From a019565abd89674bb6657f5449954cc2690d4161 Mon Sep 17 00:00:00 2001
From: barillac <barillac>
Date: Thu, 18 Jun 2015 14:46:39 +0000
Subject: [PATCH] experimental step + vocabularies + annotations_state added
SVN: 34215
---
.../weismigration/1/as/definitions.py | 25 +-
.../weismigration/1/as/definitionsVoc.py | 602 +-----------------
.../1/as/initialize-master-data.py | 24 +-
3 files changed, 63 insertions(+), 588 deletions(-)
diff --git a/plasmid/source/core-plugins/weismigration/1/as/definitions.py b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
index 24270a4b371..5674e9f144c 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/definitions.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/definitions.py
@@ -80,7 +80,7 @@ antibodyDefinition = [
["BOX", "General", "Box", DataType.VARCHAR, None, "", None, None, False],
["EMPTY", "General", "empty?", DataType.VARCHAR, None, "", None, None, False],
["CATALOG_NUM", "General", "Catalog#", DataType.VARCHAR, None, "", None, None, False]
-
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
@@ -99,7 +99,7 @@ strainDefinition = [
["REMOVED", "General", "removed", DataType.VARCHAR, None, "", None, None, False],
["UNMARKED_MUTATIONS", "General", "unmarked mutations", DataType.VARCHAR, None, "", None, None, False],
["WHO_ENTERED", "General", "who entered", DataType.VARCHAR, None, "", None, None, False]
-
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
oligoDefinition = [
@@ -135,6 +135,7 @@ oligoDefinition = [
["CATEGORY", "General", "category", DataType.CONTROLLEDVOCABULARY, "OLIGO_CATEGORY", "", None, None, False],
["REORDERED", "General", "Reordered", DataType.VARCHAR, None, "", None, None, False],
["NOTES", "Comments", "Notes", DataType.VARCHAR, None, "", None, None, False]
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
plasmidDefinition = [
@@ -165,6 +166,7 @@ plasmidDefinition = [
["SIZE_PARENT", "General", "Size parent", DataType.REAL, None, "", None, None, False],
["VECTOR", "General", "Vector", DataType.VARCHAR, None, "", None, None, False],
["VECTOR_TYPE", "General", "Vector Type", DataType.VARCHAR, None, "", None, None, False]
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
chemicalDefinition = [
@@ -181,6 +183,7 @@ chemicalDefinition = [
["USED_BY", "General", "used by", DataType.VARCHAR, None, "", None, None, False],
["LOCATION", "Storage", "Location", DataType.VARCHAR, None, "", None, None, False],
["COMMENTS", "Comments", "Comments", DataType.VARCHAR, None, "", None, None, False],
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
RestrictionEnzymeDefinition = [
@@ -188,7 +191,21 @@ RestrictionEnzymeDefinition = [
["BLOCK", "Storage", "Block", DataType.VARCHAR, None, "", None, None, False],
["POSITION", "Storage", "Position", DataType.VARCHAR, None, "", None, None, False],
["COMMENT", "Comments", "Comment", DataType.VARCHAR, None, "", None, None, False]
-
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
];
-
+ExperimentalStepDefinition= [
+ ["NAME", "General", "Name", DataType.MULTILINE_VARCHAR, None, "Name", None, None],
+ ["OWNER", "General", "Owner", DataType.CONTROLLEDVOCABULARY, "LAB_MEMBERS", "Who produced/owned the sample", None, None],
+ ["EXPERIMENTAL_GOALS", "General", "Experimental Goals", DataType.MULTILINE_VARCHAR, None, "Goal of the experiment", None, None],
+ ["EXPERIMENTAL_RESULTS", "General", "Experimental Results", DataType.MULTILINE_VARCHAR, None, "Brief summary of the results obtained", None, None],
+ ["START_DATE", "General", "Start date", DataType.TIMESTAMP, None, "Date when the experimental step is started", None, None],
+ ["END_DATE", "General", "End date", DataType.TIMESTAMP, None, "Date when the experimental step is completed", None, None],
+ ["EXPERIMENTAL_READOUT", "Readout details", "Experimental readout", DataType.CONTROLLEDVOCABULARY, "EXPERIMENTAL_READOUT", "Experimental readout used in the experiment", None, None],
+ ["MACHINE", "Readout details", "Machine", DataType.CONTROLLEDVOCABULARY, "MACHINE", "Machine used to perform the experiment", None, None],
+ ["FREEFORM_TABLE_STATE", "Readout details", "Freeform Table State", DataType.MULTILINE_VARCHAR, None, "Table describing how the order of samples measured in the experiments", None, None],
+ ["PUBLICATION", "Comments", "Publication", DataType.MULTILINE_VARCHAR, None, "Publication from where the information was first found OR technical sheet given by the manufacturer", None, None],
+ ["NOTES", "Comments", "Notes", DataType.MULTILINE_VARCHAR, None, "Notes", None, None],
+ ["XMLCOMMENTS", "Comments", "Comments List", DataType.XML, None, "Several comments can be added by different users", commentsSampleScriptName, None],
+ ["ANNOTATIONS_STATE", "Comments", "Annotations State", DataType.XML, None, "Annotations State", annotationsScriptName, None]
+];
diff --git a/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py b/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
index 90660044107..a8a1f718bf1 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/definitionsVoc.py
@@ -148,582 +148,28 @@ vocabularyDefinitions = {
"OLIGO_TYPE" : [
["DNA", "DNA"]
],
-
-
-
- # "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" : [
- ["BENCH-20", "Bench -20�C"],
- ["BENCH-80", "Bench -80�C"],
- ["BENCH-RT", "Bench RT"],
- ["BENCH", "Bench"]
- ]
+ "EXPERIMENTAL_READOUT":
+ [
+ ["FLOW_CYTOMETRY", "flow citometry", None],
+ ["SORTING", "cell sorting", None],
+ ["GROWTH", "growth", None],
+ ["WESTERN_BLOTTING", "western blotting", None],
+ ["RT_QPCR", "RT-qPCR", None]
+ ],
+ "MACHINE":
+ [
+ ["LSRII_FORTESSA", "SRII Fortessa", None],
+ ["TECAN_READER", "Tecan reader", None],
+ ["BIOLECTOR", "BioLector", None],
+ ["LICOR_ODYSSEY", "LI-COR Odyssey", None],
+ ["TI_ECLIPSE", "TI Eclipse (Nikon)", None],
+ ["SRX_101A", "Konica Minolta SRX-101A", None],
+ ["LIGHT_CYCLER", "LightCycler 480", None]
+ ],
+ "FREEZER" : [
+ ["BENCH-20", "Bench -20�C"],
+ ["BENCH-80", "Bench -80�C"],
+ ["BENCH-RT", "Bench RT"],
+ ["BENCH", "Bench"]
+ ]
}
\ No newline at end of file
diff --git a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
index ec023c777a3..a9763c5223d 100644
--- a/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/weismigration/1/as/initialize-master-data.py
@@ -147,13 +147,25 @@ commentsScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "comments.py",
-thymidineScript = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "thymidine_count.py",
- definitions.thymidineScriptName,
- "Count number of thymidine in sequence",
+gcScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "gc.py",
+ definitions.gcScriptName,
+ "Count percentage of G and C in sequence",
"DYNAMIC_PROPERTY",
"SAMPLE");
+atScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "at.py",
+ definitions.atScriptName,
+ "Count percentage of A and T in sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
+
+
+lengthScriptName = createScript(PATH_TO_MANAGE_PROPERTIES_SCRIPTS + "length.py",
+ definitions.lengthScriptName,
+ "Count length sequence",
+ "DYNAMIC_PROPERTY",
+ "SAMPLE");
##
## Vocabulary Types
##
@@ -171,11 +183,11 @@ createExperimentTypeWithProperties("METHOD", "FOLDER FOR ORGANIZING METHODS SAMP
##
## Sample Types
##
-#createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
+createSampleTypeWithProperties("ANTIBODY", "", definitions.antibodyDefinition);
#addStorageGroups(definitions.numberOfStorageGroups, "ANTIBODY");
-# createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
+createSampleTypeWithProperties("STRAIN", "", definitions.strainDefinition);
# addStorageGroups(definitions.numberOfStorageGroups, "STRAIN");
-# createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
+createSampleTypeWithProperties("PLASMID", "", definitions.plasmidDefinition);
# addStorageGroups(definitions.numberOfStorageGroups, "PLASMID");
createSampleTypeWithProperties("OLIGO", "", definitions.oligoDefinition);
createSampleTypeWithProperties("CHEMICAL", "", definitions.chemicalDefinition);
--
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