This worklfow load a TSV file from the ChEBI database. (normally structures.tsv) After the extraction of the molecules from the TSV file all non MDL mol files are removed before the valid molecules are inserted into a database.
org.openscience.cdk.applications.taverna.io.FileWriter
org.openscience.cdk.applications.taverna.io.TextFileReader
org.openscience.cdk.applications.taverna.tools.chebi.ExtractDataFromChebiStructureTSV
chebi
org.openscience.cdk.applications.taverna.database.pgchem.InsertMoleculeIntoDB
jdbc:postgresql://localhost/cdktaverna
INSERT INTO chebimolecules (molecule,originalid,origin,comment) VALUES(migrate_molecule(?),?,?,?)
org.openscience.cdk.applications.taverna.tools.chebi.RemoveAllNonMolFilesFromChebiStructureExtraction