Examples with Column org.molgenis.emx2.Column used on opensource projects

Example 21 with Column

use of org.molgenis.emx2.Column in project molgenis-emx2 by molgenis.

the class FileApi method getFile.

public static String getFile(Request request, Response response) throws IOException {
    String tableName = request.params("table");
    String columnName = request.params("column");
    String id = request.params("id");
    Schema schema = getSchema(request);
    Table t = schema.getTable(tableName);
    if (t == null) {
        throw new MolgenisException("Download failed: Table '" + tableName + "' not found in schema " + schema.getName());
    }
    Column c = t.getMetadata().getColumn(columnName);
    if (c == null) {
        throw new MolgenisException("Download failed: Column '" + columnName + "' not found in table " + schema.getName() + "." + tableName);
    }
    List<Row> result = t.query().select(t.getMetadata().getPrimaryKeyFields().stream().map(f -> s(f.getName())).toArray(SelectColumn[]::new)).select(s(columnName, s("contents"), s("mimetype"), s("extension"))).where(f(columnName, f("id", EQUALS, id))).retrieveRows();
    if (result.size() != 1) {
        throw new MolgenisException("Download failed: file id '" + id + "' not found in table " + tableName);
    }
    String ext = result.get(0).getString(columnName + "_extension");
    String mimetype = result.get(0).getString(columnName + "_mimetype");
    byte[] contents = result.get(0).getBinary(columnName + "_contents");
    response.raw().setHeader("Content-Disposition", "attachment; filename=" + c.getName() + "." + ext);
    response.raw().setContentType(mimetype);
    try (OutputStream out = response.raw().getOutputStream()) {
        // autoclosing
        out.write(contents);
        out.flush();
    }
    return "";
}

Example 22 with Column

use of org.molgenis.emx2.Column in project molgenis-emx2 by molgenis.

the class SqlTableMetadata method alterColumnTransaction.

// static to ensure we don't touch 'this' until transaction succesfull
private static SqlTableMetadata alterColumnTransaction(String schemaName, String tableName, String columnName, Column column, Database db) {
    SqlTableMetadata tm = (SqlTableMetadata) db.getSchema(schemaName).getMetadata().getTableMetadata(tableName);
    Column newColumn = new Column(tm, column);
    Column oldColumn = tm.getColumn(columnName);
    // primary keys by definition are required
    if (newColumn.getKey() == 1) {
        newColumn.setRequired(true);
    }
    validateColumn(newColumn);
    // check if reference and of different size
    if (newColumn.isRefArray() && !newColumn.getName().equals(oldColumn.getName()) && !newColumn.getColumnType().equals(oldColumn.getColumnType()) && newColumn.getRefTable().getPrimaryKeyFields().size() > 1) {
        throw new MolgenisException("Alter column of '" + oldColumn.getName() + " failed: REF_ARRAY is not supported for composite keys of table " + newColumn.getRefTableName());
    }
    // if changing 'ref' then check if not refBack exists
    if (!oldColumn.getColumnType().equals(newColumn.getColumnType())) {
        tm.checkNotRefback(columnName, oldColumn);
    }
    // drop old key, if touched
    if (oldColumn.getKey() > 0 && newColumn.getKey() != oldColumn.getKey()) {
        executeDropKey(tm.getJooq(), oldColumn.getTable(), oldColumn.getKey());
    }
    // drop referential constraints around this column
    executeRemoveRefConstraints(tm.getJooq(), oldColumn);
    // remove refBacks if exist
    executeRemoveRefback(oldColumn, newColumn);
    // add ontology table if needed
    if (newColumn.isOntology()) {
        createOntologyTable(newColumn);
    }
    // rename and retype if needed
    executeAlterType(tm.getJooq(), oldColumn, newColumn);
    executeAlterName(tm.getJooq(), oldColumn, newColumn);
    // only applies to key=1
    if ((oldColumn.isPrimaryKey() || newColumn.isPrimaryKey()) && oldColumn.isRequired() && !oldColumn.isRequired() == newColumn.isRequired()) {
        executeSetRequired(tm.getJooq(), newColumn);
    }
    // update the metadata so we can use it for new keys and references
    if (column.getPosition() == null) {
        column.setPosition(tm.columns.get(columnName).getPosition());
    }
    // remove the old
    tm.columns.remove(columnName);
    // add the new
    tm.columns.put(column.getName(), column);
    // reapply ref constrainst
    executeCreateRefConstraints(tm.getJooq(), newColumn);
    // check if refBack constraints need updating
    reapplyRefbackContraints(oldColumn, newColumn);
    // create/update key, if touched
    if (newColumn.getKey() != oldColumn.getKey()) {
        createOrReplaceKey(tm.getJooq(), tm, newColumn.getKey(), tm.getKeyFields(newColumn.getKey()));
    }
    // delete old column if name changed, then save any other metadata changes
    if (!oldColumn.getName().equals(newColumn.getName()))
        deleteColumn(tm.getJooq(), oldColumn);
    saveColumnMetadata(tm.getJooq(), newColumn);
    return tm;
}

Example 23 with Column

use of org.molgenis.emx2.Column in project molgenis-emx2 by molgenis.

the class SqlTableMetadata method addTransaction.

// static to ensure we don't touch 'this' until complete
private static SqlTableMetadata addTransaction(Database db, String schemaName, String tableName, Column[] column) {
    SqlTableMetadata tm = (SqlTableMetadata) db.getSchema(schemaName).getMetadata().getTableMetadata(tableName);
    // first per-column actions, then multi-column action such as composite keys/refs
    int position = MetadataUtils.getMaxPosition(tm.getJooq(), schemaName) + 1;
    for (Column c : column) {
        long start = System.currentTimeMillis();
        if (tm.getLocalColumn(c.getName()) != null) {
            tm.alterColumn(c);
        } else {
            Column newColumn = new Column(tm, c);
            if (tm.getInherit() != null && tm.getInheritedTable().getColumn(c.getName()) != null && // this column is replicated in all subclass tables
            !c.getName().equals(MG_TABLECLASS)) {
                throw new MolgenisException("Cannot add column " + tm.getTableName() + "." + c.getName() + ": column exists in inherited class " + tm.getInherit());
            }
            if (!newColumn.isHeading()) {
                validateColumn(newColumn);
                if (newColumn.getPosition() == null) {
                    // positions are asumed to number up in a schema
                    newColumn.setPosition(position++);
                }
                executeCreateColumn(tm.getJooq(), newColumn);
                tm.columns.put(c.getName(), newColumn);
                if (newColumn.getKey() > 0) {
                    createOrReplaceKey(tm.getJooq(), newColumn.getTable(), newColumn.getKey(), newColumn.getTable().getKeyFields(newColumn.getKey()));
                }
                executeCreateRefConstraints(tm.getJooq(), newColumn);
            } else {
                saveColumnMetadata(tm.getJooq(), newColumn);
                tm.columns.put(c.getName(), newColumn);
            }
            log(tm, start, "added column '" + newColumn.getName() + "' to table " + tm.getTableName());
        }
    }
    return tm;
}

Example 24 with Column

use of org.molgenis.emx2.Column in project molgenis-emx2 by molgenis.

the class SqlTableMetadata method alterNameTransaction.

// ensure the transaction has no side effects on 'this' until completed
private static SqlTableMetadata alterNameTransaction(Database db, String schemaName, String tableName, String newName) {
    SqlTableMetadata tm = (SqlTableMetadata) db.getSchema(schemaName).getMetadata().getTableMetadata(tableName);
    // drop triggers for this table
    for (Column column : tm.getStoredColumns()) {
        SqlColumnExecutor.executeRemoveRefConstraints(tm.getJooq(), column);
    }
    // rename table and triggers
    SqlTableMetadataExecutor.executeAlterName(tm.getJooq(), tm, newName);
    // update metadata
    MetadataUtils.alterTableName(tm.getJooq(), tm, newName);
    tm.tableName = newName;
    // recreate triggers for this table
    for (Column column : tm.getStoredColumns()) {
        SqlColumnExecutor.executeCreateRefConstraints(tm.getJooq(), column);
    }
    return tm;
}

Example 25 with Column

use of org.molgenis.emx2.Column in project molgenis-emx2 by molgenis.

the class SqlTableMetadata method alterColumn.

@Override
public TableMetadata alterColumn(String columnName, Column column) {
    // ignore mg_ columns
    if (column.getName().startsWith("mg_"))
        return this;
    Column oldColumn = getColumn(columnName);
    if (oldColumn == null) {
        throw new MolgenisException("Alter column failed: Column  '" + getTableName() + "." + column.getName() + "' does not exist");
    }
    if (getInherit() != null && getInheritedTable().getColumn(columnName) != null) {
        throw new MolgenisException("Alter column " + getTableName() + "." + columnName + " failed: column is part of inherited table " + getInherit());
    }
    if (getInherit() != null && getInheritedTable().getColumn(column.getName()) != null) {
        throw new MolgenisException("Rename column from " + getTableName() + "." + columnName + " to " + getTableName() + "." + column.getName() + " failed: column '" + column.getName() + "' is part of inherited table " + getInherit());
    }
    getDatabase().tx(db -> sync(alterColumnTransaction(getSchemaName(), getTableName(), columnName, column, db)));
    // reload the state
    ((SqlSchemaMetadata) getSchema()).sync(getDatabase().getSchema(getSchemaName()).getMetadata());
    return this;
}