diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitions.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitions.py
deleted file mode 120000
index 7c34540377aa3237514f65a3e6bb1ba8771db965..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitions.py
+++ /dev/null
@@ -1 +0,0 @@
-/Users/barillac/openbis-weis/servers/core-plugins/weismigration/1/as/definitions.py
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitionsVoc.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitionsVoc.py
deleted file mode 120000
index 3c701d72a254d0853e45059e9ea8984e1af5060c..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/definitionsVoc.py
+++ /dev/null
@@ -1 +0,0 @@
-/Users/barillac/openbis-weis/servers/core-plugins/weismigration/1/as/definitionsVoc.py
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitions.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitions.py
deleted file mode 100644
index 67f4986e22a26dc0aed0b7262676b19cb2e559b2..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitions.py
+++ /dev/null
@@ -1,374 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
-
-#
-# Helper Methods
-#
-def getPropertyDefinitionByCode(definition, code):
- for property in definition:
- if property[0] == code:
- return property
- return None
-
-#
-# Scripts
-#
-commentsScriptName = "COMMENTS";
-adenosineScriptName = "ADENOSINE_COUNT"
-cytosineScriptName= "CYTOSINE_COUNT"
-gcScriptName= "GC"
-guanosineScriptName= "GUANOSINE_COUNT"
-lengthScriptName= "SEQUENCE_LENGTH"
-nucelotideScriptName= "ONUCLEOTIDE_COUNT"
-thymidineScriptName= "THYMIDINE_COUNT"
-tmScriptName= "TM"
-
-#
-# Storage
-#
-numberOfStorageGroups = 65
-
-def getStorageGroupPropertyCodes():
- propertyCodes = [];
- for property in getStorageGroupDefinition():
- propertyCodes.append(property[0]);
- return propertyCodes;
-
-def getStorageGroupDefinition():
- return [
- ["STORAGE_NAME", "Physical Storage", "location", DataType.CONTROLLEDVOCABULARY, "FREEZER", "Storage Name", None, None, False],
- ["STORAGE_ROW", "Physical Storage", "Storage Row", DataType.INTEGER, None, "Storage Row", None, None, False],
- ["STORAGE_COLUMN", "Physical Storage", "Storage Column", DataType.INTEGER, None, "Storage Column", None, None, False],
- ["STORAGE_BOX_NAME", "Physical Storage", "box label", DataType.VARCHAR, None, "Storage Box Name", None, None, False],
- ["STORAGE_USER", "Physical Storage", "frozen by", DataType.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/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitionsVoc.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitionsVoc.py
deleted file mode 100644
index 83fc17f19b34ba3d65064d86fb5089432afbf91c..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/defs/definitionsVoc.py
+++ /dev/null
@@ -1,846 +0,0 @@
-#!/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"]
- ]
- }
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/doc/fm11_odbc_jdbc_guide_en.pdf b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/doc/fm11_odbc_jdbc_guide_en.pdf
deleted file mode 100644
index 36aaa0f12220dbde26b7ece4e3b78914087893b0..0000000000000000000000000000000000000000
Binary files a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/doc/fm11_odbc_jdbc_guide_en.pdf and /dev/null differ
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/lib/FileMakerMain.java b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/lib/FileMakerMain.java
deleted file mode 100644
index a2206338c1ccb79267396fbe2751fbb529304ab8..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/lib/FileMakerMain.java
+++ /dev/null
@@ -1,77 +0,0 @@
-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/weismigration/1/dss/drop-boxes copy/weismigration/lib/fmjdbc.jar b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/lib/fmjdbc.jar
deleted file mode 100644
index 34cae1d60b916205b9039fe765c971229cef1a32..0000000000000000000000000000000000000000
Binary files a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/lib/fmjdbc.jar and /dev/null differ
diff --git a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/migration.py b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/migration.py
deleted file mode 100644
index f5a3da472f05ce2c13b0cd4b5d35d4351eafa910..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/migration.py
+++ /dev/null
@@ -1,647 +0,0 @@
-# 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.REAL and propertyValue is not None:
- if propertyValue =="?":
- propertyValue=""
-
- 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
- print "EXISTING VALUE:", propertyValue
- else:
- print "MISSING VALUE FOR:", propertyValue
-
- if propertyDefinition is not None: #Sometimes special fields are added for other purposes, these should not be set
- if propertyDefinition[0] =="COMPANY":
- if propertyValue == "Sgmal-Aldrich":
- entity.setPropertyValue("COMPANY", "SIGMA-ALDRICH")
- elif propertyValue =="fluka":
- entity.setPropertyValue("COMPANY", "FLUKA")
- elif propertyValue =="Bio rad":
- entity.setPropertyValue("COMPANY", "BIO-RAD")
- elif propertyValue =="merk":
- entity.setPropertyValue("COMPANY", "MERCK")
- elif propertyValue =="JT Baker":
- entity.setPropertyValue("COMPANY", "JTBAKER")
- elif propertyValue =="Sigma":
- entity.setPropertyValue("COMPANY", "SIGMA-ALDRICH")
- elif propertyValue =="sigma":
- entity.setPropertyValue("COMPANY", "SIGMA-ALDRICH")
- elif propertyValue =="BioChemica":
- entity.setPropertyValue("COMPANY", "BIOCHEMICA")
- elif propertyValue =="molecular Probes":
- entity.setPropertyValue("COMPANY", "MOLECULAR_PROBES")
- elif propertyValue =="SIGMA":
- entity.setPropertyValue("COMPANY", "SIGMA-ALDRICH")
- elif propertyValue =="Invitrogen\r\r\r":
- entity.setPropertyValue("COMPANY", "INVITROGEN")
- elif propertyValue =="Sigma Aldrich":
- entity.setPropertyValue("COMPANY", "SIGMA-ALDRICH")
- elif propertyValue =="pierce":
- entity.setPropertyValue("COMPANY", "PIERCE")
- elif propertyValue =="Merck":
- entity.setPropertyValue("COMPANY", "MERCK")
- elif propertyValue =="calbiochem":
- entity.setPropertyValue("COMPANY", "CALBIOCHEM")
- elif propertyValue =="Biorad":
- entity.setPropertyValue("COMPANY", "BIO-RAD")
- elif propertyValue =="bd":
- entity.setPropertyValue("COMPANY", "BD")
- elif propertyValue =="AppliChem":
- entity.setPropertyValue("COMPANY", "APPLICHEM")
- elif propertyValue =="?":
- entity.setPropertyValue("COMPANY", "UNKNOWN")
- else:
- entity.setPropertyValue("COMPANY", propertyValue)
- else:
- entity.setPropertyValue(propertyCode, propertyValue)
-
-
-
-
-
-def setPlasmidParents(tr, definition, entity, properties):
- for propertyCode, propertyValue in properties.iteritems():
-
- propertyDefinition = definitions.getPropertyDefinitionByCode(definition, propertyCode)
- if propertyValue is not None and propertyDefinition[0] == "PCR_3_OLIGO" or propertyDefinition[0] == "PCR_5_OLIGO":
- propertyValue = unicode(propertyValue)
- print "PROP_PARENTS", propertyDefinition[0], propertyValue
- if re.match ("UC# ", propertyValue) and not re.search("/", propertyValue):
- parentCode = "/MATERIALS/"+ propertyValue.replace("UC# ", "US").strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- elif re.match ("UC#", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC#", "US").strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- elif re.match ("UC #", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC #", "US").strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- elif re.match ("UC ", propertyValue) and not re.search("/", propertyValue):
- parentCode="/MATERIALS/"+ propertyValue.replace("UC ", "US").strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- elif re.match ("UC", propertyValue) and not re.search("/", propertyValue):
- parentCode= "/MATERIALS/"+ propertyValue.replace("UC", "US").strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- elif re.match ("CH", propertyValue):
- parentCode="/MATERIALS/"+ propertyValue.strip(" ")
- currentParentsList = entity.getParentSampleIdentifiers()
- currentParentsList.add(parentCode)
- entity.setParentSampleIdentifiers(currentParentsList)
- else:
- print "NO PARENT WAS SET FOR THIS FOUND VALUE:", 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):
- experimentType ="MATERIAL"
- 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 == "STRAIN":
- experiment = getExperimentForUpdate("/MATERIALS/YEASTS/YEAST_COLLECTION_1", 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 == "RESTRICTION_ENZYME":
- experiment = getExperimentForUpdate("/MATERIALS/REAGENTS/RESTRICTION_ENZYMES", 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:
- if property[0]=="ANNOTATIONS_STATE":
- values[property[0]] =""
- else:
- 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 FMPeterMultipleValuesAdaptor(FileMakerEntityAdaptor):
- selectMultipleValuesQuery = None
- entityIdFieldName = None
- entityCodeFieldName = None
-
- def addEntity(self, values):
- self.entities.append(FMPeterEntityMultipleValuesOpenBISDTO(values, self.definition))
-
- def init(self):
- print "Reading MultipleValueses for: " + self.__class__.__name__
- emptyMultipleValues = 0
- MultipleValueses = {}
- EntityAdaptor.init(self)
- preparedStatement = self.connection.prepareStatement(self.selectMultipleValuesQuery)
- result = preparedStatement.executeQuery()
- while result.next():
- entityId = unicode(result.getString(self.entityIdFieldName))
- if entityId is not None:
- if entityId in sampleID2Sample:
- entityNumber = sampleID2Sample[entityId][self.entityCodeFieldName]
- if entityNumber is not None:
- values = {}
- values["DISRUPTIONS"] = result.getString("disruptions")
- values["MARKERS"] = result.getString("markers")
- values["UNMARKED_MUTATIONS"] = result.getString("unmarked mutations")
-
-
- allMultipleValueses = []
- if entityNumber in MultipleValueses:
- allMultipleValueses = MultipleValueses[entityNumber]
- else:
- MultipleValueses[entityNumber] = allMultipleValueses
- allMultipleValueses.append(values)
- else:
- #The entity is not there. What the *#%$&
- emptyMultipleValues += 1
- else:
- #The entity is not there. What the *#%$&
- emptyMultipleValues += 1
-
- print "- ERROR ADAPTOR MultipleValueses positions with empty entityId for " + self.__class__.__name__ + ":" + str(emptyMultipleValues)
-
- for entiyCode, allMultipleValueses in MultipleValueses.iteritems():
- self.addEntity({
- "*CODE" : entiyCode,
- "*MultipleValuesESLIST" : allMultipleValueses
- })
-
- result.close()
- preparedStatement.close()
-
-class FMPeterEntityMultipleValuesOpenBISDTO(OpenBISDTO):
- def getIdentifier(self, tr):
- return self.values["*CODE"]
-
- def write(self, tr):
- sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
- print "* INFO MultipleValueses size: " + str(len(self.values["*MultipleValuesESLIST"]))
- #Delete old MultipleValueses
- for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
- for propertyCode in definitions.getRepetitionPropertyCodes():
- sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), None)
-
-
- #Add new MultipleValueses
- MultipleValuesNum = 0
- for MultipleValues in self.values["*MultipleValuesESLIST"]:
- MultipleValuesNum += 1
- for propertyCode, propertyValue in MultipleValues.iteritems():
-
- if propertyValue is not None:
- propertyValue = unicode(propertyValue)
- print "PROPCODE", propertyCode, str(MultipleValuesNum), propertyValue
- sample.setPropertyValue(propertyCode + "_" + str(MultipleValuesNum), propertyValue)
-
- def isMultipleValuesPressent(self, MultipleValuesSignature, tr):
- sample = getSampleForUpdate("/MATERIALS/"+self.values["*CODE"], None, tr)
- if sample is not None:
- for MultipleValuesNum in range(1, definitions.numberOfRepetitions+1):
- storedSignature = "";
- for propertyCode in definitions.getRepetitionPropertyCodes():
- propertyValue = sample.getPropertyValue(propertyCode + "_" + str(MultipleValuesNum))
- print propertyCode+ "_" + str(MultipleValuesNum), propertyValue
- if propertyValue is not None:
- propertyValue = unicode(propertyValue)
- storedSignature += propertyValue
- if storedSignature == MultipleValuesSignature:
- #print "Found MultipleValues " + storedSignature.encode('ascii', 'ignore')
- return True
- return False
-
- def isInOpenBIS(self, tr):
- for MultipleValues in self.values["*MultipleValuesESLIST"]:
- MultipleValuesSignature = "";
- for propertyCode in definitions.getRepetitionPropertyCodes():
- propertyValue = MultipleValues[propertyCode]
-
- if propertyValue is not None:
- propertyValue = unicode(propertyValue)
- MultipleValuesSignature += propertyValue
- if not self.isMultipleValuesPressent(MultipleValuesSignature, tr):
- return False
- return True
-##
-## Antibodies
-##
-
-class AntibodyAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"Weis Lab Antibodies\""
- self.definition = definitions.antibodyDefinition
- FileMakerEntityAdaptor.init(self)
-
- def addEntity(self, values):
- self.entities.append(AntibodyOpenBISDTO(values, self.definition))
-
-
-class AntibodyOpenBISDTO(FMPeterOpenBISDTO):
- def isSampleCacheable(self):
- return False
-
- def write(self, tr):
- code = "AB_" + self.values["REF_NUM"]
- if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"ANTIBODY", tr)
- setEntityProperties(tr, self.definition, sample, self.values);
-
- def getIdentifier(self, tr):
- code = "AB_"+ self.values["REF_NUM"]
- return code
-
-
-
-##
-## Strains
-##
-class StrainAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"Weis Lab Yeast 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["NAME"]
- if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"STRAIN", tr)
- setEntityProperties(tr, self.definition, sample, self.values)
- print setEntityProperties(tr, self.definition, sample, self.values)
-
- def getIdentifier(self, tr):
- code = self.values["NAME"]
- return code
-
-class StrainMultipleValuesAdaptor(FMPeterMultipleValuesAdaptor):
- selectMultipleValuesQuery = "SELECT * FROM \"Weis Lab Yeast Strains\""
- entityIdFieldName = "KWY number"
- entityCodeFieldName = "NAME"
-##
-## Plasmids
-##
-class PlasmidAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"Weis Lab 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 = "PKW" + self.values["NAME"]
- if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"PLASMID", tr)
- setEntityProperties(tr, self.definition, sample, self.values)
- setPlasmidParents(tr, self.definition, sample, self.values)
- print "SETPARENTS", setPlasmidParents(tr, self.definition, sample, self.values)
-
- def getIdentifier(self, tr):
- code = "PKW" +self.values["NAME"]
- return code
-
-
-
-##
-## Oligos
-##
-class OligoAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"WLO\""
- 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["NAME"]
- 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["NAME"]
- return code
-
-
-
-##
-## Chemical
-##
-class ChemicalAdaptor(FileMakerEntityAdaptor):
-
- def init(self):
- self.selectQuery = "SELECT * FROM \"Table\""
- 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["ID"]
- 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["ID"]
- return code
-
-##
-## Restriction enzymes
-##
-class EnzymeAdaptor(FileMakerEntityAdaptor):
- def init(self):
- self.selectQuery = "SELECT * FROM \"Restriction_Enzymes\""
- self.definition = definitions.RestrictionEnzymeDefinition
- FileMakerEntityAdaptor.init(self)
-
- def addEntity(self, values):
- self.entities.append(EnzymeOpenBISDTO(values, self.definition))
-
-class EnzymeOpenBISDTO(FMPeterOpenBISDTO):
- def isSampleCacheable(self):
- return False
-
- def write(self, tr):
- code = self.values["NAME"]
-
- if code is not None:
- sample = getSampleForUpdate("/MATERIALS/"+code,"RESTRICTION_ENZYME", tr)
- setEntityProperties(tr, self.definition, sample, self.values);
-
- def getIdentifier(self, tr):
- code = self.values["NAME"]
- return code
-
-
-
-fmConnString = "jdbc:filemaker://127.0.0.1/"
-#fmConnString = "jdbc:filemaker://fmsrv.ethz.ch/"
-fmUser= "admin"
-fmPass = "nucleus"
-
-# adaptors = [ AntibodyAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibodies_Peter"),
-# AntibodyMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_antibody_MultipleValueses_Peter"),
-# PlasmidAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmids_Peter"),
-# PlasmidMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_plasmid_MultipleValueses_Peter"),
-# StrainAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strains_Peter"),
-# StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_strain_MultipleValueses_Peter"),
-# OligoAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligos_Peter"),
-# OligoMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_oligo_MultipleValueses_Peter"),
-# CellAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cells_Peter"),
-# CellMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_cell_MultipleValueses_Peter"),
-# SirnaAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
-# ChemicalAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_Main_Menu_Peter"),
-# DocumentsAdaptor(fmConnString, fmUser, fmPass, "MultipleValuesIT_documents_Peter")]
-
-
-
-adaptors = [
- #EnzymeAdaptor(fmConnString, fmUser, fmPass, "Weis_Restriction_enzymes")
- #ChemicalAdaptor(fmConnString, fmUser, fmPass, "Weis_Chemicals")
- #OligoAdaptor(fmConnString, fmUser, fmPass, "Weis_Oligos"),
- #AntibodyAdaptor(fmConnString, fmUser, fmPass, "Weis _Antibodies")
- #PlasmidAdaptor(fmConnString, fmUser, fmPass, "Weis_Plasmids")
- StrainAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains"),
- StrainMultipleValuesAdaptor(fmConnString, fmUser, fmPass, "Weis_Yeast_Strains")
- ]
-
-
-def createDataHierarchy(tr):
- inventorySpace = tr.getSpace("MATERIALS")
- if inventorySpace == None:
- tr.createNewSpace("MATERIALS", None)
- tr.createNewProject("/MATERIALS/REAGENTS")
- 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/weismigration/1/dss/drop-boxes copy/weismigration/plugin.properties b/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/plugin.properties
deleted file mode 100644
index 238e3eb903c49960826af70ba5a6983b7836c480..0000000000000000000000000000000000000000
--- a/plasmid/source/core-plugins/weismigration/1/dss/drop-boxes copy/weismigration/plugin.properties
+++ /dev/null
@@ -1,9 +0,0 @@
-##
-## 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 = weismigration
-incoming-dir = ${root-dir}/weismigration
\ No newline at end of file