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Commit 4cfcdbcd authored by juanf's avatar juanf
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SSDM-1078 : PAPER - Provide sensible defaults - Implementation 

SVN: 32710
parent 6fbada11
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plasmid/source/core-plugins/newbrowser/1/as/initialize-master-data.py
+ 364
− 18
View file @ 4cfcdbcd
......@@ -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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