diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java index 51c92a5c..9bd78978 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/DiseasePanelParsers.java @@ -208,6 +208,10 @@ public static DiseasePanel parsePanelApp(Path panelAppJsonFile) throws IOExcepti Map panelInfo = objectMapper.readValue(panelAppJsonFile.toFile(), Map.class); + return parsePanelApp(panelInfo); + } + + public static DiseasePanel parsePanelApp(Map panelInfo) { List categories = new ArrayList<>(2); categories.add(new DiseasePanel.PanelCategory(String.valueOf(panelInfo.get("disease_group")), 1)); categories.add(new DiseasePanel.PanelCategory(String.valueOf(panelInfo.get("disease_sub_group")), 2)); diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringClinicalVariantCreator.java similarity index 99% rename from biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java rename to biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringClinicalVariantCreator.java index 25df27a9..cf62b4d5 100644 --- a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringClinicalVariantCreator.java @@ -17,7 +17,7 @@ * */ -package org.opencb.biodata.tools.clinical; +package org.opencb.biodata.tools.clinical.tiering; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.collections4.MapUtils; @@ -35,6 +35,7 @@ import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.ConsequenceType; import org.opencb.biodata.models.variant.avro.SequenceOntologyTerm; +import org.opencb.biodata.tools.clinical.ClinicalVariantCreator; import java.util.*; import java.util.stream.Collectors; diff --git a/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringConfiguration.java b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringConfiguration.java new file mode 100644 index 00000000..7b74401c --- /dev/null +++ b/biodata-tools/src/main/java/org/opencb/biodata/tools/clinical/tiering/TieringConfiguration.java @@ -0,0 +1,58 @@ +package org.opencb.biodata.tools.clinical.tiering; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +import java.util.Map; + +@JsonIgnoreProperties(ignoreUnknown = true) +public class TieringConfiguration { + private String penetrance; + private Map queries; + private Map> tiers; + + public TieringConfiguration() { + } + + public TieringConfiguration(String penetrance, Map queries, Map> tiers) { + this.penetrance = penetrance; + this.queries = queries; + this.tiers = tiers; + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("TieringConfiguration{"); + sb.append("penetrance='").append(penetrance).append('\''); + sb.append(", queries=").append(queries); + sb.append(", tiers=").append(tiers); + sb.append('}'); + return sb.toString(); + } + + public String getPenetrance() { + return penetrance; + } + + public TieringConfiguration setPenetrance(String penetrance) { + this.penetrance = penetrance; + return this; + } + + public Map getQueries() { + return queries; + } + + public TieringConfiguration setQueries(Map queries) { + this.queries = queries; + return this; + } + + public Map> getTiers() { + return tiers; + } + + public TieringConfiguration setTiers(Map> tiers) { + this.tiers = tiers; + return this; + } +}