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Admin cannot assign protected tag to entity #2119 #2120

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a475311
JobServiceIT test fails #2109
anton-abushkevich Oct 5, 2022
e4230e5
REST endpoint documentation (#2118)
anthonysena Oct 6, 2022
2ffc9c7
Admin cannot assign protected tag to entity #2119
anton-abushkevich Oct 7, 2022
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6 changes: 5 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,11 @@ OHDSI WebAPI contains all OHDSI RESTful services that can be called from OHDSI a

## Technology

OHDSI WebAPI is a Java 8 web application that utilizes a database (PostgreSQL, SQL Server or Oracle) for storage.
OHDSI WebAPI is a Java 8 web application that utilizes a PostgreSQL database for storage.

## API Documentation

The API Documentation is found at [http://webapidoc.ohdsi.org/](http://webapidoc.ohdsi.org/)

## System Requirements & Installation

Expand Down
130 changes: 127 additions & 3 deletions src/main/java/org/ohdsi/webapi/cohortcharacterization/CcController.java
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Expand Up @@ -105,6 +105,13 @@ public CcController(
FeatureExtraction.init(null);
}

/**
* Create a new cohort characterization
*
* @param dto A cohort characterization JSON definition (name, cohorts, featureAnalyses, etc.)
* @return The cohort characterization definition passed in as input
* with additional fields (createdDate, hasWriteAccess, tags, id, hashcode).
*/
@POST
@Path("/")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -115,6 +122,12 @@ public CohortCharacterizationDTO create(final CohortCharacterizationDTO dto) {
return conversionService.convert(createdEntity, CohortCharacterizationDTO.class);
}

/**
* Create a copy of an existing cohort characterization
*
* @param id An existing cohort characterization id
* @return The cohort characterization definition of the newly created copy
*/
@POST
@Path("/{id}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -128,6 +141,11 @@ public CohortCharacterizationDTO copy(@PathParam("id") final Long id) {
return create(dto);
}

/**
* Get information about the cohort characterization analyses in WebAPI
*
* @return A json object with information about the characterization analyses in WebAPI.
*/
@GET
@Path("/")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -140,6 +158,11 @@ public Page<CcShortDTO> list(@Pagination Pageable pageable) {
});
}

/**
* Get the design specification for every cohort-characterization analysis in WebAPI.
*
* @return A json object with all characterization design specifications.
*/
@GET
@Path("/design")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -148,6 +171,12 @@ public Page<CohortCharacterizationDTO> listDesign(@Pagination Pageable pageable)
return service.getPageWithLinkedEntities(pageable).map(this::convertCcToDto);
}

/**
* Get metadata about a cohort characterization.
*
* @param id The id for an existing cohort characterization
* @return name, createdDate, tags, etc for a single cohort characterization.
*/
@GET
@Path("/{id}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -156,6 +185,12 @@ public CcShortDTO get(@PathParam("id") final Long id) {
return convertCcToShortDto(service.findById(id));
}

/**
* Get the complete design specification for a single cohort characterization.
*
* @param id The id for an existing cohort characterization
* @return JSON containing the cohort characterization specification
*/
@GET
@Path("/{id}/design")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -166,6 +201,15 @@ public CohortCharacterizationDTO getDesign(@PathParam("id") final Long id) {
return convertCcToDto(cc);
}

/**
* Check if a cohort characterization with the same name exists
*
* <p>This endpoint is used to check that a desired name for a characterization does not already exist in WebAPI</p>
*
* @param id The id for a new characterization that does not currently exist in WebAPI
* @param name The desired name for the new cohort characterization
* @return The number of existing characterizations with the same name that was passed as a query parameter
*/
@GET
@Path("/{id}/exists")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -174,6 +218,11 @@ public int getCountCcWithSameName(@PathParam("id") @DefaultValue("0") final long
return service.getCountCcWithSameName(id, name);
}

/**
* Remove a characterization from WebAPI
*
* @param id The id for a characterization that currently exists in WebAPI
*/
@DELETE
@Path("/{id}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -189,7 +238,7 @@ private CohortCharacterizationDTO convertCcToDto(final CohortCharacterizationEnt
private CcShortDTO convertCcToShortDto(final CohortCharacterizationEntity entity) {
return conversionService.convert(entity, CcShortDTO.class);
}

@PUT
@Path("/{id}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -202,6 +251,14 @@ public CohortCharacterizationDTO update(@PathParam("id") final Long id, final Co
return conversionService.convert(updatedEntity, CohortCharacterizationDTO.class);
}

/**
* Add a new cohort characterization analysis to WebAPI
*
* @chrisknoll this endpoint did not work when I tried it.
*
* @param dto A cohort characterization definition
* @return The same cohort characterization definition that was passed as input
*/
@POST
@Path("/import")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -213,6 +270,12 @@ public CohortCharacterizationDTO doImport(final CcExportDTO dto) {
return conversionService.convert(service.importCc(entity), CohortCharacterizationDTO.class);
}

/**
* Get a cohort characterization definition
*
* @param id The id of an existing cohort characterization definition
* @return JSON containing the cohort characterization definition
*/
@GET
@Path("/{id}/export")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -221,6 +284,11 @@ public String export(@PathParam("id") final Long id) {
return service.serializeCc(id);
}

/**
* Get csv files containing concept sets used in a characterization analysis
* @param id The id for a cohort characterization analysis
* @return A zip file containing three csv files (mappedConcepts, includedConcepts, conceptSetExpression)
*/
@GET
@Path("/{id}/export/conceptset")
@Produces(MediaType.APPLICATION_OCTET_STREAM)
Expand All @@ -232,8 +300,13 @@ public Response exportConceptSets(@PathParam("id") final Long id) {
ByteArrayOutputStream stream = ExportUtil.writeConceptSetExportToCSVAndZip(exportList);
return HttpUtils.respondBinary(stream, String.format("cc_%d_export.zip", id));
}


/**
* Check that a cohort characterization definition is correct
* @summary Check a cohort characterization definition
* @param characterizationDTO A cohort characterization definition object
* @return A list of warnings that is possibly empty
*/
@POST
@Path("/check")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -242,6 +315,12 @@ public CheckResult runDiagnostics(CohortCharacterizationDTO characterizationDTO)
return new CheckResult(checker.check(characterizationDTO));
}

/**
* Generate a cohort characterization on a single data source
* @param id The id of an existing cohort characterization in WebAPI
* @param sourceKey The identifier for the data source to generate against
* @return A json object with information about the generation job included the status and execution id.
*/
@POST
@Path("/{id}/generation/{sourceKey}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -256,13 +335,24 @@ public JobExecutionResource generate(@PathParam("id") final Long id, @PathParam(
return service.generateCc(id, sourceKey);
}

/**
* Cancel a cohort characterization generation
* @param id The id of an existing cohort characterization
* @param sourceKey The sourceKey for the data source to generate against
* @return Status code
*/
@DELETE
@Path("/{id}/generation/{sourceKey}")
public Response cancelGeneration(@PathParam("id") final Long id, @PathParam("sourceKey") final String sourceKey) {
service.cancelGeneration(id, sourceKey);
return Response.ok().build();
}

/**
* Get all generations for a cohort characterization
* @param id The id for an existing cohort characterization
* @return An array of all generations that includes the generation id, sourceKey, start and end times
*/
@GET
@Path("/{id}/generation")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -274,6 +364,11 @@ public List<CommonGenerationDTO> getGenerationList(@PathParam("id") final Long i
info -> Collections.singletonMap(Constants.Variables.SOURCE, sourcesMap.get(info.getSourceKey())));
}

/**
* Get generation information by generation id
* @param generationId The generation id to look up
* @return Data about the generation including the generation id, sourceKey, hashcode, start and end times
*/
@GET
@Path("/generation/{generationId}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -285,6 +380,10 @@ public CommonGenerationDTO getGeneration(@PathParam("generationId") final Long g
Collections.singletonMap(Constants.Variables.SOURCE, generationEntity.getSource()));
}

/**
* Delete a cohort characterization generation
* @param generationId
*/
@DELETE
@Path("/generation/{generationId}")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -293,6 +392,11 @@ public void deleteGeneration(@PathParam("generationId") final Long generationId)
service.deleteCcGeneration(generationId);
}

/**
* Get the definition of a cohort characterization for a given generation id
* @param generationId
* @return A cohort characterization definition
*/
@GET
@Path("/generation/{generationId}/design")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -302,6 +406,12 @@ public CcExportDTO getGenerationDesign(
return conversionService.convert(service.findDesignByGenerationId(generationId), CcExportDTO.class);
}

/**
* Get the total number of analyses in a cohort characterization
*
* @param generationId
* @return The total number of analyses in the given cohort characterization
*/
@GET
@Path("/generation/{generationId}/result/count")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -310,6 +420,13 @@ public Long getGenerationsResultsCount( @PathParam("generationId") final Long ge
return service.getCCResultsTotalCount(generationId);
}

/**
* Get cohort characterization results
* @param generationId id for generation
* @param thresholdLevel The max prevelance for a covariate. Covariates that occur in less than {threholdLevel}%
* of the cohort will not be returned. Default is 0.01 = 1%
* @return The complete set of characterization analyses filtered by the thresholdLevel parameter
*/
@GET
@Path("/generation/{generationId}/result")
@Produces(MediaType.APPLICATION_JSON)
Expand All @@ -318,7 +435,7 @@ public List<CcResult> getGenerationsResults(
@PathParam("generationId") final Long generationId, @DefaultValue("0.01") @QueryParam("thresholdLevel") final float thresholdLevel) {
return service.findResultAsList(generationId, thresholdLevel);
}

@POST
@Path("/generation/{generationId}/result")
@Produces(MediaType.APPLICATION_JSON)
Expand Down Expand Up @@ -398,6 +515,13 @@ public List<CcPrevalenceStat> getPrevalenceStat(@PathParam("generationId") Long
return stats;
}

/**
* Download a cohort characterization R study package that can be used to run the characterization on an OMOP CDM from R
* @summary Download a cohort characterization R package
* @param analysisId id of the cohort characterization to convert to an R study package
* @param packageName The name of the R study package
* @return A zip file containing the cohort characterization R study package
*/
@GET
@Path("{id}/download")
@Consumes(MediaType.APPLICATION_JSON)
Expand Down
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