From 4cfcdbcd23242fd7a10f6408b0c91cf2ea4b2463 Mon Sep 17 00:00:00 2001
From: juanf <juanf>
Date: Mon, 3 Nov 2014 16:00:10 +0000
Subject: [PATCH] SSDM-1078 : PAPER - Provide sensible defaults -
Implementation
SVN: 32710
---
.../newbrowser/1/as/initialize-master-data.py | 382 +++++++++++++++++-
1 file changed, 364 insertions(+), 18 deletions(-)
diff --git a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
index e0a1bbea988..6364474ab58 100644
--- a/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
+++ b/plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
@@ -14,25 +14,371 @@
# limitations under the License.
#
+# MasterDataRegistrationTransaction Class
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType as DataType
+##
+## Help Methods
+##
+propertiesCache = {};
tr = service.transaction()
-# The default ELN Experiment
-elnExperimentTypeE = tr.getOrCreateNewExperimentType("SYSTEM_EXPERIMENT")
-elnExperimentTypeE.setDescription("Lab Experiment")
-elnExperimentTypeS = tr.getOrCreateNewSampleType("SYSTEM_EXPERIMENT")
-elnExperimentTypeS.setDescription("Lab Experiment")
-elnExperimentTypeS.setListable(True)
-elnExperimentTypeS.setSubcodeUnique(False)
-elnExperimentTypeS.setAutoGeneratedCode(False)
-elnExperimentTypeS.setGeneratedCodePrefix('C')
-
-# The default experiment used by the UI, assigned automatically to new samples
-folderType = tr.getOrCreateNewExperimentType("ELN_FOLDER")
-folderType.setDescription("Folder")
-
-# Preview Image
-elnDataSetPreviewType = tr.getOrCreateNewDataSetType("ELN_PREVIEW")
-elnDataSetPreviewType.setDescription("ELN Preview");
-elnDataSetPreviewType.setDataSetKind("PHYSICAL");
\ No newline at end of file
+def createVocabularyWithTerms(vocabularyCode, terms):
+ vocabulary = tr.createNewVocabulary(vocabularyCode);
+ addTerms(vocabulary, terms);
+
+def addTerms(vocabulary, terms):
+ for term in terms:
+ addTermWithLabel(vocabulary, term[0], term[1])
+
+def addTermWithLabel(vocabulary, termCode, termLabel):
+ newTerm = tr.createNewVocabularyTerm(termCode);
+ newTerm.setLabel(termLabel);
+ vocabulary.addTerm(newTerm);
+
+def createExperimentTypeWithProperties(experimentTypeCode, description, properties):
+ newExperiment = tr.getOrCreateNewExperimentType(experimentTypeCode);
+ newExperiment.setDescription(description);
+ addProperties(newExperiment, properties);
+
+def addProperties(entity, properties):
+ for property in properties:
+ addProperty(entity, property[0], property[1], property[2], property[3], property[4]);
+
+def addProperty(entity, propertyCode, section, propertyLabel, dataType, propertyDescription):
+ property = None;
+
+ if propertyCode in propertiesCache:
+ property = propertiesCache[propertyCode];
+ else:
+ property = tr.getOrCreateNewPropertyType(propertyCode, dataType);
+ property.setDescription(propertyDescription);
+ property.setLabel(propertyLabel);
+ propertiesCache[propertyCode] = property;
+
+ propertyAssignment = tr.assignPropertyType(entity, property);
+ propertyAssignment.setSection(section);
+
+##
+## Vocabularies
+##
+
+createVocabularyWithTerms("HOST", [
+ ["MOUSE", "mouse"],
+ ["RAT", "rat"],
+ ["GUINEA_PIG", "guinea pig"],
+ ["RABBIT", "rabbit"],
+ ["DONKEY", "donkey"]
+ ]);
+
+createVocabularyWithTerms("DETECTION", [
+ ["HRP", "horseradish peroxydase"],
+ ["FLUORESCENCE", "fluorescent probe"]
+ ]);
+
+createVocabularyWithTerms("STORAGE", [
+ ["RT", "room temperature"],
+ ["4", "+4 degrees"],
+ ["-20", "-20 degrees"],
+ ["-80", "-80 degrees"]
+ ]);
+
+createVocabularyWithTerms("CLONALITY", [
+ ["MONOCLONAL", "monoclonal"],
+ ["POLYCLONAL", "polyclonal"],
+ ["UNKNOWN", "unknown"]
+ ]);
+
+createVocabularyWithTerms("BACKBONE", [
+ ["PBLUESCRIPT_II_KS_PLUS", "pBluescript II KS +"],
+ ["PBSN", "pBSN"],
+ ["PSPPOLY_A", "pSPpoly(A)"],
+ ["PKERG10Y", "pKERG10y"],
+ ["PRS30Y", "pRS30y"],
+ ["PRS31Y", "pRS31y"],
+ ["PRS40Y", "pRS40y"],
+ ["PRS41Y", "pRS41y"],
+ ["PRS42Y", "pRS42y"],
+ ["PET22B", "pET22b"],
+ ["UNKNOWN", "unknown"],
+ ["PFA6", "pFA6"],
+ ["PGEX4T1", "pGEX4T1"],
+ ["PEG202", "pEG202"],
+ ["PJEXPRESS", "pJexpress"],
+ ["PJEXPRESS2", "pJexpress2"],
+ ["POLYLYS-PJEXPRESS2", "polyLys-pJexpress2"],
+ ["OSER", "OSER"]
+ ]);
+
+createVocabularyWithTerms("BACTERIAL_ANTIBIOTIC_RESISTANCE", [
+ ["BLA", "bla"],
+ ["KAN", "kan"],
+ ["CAM", "cam"]
+ ]);
+
+createVocabularyWithTerms("MARKER", [
+ ["URA3", "URA3"],
+ ["HIS3", "HIS3"],
+ ["LEU2", "LEU2"],
+ ["TRP1", "TRP1"],
+ ["MET15", "MET15"],
+ ["LYS2", "LYS2"],
+ ["ADE1", "ADE1"],
+ ["KANMX", "KanMX"],
+ ["NATMX", "NatMX"],
+ ["HYGMX", "HygMX"],
+ ["URA3MX", "Ura3MX"],
+ ["HIS3MX", "His3MX"],
+ ["BAR", "bar"],
+ ["CY_1", "Cy1"],
+ ["E_1", "e1"],
+ ["SB_1", "Sb1"],
+ ["W_1", "w1"],
+ ["Y1", "y1"],
+ ]);
+
+createVocabularyWithTerms("STERILIZATION", [
+ ["AUTOCLAVATION", "autoclavation"],
+ ["FILTRATION", "filtration"],
+ ["NONE", "none"]
+ ]);
+
+createVocabularyWithTerms("GENETIC_BACKGROUND", [
+ ["BY4743", "BY4743"],
+ ["BY4741", "BY4741"],
+ ["BY4742", "BY4742"],
+ ["CEN.PK2-1C", "CEN.PK2-1C"],
+ ["CEN.PK2-1D", "CEN.PK2-1D"],
+ ["CEN.PK2", "CEN.PK2"],
+ ["W303", "W303"],
+ ["W303-1A", "W303-1A"],
+ ["W303-1B", "W303-1B"],
+ ["S288C", "S288C"],
+ ["RM11", "RM11"],
+ ["RM11-A", "RM11-A"],
+ ["RM11-B", "RM11-B"],
+ ["UNKNOWN", "unknown"],
+ ["FY4", "FY4"]
+ ]);
+
+createVocabularyWithTerms("MATING_TYPE", [
+ ["A", "a"],
+ ["ALPHA", "alpha"],
+ ["DIPLOID", "diploid"],
+ ["UNKNOWN", "unknown"]
+ ]);
+
+createVocabularyWithTerms("BACKGROUND_SPECIFIC_MARKERS", [
+ ["MET15_LYS2", "met15- lys2-"],
+ ["MET15", "met15-"],
+ ["LYS2", "lys2-"],
+ ["TRP1_ADE2", "trp1- ade2-"],
+ ["TRP1", "trp1-"],
+ ["ADE2", "ade2-"],
+ ["MET15_TRP1", "met15- trp1-"],
+ ["HO_KAN", "ho::kanMX"],
+ ["NONE", "none"],
+ ["UNKNOWN", "unknown"],
+ ["MET15_LYS2_TRP1_ADE2", "met15- lys2- trp1- ade2-"],
+ ["LYS2_TRP1", "lys2- trp1-"],
+ ["MET15_LYS2_TRP1", "met15- lys2- trp1-"]
+ ]);
+
+createVocabularyWithTerms("COMMON_MARKERS", [
+ ["URA3_HIS3_LEU2", "ura3- his3- leu2-"],
+ ["URA3_HIS3", "ura3- his3-"],
+ ["URA3_LEU2", "ura3- leu2-"],
+ ["URA3", "ura3-"],
+ ["HIS3_LEU2", "his3- leu2-"],
+ ["HIS3", "his3-"],
+ ["LEU2", "leu2-"],
+ ["NONE", "none"],
+ ["UNKNOWN", "unknown"]
+ ]);
+
+createVocabularyWithTerms("ENDOGENOUS_PLASMID", [
+ ["CIR_PLUS", "cir+"],
+ ["CIR_ZERO", "cir0"],
+ ["UNKNOWN", "unknown"]
+ ]);
+
+createVocabularyWithTerms("DIRECTION", [
+ ["FORWARD", "forward"],
+ ["REVERSE", "reverse"]
+ ]);
+
+createVocabularyWithTerms("STRAND", [
+ ["DS", "double strand"],
+ ["SS", "single strand"]
+ ]);
+
+createVocabularyWithTerms("RNA_TYPE", [
+ ["MIMIC", "mimic"],
+ ["INHIBITOR", "inhibitor"]
+ ]);
+
+createVocabularyWithTerms("RNA_BACKBONE", [
+ ["LNA", "LNA"],
+ ["2_O_METHYL", "2-O-methylation"]
+ ]);
+
+createVocabularyWithTerms("ORIGIN", [
+ ["CROSS", "cross"],
+ ["TRANSFORMATION", "transformation"],
+ ["SPORULATION", "transformation sporulation"],
+ ["NEGATIVE_SELECTION", "negative selection"],
+ ["TRANSFECTION", "transfection"]
+ ]);
+
+createVocabularyWithTerms("CHECK", [
+ ["PCR", "PCR"],
+ ["MICROSCOPY", "microscopy"],
+ ["WB", "western blotting"],
+ ["SB", "southern blotting"],
+ ["PCR_MICROSCOPY", "PCR and microscopy"],
+ ["FLOWCYTOMETRY", "flow cytometry"],
+ ["PCR_FLOWCYTOMETRY", "PCR and flow cytometry"],
+ ["MORPHOLOGY", "morphology"],
+ ["OTHER", "other"],
+ ["NOTHING", "nothing"]
+ ]);
+
+createVocabularyWithTerms("PROTOCOL_TYPE", [
+ ["DNA", "DNA method"],
+ ["RNA", "RNA method"],
+ ["PROTEINS", "proteins method"],
+ ["YEAST_BASICS", "yeast basic method"],
+ ["BACTERIA_BASICS", "bacteria basic method"],
+ ["FLUORESCENCE_MICROSCOPY", "fluorescence microscopy method"],
+ ["FLOW_CYTOMETRY", "flow cytometry method"],
+ ["CELL_SORTING", "cell sorting method"],
+ ["CELL_LINE_BASICS", "cell line basics"]
+ ]);
+
+createVocabularyWithTerms("TEMPLATE", [
+ ["DNA", "DNA"],
+ ["RNA", "RNA"],
+ ["BACTERIA_COLONY", "bacteria colony"],
+ ["YEAST_COLONY", "yeast colony"]
+ ]);
+
+createVocabularyWithTerms("YES_NO", [
+ ["YES", "yes"],
+ ["NO", "no"],
+ ["UNKNOWN", "unknown"]
+ ]);
+
+createVocabularyWithTerms("MEMBRANE", [
+ ["PVDF", "PVDF"],
+ ["NITROCELLULOSE", "nitrocellulose"],
+ ["PVDF_NITROCELLULOSE", "Either PVDF or nitrocellulose"]
+ ]);
+
+createVocabularyWithTerms("SPECIES", [
+ ["HOMO", "Homo sapiens"],
+ ["MOUSE", "Mus musculus"],
+ ["RAT", "Rattus norvegicus"],
+ ["PIG", "Sus scrofa"],
+ ["DROSOPHILA_MELANOGASTER", "Drosophila melanogaster"]
+ ]);
+
+createVocabularyWithTerms("CELL_MEDIUM", [
+ ["RPMI", "rpmi"],
+ ["1640", "1640"],
+ ["ISCOVES", "iscoves"],
+ ["DMEM", "DMEM"],
+ ["DMEM_NUTRIENT_MIXTURE_F-12_HAM", "DMEM nutrient mixture F-12 HAM"],
+ ["DMEM_HIGH_GLUC", "DMEM high glucose"],
+ ["DMEM_LOW_GLUC", "DMEM low glucose"]
+ ]);
+
+createVocabularyWithTerms("OWNER", [
+ ["FILL_ME_1", "Fill me with the people of your lab"],
+ ["FILL_ME_2", "Fill me with the people of your lab 2"]
+ ]);
+
+createVocabularyWithTerms("CELL_TYPE", [
+ ["FIBROBLAST", "fibroblast"],
+ ["NEURON", "neuron"]
+ ]);
+
+createVocabularyWithTerms("ORGANISM", [
+ ["BACTERIA", "Bacteria"],
+ ["BUDDING_YEAST", "Saccharomyces cerevisiae"],
+ ["MAMMALIAN", "mammalian"],
+ ["DROSOPHILA_MELANOGASTER", "Drosophila melanogaster"]
+ ]);
+
+createVocabularyWithTerms("EXPERIMENTAL_READOUT", [
+ ["FLOW_CYTOMETRY", "flow citometry"],
+ ["SORTING", "cell sorting"],
+ ["GROWTH", "growth"],
+ ["WESTERN_BLOTTING", "western blottong"],
+ ["RT_QPCR", "RT-qPCR"]
+ ]);
+
+createVocabularyWithTerms("MACHINE", [
+ ["LSRII_FORTESSA", "SRII Fortessa"],
+ ["TECAN_READER", "Tecan reader"],
+ ["BIOLECTOR", "BioLector"],
+ ["LICOR_ODYSSEY", "LI-COR Odyssey"],
+ ["TI_ECLIPSE", "TI Eclipse (Nikon)"],
+ ["SRX_101A", "Konica Minolta SRX-101A"],
+ ["LIGHT_CYCLER", "LightCycler 480"]
+ ]);
+##
+## Property Types
+##
+NOTES = tr.getOrCreateNewPropertyType("NOTES", DataType.MULTILINE_VARCHAR);
+NOTES.setDescription("Notes regarding the dataset");
+NOTES.setLabel("Notes");
+
+##
+## Experiment Types
+##
+createExperimentTypeWithProperties("ANTIBODY", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("BACTERIA", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("CHEMICAL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("ENZYME", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("MEDIA", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("OLIGO", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("RNA", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("PLASMID", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("SOLUTION_BUFFER", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("YEAST", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("CELL_LINE", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("FLY", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+
+createExperimentTypeWithProperties("GENERAL_PROTOCOL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("PCR_PROTOCOL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+createExperimentTypeWithProperties("WESTERN_BLOTTING_PROTOCOL", "BOX TO HOLD SAMPLES OF THIS TYPE FOR ORGANIZATIONAL PURPOSES", []);
+
+createExperimentTypeWithProperties("DEFAULT_EXPERIMENT", "Default Experiment", [
+ ["NAME", "General", "Name", DataType.VARCHAR, "Name"],
+ ["EXPERIMENTAL_GOALS", "General", "Experimental goals", DataType.MULTILINE_VARCHAR, "Goal of the experiment"],
+ ["GRANT", "General", "Grant", DataType.VARCHAR, "grant name"],
+ ["START_DATE", "General", "Start Date", DataType.TIMESTAMP, "Start Date"],
+ ["END_DATE", "General", "End Date", DataType.TIMESTAMP, "End Date"],
+ ["EXPERIMENTAL_RESULTS", "General", "Experimental results", DataType.MULTILINE_VARCHAR, "Brief summary of the results obtained"]
+]);
+
+##
+## Dataset
+##
+ELN_PREVIEW = tr.getOrCreateNewDataSetType("ELN_PREVIEW")
+ELN_PREVIEW.setDescription("ELN Preview");
+ELN_PREVIEW.setDataSetKind("PHYSICAL");
+
+SEQ_FILE = tr.getOrCreateNewDataSetType("SEQ_FILE")
+SEQ_FILE.setDescription("");
+SEQ_FILE.setDataSetKind("PHYSICAL");
+
+SEQ_FILE_NOTES = tr.assignPropertyType(SEQ_FILE, NOTES);
+SEQ_FILE_NOTES.setSection("General information");
+
+RAW_DATA = tr.getOrCreateNewDataSetType("RAW_DATA")
+RAW_DATA.setDescription("");
+RAW_DATA.setDataSetKind("PHYSICAL");
+
+RAW_DATA_NOTES = tr.assignPropertyType(RAW_DATA, NOTES);
+RAW_DATA_NOTES.setSection("General information");
\ No newline at end of file
--
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