Example usage for org.apache.commons.csv CSVFormat TDF

List of usage examples for org.apache.commons.csv CSVFormat TDF

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Introduction

In this page you can find the example usage for org.apache.commons.csv CSVFormat TDF.

Prototype

CSVFormat TDF

To view the source code for org.apache.commons.csv CSVFormat TDF.

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Document

Tab-delimited format.

Usage

From source file:org.ohdsi.whiteRabbit.WhiteRabbitMain.java

private DbSettings getTargetDbSettings() {
    DbSettings dbSettings = new DbSettings();
    if (targetType.getSelectedItem().equals("Delimited text files")) {
        dbSettings.dataType = DbSettings.CSVFILES;

        switch ((String) targetCSVFormat.getSelectedItem()) {
        case "Default (comma, CRLF)":
            dbSettings.csvFormat = CSVFormat.DEFAULT;
            break;
        case "RFC4180":
            dbSettings.csvFormat = CSVFormat.RFC4180;
            break;
        case "Excel CSV":
            dbSettings.csvFormat = CSVFormat.EXCEL;
            break;
        case "TDF (tab, CRLF)":
            dbSettings.csvFormat = CSVFormat.TDF;
            break;
        case "MySQL (tab, LF)":
            dbSettings.csvFormat = CSVFormat.MYSQL;
            break;
        default://from   w w  w .  j av a 2 s  .  c o m
            dbSettings.csvFormat = CSVFormat.RFC4180;
        }

    } else {
        dbSettings.dataType = DbSettings.DATABASE;
        dbSettings.user = targetUserField.getText();
        dbSettings.password = targetPasswordField.getText();
        dbSettings.server = targetServerField.getText();
        dbSettings.database = targetDatabaseField.getText();
        if (targetType.getSelectedItem().toString().equals("MySQL"))
            dbSettings.dbType = DbType.MYSQL;
        else if (targetType.getSelectedItem().toString().equals("Oracle"))
            dbSettings.dbType = DbType.ORACLE;
        else if (sourceType.getSelectedItem().toString().equals("PostgreSQL"))
            dbSettings.dbType = DbType.POSTGRESQL;
        else if (sourceType.getSelectedItem().toString().equals("SQL Server")) {
            dbSettings.dbType = DbType.MSSQL;
            if (sourceUserField.getText().length() != 0) { // Not using windows authentication
                String[] parts = sourceUserField.getText().split("/");
                if (parts.length == 2) {
                    dbSettings.user = parts[1];
                    dbSettings.domain = parts[0];
                }
            }
        } else if (sourceType.getSelectedItem().toString().equals("PDW")) {
            dbSettings.dbType = DbType.PDW;
            if (sourceUserField.getText().length() != 0) { // Not using windows authentication
                String[] parts = sourceUserField.getText().split("/");
                if (parts.length == 2) {
                    dbSettings.user = parts[1];
                    dbSettings.domain = parts[0];
                }
            }
        }

        if (dbSettings.database.trim().length() == 0) {
            String message = "Please specify a name for the target database";
            JOptionPane.showMessageDialog(frame, StringUtilities.wordWrap(message, 80), "Database error",
                    JOptionPane.ERROR_MESSAGE);
            return null;
        }
    }
    return dbSettings;
}

From source file:org.phenotips.oo.OmimSourceParser.java

private void loadSymptoms(boolean positive) {
    try (BufferedReader in = new BufferedReader(
            new InputStreamReader(new URL(positive ? POSITIVE_ANNOTATIONS_URL : NEGATIVE_ANNOTATIONS_URL)
                    .openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.parse(in)) {
            if ("OMIM".equals(row.get(0))) {
                SolrInputDocument term = this.data.get(row.get(1));
                if (term != null) {
                    term.addField(positive ? "actual_symptom" : "actual_not_symptom", row.get(4));
                }/*from ww w.  jav a2  s .c o  m*/
            }
        }
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-HPO links: {}", ex.getMessage(), ex);
    }
}

From source file:org.phenotips.oo.OmimSourceParser.java

private void loadGenes() {
    final String missing = "-";
    try (BufferedReader in = new BufferedReader(
            new InputStreamReader(new URL(GENE_ANNOTATIONS_URL).openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.withHeader().parse(in)) {
            if (!row.get("Type").contains("gene")) {
                continue;
            }/*from   www .  j a v a 2s.  com*/
            SolrInputDocument term = this.data.get(row.get(2));
            if (term != null) {
                String gs = row.get("Approved Gene Symbol");
                if (!missing.equals(gs)) {
                    term.addField(GENE_FIELD, gs);
                }
                String eid = row.get("Ensembl Gene ID");
                if (!missing.equals(eid)) {
                    term.addField(GENE_FIELD, eid);
                }
            }
        }
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-Gene links: {}", ex.getMessage(), ex);
    }
}

From source file:org.phenotips.oo.OmimSourceParser.java

private void loadGeneReviews() {
    try (BufferedReader in = new BufferedReader(new InputStreamReader(
            new URL(GENEREVIEWS_MAPPING_URL).openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.withHeader().parse(in)) {
            SolrInputDocument term = this.data.get(row.get(2));
            if (term != null) {
                term.addField("gene_reviews_link", "https://www.ncbi.nlm.nih.gov/books/" + row.get(0));
            }//from www  . j a  v a2 s  .c om
        }
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-GeneReviews links: {}", ex.getMessage(), ex);
    }
}

From source file:org.phenotips.variantstore.input.exomiser6.tsv.Exomiser6TSVIterator.java

/**
 * Create a new TSV iterator for files output by Exomiser.
 *
 * @param path          the path to the file
 * @param variantHeader the header with file meta-information
 *///from  www.j  a v a  2 s  .c o  m
public Exomiser6TSVIterator(Path path, VariantHeader variantHeader) {
    super(path, variantHeader);

    Reader reader = null;
    try {
        reader = new FileReader(this.path.toString());
        this.tsvParser = CSVFormat.TDF.parse(reader);
    } catch (IOException e) {
        logger.error(String.format("Error when opening file %s, this should NOT be happening", this.path), e);
    }

    this.tsvRecordIterator = tsvParser.iterator();
    // skip first row >.>
    if (this.hasNext()) {
        tsvRecordIterator.next();
    }
}

From source file:org.phenotips.variantstore.input.tsv.AbstractTSVIterator.java

/**
 * Create a new TSV iterator for files, such as those outputted by Exomiser.
 *
 * @param path          the path to the file
 * @param variantHeader the header with file meta-information
 *//* w w w .  j a v  a  2  s .  co m*/
public AbstractTSVIterator(Path path, VariantHeader variantHeader) {
    super(path, variantHeader);

    Reader reader = null;
    try {
        reader = new FileReader(this.path.toString());
        this.tsvParser = CSVFormat.TDF.parse(reader);
    } catch (IOException e) {
        logger.error(String.format("Error when opening file %s, this should NOT be happening", this.path), e);
    }

    this.tsvRecordIterator = tsvParser.iterator();
    // Read column names
    if (this.hasNext()) {
        this.columns = new ArrayList<String>();
        for (String field : tsvRecordIterator.next()) {
            // Remove leading hashes
            columns.add(field.replaceAll("^#+", ""));
        }
    }
}

From source file:org.phenotips.variantstore.input.tsv.ExomiserTSVIterator.java

/**
 * Create a new TSV iterator for files output by Exomiser.
 *
 * @param path          the path to the file
 * @param variantHeader the header with file meta-information
 *///  ww  w  .jav  a2  s  .  c o m
public ExomiserTSVIterator(Path path, VariantHeader variantHeader) {
    super(path, variantHeader);

    Reader reader = null;
    try {
        reader = new FileReader(this.path.toString());
        this.tsvParser = CSVFormat.TDF.parse(reader);
    } catch (IOException e) {
        logger.error(String.format("Error when opening file %s, this should NOT be happening", this.path), e);
    }

    this.tsvRecordIterator = tsvParser.iterator();
    // skip first row >.>
    if (this.hasNext()) {
        tsvRecordIterator.next();
    }
}

From source file:org.phenotips.vocabulary.internal.GeneNomenclature.java

@Override
protected Collection<SolrInputDocument> load(URL url) {
    try {//from w  w  w.  java2  s. c om
        Collection<SolrInputDocument> solrDocuments = new HashSet<>();

        Reader in = new InputStreamReader(url.openConnection().getInputStream(), Charset.forName("UTF-8"));
        for (CSVRecord row : CSVFormat.TDF.withHeader().parse(in)) {
            SolrInputDocument crtTerm = new SolrInputDocument();
            for (Map.Entry<String, String> item : row.toMap().entrySet()) {
                if ("hgnc_id".equals(item.getKey())) {
                    crtTerm.addField(ID_FIELD_NAME, item.getValue());
                } else if (StringUtils.isNotBlank(item.getValue())) {
                    crtTerm.addField(item.getKey(), StringUtils.split(item.getValue(), "|"));
                }
            }
            solrDocuments.add(crtTerm);
        }
        addMetaInfo(solrDocuments);
        return solrDocuments;
    } catch (IOException ex) {
        this.logger.warn("Failed to read/parse the HGNC source: {}", ex.getMessage());
    }
    return null;
}

From source file:org.phenotips.vocabulary.internal.hpoannotations.AbstractPhenotypeForDiseaseAnnotationsExtension.java

@Override
protected CSVFormat setupCSVParser(Vocabulary vocabulary) {
    return CSVFormat.TDF;
}

From source file:org.phenotips.vocabulary.internal.hpoannotations.GeneForPhenotypesAnnotationsExtension.java

@Override
protected CSVFormat setupCSVParser(Vocabulary vocabulary) {
    // Bug in commons-csv: although duplicate null headers are allowed in CSVParser, CSVFormat#validate doesn't
    // allow more than one null header
    return CSVFormat.TDF.withHeader("id", null, "", "associated_genes").withAllowMissingColumnNames()
            .withCommentMarker('#');
}