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update model to the 'OR' filters
1 parent 2d30bb9 commit b8b3be5

18 files changed

+108
-30
lines changed

‎beacon-framework/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/requests/BeaconQueryFilter.java‎

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@@ -37,7 +37,7 @@
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* @author Dmitry Repchevsky
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*/
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public interface BeaconQueryFilter {
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public interface BeaconQueryFilter extends BeaconQueryFilterGroupInterface {
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String getId();
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void setId(String id);

‎beacon-framework/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/requests/BeaconQueryFilterGroup.java‎

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/**
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* *****************************************************************************
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* Copyright (C) 2025 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
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* and Barcelona Supercomputing Center (BSC)
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*
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* Modifications to the initial code base are copyright of their respective
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* authors, or their employers as appropriate.
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*
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* This library is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
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* version 2.1 of the License, or (at your option) any later version.
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*
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* This library is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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* Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with this library; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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* *****************************************************************************
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*/
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package es.bsc.inb.ga4gh.beacon.framework.model.v200.requests;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Logical 'OR' query filters group.
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*
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* @author Dmitry Repchevsky
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*/
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public class BeaconQueryFilterGroup extends ArrayList<BeaconQueryFilter>
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implements List<BeaconQueryFilter>, BeaconQueryFilterGroupInterface {
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}

‎beacon-framework/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/requests/BeaconQueryFilterGroupInterface.java‎

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/**
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* *****************************************************************************
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* Copyright (C) 2025 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
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* and Barcelona Supercomputing Center (BSC)
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*
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* Modifications to the initial code base are copyright of their respective
7+
* authors, or their employers as appropriate.
8+
*
9+
* This library is free software; you can redistribute it and/or
10+
* modify it under the terms of the GNU Lesser General Public
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* License as published by the Free Software Foundation; either
12+
* version 2.1 of the License, or (at your option) any later version.
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*
14+
* This library is distributed in the hope that it will be useful,
15+
* but WITHOUT ANY WARRANTY; without even the implied warranty of
16+
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17+
* Lesser General Public License for more details.
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*
19+
* You should have received a copy of the GNU Lesser General Public
20+
* License along with this library; if not, write to the Free Software
21+
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
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* MA 02110-1301 USA
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* *****************************************************************************
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*/
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package es.bsc.inb.ga4gh.beacon.framework.model.v200.requests;
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/**
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* The common interface for the single filter and a group of filters.
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*
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* @author Dmitry Repchevsky
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*/
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public interface BeaconQueryFilterGroupInterface {
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}

‎beacon-framework/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/requests/BeaconRequestQuery.java‎

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@@ -35,7 +35,7 @@
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public class BeaconRequestQuery {
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private BeaconRequestParameters request_parameters;
38-
private List<BeaconQueryFilter> filters;
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private List<BeaconQueryFilterGroupInterface> filters;
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private String include_resultset_responses;
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private Pagination pagination;
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private String granularity;
@@ -49,11 +49,11 @@ public void setRequestParameters(BeaconRequestParameters request_parameters) {
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this.request_parameters = request_parameters;
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}
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public List<BeaconQueryFilter> getFilters() {
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public List<BeaconQueryFilterGroupInterface> getFilters() {
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return filters;
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}
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public void setFilters(List<BeaconQueryFilter> filters) {
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public void setFilters(List<BeaconQueryFilterGroupInterface> filters) {
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this.filters = filters;
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}
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‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
28+
import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
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import java.util.List;
@@ -51,7 +51,7 @@ public interface AnalysesInterface {
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*/
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BeaconResultsetsResponse getAnalyses(
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String requested_schema, Integer skip, Integer limit,
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String include_responses, List<BeaconQueryFilter> filters);
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String include_responses, List<BeaconQueryFilterGroupInterface> filters);
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/**
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* Get a list of bioinformatics analyses.

‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/BiosamplesInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
28+
import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
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import java.util.List;
@@ -50,7 +50,7 @@ public interface BiosamplesInterface {
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*/
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BeaconResultsetsResponse getBiosamples(
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String requested_schema, Integer skip, Integer limit,
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String include_responses, List<BeaconQueryFilter> filters);
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String include_responses, List<BeaconQueryFilterGroupInterface> filters);
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/**
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* Get a list of biosamples.

‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/CohortsInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
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* @return
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*/
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BeaconCollectionsResponse getCohorts(
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String requested_schema, Integer skip, Integer limit, List<BeaconQueryFilter> filters);
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String requested_schema, Integer skip, Integer limit, List<BeaconQueryFilterGroupInterface> filters);
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/**
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* Get a list of cohorts.

‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/DatasetsInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse;
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* @return
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*/
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BeaconCollectionsResponse getDatasets(String requested_schema, Integer skip,
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Integer limit, List<BeaconQueryFilter> filters);
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Integer limit, List<BeaconQueryFilterGroupInterface> filters);
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/**
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* Get a list of datasets.

‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/GenomicVariationsInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
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import java.util.List;
@@ -65,7 +65,7 @@ BeaconResultsetsResponse getGenomicVariations(
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String include_responses, long[] start, long[] end, String assembly_id,
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String reference_name, String reference_bases, String alternate_bases,
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Long variant_min_length, Long variant_max_length, String genomic_allele_short_form,
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String gene_id, String aminoacid_change, List<BeaconQueryFilter> filters);
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String gene_id, String aminoacid_change, List<BeaconQueryFilterGroupInterface> filters);
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BeaconResultsetsResponse postGenomicVariationsRequest(BeaconRequestBody request);
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‎beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/IndividualsInterface.java‎

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package es.bsc.inb.ga4gh.beacon.framework;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter;
28+
import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilterGroupInterface;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody;
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import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse;
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import java.util.List;
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*/
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BeaconResultsetsResponse getIndividuals(
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String requested_schema, Integer skip, Integer limit,
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String include_responses, List<BeaconQueryFilter> filters);
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String include_responses, List<BeaconQueryFilterGroupInterface> filters);
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/**
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* Get a list of individuals.

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