Import or Export a Saved Query SDF Button

This script can be used in conjunction with an edited version of the Batch Searching script, for use on the Markush data infrastructure. The batch searching script keeps all queries in a query table, with a many:many relationship to the markush structures in the VMNS table they were found in. This may be a privacy concern for researchers who wish to keep the queries and results private, or only shared via external files. In that case, these two buttons can export a query with the resulting relationships to the VMNS structures, and then reimported to the same data structure for analysis.

This button is written to go on a query results form, which has the VMNS table as a child, connected via a n:n relationship. This button also has two handy file formatting features: it will check for the existence of a file and confirm if you want to overwrite it, and it will check the extension to ensure it is a SDF.

/** Export a saved batch query button
 *
 * @author Erin Bolstad ([email protected])
 * Dec 2011
 */
import com.im.commons.progress.*
import chemaxon.formats.MolExporter
import chemaxon.struc.Molecule
import chemaxon.formats.MolImporter
import javax.swing.JFileChooser
import javax.swing.*

evaluate = { widget ->
    if (SwingUtilities.isEventDispatchThread()) {
        Thread.start() {
            evaluateImpl(widget)
        }
    } else {
        evaluateImpl(widget)
    }
}

evaluateImpl = { widget ->
    def STRUCTURE_FIELD = 'Cd Structure' // field name of the structure field
    def FIELDS_FROM_CHILD = [ 'DCR Number', 'ROLE1 CODES', 'ROLE1 NAMES', 'ROLE2 CODES', 'ROLE2 NAMES' ] // list of field names from the child entity to export. Do not include structure field

    // Prompt for save file location
    def chooser = new JFileChooser()
    if (chooser.showSaveDialog(null)==JFileChooser.APPROVE_OPTION) {
        File fileName = chooser.getSelectedFile()
        name = fileName.getCanonicalPath()

        // Check to see if file has the correct extension

        if (!name.endsWith('.sdf')){
            FILE_NAME = name + '.sdf'
        } else {
            FILE_NAME = fileName.getCanonicalPath()
        }

        // See if file already exists

        File existFile = new File(FILE_NAME)
        if (existFile.exists () ) {
            def response = JOptionPane.showConfirmDialog (null, "$existFile exists \nOverwrite existing file?", "Confirm Overwrite", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE)
            if (response == JOptionPane.CANCEL_OPTION) {
                return
            }
        }
    } else {
        return}

    def rs = widget.form.resultSet
    def dataTree = rs.dataTree
    def parent = dataTree.rootVertex.entity
    def molEdge = dataTree.rootVertex.edges.find { it.destination.entity.name == 'V Examples' }
    def molEntity = molEdge.destination.entity
    def fldMol = molEntity.fields.items.find { it.name == STRUCTURE_FIELD }

    def fieldsFromChild = [ ]
    FIELDS_FROM_CHILD.each { name ->
        def fld = molEntity.fields.items.find { it.name == name }
        if (fld) {
            fieldsFromChild << fld
        } else {
            JOptionPane.showMessageDialog(null, "WARNING: field $name not found", "Oh no!", JOptionPane.INFORMATION_MESSAGE)
        }
    }

    def ors = parent.schema.dataProvider.getDefaultResultSet(dataTree, false, DFEnvironmentRO.DEV_NULL)
    def parentVS = ors.getVertexState(dataTree.rootVertex)
    def molVS = ors.getVertexState(molEdge.destination)
    def ids = parentVS.selectedRowsIds

    if (ids.size == 1) {
    } else {
        throw new RuntimeException('Must select single record for export')
    }
    def id = ids[0]

    // now read the data
    def good = 0

    def exporter = new MolExporter(FILE_NAME, 'sdf')

    def lock = ors.lockable.obtainLock('exporting')
    try {
        def envRW = new DFEnvironmentRW() {
            public DFLock getLock() {
                return lock;
            }

            public DFFeedback getFeedback() {
                return DFEnvironmentRO.DEV_NULL.feedback;
            }
        };

        def mol = null
        def childIDs = molVS.ids
        def values = [ : ]
        childIDs.eachWithIndex { childID, i ->

            def molData = molVS.getData([childID], DFEnvironmentRO.DEV_NULL)
            mol = molData[childID][fldMol.id]
            fieldsFromChild.each {
                values.put(it, molData[childID][it.id])
            }

            def expMol
            if (!mol ) {
                expMol = new Molecule()
            } else {
                expMol = MolImporter.importMol(mol)
            }
            values.each { k,v ->
                if (v) {
                    expMol.setProperty(k.name, v.toString())
                }
            }
            exporter.write(expMol)
            good++
        }

    } finally {
        lock?.release()
        exporter.flush()
        exporter.close()
    }

    JOptionPane.showMessageDialog(null, "Finished exporting data to file $FILE_NAME \n $good structures exported", "Export Complete", JOptionPane.INFORMATION_MESSAGE)

}

Versions: This script has been tested on IJC versions 5.7 and 6.0