Skip to content

Commit

Permalink
more text replacements #522
Browse files Browse the repository at this point in the history
  • Loading branch information
@julie-sullivan
julie-sullivan committed Feb 4, 2020
1 parent f3a672d commit 82afad0
Show file tree
Hide file tree
Showing 3 changed files with 39 additions and 51 deletions.
33 changes: 23 additions & 10 deletions cellbase-core/src/main/java/org/opencb/cellbase/core/ParamConstants.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -124,44 +124,57 @@ public class ParamConstants {

public static final String SOURCE = "Comma separated list of database sources of the documents to be returned."
+ " Possible values are clinvar,cosmic or iarctp53. E.g.: clinvar,cosmic";

public static final String SEQUENCE_ONTOLOGY = "Comma separated list of sequence ontology term names, "
+ "e.g. missense_variant. Exact text matches will be returned. A list of searchable SO term names can be"
+ " accessed at https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/variation/consequence_types";

public static final String FEATURE_IDS = "Comma separated list of feature ids, which can be either ENSEMBL gene "
+ "ids, HGNC gene symbols, transcript symbols or ENSEMBL transcript ids, e.g.: BRCA2, ENST00000409047. "
+ "Exact text matches will be returned.";

public static final String TRAITS = "Keywords search. Comma separated (no spaces in between) list of "
+ "keywords describing required phenotype/disease. All variants related somehow with all those keywords "
+ "(case insensitive) will be returned, e.g: carcinoma,lung or acute,myeloid,leukaemia. WARNING: returned "
+ "numTotalResults will always be -1 when searching by trait keywords.";

public static final String VARIANT_ACCESSIONS = "Comma separated list of database accessions, "
+ "e.g. RCV000033215,COSM306824 Exact text matches will be returned.";

public static final String VARIANT_IDS = "Comma separated list of ids, e.g. rs6025,COSM306824. "
+ "Exact text matches will be returned.";

public static final String VARIANT_TYPES = "Comma separated list of variant types, e.g. \"SNV\" A list of "
+ "searchable types can be accessed at "
+ "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/type";

public static final String CONSISTENCY_STATUS = "Comma separated list of consistency labels. A list of searchable "
+ "consistency labels can be accessed at "
+ "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/consistency_labels";

public static final String CLINICAL_SIGNFICANCE = "Comma separated list of clinical significance labels. "
+ "A list of searchable clinical significance labels can be accessed at "
+ "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/clinsig_labels"
+ " WARNING: returned numTotalResults will always be -1 if more than 1 label is provided.";

public static final String MODE_INHERITANCE = "Comma separated list of mode of inheritance labels. A list of "
+ "searchable mode of inheritance labels can be accessed at "
+ "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/mode_inheritance_labels";

public static final String ALLELE_ORIGIN = "Comma separated list of allele origin labels. A list of searchable "
+ "allele origin labels can be accessed at "
+ "https://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/clinical/variant/allele_origin_labels";


// ---------------------------------------------

public static final String VARIANTS = "Comma separated list of variants to annotate, e.g. "
+ "19:45411941:T:C,14:38679764:-:GATCTG,1:6635210:G:-,"
+ "2:114340663:GCTGGGCATCCT:ACTGGGCATCCT,1:816505-825225:<CNV>";
public static final String NORMALISE = "Boolean to indicate whether input variants shall be "
+ "normalized or not. Normalization process does NOT include decomposing ";
public static final String SKIP_DECOMPOSE = "Boolean to indicate whether input MNVs should be "
+ "decomposed or not as part of the normalisation step. MNV decomposition is strongly encouraged.";
public static final String IGNORE_PHASE = "Boolean to indicate whether phase data should be taken into account.";
public static final String PHASED = "DEPRECATED. Will be removed in next release. Please, use ignorePhase instead. " +
" Boolean to indicate whether phase should be considered during the annotation process";
public static final String IMPRECISE = "Boolean to indicate whether imprecise search must be used or not";
public static final String SV_EXTRA_PADDING = "Integer to optionally provide the size of the extra"
+ " padding to be used when annotating imprecise (or not) structural variants";
public static final String CNV_EXTRA_PADDING = "Integer to optionally provide the size of the extra"
+ " padding to be used when annotating imprecise (or not) CNVs";

// ---------------------------------------------

public static final String STRAND = "Strand to query, either 1 or -1";
}
16 changes: 5 additions & 11 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/RegionWSServer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -306,16 +306,11 @@ public Response getRepeatByRegion(@PathParam("chrRegionId")
@ApiImplicitParam(name = "interval",
value = "Use only if histogram=true. Boolean indicating the size of the histogram interval",
defaultValue = "200000", required = false, dataType = "Integer", paramType = "query"),
@ApiImplicitParam(name = "consequenceType",
value = "Comma separated list of sequence ontology term names, e.g.: missense_variant. Exact text "
+ "matches will be returned.",
@ApiImplicitParam(name = "consequenceType", value = ParamConstants.SNP_CONSEQUENCE_TYPE,
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 "
+ " ENSEMBL gene ids. Exact text matches will be returned.",
@ApiImplicitParam(name = "gene", value = ParamConstants.GENE_IDS,
required = false, dataType = "java.util.List", paramType = "query"),
@ApiImplicitParam(name = "id",
value = "Comma separated list of rs ids, e.g.: rs6025",
@ApiImplicitParam(name = "id", value = "Comma separated list of rs ids, e.g.: rs6025",
required = false, dataType = "java.util.List", paramType = "query"),
@ApiImplicitParam(name = "reference", value = ParamConstants.SNP_REFERENCE,
required = false, dataType = "java.util.List", paramType = "query"),
Expand Down Expand Up @@ -404,9 +399,8 @@ public Response getSnpByRegion(@PathParam("chrRegionId") String region,
public Response getSequenceByRegion(@PathParam("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",
@DefaultValue("1") @QueryParam("strand")
@ApiParam(name = "strand", value = ParamConstants.STRAND,
allowableValues = "1,-1", defaultValue = "1", required = true) String strand) {
try {
parseQueryParams();
Expand Down
41 changes: 11 additions & 30 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 @@ -167,54 +167,35 @@ public Response getAnnotationByVariantsPOST(@ApiParam(name = "variants", value =
+ " expression, geneDisease, drugInteraction, populationFrequencies, repeats}.",
response = VariantAnnotation.class, responseContainer = "QueryResponse")
public Response getAnnotationByVariantsGET(@PathParam("variants")
@ApiParam(name = "variants", value = "Comma separated list of variants to"
+ "annotate, e.g. "
+ "19:45411941:T:C,14:38679764:-:GATCTG,1:6635210:G:-,"
+ "2:114340663:GCTGGGCATCCT:ACTGGGCATCCT,1:816505-825225:<CNV>",
@ApiParam(name = "variants", value = ParamConstants.VARIANTS,
required = true) String variants,
@QueryParam("normalize")
@ApiParam(name = "normalize",
value = "Boolean to indicate whether input variants shall be "
+ "normalized or not. Normalization process does NOT "
+ "include decomposing ", allowableValues = "false,true",
@ApiParam(name = "normalize", value = ParamConstants.NORMALISE,
allowableValues = "false,true",
defaultValue = "true", required = false) Boolean normalize,
@QueryParam("skipDecompose")
@ApiParam(name = "skipDecompose",
value = "Boolean to indicate whether input MNVs should be "
+ "decomposed or not as part of the normalisation step."
+ " MNV decomposition is strongly encouraged.",
@ApiParam(name = "skipDecompose", value = ParamConstants.SKIP_DECOMPOSE,
allowableValues = "false,true",
defaultValue = "false", required = false) Boolean skipDecompose,
@QueryParam("ignorePhase")
@ApiParam(name = "ignorePhase",
value = "Boolean to indicate whether phase data should be "
+ "taken into account.", allowableValues = "false,true",
@ApiParam(name = "ignorePhase", value = ParamConstants.IGNORE_PHASE,
allowableValues = "false,true",
required = false) Boolean ignorePhase,
@Deprecated
@QueryParam("phased")
@ApiParam(name = "phased",
value = "DEPRECATED. Will be removed in next release. "
+ "Please, use ignorePhase instead. Boolean to "
+ "indicate whether phase should be considered "
+ "during the annotation process",
allowableValues = "false,true",
required = false) Boolean phased,
@ApiParam(name = "phased", value = ParamConstants.PHASED,
allowableValues = "false,true", required = false) Boolean phased,
@QueryParam("imprecise")
@ApiParam(name = "imprecise",
value = "Boolean to indicate whether imprecise search must be"
+ " used or not", allowableValues = "false,true",
value = ParamConstants.IMPRECISE, allowableValues = "false,true",
defaultValue = "true", required = false) Boolean imprecise,
@QueryParam("svExtraPadding")
@ApiParam(name = "svExtraPadding",
value = "Integer to optionally provide the size of the extra"
+ " padding to be used when annotating imprecise (or not)"
+ " structural variants",
value = ParamConstants.SV_EXTRA_PADDING,
defaultValue = "0", required = false) Integer svExtraPadding,
@QueryParam("cnvExtraPadding")
@ApiParam(name = "cnvExtraPadding",
value = "Integer to optionally provide the size of the extra"
+ " padding to be used when annotating imprecise (or not)"
+ " CNVs",
value = ParamConstants.CNV_EXTRA_PADDING,
defaultValue = "0", required = false) Integer cnvExtraPadding,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
Expand Down

0 comments on commit 82afad0

Please sign in to comment.