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Add support for adding Markdown descriptions to models in OpenAPI spec
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@arteymix
arteymix committed Dec 13, 2022
1 parent 281c92c commit a982a01
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Showing 19 changed files with 227 additions and 197 deletions.
3 changes: 3 additions & 0 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/AnalysisResultSetsWebService.java
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Expand Up @@ -21,6 +21,8 @@
import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.enums.Explode;
import io.swagger.v3.oas.annotations.extensions.Extension;
import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.ExampleObject;
import io.swagger.v3.oas.annotations.media.Schema;
Expand Down Expand Up @@ -86,6 +88,7 @@ public class AnalysisResultSetsWebService {
public PaginatedResponseDataObject<DifferentialExpressionAnalysisResultSetValueObject> getResultSets(
@Parameter(schema = @Schema(implementation = DatasetArrayArg.class), explode = Explode.FALSE) @QueryParam("datasets") DatasetArrayArg datasets,
@Parameter(schema = @Schema(implementation = DatabaseEntryArrayArg.class), explode = Explode.FALSE) @QueryParam("databaseEntries") DatabaseEntryArrayArg databaseEntries,
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionAnalysisResultSetService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filters,
@QueryParam("offset") @DefaultValue("0") OffsetArg offset,
@QueryParam("limit") @DefaultValue("20") LimitArg limit,
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6 changes: 6 additions & 0 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/AnnotationsWebService.java
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Expand Up @@ -22,6 +22,8 @@
import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.enums.Explode;
import io.swagger.v3.oas.annotations.extensions.Extension;
import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
Expand Down Expand Up @@ -155,6 +157,7 @@ public ResponseDataObject<List<AnnotationSearchResultValueObject>> searchAnnotat
})
public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatasets( // Params:
@Parameter(schema = @Schema(implementation = StringArrayArg.class), explode = Explode.FALSE) @QueryParam("query") @DefaultValue("") StringArrayArg query,
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filterArg, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
Expand Down Expand Up @@ -206,6 +209,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatase
}, deprecated = true)
public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatasetsByQueryInPath( // Params:
@PathParam("query") @DefaultValue("") StringArrayArg query, // Required
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filterArg, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
Expand All @@ -228,6 +232,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchDatase
public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonDatasets( // Params:
@PathParam("taxon") TaxonArg<?> taxonArg, // Required
@Parameter(schema = @Schema(implementation = StringArrayArg.class), explode = Explode.FALSE) @QueryParam("query") @DefaultValue("") StringArrayArg query,
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
Expand Down Expand Up @@ -273,6 +278,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonD
public PaginatedResponseDataObject<ExpressionExperimentValueObject> searchTaxonDatasetsByQueryInPath( // Params:
@PathParam("taxon") TaxonArg<?> taxonArg, // Required
@PathParam("query") @DefaultValue("") StringArrayArg query, // Required
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
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4 changes: 4 additions & 0 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/DatasetsWebService.java
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Expand Up @@ -15,6 +15,8 @@
package ubic.gemma.web.services.rest;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.extensions.Extension;
import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
Expand Down Expand Up @@ -128,6 +130,7 @@ public DatasetsWebService( ExpressionExperimentService expressionExperimentServi
@Produces(MediaType.APPLICATION_JSON)
@Operation(summary = "Retrieve all datasets")
public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasets( // Params:
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
Expand Down Expand Up @@ -159,6 +162,7 @@ public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasets(
@Operation(summary = "Retrieve datasets by their identifiers")
public PaginatedResponseDataObject<ExpressionExperimentValueObject> getDatasetsByIds( // Params:
@PathParam("dataset") DatasetArrayArg datasetsArg, // Optional
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
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4 changes: 4 additions & 0 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/PlatformsWebService.java
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Expand Up @@ -15,6 +15,8 @@
package ubic.gemma.web.services.rest;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.extensions.Extension;
import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
Expand Down Expand Up @@ -88,6 +90,7 @@ public PlatformsWebService( GeneService geneService, ArrayDesignService arrayDes
@Produces(MediaType.APPLICATION_JSON)
@Operation(summary = "Retrieve all platforms")
public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatforms( // Params:
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "arrayDesignService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
Expand Down Expand Up @@ -115,6 +118,7 @@ public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatforms( // Para
@Operation(summary = "Retrieve all platforms matching a set of platform identifiers")
public PaginatedResponseDataObject<ArrayDesignValueObject> getPlatformsByIds( // Params:
@PathParam("platform") PlatformArrayArg datasetsArg, // Optional
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "arrayDesignService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
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3 changes: 1 addition & 2 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/SearchWebService.java
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Expand Up @@ -29,7 +29,6 @@
import ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject;
import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
import ubic.gemma.persistence.service.genome.taxon.TaxonService;
import ubic.gemma.web.services.rest.swagger.resolvers.SearchResultTypeAllowableValuesModelResolver;
import ubic.gemma.web.services.rest.util.ResponseDataObject;
import ubic.gemma.web.services.rest.util.args.LimitArg;
import ubic.gemma.web.services.rest.util.args.PlatformArg;
Expand Down Expand Up @@ -75,7 +74,7 @@ public class SearchWebService {
/**
* Search everything subject to taxon and platform constraints.
* <p>
* Naming the schema in for the result types is necessary so that it can be resolved in {@link SearchResultTypeAllowableValuesModelResolver}.
* 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}.
*/
@GET
@Produces(MediaType.APPLICATION_JSON_VALUE)
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3 changes: 3 additions & 0 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/TaxaWebService.java
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Expand Up @@ -17,6 +17,8 @@
import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.enums.Explode;
import io.swagger.v3.oas.annotations.extensions.Extension;
import io.swagger.v3.oas.annotations.extensions.ExtensionProperty;
import io.swagger.v3.oas.annotations.media.Schema;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
Expand Down Expand Up @@ -225,6 +227,7 @@ public ResponseDataObject<List<PhysicalLocationValueObject>> getGeneLocationsInT
@Operation(summary = "Retrieve the datasets for a given taxon")
public PaginatedResponseDataObject<ExpressionExperimentValueObject> getTaxonDatasets( // Params:
@PathParam("taxon") TaxonArg<?> taxonArg, // Required
@Schema(extensions = { @Extension(name = "gemma", properties = { @ExtensionProperty(name = "filteringService", value = "expressionExperimentService") }) })
@QueryParam("filter") @DefaultValue("") FilterArg filter, // Optional, default null
@QueryParam("offset") @DefaultValue("0") OffsetArg offset, // Optional, default 0
@QueryParam("limit") @DefaultValue("20") LimitArg limit, // Optional, default 20
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15 changes: 0 additions & 15 deletions gemma-web/src/main/java/ubic/gemma/web/services/rest/swagger/CustomModelConverter.java
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51 changes: 0 additions & 51 deletions .../java/ubic/gemma/web/services/rest/swagger/CustomModelConvertersRegistrationListener.java
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