Example usage for org.hibernate SessionFactory close

List of usage examples for org.hibernate SessionFactory close

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Introduction

In this page you can find the example usage for org.hibernate SessionFactory close.

Prototype

void close() throws HibernateException;

Source Link

Document

Destroy this SessionFactory and release all resources (caches, connection pools, etc).

Usage

From source file:module.script.pro12.CreatePro12.java

License:Open Source License

@SuppressWarnings({ "unchecked" })
public CreatePro12() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    // MongoDatabase db = mongoClient.getDatabase("geo");

    MongoCollection<Document> collectionSeries = db.getCollection("series");

    Date submissionDate = null;//from  w  w w  .j  ava  2 s  .  c o m
    try {
        submissionDate = dateFormat.parse("2010-01-01");
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    List<String> platforms = new ArrayList<String>();
    platforms.add("GPL570");

    Document docSeries = new Document();
    docSeries.append("_id", "PRO12").append("title", "Project 12: Reference tissues and cell lines")
            .append("platforms", platforms).append("submission_date", submissionDate)
            .append("last_update", submissionDate).append("import_date", new Date());

    System.out.println(docSeries);
    collectionSeries.insertOne(docSeries);

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.pro12.TransferPro12.java

License:Open Source License

@SuppressWarnings({ "unchecked" })
public TransferPro12() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    String sql = "select id_sample from epimed_prod.om_sample join epimed_prod.om_sample_series using (id_sample) "
            + "join epimed_prod.om_series using (id_series) where id_series='PRO12'";

    List<String> list = session.createSQLQuery(sql).list();

    Document pro12 = new Document();
    pro12.append("series", "PRO12");

    for (String gsmNumber : list) {

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        System.out.println("-----------------------------");
        System.out.println(gsmNumber + " " + doc);

        if (doc != null) {
            // Update Mongo document
            collection.updateOne(Filters.eq("_id", gsmNumber), new Document("$push", pro12));
        }//w  w w .  ja  v  a2  s. c  o m

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.proallchen.CreateProallChen.java

License:Open Source License

public CreateProallChen() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    // MongoDatabase db = mongoClient.getDatabase("geo");

    MongoCollection<Document> collectionSeries = db.getCollection("series");

    Date submissionDate = null;// w w w  . ja  va  2  s.  c o m
    try {
        submissionDate = dateFormat.parse("2016-05-13");
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // List<String> platforms = new ArrayList<String>();
    // platforms.add("GPL570");

    Document docSeries = new Document();
    docSeries.append("_id", "PROALL_CHEN")
            .append("title", "Genomic Profiling of Adult and Pediatric B-cell Acute Lymphoblastic Leukemia")
            .append("platforms", null).append("submission_date", submissionDate)
            .append("last_update", submissionDate).append("import_date", new Date());

    System.out.println(docSeries);
    collectionSeries.insertOne(docSeries);

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.probcp.ImportSamplesProbcp.java

License:Open Source License

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();/*from  www.j  a va 2  s.  co  m*/
        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();

}

From source file:module.script.probcp.UpdateSamplesProbcp.java

License:Open Source License

public UpdateSamplesProbcp() {

    // ===== 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" };
    List<String> series = new ArrayList<String>();

    for (int l = 0; l < studies.length; l++) {

        String idStudy = studies[l];
        String studyName = idStudy.toUpperCase();

        series.clear();//  w ww  .  j  a  va  2s  . c o  m
        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));

            String id = studyName + "_" + idSample;

            Document docSample = collectionSamples.find(Filters.eq("_id", id)).first();
            Document expgroup = (Document) docSample.get("exp_group");
            expgroup.append("tnm_grade", grade);
            expgroup.append("tnm_stage", null);
            docSample.append("exp_group", expgroup);

            UpdateResult updateResult = collectionSamples.updateOne(Filters.eq("_id", id),
                    new Document("$set", docSample));

            System.out.println(docSample);

        }

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();

}

From source file:module.script.TransferBrbAnnotations.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public TransferBrbAnnotations() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    String sql = "select id_sample, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
            + "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
            + "where exposed=true group by id_sample";

    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    for (Object item : list) {

        Map<String, Object> map = (HashMap<String, Object>) item;

        String gsmNumber = (String) map.get("id_sample");
        String gseNumber = (String) map.get("main_gse_number");

        System.out.println("-----------------------------");
        System.out.println(gseNumber + " " + gsmNumber);

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        if (doc != null) {
            Document expGroup = (Document) doc.get("exp_group");
            expGroup.put("exposure", map.get("list_substances"));
            System.out.println(expGroup);

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", true);
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                    new Document("$set", doc));
        }//from  w  w w  .j  a  va2  s  . c om

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.TransferBrbHistologyCodes.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public TransferBrbHistologyCodes() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    String sql = "select id_sample, main_gse_number, index_histology_code, histology_code, ordered_histology_code from db_brb_lung.view_exp_group";

    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    for (Object item : list) {

        Map<String, Object> map = (HashMap<String, Object>) item;

        String gsmNumber = (String) map.get("id_sample");
        String gseNumber = (String) map.get("main_gse_number");

        System.out.println("-----------------------------");
        System.out.println(gseNumber + " " + gsmNumber);

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        if (doc != null) {
            Document expGroup = (Document) doc.get("exp_group");
            expGroup.put("index_histology_code", map.get("index_histology_code"));
            expGroup.put("histology_code", map.get("histology_code"));
            expGroup.put("ordered_histology_code", map.get("ordered_histology_code"));
            System.out.println(expGroup);

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", true);
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                    new Document("$set", doc));
        }//from  ww  w .  j  a v a 2s . c  o m

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.TransferExposure.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public TransferExposure() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    String sql = "select id_sample, main_gse_number, string_agg(id_substance, ', ') as list_substances from epimed_prod.om_sample "
            + "join epimed_prod.cl_biopatho using (id_biopatho) join epimed_prod.cl_patient using (id_patient) join epimed_prod.cl_exposure using (id_patient) "
            + "where exposed=true group by id_sample";

    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    for (Object item : list) {

        Map<String, Object> map = (HashMap<String, Object>) item;

        String gsmNumber = (String) map.get("id_sample");
        String gseNumber = (String) map.get("main_gse_number");

        System.out.println("-----------------------------");
        System.out.println(gseNumber + " " + gsmNumber);

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        if (doc != null) {
            Document expGroup = (Document) doc.get("exp_group");
            expGroup.put("exposure", map.get("list_substances"));
            System.out.println(expGroup);

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", true);
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                    new Document("$set", doc));
        }//from w w w.  jav  a2 s.c o m

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.script.TransferFromEpimedProd.java

License:Open Source License

@SuppressWarnings({ "unused", "unchecked" })
public TransferFromEpimedProd() {

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    // ===== Session Mongo =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");

    MongoCollection<Document> collection = db.getCollection("samples");

    String sql = "select * from epimed_prod.view_exp_group order by main_gse_number, id_sample";
    List<Object> list = session.createSQLQuery(sql).setResultTransformer(Criteria.ALIAS_TO_ENTITY_MAP).list();

    String[] commonAttributes = { "pathology", "tnm_stage", "id_topology_group", "histology_subtype",
            "tissue_stage", "dead", "dfs_months", "age_max", "morphology", "id_tissue_stage", "topology", "sex",
            "age_min", "m", "topology_group", "n", "t", "collection_method", "id_morphology", "relapsed",
            "histology_type", "os_months", "id_topology" };

    List<ClPathology> listPathology = session.createCriteria(ClPathology.class).list();
    Map<String, ClPathology> mapPathology = new HashMap<String, ClPathology>();
    for (ClPathology p : listPathology) {
        mapPathology.put(p.getName(), p);
    }//from w w  w.j  a  v  a  2  s  .com

    List<ClTissueStatus> listTissueStatus = session.createCriteria(ClTissueStatus.class).list();
    Map<Integer, ClTissueStatus> mapTissueStatus = new HashMap<Integer, ClTissueStatus>();
    for (ClTissueStatus t : listTissueStatus) {
        mapTissueStatus.put(t.getIdTissueStatus(), t);
    }

    System.out.println(listTissueStatus);

    for (Object item : list) {

        Map<String, Object> map = (HashMap<String, Object>) item;

        String gsmNumber = (String) map.get("id_sample");
        String gseNumber = (String) map.get("main_gse_number");

        System.out.println("-----------------------------");
        System.out.println(gseNumber + " " + gsmNumber);

        Document doc = collection.find(Filters.eq("_id", gsmNumber)).first();

        if (doc != null) {
            Document expGroup = (Document) doc.get("exp_group");
            for (int j = 0; j < commonAttributes.length; j++) {
                String attr = commonAttributes[j];
                expGroup.put(attr, map.get(attr));
            }

            // Treatment
            expGroup.put("treatment", map.get("treatment_type"));

            // Pathology
            String pathoString = (String) map.get("pathology");
            ClPathology pathology = mapPathology.get(pathoString);
            if (pathology != null) {
                expGroup.put("id_pathology", pathology.getIdPathology());
                expGroup.put("pathology", pathology.getName());
            }

            // Tissue status
            Integer idTissueStatus = (Integer) map.get("id_tissue_status");
            if (idTissueStatus != null && idTissueStatus > 3) {
                idTissueStatus = 3;
            }
            ClTissueStatus tissueStatus = mapTissueStatus.get(idTissueStatus);
            if (tissueStatus != null) {
                expGroup.put("id_tissue_status", tissueStatus.getIdTissueStatus());
                expGroup.put("tissue_status", tissueStatus.getName());
            }

            System.out.println("idTissueStatus=" + tissueStatus + ", pathology=" + pathology);
            System.out.println(expGroup);

            // Update Mongo document
            doc.put("exp_group", expGroup);
            doc.put("analyzed", true);
            UpdateResult updateResult = collection.updateOne(Filters.eq("_id", gsmNumber),
                    new Document("$set", doc));
        }

    }

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();

    mongoClient.close();
}

From source file:module.test.ImportProbesets.java

License:Open Source License

public ImportProbesets() {

    // === Display ===
    System.out.println("\n================ BEGIN Module " + this.getClass().getName() + "================");

    // ===== Connection =====

    MongoClient mongoClient = MongoUtil.buildMongoClient();
    MongoDatabase db = mongoClient.getDatabase("epimed_experiments");
    MongoCollection<Document> collectionProbesets = db.getCollection("probesets");

    // ===== Session PostgreSQL =====
    SessionFactory sessionFactory = HibernateUtil
            .buildSessionFactory("config/epimed_semantic.hibernate.cfg.xml");
    Session session = sessionFactory.openSession();

    String idPlatform = "GPL570";
    String gpl = idPlatform.toLowerCase();

    // ===== Load file =====

    String inputfile = this.getInputDirectory() + this.getDirSeparator() + "HG-U133_Plus_2.na36.annot.csv";

    System.out.println("ID Platform " + gpl);
    System.out.println("LOADING \t " + inputfile);
    System.out.println("Please wait... ");
    List<String> listRows = fileService.loadTextFile(inputfile);
    System.out.println("File sucessfully LOADED");

    // ===== Recognize header =====

    List<String> header = fileService.readHeader(listRows, "\",\"");
    System.out.println("Header " + header);
    List<List<String>> data = fileService.readData(listRows, "\",\"");
    System.out.println(/*ww w  .java  2  s .co  m*/
            "The data are sucessfully loaded: rows " + data.size() + ", columns " + data.get(0).size());

    Integer indProbeset = fileService.findIndex(header, "Probe Set ID");
    Integer indGenes = fileService.findIndex(header, "Entrez Gene");
    Integer indUnigenes = fileService.findIndex(header, "UniGene ID");
    Integer indTranscripts = fileService.findIndex(header, "RefSeq Transcript ID");
    Integer indGb = fileService.findIndex(header, "Representative Public ID");

    for (int i = 0; i < 5; i++) {
        List<String> dataline = data.get(i);

        String probeset = dataline.get(indProbeset);
        String genes = dataline.get(indGenes);
        String unigenes = dataline.get(indUnigenes);
        String transcripts = dataline.get(indTranscripts);
        String gb = dataline.get(indGb);

        System.out.println(probeset + "\t" + genes + "\t" + formatService.splitInArray(unigenes, "///") + "\t"
                + gb + "\t" + transcripts);

        Document docProbeset = mongoService.createProbeset(idPlatform, probeset);
        docProbeset.put("genes", formatService.splitInArray(genes, "///"));
        docProbeset.put("unigenes", formatService.splitInArray(unigenes, "///"));

        List<String> listTranscripts = formatService.splitInArray(transcripts, "///");
        listTranscripts.addAll(formatService.splitInArray(gb, "///"));

        docProbeset.put("transcripts", listTranscripts);

        collectionProbesets.insertOne(docProbeset);

        /*
        for (int j=0; j<dataline.size(); j++) {
           String key = header.get(j);
           String value = dataline.get(j);
           System.out.println(key + ": " + value);
        }
        */
    }

    /*
    String tableProbe = "hs.om_probe_" + gpl;
    String tableGP = "hs.om_gp_" + gpl;
    List<Object []> listProbesets = session.createNativeQuery("select * from " + tableProbe + " order by id_probe").getResultList();
    for (int i=0; i<10; i++) {
            
       Object[] line = listProbesets.get(i);
            
       System.out.println(Arrays.toString(line));
       // Document docProbeset = mongoService.createProbeset(idPlatform, "1007_s_at");
       // collectionProbesets.insertOne(docProbeset);
    }
     */

    // === Close connections ===

    if (session.isOpen()) {
        session.close();
    }
    sessionFactory.close();
    mongoClient.close();

    // === Display ===
    System.out.println("================ END Module " + this.getClass().getName() + "================");

}