#!/usr/bin/env python # -*- coding: utf-8 -*- import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType ## ## Documentation ## ## Properties starting by "+" will be created in openBIS, but will not be read from FileMaker but if set programmatically will be put back in openBIS. ## Properties starting by "-" will not be created in openBIS but will be read from FileMaker. # # Helper Methods # def getPropertyDefinitionByCode(definition, code): for property in definition: if property[0] == code: return property return None # # Scripts # commentsScriptName = "COMMENTS"; annotationsScriptName="ANNOTATIONS" geneticModificationsScriptName = "GENETIC_MODIFICATIONS"; seqFileDefinition = [ ["NAME", "General", "Name", DataType.VARCHAR, None, "Name", None, None, False], ["NOTES", "General information", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes regarding the dataset", None, None,False], ["XMLCOMMENTS", "Comments","Comments List", DataType.XML, None, "Several comments can be added by different users", "COMMENTS_DATA_SET", None,False] ]; # #Sample Types # strainDefinition = [ ["NAME", "General", "Name", DataType.VARCHAR, None, "", None, None, False], ["BBPL_NUM", "General", "bBPL Number", DataType.VARCHAR, None, "", None, None, False], ["PLASMID", "General", "Plasmid", DataType.VARCHAR, None, "", None, None, False], ["GENOTYPE", "General", "Genotype", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["SOURCE", "General", "Source", DataType.VARCHAR, None, "", None, None, False], ["DEPOSITOR", "General", "Depositor", DataType.CONTROLLEDVOCABULARY, "LAB_MEMBERS", "", None, None, False], ["REFERENCE", "General", "Reference", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["OTHER_COLLECTION_NUMBER", "General", "Other Collection Number", DataType.VARCHAR, None, "", None, None, False], ["MEDIUM", "General", "Medium", DataType.VARCHAR, None, "", None, None, False], ["RESISTANCE", "General", "Resistance", DataType.VARCHAR, None, "", None, None, False], ["REMARKS", "General", "Application/Remarks", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["DATE", "General", "Date", DataType.TIMESTAMP, None, "", None, None, False], ["OTHER", "General", "Other", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["-BPL_NUMBER", "General", "BPL Number", DataType.VARCHAR, None, "", None, None, False], ["+GENETIC_MODIFICATIONS", "Genotype", "Genetic modifications", DataType.MULTILINE_VARCHAR, None, "", None, geneticModificationsScriptName, False], ["+STORAGE_NAMES", "Physical Storage", "Storage Name", DataType.CONTROLLEDVOCABULARY, "STORAGE_NAMES", "Storage Name", None, None, False], ["+STORAGE_ROW", "Physical Storage", "Storage Row", DataType.INTEGER, None, "Storage Row", None, None, False], ["+STORAGE_COLUMN", "Physical Storage", "Storage Column", DataType.INTEGER, None, "Storage Column", None, None, False], ["STORAGE_BOX_NAME", "Physical Storage", "Box", DataType.VARCHAR, None, "Storage Box Name", None, None, False], ["+STORAGE_BOX_SIZE", "Physical Storage", "Storage Box Size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box Size", None, None, False], ["+STORAGE_USER", "Physical Storage", "Storage User Id", DataType.VARCHAR, None, "Storage User Id", None, None, False], ["STORAGE_POSITION", "Physical Storage", "Location", DataType.VARCHAR, None, "Storage Position", None, None, False], ["+ANNOTATIONS_STATE", "Comments", " Annotations State", DataType.XML, None,"Annotations State", annotationsScriptName, None, False] ]; oligoDefinition = [ ["NAME", "General", "Name", DataType.VARCHAR, None, "", None, None, False], ["DESCRIPTION", "General", "Description", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["DEPOSITOR", "General", "Depositor", DataType.CONTROLLEDVOCABULARY, "LAB_MEMBERS", "", None, None, False], ["DATE", "General", "Date", DataType.TIMESTAMP, None, "", None, None, False], ["REMARKS", "General", "Application/Remarks", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["SEQUENCE", "General", "Sequence", DataType.VARCHAR, None, "", None, None, False], ["ALTERNATE_OL_NAME", "General", "Alternate Oligo Name", DataType.VARCHAR, None, "", None, None, False], ["OBPL_NUMBER", "General", "oBPL Number", DataType.VARCHAR, None, "", None, None, False], ["+STORAGE_NAMES", "Physical Storage", "Storage Name", DataType.CONTROLLEDVOCABULARY, "STORAGE_NAMES", "Storage Name", None, None, False], ["+STORAGE_ROW", "Physical Storage", "Storage Row", DataType.INTEGER, None, "Storage Row", None, None, False], ["+STORAGE_COLUMN", "Physical Storage", "Storage Column", DataType.INTEGER, None, "Storage Column", None, None, False], ["STORAGE_BOX_NAME", "Physical Storage", "Box", DataType.VARCHAR, None, "Storage Box Name", None, None, False], ["+STORAGE_BOX_SIZE", "Physical Storage", "Storage Box Size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box Size", None, None, False], ["+STORAGE_USER", "Physical Storage", "Storage User Id", DataType.VARCHAR, None, "Storage User Id", None, None, False], ["STORAGE_POSITION", "Physical Storage", "Location", DataType.VARCHAR, None, "Storage Position", None, None, False], ["+ANNOTATIONS_STATE", "Comments", " Annotations State", DataType.XML, None,"Annotations State", annotationsScriptName, None, False] ]; plasmidDefinition = [ ["NAME", "General", "Name", DataType.VARCHAR, None, "", None, None, False], ["DESCRIPTION", "General", "Description", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["SOURCE", "General", "Source", DataType.VARCHAR, None, "", None, None, False], ["DEPOSITOR", "General", "Depositor", DataType.CONTROLLEDVOCABULARY, "LAB_MEMBERS", "", None, None, False], ["DATE", "General", "Date", DataType.TIMESTAMP, None, "", None, None, False], ["REFERENCE", "General", "Reference", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["DERIVATIVE_OF", "General", "Derivative of", DataType.VARCHAR, None, "", None, None, False], ["RESISTANCE", "General", "Resistance", DataType.VARCHAR, None, "", None, None, False], ["REMARKS", "General", "Application/Remarks", DataType.MULTILINE_VARCHAR, None, "", None, None, False], ["ALTERNATE_PL_NUMBER", "General", "Alternate Plasmid Number", DataType.VARCHAR, None, "", None, None, False], ["PL_NUMBER", "General", "Plasmid Number", DataType.INTEGER, None, "", None, None, False], ["ORIGIN", "General", "Origin", DataType.VARCHAR, None, "", None, None, False], ["VERIFIED_BY", "General", "Verified by:", DataType.VARCHAR, None, "", None, None, False], ["VERIFIED_BY_2", "General", "Verified by 2", DataType.VARCHAR, None, "", None, None, False], ["VERIFIED_BY_3", "General", "Verified by 3", DataType.VARCHAR, None, "", None, None, False], ["VERIFIED_BY_4", "General", "Verified by 4", DataType.VARCHAR, None, "", None, None, False], ["GLYCEROL", "General", "Glycerol", DataType.VARCHAR, None, "", None, None, False], ["PROMOTER", "General", "Promoter", DataType.VARCHAR, None, "", None, None, False], ["-SEQUENCE", "General", "Sequence", DataType.VARCHAR, None, "", None, None, False], ["+STORAGE_NAMES", "Physical Storage", "Storage Name", DataType.CONTROLLEDVOCABULARY, "STORAGE_NAMES", "Storage Name", None, None, False], ["+STORAGE_ROW", "Physical Storage", "Storage Row", DataType.INTEGER, None, "Storage Row", None, None, False], ["+STORAGE_COLUMN", "Physical Storage", "Storage Column", DataType.INTEGER, None, "Storage Column", None, None, False], ["STORAGE_BOX_NAME", "Physical Storage", "Box", DataType.VARCHAR, None, "Storage Box Name", None, None, False], ["+STORAGE_BOX_SIZE", "Physical Storage", "Storage Box Size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box Size", None, None, False], ["+STORAGE_USER", "Physical Storage", "Storage User Id", DataType.VARCHAR, None, "Storage User Id", None, None, False], ["STORAGE_POSITION", "Physical Storage", "Location", DataType.VARCHAR, None, "Storage Position", None, None, False], ["+ANNOTATIONS_STATE", "Comments", " Annotations State", DataType.XML, None,"Annotations State", annotationsScriptName, None, False] ];