Java tutorial
/** * EpiMed - Information system for bioinformatics developments in the field of epigenetics * * This software is a computer program which performs the data management * for EpiMed platform of the Institute for Advances Biosciences (IAB) * * Copyright University of Grenoble Alps (UGA) * GNU GENERAL PUBLIC LICENSE * Please check LICENSE file * * Author: Ekaterina Bourova-Flin * */ package module.script.probcp; import java.util.ArrayList; import java.util.Arrays; import java.util.Date; import java.util.List; import org.bson.Document; import org.hibernate.Session; import org.hibernate.SessionFactory; import com.mongodb.MongoClient; import com.mongodb.client.MongoCollection; import com.mongodb.client.MongoDatabase; import config.HibernateUtil; import config.MongoUtil; import model.entity.ClMorphology; import model.entity.ClTopology; import module.BaseModule; @SuppressWarnings("unchecked") public class ImportSamplesProbcp extends BaseModule { private Date today = new Date(); public ImportSamplesProbcp() { // ===== Connection ===== MongoClient mongoClient = MongoUtil.buildMongoClient(); MongoDatabase db = mongoClient.getDatabase("epimed_experiments"); MongoCollection<Document> collectionSamples = db.getCollection("samples"); // ===== Session PostgreSQL ===== SessionFactory sessionFactory = HibernateUtil .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml"); Session session = sessionFactory.openSession(); String[] studies = { "tya16", "law15" }; List<String> series = new ArrayList<String>(); for (int l = 0; l < studies.length; l++) { String idStudy = studies[l]; String studyName = idStudy.toUpperCase(); series.clear(); series.add(studyName); series.add("PROBCP"); String sql = "select * from st_bcp." + idStudy + "_sample order by id_sample"; List<Object> listSamples = session.createSQLQuery(sql).list(); for (int i = 0; i < listSamples.size(); i++) { Object[] lineSample = (Object[]) listSamples.get(i); String idSample = (String) lineSample[0]; String clinicalClassification = (String) lineSample[1]; String tnmStage = (String) lineSample[2]; Integer grade = (Integer) lineSample[3]; String type = (String) lineSample[4]; System.out.println(Arrays.toString(lineSample)); // ===== Collection method ==== String collectionMethod = "biopsy"; if (idStudy.equals("law15") && !idSample.startsWith("Tumor")) { collectionMethod = "cell line"; } // ==== Topology ==== ClTopology topology = session.get(ClTopology.class, "C50.9"); // === Morphology === ClMorphology morphology = session.get(ClMorphology.class, "8010/3"); // carcinoma ClMorphology idc = session.get(ClMorphology.class, "8500/3"); // inf. duct. carcinoma ClMorphology lo = session.get(ClMorphology.class, "8520/3"); // lobular carcinoma ClMorphology ac = session.get(ClMorphology.class, "8140/3"); // adenocarcinoma if (type != null && (type.contains("IDC") || type.contains("DC") || type.contains("ductal"))) { morphology = idc; } if (type != null && type.contains("Lo")) { morphology = lo; } if (type != null && (type.contains("AC") || type.contains("adeno"))) { morphology = ac; } // ===== Sample Document ===== Document docSample = new Document(); docSample.append("_id", studyName + "_" + idSample).append("main_gse_number", studyName) .append("series", series).append("organism", "Homo sapiens") .append("submission_date", today).append("last_update", today).append("import_date", today) .append("analyzed", true); // ===== Mandatory parameters ===== Document expGroup = this.generateExpGroup(idSample, studyName, tnmStage, grade, type, collectionMethod, topology, morphology); docSample.append("exp_group", expGroup); // ===== Supplementary parameters ===== Document parameters = this.generateParameters(idSample); docSample.append("parameters", parameters); parameters.append("clinical_classification", clinicalClassification); parameters.append("tnm_stage", tnmStage); parameters.append("grade", grade); parameters.append("type", type); // === Append parameters to document === docSample.append("parameters", parameters); // === Save === collectionSamples.insertOne(docSample); System.out.println(docSample); } } if (session.isOpen()) { session.close(); } sessionFactory.close(); mongoClient.close(); } /** =============================================================== */ public static void main(String[] args) { new ImportSamplesProbcp(); } /** =============================================================== */ public Document generateExpGroup(String idSample, String mainGse, String tnmStage, Integer grade, String type, String collectionMethod, ClTopology topology, ClMorphology morphology) { Document expGroup = new Document(); expGroup.append("id_sample", idSample).append("main_gse_number", mainGse) .append("id_platform", "proteomics").append("sample_title", null).append("sample_source", null) .append("sex", null).append("ethnic_group", null).append("age_min", null).append("age_max", null) .append("id_tissue_stage", 1).append("tissue_stage", "adult").append("id_tissue_status", 3) .append("tissue_status", "Pathological tumoral").append("id_pathology", "C80.9") .append("pathology", "Cancer").append("collection_method", collectionMethod) .append("id_topology", topology.getIdTopology()).append("topology", topology.getName()) .append("id_topology_group", topology.getClTopologyGroup().getIdGroup()) .append("topology_group", topology.getClTopologyGroup().getName()) .append("id_morphology", morphology.getIdMorphology()).append("morphology", morphology.getName()) .append("histology_type", type).append("histology_subtype", null).append("t", null) .append("n", null).append("m", null).append("tnm_stage", tnmStage).append("tnm_grade", grade) .append("dfs_months", null).append("os_months", null).append("relapsed", null).append("dead", null) .append("treatment", null).append("exposure", null); return expGroup; } /** =============================================================== */ public Document generateParameters(String idSample) { Document parameters = new Document(); parameters.append("id_sample", idSample); ; return parameters; } /** =============================================================== */ }