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add exclude,include for consistency. more text replacements. #522
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@julie-sullivan
julie-sullivan committed Feb 4, 2020
1 parent 547871f commit f3a672d
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Showing 2 changed files with 104 additions and 24 deletions.
107 changes: 87 additions & 20 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -263,8 +263,20 @@ public Response getTranscriptByRegion(@PathParam("chrRegionId") @ApiParam(name =
responseContainer = "QueryResponse")
public Response getRepeatByRegion(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId",
value = ParamConstants.REGION_DESCRIPTION, required = true) String region) {
value = ParamConstants.REGION_DESCRIPTION, required = true) String region,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
RepeatsDBAdaptor repeatsDBAdaptor = dbAdaptorFactory.getRepeatsDBAdaptor(this.species, this.assembly);
List<Query> queries = createQueries(region, RepeatsDBAdaptor.QueryParams.REGION.key());
Expand Down Expand Up @@ -312,10 +324,21 @@ public Response getRepeatByRegion(@PathParam("chrRegionId")
})
public Response getVariationByRegion(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId",
value = "Comma separated list of genomic regions to be queried, "
+ "e.g.: 1:6635137-6635325",
required = true) String chrRegionId) {
value = ParamConstants.REGION_DESCRIPTION,
required = true) String chrRegionId,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
VariantDBAdaptor variationDBAdaptor = dbAdaptorFactory.getVariationDBAdaptor(this.species, this.assembly);

Expand Down Expand Up @@ -359,8 +382,18 @@ public Response getVariationByRegion(@PathParam("chrRegionId")
@ApiOperation(httpMethod = "GET", value = "Retrieves all SNP objects", hidden = true)
public Response getSnpByRegion(@PathParam("chrRegionId") String region,
@DefaultValue("") @QueryParam("consequence_type") String consequenceTypes,
@DefaultValue("") @QueryParam("phenotype") String phenotype) {
return getVariationByRegion(region);
@DefaultValue("") @QueryParam("phenotype") String phenotype,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
return getVariationByRegion(region, exclude, include, sort, limit, skip);
}


Expand All @@ -369,8 +402,8 @@ public Response getSnpByRegion(@PathParam("chrRegionId") String region,
@ApiOperation(httpMethod = "GET", value = "Retrieves genomic sequence", response = String.class,
responseContainer = "QueryResponse")
public Response getSequenceByRegion(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId", value = "Comma separated list of genomic coordinates, "
+ "e.g. 9:3242335-3272335,13:3425245-3525245", required = true) String chrRegionId,
@ApiParam(name = "chrRegionId", value = ParamConstants.REGION_DESCRIPTION,
required = true) String chrRegionId,
@DefaultValue("1")
@QueryParam("strand")
@ApiParam(name = "strand", value = "Strand to query, either 1 or -1",
Expand Down Expand Up @@ -408,9 +441,7 @@ public Response getSequenceByRegion(@PathParam("chrRegionId")
+ "https://github.com/opencb/cellbase/wiki/MongoDB-implementation#clinical for further details.",
response = Document.class, responseContainer = "QueryResponse")
@ApiImplicitParams({
@ApiImplicitParam(name = "so",
value = "Comma separated list of sequence ontology term names, e.g.: missense_variant. Exact text "
+ "matches will be returned.",
@ApiImplicitParam(name = "so", value = ParamConstants.SEQUENCE_ONTOLOGY,
required = false, dataType = "java.util.List", paramType = "query"),
@ApiImplicitParam(name = "gene",
value = "Comma separated list gene ids, e.g.: BRCA2. Gene ids can be either HGNC symbols or "
Expand Down Expand Up @@ -438,8 +469,22 @@ public Response getSequenceByRegion(@PathParam("chrRegionId")
+ "for ClinVar variants), e.g.: Benign",
required = false, dataType = "java.util.List", paramType = "query"),
})
public Response getClinicalByRegion(@PathParam("chrRegionId") String chrRegionId) {
public Response getClinicalByRegion(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId", value = ParamConstants.REGION_DESCRIPTION,
required = true) String chrRegionId,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
ClinicalDBAdaptor clinicalDBAdaptor = dbAdaptorFactory.getClinicalDBAdaptor(this.species, this.assembly);
query.put(ClinicalDBAdaptor.QueryParams.REGION.key(), chrRegionId);
Expand Down Expand Up @@ -471,9 +516,21 @@ public Response getClinicalByRegion(@PathParam("chrRegionId") String chrRegionId
required = false, dataType = "java.util.List", paramType = "query"),
})
public Response getFeatureMap(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId", value = "Comma separated list of genomic coordinates, "
+ "e.g. 9:3242335-3272335,13:3425245-3525245", required = true) String chrRegionId) {
@ApiParam(name = "chrRegionId", value = ParamConstants.REGION_DESCRIPTION,
required = true) String chrRegionId,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
RegulationDBAdaptor regRegionDBAdaptor = dbAdaptorFactory.getRegulationDBAdaptor(this.species, this.assembly);
List<Query> queries = createQueries(chrRegionId, RegulationDBAdaptor.QueryParams.REGION.key());
Expand All @@ -499,11 +556,21 @@ public Response getFeatureMap(@PathParam("chrRegionId")
+ "If histogram=true Document objects with keys start,end,chromosome & feature_count will be returned.",
responseContainer = "QueryResponse")
public Response getTfByRegion(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId",
value = "Comma separated list of genomic regions to be queried, e.g.: "
+ "1:6635137-6635325",
required = false) String chrRegionId) {
@ApiParam(name = "chrRegionId", value = ParamConstants.REGION_DESCRIPTION,
required = false) String chrRegionId,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
RegulationDBAdaptor regulationDBAdaptor = dbAdaptorFactory.getRegulationDBAdaptor(this.species, this.assembly);

Expand Down Expand Up @@ -536,8 +603,8 @@ public Response getTfByRegion(@PathParam("chrRegionId")
@ApiOperation(httpMethod = "GET", value = "Retrieves all the conservation scores", response = GenomicScoreRegion.class,
responseContainer = "QueryResponse")
public Response conservation(@PathParam("chrRegionId")
@ApiParam(name = "chrRegionId", value = "Comma separated list of genomic coordinates, "
+ "e.g. 9:3242335-3272335,13:3425245-3525245", required = true) String chrRegionId) {
@ApiParam(name = "chrRegionId", value = ParamConstants.REGION_DESCRIPTION,
required = true) String chrRegionId) {
try {
parseQueryParams();
GenomeDBAdaptor conservationDBAdaptor = dbAdaptorFactory.getGenomeDBAdaptor(this.species, this.assembly);
Expand Down
21 changes: 17 additions & 4 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ public Response getAnnotationByVariantsPOST(@ApiParam(name = "variants", value =
phased,
imprecise,
svExtraPadding,
cnvExtraPadding);
cnvExtraPadding, null, null, null, null, null);
}

@GET
Expand Down Expand Up @@ -215,15 +215,25 @@ public Response getAnnotationByVariantsGET(@PathParam("variants")
value = "Integer to optionally provide the size of the extra"
+ " padding to be used when annotating imprecise (or not)"
+ " CNVs",
defaultValue = "0", required = false) Integer cnvExtraPadding) {
defaultValue = "0", required = false) Integer cnvExtraPadding,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
@QueryParam("include")
@ApiParam(value = ParamConstants.INCLUDE_DESCRIPTION) String include,
@QueryParam("sort")
@ApiParam(value = ParamConstants.SORT_DESCRIPTION) String sort,
@QueryParam("limit") @DefaultValue("10")
@ApiParam(value = ParamConstants.LIMIT_DESCRIPTION) Integer limit,
@QueryParam("skip") @DefaultValue("0")
@ApiParam(value = ParamConstants.SKIP_DESCRIPTION) Integer skip) {
return getAnnotationByVariant(variants,
normalize,
skipDecompose,
ignorePhase,
phased,
imprecise,
svExtraPadding,
cnvExtraPadding);
cnvExtraPadding, exclude, include, sort, limit, skip);
}

private Response getAnnotationByVariant(String variants,
Expand All @@ -233,8 +243,11 @@ private Response getAnnotationByVariant(String variants,
@Deprecated Boolean phased,
Boolean imprecise,
Integer svExtraPadding,
Integer cnvExtraPadding) {
Integer cnvExtraPadding,
String exclude, String include, String sort, Integer limit, Integer skip) {
try {
parseIncludesAndExcludes(exclude, include, sort);
parseLimitAndSkip(limit, skip);
parseQueryParams();
List<Variant> variantList = parseVariants(variants);
logger.debug("queryOptions: " + queryOptions);
Expand Down

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