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Merge pull request #653 from opencb/TASK-1111
TASK-1111 Add Pharmagenomics data to CellBase
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cellbase-core/src/main/java/org/opencb/cellbase/core/api/PharmaChemicalQuery.java
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| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package org.opencb.cellbase.core.api; | ||
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| import org.apache.commons.collections4.CollectionUtils; | ||
| import org.opencb.cellbase.core.api.query.AbstractQuery; | ||
| import org.opencb.cellbase.core.api.query.QueryException; | ||
| import org.opencb.cellbase.core.api.query.QueryParameter; | ||
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| import java.util.List; | ||
| import java.util.Map; | ||
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| public class PharmaChemicalQuery extends AbstractQuery { | ||
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| @QueryParameter(id = "id") | ||
| private List<String> ids; | ||
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| @QueryParameter(id = "name") | ||
| private List<String> names; | ||
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| @QueryParameter(id = "source", allowedValues = {"PharmGKB"}) | ||
| private List<String> sources; | ||
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| @QueryParameter(id = "types", alias = {"type"}) | ||
| private List<String> types; | ||
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| @QueryParameter(id = "variants.variantId", alias = {"variant"}) | ||
| private List<String> variants; | ||
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| @QueryParameter(id = "variants.location", alias = {"location"}) | ||
| private List<String> locations; | ||
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| @QueryParameter(id = "variants.chromosome", alias = {"chromosome"}) | ||
| private List<String> chromosomes; | ||
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| @QueryParameter(id = "variants.haplotypes", alias = {"haplotype"}) | ||
| private List<String> hapolotypes; | ||
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| @QueryParameter(id = "variants.geneNames", alias = {"geneName"}) | ||
| private List<String> geneNames; | ||
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| @QueryParameter(id = "variants.phenotypes", alias = {"phenotype"}) | ||
| private List<String> phenotypes; | ||
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| @QueryParameter(id = "variants.phenotypeTypes", alias = {"phenotypeType"}) | ||
| private List<String> phenotypeTypes; | ||
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| @QueryParameter(id = "variants.confidence", alias = {"confidence"}) | ||
| private List<String> confidences; | ||
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| @QueryParameter(id = "variants.evidences.pubmed", alias = {"pubmedId"}) | ||
| private List<String> pubmedIds; | ||
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| public PharmaChemicalQuery() { | ||
| } | ||
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| public PharmaChemicalQuery(Map<String, String> params) throws QueryException { | ||
| super(params); | ||
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| objectMapper.readerForUpdating(this); | ||
| objectMapper.readerFor(PharmaChemicalQuery.class); | ||
| objectWriter = objectMapper.writerFor(PharmaChemicalQuery.class); | ||
| } | ||
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| @Override | ||
| protected void validateQuery() throws QueryException { | ||
| if (CollectionUtils.isNotEmpty(variants)) { | ||
| for (String variant : variants) { | ||
| if (!variant.startsWith("rs")) { | ||
| throw new QueryException("Invalid variant ID: '" + variant + "'; it has to start with rs"); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| @Override | ||
| public String toString() { | ||
| final StringBuilder sb = new StringBuilder("PharmaChemicalQuery{"); | ||
| sb.append("ids=").append(ids); | ||
| sb.append(", names=").append(names); | ||
| sb.append(", sources=").append(sources); | ||
| sb.append(", types=").append(types); | ||
| sb.append(", variants=").append(variants); | ||
| sb.append(", locations=").append(locations); | ||
| sb.append(", chromosomes=").append(chromosomes); | ||
| sb.append(", hapolotypes=").append(hapolotypes); | ||
| sb.append(", geneNames=").append(geneNames); | ||
| sb.append(", phenotypes=").append(phenotypes); | ||
| sb.append(", phenotypeTypes=").append(phenotypeTypes); | ||
| sb.append(", confidences=").append(confidences); | ||
| sb.append(", pubmedIds=").append(pubmedIds); | ||
| sb.append('}'); | ||
| return sb.toString(); | ||
| } | ||
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| public List<String> getIds() { | ||
| return ids; | ||
| } | ||
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| public PharmaChemicalQuery setIds(List<String> ids) { | ||
| this.ids = ids; | ||
| return this; | ||
| } | ||
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| public List<String> getNames() { | ||
| return names; | ||
| } | ||
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| public PharmaChemicalQuery setNames(List<String> names) { | ||
| this.names = names; | ||
| return this; | ||
| } | ||
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| public List<String> getSources() { | ||
| return sources; | ||
| } | ||
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| public PharmaChemicalQuery setSources(List<String> sources) { | ||
| this.sources = sources; | ||
| return this; | ||
| } | ||
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| public List<String> getTypes() { | ||
| return types; | ||
| } | ||
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| public PharmaChemicalQuery setTypes(List<String> types) { | ||
| this.types = types; | ||
| return this; | ||
| } | ||
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| public List<String> getVariants() { | ||
| return variants; | ||
| } | ||
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| public PharmaChemicalQuery setVariants(List<String> variants) { | ||
| this.variants = variants; | ||
| return this; | ||
| } | ||
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| public List<String> getLocations() { | ||
| return locations; | ||
| } | ||
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| public PharmaChemicalQuery setLocations(List<String> locations) { | ||
| this.locations = locations; | ||
| return this; | ||
| } | ||
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| public List<String> getChromosomes() { | ||
| return chromosomes; | ||
| } | ||
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| public PharmaChemicalQuery setChromosomes(List<String> chromosomes) { | ||
| this.chromosomes = chromosomes; | ||
| return this; | ||
| } | ||
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| public List<String> getHapolotypes() { | ||
| return hapolotypes; | ||
| } | ||
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| public PharmaChemicalQuery setHapolotypes(List<String> hapolotypes) { | ||
| this.hapolotypes = hapolotypes; | ||
| return this; | ||
| } | ||
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| public List<String> getGeneNames() { | ||
| return geneNames; | ||
| } | ||
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| public PharmaChemicalQuery setGeneNames(List<String> geneNames) { | ||
| this.geneNames = geneNames; | ||
| return this; | ||
| } | ||
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| public List<String> getPhenotypes() { | ||
| return phenotypes; | ||
| } | ||
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| public PharmaChemicalQuery setPhenotypes(List<String> phenotypes) { | ||
| this.phenotypes = phenotypes; | ||
| return this; | ||
| } | ||
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| public List<String> getPhenotypeTypes() { | ||
| return phenotypeTypes; | ||
| } | ||
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| public PharmaChemicalQuery setPhenotypeTypes(List<String> phenotypeTypes) { | ||
| this.phenotypeTypes = phenotypeTypes; | ||
| return this; | ||
| } | ||
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| public List<String> getConfidences() { | ||
| return confidences; | ||
| } | ||
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| public PharmaChemicalQuery setConfidences(List<String> confidences) { | ||
| this.confidences = confidences; | ||
| return this; | ||
| } | ||
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| public List<String> getPubmedIds() { | ||
| return pubmedIds; | ||
| } | ||
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| public PharmaChemicalQuery setPubmedIds(List<String> pubmedIds) { | ||
| this.pubmedIds = pubmedIds; | ||
| return this; | ||
| } | ||
| } |
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