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public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatforms( // Params:
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "arrayDesignService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
@@ -115,6 +118,7 @@ public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatforms( // Para
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@Operation(summary = "Retrieve all platforms matching a set of platform identifiers")
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public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatformsByIds( // Params:
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@PathParam("platform") PlatformArrayArg datasetsArg, // Optional
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "arrayDesignService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/SearchWebService.java

+1-2
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@@ -29,7 +29,6 @@
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import ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject;
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import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
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import ubic.gemma.persistence.service.genome.taxon.TaxonService;
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import ubic.gemma.web.services.rest.swagger.resolvers.SearchResultTypeAllowableValuesModelResolver;
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import ubic.gemma.web.services.rest.util.ResponseDataObject;
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import ubic.gemma.web.services.rest.util.args.LimitArg;
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import ubic.gemma.web.services.rest.util.args.PlatformArg;
@@ -75,7 +74,7 @@ public class SearchWebService {
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/**
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* Search everything subject to taxon and platform constraints.
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* <p>
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* Naming the schema in for the result types is necessary so that it can be resolved in {@link SearchResultTypeAllowableValuesModelResolver}.
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* Naming the schema in for the result types is necessary so that it can be resolved in {@link ubic.gemma.web.services.rest.swagger.resolver.CustomModelResolver}.
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*/
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@GET
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@Produces(MediaType.APPLICATION_JSON_VALUE)

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/TaxaWebService.java

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@@ -17,6 +17,8 @@
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import io.swagger.v3.oas.annotations.Operation;
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import io.swagger.v3.oas.annotations.Parameter;
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import io.swagger.v3.oas.annotations.enums.Explode;
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import io.swagger.v3.oas.annotations.extensions.Extension;
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import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
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import io.swagger.v3.oas.annotations.media.Schema;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
@@ -225,6 +227,7 @@ public ResponseDataObject<List<PhysicalLocationValueObject>> getGeneLocationsInT
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@Operation(summary = "Retrieve the datasets for a given taxon")
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public PaginatedResponseDataObject<ExpressionExperimentValueObject> getTaxonDatasets( // Params:
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@PathParam("taxon") TaxonArg<?> taxonArg, // Required
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@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
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@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
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@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
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@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20

‎gemma-web/src/main/java/ubic/gemma/web/services/rest/swagger/CustomModelConverter.java

-15
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‎gemma-web/src/main/java/ubic/gemma/web/services/rest/swagger/CustomModelConvertersRegistrationListener.java

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