#!/usr/bin/env python # -*- coding: utf-8 -*- import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType # # Helper Methods # def getPropertyDefinitionByCode(definition, code): for property in definition: if property[0] == code: return property return None # # Scripts # commentsScriptName = "COMMENTS"; adenosineScriptName = "ADENOSINE_COUNT" cytosineScriptName= "CYTOSINE_COUNT" gcScriptName= "GC" guanosineScriptName= "GUANOSINE_COUNT" lengthScriptName= "SEQUENCE_LENGTH" nucelotideScriptName= "ONUCLEOTIDE_COUNT" thymidineScriptName= "THYMIDINE_COUNT" tmScriptName= "TM" # # Storage # numberOfStorageGroups = 65 def getStorageGroupPropertyCodes(): propertyCodes = []; for property in getStorageGroupDefinition(): propertyCodes.append(property[0]); return propertyCodes; def getStorageGroupDefinition(): return [ ["STORAGE_NAME", "Physical Storage", "location", DataType.CONTROLLEDVOCABULARY, "FREEZER", "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 label", DataType.VARCHAR, None, "Storage Box Name", None, None, False], ["STORAGE_USER", "Physical Storage", "frozen by", DataType.VARCHAR, None, "Storage User Id", None, None, False], ["STORAGE_BOX_SIZE", "Physical Storage", "box size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box size", None, None, False], ["STORAGE_BOX_POSITION", "Physical Storage", "position", DataType.VARCHAR, None, "Storage Box Position", None, None, False] ]; # # Experiment Types # experimentDefinition = [ ["NAME", "General", "Name", DataType.VARCHAR, None, "Name", None, None, False], ["EXPERIMENTAL_GOALS", "General", "Experimental goals", DataType.MULTILINE_VARCHAR, None, "Goal of the experiment", None, None, False], ["GRANT", "General", "Grant", DataType.VARCHAR, None, "grant name", None, None, False], ["START_DATE", "General", "Start Date", DataType.TIMESTAMP, None, "Start Date", None, None, False], ["END_DATE", "General", "End Date", DataType.TIMESTAMP, None, "End Date", None, None, False], ["EXPERIMENTAL_RESULTS", "General", "Experimental results", DataType.MULTILINE_VARCHAR, None, "Brief summary of the results obtained", None, None, False], ["XMLCOMMENTS", "Comments","Comments List", DataType.XML, None, "Several comments can be added by different users", commentsScriptName, None, False] ]; # # Sample Types # antibodyDefinition = [ ["NAME", "General", "antibody ID", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_ID_NR", "General", "antibody_id_nr", DataType.VARCHAR, None, "", None, None, False], ["ANTIGEN", "General", "antigen", DataType.VARCHAR, None, "", None, None, False], ["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False], ["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_FACS_BLOCK", "General", "block facs", DataType.CONTROLLEDVOCABULARY, "BLOCK", "", None, None, False], ["ANTIBODY_IF_BLOCK", "General", "block IFF", DataType.CONTROLLEDVOCABULARY, "BLOCK", "", None, None, False], ["ANTIBODY_WB_BLOCK", "General", "block western", DataType.CONTROLLEDVOCABULARY, "BLOCK", "", None, None, False], ["CATALOGUE_NUMBER", "General", "catalog id #", DataType.VARCHAR, None, "", None, None, False], ["CLASS", "General", "class", DataType.CONTROLLEDVOCABULARY, "CLASS", "", None, None, False], ["CLONE", "General", "clone", DataType.VARCHAR, None, "", None, None, False], ["COMPANY", "General", "company", DataType.CONTROLLEDVOCABULARY, "COMPANY", "", None, None, False], ["ANTIBODY_FACS_CONC", "General", "conc facs", DataType.CONTROLLEDVOCABULARY, "CONCENTRATION_FACS", "", None, None, False], ["ANTIBODY_IF_CONC", "General", "conc IFF", DataType.CONTROLLEDVOCABULARY, "CONCENTRATION_FACS", "", None, None, False], ["ANTIBODY_IP_CONC", "General", "conc ip", DataType.CONTROLLEDVOCABULARY, "CONCENTRATION_IP", "", None, None, False], ["ANTIBODY_WB_CONC", "General", "conc western", DataType.CONTROLLEDVOCABULARY, "CONCENTRATION_WESTERN", "", None, None, False], ["ANTIBODY_CONCENTRATION", "General", "concentration", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_CROSSREACTIVITY", "General", "crossreactivity", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_FACS_FIX", "General", "fix facs", DataType.CONTROLLEDVOCABULARY, "FIX", "", None, None, False], ["ANTIBODY_IF_FIX", "General", "fix IFF", DataType.CONTROLLEDVOCABULARY, "FIX", "", None, None, False], ["ANTIBODY_WB_FIX", "General", "fix western", DataType.CONTROLLEDVOCABULARY, "FIX", "", None, None, False], ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["LABEL", "General", "label", DataType.CONTROLLEDVOCABULARY, "LABEL", "", None, None, False], ["LOTNUMBER", "General", "lotnumber", DataType.VARCHAR, None, "", None, None, False], ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["MONO_POLYCLONAL", "General", "mono/polyclonal", DataType.CONTROLLEDVOCABULARY, "MONO-POLYCLONAL", "", None, None, False], ["ANTIBODY_FACS_NOTES", "General", "notes FACS", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_IF_NOTES", "General", "notes IFF", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_IP_NOTES", "General", "notes IP", DataType.VARCHAR, None, "", None, None, False], ["ANTIBODY_WB_NOTES", "General", "notes western", DataType.VARCHAR, None, "", None, None, False], ["SERIAL_NUMBER", "General", "serial number", DataType.INTEGER, None, "", None, None, False], ["ANTIGEN_SIZE", "General", "size", DataType.VARCHAR, None, "", None, None, False], ["SOURCE", "General", "source", DataType.CONTROLLEDVOCABULARY, "SOURCE", "", None, None, False], ["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False], ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False], ["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False], ["BOX", "Storage", "box", DataType.VARCHAR, None, "", None, None, False], ["RACK", "Storage", "rack", DataType.VARCHAR, None, "", None, None, False], ["PUBLISHED_IN", "Reference", "reference", DataType.VARCHAR, None, "", None, None, False], ["COMMENTS", "Comments", "info", DataType.VARCHAR, None, "", None, None, False] ]; cellDefinition = [ ["CO2", "General", "%CO2", DataType.CONTROLLEDVOCABULARY, "CO2", "", None, None, False], ["ATCC_NUM", "General", "ATCC No.", DataType.VARCHAR, None, "", None, None, False], ["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False], ["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False], ["CELL_ID_NR", "General", "cell_id_nr", DataType.VARCHAR, None, "", None, None, False], ["CELL_ID_NR_COPY", "General", "cell_id_nr Copy", DataType.VARCHAR, None, "", None, None, False], ["NAME", "General", "cell ID", DataType.VARCHAR, None, "", None, None, False], ["CELL_ID_COPY", "General", "cell ID Copy", DataType.VARCHAR, None, "", None, None, False], ["CLONE", "General", "clone #", DataType.INTEGER, None, "", None, None, False], ["COMPARE_FIELD", "General", "compare field", DataType.VARCHAR, None, "", None, None, False], ["CONC1", "General", "conc.1", DataType.REAL, None, "", None, None, False], ["CONC_UNIT1", "General", "concentration unit 1", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CONC2", "General", "conc.2", DataType.REAL, None, "", None, None, False], ["CONC_UNIT2", "General", "concentration unit 2", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CONC3", "General", "conc.3", DataType.REAL, None, "", None, None, False], ["CONC_UNIT3", "General", "concentration unit 3", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CONC4", "General", "conc.4", DataType.REAL, None, "", None, None, False], ["CONC_UNIT4", "General", "concentration unit 4", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False], ["DATE", "General", "date", DataType.TIMESTAMP, None, "", None, None, False], ["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False], ["GROWTH_TEMPERATURE", "General", "growth temperature", DataType.CONTROLLEDVOCABULARY, "GROWTH_TEMPERATURE", "", None, None, False], ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["LINE_NAME", "General", "line name", DataType.VARCHAR, None, "", None, None, False], ["MEDIUM", "General", "medium", DataType.CONTROLLEDVOCABULARY, "MEDIUM", "", None, None, False], ["MEDIUM_SPECIALS", "General", "medium specials", DataType.VARCHAR, None, "", None, None, False], ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False], ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["MYCOPLASM_TESTED", "General", "mycoplasm_tested", DataType.BOOLEAN, None, "", None, None, False], ["OBTAINED_FROM", "General", "obtained from", DataType.CONTROLLEDVOCABULARY, "CELL_OBTAINED_FROM", "", None, None, False], ["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False], ["PARENTAL_CELL", "General", "parental cell", DataType.VARCHAR, None, "", None, None, False], ["PASSAGE", "General", "passage", DataType.VARCHAR, None, "", None, None, False], ["PERS_CELL_NUMBER", "General", "PersCellNumber", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_ID1", "General", "plasmid ID 1", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_ID2", "General", "plasmid ID 2", DataType.VARCHAR, None, "", None, None, False], ["SELECTION_PLASMID1", "General", "sel.1", DataType.CONTROLLEDVOCABULARY, "SELECTION", "", None, None, False], ["SELECTION_PLASMID2", "General", "sel.2", DataType.CONTROLLEDVOCABULARY, "SELECTION", "", None, None, False], ["SELECTION_PLASMID3", "General", "sel.3", DataType.CONTROLLEDVOCABULARY, "SELECTION", "", None, None, False], ["SELECTION_PLASMID4", "General", "sel.4", DataType.CONTROLLEDVOCABULARY, "SELECTION", "", None, None, False], ["SERIAL_NUMBER", "General", "serial number", DataType.INTEGER, None, "", None, None, False], ["SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "CELL_SPECIES", "", None, None, False], ["VIRUS_ID1", "General", "virus ID 1", DataType.VARCHAR, None, "", None, None, False], ["VIRUS_ID2", "General", "virus ID 2", DataType.VARCHAR, None, "", None, None, False], ["PUBLISHED_IN", "Reference", "reference", DataType.VARCHAR, None, "", None, None, False], ["COMMENTS", "Comments", "info", DataType.VARCHAR, None, "", None, None, False] ]; strainDefinition = [ ["CO2", "General", "%CO2", DataType.CONTROLLEDVOCABULARY, "CO2", "", None, None, False], ["BACKGROUND", "General", "background", DataType.CONTROLLEDVOCABULARY, "STRAIN_BACKGROUND", "", None, None, False], ["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False], ["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False], ["CIR", "General", "cir", DataType.CONTROLLEDVOCABULARY, "CIR", "", None, None, False], ["CONC_INDUCER1", "General", "conc. inducer 1", DataType.VARCHAR, None, "", None, None, False], ["CONC_INDUCER2", "General", "conc. inducer 2", DataType.VARCHAR, None, "", None, None, False], ["CONC_INDUCER3", "General", "conc. inducer 3", DataType.VARCHAR, None, "", None, None, False], ["CONC1", "General", "conc.1", DataType.REAL, None, "", None, None, False], ["CONC_UNIT1", "General", "concentration unit 1", DataType.VARCHAR, None, "", None, None, False], ["CONC2", "General", "conc.2", DataType.REAL, None, "", None, None, False], ["CONC_UNIT2", "General", "concentration unit 2", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CONC3", "General", "conc.3", DataType.REAL, None, "", None, None, False], ["CONC_UNIT3", "General", "concentration unit 3", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False], ["DATE", "General", "date", DataType.VARCHAR, None, "", None, None, False], ["DERIVATION", "General", "derivation", DataType.CONTROLLEDVOCABULARY, "DERIVATION", "", None, None, False], ["EXPRESSED_PROTEIN1", "General", "expressed protein 1", DataType.VARCHAR, None, "", None, None, False], ["EXPRESSED_PROTEIN2", "General", "expressed protein 2", DataType.VARCHAR, None, "", None, None, False], ["EXPRESSED_PROTEIN3", "General", "expressed protein 3", DataType.VARCHAR, None, "", None, None, False], ["FREE_PLASMID", "General", "freeplasmid", DataType.VARCHAR, None, "", None, None, False], ["FREEZEDATE", "General", "freezedate", DataType.VARCHAR, None, "", None, None, False], ["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False], ["GAL", "General", "gal", DataType.CONTROLLEDVOCABULARY, "GAL", "", None, None, False], ["GENE_EXPRESSION1", "General", "gene expression 1", DataType.VARCHAR, None, "", None, None, False], ["GENE_EXPRESSION2", "General", "gene expression 2", DataType.VARCHAR, None, "", None, None, False], ["GROWTH_TEMPERATURE", "General", "growth temperature", DataType.CONTROLLEDVOCABULARY, "GROWTH_TEMPERATURE", "", None, None, False], ["INDUCER1", "General", "inducer 1", DataType.VARCHAR, None, "", None, None, False], ["INDUCER2", "General", "inducer 2", DataType.VARCHAR, None, "", None, None, False], ["INDUCER3", "General", "inducer 3", DataType.VARCHAR, None, "", None, None, False], ["COMMENTS", "General", "info", DataType.VARCHAR, None, "", None, None, False], ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["MARKERS", "General", "markers", DataType.VARCHAR, None, "", None, None, False], ["MAT", "General", "mat", DataType.CONTROLLEDVOCABULARY, "MAT", "", None, None, False], ["MEDIUM", "General", "medium", DataType.CONTROLLEDVOCABULARY, "MEDIUM", "", None, None, False], ["MEDIUM_SPECIALS", "General", "medium specials", DataType.VARCHAR, None, "", None, None, False], ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False], ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["NUMBER", "General", "number", DataType.VARCHAR, None, "", None, None, False], ["STRAIN_OBTAINED_FROM", "General", "obtained from", DataType.VARCHAR, None, "", None, None, False], ["ORF", "General", "orf", DataType.VARCHAR, None, "", None, None, False], ["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False], ["PARENTAL_CELL", "General", "parental cell", DataType.VARCHAR, None, "", None, None, False], ["PASSAGE", "General", "passage", DataType.VARCHAR, None, "", None, None, False], ["PERSYEASTNUMBER", "General", "persyeastnumber", DataType.INTEGER, None, "", None, None, False], ["PETERYEASTNUMBER", "General", "peteryeastnumber", DataType.INTEGER, None, "", None, None, False], ["PLASMID_ID1", "General", "plasmid ID 1", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_ID2", "General", "plasmid ID 2", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_ID3", "General", "plasmid ID 3", DataType.VARCHAR, None, "", None, None, False], ["PROMOTER1", "General", "promoter 1", DataType.VARCHAR, None, "", None, None, False], ["PROMOTER2", "General", "promoter 2", DataType.VARCHAR, None, "", None, None, False], ["PROMOTER3", "General", "promoter 3", DataType.VARCHAR, None, "", None, None, False], ["PUBLISHED_IN", "General", "reference", DataType.VARCHAR, None, "", None, None, False], ["SELECTION1", "General", "sel.1", DataType.VARCHAR, None, "", None, None, False], ["SELECTION2", "General", "sel.2", DataType.VARCHAR, None, "", None, None, False], ["SELECTION3", "General", "sel.3", DataType.VARCHAR, None, "", None, None, False], ["SELECTION", "General", "selection", DataType.CONTROLLEDVOCABULARY, "SELECTION_YEAST", "", None, None, False], ["SERIAL_NUMBER", "General", "serial number", DataType.INTEGER, None, "", None, None, False], ["STRAIN_SOURCE", "General", "source", DataType.CONTROLLEDVOCABULARY, "STRAIN_SOURCE", "", None, None, False], ["SPECIES", "General", "species", DataType.VARCHAR, None, "", None, None, False], ["STRAIN_ID_NR", "General", "strain_id_nr", DataType.VARCHAR, None, "", None, None, False], ["NAME", "General", "strain ID", DataType.VARCHAR, None, "", None, None, False], ["STRAIN_NAME", "General", "strain name", DataType.VARCHAR, None, "", None, None, False] ]; oligoDefinition = [ ["AMOUNT", "General", "amount", DataType.REAL, None, "", None, None, False], ["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False], ["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False], ["OLIGO_COMPANY", "General", "company", DataType.CONTROLLEDVOCABULARY, "OLIGO_COMPANY", "", None, None, False], ["CONCENTRATION", "General", "concentration", DataType.REAL, None, "", None, None, False], ["CONCENTRATION_UNIT", "General", "concentration unit", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False], ["DATE", "General", "date", DataType.VARCHAR, None, "", None, None, False], ["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False], ["GENE_LOCUS", "General", "gene locus", DataType.VARCHAR, None, "", None, None, False], ["GRADE", "General", "grade", DataType.CONTROLLEDVOCABULARY, "OLIGO_GRADE", "", None, None, False], ["COMMENTS", "General", "Info", DataType.VARCHAR, None, "", None, None, False], ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["MODIFICATION_DATE", "General", "modification date", DataType.TIMESTAMP, None, "", None, None, False], ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["OD", "General", "od", DataType.INTEGER, None, "", None, None, False], ["NAME", "General", "oligo ID", DataType.INTEGER, None, "", None, None, False], ["OLIGO_ID_NR", "General", "oligo_id_nr", DataType.VARCHAR, None, "", None, None, False], ["ORDER_DATE", "General", "order date", DataType.VARCHAR, None, "", None, None, False], ["OLIGO_ORGANISM", "General", "organism", DataType.CONTROLLEDVOCABULARY, "OLIGO_ORGANISM", "", None, None, False], ["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False], ["PRIMER_PARTNER", "General", "primer partner", DataType.VARCHAR, None, "", None, None, False], ["PRIMER_POSITION", "General", "primer position", DataType.CONTROLLEDVOCABULARY, "PRIMER_POSITION", "", None, None, False], ["PUBLISHED_IN", "General", "PublishedIn", DataType.VARCHAR, None, "", None, None, False], ["RESTRICTION_SITE", "General", "restriction site", DataType.CONTROLLEDVOCABULARY, "RESTRICTION", "", None, None, False], ["SEQUENCE", "General", "sequence", DataType.VARCHAR, None, "", None, None, False], ["SERIAL_NUMBER", "General", "serial number", DataType.VARCHAR, None, "", None, None, False], ["USAGE", "General", "usage", DataType.CONTROLLEDVOCABULARY, "OLIGO_USAGE", "", None, None, False], ["ADENOSINE", "Calculated fields", "adenosine", DataType.INTEGER, None, "", adenosineScriptName, None, False], ["CYTOSINE", "Calculated fields", "cytosine", DataType.INTEGER, None, "", cytosineScriptName, None, False], ["GUANOSINE", "Calculated fields", "guanosine", DataType.INTEGER, None, "", guanosineScriptName, None, False], ["THYMIDINE", "Calculated fields", "thymidine", DataType.INTEGER, None, "", thymidineScriptName, None, False], ["LENGTH", "Calculated fields", "length", DataType.INTEGER, None, "", lengthScriptName, None, False], ["GC", "Calculated fields", "gc", DataType.REAL, None, "", gcScriptName, None, False], ["TM", "Calculated fields", "tm", DataType.REAL, None, "", tmScriptName, None, False], ["O_NUCLEOTIDE", "Calculated fields", "O nucleotide", DataType.INTEGER, None, "", nucelotideScriptName, None, False] ]; plasmidDefinition = [ ["BACKBONE", "General", "backbone", DataType.CONTROLLEDVOCABULARY, "BACKBONE", "", None, None, False], ["BACKUP_STORAGE", "General", "backup storage", DataType.VARCHAR, None, "", None, None, False], ["BACTERIAL_HOST", "General", "bacterial host", DataType.CONTROLLEDVOCABULARY, "BACTERIAL_HOST", "", None, None, False], ["BARCODE", "General", "barcode", DataType.VARCHAR, None, "", None, None, False], ["BARCODE_LABEL", "General", "barcode label", DataType.VARCHAR, None, "", None, None, False], ["BIOSAFETY_LEVEL", "General", "biosafety level", DataType.CONTROLLEDVOCABULARY, "BIOSAFETY_LEVEL", "", None, None, False], ["BOXNR", "General", "boxNr", DataType.VARCHAR, None, "", None, None, False], ["CONCENTRATION_UNIT", "General", "concentration unit", DataType.CONTROLLEDVOCABULARY, "CONC_UNITS", "", None, None, False], ["CONSTRUCTION_METHOD", "General", "construction method", DataType.VARCHAR, None, "", None, None, False], ["CREATION_DATE", "General", "creation date", DataType.TIMESTAMP, None, "", None, None, False], ["CTERMTAG", "General", "Ctermtag", DataType.VARCHAR, None, "", None, None, False], ["DATE", "General", "date", DataType.VARCHAR, None, "", None, None, False], ["DATE_OF_CONSTRUCTION", "General", "date of construction", DataType.TIMESTAMP, None, "", None, None, False], ["DERIVATIVE_OF", "General", "Derivative of", DataType.VARCHAR, None, "", None, None, False], ["ECOLI_STRAIN", "General", "E.coli strain", DataType.VARCHAR, None, "", None, None, False], ["EXCISE_INSERT", "General", "excise insert", DataType.VARCHAR, None, "", None, None, False], ["EXCISE_INSERT2", "General", "excise insert 2", DataType.VARCHAR, None, "", None, None, False], ["FREEZEDATE", "General", "freezedate", DataType.VARCHAR, None, "", None, None, False], ["FROZEN", "General", "frozen", DataType.TIMESTAMP, None, "", None, None, False], ["FUNCTIONAL_ELEMENTS_INSERT", "General", "functional elements insert", DataType.VARCHAR, None, "", None, None, False], ["HYPERCARD_FILE", "General", "hypercard file", DataType.VARCHAR, None, "", None, None, False], ["INFO", "General", "info", DataType.VARCHAR, None, "", None, None, False], ["INSERT", "General", "insert", DataType.VARCHAR, None, "", None, None, False], ["INSERTION_SITE", "General", "insertion site", DataType.VARCHAR, None, "", None, None, False], ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["LINEARIZE", "General", "linearize", DataType.VARCHAR, None, "", None, None, False], ["MARKER", "General", "Marker", DataType.VARCHAR, None, "", None, None, False], ["MODIFICATION_DATE", "General", "modification date", DataType.VARCHAR, None, "", None, None, False], ["MODIFIED_BY", "General", "modified by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["NAME_OF_PARENTAL_CLONE", "General", "name of parental clone", DataType.VARCHAR, None, "", None, None, False], ["NAME_OF_VECTOR", "General", "name of vector", DataType.VARCHAR, None, "", None, None, False], ["NTERMTAG", "General", "Ntermtag", DataType.VARCHAR, None, "", None, None, False], ["NUCLEOTIDE_SEQUENCE", "General", "nucleotide sequence", DataType.VARCHAR, None, "", None, None, False], ["OLIGOS_USED", "General", "oligos used", DataType.VARCHAR, None, "", None, None, False], ["ORGANISM", "General", "organism", DataType.VARCHAR, None, "", None, None, False], ["ORIGIN_OF_REPLICATION", "General", "origin of replication", DataType.VARCHAR, None, "", None, None, False], ["OTHER_MARKER", "General", "other marker", DataType.VARCHAR, None, "", None, None, False], ["PAGE_NUMBER", "General", "page number", DataType.VARCHAR, None, "", None, None, False], ["PERSPLASMIDNUM", "General", "persPlasmidnum", DataType.REAL, None, "", None, None, False], ["PETERPLASMIDNUM", "General", "PeterPlasmidNum", DataType.INTEGER, None, "", None, None, False], ["NAME", "General", "plasmid ID", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_ID_NR", "General", "plasmid_id_nr", DataType.VARCHAR, None, "", None, None, False], ["PLASMIDNAME", "General", "plasmidname", DataType.VARCHAR, None, "", None, None, False], ["PRIMERS", "General", "primers", DataType.VARCHAR, None, "", None, None, False], ["PROMOTER", "General", "promoter", DataType.CONTROLLEDVOCABULARY, "PROMOTER", "", None, None, False], ["SELECTION_IN_BACTERIA", "General", "selection in bacteria", DataType.CONTROLLEDVOCABULARY, "SELECTION_IN_BACTERIA", "", None, None, False], ["SELECTION_IN_EUKARYOTES", "General", "selection in eukaryotes", DataType.CONTROLLEDVOCABULARY, "SELECTION_IN_EUKARYOTES", "", None, None, False], ["SEQUENCE_FILE_NAME", "General", "sequence file name", DataType.VARCHAR, None, "", None, None, False], ["SEQUENCING_DATE", "General", "sequencing date", DataType.TIMESTAMP, None, "", None, None, False], ["SERIAL_NUMBER", "General", "serial number", DataType.INTEGER, None, "", None, None, False], ["SHELF", "General", "shelf", DataType.VARCHAR, None, "", None, None, False], ["SIZE_INSERT", "General", "size insert", DataType.REAL, None, "", None, None, False], ["SIZE_OF_INSERT", "General", "size of insert", DataType.VARCHAR, None, "", None, None, False], ["SIZE_VECTOR", "General", "size vector", DataType.REAL, None, "", None, None, False], ["PLASMID_SOURCE", "General", "source", DataType.VARCHAR, None, "", None, None, False], ["PLASMID_SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "PLASMID_ORGANISM", "", None, None, False], #["TUBES", "General", "TUBES", DataType.VARCHAR, None, "", None, None, False], ["URL", "Reference", "url", DataType.VARCHAR, None, "", None, None, False], ["PUBLISHED_IN", "Reference", "published in", DataType.VARCHAR, None, "", None, None, False] ]; chemicalDefinition = [ ["ARTICLE", "General", "Article", DataType.VARCHAR, None, "", None, None, False], ["COMPANY", "General", "Company", DataType.CONTROLLEDVOCABULARY, "COMPANY", "", None, None, False], ["ARTICLE_NUM", "General", "Article Number", DataType.VARCHAR, None, "", None, None, False], ["RECORD_NUMBER", "General", "RecordNumber", DataType.VARCHAR, None, "", None, None, False], ["LOCATION", "Location", "Location", DataType.VARCHAR, None, "", None, None, False] ]; siRNADefinition = [ ["INVESTIGATOR", "General", "investigator", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "", None, None, False], ["GENE_LOCUS", "General", "gene locus", DataType.VARCHAR, None, "", None, None, False], ["EXON_OR_THREE_PRIME", "General", "exon or three prime", DataType.CONTROLLEDVOCABULARY, "EXON_OR_THREE_PRIME", "", None, None, False], ["EXON", "General", "exon #", DataType.INTEGER, None, "", None, None, False], ["3_PRIME_POSITION", "General", "3' position", DataType.VARCHAR, None, "", None, None, False], ["SIRNA_SPECIES", "General", "species", DataType.CONTROLLEDVOCABULARY, "SIRNA_SPECIES", "", None, None, False], ["SEQUENCE", "General", "SEQUENCE", DataType.VARCHAR, None, "", None, None, False], ["SIRNA_COMPANY", "General", "Company", DataType.CONTROLLEDVOCABULARY, "SIRNA_COMPANY", "", None, None, False], ["STOCK_CONCENTRATION", "General", "Stock concentration", DataType.REAL, None, "", None, None, False], ["WORKING_CONCENTRATION", "General", "Working concentration", DataType.REAL, None, "", None, None, False], ["EFFICIENCY", "General", "Efficiency", DataType.VARCHAR, None, "", None, None, False], ["EFFICIENCY_QPCR", "General", "Efficiency_qPCR", DataType.VARCHAR, None, "", None, None, False], ["EFFICIENCY_WESTERN", "General", "Efficiency_Western", DataType.VARCHAR, None, "", None, None, False], ["EFFICIENCY_OTHER", "General", "Efficiency_other", DataType.VARCHAR, None, "", None, None, False], ["OFF_TARGET_EFFECTS", "General", "Off target effects", DataType.VARCHAR, None, "", None, None, False], ["INFO", "General", "Info", DataType.VARCHAR, None, "", None, None, False], ["SPECIFIC_SPLICE_VARIANT", "General", "Specific splice variant", DataType.VARCHAR, None, "", None, None, False], ["TRANSFECTION_AGENT", "General", "Transfection agent", DataType.CONTROLLEDVOCABULARY, "TRANSFECTION_AGENT", "", None, None, False], ["LIBRARY", "General", "Library", DataType.VARCHAR, None, "", None, None, False], ["CHARACTERIZED_BY_COMPANY", "General", "Characterized by company", DataType.VARCHAR, None, "", None, None, False], ["NUMBERINPOOL", "General", "NumberINpool", DataType.INTEGER, None, "", None, None, False], ["TEST", "General", "Test", DataType.VARCHAR, None, "", None, None, False], ["CHEMICAL_MODIFICATION", "General", "Chemical modification", DataType.VARCHAR, None, "", None, None, False], ["OLIGO_NAME", "General", "Oligo name", DataType.VARCHAR, None, "", None, None, False], ["SIRNA_OLIGONUMBER", "General", "siRNA_OligoNumber", DataType.VARCHAR, None, "", None, None, False], ["SIRNA_FREEZER_LOCATION", "General", "Freezer Location", DataType.CONTROLLEDVOCABULARY, "SIRNA_FREEZER_LOCATION", "", None, None, False], ["DRAWER", "General", "Drawer", DataType.VARCHAR, None, "", None, None, False], ["PUBLISHED", "Reference", "Published", DataType.VARCHAR, None, "", None, None, False] ]; # # Data Set Types # documentDefinition = [ ["CREATION_DATE", "General", "date created", DataType.TIMESTAMP, None, "", None, None, False], ["MODIFICATION_DATE", "General", "date modified", DataType.TIMESTAMP, None, "", None, None, False], ["INFO", "General", "info", DataType.VARCHAR, None, "", None, None, False], ["ID_NR", "General", "id_nr", DataType.VARCHAR, None, "", None, None, False], ["FILE", "General", "file", DataType.VARCHAR, None, "", None, None, False], ["SERIAL", "General", "serial", DataType.INTEGER, None, "", None, None, False] ];