This workflow loads molecules from a database. For each molecule the atom type gets perceived. The output of this workflow are a couple of text files. The frist text file contains all molecule id's which are loaded from the database. The second text file contains all molecules which had problems with the atom typing. This file contains the molecule id and the atom which caused the problem. The last output file, a pdf, contains all structures of the molecules which caused problems during the atom typing to visual inspect the molecules.
org.openscience.cdk.applications.taverna.database.pgchem.IterativeMoleculeFromDBReader
jdbc:postgresql://localhost/cdk-taverna
testuser
testpwd
SELECT * FROM molecules ORDER BY id LIMIT ? OFFSET ?
org.embl.ebi.escience.scuflworkers.java.FailIfTrue
org.openscience.cdk.applications.taverna.tools.ExtractDatabaseIDFromMolecule
org.openscience.cdk.applications.taverna.atomtype.PerceiveAtomType
org.openscience.cdk.applications.taverna.renderers.CreatePDFWith2DStructures
org.openscience.cdk.applications.taverna.database.pgchem.IterativeGetMoleculeFromDB
org.openscience.cdk.applications.taverna.database.pgchem.IterativeHasNextMoleculeFromDB
org.openscience.cdk.applications.taverna.tools.ExtractDatabaseIDFromMolecule
org.openscience.cdk.applications.taverna.io.iterative.IterativeFileWriter
org.openscience.cdk.applications.taverna.io.iterative.IterativeFileWriter
org.openscience.cdk.applications.taverna.io.WriteToMDLMolFile
org.openscience.cdk.applications.taverna.io.iterative.IterativeFileWriter
Completed
Iterative_File_Writer
Has_Next_Molecule_from_database
Scheduled
Running
Completed
Create_PDF_File_with_2D_Structures
Has_Next_Molecule_from_database
Scheduled
Running
Completed
Write_MDL_Mol_File_to_File
Has_Next_Molecule_from_database
Scheduled
Running
Completed
Iterative_File_Writer2
Has_Next_Molecule_from_database
Scheduled
Running
Completed
Iterative_File_Writer1
Has_Next_Molecule_from_database
Scheduled
Running