diff --git a/README.md b/README.md new file mode 100644 index 0000000..6c361fc --- /dev/null +++ b/README.md @@ -0,0 +1,36 @@ +These are Java Beans classes for the Beacon API v2.0.0 specification JSON schema. + +Compiling: +```shell +>git https://github.com/elixir-europe/java-beacon-v2.api.git +>cd java-beacon-v2-api +>mvn install +``` +Maven will build three libraries: +1. beacon-framework/target/beacon-framework-2.x.x.jar +these are java model classes for Beacon v2 framwork +2. beacon-data-model/target/beacon-data-model-2.x.x.jar +these are the java interfaces for Beacon v2 models +3. beacon-model/target/beacon-model-2.x.x.jar +these are the java interfaces for Beacon v2 endpoints + +Most probably, you wont be needed to manually compile this project, but rather include the libararies in your own project + +To include Beacon beans in a maven project (pom.xml): + +```xml + + + es.bsc.inb.ga4gh + beacon-model + 2.x.x + + + + + + gitlab-bsc-maven + https://inb.bsc.es/maven + + +``` diff --git a/beacon-model/LICENSE b/beacon-model/LICENSE new file mode 100644 index 0000000..d3286f2 --- /dev/null +++ b/beacon-model/LICENSE @@ -0,0 +1,504 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +(This is the first released version of the Lesser GPL. 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Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random + Hacker. + + {signature of Ty Coon}, 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff --git a/beacon-model/pom.xml b/beacon-model/pom.xml new file mode 100644 index 0000000..0af80d9 --- /dev/null +++ b/beacon-model/pom.xml @@ -0,0 +1,105 @@ + + + + 4.0.0 + + + es.bsc.inb.ga4gh + beacon-v2-api + 2.0.4 + + + beacon-model + jar + + + Beacon Java Data Model version 2.0.0 + + + + Barcelona Supercomputing Center + https://www.bsc.es/ + + + + + LGPL-2.1-or-later + https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt + repo + + + + + + redmitry + Dmitry Repchevsky + redmitry@list.ru + + + + + UTF-8 + 17 + 17 + + 3.1.0 + + + + + + es.bsc.inb.ga4gh + beacon-framework + 2.0.4 + + + + es.bsc.inb.ga4gh + beacon-data-model + 2.0.4 + + + + jakarta.ws.rs + jakarta.ws.rs-api + ${jakarta.ws.rs-api.version} + provided + + + + jakarta.json + jakarta.json-api + ${jakarta.json.version} + provided + + + jakarta.json.bind + jakarta.json.bind-api + ${jakarta.json.bind.version} + provided + + + + + diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java new file mode 100644 index 0000000..ef184cf --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/AnalysesInterface.java @@ -0,0 +1,120 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Analysis endpoints + * + * @author Dmitry Repchevsky + */ + +public interface AnalysesInterface { + + /** + * Get a list of bioinformatics analyses. + * + * @param requested_schema + * @param skip + * @param limit + * @param include_responses + * @param filters + * + * @return + */ + BeaconResultsetsResponse getAnalyses( + String requested_schema, Integer skip, Integer limit, + String include_responses, List filters); + + /** + * Get a list of bioinformatics analyses. + * + * @param request + * @return + */ + BeaconResultsetsResponse postAnalyses(BeaconRequestBody request); + + /** + * Get details about one bioinformatics analysis, identified by its (unique) 'id' + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneAnalysis(String id); + + /** + * Get details about one bioinformatics analysis, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneAnalysisRequest(String id, BeaconRequestBody request); + + /** + * Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneAnalysisGenomicVariants( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the list of variants instances for one bioinformatics analysis, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneAnalysisGenomicVariantsRequest(String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with analyses. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getAnalysesFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with analyses. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postAnalysesFilteringTermsRequest(BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/BiosamplesInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/BiosamplesInterface.java new file mode 100644 index 0000000..dfee2f6 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/BiosamplesInterface.java @@ -0,0 +1,162 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Biosamples endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface BiosamplesInterface { + + /** + * Get a list of biosamples. + * + * @param requested_schema + * @param skip + * @param limit + * @param include_responses + * @param filters + * @return + */ + BeaconResultsetsResponse getBiosamples( + String requested_schema, Integer skip, Integer limit, + String include_responses, List filters); + + /** + * Get a list of biosamples. + * + * @param request + * @return + */ + BeaconResultsetsResponse postBiosamplesRequest(BeaconRequestBody request); + + /** + * Get details about one Biosample, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneBiosample(String id); + + /** + * Get details about one Biosample, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneBiosampleRequest(String id, BeaconRequestBody request); + + /** + * Get the genomic variants list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneBiosampleGenomicVariants( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the genomic variants list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneBiosampleGenomicVariantsRequest( + String id, BeaconRequestBody request); + + /** + * Get the analysis list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneBiosampleAnalysis( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the analysis list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneBiosampleAnalysisRequest(String id, BeaconRequestBody request); + + /** + * Get the runs list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneBiosampleRuns( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the runs list from one biosample, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse getOneBiosampleRuns(String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with biosamples. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getBiosamplesFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with biosamples. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postBiosamplesFilteringTermsRequest(BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/CohortsInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/CohortsInterface.java new file mode 100644 index 0000000..854f9c5 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/CohortsInterface.java @@ -0,0 +1,120 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Cohorts Endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface CohortsInterface { + + /** + * Get a list of cohorts. + * + * @param requested_schema + * @param skip + * @param limit + * @param filters + * + * @return + */ + BeaconCollectionsResponse getCohorts( + String requested_schema, Integer skip, Integer limit, List filters); + + /** + * Get a list of cohorts. + * + * @param request + * @return + */ + BeaconCollectionsResponse postCohortsRequest(BeaconRequestBody request); + + /** + * Get details about one cohort, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneCohort(String id); + + /** + * Get details about one cohort, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneCohortRequest(String id, BeaconRequestBody request); + + /** + * Get the individuals from one cohort, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneCohortIndividuals( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the individuals from one cohort, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneCohortIndividualsRequest(String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'. + * + * @param id + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getOneCohortFilteringTerms(String id, Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with a given cohort, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconFilteringTermsResponse postOneCohortFilteringTermsRequest(String id, BeaconRequestBody request); +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/DatasetsInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/DatasetsInterface.java new file mode 100644 index 0000000..419f9d9 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/DatasetsInterface.java @@ -0,0 +1,184 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Datasets Endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface DatasetsInterface { + + /** + * Get a list of datasets. + * + * @param requested_schema + * @param skip + * @param limit + * @param filters + * + * @return + */ + BeaconCollectionsResponse getDatasets(String requested_schema, Integer skip, + Integer limit, List filters); + + /** + * Get a list of datasets. + * + * @param request + * @return + */ + BeaconCollectionsResponse postDatasetsRequest(BeaconRequestBody request); + + /** + * Get details about one dataset, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneDataset(String id); + + /** + * Get details about one dataset, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneDatasetRequest(String id, BeaconRequestBody request); + + /** + * Get details about one dataset, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneDatasetGenomicVariants( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get details about one dataset, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneDatasetGenomicVariantsRequest( + String id, BeaconRequestBody request); + + /** + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneDatasetBiosamples( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the biosamples list from one dataset, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneDatasetBiosamplesRequest( + String id, BeaconRequestBody request); + + /** + * Get the individuals list from one dataset, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneDatasetIndividuals( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the individuals list from one dataset, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneDatasetIndividualsRequest( + String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getOneDatasetFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with a given dataset, identified by its (unique) 'id'. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postOneDatasetFilteringTermsRequest(BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with defined dataset. + * + * @param id + * @param skip + * @param limit + * + * @return + */ + BeaconFilteringTermsResponse getOneDatasetFilteringTerms(String id, Integer skip, Integer limit); + + + /** + * Get the list of filtering terms that could be used with defined dataset. + * + * @param id + * @param request + * @return + */ + BeaconFilteringTermsResponse postOneDatasetFilteringTermsRequest(String id, BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/GenomicVariationsInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/GenomicVariationsInterface.java new file mode 100644 index 0000000..31cff44 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/GenomicVariationsInterface.java @@ -0,0 +1,149 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Genomic Variations Endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface GenomicVariationsInterface { + + /** + * Get details about one genomic variation, identified by its (unique) 'id'. + * + * @param requested_schema + * Schema to be used to format the 'result' field in the response + * @param skip + * @param limit + * @param include_responses + * @param start + * @param end + * @param assembly_id + * @param reference_name + * @param reference_bases + * @param alternate_bases + * @param variant_min_length + * @param variant_max_length + * @param genomic_allele_short_form + * @param gene_id + * @param aminoacid_change + * @param filters + * @return + */ + BeaconResultsetsResponse getGenomicVariations( + String requested_schema, Integer skip, Integer limit, + String include_responses, long[] start, long[] end, String assembly_id, + String reference_name, String reference_bases, String alternate_bases, + Long variant_min_length, Long variant_max_length, String genomic_allele_short_form, + String gene_id, String aminoacid_change, List filters); + + BeaconResultsetsResponse postGenomicVariationsRequest(BeaconRequestBody request); + + /** + * Get details about one genomic variation, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneGenomicVariation(String id); + + /** + * Get details about one genomic variation, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneGenomicVariationRequest(String id, BeaconRequestBody request); + + /** + * Get the biosamples list from one genomic variant, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getBiosamples( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the biosamples list from one genomic variant, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postBiosamplesRequest(String id, BeaconRequestBody request); + + /** + * Get the individuals list from one genomic variant, identified by its (unique) 'id' + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getIndividuals( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the individuals list from one genomic variant, identified by its (unique) 'id' + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postIndividualsRequest(String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with genomic variations. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getGenomicVariationsFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with genomic variations. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postGenomicVariationsFilteringTermsRequest(BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/IndividualsInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/IndividualsInterface.java new file mode 100644 index 0000000..d693d75 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/IndividualsInterface.java @@ -0,0 +1,142 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Individuals Endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface IndividualsInterface { + + /** + * Get a list of individuals. + * + * @param requested_schema + * @param skip + * @param limit + * @param include_responses + * @param filters + * @return + */ + BeaconResultsetsResponse getIndividuals( + String requested_schema, Integer skip, Integer limit, + String include_responses, List filters); + + /** + * Get a list of individuals. + * + * @param request + * @return + */ + BeaconResultsetsResponse postIndividualsRequest(BeaconRequestBody request); + + /** + * Get details about one individual, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneIndividual(String id); + + /** + * Get details about one individual, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneIndividualRequest(String id, BeaconRequestBody request); + + /** + * Get the genomic variants list from one individual, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneIndividualGenomicVariants( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the genomic variants list from one individual, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneIndividualGenomicVariantsRequest( + String id, BeaconRequestBody request); + + /** + * Get the biosamples list from one individual, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneIndividualBiosamples( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the biosamples list from one individual, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneIndividualBiosamplesRequest( + String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with individuals. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getIndividualsFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with individuals. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postIndividualsFilteringTermsRequest(BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/RunsInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/RunsInterface.java new file mode 100644 index 0000000..6c32923 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/RunsInterface.java @@ -0,0 +1,146 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.List; + +/** + * GA4GH Beacon API Specification - Runs Endpoints. + * + * @author Dmitry Repchevsky + */ + +public interface RunsInterface { + + /** + * Get a list of sequencing runs. + * + * @param requested_schema + * schema to be used to format the 'result' field in the response + * @param skip + * number of pages to skip + * @param limit + * size of the page + * @param include_responses + * @param filters + * + * @return + */ + BeaconResultsetsResponse getRuns( + String requested_schema, Integer skip, Integer limit, + String include_responses, List filters); + + /** + * Get a list of sequencing runs. + * + * @param request + * @return + */ + BeaconResultsetsResponse postRunsRequest(BeaconRequestBody request); + + /** + * Get details about one sequencing run, identified by its (unique) 'id'. + * + * @param id + * @return + */ + BeaconResultsetsResponse getOneRun(String id); + + /** + * Get details about one sequencing run, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneRun(String id, BeaconRequestBody request); + + /** + * Get the genomic variants list from one run, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneRunGenomicVariants( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the genomic variants list from one run, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneRunGenomicVariantsRequest( + String id, BeaconRequestBody request); + + /** + * Get the analysis list from one sequencing run, identified by its (unique) 'id'. + * + * @param id + * @param requested_schema + * @param skip + * @param limit + * @return + */ + BeaconResultsetsResponse getOneRunAnalyses( + String id, String requested_schema, Integer skip, Integer limit); + + /** + * Get the analysis list from one sequencing run, identified by its (unique) 'id'. + * + * @param id + * @param request + * @return + */ + BeaconResultsetsResponse postOneRunAnalysesRequest( + String id, BeaconRequestBody request); + + /** + * Get the list of filtering terms that could be used with runs. + * + * @param skip + * @param limit + * @return + */ + BeaconFilteringTermsResponse getRunsFilteringTerms(Integer skip, Integer limit); + + /** + * Get the list of filtering terms that could be used with runs. + * + * @param request + * @return + */ + BeaconFilteringTermsResponse postRunsFilteringTermsRequest(BeaconRequestBody request); + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/AnalysesRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/AnalysesRequestParameters.java new file mode 100644 index 0000000..97d1759 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/AnalysesRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class AnalysesRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/BiosamplesRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/BiosamplesRequestParameters.java new file mode 100644 index 0000000..40d7a9d --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/BiosamplesRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class BiosamplesRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/CohortsRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/CohortsRequestParameters.java new file mode 100644 index 0000000..a27934a --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/CohortsRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class CohortsRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/DatasetsRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/DatasetsRequestParameters.java new file mode 100644 index 0000000..070f808 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/DatasetsRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class DatasetsRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/GenomicVariationsRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/GenomicVariationsRequestParameters.java new file mode 100644 index 0000000..6fd05d0 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/GenomicVariationsRequestParameters.java @@ -0,0 +1,153 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class GenomicVariationsRequestParameters extends BeaconRequestParameters { + + private String assembly_id; + private String reference_name; + private long[] start; + private long[] end; + private String reference_bases; + private String alternate_bases; + private String variant_type; + private Long variant_min_length; + private Long variant_max_length; + private String mate_name; + private String gene_id; + private String aminoacid_change; + private String genomic_allele_short_form; + + public String getAssemblyId() { + return assembly_id; + } + + public void setAssemblyId(String assembly_id) { + this.assembly_id = assembly_id; + } + + public String getReferenceName() { + return reference_name; + } + + public void setReferenceName(String reference_name) { + this.reference_name = reference_name; + } + + public long[] getStart() { + return start; + } + + public void setStart(long[] start) { + this.start = start; + } + + public long[] getEnd() { + return end; + } + + public void setEnd(long[] end) { + this.end = end; + } + + public String getReferenceBases() { + return reference_bases; + } + + public void setReferenceBases(String reference_bases) { + this.reference_bases = reference_bases; + } + + public String getAlternateBases() { + return alternate_bases; + } + + public void setAlternateBases(String alternate_bases) { + this.alternate_bases = alternate_bases; + } + + public String getVariantType() { + return variant_type; + } + + public void setVariantType(String variant_type) { + this.variant_type = variant_type; + } + + public Long getVariantMinLength() { + return variant_min_length; + } + + public void setVariantMinLength(Long variant_min_length) { + this.variant_min_length = variant_min_length; + } + + public Long getVariantMaxLength() { + return variant_max_length; + } + + public void setVariantMaxLength(Long variant_max_length) { + this.variant_max_length = variant_max_length; + } + + public String getMateName() { + return mate_name; + } + + public void setMateName(String mate_name) { + this.mate_name = mate_name; + } + + public String getGeneId() { + return gene_id; + } + + public void setGeneId(String gene_id) { + this.gene_id = gene_id; + } + + public String getAminoacidChange() { + return aminoacid_change; + } + + public void setAminoacidChange(String aminoacid_change) { + this.aminoacid_change = aminoacid_change; + } + + public String getGenomicAlleleShortForm() { + return genomic_allele_short_form; + } + + public void setGenomicAlleleShortForm(String genomic_allele_short_form) { + this.genomic_allele_short_form = genomic_allele_short_form; + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/IndividualsRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/IndividualsRequestParameters.java new file mode 100644 index 0000000..b5e70a8 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/IndividualsRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class IndividualsRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RequestParametersDeserializer.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RequestParametersDeserializer.java new file mode 100644 index 0000000..e2d5af8 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RequestParametersDeserializer.java @@ -0,0 +1,68 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; +import jakarta.json.JsonObject; +import jakarta.json.JsonValue; +import jakarta.json.bind.Jsonb; +import jakarta.json.bind.JsonbBuilder; +import jakarta.json.bind.JsonbException; +import jakarta.json.bind.serializer.DeserializationContext; +import jakarta.json.bind.serializer.JsonbDeserializer; +import jakarta.json.stream.JsonParser; +import java.lang.reflect.Type; +import java.util.logging.Level; +import java.util.logging.Logger; + +/** + * @author Dmitry Repchevsky + */ + +public class RequestParametersDeserializer implements JsonbDeserializer { + + private static final Jsonb JSONB = JsonbBuilder.create(); + + @Override + public BeaconRequestParameters deserialize(JsonParser parser, DeserializationContext dc, Type type) { + final JsonValue value = parser.getValue(); + if (value != null && value.getValueType() == JsonValue.ValueType.OBJECT) { + final JsonObject obj = value.asJsonObject(); + if (!obj.isEmpty()) { + try { + return JSONB.fromJson(value.toString(), GenomicVariationsRequestParameters.class); +// return dc.deserialize(GenomicVariationsRequestParameters.class, +// Json.createParserFactory(Collections.EMPTY_MAP).createParser(obj)); + } catch(JsonbException ex) { + Logger.getLogger(RequestParametersDeserializer.class.getName()).log( + Level.INFO, ex.getMessage()); + } + } + } + return null; + } + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RunsRequestParameters.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RunsRequestParameters.java new file mode 100644 index 0000000..ecec9a0 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/model/v200/RunsRequestParameters.java @@ -0,0 +1,36 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.model.v200; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestParameters; + +/** + * @author Dmitry Repchevsky + */ + +public class RunsRequestParameters extends BeaconRequestParameters { + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/package-info.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/package-info.java new file mode 100644 index 0000000..cdfaf24 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/package-info.java @@ -0,0 +1,5 @@ +/** + * Java interfaces for the Beacon 2.0 endpoints. + */ + +package es.bsc.inb.ga4gh.beacon.framework; diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AnalysesEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AnalysesEndpointInterface.java new file mode 100644 index 0000000..0aab81e --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AnalysesEndpointInterface.java @@ -0,0 +1,288 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.AnalysesInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/analyses") +public interface AnalysesEndpointInterface + extends AnalysesInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getAnalyses( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("includeResultsetResponses") String include_responses, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getAnalyses(requested_schema, + skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getAnalyses(requested_schema, + skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postAnalyses( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postAnalyses(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postAnalyses(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneAnalysis( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneAnalysis(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneAnalysis(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneAnalysisRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneAnalysisRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneAnalysisRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void getOneAnalysisGenomicVariants( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneAnalysisGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneAnalysisGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void postOneAnalysisGenomicVariantsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneAnalysisGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneAnalysisGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getAnalysesFilteringTerms( + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getAnalysesFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getAnalysesFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postAnalysesFilteringTermsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postAnalysesFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postAnalysesFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AsyncEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AsyncEndpointInterface.java new file mode 100644 index 0000000..31ec90b --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/AsyncEndpointInterface.java @@ -0,0 +1,46 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import java.util.concurrent.ExecutorService; + +/** + * @author Dmitry Repchevsky + */ + +public interface AsyncEndpointInterface { + + /** + * Implementers may provide the executor service to be used for the + * asynchronous web service execution. + * + * @return ExecutorService for asynchronous execution or null. + */ + default ExecutorService getExecutorService() { + return null; + } + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconEndpointInterface.java new file mode 100644 index 0000000..c1e9cb5 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconEndpointInterface.java @@ -0,0 +1,89 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.v200.BeaconInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconInfoResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconMapResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconEntryTypesResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.configuration.ServiceConfiguration; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.service_info.model.v100.Service; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.core.MediaType; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/") +public interface BeaconEndpointInterface extends BeaconInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + @Override + BeaconInfoResponse getBeaconInfoRoot(@QueryParam("requestedSchema") String requestedSchema); + + @GET + @Path("/info") + @Produces(MediaType.APPLICATION_JSON) + @Override + BeaconInfoResponse getBeaconInfo(@QueryParam("requestedSchema") String requestedSchema); + + @GET + @Path("/service-info") + @Produces(MediaType.APPLICATION_JSON) + @Override + Service getBeaconServiceInfo(); + + @GET + @Path("/configuration") + @Produces(MediaType.APPLICATION_JSON) + @Override + ServiceConfiguration getBeaconConfiguration(); + + @GET + @Path("/map") + @Produces(MediaType.APPLICATION_JSON) + @Override + BeaconMapResponse getBeaconMap(); + + @GET + @Path("/entry_types") + @Produces(MediaType.APPLICATION_JSON) + @Override + BeaconEntryTypesResponse getEntryTypes(); + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + @Override + BeaconFilteringTermsResponse getFilteringTerms(); +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconErrorResponseProvider.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconErrorResponseProvider.java new file mode 100644 index 0000000..b6c9926 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BeaconErrorResponseProvider.java @@ -0,0 +1,78 @@ +/** + * ***************************************************************************** + * Copyright (C) 2022 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconError; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconErrorResponse; +import jakarta.ws.rs.WebApplicationException; +import jakarta.ws.rs.core.Response; +import jakarta.ws.rs.ext.ExceptionMapper; +import jakarta.ws.rs.ext.Provider; +import java.net.HttpURLConnection; + +/** + * Provider that automatically generates BeaconErrorResponse response + * catching WebApplicationException exceptions thrown from by the endpoints. + * + * @author Dmitry Repchevsky + */ + +@Provider +public class BeaconErrorResponseProvider implements ExceptionMapper { + + @Override + public Response toResponse(Exception ex) { + + if (ex instanceof WebApplicationException) { + final WebApplicationException wex = (WebApplicationException)ex; + final Response response = wex.getResponse(); + + final Object entity = response.getEntity(); + if (entity instanceof BeaconErrorResponse) { + // if exception already has the BeaconErrorResponse - just proxy it + return response; + } + + BeaconErrorResponse error_response = new BeaconErrorResponse(); + BeaconError error = new BeaconError(); + error.setErrorCode(response.getStatus()); + error.setErrorMessage(ex.getMessage()); + + error_response.setBeaconError(error); + + return Response.status(response.getStatus()).entity(error_response).build(); + } + BeaconErrorResponse error_response = new BeaconErrorResponse(); + BeaconError error = new BeaconError(); + + error.setErrorCode(HttpURLConnection.HTTP_INTERNAL_ERROR); + error.setErrorMessage(ex.getMessage()); + + error_response.setBeaconError(error); + + return Response.status(HttpURLConnection.HTTP_INTERNAL_ERROR).entity(error_response).build(); + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BiosamplesEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BiosamplesEndpointInterface.java new file mode 100644 index 0000000..edc326b --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/BiosamplesEndpointInterface.java @@ -0,0 +1,415 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.BiosamplesInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/biosamples") +public interface BiosamplesEndpointInterface + extends BiosamplesInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getBiosamples( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("includeResultsetResponses") String include_responses, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getBiosamples(requested_schema, skip, limit, + include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getBiosamples(requested_schema, skip, limit, + include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postBiosamplesRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postBiosamplesRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postBiosamplesRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneBiosample( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneBiosample(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneBiosample(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneBiosampleRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneBiosampleRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneBiosampleRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void getOneBiosampleGenomicVariants( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneBiosampleGenomicVariants( + id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneBiosampleGenomicVariants( + id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void postOneBiosampleGenomicVariantsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneBiosampleGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneBiosampleGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/analyses") + @Produces(MediaType.APPLICATION_JSON) + default void getOneBiosampleAnalysis( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneBiosampleAnalysis(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneBiosampleAnalysis(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/analyses") + @Produces(MediaType.APPLICATION_JSON) + default void postOneBiosampleAnalysisRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneBiosampleAnalysisRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneBiosampleAnalysisRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/runs") + @Produces(MediaType.APPLICATION_JSON) + default void getOneBiosampleRuns( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneBiosampleRuns(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneBiosampleRuns(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/runs") + @Produces(MediaType.APPLICATION_JSON) + default void getOneBiosampleRuns( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneBiosampleRuns(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneBiosampleRuns(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getBiosamplesFilteringTerms( + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getBiosamplesFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getBiosamplesFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postBiosamplesFilteringTermsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postBiosamplesFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postBiosamplesFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/CohortsEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/CohortsEndpointInterface.java new file mode 100644 index 0000000..4ba9aa3 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/CohortsEndpointInterface.java @@ -0,0 +1,290 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.CohortsInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/cohorts") +public interface CohortsEndpointInterface + extends CohortsInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getCohorts( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconCollectionsResponse response = + getCohorts(requested_schema, skip, limit, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconCollectionsResponse response = + getCohorts(requested_schema, skip, limit, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postCohortsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconCollectionsResponse response = postCohortsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconCollectionsResponse response = postCohortsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneCohort( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneCohort(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneCohort(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneCohortRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneCohortRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneCohortRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void getOneCohortIndividuals( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneCohortIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneCohortIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void postOneCohortIndividualsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneCohortIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneCohortIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getOneCohortFilteringTerms( + @PathParam("id") String id, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getOneCohortFilteringTerms(id, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getOneCohortFilteringTerms(id, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postOneCohortFilteringTermsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postOneCohortFilteringTermsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postOneCohortFilteringTermsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/DatasetsEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/DatasetsEndpointInterface.java new file mode 100644 index 0000000..546ede8 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/DatasetsEndpointInterface.java @@ -0,0 +1,407 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.DatasetsInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconCollectionsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/datasets") +public interface DatasetsEndpointInterface + extends DatasetsInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getDatasets( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconCollectionsResponse response = getDatasets(requested_schema, + skip, limit, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconCollectionsResponse response = getDatasets(requested_schema, + skip, limit, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postDatasetsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconCollectionsResponse response = postDatasetsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconCollectionsResponse response = postDatasetsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneDataset( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneDataset(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneDataset(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneDatasetRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneDatasetRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneDatasetRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void getOneDatasetGenomicVariants( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneDatasetGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneDatasetGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void postOneDatasetGenomicVariantsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneDatasetGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneDatasetGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void getOneDatasetBiosamples( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneDatasetBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneDatasetBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void postOneDatasetBiosamplesRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneDatasetBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneDatasetBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void getOneDatasetIndividuals( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneDatasetIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneDatasetIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void postOneDatasetIndividualsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneDatasetIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneDatasetIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getOneDatasetFilteringTerms( + @PathParam("id") String id, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getOneDatasetFilteringTerms(id, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getOneDatasetFilteringTerms(id, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postOneDatasetFilteringTermsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postOneDatasetFilteringTermsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postOneDatasetFilteringTermsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/GenomicVariationsEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/GenomicVariationsEndpointInterface.java new file mode 100644 index 0000000..629d401 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/GenomicVariationsEndpointInterface.java @@ -0,0 +1,371 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.GenomicVariationsInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/g_variants") +public interface GenomicVariationsEndpointInterface + extends GenomicVariationsInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getGenomicVariations( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("includeResultsetResponses") String include_responses, + @QueryParam("start") long[] start, + @QueryParam("end") long[] end, + @QueryParam("assemblyId") String assembly_id, + @QueryParam("referenceName") String reference_name, + @QueryParam("referenceBases") String reference_bases, + @QueryParam("alternateBases") String alternate_bases, + @QueryParam("variantMinLength") Long variant_min_length, + @QueryParam("variantMaxLength") Long variant_max_length, + @QueryParam("genomicAlleleShortForm") String genomic_allele_short_form, + @QueryParam("geneid") String gene_id, + @QueryParam("aminoacidChange") String aminoacid_change, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getGenomicVariations(requested_schema, skip, limit, + include_responses, start, end, assembly_id, + reference_name, reference_bases, alternate_bases, + variant_min_length, variant_max_length, + genomic_allele_short_form, gene_id, aminoacid_change, + filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getGenomicVariations(requested_schema, skip, limit, + include_responses, start, end, assembly_id, + reference_name, reference_bases, alternate_bases, + variant_min_length, variant_max_length, + genomic_allele_short_form, gene_id, aminoacid_change, + filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postGenomicVariationsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postGenomicVariationsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postGenomicVariationsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneGenomicVariation( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneGenomicVariation(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneGenomicVariation(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneGenomicVariationRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneGenomicVariationRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneGenomicVariationRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void getBiosamples( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void postBiosamplesRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void getIndividuals( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getIndividuals(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/individuals") + @Produces(MediaType.APPLICATION_JSON) + default void postIndividualsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postIndividualsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getGenomicVariationsFilteringTerms( + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getGenomicVariationsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getGenomicVariationsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postGenomicVariationsFilteringTermsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postGenomicVariationsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postGenomicVariationsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/IndividualsEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/IndividualsEndpointInterface.java new file mode 100644 index 0000000..7233e26 --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/IndividualsEndpointInterface.java @@ -0,0 +1,350 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.IndividualsInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/individuals") +public interface IndividualsEndpointInterface + extends IndividualsInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getIndividuals( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("includeResultsetResponses") String include_responses, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getIndividuals(requested_schema, skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getIndividuals(requested_schema, skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postIndividualsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postIndividualsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postIndividualsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneIndividual( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneIndividual(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneIndividual(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneIndividualRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneIndividualRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneIndividualRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void getOneIndividualGenomicVariants( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneIndividualGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneIndividualGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void postOneIndividualGenomicVariantsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneIndividualGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneIndividualGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void getOneIndividualBiosamples( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneIndividualBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneIndividualBiosamples(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/biosamples") + @Produces(MediaType.APPLICATION_JSON) + default void postOneIndividualBiosamplesRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneIndividualBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneIndividualBiosamplesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getIndividualsFilteringTerms( + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getIndividualsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getIndividualsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postIndividualsFilteringTermsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postIndividualsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postIndividualsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/RunsEndpointInterface.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/RunsEndpointInterface.java new file mode 100644 index 0000000..3f6bb2e --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/RunsEndpointInterface.java @@ -0,0 +1,350 @@ +/** + * ***************************************************************************** + * Copyright (C) 2023 ELIXIR ES, Spanish National Bioinformatics Institute (INB) + * and Barcelona Supercomputing Center (BSC) + * + * Modifications to the initial code base are copyright of their respective + * authors, or their employers as appropriate. + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, + * MA 02110-1301 USA + * ***************************************************************************** + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; + +import es.bsc.inb.ga4gh.beacon.framework.RunsInterface; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconQueryFilter; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.requests.BeaconRequestBody; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconFilteringTermsResponse; +import es.bsc.inb.ga4gh.beacon.framework.model.v200.responses.BeaconResultsetsResponse; +import java.util.concurrent.ExecutorService; +import jakarta.ws.rs.GET; +import jakarta.ws.rs.POST; +import jakarta.ws.rs.Path; +import jakarta.ws.rs.PathParam; +import jakarta.ws.rs.Produces; +import jakarta.ws.rs.QueryParam; +import jakarta.ws.rs.container.AsyncResponse; +import jakarta.ws.rs.container.Suspended; +import jakarta.ws.rs.core.MediaType; +import java.util.List; + +/** + * @author Dmitry Repchevsky + */ + +@Path("/runs") +public interface RunsEndpointInterface + extends RunsInterface, AsyncEndpointInterface { + + @GET + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void getRuns( + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @QueryParam("includeResultsetResponses") String include_responses, + @QueryParam("filters") List filters, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getRuns(requested_schema, + skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getRuns(requested_schema, + skip, limit, include_responses, filters); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/") + @Produces(MediaType.APPLICATION_JSON) + default void postRunsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postRunsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postRunsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void getOneRun( + @PathParam("id") String id, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = getOneRun(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = getOneRun(id); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}") + @Produces(MediaType.APPLICATION_JSON) + default void postOneRun( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = postOneRun(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = postOneRun(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void getOneRunGenomicVariants( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneRunGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneRunGenomicVariants(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/g_variants") + @Produces(MediaType.APPLICATION_JSON) + default void postOneRunGenomicVariantsRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneRunGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneRunGenomicVariantsRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/{id}/analyses") + @Produces(MediaType.APPLICATION_JSON) + default void getOneRunAnalyses( + @PathParam("id") String id, + @QueryParam("requestedSchema") String requested_schema, + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + getOneRunAnalyses(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + getOneRunAnalyses(id, requested_schema, skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/{id}/analyses") + @Produces(MediaType.APPLICATION_JSON) + default void postOneRunAnalysesRequest( + @PathParam("id") String id, + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconResultsetsResponse response = + postOneRunAnalysesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconResultsetsResponse response = + postOneRunAnalysesRequest(id, request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @GET + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void getRunsFilteringTerms( + @QueryParam("skip") Integer skip, + @QueryParam("limit") Integer limit, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + getRunsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + getRunsFilteringTerms(skip, limit); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } + + @POST + @Path("/filtering_terms") + @Produces(MediaType.APPLICATION_JSON) + default void postRunsFilteringTermsRequest( + BeaconRequestBody request, + @Suspended AsyncResponse asyncResponse) { + + final ExecutorService executor = getExecutorService(); + if (executor != null) { + executor.submit(() -> { + try { + final BeaconFilteringTermsResponse response = + postRunsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + }); + } else { + try { + final BeaconFilteringTermsResponse response = + postRunsFilteringTermsRequest(request); + asyncResponse.resume(response); + } catch (Exception ex) { + asyncResponse.resume(ex); + } + } + } +} diff --git a/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/package-info.java b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/package-info.java new file mode 100644 index 0000000..70343dc --- /dev/null +++ b/beacon-model/src/main/java/es/bsc/inb/ga4gh/beacon/framework/rest/package-info.java @@ -0,0 +1,8 @@ +/** + * Java JAX-RS interfaces for the Beacon 2.0 endpoints. + * + * Implementers will implement these interfaces to + * provide real functionality. + */ + +package es.bsc.inb.ga4gh.beacon.framework.rest; 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You can do so by permitting +redistribution under these terms (or, alternatively, under the terms of the +ordinary General Public License). + + To apply these terms, attach the following notices to the library. It is +safest to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least the +"copyright" line and a pointer to where the full notice is found. + + beacon-data-model + Copyright (C) 2019 INB / ga4gh + + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + This library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 + USA + +Also add information on how to contact you by electronic and paper mail. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the library, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the + library `Frob' (a library for tweaking knobs) written by James Random + Hacker. + + {signature of Ty Coon}, 1 April 1990 + Ty Coon, President of Vice + +That's all there is to it! diff --git a/pom.xml b/pom.xml index d47d593..a7252f2 100644 --- a/pom.xml +++ b/pom.xml @@ -56,6 +56,7 @@ beacon-framework beacon-data-model + beacon-model