#!/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 = { "LAB_MEMBERS" : [ ["ELISA_DULTZ", "E. Dultz"], ["A_KOEK", "A. Koek"], ["A_MADRID", "A. Madrid"], ["AC_STROM", "A.C. Strom"], ["A_HIBBEL", "A. Hibbel"], ["B_ZEITLER", "B. Zeitler"], ["B_MONTPETIT", "B. Montpetit"], ["C_BRUNE", "C. Brune"], ["C_DERRER", "C. Derrer"], ["C_SMOLKE", "C. Smolke"], ["C_WEIRICH", "C. Weirich"], ["C_MUGLER", "C. Mugler"], ["E_GREEN", "E. Green"], ["E_ONISHCHENKO", "E. Onishchenko"], ["E_WEIDER", "E. Weider"], ["J_CARROLL", "J. Carroll"], ["J_TANG", "J. Tang"], ["J_SODERHOLM", "Jon Soderholm"], ["K_WEIS", "K. Weis"], ["L_STANTON", "L. Stanton"], ["M_BLOWER", "M. Blower"], ["M_HERZOG", "M. Herzog"], ["M_HOCHSTRASSER", "M. Hochstrasser"], ["M_HONDELE", "M. Hondele"], ["M_NACHURY", "M. Nachury"], ["N_FISCHER", "N. Fischer"], ["L_CHAN", "L. Chan"], ["P_KALAB", "P. Kalab"], ["R_JOYNER", "R. Joyner"], ["R_SACHDEV", "R. Sachdev"], ["R_MANCINI", "R. Mancini"], ["S_MUNCHEL", "S. Munchel"], ["N_TAKIZAWA", "N. Takizawa"], ["S_BIRD", "S. Bird"], ["S_HEINRICH", "S. Heinrich"], ["S_RAJOO", "S. Rajoo"], ["Y_JIANG", "Y. Jiang"], ["Z_DOSSANI", "Z. Dossani"], ["B_ROBINSON", "B. Robison"], ["C_MCGOURTY", "C. McGourty"], ["SEE_COMMENTS", "See comments"], ], "AB_CLONALITY" : [ ["MONOCLONAL", "monoclonal"], ["POLYCLONAL", "polyclonal"], ], "AB_SPECIES" : [ ["HUMAN", "Human"], ["RABBIT", "Rabbit"], ["MOUSE", "Mouse"], ["CHICKEN", "Chicken"], ["DONKEY", "Donkey"], ["CAMEL", "Camel"], ["GOAT", "Goat"], ["SHEEP", "Sheep"], ["RAT", "Rat"], ["UNKWOWN", "?"], ["SEE_COMMENTS", "see comments"], ], "AB_TYPE" : [ ["IGG", "IgG"], ["IGM", "IgM"], ["IGY", "IgY"], ["UNKNOWN", "?"], ["SEE_COMMENTS", "see comments"], ], "AB_FORM" : [ ["SERUM", "serum"], ["AFFINITY_PURIFIED", "affinity purified"], ["TISSUE_CULT_SUPERNATANT", "tissue culture supernatant"], ["SEE_COMMENTS", "see comments"], ], "AB_PRIMSEC" : [ ["PRIMARY", "primary"], ["SECONDAY", "secondary"], ], "AB_LOCATION" : [ ["FOUR_DEG", "4C"], ["MINUS_20", "-20C"], ["MINUS_80", "-80C"], ["RT", "RT"], ["SEE_COMMENTS", "see comments"], ], "CHEMICALS_LOCATION" : [ ["CHEM_CABINET", "Chemical cabinet"], ["CHEM_CABINET_E8", "Chemical cabinet E8"], ["MINUS_20", "-20C"], ["FOUR_DEG", "4C"], ["MINUS_80", "-80C"], ["SMALL_CHEMICALS", "Small chemicals"], ["DYES", "Dyes"], ["SEE_COMMENTS", "see comments"], ], "YEAST_BACKGROUND" : [ ["UNKWNOWN", "?"] ], "OLIGO_CATEGORY" : [ ["CHECKING", "Checking"], ["CLONING", "Cloning"], ["MUTAGENESIS", "Mutagenesis"], ["PRINGLE", "Pringle"], ["QPCR", "qPCR"], ["SEQUENCING", "qPCR"], ], "OLIGO_SENSE" : [ ["SENSE", "sense"], ["ANTISENSE", "antisense"], ], "PLASMID_BACTERIAL_STRAIN" : [ ["XL1BLUE", "XL1blue"], ["XL10-GOLD", "XL10-Gold"], ["XL1-BLUE", "XL1-Blue"], ["TG2", "TG2"], ["TG1", "TG1"], ["SURE", "SURE"], ["STBL3", "STBL3"], ["STBL2", "STBL2"], ["SOLR_CELLS", "SOLR cells"], ["SG13", "SG13"], ["SCS110", "SCS110"], ["MC1061", "MC1061"], ["MACH1", "MACH1"], ["M15PREP4", "M15prep4"], ["KC8", "KC8"], ["HB101", "HB101"], ["E_COLI", "E.coli"], ["DH5ALPHA", "DH5alpha"], ["DH10B", "DH10B"], ["DH1", "DH1"], ["CCDB_SURVIVAL", "ccdB Survival"], ["BLR", "BLR"], ["BL21_PLUS", "BL21+"], ["BL21-LYSS", "BL21[LysS]"], ["BL21", "BL21"], ["UNKNOWN", "???"] ], "PLASMID_DRUG_RES" : [ ["AMP", "Amp"], ["AMP_MAYBE", "AMP?"], ["CAM", "CAM"], ["KAN", "KAN"], ["KAN_CAM", "kan cam"], ["KAN-CAM-CCDB_CELLS", "KAN,CAM, ccdB cells"], ["TET", "tet"], ["ZEO", "Zeo"] ], "PLASMID_SELECTION_MAKER" : [ ["URA3_ADE3", "URA3, ADE3"], ["ADE2", "ADE2"], ["CAURA", "CaURA"], ["CAURA3", "CaURA3"], ["CEN_HIS3", "CEN, HIS3"], ["G418", "G418"], ["HIS3", "HIS3"], ["HIS3_OR_LEU2", "HIS3 or LEU2"], ["HIS3MX", "HIS3MX"], ["HIS5", "HIS5"], ["HIS5MX", "His5MX"], ["HISMX", "HisMX"], ["HISMX6", "HISMX6"], ["HPHMX", "HphMx"], ["HYG", "Hyg"], ["HYGB", "HYGB"], ["HYGB_R", "HygB R"], ["KAN", "kan"], ["KANMX", "KanMX"], ["LEU", "Leu"], ["LEU2", "LEU2"], ["MET15", "MET15"], ["NAT", "Nat"], ["NATMX", "NatMX"], ["NEO", "Neo"], ["NOTHING", "nothing"], ["S_POMBE_HIS5", "S. pombe His5"], ["SPHIS5", "SpHIS5"], ["TRP1", "TRP1"], ["URA", "URA"], ["URA3", "URA3"], ["URA3_CA", "URA3 (C.a.)"] ], "PLASMID_VECTOR_TYPE" : [ ["BACTERIAL_EXPRESSION", "Bacterial expression"], ["YEAST_INTEGRATION", "Yeast integration"], ["PRINGLE", "Pringle"], ["MAMMALIAN_EXPRESSION", "Mammalian expression"], ["YEAST_CEN", "Yeast CEN"], ["YEAST_CENLESS", "Yeast CEN-less with ARS"], ["YEAST_2U", "Yeast 2u"], ["CLONING_INTERMEDIATE", "Cloning intermediate"], ["PLASMID", "Plasmid"], ["PHAGEMID", "Phagemid"] ], "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"] ], "MAT" : [ ["ALPHA", "a"], ["A", "A"], ["ALPHA_A", "a/A"], ["A_A", "A/A"], ["ALPHA_ALPHA", "a/a"], ["UNKNOWN", "?"], ] }