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rename to groupby, move path for distinct endpoint so it better match…
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…es the standard pattern. remove merge param. change pathparam geneId to be genes. rename snp to be variant. #522
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@julie-sullivan
julie-sullivan committed Feb 4, 2020
1 parent 053c8fa commit ebea718
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Showing 7 changed files with 225 additions and 286 deletions.
15 changes: 7 additions & 8 deletions cellbase-core/src/main/java/org/opencb/cellbase/core/ParamConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -56,11 +56,14 @@ public class ParamConstants {

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


public static final String TRANSCRIPT_IDS = "Comma separated list of transcript IDs, e.g. ENST00000342992. Other transcript symbols "
+ "such as HGNC symbols are allowed as well, e.g.: BRCA2-001";
public static final String TRANSCRIPT_BIOTYPES = "Comma separated list of transcript gencode biotypes, "
+ "e.g. protein_coding,miRNA,lincRNA. Exact text matches will be returned";
public static final String TRANSCRIPT_XREFS = "Comma separated list transcript xrefs ids, "
+ "e.g. ENSG00000145113,35912_at,GO:0002020. Exact text matches will be returned";
public static final String TRANSCRIPT_IDS = "Comma separated list of ENSEMBL transcript ids, "
public static final String TRANSCRIPT_ENSEMBL_IDS = "Comma separated list of ENSEMBL transcript ids, "
+ "e.g. ENST00000342992,ENST00000380152,ENST00000544455. Exact text matches will be returned";
public static final String TRANSCRIPT_NAMES = "Comma separated list of transcript names, e.g. BRCA2-201,TTN-003."
+ " Exact text matches will be returned";
Expand Down Expand Up @@ -91,17 +94,13 @@ public class ParamConstants {

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

public static final String SNP_REFERENCE = "Comma separated list of possible reference to be queried, e.g. A,T";
public static final String SNP_ALTERNATE = "Comma separated list of possible alternate to be queried, e.g. A,T";
public static final String SNP_CONSEQUENCE_TYPE = "Comma separated list of possible SO names describing consequence"
public static final String REFERENCE = "Comma separated list of possible reference to be queried, e.g. A,T";
public static final String ALTERNATE = "Comma separated list of possible alternate to be queried, e.g. A,T";
public static final String CONSEQUENCE_TYPE = "Comma separated list of possible SO names describing consequence"
+ " types to be queried, e.g. missense_variant,downstream_variant. Exact text matches will be retrieved.";
public static final String SNP_MERGE = "Return variants for a gene per CellBaseDataResult or all of them merged"
+ " into the same CellBaseDataResult object.";

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

public static final String TFBS_MERGE = "Return one TFBs per CellBaseDataResult or all of them merged"
+ " into the same CellBaseDataResult object.";
public static final String TFBS_IDS = "String containing a comma separated list of TF names to search, e.g. CTCF";

// ---------------------------------------------
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166 changes: 68 additions & 98 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/GeneWSServer.java
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36 changes: 18 additions & 18 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/feature/ProteinWSServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,15 +65,15 @@ public Response getModel() {
}

@GET
@Path("/{proteinId}/info")
@Path("/{proteins}/info")
@ApiOperation(httpMethod = "GET", value = "Get the protein info", response = Entry.class,
responseContainer = "QueryResponse")
@ApiImplicitParams({
@ApiImplicitParam(name = "keyword", value = ParamConstants.PROTEIN_KEYWORD,
required = false, dataType = "java.util.List", paramType = "query")
})
public Response getInfoByEnsemblId(@PathParam("proteinId")
@ApiParam(name = "proteinId", value = ParamConstants.PROTEIN_XREF_IDS,
public Response getInfoByEnsemblId(@PathParam("proteins")
@ApiParam(name = "proteins", value = ParamConstants.PROTEIN_XREF_IDS,
required = true) String id,
@QueryParam("exclude")
@ApiParam(value = ParamConstants.EXCLUDE_DESCRIPTION) String exclude,
Expand Down Expand Up @@ -137,7 +137,7 @@ public Response getAll(@QueryParam("exclude")
}

@GET
@Path("/{proteinId}/substitutionScores")
@Path("/{proteins}/substitutionScores")
@ApiOperation(httpMethod = "GET", value = "Get the gene corresponding substitution scores for the input protein",
notes = "Schema of returned objects will vary depending on provided query parameters. If the amino acid "
+ " position is provided, all scores will be returned for every possible amino acid"
Expand All @@ -156,8 +156,8 @@ public Response getAll(@QueryParam("exclude")
+ " of aminoacid names, e.g.: CYS",
required = false, dataType = "String", paramType = "query")
})
public Response getSubstitutionScores(@PathParam("proteinId")
@ApiParam(name = "proteinId",
public Response getSubstitutionScores(@PathParam("proteins")
@ApiParam(name = "proteins",
value = "String indicating one xref id, e.g.: Q9UL59, Exact text "
+ "matches will be returned",
required = true) String id,
Expand Down Expand Up @@ -203,10 +203,10 @@ public Response getSubstitutionScores(@PathParam("proteinId")
}

@GET
@Path("/{proteinId}/name")
@Path("/{proteins}/name")
@ApiOperation(httpMethod = "GET", value = "Deprecated", hidden = true)
@Deprecated
public Response getproteinByName(@PathParam("proteinId") String id) {
public Response getproteinByName(@PathParam("proteins") String id) {
try {
parseQueryParams();
ProteinDBAdaptor geneDBAdaptor = dbAdaptorFactory.getProteinDBAdaptor(this.species, this.assembly);
Expand All @@ -217,35 +217,35 @@ public Response getproteinByName(@PathParam("proteinId") String id) {
}

@GET
@Path("/{proteinId}/gene")
@Path("/{proteins}/gene")
@ApiOperation(httpMethod = "GET", value = "Get the gene corresponding to the input protein", hidden = true)
public Response getGene(@PathParam("proteinId") String query) {
public Response getGene(@PathParam("proteins") String query) {
return null;
}

@GET
@Path("/{proteinId}/transcript")
@Path("/{proteins}/transcript")
@ApiOperation(httpMethod = "GET", value = "To be implemented", hidden = true)
public Response getTranscript(@PathParam("proteinId") String query) {
public Response getTranscript(@PathParam("proteins") String query) {
return null;
}

@GET
@Path("/{proteinId}/sequence")
@Path("/{proteins}/sequence")
@ApiOperation(httpMethod = "GET", value = "Get the aa sequence for the given protein", response = String.class,
responseContainer = "QueryResponse")
public Response getSequence(@PathParam("proteinId")
@ApiParam (name = "proteinId", value = "UniProt accession id, e.g: Q9UL59",
required = true) String proteinId) {
public Response getSequence(@PathParam("proteins")
@ApiParam (name = "proteins", value = "UniProt accession id, e.g: Q9UL59",
required = true) String proteins) {
ProteinDBAdaptor proteinDBAdaptor = dbAdaptorFactory.getProteinDBAdaptor(this.species, this.assembly);
query.put(ProteinDBAdaptor.QueryParams.ACCESSION.key(), proteinId);
query.put(ProteinDBAdaptor.QueryParams.ACCESSION.key(), proteins);
queryOptions.put("include", "sequence.value");
// split by comma
CellBaseDataResult<Entry> queryResult = proteinDBAdaptor.get(query, queryOptions);
CellBaseDataResult<String> queryResult1 = new CellBaseDataResult<>(queryResult.getId(), queryResult.getTime(),
queryResult.getEvents(), queryResult.getNumResults(), Collections.emptyList(), 1);
queryResult1.setResults(Collections.singletonList(queryResult.first().getSequence().getValue()));
queryResult1.setId(proteinId);
queryResult1.setId(proteins);
return createOkResponse(queryResult1);
}

Expand Down
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