diff --git a/plasmid/source/core-plugins/petermigration/2/as/definitions.py b/plasmid/source/core-plugins/petermigration/2/as/definitions.py
new file mode 100644
index 0000000000000000000000000000000000000000..6cf0d515317babb43e8d21a5145016ef89930064
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/as/definitions.py
@@ -0,0 +1,375 @@
+#!/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_BOX_SIZE", "Physical Storage", "box size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box size", None, None, False],
+ ["STORAGE_USER", "Physical Storage", "frozen by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "Storage User Id", 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]
+
+];
diff --git a/plasmid/source/core-plugins/petermigration/2/as/definitionsVoc.py b/plasmid/source/core-plugins/petermigration/2/as/definitionsVoc.py
new file mode 100644
index 0000000000000000000000000000000000000000..6c41596dc8dd2ff2c3e1aff1b0ae83ddf1961722
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/as/definitionsVoc.py
@@ -0,0 +1,852 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#
+# Helper Methods
+#
+def getVocabularyTermCodeForVocabularyAndTermLabel(vocabularyCode, termLabel):
+ vocabulary = vocabularyDefinitions[vocabularyCode]
+ for term in vocabulary:
+ if term[1] == termLabel:
+ #print repr("TERM NOT FOUND IN VOCABULARY LIST: " + unicode(vocabularyCode) + " : '" + unicode(termLabel) + "'")
+ return term[0]
+ return None
+
+# "VOCABULARY_CODE" : { "TERM_CODE" : "OBJECT" }
+createdVocabularyTerms = { }
+
+def printCreatedTerms():
+ print "--- Created Vocabulary Terms Report"
+ for vocabularyCode in createdVocabularyTerms:
+ print "Vocabulary [" + vocabularyCode + "]"
+ for vocabularyTermCode in createdVocabularyTerms[vocabularyCode]:
+ print "Term [" + vocabularyTermCode + "] Label: [" + repr(createdVocabularyTerms[vocabularyCode][vocabularyTermCode].getLabel()) + "]"
+ print "---"
+
+def getCreatedTerm(vocabularyCode, termCode):
+ if vocabularyCode in createdVocabularyTerms:
+ if termCode in createdVocabularyTerms[vocabularyCode]:
+ return createdVocabularyTerms[vocabularyCode][termCode]
+ return None
+
+def addCreatedTerm(vocabularyCode, termCode, object):
+ if vocabularyCode not in createdVocabularyTerms:
+ createdVocabularyTerms[vocabularyCode] = {}
+ createdVocabularyTerms[vocabularyCode][termCode] = object
+
+def createVocabularyTerm(tr, vocabularyCode, termCode, termLabel):
+ createdTerm = getCreatedTerm(vocabularyCode, termCode)
+ if createdTerm is None:
+ vocabulary = tr.getVocabularyForUpdate(vocabularyCode)
+
+ for term in vocabulary.getTerms():
+ if term.getCode() == termCode:
+ createdTerm = term
+
+ if createdTerm is None:
+ createdTerm = tr.createNewVocabularyTerm()
+ createdTerm.setCode(termCode)
+ createdTerm.setLabel(termLabel)
+ createdTerm.setOrdinal(vocabulary.getTerms().size())
+ vocabulary.addTerm(createdTerm)
+ addCreatedTerm(vocabularyCode, termCode, createdTerm)
+ return createdTerm
+
+#
+# Vocabularies
+#
+
+vocabularyDefinitions = {
+ "ALL_LAB_MEMBERS" : [
+ ["ANNA_DEPLAZES", "Anna Deplazes"],
+ ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"],
+ ["BRIAN_LUKE", "Brian Luke"],
+ ["CAROLINE_ZBINDEN", "Caroline Zbinden"],
+ ["CELINE_LAFOURCADE", "Celine Lafourcade"],
+ ["CHRISTINE_RUPP", "Christine Rupp"],
+ ["CLAUDINE_KRAFT", "Claudine Kraft"],
+ ["EDYTA_SIERGIEJUK", "Edyta Siergiejuk"],
+ ["FABIAN_HERZOG", "Fabian Herzog"],
+ ["FABIAN_RUDOLF", "Fabian Rudolf"],
+ ["FRANK_VAN_DROGEN", "Frank Van Drogen"],
+ ["GERDA_JORRITSMA", "Gerda Jorritsma"],
+ ["GWEN_RABUT", "Gw\xe9nael Rabut"],
+ ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"],
+ ["IRAM_ZAIDI", "Iram Zaidi"],
+ ["IZABELA_SUMARA", "Izabela Sumara"],
+ ["LIONEL_PINTARD", "Lionel Pintard"],
+ ["MALIKAJAQUENOUD", "MalikaJaquenoud"],
+ ["MARC_SOHRMANN", "Marc Sohrmann"],
+ ["MARIE-LYN_HECHT", "Marie-Lyn Hecht"],
+ ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["MICHAEL_OLMA", "Michael Olma"],
+ ["MICHAEL_SCHNEIDER", "Michael Schneider"],
+ ["MICHELE_KNAUS", "Michele Knaus"],
+ ["MONIKA_GERSBACH", "Monika Gersbach"],
+ ["NATHALIE_MEYER-SCHALLER", "Nathalie Meyer-Schaller"],
+ ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"],
+ ["NICOLAS_DARD", "Nicolas Dard"],
+ ["NICOLAS_PAGE", "Nicolas Page"],
+ ["PATRICK_PEDRIOLI", "Patrick Pedrioli"],
+ ["PHILIPPE_WIGET", "Philippe Wiget"],
+ ["PIERRE_MAILLARD", "Pierre Maillard"],
+ ["REINHARD_DECHANT", "Reinhard Dechant"],
+ ["SANDER_SPRINGER", "Sander Springer"],
+ ["SARAH_GLASER", "Sarah Glaser"],
+ ["SARAH_MAERKI", "Sarah M\xe4rki"],
+ ["SEBASTIAN_LEIDEL", "Sebastian Leidel"],
+ ["SERGE_PELET", "Serge Pelet"],
+ ["STEFAN_MUELLER", "Stefan M�ller"],
+ ["TANIA_ROBERTS", "Tania Roberts"],
+ ["THIMO_KURZ", "Thimo Kurz"],
+ ["TOBIAS_BRAUN", "Tobias Braun"],
+ ["VANESSA_REZGUI", "Vanessa Rezgui"],
+ ["WOJCIECH_PIWKO", "Wojciech Piwko"],
+ ["YUKIKO_SHIMADA", "Yukiko Shimada"],
+ ["YVONNE_GLOOR", "Yvonne Gloor"],
+ ["JOCHEN_BECK", "Jochen Beck"],
+ ["MONIKA_KIJANSKA", "Monika Kijanska"],
+ ["ANGIE_RAGHEB", "Angie Ragheb"],
+ ["ANNE_PACQUELET", "Anne Pacquelet"],
+ ["BJORN_HEGEMANN", "Bj\xf6rn Hegemann"],
+ ["JANNY_TILMA", "Janny Tilma"],
+ ["THIBAULT_COURTHEOUX", "Thibault Courtheoux"],
+ ["SAMUEL_GILBERTO", "Samuel Gilberto"],
+ ["REMY_BUSER", "Remy Buser"],
+ ["RADOSLAV_ENCHEV", "Radoslav Enchev"],
+ ["MICHAELA_HUBNER", "Michaela Hubner"],
+ ["MIA_LI", "Mia Li"],
+ ["JULIEN_MOUYSSET", "Julien Mouysset"]
+ ],
+ "LAB_MEMBERS_INITIALS" : [
+ ["AD", "AD"],
+ ["ACB", "ACB"],
+ ["BL", "BL"],
+ ["CZ", "CZ"],
+ ["CL", "CL"],
+ ["CR", "CR"],
+ ["CK", "CK"],
+ ["ES", "ES"],
+ ["FH", "FH"],
+ ["FR", "FR"],
+ ["FD", "FD"],
+ ["GJ", "GJ"],
+ ["GR", "GR"],
+ ["ISS", "ISS"],
+ ["IZ", "IZ"],
+ ["IS", "IS"],
+ ["LP", "LP"],
+ ["MJ", "MJ"],
+ ["MSO", "MSo"],
+ ["MH", "MH"],
+ ["MG", "MG"],
+ ["MP", "MP"],
+ ["MO", "MO"],
+ ["MSC", "MSc"],
+ ["MK", "MK"],
+ ["MG", "MG"],
+ ["NS", "NS"],
+ ["NPE", "NPe"],
+ ["ND", "ND"],
+ ["NPA", "NPa"],
+ ["PP", "PP"],
+ ["PW", "PW"],
+ ["PM", "PM"],
+ ["RD", "RD"],
+ ["SS", "SS"],
+ ["SG", "SG"],
+ ["SMA", "SMa"],
+ ["SL", "SL"],
+ ["SP", "SP"],
+ ["SM", "SM"],
+ ["TR", "TR"],
+ ["TK", "TK"],
+ ["TB", "TB"],
+ ["VR", "VR"],
+ ["WP", "WP"],
+ ["YS", "YS"],
+ ["YG", "YG"],
+ ["JB", "JB"],
+ ["MKI", "MKi"]
+ ],
+ "BLOCK" : [
+ ["1BSA_01TRITON-X100", "1% BSA; 0.1% Triton-X100"],
+ ],
+ "CLASS" : [
+ ["IGM", "IgM"],
+ ["IGG1", "IgG1"],
+ ["IGG2", "IgG2"]
+ ],
+ "COMPANY" : [
+ ["ABCAM", "abcam"],
+ ["CELL_SIGNALING", "cell signaling"],
+ ["STRATAGEN", "stratagene"],
+ ["CLONTECH", "clontech"],
+ ["UBI", "ubi"],
+ ["SOUTHERN_BIOTECH", "southern biotech"],
+ ["PIERCE", "pierce"],
+ ["PHARMIGEN", "pharmingen"],
+ ["MOLECULAR_PROBES", "molecular probes"],
+ ["PHARMACIA", "pharmacia"],
+ ["BIORAD", "biorad"],
+ ["EUROGENETIC", "eurogentec"],
+ ["HOMEMADE", "homemade"],
+ ["BD_BIOSCIENCE", "BD bioscience"],
+ ["OBTAINED_FROM", "obtained from "],
+ ["ZYMED", "Zymed"],
+ ["UNKNOWN", "Unknown"],
+ ["SANTA_CRUZ", "Santa Cruz"],
+ ["BIOLEGEND", "Biolegend"],
+ ["BETHYL", "Bethyl"],
+ ["UPSTATE", "Upstate"],
+ ["ROCKLAND", "Rockland"],
+ ["NOVUS_BIOLOGICALS", "Novus Biologicals"],
+ ["CHEMICON_INTERNATIONAL", "Chemicon International"],
+ ["SIGMA", "Sigma"],
+ ["ALPHA_DIAGNOSTIC_INTERNATIONAL", "Alpha Diagnostic International"],
+ ["MILLIPORE", "Millipore"],
+ ["ACTIVE_MOTIF", "Active motif"],
+ ["NEB", "NEB"],
+ ["NEOMARKERS", "Neomarkers"],
+ ["LUBIOSCIENCE", "LubioScience"],
+ ["EBIOSCIENCE", "eBioscience"],
+ ["INVITROGEN", "Invitrogen"],
+ ["STRESSGEN", "Stressgen"],
+ ["COVANCE", "Covance"],
+ ["ENZO_LIFE_SCIENCES", "Enzo Life Sciences"],
+ ["CALBIOCHEM", "Calbiochem"],
+ ["ROCHE", "Roche"],
+ ["CYTOSKELETON", "Cytoskeleton"],
+ ["OPEN_BIOSYSTEMS", "Open Biosystems"],
+ ["BD_TRANSDUCTION", "BD Transduction"],
+ ["ATLAS_ANTIBODIES_AB", "Atlas Antibodies AB"],
+ ["GENENTECH", "Genentech"],
+ ["TRANSDUCTION_LABS", "Transduction Labs"],
+ ["ANTIBODIES_INCORPORATED", "Antibodies Incorporated"],
+ ["BABCO", "BAbCO"],
+ ["ERICH_NIGG_LAB_BASEL", "Erich Nigg lab (Basel)"],
+ ["FRANCIS_BARR", "Francis Barr"],
+ ["AVIVA_SYSTEMS_BIOLOGY", "Aviva Systems Biology"],
+ ["LUCERNACHEM", "LucernaChem"],
+ ["LI-COR", "LI-COR"],
+ ["ABGENT", "Abgent"],
+ ["CHROMOTEK", "Chromotek"],
+ ["ABNOVA", "Abnova"],
+ ["UNKNOWN", "Unknown"],
+ ["ABSEA", "Absea"],
+ ["GE_HEALTHCARE", "GE Healthcare"],
+ ["GRAMSCH_LABORATORIES", "Gramsch Laboratories"],
+ ["ADIPOGEN", "Adipogen"],
+ ["COSMO_BIO_CO", "Cosmo bio co."],
+ ["BECKTON_DICKINSON", "Beckton Dickinson"],
+ ["BIOTIUM", "Biotium"]
+ ],
+ "CONCENTRATION_FACS" : [
+ ["1_TO_10", "1 : 10"],
+ ["1_TO_20", "1 : 20"],
+ ["1_TO_30", "1 : 30"],
+ ["1_TO_40", "1 : 40"],
+ ["1_TO_50", "1 : 50"],
+ ["1_TO_100", "1 : 100"],
+ ["1_TO_200", "1 : 200"],
+ ["1_TO_500", "1 : 500"],
+ ["1_TO_1000", "1 : 1000"],
+ ["1_TO_2000", "1 : 2000"],
+ ["1_TO_3000", "1 : 3000"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CONCENTRATION_IP" : [
+ ["1UL", "1 �l"],
+ ["5UL", "5 �l"],
+ ["10UL", "10 �l"],
+ ["15UL", "15 �l"],
+ ["20UL", "20 �l"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CONCENTRATION_WESTERN" : [
+ ["1_TO_100", "1 : 100"],
+ ["1_TO_500", "1 : 500"],
+ ["1_TO_1000", "1 : 1000"],
+ ["1_TO_2000", "1 : 2000"],
+ ["1_TO_3000", "1 : 3000"],
+ ["1_TO_5000", "1 : 5000"],
+ ["1_TO_10000", "1 : 10000"],
+ ["1_TO_20000", "1 : 20000"],
+ ["1_TO_25000", "1 : 25000"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CURRENT_LAB_MEMBERS" : [
+ ["CAROLINE_ZBINDEN", "Caroline Zbinden"],
+ ["FRANK_VAN_DROGEN", "Frank Van Drogen"],
+ ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["REINHARD_DECHANT", "Reinhard Dechant"],
+ ["WOJCIECH_PIWKO", "Wojciech Piwko"],
+ ["JOCHEN_BECK", "Jochen Beck"]
+ ],
+ "FIX" : [
+ ["1H-RT", "1h, RT"],
+ ["PTEMF", "PTEMF"],
+ ["PFA", "PFA"],
+ ["MEOH", "MeOH"]
+ ],
+ "LABEL" : [
+ ["HRP", "hrp"],
+ ["AP", "ap"],
+ ["FITC", "fitc"],
+ ["CY3", "Cy3"],
+ ["ALEXA647", "Alexa 647"]
+ ],
+ "ANTIBODY_LOCATION" : [
+ ["SMALL_PETER_LAB", "Small Peter Lab"],
+ ["BIG_PETER_LAB", "Big Peter Lab"],
+ ["NEW_PETER_LAB", "New Peter Lab"],
+ ["MINUS20_C-FLOOR", "-20C C-Floor"]
+ ],
+ "MONO-POLYCLONAL" : [
+ ["MONOCLONAL", "Monoclonal"],
+ ["POLYCLONAL", "Polyclonal"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "SOURCE" : [
+ ["MOUSE", "Mouse"],
+ ["RABBIT", "Rabbit"],
+ ["HAMSTER", "Hamster"],
+ ["GOAT", "Goat"],
+ ["RAT", "Rat"],
+ ["CHICKEN", "Chicken"],
+ ["SHEEP", "Sheep"],
+ ["HUMAN", "Human"],
+ ["GUINEA_PIG", "Guinea pig"],
+ ["DONEKY", "Donkey"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "CELL_LOCATION" : [
+ ["FRIDGE", "fridge"],
+ ["FREEZER", "freezer"],
+ ["REFCO", "refco"],
+ ["TANK", "tank"]
+ ],
+ "SELECTION" : [
+ ["NEOMYCIN_G418", "Neomycin/G418"],
+ ["HYGROMYCIN", "Hygromycin"],
+ ["MPA", "MPA"],
+ ["G418", "G418"],
+ ["PUROMYCIN", "puromycin"],
+ ["BLASTICIDIN", "Blasticidin"],
+ ["ZEOCIN", "Zeocin"]
+ ],
+ "CO2" : [
+ ["5", "5"],
+ ["7.5", "7.5"]
+ ],
+ "GROWTH_TEMPERATURE" : [
+ ["37", "37"],
+ ["28", "28"],
+ ["34", "34"]
+ ],
+ "MEDIUM" : [
+ ["RPMI1640", "RPMI 1640"],
+ ["ISCOVES", "Iscoves"],
+ ["DMEM", "DMEM"],
+ ["LB", "LB"],
+ ["DMEM_NUTRIENT", "DMEM nutrient mixture F-12 HAM [D8437]"]
+ ],
+ "CELL_OBTAINED_FROM" : [
+ ["FREIBURG", "Freiburg"],
+ ["ATCC", "ATCC"],
+ ["DANIEL_GERLICH", "Daniel Gerlich"],
+ ["ERICH_NIGG", "Erich Nigg"],
+ ["KREK", "Krek"],
+ ["TONY_HEYMAN", "Tony Heyman"],
+ ["THOMAS-WILD_ULRIKE-KUTAY", "Thomas Wild/Ulrike Kutay"],
+ ["JAN_MICHAEL_PETERS", "Jan-Michael Peters"],
+ ["M_BRANDEIS", "M Brandeis"],
+ ["ARI_HELENIUS", "Ari Helenius"],
+ ["ROMEO_RICCI", "Romeo Ricci"]
+ ],
+ "CELL_SPECIES" : [
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["CHINESE_HAMSTER", "chines hamster"],
+ ["HYBRIDOMA", "hybridoma (human & mouse)"]
+ ],
+ "CONC_UNITS" : [
+ ["MICROG_MICROL", "�g/�l"],
+ ["MG_ML", "mgl/ml"],
+ ["UG_ML", "ug/ml"]
+ ],
+ "STRAIN_SOURCE" : [
+ ["F_CHANG", "F. Chang"],
+ ["J_CHANT", "J. Chant"],
+ ["R_DESHAIES", "R. Deshaies"],
+ ["E_ELION", "E. Elion"],
+ ["P_HIETER", "P. Hieter"],
+ ["I_HERSKOWITZ", "I. Herskowitz"],
+ ["A_NEIMAN", "A. Neiman"],
+ ["P_SORGER", "P. Sorger"],
+ ["T_STEARNS", "T. Stearns"],
+ ["MARC_BONDEL", "Marc Bondel"],
+ ["G_SUMARA", "G. Sumara"],
+ ["MICHAEL_ALTMANN", "Michael Altmann"],
+ ["HETEROZYGOUS_DIPLOID_COLLECTION", "Heterozygous diploid collection"],
+ ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"],
+ ["ANNE_PAQUELET", "Anne Paquelet"],
+ ["YAGMUR-TURGAY_KUTAY-GROUP", "Yagmur Turgay - Kutay group"],
+ ["BARBAR_CATARIN", "Barbar Catarin"],
+ ["FRANK_VAN-DROGEN", "Frank van Drogen"],
+ ["HEMMO_MEYER", "Hemmo Meyer"],
+ ["JEAN-MARC_GALLAND", "Jean-Marc Galland"],
+ ["JEFF_PARVIN", "Jeff Parvin"],
+ ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"],
+ ["MIKIKO_TAKAHASHI", "Mikiko Takahashi"],
+ ["SANDRA_HENCHOZ", "Sandra Henchoz"],
+ ["MALIKA_JAQUENOUD", "Malika Jaquenoud"],
+ ["GERDA_JORRITSMA", "Gerda Jorritsma"],
+ ["CELINE_LAFOURCADE", "Céline Lafourcade"],
+ ["CELINE_LONGARETTI", "Céline Longaretti"],
+ ["BRIAN_LUKE", "Brian Luke"],
+ ["GUY_NIEDERHAUSER", "Guy Niederhäuser"],
+ ["NICOLAS_PAGE", "Nicolas Pag�"],
+ ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["AUDREY_PETIT", "Audrey Petit"],
+ ["LIONEL_PINTARD", "Lionel Pintard"],
+ ["YUKIKO_SHIMADA", "Yukiko Shimada"],
+ ["PHILIPPE_WIGET", "Philippe Wiget"],
+ ["VOLKER_STUCKE", "Volker Stucke"],
+ ["KATRIN_PETER", "Katrin Peter"],
+ ["MARC_BLONDEL", "marc blondel"],
+ ["M_FUNK", "M. Funk"],
+ ["ATTILA_BECSKEI", "Attila Becskei"],
+ ["GWENAEL_RABUT", "Gwenael Rabut"],
+ ["PHILIP_JERMANN", "Philip Jermann"],
+ ["P_PRYCIAK", "P.Pryciak"],
+ ["LINDA_HICKE", "Linda Hicke"],
+ ["RZPD", "RZPD"],
+ ["OPENBIO", "OpenBio"],
+ ["F_POSAS", "F. Posas"],
+ ["HAPLOID_COLLECTION", "Haploid collection"],
+ ["MIRIAM_BORTFELD", "Miriam Bortfeld"],
+ ["EUROSCARF", "Euroscarf"],
+ ["TS_COLLECTION", "ts collection"],
+ ["CONZELMANN_LAB", "Conzelmann lab"],
+ ["SEBASTIAN_LEIDEL", "Sebastian Leidel"],
+ ["ANNA_DEPLAZES", "Anna Deplazes"],
+ ["BIBOU", "Bibou"],
+ ["MARC_SOHRMANN", "Marc sohrmann"]
+ ],
+ "SELECTION_YEAST" : [
+ ["NONE", "None"],
+ ["URA", "Ura"],
+ ["LEU", "Leu"],
+ ["TRP", "Trp"],
+ ["HIS", "His"],
+ ["VIABILITY", "Viability"],
+ ["NAT", "nat"],
+ ["KAN", "kan"],
+ ["KAN_NAT", "kan + nat"],
+ ["HIS_KAN", "HIS + kan"],
+ ["HIS_KAN_NAT", "HIS + kan + nat"],
+ ["HIS", "HIS"],
+ ["LEU_NAT", "leu + nat"],
+ ["ADE2", "ade2"]
+ ],
+ "DERIVATION" : [
+ ["GAMMA_INTEG", "gamma integ"],
+ ["DELTA_INTEG", "� integ"],
+ ["5FAO_LOOPOUT", "5-FAO loopout"],
+ ["PLASMID_SHUFFLE", "plasmid shuffle"],
+ ["TETRAD", "tetrad"],
+ ["LOOP-IN_LOOP-OUT", "loop-in/loop-out"],
+ ["GALPHO", "GalpHO mating type switch"],
+ ["DELETION", "Deletion"],
+ ["INTEGRATION", "Integration"]
+ ],
+ "STRAIN_BACKGROUND" : [
+ ["W303", "W303"],
+ ["K699", "K699"],
+ ["K700", "K700"],
+ ["S288C", "S288C"],
+ ["1278", "*1278*"],
+ ["EG123", "EG123"],
+ ["DF5", "DF5"],
+ ["SIGMA", "Sigma"],
+ ["UNKNOWN", "Don't know"],
+ ["BY7092", "BY7092"],
+ ["BY5565", "BY5565"],
+ ["BY4741", "BY4741"]
+ ],
+ "CIR" : [
+ ["CIR_PLUS", "cir+"],
+ ["CIR_DEG", "cir�"],
+ ],
+ "GAL" : [
+ ["PLUS", "Plus"],
+ ["PLUS_PLUS", "Plus/Plus"],
+ ["GAL1", "gal1"],
+ ["GAL1_GAL1", "gal1/gal1"],
+ ["GAL2", "gal2"],
+ ["GAL2_GAL2", "gal2/gal2"],
+ ],
+ "MAT" : [
+ ["AT", "@"],
+ ["A", "a"],
+ ["ALPHA", "alpha"],
+ ["DIPLOID", "diploid"],
+ ["UNKNOWN", "unknown"]
+ ],
+ "OLIGO_ORGANISM" : [
+ ["BMV", "BMV"],
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["XENOPUS", "xenopus"],
+ ["DROSOPHILA", "drosophila"],
+ ["YEAST", "yeast"],
+ ["ECOLI", "E.coli"],
+ ["SYNTHETIC", "synthetic"],
+ ["HIV1", "HIV-1"],
+ ["CELEGANS", "C.elegans"],
+ ["MYCOPLASMA", "mycoplasma"]
+ ],
+ "OLIGO_GRADE" : [
+ ["DESALTED", "desalted"],
+ ["HPLC", "hplc"],
+ ["PURITY", "purity"],
+ ["UNKNOWN", "?"]
+ ],
+ "PRIMER_POSITION" : [
+ ["FORWARD", "forward"],
+ ["REVERSE", "reverse"]
+ ],
+ "OLIGO_COMPANY" : [
+ ["MWG", "MWG"],
+ ["BIG", "BIG"],
+ ["PHARMACIA", "Pharmacia"],
+ ["IGLOI", "Igloi"],
+ ["INVITROGEN", "invitrogen"],
+ ["MICROSYNTH", "microsynth"]
+ ],
+ "OLIGO_USAGE" : [
+ ["PCR", "pcr"],
+ ["SEQUENCING", "sequencing"],
+ ["HYBRIDIZE", "hybridize"],
+ ["MUTAGENESIS", "mutagenesis"],
+ ["RT-PCR", "Real-Time PCR"]
+ ],
+ "RESTRICTION" : [
+ ["AATII", "AatII"],
+ ["ACCI", "AccI"],
+ ["ACII", "AciI"],
+ ["AFLII", "AflII"],
+ ["AFLIII", "AflIII"],
+ ["AGEI", "AgeI"],
+ ["ALUI", "AluI"],
+ ["ALWI", "AlwI"],
+ ["ALWNI", "AlwNI"],
+ ["APAI", "ApaI"],
+ ["APALI", "ApaLI"],
+ ["APOI", "ApoI"],
+ ["ASCI", "AscI"],
+ ["ASEI", "AseI"],
+ ["AVAI", "AvaI"],
+ ["AVAII", "AvaII"],
+ ["AVRII", "AvrII"],
+ ["BAMHI", "BamHI"],
+ ["BANI", "BanI"],
+ ["BANII", "BanII"],
+ ["BBSI", "BbsI"],
+ ["BBVI", "BbvI"],
+ ["BCGI-1", "BcgI-1"],
+ ["BCGI-2", "BcgI-2"],
+ ["BCLI", "BclI"],
+ ["BFAI", "BfaI"],
+ ["BGLI", "BglI"],
+ ["BGLII", "BglII"],
+ ["BLPI", "BlpI"],
+ ["BPMI", "BpmI"],
+ ["BSAAI", "BsaAI"],
+ ["BSABI", "BsaBI"],
+ ["BSAHI", "BsaHI"],
+ ["BSAI", "BsaI"],
+ ["BSAJI", "BsaJI"],
+ ["BSAWI", "BsaWI"],
+ ["BSERI", "BseRI"],
+ ["BSGI", "BsgI"],
+ ["BSIEI", "BsiEI"],
+ ["BSIHKAI", "BsiHKAI"],
+ ["BSIWI", "BsiWI"],
+ ["BSLI", "BslI"],
+ ["BSMAI", "BsmAI"],
+ ["BSMBI", "BsmBI"],
+ ["BSMFI", "BsmFI"],
+ ["BSMI", "BsmI"],
+ ["BSOFI", "BsoFI"],
+ ["BSP1286I", "Bsp1286I"],
+ ["BSPEI", "BspEI"],
+ ["BSPHI", "BspHI"],
+ ["BSPMI", "BspMI"],
+ ["BSRBI", "BsrBI"],
+ ["BSRDI", "BsrDI"],
+ ["BSRFI", "BsrFI"],
+ ["BSRGI", "BsrGI"],
+ ["BSRI", "BsrI"],
+ ["BSSHII", "BssHII"],
+ ["BST1107I", "Bst1107I"],
+ ["BSTBI", "BstBI"],
+ ["BSTEII", "BstEII"],
+ ["BSTNI", "BstNI"],
+ ["BSTUI", "BstUI"],
+ ["BSTXI", "BstXI"],
+ ["BSTYI", "BstYI"],
+ ["BSU36I", "Bsu36I"],
+ ["CAC8I", "Cac8I"],
+ ["CLAI", "ClaI"],
+ ["CVIJI", "CviJI"],
+ ["DDEI", "DdeI"],
+ ["DPNI", "DpnI"],
+ ["DRAI", "DraI"],
+ ["DRAIII", "DraIII"],
+ ["DRDI", "DrdI"],
+ ["DSAI", "DsaI"],
+ ["EAEI", "EaeI"],
+ ["EAGI", "EagI"],
+ ["EAM1105I", "Eam1105I"],
+ ["EARI", "EarI"],
+ ["ECO47III", "Eco47III"],
+ ["ECO57I", "Eco57I"],
+ ["ECONI", "EcoNI"],
+ ["ECOO109I", "EcoO109I"],
+ ["ECORI", "EcoRI"],
+ ["ECORV", "EcoRV"],
+ ["FOKI", "FokI"],
+ ["FSEI", "FseI"],
+ ["FSPI", "FspI"],
+ ["HAEII", "HaeII"],
+ ["HAEIII", "HaeIII"],
+ ["HGAI", "HgaI"],
+ ["HHAI", "HhaI"],
+ ["HINCII", "HincII"],
+ ["HINDIII", "HindIII"],
+ ["HINFI", "HinfI"],
+ ["HPAI", "HpaI"],
+ ["HPAII", "HpaII"],
+ ["HPHI", "HphI"],
+ ["KPNI", "KpnI"],
+ ["MAEII", "MaeII"],
+ ["MAEIII", "MaeIII"],
+ ["MBOI", "MboI"],
+ ["MBOII", "MboII"],
+ ["MLUI", "MluI"],
+ ["MNLI", "MnlI"],
+ ["MSCI", "MscI"],
+ ["MSEI", "MseI"],
+ ["MSLI", "MslI"],
+ ["MSPA1I", "MspA1I"],
+ ["MUNI", "MunI"],
+ ["MWOI", "MwoI"],
+ ["NAEI", "NaeI"],
+ ["NARI", "NarI"],
+ ["NCII", "NciI"],
+ ["NCOI", "NcoI"],
+ ["NDEI", "NdeI"],
+ ["NHEI", "NheI"],
+ ["NLAIII", "NlaIII"],
+ ["NLAIV", "NlaIV"],
+ ["NOTI", "NotI"],
+ ["NRUI", "NruI"],
+ ["NSII", "NsiI"],
+ ["NSPI", "NspI"],
+ ["PACI", "PacI"],
+ ["PFLMI", "PflMI"],
+ ["PLEI", "PleI"],
+ ["PMEI", "PmeI"],
+ ["PMLI", "PmlI"],
+ ["PPUMI", "PpuMI"],
+ ["PSHAI", "PshAI"],
+ ["PSP1406I", "Psp1406I"],
+ ["PSTI", "PstI"],
+ ["PVUI", "PvuI"],
+ ["PVUII", "PvuII"],
+ ["RSAI", "RsaI"],
+ ["RSRII", "RsrII"],
+ ["SACI", "SacI"],
+ ["SACII", "SacII"],
+ ["SALI", "SalI"],
+ ["SAPI", "SapI"],
+ ["SAU96I", "Sau96I"],
+ ["SCAI", "ScaI"],
+ ["SCRFI", "ScrFI"],
+ ["SEXAI", "SexAI"],
+ ["SFANI", "SfaNI"],
+ ["SFCI", "SfcI"],
+ ["SFII", "SfiI"],
+ ["SGFI", "SgfI"],
+ ["SGRAI", "SgrAI"],
+ ["SMAI", "SmaI"],
+ ["SNABI", "SnaBI"],
+ ["SPEI", "SpeI"],
+ ["SPHI", "SphI"],
+ ["SRFI", "SrfI"],
+ ["SSE8387I", "Sse8387I"],
+ ["SSPI", "SspI"],
+ ["STUI", "StuI"],
+ ["STYI", "StyI"],
+ ["SWAI", "SwaI"],
+ ["TAQI", "TaqI"],
+ ["TFII", "TfiI"],
+ ["TSP45I", "Tsp45I"],
+ ["TSP509I", "Tsp509I"],
+ ["TTH111I", "Tth111I"],
+ ["XBAI", "XbaI"],
+ ["XCMI", "XcmI"],
+ ["XHOI", "XhoI"],
+ ["XMNI", "XmnI"],
+ ["SACI_NHEI", "sacI NheI"],
+ ["XMAI", "XmaI"],
+ ["BAMHI", "BamHI"],
+ ["CLAI", "ClaI"],
+ ["PACI", "PacI"],
+ ["NOTI", "NotI"],
+ ["SALI", "SalI"],
+ ["XHOI", "XhoI"],
+ ["NONE", "none"]
+ ],
+ "BACKBONE" : [
+ ["PCDNA3", "pCDNA3"],
+ ["PABES-NEO2000", "pABES-neo 2000"],
+ ["PUC19", "pUC 19"],
+ ["PMX-1", "pMX-1"],
+ ["PRMHA-3", "pRmHa-3"]
+ ],
+ "BACTERIAL_HOST" : [
+ ["DH10B", "DH10B"],
+ ["JM110", "JM110"],
+ ["BL21", "BL21"],
+ ["DH5A", "DH5a"],
+ ["PB3", "PB3"],
+ ["DB31", "DB3.1"],
+ ["CCDB_SURVIVAL", "ccdB survival"]
+ ],
+ "BIOSAFETY_LEVEL" : [
+ ["S1", "S1"],
+ ["S2", "S2"],
+ ["S3", "S3"]
+ ],
+ "SELECTION_IN_BACTERIA" : [
+ ["AMPICILLIN", "Ampicillin"],
+ ["KANAMYCIN", "Kanamycin"],
+ ["SPECTINOMCIN", "Spectinomcin"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "SELECTION_IN_EUKARYOTES" : [
+ ["G418_NEO", "G418/neo"],
+ ["MPA", "MPA"],
+ ["HYGROMYCIN", "Hygromycin"]
+ ],
+ "SOURCE_OF_REPLICON" : [
+ ["CMV", "CMV"]
+ ],
+ "PLASMID_ORGANISM" : [
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["XENOPUS", "xenopus"],
+ ["DROSOPHILA", "drosophila"],
+ ["YEAST", "yeast"],
+ ["ECOLI", "E.coli"],
+ ["SYNTHETIC", "synthetic"]
+ ],
+ "PROMOTER" : [
+ ["ENDOGENOUS", "endogenous"],
+ ["GAL1", "gal1"],
+ ["GALL", "galL"],
+ ["GALS", "galS"],
+ ["TET", "tet"],
+ ["ADH", "adh"],
+ ["CYC", "cyc"],
+ ["GPD", "gpd"],
+ ["DASH", "\"-\""],
+ ["CMV", "cmv"],
+ ["SV40", "SV40"],
+ ["TET_ON", "tet on"],
+ ["TET_OFF", "tet off"],
+ ["RIM1", "rim1"]
+ ],
+ "EXON_OR_THREE_PRIME" : [
+ ["EXON", "exon"],
+ ["3P", "3'"],
+ ["5P", "5'"]
+ ],
+ "SIRNA_SPECIES" : [
+ ["HUMAN", "Human"],
+ ["MOUSE", "Mouse'"],
+ ],
+ "SIRNA_COMPANY" : [
+ ["AMBION", "Ambion"],
+ ["DHARMACON", "Dharmacon'"],
+ ["INVITORGEN", "Invitrogen'"],
+ ["MICROSYNTH", "Microsynth'"],
+ ["QIAGEN", "Qiagen'"],
+ ["GIFT", "Gift'"]
+ ],
+ "SIRNA_FREEZER_LOCATION" : [
+ ["BIGLABFREEZER", "BigLab freezer"],
+ ["SMALLLAB_BIGFREEZER", "SmallLab Big freezer'"],
+ ["FREEZER_G17", "Freezer G17'"],
+ ["G93-FRANK", "G9.3--Frank'"],
+ ["FREEZER-G17_BOX_NATHALIE", "Freezer G17 Box Nathalie'"],
+ ["BOX-THIBAULT-BIGFREEZER-SMALLLAB", "Box thibault Big freezer small lab'"],
+ ["BOX-NATHALIE", "Box Nathalie'"]
+ ],
+ "TRANSFECTION_AGENT" : [
+ ["FUGENE", "Fugene"],
+ ["LIPOFECTAMINE", "Lipofectamine'"],
+ ["OLIGOFECTAMINE", "Oligofectamine'"],
+ ["RNAIMAX", "RNAimax'"]
+ ],
+ "FREEZER" : [
+ ["G9_FRIDGE-1", "G9 Fridge 1"],
+ ["G9_FRIDGE-2", "G9 Fridge 2"],
+ ["G9_FREEZER-A", "-20C Small Peter Lab"],
+ ["G9_FREEZER-B", "G9 Freezer B"],
+ ["G9_FREEZER-C", "G9 Freezer C"],
+ ["G10_FREEZER-D", "G10 Freezer D"],
+ ["G10_FREEZER-E", "G10 Freezer E"],
+ ["G10_FREEZER-F", "G10 Freezer F"],
+ ["G10_FREEZER-G", "G10 Freezer G"],
+ ["G10_FREEZER-H", "G10 Freezer H"],
+ ["G10_FREEZER-I", "G10 Freezer I"],
+ ["G10_FRIDGE-3", "+4C Big Peter Lab"],
+ ["G10_FRIDGE-4", "G10 Fridge 4"],
+ ["G10_FRIDGE-5", "G10 Fridge 5"],
+ ["G10_FRIDGE-6", "G10 Fridge 6"],
+ ["G10_FRIDGE-7", "G10 Fridge 7"],
+ ["G11_FRIDGE-8", "G10 Fridge 8"],
+ ["G14_FREEZER-J", "G14 Freezer J"],
+ ["G14_FREEZER-K", "G14 Freezer K"],
+ ["G14_FREEZER-L", "G14 Freezer L"],
+ ["G14_FREEZER-M", "G14 Freezer M"],
+ ["G14_FRIDGE-9", "G14 Fridge 9"],
+ ["G14_FRIDGE-10", "G14 Fridge 10"],
+ ["G17_FRIDGE-11", "G17 Fridge 11"],
+ ["G17_FRIDGE-12", "G17 Fridge 12"],
+ ["G17_FREEZER-N", "G17 Freezer N"],
+ ["USER_BENCH-20", "Bench -20�C"],
+ ["USER_BENCH-80", "Bench -80�C"],
+ ["USER_BENCH-RT", "Bench RT"],
+ ["USER_BENCH", "Bench"]
+ ],
+ "STORAGE_BOX_SIZE" : [
+ ["9X9", "9 x 9 box"],
+ ["5X5", "5 x 5 box"],
+ ["10X10", "10 x 10 box"],
+ ["10X12", "10 x 12 box"]
+ ],
+ }
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/2/as/initialize-master-data.py b/plasmid/source/core-plugins/petermigration/2/as/initialize-master-data.py
new file mode 100644
index 0000000000000000000000000000000000000000..ddb26f48fbfb39bb26663af7e353b0a4a1d41efc
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/as/initialize-master-data.py
@@ -0,0 +1,155 @@
+#
+# Copyright 2014 ETH Zuerich, Scientific IT Services
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# MasterDataRegistrationTransaction Class
+import definitions
+import definitionsVoc
+import os
+import copy
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+
+##
+## Globals
+##
+vocabulariesCache = {};
+propertiesCache = {};
+samplesCache = {};
+tr = service.transaction()
+
+##
+## API Facade
+##
+def createVocabularyWithTerms(vocabularyCode, terms):
+ vocabulary = tr.createNewVocabulary(vocabularyCode);
+ vocabulary.setChosenFromList(True);
+ addTerms(vocabulary, terms);
+ vocabulariesCache[vocabularyCode] = vocabulary;
+
+def addTerms(vocabulary, terms):
+ for term in terms:
+ addTermWithLabel(vocabulary, term[0], term[1])
+
+def addTermWithLabel(vocabulary, termCode, termLabel):
+ newTerm = tr.createNewVocabularyTerm(termCode);
+ newTerm.setLabel(termLabel);
+ vocabulary.addTerm(newTerm);
+
+def createSampleTypeWithProperties(sampleTypeCode, description, properties):
+ newSampleType = tr.getOrCreateNewSampleType(sampleTypeCode);
+ newSampleType.setDescription(description);
+ newSampleType.setShowParents(True);
+ newSampleType.setAutoGeneratedCode(True);
+ newSampleType.setGeneratedCodePrefix(sampleTypeCode[:3]);
+ addProperties(newSampleType, properties);
+ samplesCache[sampleTypeCode] = newSampleType;
+
+def createDataSetTypeWithProperties(dataSetCode, kind, description, properties):
+ newDataSet = tr.getOrCreateNewDataSetType(dataSetCode);
+ newDataSet.setDataSetKind(kind);
+ newDataSet.setDescription(description);
+ addProperties(newDataSet, properties);
+
+def createExperimentTypeWithProperties(experimentTypeCode, description, properties):
+ newExperiment = tr.getOrCreateNewExperimentType(experimentTypeCode);
+ newExperiment.setDescription(description);
+ addProperties(newExperiment, properties);
+
+def addPropertiesToSamples(sampleTypeCodes, properties):
+ for sampleTypeCode in sampleTypeCodes:
+ sampleType = samplesCache[sampleTypeCode];
+ if sampleType is None:
+ sampleType = tr.getSampleType(sampleType)
+ addProperties(sampleType, properties);
+
+def addProperties(entity, properties):
+ for property in properties:
+ addProperty(entity, property[0], property[1], property[2], property[3], property[4], property[5], property[6], property[7], property[8]);
+
+def addProperty(entity, propertyCode, section, propertyLabel, dataType, vocabularyCode, propertyDescription, managedScript, dynamicScript, isMandatory):
+ property = None;
+
+ if propertyCode in propertiesCache:
+ property = propertiesCache[propertyCode];
+ else:
+ property = createProperty(propertyCode, dataType, propertyLabel, propertyDescription, vocabularyCode);
+
+ propertyAssignment = tr.assignPropertyType(entity, property);
+ propertyAssignment.setSection(section);
+ propertyAssignment.setMandatory(isMandatory);
+ if managedScript != None:
+ propertyAssignment.setManaged(True);
+ propertyAssignment.setShownEdit(True);
+ propertyAssignment.setScriptName(managedScript);
+ if dynamicScript != None:
+ propertyAssignment.setDynamic(True);
+ propertyAssignment.setShownEdit(True);
+ propertyAssignment.setScriptName(dynamicScript);
+
+def createProperty(propertyCode, dataType, propertyLabel, propertyDescription, vocabularyCode):
+ property = tr.getOrCreateNewPropertyType(propertyCode, dataType);
+ property.setDescription(propertyDescription);
+ property.setLabel(propertyLabel);
+ propertiesCache[propertyCode] = property;
+ if dataType == DataType.CONTROLLEDVOCABULARY:
+ property.setVocabulary(vocabulariesCache[vocabularyCode]);
+ return property;
+
+def addStorageGroups(numGroups, sampleType):
+ for storageIdx in range(1,(numGroups + 1)):
+ storageGroup = definitions.getStorageGroupDefinition();
+ for property in storageGroup:
+ property[0] = property[0] + "_" + str(storageIdx);
+ property[1] = property[1] + "_" + str(storageIdx);
+ property[5] = property[5] + "_" + str(storageIdx);
+ addPropertiesToSamples([sampleType], storageGroup);
+
+def addBoxSizeProperty(numGroups, sampleType):
+ for storageIdx in range(1,(numGroups + 1)):
+ property = ["STORAGE_BOX_SIZE", "Physical Storage", "box size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box size", None, None, False];
+ property[0] = property[0] + "_" + str(storageIdx);
+ property[1] = property[1] + "_" + str(storageIdx);
+ property[5] = property[5] + "_" + str(storageIdx);
+ addPropertiesToSamples([sampleType], storageGroup);
+
+#Valid Script Types: DYNAMIC_PROPERTY, MANAGED_PROPERTY, ENTITY_VALIDATION
+def createScript(path, name, description, scriptType, entityType):
+ scriptAsString = open(path, 'r').read();
+ script = tr.getOrCreateNewScript(name);
+ script.setName(name);
+ script.setDescription(description);
+ script.setScript(scriptAsString);
+ script.setScriptType(scriptType);
+ script.setEntityForScript(entityType);
+ return script;
+
+##
+## Vocabulary Types
+##
+createVocabularyWithTerms("STORAGE_BOX_SIZE", [
+ ["9X9", "9 x 9 box"],
+ ["5X5", "5 x 5 box"],
+ ["10X10", "10 x 10 box"],
+ ["10X12", "10 x 12 box"]
+ ]);
+
+##
+## New Position Property
+##
+addBoxSizeProperty(definitions.numberOfStorageGroups, "ANTIBODY");
+addBoxSizeProperty(definitions.numberOfStorageGroups, "CELL");
+addBoxSizeProperty(definitions.numberOfStorageGroups, "STRAIN");
+addBoxSizeProperty(definitions.numberOfStorageGroups, "PLASMID");
+addBoxSizeProperty(definitions.numberOfStorageGroups, "OLIGO");
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitions.py b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitions.py
new file mode 100644
index 0000000000000000000000000000000000000000..6cf0d515317babb43e8d21a5145016ef89930064
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitions.py
@@ -0,0 +1,375 @@
+#!/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_BOX_SIZE", "Physical Storage", "box size", DataType.CONTROLLEDVOCABULARY, "STORAGE_BOX_SIZE", "Storage Box size", None, None, False],
+ ["STORAGE_USER", "Physical Storage", "frozen by", DataType.CONTROLLEDVOCABULARY, "ALL_LAB_MEMBERS", "Storage User Id", 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]
+
+];
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitionsVoc.py b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitionsVoc.py
new file mode 100644
index 0000000000000000000000000000000000000000..6c41596dc8dd2ff2c3e1aff1b0ae83ddf1961722
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/definitionsVoc.py
@@ -0,0 +1,852 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+#
+# Helper Methods
+#
+def getVocabularyTermCodeForVocabularyAndTermLabel(vocabularyCode, termLabel):
+ vocabulary = vocabularyDefinitions[vocabularyCode]
+ for term in vocabulary:
+ if term[1] == termLabel:
+ #print repr("TERM NOT FOUND IN VOCABULARY LIST: " + unicode(vocabularyCode) + " : '" + unicode(termLabel) + "'")
+ return term[0]
+ return None
+
+# "VOCABULARY_CODE" : { "TERM_CODE" : "OBJECT" }
+createdVocabularyTerms = { }
+
+def printCreatedTerms():
+ print "--- Created Vocabulary Terms Report"
+ for vocabularyCode in createdVocabularyTerms:
+ print "Vocabulary [" + vocabularyCode + "]"
+ for vocabularyTermCode in createdVocabularyTerms[vocabularyCode]:
+ print "Term [" + vocabularyTermCode + "] Label: [" + repr(createdVocabularyTerms[vocabularyCode][vocabularyTermCode].getLabel()) + "]"
+ print "---"
+
+def getCreatedTerm(vocabularyCode, termCode):
+ if vocabularyCode in createdVocabularyTerms:
+ if termCode in createdVocabularyTerms[vocabularyCode]:
+ return createdVocabularyTerms[vocabularyCode][termCode]
+ return None
+
+def addCreatedTerm(vocabularyCode, termCode, object):
+ if vocabularyCode not in createdVocabularyTerms:
+ createdVocabularyTerms[vocabularyCode] = {}
+ createdVocabularyTerms[vocabularyCode][termCode] = object
+
+def createVocabularyTerm(tr, vocabularyCode, termCode, termLabel):
+ createdTerm = getCreatedTerm(vocabularyCode, termCode)
+ if createdTerm is None:
+ vocabulary = tr.getVocabularyForUpdate(vocabularyCode)
+
+ for term in vocabulary.getTerms():
+ if term.getCode() == termCode:
+ createdTerm = term
+
+ if createdTerm is None:
+ createdTerm = tr.createNewVocabularyTerm()
+ createdTerm.setCode(termCode)
+ createdTerm.setLabel(termLabel)
+ createdTerm.setOrdinal(vocabulary.getTerms().size())
+ vocabulary.addTerm(createdTerm)
+ addCreatedTerm(vocabularyCode, termCode, createdTerm)
+ return createdTerm
+
+#
+# Vocabularies
+#
+
+vocabularyDefinitions = {
+ "ALL_LAB_MEMBERS" : [
+ ["ANNA_DEPLAZES", "Anna Deplazes"],
+ ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"],
+ ["BRIAN_LUKE", "Brian Luke"],
+ ["CAROLINE_ZBINDEN", "Caroline Zbinden"],
+ ["CELINE_LAFOURCADE", "Celine Lafourcade"],
+ ["CHRISTINE_RUPP", "Christine Rupp"],
+ ["CLAUDINE_KRAFT", "Claudine Kraft"],
+ ["EDYTA_SIERGIEJUK", "Edyta Siergiejuk"],
+ ["FABIAN_HERZOG", "Fabian Herzog"],
+ ["FABIAN_RUDOLF", "Fabian Rudolf"],
+ ["FRANK_VAN_DROGEN", "Frank Van Drogen"],
+ ["GERDA_JORRITSMA", "Gerda Jorritsma"],
+ ["GWEN_RABUT", "Gw\xe9nael Rabut"],
+ ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"],
+ ["IRAM_ZAIDI", "Iram Zaidi"],
+ ["IZABELA_SUMARA", "Izabela Sumara"],
+ ["LIONEL_PINTARD", "Lionel Pintard"],
+ ["MALIKAJAQUENOUD", "MalikaJaquenoud"],
+ ["MARC_SOHRMANN", "Marc Sohrmann"],
+ ["MARIE-LYN_HECHT", "Marie-Lyn Hecht"],
+ ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["MICHAEL_OLMA", "Michael Olma"],
+ ["MICHAEL_SCHNEIDER", "Michael Schneider"],
+ ["MICHELE_KNAUS", "Michele Knaus"],
+ ["MONIKA_GERSBACH", "Monika Gersbach"],
+ ["NATHALIE_MEYER-SCHALLER", "Nathalie Meyer-Schaller"],
+ ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"],
+ ["NICOLAS_DARD", "Nicolas Dard"],
+ ["NICOLAS_PAGE", "Nicolas Page"],
+ ["PATRICK_PEDRIOLI", "Patrick Pedrioli"],
+ ["PHILIPPE_WIGET", "Philippe Wiget"],
+ ["PIERRE_MAILLARD", "Pierre Maillard"],
+ ["REINHARD_DECHANT", "Reinhard Dechant"],
+ ["SANDER_SPRINGER", "Sander Springer"],
+ ["SARAH_GLASER", "Sarah Glaser"],
+ ["SARAH_MAERKI", "Sarah M\xe4rki"],
+ ["SEBASTIAN_LEIDEL", "Sebastian Leidel"],
+ ["SERGE_PELET", "Serge Pelet"],
+ ["STEFAN_MUELLER", "Stefan M�ller"],
+ ["TANIA_ROBERTS", "Tania Roberts"],
+ ["THIMO_KURZ", "Thimo Kurz"],
+ ["TOBIAS_BRAUN", "Tobias Braun"],
+ ["VANESSA_REZGUI", "Vanessa Rezgui"],
+ ["WOJCIECH_PIWKO", "Wojciech Piwko"],
+ ["YUKIKO_SHIMADA", "Yukiko Shimada"],
+ ["YVONNE_GLOOR", "Yvonne Gloor"],
+ ["JOCHEN_BECK", "Jochen Beck"],
+ ["MONIKA_KIJANSKA", "Monika Kijanska"],
+ ["ANGIE_RAGHEB", "Angie Ragheb"],
+ ["ANNE_PACQUELET", "Anne Pacquelet"],
+ ["BJORN_HEGEMANN", "Bj\xf6rn Hegemann"],
+ ["JANNY_TILMA", "Janny Tilma"],
+ ["THIBAULT_COURTHEOUX", "Thibault Courtheoux"],
+ ["SAMUEL_GILBERTO", "Samuel Gilberto"],
+ ["REMY_BUSER", "Remy Buser"],
+ ["RADOSLAV_ENCHEV", "Radoslav Enchev"],
+ ["MICHAELA_HUBNER", "Michaela Hubner"],
+ ["MIA_LI", "Mia Li"],
+ ["JULIEN_MOUYSSET", "Julien Mouysset"]
+ ],
+ "LAB_MEMBERS_INITIALS" : [
+ ["AD", "AD"],
+ ["ACB", "ACB"],
+ ["BL", "BL"],
+ ["CZ", "CZ"],
+ ["CL", "CL"],
+ ["CR", "CR"],
+ ["CK", "CK"],
+ ["ES", "ES"],
+ ["FH", "FH"],
+ ["FR", "FR"],
+ ["FD", "FD"],
+ ["GJ", "GJ"],
+ ["GR", "GR"],
+ ["ISS", "ISS"],
+ ["IZ", "IZ"],
+ ["IS", "IS"],
+ ["LP", "LP"],
+ ["MJ", "MJ"],
+ ["MSO", "MSo"],
+ ["MH", "MH"],
+ ["MG", "MG"],
+ ["MP", "MP"],
+ ["MO", "MO"],
+ ["MSC", "MSc"],
+ ["MK", "MK"],
+ ["MG", "MG"],
+ ["NS", "NS"],
+ ["NPE", "NPe"],
+ ["ND", "ND"],
+ ["NPA", "NPa"],
+ ["PP", "PP"],
+ ["PW", "PW"],
+ ["PM", "PM"],
+ ["RD", "RD"],
+ ["SS", "SS"],
+ ["SG", "SG"],
+ ["SMA", "SMa"],
+ ["SL", "SL"],
+ ["SP", "SP"],
+ ["SM", "SM"],
+ ["TR", "TR"],
+ ["TK", "TK"],
+ ["TB", "TB"],
+ ["VR", "VR"],
+ ["WP", "WP"],
+ ["YS", "YS"],
+ ["YG", "YG"],
+ ["JB", "JB"],
+ ["MKI", "MKi"]
+ ],
+ "BLOCK" : [
+ ["1BSA_01TRITON-X100", "1% BSA; 0.1% Triton-X100"],
+ ],
+ "CLASS" : [
+ ["IGM", "IgM"],
+ ["IGG1", "IgG1"],
+ ["IGG2", "IgG2"]
+ ],
+ "COMPANY" : [
+ ["ABCAM", "abcam"],
+ ["CELL_SIGNALING", "cell signaling"],
+ ["STRATAGEN", "stratagene"],
+ ["CLONTECH", "clontech"],
+ ["UBI", "ubi"],
+ ["SOUTHERN_BIOTECH", "southern biotech"],
+ ["PIERCE", "pierce"],
+ ["PHARMIGEN", "pharmingen"],
+ ["MOLECULAR_PROBES", "molecular probes"],
+ ["PHARMACIA", "pharmacia"],
+ ["BIORAD", "biorad"],
+ ["EUROGENETIC", "eurogentec"],
+ ["HOMEMADE", "homemade"],
+ ["BD_BIOSCIENCE", "BD bioscience"],
+ ["OBTAINED_FROM", "obtained from "],
+ ["ZYMED", "Zymed"],
+ ["UNKNOWN", "Unknown"],
+ ["SANTA_CRUZ", "Santa Cruz"],
+ ["BIOLEGEND", "Biolegend"],
+ ["BETHYL", "Bethyl"],
+ ["UPSTATE", "Upstate"],
+ ["ROCKLAND", "Rockland"],
+ ["NOVUS_BIOLOGICALS", "Novus Biologicals"],
+ ["CHEMICON_INTERNATIONAL", "Chemicon International"],
+ ["SIGMA", "Sigma"],
+ ["ALPHA_DIAGNOSTIC_INTERNATIONAL", "Alpha Diagnostic International"],
+ ["MILLIPORE", "Millipore"],
+ ["ACTIVE_MOTIF", "Active motif"],
+ ["NEB", "NEB"],
+ ["NEOMARKERS", "Neomarkers"],
+ ["LUBIOSCIENCE", "LubioScience"],
+ ["EBIOSCIENCE", "eBioscience"],
+ ["INVITROGEN", "Invitrogen"],
+ ["STRESSGEN", "Stressgen"],
+ ["COVANCE", "Covance"],
+ ["ENZO_LIFE_SCIENCES", "Enzo Life Sciences"],
+ ["CALBIOCHEM", "Calbiochem"],
+ ["ROCHE", "Roche"],
+ ["CYTOSKELETON", "Cytoskeleton"],
+ ["OPEN_BIOSYSTEMS", "Open Biosystems"],
+ ["BD_TRANSDUCTION", "BD Transduction"],
+ ["ATLAS_ANTIBODIES_AB", "Atlas Antibodies AB"],
+ ["GENENTECH", "Genentech"],
+ ["TRANSDUCTION_LABS", "Transduction Labs"],
+ ["ANTIBODIES_INCORPORATED", "Antibodies Incorporated"],
+ ["BABCO", "BAbCO"],
+ ["ERICH_NIGG_LAB_BASEL", "Erich Nigg lab (Basel)"],
+ ["FRANCIS_BARR", "Francis Barr"],
+ ["AVIVA_SYSTEMS_BIOLOGY", "Aviva Systems Biology"],
+ ["LUCERNACHEM", "LucernaChem"],
+ ["LI-COR", "LI-COR"],
+ ["ABGENT", "Abgent"],
+ ["CHROMOTEK", "Chromotek"],
+ ["ABNOVA", "Abnova"],
+ ["UNKNOWN", "Unknown"],
+ ["ABSEA", "Absea"],
+ ["GE_HEALTHCARE", "GE Healthcare"],
+ ["GRAMSCH_LABORATORIES", "Gramsch Laboratories"],
+ ["ADIPOGEN", "Adipogen"],
+ ["COSMO_BIO_CO", "Cosmo bio co."],
+ ["BECKTON_DICKINSON", "Beckton Dickinson"],
+ ["BIOTIUM", "Biotium"]
+ ],
+ "CONCENTRATION_FACS" : [
+ ["1_TO_10", "1 : 10"],
+ ["1_TO_20", "1 : 20"],
+ ["1_TO_30", "1 : 30"],
+ ["1_TO_40", "1 : 40"],
+ ["1_TO_50", "1 : 50"],
+ ["1_TO_100", "1 : 100"],
+ ["1_TO_200", "1 : 200"],
+ ["1_TO_500", "1 : 500"],
+ ["1_TO_1000", "1 : 1000"],
+ ["1_TO_2000", "1 : 2000"],
+ ["1_TO_3000", "1 : 3000"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CONCENTRATION_IP" : [
+ ["1UL", "1 �l"],
+ ["5UL", "5 �l"],
+ ["10UL", "10 �l"],
+ ["15UL", "15 �l"],
+ ["20UL", "20 �l"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CONCENTRATION_WESTERN" : [
+ ["1_TO_100", "1 : 100"],
+ ["1_TO_500", "1 : 500"],
+ ["1_TO_1000", "1 : 1000"],
+ ["1_TO_2000", "1 : 2000"],
+ ["1_TO_3000", "1 : 3000"],
+ ["1_TO_5000", "1 : 5000"],
+ ["1_TO_10000", "1 : 10000"],
+ ["1_TO_20000", "1 : 20000"],
+ ["1_TO_25000", "1 : 25000"],
+ ["NOT_TESTED", "not tested"],
+ ["NOT_WORKING", "not working"]
+ ],
+ "CURRENT_LAB_MEMBERS" : [
+ ["CAROLINE_ZBINDEN", "Caroline Zbinden"],
+ ["FRANK_VAN_DROGEN", "Frank Van Drogen"],
+ ["INGRID_STOFFEL-STUDER", "Ingrid Stoffel-Studer"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["REINHARD_DECHANT", "Reinhard Dechant"],
+ ["WOJCIECH_PIWKO", "Wojciech Piwko"],
+ ["JOCHEN_BECK", "Jochen Beck"]
+ ],
+ "FIX" : [
+ ["1H-RT", "1h, RT"],
+ ["PTEMF", "PTEMF"],
+ ["PFA", "PFA"],
+ ["MEOH", "MeOH"]
+ ],
+ "LABEL" : [
+ ["HRP", "hrp"],
+ ["AP", "ap"],
+ ["FITC", "fitc"],
+ ["CY3", "Cy3"],
+ ["ALEXA647", "Alexa 647"]
+ ],
+ "ANTIBODY_LOCATION" : [
+ ["SMALL_PETER_LAB", "Small Peter Lab"],
+ ["BIG_PETER_LAB", "Big Peter Lab"],
+ ["NEW_PETER_LAB", "New Peter Lab"],
+ ["MINUS20_C-FLOOR", "-20C C-Floor"]
+ ],
+ "MONO-POLYCLONAL" : [
+ ["MONOCLONAL", "Monoclonal"],
+ ["POLYCLONAL", "Polyclonal"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "SOURCE" : [
+ ["MOUSE", "Mouse"],
+ ["RABBIT", "Rabbit"],
+ ["HAMSTER", "Hamster"],
+ ["GOAT", "Goat"],
+ ["RAT", "Rat"],
+ ["CHICKEN", "Chicken"],
+ ["SHEEP", "Sheep"],
+ ["HUMAN", "Human"],
+ ["GUINEA_PIG", "Guinea pig"],
+ ["DONEKY", "Donkey"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "CELL_LOCATION" : [
+ ["FRIDGE", "fridge"],
+ ["FREEZER", "freezer"],
+ ["REFCO", "refco"],
+ ["TANK", "tank"]
+ ],
+ "SELECTION" : [
+ ["NEOMYCIN_G418", "Neomycin/G418"],
+ ["HYGROMYCIN", "Hygromycin"],
+ ["MPA", "MPA"],
+ ["G418", "G418"],
+ ["PUROMYCIN", "puromycin"],
+ ["BLASTICIDIN", "Blasticidin"],
+ ["ZEOCIN", "Zeocin"]
+ ],
+ "CO2" : [
+ ["5", "5"],
+ ["7.5", "7.5"]
+ ],
+ "GROWTH_TEMPERATURE" : [
+ ["37", "37"],
+ ["28", "28"],
+ ["34", "34"]
+ ],
+ "MEDIUM" : [
+ ["RPMI1640", "RPMI 1640"],
+ ["ISCOVES", "Iscoves"],
+ ["DMEM", "DMEM"],
+ ["LB", "LB"],
+ ["DMEM_NUTRIENT", "DMEM nutrient mixture F-12 HAM [D8437]"]
+ ],
+ "CELL_OBTAINED_FROM" : [
+ ["FREIBURG", "Freiburg"],
+ ["ATCC", "ATCC"],
+ ["DANIEL_GERLICH", "Daniel Gerlich"],
+ ["ERICH_NIGG", "Erich Nigg"],
+ ["KREK", "Krek"],
+ ["TONY_HEYMAN", "Tony Heyman"],
+ ["THOMAS-WILD_ULRIKE-KUTAY", "Thomas Wild/Ulrike Kutay"],
+ ["JAN_MICHAEL_PETERS", "Jan-Michael Peters"],
+ ["M_BRANDEIS", "M Brandeis"],
+ ["ARI_HELENIUS", "Ari Helenius"],
+ ["ROMEO_RICCI", "Romeo Ricci"]
+ ],
+ "CELL_SPECIES" : [
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["CHINESE_HAMSTER", "chines hamster"],
+ ["HYBRIDOMA", "hybridoma (human & mouse)"]
+ ],
+ "CONC_UNITS" : [
+ ["MICROG_MICROL", "�g/�l"],
+ ["MG_ML", "mgl/ml"],
+ ["UG_ML", "ug/ml"]
+ ],
+ "STRAIN_SOURCE" : [
+ ["F_CHANG", "F. Chang"],
+ ["J_CHANT", "J. Chant"],
+ ["R_DESHAIES", "R. Deshaies"],
+ ["E_ELION", "E. Elion"],
+ ["P_HIETER", "P. Hieter"],
+ ["I_HERSKOWITZ", "I. Herskowitz"],
+ ["A_NEIMAN", "A. Neiman"],
+ ["P_SORGER", "P. Sorger"],
+ ["T_STEARNS", "T. Stearns"],
+ ["MARC_BONDEL", "Marc Bondel"],
+ ["G_SUMARA", "G. Sumara"],
+ ["MICHAEL_ALTMANN", "Michael Altmann"],
+ ["HETEROZYGOUS_DIPLOID_COLLECTION", "Heterozygous diploid collection"],
+ ["ANNE-CHRISTINE_BUTTY", "Anne-Christine Butty"],
+ ["ANNE_PAQUELET", "Anne Paquelet"],
+ ["YAGMUR-TURGAY_KUTAY-GROUP", "Yagmur Turgay - Kutay group"],
+ ["BARBAR_CATARIN", "Barbar Catarin"],
+ ["FRANK_VAN-DROGEN", "Frank van Drogen"],
+ ["HEMMO_MEYER", "Hemmo Meyer"],
+ ["JEAN-MARC_GALLAND", "Jean-Marc Galland"],
+ ["JEFF_PARVIN", "Jeff Parvin"],
+ ["MARIE-PIERRE_GULLI", "Marie-Pierre Gulli"],
+ ["MIKIKO_TAKAHASHI", "Mikiko Takahashi"],
+ ["SANDRA_HENCHOZ", "Sandra Henchoz"],
+ ["MALIKA_JAQUENOUD", "Malika Jaquenoud"],
+ ["GERDA_JORRITSMA", "Gerda Jorritsma"],
+ ["CELINE_LAFOURCADE", "Céline Lafourcade"],
+ ["CELINE_LONGARETTI", "Céline Longaretti"],
+ ["BRIAN_LUKE", "Brian Luke"],
+ ["GUY_NIEDERHAUSER", "Guy Niederhäuser"],
+ ["NICOLAS_PAGE", "Nicolas Pag�"],
+ ["NATHALIE_PERRINJAQUET", "Nathalie Perrinjaquet"],
+ ["MATTHIAS_PETER", "Matthias Peter"],
+ ["AUDREY_PETIT", "Audrey Petit"],
+ ["LIONEL_PINTARD", "Lionel Pintard"],
+ ["YUKIKO_SHIMADA", "Yukiko Shimada"],
+ ["PHILIPPE_WIGET", "Philippe Wiget"],
+ ["VOLKER_STUCKE", "Volker Stucke"],
+ ["KATRIN_PETER", "Katrin Peter"],
+ ["MARC_BLONDEL", "marc blondel"],
+ ["M_FUNK", "M. Funk"],
+ ["ATTILA_BECSKEI", "Attila Becskei"],
+ ["GWENAEL_RABUT", "Gwenael Rabut"],
+ ["PHILIP_JERMANN", "Philip Jermann"],
+ ["P_PRYCIAK", "P.Pryciak"],
+ ["LINDA_HICKE", "Linda Hicke"],
+ ["RZPD", "RZPD"],
+ ["OPENBIO", "OpenBio"],
+ ["F_POSAS", "F. Posas"],
+ ["HAPLOID_COLLECTION", "Haploid collection"],
+ ["MIRIAM_BORTFELD", "Miriam Bortfeld"],
+ ["EUROSCARF", "Euroscarf"],
+ ["TS_COLLECTION", "ts collection"],
+ ["CONZELMANN_LAB", "Conzelmann lab"],
+ ["SEBASTIAN_LEIDEL", "Sebastian Leidel"],
+ ["ANNA_DEPLAZES", "Anna Deplazes"],
+ ["BIBOU", "Bibou"],
+ ["MARC_SOHRMANN", "Marc sohrmann"]
+ ],
+ "SELECTION_YEAST" : [
+ ["NONE", "None"],
+ ["URA", "Ura"],
+ ["LEU", "Leu"],
+ ["TRP", "Trp"],
+ ["HIS", "His"],
+ ["VIABILITY", "Viability"],
+ ["NAT", "nat"],
+ ["KAN", "kan"],
+ ["KAN_NAT", "kan + nat"],
+ ["HIS_KAN", "HIS + kan"],
+ ["HIS_KAN_NAT", "HIS + kan + nat"],
+ ["HIS", "HIS"],
+ ["LEU_NAT", "leu + nat"],
+ ["ADE2", "ade2"]
+ ],
+ "DERIVATION" : [
+ ["GAMMA_INTEG", "gamma integ"],
+ ["DELTA_INTEG", "� integ"],
+ ["5FAO_LOOPOUT", "5-FAO loopout"],
+ ["PLASMID_SHUFFLE", "plasmid shuffle"],
+ ["TETRAD", "tetrad"],
+ ["LOOP-IN_LOOP-OUT", "loop-in/loop-out"],
+ ["GALPHO", "GalpHO mating type switch"],
+ ["DELETION", "Deletion"],
+ ["INTEGRATION", "Integration"]
+ ],
+ "STRAIN_BACKGROUND" : [
+ ["W303", "W303"],
+ ["K699", "K699"],
+ ["K700", "K700"],
+ ["S288C", "S288C"],
+ ["1278", "*1278*"],
+ ["EG123", "EG123"],
+ ["DF5", "DF5"],
+ ["SIGMA", "Sigma"],
+ ["UNKNOWN", "Don't know"],
+ ["BY7092", "BY7092"],
+ ["BY5565", "BY5565"],
+ ["BY4741", "BY4741"]
+ ],
+ "CIR" : [
+ ["CIR_PLUS", "cir+"],
+ ["CIR_DEG", "cir�"],
+ ],
+ "GAL" : [
+ ["PLUS", "Plus"],
+ ["PLUS_PLUS", "Plus/Plus"],
+ ["GAL1", "gal1"],
+ ["GAL1_GAL1", "gal1/gal1"],
+ ["GAL2", "gal2"],
+ ["GAL2_GAL2", "gal2/gal2"],
+ ],
+ "MAT" : [
+ ["AT", "@"],
+ ["A", "a"],
+ ["ALPHA", "alpha"],
+ ["DIPLOID", "diploid"],
+ ["UNKNOWN", "unknown"]
+ ],
+ "OLIGO_ORGANISM" : [
+ ["BMV", "BMV"],
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["XENOPUS", "xenopus"],
+ ["DROSOPHILA", "drosophila"],
+ ["YEAST", "yeast"],
+ ["ECOLI", "E.coli"],
+ ["SYNTHETIC", "synthetic"],
+ ["HIV1", "HIV-1"],
+ ["CELEGANS", "C.elegans"],
+ ["MYCOPLASMA", "mycoplasma"]
+ ],
+ "OLIGO_GRADE" : [
+ ["DESALTED", "desalted"],
+ ["HPLC", "hplc"],
+ ["PURITY", "purity"],
+ ["UNKNOWN", "?"]
+ ],
+ "PRIMER_POSITION" : [
+ ["FORWARD", "forward"],
+ ["REVERSE", "reverse"]
+ ],
+ "OLIGO_COMPANY" : [
+ ["MWG", "MWG"],
+ ["BIG", "BIG"],
+ ["PHARMACIA", "Pharmacia"],
+ ["IGLOI", "Igloi"],
+ ["INVITROGEN", "invitrogen"],
+ ["MICROSYNTH", "microsynth"]
+ ],
+ "OLIGO_USAGE" : [
+ ["PCR", "pcr"],
+ ["SEQUENCING", "sequencing"],
+ ["HYBRIDIZE", "hybridize"],
+ ["MUTAGENESIS", "mutagenesis"],
+ ["RT-PCR", "Real-Time PCR"]
+ ],
+ "RESTRICTION" : [
+ ["AATII", "AatII"],
+ ["ACCI", "AccI"],
+ ["ACII", "AciI"],
+ ["AFLII", "AflII"],
+ ["AFLIII", "AflIII"],
+ ["AGEI", "AgeI"],
+ ["ALUI", "AluI"],
+ ["ALWI", "AlwI"],
+ ["ALWNI", "AlwNI"],
+ ["APAI", "ApaI"],
+ ["APALI", "ApaLI"],
+ ["APOI", "ApoI"],
+ ["ASCI", "AscI"],
+ ["ASEI", "AseI"],
+ ["AVAI", "AvaI"],
+ ["AVAII", "AvaII"],
+ ["AVRII", "AvrII"],
+ ["BAMHI", "BamHI"],
+ ["BANI", "BanI"],
+ ["BANII", "BanII"],
+ ["BBSI", "BbsI"],
+ ["BBVI", "BbvI"],
+ ["BCGI-1", "BcgI-1"],
+ ["BCGI-2", "BcgI-2"],
+ ["BCLI", "BclI"],
+ ["BFAI", "BfaI"],
+ ["BGLI", "BglI"],
+ ["BGLII", "BglII"],
+ ["BLPI", "BlpI"],
+ ["BPMI", "BpmI"],
+ ["BSAAI", "BsaAI"],
+ ["BSABI", "BsaBI"],
+ ["BSAHI", "BsaHI"],
+ ["BSAI", "BsaI"],
+ ["BSAJI", "BsaJI"],
+ ["BSAWI", "BsaWI"],
+ ["BSERI", "BseRI"],
+ ["BSGI", "BsgI"],
+ ["BSIEI", "BsiEI"],
+ ["BSIHKAI", "BsiHKAI"],
+ ["BSIWI", "BsiWI"],
+ ["BSLI", "BslI"],
+ ["BSMAI", "BsmAI"],
+ ["BSMBI", "BsmBI"],
+ ["BSMFI", "BsmFI"],
+ ["BSMI", "BsmI"],
+ ["BSOFI", "BsoFI"],
+ ["BSP1286I", "Bsp1286I"],
+ ["BSPEI", "BspEI"],
+ ["BSPHI", "BspHI"],
+ ["BSPMI", "BspMI"],
+ ["BSRBI", "BsrBI"],
+ ["BSRDI", "BsrDI"],
+ ["BSRFI", "BsrFI"],
+ ["BSRGI", "BsrGI"],
+ ["BSRI", "BsrI"],
+ ["BSSHII", "BssHII"],
+ ["BST1107I", "Bst1107I"],
+ ["BSTBI", "BstBI"],
+ ["BSTEII", "BstEII"],
+ ["BSTNI", "BstNI"],
+ ["BSTUI", "BstUI"],
+ ["BSTXI", "BstXI"],
+ ["BSTYI", "BstYI"],
+ ["BSU36I", "Bsu36I"],
+ ["CAC8I", "Cac8I"],
+ ["CLAI", "ClaI"],
+ ["CVIJI", "CviJI"],
+ ["DDEI", "DdeI"],
+ ["DPNI", "DpnI"],
+ ["DRAI", "DraI"],
+ ["DRAIII", "DraIII"],
+ ["DRDI", "DrdI"],
+ ["DSAI", "DsaI"],
+ ["EAEI", "EaeI"],
+ ["EAGI", "EagI"],
+ ["EAM1105I", "Eam1105I"],
+ ["EARI", "EarI"],
+ ["ECO47III", "Eco47III"],
+ ["ECO57I", "Eco57I"],
+ ["ECONI", "EcoNI"],
+ ["ECOO109I", "EcoO109I"],
+ ["ECORI", "EcoRI"],
+ ["ECORV", "EcoRV"],
+ ["FOKI", "FokI"],
+ ["FSEI", "FseI"],
+ ["FSPI", "FspI"],
+ ["HAEII", "HaeII"],
+ ["HAEIII", "HaeIII"],
+ ["HGAI", "HgaI"],
+ ["HHAI", "HhaI"],
+ ["HINCII", "HincII"],
+ ["HINDIII", "HindIII"],
+ ["HINFI", "HinfI"],
+ ["HPAI", "HpaI"],
+ ["HPAII", "HpaII"],
+ ["HPHI", "HphI"],
+ ["KPNI", "KpnI"],
+ ["MAEII", "MaeII"],
+ ["MAEIII", "MaeIII"],
+ ["MBOI", "MboI"],
+ ["MBOII", "MboII"],
+ ["MLUI", "MluI"],
+ ["MNLI", "MnlI"],
+ ["MSCI", "MscI"],
+ ["MSEI", "MseI"],
+ ["MSLI", "MslI"],
+ ["MSPA1I", "MspA1I"],
+ ["MUNI", "MunI"],
+ ["MWOI", "MwoI"],
+ ["NAEI", "NaeI"],
+ ["NARI", "NarI"],
+ ["NCII", "NciI"],
+ ["NCOI", "NcoI"],
+ ["NDEI", "NdeI"],
+ ["NHEI", "NheI"],
+ ["NLAIII", "NlaIII"],
+ ["NLAIV", "NlaIV"],
+ ["NOTI", "NotI"],
+ ["NRUI", "NruI"],
+ ["NSII", "NsiI"],
+ ["NSPI", "NspI"],
+ ["PACI", "PacI"],
+ ["PFLMI", "PflMI"],
+ ["PLEI", "PleI"],
+ ["PMEI", "PmeI"],
+ ["PMLI", "PmlI"],
+ ["PPUMI", "PpuMI"],
+ ["PSHAI", "PshAI"],
+ ["PSP1406I", "Psp1406I"],
+ ["PSTI", "PstI"],
+ ["PVUI", "PvuI"],
+ ["PVUII", "PvuII"],
+ ["RSAI", "RsaI"],
+ ["RSRII", "RsrII"],
+ ["SACI", "SacI"],
+ ["SACII", "SacII"],
+ ["SALI", "SalI"],
+ ["SAPI", "SapI"],
+ ["SAU96I", "Sau96I"],
+ ["SCAI", "ScaI"],
+ ["SCRFI", "ScrFI"],
+ ["SEXAI", "SexAI"],
+ ["SFANI", "SfaNI"],
+ ["SFCI", "SfcI"],
+ ["SFII", "SfiI"],
+ ["SGFI", "SgfI"],
+ ["SGRAI", "SgrAI"],
+ ["SMAI", "SmaI"],
+ ["SNABI", "SnaBI"],
+ ["SPEI", "SpeI"],
+ ["SPHI", "SphI"],
+ ["SRFI", "SrfI"],
+ ["SSE8387I", "Sse8387I"],
+ ["SSPI", "SspI"],
+ ["STUI", "StuI"],
+ ["STYI", "StyI"],
+ ["SWAI", "SwaI"],
+ ["TAQI", "TaqI"],
+ ["TFII", "TfiI"],
+ ["TSP45I", "Tsp45I"],
+ ["TSP509I", "Tsp509I"],
+ ["TTH111I", "Tth111I"],
+ ["XBAI", "XbaI"],
+ ["XCMI", "XcmI"],
+ ["XHOI", "XhoI"],
+ ["XMNI", "XmnI"],
+ ["SACI_NHEI", "sacI NheI"],
+ ["XMAI", "XmaI"],
+ ["BAMHI", "BamHI"],
+ ["CLAI", "ClaI"],
+ ["PACI", "PacI"],
+ ["NOTI", "NotI"],
+ ["SALI", "SalI"],
+ ["XHOI", "XhoI"],
+ ["NONE", "none"]
+ ],
+ "BACKBONE" : [
+ ["PCDNA3", "pCDNA3"],
+ ["PABES-NEO2000", "pABES-neo 2000"],
+ ["PUC19", "pUC 19"],
+ ["PMX-1", "pMX-1"],
+ ["PRMHA-3", "pRmHa-3"]
+ ],
+ "BACTERIAL_HOST" : [
+ ["DH10B", "DH10B"],
+ ["JM110", "JM110"],
+ ["BL21", "BL21"],
+ ["DH5A", "DH5a"],
+ ["PB3", "PB3"],
+ ["DB31", "DB3.1"],
+ ["CCDB_SURVIVAL", "ccdB survival"]
+ ],
+ "BIOSAFETY_LEVEL" : [
+ ["S1", "S1"],
+ ["S2", "S2"],
+ ["S3", "S3"]
+ ],
+ "SELECTION_IN_BACTERIA" : [
+ ["AMPICILLIN", "Ampicillin"],
+ ["KANAMYCIN", "Kanamycin"],
+ ["SPECTINOMCIN", "Spectinomcin"],
+ ["UNKNOWN", "Unknown"]
+ ],
+ "SELECTION_IN_EUKARYOTES" : [
+ ["G418_NEO", "G418/neo"],
+ ["MPA", "MPA"],
+ ["HYGROMYCIN", "Hygromycin"]
+ ],
+ "SOURCE_OF_REPLICON" : [
+ ["CMV", "CMV"]
+ ],
+ "PLASMID_ORGANISM" : [
+ ["HUMAN", "human"],
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["XENOPUS", "xenopus"],
+ ["DROSOPHILA", "drosophila"],
+ ["YEAST", "yeast"],
+ ["ECOLI", "E.coli"],
+ ["SYNTHETIC", "synthetic"]
+ ],
+ "PROMOTER" : [
+ ["ENDOGENOUS", "endogenous"],
+ ["GAL1", "gal1"],
+ ["GALL", "galL"],
+ ["GALS", "galS"],
+ ["TET", "tet"],
+ ["ADH", "adh"],
+ ["CYC", "cyc"],
+ ["GPD", "gpd"],
+ ["DASH", "\"-\""],
+ ["CMV", "cmv"],
+ ["SV40", "SV40"],
+ ["TET_ON", "tet on"],
+ ["TET_OFF", "tet off"],
+ ["RIM1", "rim1"]
+ ],
+ "EXON_OR_THREE_PRIME" : [
+ ["EXON", "exon"],
+ ["3P", "3'"],
+ ["5P", "5'"]
+ ],
+ "SIRNA_SPECIES" : [
+ ["HUMAN", "Human"],
+ ["MOUSE", "Mouse'"],
+ ],
+ "SIRNA_COMPANY" : [
+ ["AMBION", "Ambion"],
+ ["DHARMACON", "Dharmacon'"],
+ ["INVITORGEN", "Invitrogen'"],
+ ["MICROSYNTH", "Microsynth'"],
+ ["QIAGEN", "Qiagen'"],
+ ["GIFT", "Gift'"]
+ ],
+ "SIRNA_FREEZER_LOCATION" : [
+ ["BIGLABFREEZER", "BigLab freezer"],
+ ["SMALLLAB_BIGFREEZER", "SmallLab Big freezer'"],
+ ["FREEZER_G17", "Freezer G17'"],
+ ["G93-FRANK", "G9.3--Frank'"],
+ ["FREEZER-G17_BOX_NATHALIE", "Freezer G17 Box Nathalie'"],
+ ["BOX-THIBAULT-BIGFREEZER-SMALLLAB", "Box thibault Big freezer small lab'"],
+ ["BOX-NATHALIE", "Box Nathalie'"]
+ ],
+ "TRANSFECTION_AGENT" : [
+ ["FUGENE", "Fugene"],
+ ["LIPOFECTAMINE", "Lipofectamine'"],
+ ["OLIGOFECTAMINE", "Oligofectamine'"],
+ ["RNAIMAX", "RNAimax'"]
+ ],
+ "FREEZER" : [
+ ["G9_FRIDGE-1", "G9 Fridge 1"],
+ ["G9_FRIDGE-2", "G9 Fridge 2"],
+ ["G9_FREEZER-A", "-20C Small Peter Lab"],
+ ["G9_FREEZER-B", "G9 Freezer B"],
+ ["G9_FREEZER-C", "G9 Freezer C"],
+ ["G10_FREEZER-D", "G10 Freezer D"],
+ ["G10_FREEZER-E", "G10 Freezer E"],
+ ["G10_FREEZER-F", "G10 Freezer F"],
+ ["G10_FREEZER-G", "G10 Freezer G"],
+ ["G10_FREEZER-H", "G10 Freezer H"],
+ ["G10_FREEZER-I", "G10 Freezer I"],
+ ["G10_FRIDGE-3", "+4C Big Peter Lab"],
+ ["G10_FRIDGE-4", "G10 Fridge 4"],
+ ["G10_FRIDGE-5", "G10 Fridge 5"],
+ ["G10_FRIDGE-6", "G10 Fridge 6"],
+ ["G10_FRIDGE-7", "G10 Fridge 7"],
+ ["G11_FRIDGE-8", "G10 Fridge 8"],
+ ["G14_FREEZER-J", "G14 Freezer J"],
+ ["G14_FREEZER-K", "G14 Freezer K"],
+ ["G14_FREEZER-L", "G14 Freezer L"],
+ ["G14_FREEZER-M", "G14 Freezer M"],
+ ["G14_FRIDGE-9", "G14 Fridge 9"],
+ ["G14_FRIDGE-10", "G14 Fridge 10"],
+ ["G17_FRIDGE-11", "G17 Fridge 11"],
+ ["G17_FRIDGE-12", "G17 Fridge 12"],
+ ["G17_FREEZER-N", "G17 Freezer N"],
+ ["USER_BENCH-20", "Bench -20�C"],
+ ["USER_BENCH-80", "Bench -80�C"],
+ ["USER_BENCH-RT", "Bench RT"],
+ ["USER_BENCH", "Bench"]
+ ],
+ "STORAGE_BOX_SIZE" : [
+ ["9X9", "9 x 9 box"],
+ ["5X5", "5 x 5 box"],
+ ["10X10", "10 x 10 box"],
+ ["10X12", "10 x 12 box"]
+ ],
+ }
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/FileMakerMain.java b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/FileMakerMain.java
new file mode 100644
index 0000000000000000000000000000000000000000..a2206338c1ccb79267396fbe2751fbb529304ab8
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/FileMakerMain.java
@@ -0,0 +1,77 @@
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+
+
+// STEP By Step:
+// 1. Open the file maker file with file maker pro
+// 2. Go to "File -> Sharing -> ODBC/JDBC" and turn sharing on
+// 3. You can go to see the names of the tables and field to "File -> Manage -> Database"
+// Without closing file maker pro you can run this script, modify it as needed
+// More info at http://www.filemaker.com/support/product/docs/fmp/fm11_odbc_jdbc_guide_en.pdf
+
+public class FileMakerMain
+{
+ // NOTE: FileMaker is so dump that you can't get the fileName and the fileData on the same query, the file data will return null, so we make a second call for this
+ public static final String GET_DOCUMENTS = "SELECT CAST(file AS VARCHAR(1000)) AS fileName, info, serial FROM documents";
+ public static final String GET_DOCUMENT_DATA = "SELECT GetAs(file, 'FILE') AS fileData FROM documents WHERE serial = ?";
+
+ static class Document {
+ String fileName;
+ String info;
+ String serial;
+
+ public String toString()
+ {
+ return fileName + " " + info;
+ }
+ }
+
+ public static List<Document> getDocuments(Connection connection) throws SQLException {
+ List<Document> documents = new ArrayList<Document>();
+ PreparedStatement preparedStatement = connection.prepareStatement(GET_DOCUMENTS);
+ ResultSet result = preparedStatement.executeQuery();
+
+ while(result.next()) {
+ Document document = new Document();
+ document.fileName = result.getString("fileName");
+ document.info = result.getString("info");
+ document.serial = result.getString("serial");
+ documents.add(document);
+ }
+ result.close();
+ preparedStatement.close();
+ return documents;
+ }
+
+ public static byte[] getFile(Connection connection, Document document) throws SQLException {
+ byte[] bytes = {};
+ PreparedStatement preparedStatement = connection.prepareStatement(GET_DOCUMENT_DATA);
+ preparedStatement.setString(1, document.serial);
+ ResultSet result = preparedStatement.executeQuery();
+ if(result.next()) {
+ byte[] value = result.getBytes("fileData");
+ if(value != null) {
+ bytes = value;
+ }
+ }
+ result.close();
+ preparedStatement.close();
+ return bytes;
+ }
+
+ public static void main(String[] args) throws Exception {
+ Class.forName("com.filemaker.jdbc.Driver").newInstance();
+ Connection connection = DriverManager.getConnection("jdbc:filemaker://127.0.0.1/BOXIT_documents_Peter.fmp12","designer", "seattle");
+
+ for(Document document: getDocuments(connection)) {
+ byte[] bytes = getFile(connection, document);
+ System.out.println(document + " " + bytes.length);
+ }
+ connection.close();
+ }
+}
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/fmjdbc.jar b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/fmjdbc.jar
new file mode 100644
index 0000000000000000000000000000000000000000..34cae1d60b916205b9039fe765c971229cef1a32
Binary files /dev/null and b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/lib/fmjdbc.jar differ
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/migration.py b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/migration.py
new file mode 100644
index 0000000000000000000000000000000000000000..44b497ae290427ddae7b09df68d7733f48e2bf63
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/migration.py
@@ -0,0 +1,657 @@
+# some_file.py
+import sys
+import definitions
+import definitionsVoc
+import re
+import random
+from datetime import datetime
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria, SearchSubCriteria
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+
+import java.lang.Class as Class
+import java.sql.DriverManager as DriverManager
+
+##
+## Generic Process Method
+##
+notMigratedEntities = {
+ "ENTITY_TYPE" : {"ENTITY ID" : {"ERROR" : "TIMES" }}
+ }
+
+def addNotMigratedEntity(type, entityID, error):
+ if type not in notMigratedEntities:
+ notMigratedEntities[type] = {}
+ if entityID not in notMigratedEntities[type]:
+ notMigratedEntities[type][entityID] = {}
+ if error not in notMigratedEntities[type][entityID]:
+ notMigratedEntities[type][entityID][error] = 1
+ else:
+ notMigratedEntities[type][entityID][error] += 1
+
+def printNotMigratedEntities():
+ print "--- Not Migrated Entities Report"
+ for type in notMigratedEntities:
+ print "Type: [" + str(type) + "]"
+ for id in notMigratedEntities[type]:
+ for error in notMigratedEntities[type][id]:
+ print "Id: [" + str(id) + "] Error: " + str(error) + " Times: " + str(notMigratedEntities[type][id][error])
+ print "---"
+
+def process(tr):
+ print "START!"
+ createDataHierarchy(tr)
+ for adaptor in adaptors:
+ print "- ADAPTOR [" + adaptor.__class__.__name__ + "] START"
+ while adaptor.next():
+ entity = adaptor.getEntity()
+ print "* ENTITY [" + str(entity.getIdentifier(tr)) + "]"
+ try:
+ if not entity.isInOpenBIS(tr):
+ entity.write(tr)
+ #print entity.getIdentifier(tr) + " - Updated"
+ else:
+ addNotMigratedEntity(adaptor.__class__.__name__, entity.getIdentifier(tr), "Already in openBIS")
+ except Exception, error:
+ addNotMigratedEntity(adaptor.__class__.__name__, entity.getIdentifier(tr), str(error.args))
+ #print entity.getIdentifier(tr) + " - Already up to date"
+ print "- ADAPTOR [" + adaptor.__class__.__name__ + "] FINISH"
+ print "REPORT START"
+ printNotMigratedEntities()
+ definitionsVoc.printCreatedTerms()
+ print "REPORT FINISH"
+ print "FINISH!"
+
+##
+## Help Methods
+##
+def setEntityProperties(tr, definition, entity, properties):
+ for propertyCode, propertyValue in properties.iteritems():
+ propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
+ if propertyValue is not None:
+ propertyValue = unicode(propertyValue)
+
+ if propertyDefinition is not None and propertyDefinition[3] == DataType.TIMESTAMP and propertyValue is not None:
+ date_val = datetime.strptime(propertyValue, "%Y")
+ propertyValue = datetime.strftime(date_val, "%Y-%m-%d")
+
+ if propertyDefinition is not None and propertyDefinition[3] == DataType.CONTROLLEDVOCABULARY and propertyValue is not None:
+ possiblePropertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel(propertyDefinition[4], propertyValue)
+ if possiblePropertyValue is not None:
+ propertyValue = possiblePropertyValue
+ else: #We rely on the Add Hock Terms if is None, since there is no API we create a new one
+ #Create new vocabulary term
+ codeToUse = re.sub(r'\W+','_',propertyValue)
+ labelToUse = propertyValue
+ if len(codeToUse) is 0:
+ codeToUse = "None" + str(random.random())
+ if len(codeToUse) > 60:
+ codeToUse = codeToUse[:50]
+ #Uses new vocabulary term
+ newTerm = definitionsVoc.createVocabularyTerm(tr, propertyDefinition[4], codeToUse, labelToUse)
+ propertyValue = newTerm.getCode()
+ print "* WARNING ENTITY [" + entity.getCode() + "]: for Vocabulary [" + propertyDefinition[4] + "], found value not in list: [" + repr(labelToUse) + "]. Created new term with code [" + codeToUse + "]"
+
+ if propertyDefinition is not None: #Sometimes special fields are added for other purposes, these should not be set
+ entity.setPropertyValue(propertyCode, propertyValue)
+
+##
+## Generic Pattern
+##
+class EntityAdaptor:
+ entities = None
+ entitiesIdx = None
+ definition = None
+
+ def init(self):
+ self.entities = []
+ self.entitiesIdx = -1
+ pass
+
+ def next(self):
+ if self.entities is None and self.entitiesIdx is None:
+ self.init()
+ self.entitiesIdx += 1
+ if len(self.entities) > self.entitiesIdx:
+ return True
+ else:
+ return False
+
+ def addEntity(self, values):
+ self.entities.append(OpenBISDTO(values, self.definition))
+
+ def getEntity(self):
+ return self.entities[self.entitiesIdx]
+
+class OpenBISDTO:
+ values = {}
+ definition = None
+
+ def __init__(self, values, definition):
+ self.values = values
+ self.definition = definition
+
+ def getIdentifier(self, tr):
+ pass
+
+ def isInOpenBIS(self, tr):
+ pass
+
+ def write(self, tr):
+ pass
+
+##
+## Costumer specific logic: generic part
+##
+experimentCache = {}
+sampleCache = {}
+sampleID2Sample = {}
+
+def getExperimentForUpdate(experimentIdentifier, experimentType, tr):
+ if experimentIdentifier not in experimentCache:
+ #print "Cache failed " + experimentIdentifier + ":" + str(experimentType)
+ experiment = tr.getExperimentForUpdate(experimentIdentifier)
+ if experiment is None and experimentType is not None:
+ #print "Cache Create " + experimentIdentifier + ":" + str(experimentType)
+ experiment = tr.createNewExperiment(experimentIdentifier, experimentType)
+ if experiment is not None:
+ experimentCache[experimentIdentifier] = experiment
+ else:
+ pass
+ #print "Cache hit " + experimentIdentifier + ":" + str(experimentType)
+ if experimentIdentifier not in experimentCache:
+ return None
+ else:
+ return experimentCache[experimentIdentifier]
+
+def getSampleForUpdate(sampleIdentifier, sampleType, tr):
+ if sampleIdentifier not in sampleCache:
+ #print "Cache failed " + sampleIdentifier + ":" + str(sampleType)
+ sample = tr.getSampleForUpdate(sampleIdentifier)
+ if sample is None and sampleType is not None:
+ #print "Cache Create " + sampleIdentifier + ":" + str(sampleType)
+ if sampleType == "ANTIBODY":
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/ANTIBODIES", sampleType, tr)
+ elif sampleType == "CELL":
+ experiment = getExperimentForUpdate("/MATERIALS/CELL_LINES/CELL_LINE_COLLECTION_1", sampleType, tr)
+ elif sampleType == "STRAIN":
+ experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION", sampleType, tr)
+ elif sampleType == "PLASMID":
+ experiment = getExperimentForUpdate("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", sampleType, tr)
+ elif sampleType == "CHEMICAL":
+ experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/CHEMICALS", sampleType, tr)
+ elif sampleType == "SIRNA":
+ experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/RNA_COLLECTION_1", sampleType, tr)
+ elif sampleType == "OLIGO":
+ experiment = getExperimentForUpdate("/MATERIALS/POLYNUCLEOTIDES/OLIGO_COLLECTION_1", sampleType, tr)
+ sample = tr.createNewSample(sampleIdentifier, sampleType)
+ sample.setExperiment(experiment)
+ if sample is not None:
+ sampleCache[sampleIdentifier] = sample
+ else:
+ pass
+ #print "Cache hit " + sampleIdentifier + ":" + str(sampleType)
+
+ if sampleIdentifier not in sampleCache:
+ return None
+ else:
+ return sampleCache[sampleIdentifier]
+
+class FileMakerEntityAdaptor(EntityAdaptor):
+ connection = None
+ selectQuery = None
+
+ def __init__(self, fileMakerConnString, fileMakerUser, fileMakerPass, db):
+ Class.forName("com.filemaker.jdbc.Driver").newInstance()
+ self.connection = DriverManager.getConnection(fileMakerConnString+db,fileMakerUser, fileMakerPass)
+
+ def init(self):
+ EntityAdaptor.init(self)
+
+ preparedStatement = self.connection.prepareStatement(self.selectQuery)
+ result = preparedStatement.executeQuery()
+
+ while result.next():
+ values = {}
+ for property in self.definition:
+ values[property[0]] = result.getString(property[2])
+ self.addEntity(values)
+ result.close()
+ preparedStatement.close()
+
+##
+## Customer specific logic: different sample types
+##
+class FMPeterOpenBISDTO(OpenBISDTO):
+ def isSampleCacheable(self):
+ return True
+
+ def isInOpenBIS(self, tr):
+ code = self.getIdentifier(tr)
+ if (code is not None) and (' ' not in code):
+ if self.isSampleCacheable():
+ sampleID2Sample[self.values["NAME"]] = self.values
+ sample = getSampleForUpdate("/MATERIALS/"+code, None, tr)
+ if sample is not None:
+ lastModificationData = self.values["MODIFICATION_DATE"].strip()
+ lastModificationData = str(datetime.strptime(lastModificationData, "%Y-%m-%d"))[:10]
+ lastModificationOpenBIS = sample.getPropertyValue("MODIFICATION_DATE")[:10]
+ return lastModificationOpenBIS == lastModificationData
+ else :
+ return False
+ else:
+ print "* ERROR [" + str(code) + "] - Invalid Code found for '" + self.__class__.__name__ + "'"
+ raise Exception('Invalid Code found ' + str(code))
+
+class FMPeterBoxAdaptor(FileMakerEntityAdaptor):
+ selectBoxQuery = None
+ entityIdFieldName = None
+ entityCodeFieldName = None
+
+ def addEntity(self, values):
+ self.entities.append(FMPeterEntityBoxOpenBISDTO(values, self.definition))
+
+ def init(self):
+ #print "Reading boxes for: " + self.__class__.__name__
+ emptyBox = 0
+ boxes = {}
+ EntityAdaptor.init(self)
+ preparedStatement = self.connection.prepareStatement(self.selectBoxQuery)
+ result = preparedStatement.executeQuery()
+ while result.next():
+ entityId = unicode(result.getString(self.entityIdFieldName))
+ if entityId is not None:
+ if entityId in sampleID2Sample:
+ antibodyNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
+ if antibodyNumber is not None:
+ values = {}
+ values["STORAGE_NAME"] = result.getString("location")
+ values["STORAGE_ROW"] = None
+ values["STORAGE_COLUMN"] = None
+ values["STORAGE_BOX_NAME"] = result.getString("box label")
+ values["STORAGE_BOX_SIZE"] = result.getString("box size")
+ values["STORAGE_USER"] = result.getString("frozen by")
+ values["STORAGE_BOX_POSITION"] = result.getString("position")
+
+ allBoxes = []
+ if antibodyNumber in boxes:
+ allBoxes = boxes[antibodyNumber]
+ else:
+ boxes[antibodyNumber] = allBoxes
+ allBoxes.append(values)
+ else:
+ #The antibody is not there. What the *#%$&
+ emptyBox += 1
+ else:
+ #The antibody is not there. What the *#%$&
+ emptyBox += 1
+
+ print "- ERROR ADAPTOR Boxes positions with empty entityId for " + self.__class__.__name__ + ":" + str(emptyBox)
+
+ for entiyCode, allBoxes in boxes.iteritems():
+ self.addEntity({
+ "*CODE" : entiyCode,
+ "*BOXESLIST" : allBoxes
+ })
+
+ result.close()
+ preparedStatement.close()
+
+class FMPeterEntityBoxOpenBISDTO(OpenBISDTO):
+ def getIdentifier(self, tr):
+ return self.values["*CODE"]
+
+ def write(self, tr):
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
+ print "* INFO Boxes size: " + str(len(self.values["*BOXESLIST"]))
+ #Delete old boxes
+ for boxNum in range(1, definitions.numberOfStorageGroups+1):
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
+ sample.setPropertyValue(propertyCode + "_" + str(boxNum), None)
+
+ #Add new boxes
+ boxNum = 0
+ for box in self.values["*BOXESLIST"]:
+ boxNum += 1
+ for propertyCode, propertyValue in box.iteritems():
+ if propertyCode == "STORAGE_NAME":
+ freezerName = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
+ if freezerName is None:
+ #print repr("NOT FOUND FEEZER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
+ propertyValue = None
+ else:
+ propertyValue = freezerName
+ if propertyCode == "STORAGE_USER":
+ storageUser = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("ALL_LAB_MEMBERS", propertyValue)
+ if storageUser is None:
+ #print repr("NOT FOUND USER: " + self.values["ANTIBODY_ID_NR"] + " : '" + unicode(propertyValue) + "'")
+ propertyValue = None
+ else:
+ propertyValue = storageUser
+
+ if propertyValue is not None:
+ propertyValue = unicode(propertyValue)
+ sample.setPropertyValue(propertyCode + "_" + str(boxNum), propertyValue)
+
+ def isBoxPressent(self, boxSignature, tr):
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
+ if sample is not None:
+ for boxNum in range(1, definitions.numberOfStorageGroups+1):
+ storedSignature = "";
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
+ propertyValue = sample.getPropertyValue(propertyCode + "_" + str(boxNum))
+ if propertyValue is not None:
+ propertyValue = unicode(propertyValue)
+ storedSignature += propertyValue
+ if storedSignature == boxSignature:
+ #print "Found Box " + storedSignature.encode('ascii', 'ignore')
+ return True
+ return False
+
+ def isInOpenBIS(self, tr):
+ for box in self.values["*BOXESLIST"]:
+ boxSignature = "";
+ for propertyCode in definitions.getStorageGroupPropertyCodes():
+ propertyValue = box[propertyCode]
+ if propertyCode == "STORAGE_NAME":
+ propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("FREEZER", propertyValue)
+ if propertyCode == "STORAGE_USER":
+ propertyValue = definitionsVoc.getVocabularyTermCodeForVocabularyAndTermLabel("LAB_MEMBERS_INITIALS", propertyValue)
+
+ if propertyValue is not None:
+ propertyValue = unicode(propertyValue)
+ boxSignature += propertyValue
+ if not self.isBoxPressent(boxSignature, tr):
+ return False
+ return True
+##
+## Antibodies
+##
+class AntibodyAdaptor(FileMakerEntityAdaptor):
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit antibodies\""
+ self.definition = definitions.antibodyDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(AntibodyOpenBISDTO(values, self.definition))
+
+class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ sample = getSampleForUpdate("/MATERIALS/"+self.values["ANTIBODY_ID_NR"],"ANTIBODY", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ return self.values["ANTIBODY_ID_NR"]
+
+class AntibodyBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"antibody boxes\""
+ entityIdFieldName = "antibody ID"
+ entityCodeFieldName = "ANTIBODY_ID_NR"
+
+##
+## Cells
+##
+class CellAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit cells\""
+ self.definition = definitions.cellDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(CellOpenBISDTO(values, self.definition))
+
+class CellOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ code = self.values["CELL_ID_NR_COPY"]
+ if code is not None and code.startswith("c_"):
+ sample = getSampleForUpdate("/MATERIALS/"+code,"CELL", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["CELL_ID_NR_COPY"]
+ return code
+
+class CellBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"cell boxes\""
+ entityIdFieldName = "cell ID"
+ entityCodeFieldName = "CELL_ID_NR_COPY"
+
+##
+## Strains
+##
+class StrainAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit strains\""
+ self.definition = definitions.strainDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(StrainOpenBISDTO(values, self.definition))
+
+class StrainOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ code = self.values["STRAIN_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["STRAIN_ID_NR"]
+ return code
+
+class StrainBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"strain boxes\""
+ entityIdFieldName = "strain ID"
+ entityCodeFieldName = "STRAIN_ID_NR"
+##
+## Plasmids
+##
+class PlasmidAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit plasmids\""
+ self.definition = definitions.plasmidDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(PlasmidOpenBISDTO(values, self.definition))
+
+class PlasmidOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ code = self.values["PLASMID_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["PLASMID_ID_NR"]
+ return code
+
+class PlasmidBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"plasmid boxes\""
+ entityIdFieldName = "plasmid ID"
+ entityCodeFieldName = "PLASMID_ID_NR"
+
+##
+## Oligos
+##
+class OligoAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"boxit oligos\""
+ self.definition = definitions.oligoDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(OligoOpenBISDTO(values, self.definition))
+
+class OligoOpenBISDTO(FMPeterOpenBISDTO):
+ def write(self, tr):
+ code = self.values["OLIGO_ID_NR"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"OLIGO", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = self.values["OLIGO_ID_NR"]
+ return code
+
+class OligoBoxAdaptor(FMPeterBoxAdaptor):
+ selectBoxQuery = "SELECT * FROM \"oligo boxes\""
+ entityIdFieldName = "oligo ID"
+ entityCodeFieldName = "OLIGO_ID_NR"
+
+##
+## Chemical
+##
+class ChemicalAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"Chemicals\""
+ self.definition = definitions.chemicalDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(ChemicalOpenBISDTO(values, self.definition))
+
+class ChemicalOpenBISDTO(FMPeterOpenBISDTO):
+ def isSampleCacheable(self):
+ return False
+
+ def write(self, tr):
+ code = "CHEM_" + self.values["RECORD_NUMBER"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"CHEMICAL", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = "CHEM_" + self.values["RECORD_NUMBER"]
+ return code
+
+##
+## Sirna
+##
+class SirnaAdaptor(FileMakerEntityAdaptor):
+ def init(self):
+ self.selectQuery = "SELECT * FROM \"siRNA\""
+ self.definition = definitions.siRNADefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ self.entities.append(SirnaOpenBISDTO(values, self.definition))
+
+class SirnaOpenBISDTO(FMPeterOpenBISDTO):
+ def isSampleCacheable(self):
+ return False
+
+ def write(self, tr):
+ code = "SI_" + self.values["SIRNA_OLIGONUMBER"]
+ if code is not None:
+ sample = getSampleForUpdate("/MATERIALS/"+code,"SIRNA", tr)
+ setEntityProperties(tr, self.definition, sample, self.values);
+
+ def getIdentifier(self, tr):
+ code = "SI_" +self.values["SIRNA_OLIGONUMBER"]
+ return code
+
+##
+## Documents
+##
+class DocumentsAdaptor(FileMakerEntityAdaptor):
+
+ def init(self):
+ self.selectQuery = "SELECT CAST(file AS VARCHAR(1000)) AS file, info, id_nr, serial, \"date created\", \"date modified\" FROM documents"
+ self.definition = definitions.documentDefinition
+ FileMakerEntityAdaptor.init(self)
+
+ def addEntity(self, values):
+ preparedStatement = self.connection.prepareStatement("SELECT GetAs(file, 'FILE') AS fileData FROM documents WHERE serial = ?");
+ preparedStatement.setString(1, values["SERIAL"]);
+ result = preparedStatement.executeQuery();
+
+ if result.next():
+ fileData = result.getBytes("fileData");
+ values["*DATA"] = fileData
+
+ self.entities.append(DocumentOpenBISDTO(values, self.definition))
+
+class DocumentOpenBISDTO(OpenBISDTO):
+ def write(self, tr):
+ sampleIdentifier = "/MATERIALS/"+self.values["ID_NR"];
+ dataSetSample = getSampleForUpdate(sampleIdentifier, None, tr)
+ if dataSetSample is not None and self.values["*DATA"] is not None and self.values["FILE"] is not None:
+ print "* INFO DATASET CREATION FOR SERIAL " + self.values["SERIAL"] + " WITH FILE " + self.values["FILE"]
+ dataSet = tr.createNewDataSet("DOCUMENT")
+ dataSet.setSample(dataSetSample)
+ setEntityProperties(tr, self.definition, dataSet, self.values)
+ absolutePath = tr.createNewFile(dataSet, self.values["FILE"].replace("/", "_"))
+ f = open(absolutePath, 'wb')
+ f.write(self.values["*DATA"])
+ f.close()
+ #incoming = tr.getIncoming()
+ #tr.moveFile(incoming.getAbsolutePath(), dataSet)
+ else:
+ if dataSetSample is None:
+ print "* ERROR No sample found for document"
+ raise Exception('No sample found for document')
+ if self.values["*DATA"] is None:
+ print "* ERROR No Data found for file"
+ raise Exception('No Data found for file')
+ if self.values["FILE"] is None:
+ print "* ERROR No file name found for file"
+ raise Exception('No file name found for file')
+
+ def getIdentifier(self, tr):
+ return self.values["SERIAL"]
+
+ def getDocumentBySerial(self, tr, serial):
+ criteria = SearchCriteria()
+ criteria.setOperator(criteria.SearchOperator.MATCH_ANY_CLAUSES)
+ criteria.addMatchClause(criteria.MatchClause.createAttributeMatch(criteria.MatchClauseAttribute.TYPE, "DOCUMENT"))
+ criteria.addMatchClause(criteria.MatchClause.createPropertyMatch("SERIAL", serial))
+ datasets = tr.getSearchService().searchForDataSets(criteria)
+ if datasets:
+ return datasets[0]
+ else:
+ return None
+
+ def isInOpenBIS(self, tr):
+ dataset = self.getDocumentBySerial(tr, self.values["SERIAL"])
+ return dataset is not None
+
+#fmConnString = "jdbc:filemaker://127.0.0.1/"
+fmConnString = "jdbc:filemaker://fm.ethz.ch/"
+fmUser= "designer"
+fmPass = "seattle"
+
+adaptors = [
+ AntibodyAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibodies_Peter"),
+ AntibodyBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_antibody_boxes_Peter"),
+ PlasmidAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmids_Peter"),
+ PlasmidBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_plasmid_boxes_Peter"),
+ StrainAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strains_Peter"),
+ StrainBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_strain_boxes_Peter"),
+ OligoAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligos_Peter"),
+ OligoBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_oligo_boxes_Peter"),
+ CellAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cells_Peter"),
+ CellBoxAdaptor(fmConnString, fmUser, fmPass, "BOXIT_cell_boxes_Peter"),
+ SirnaAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
+ ChemicalAdaptor(fmConnString, fmUser, fmPass, "BOXIT_Main_Menu_Peter"),
+ DocumentsAdaptor(fmConnString, fmUser, fmPass, "BOXIT_documents_Peter")
+ ]
+
+
+
+def createDataHierarchy(tr):
+ inventorySpace = tr.getSpace("MATERIALS")
+ if inventorySpace == None:
+ tr.createNewSpace("MATERIALS", None)
+ tr.createNewProject("/MATERIALS/REAGENTS")
+ tr.createNewProject("/MATERIALS/CELL_LINES")
+ tr.createNewProject("/MATERIALS/POLYNUCLEOTIDES")
+ tr.createNewProject("/MATERIALS/PLASMIDS")
+ tr.createNewProject("/MATERIALS/YEASTS")
+
+
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/plugin.properties b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..54f2044ddda7bb67c827931911974a3ed40540c7
--- /dev/null
+++ b/plasmid/source/core-plugins/petermigration/2/dss/drop-boxes/petermigration/plugin.properties
@@ -0,0 +1,9 @@
+##
+## Defaults
+##
+incoming-data-completeness-condition = auto-detection
+top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2
+storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+script-path = migration.py
+dropbox-name = petermigration
+incoming-dir = ${root-dir}/petermigration
\ No newline at end of file