def AddDefaultExpertiments(sess, mCls): # add a couple of experiments to use... SqlDataModel.Insert( sess, mCls.ExpMeta(Name="Image", Description="", SourceFile="Image.pxp")) SqlDataModel.Insert( sess, mCls.ExpMeta(Name="Image1", Description="", SourceFile="Image1.pxp"))
def AddDefaultUsers(sess, mCls): Names = [ "Patrick_Heenan", "William_'John'_Van_Patten", "Devin_Edwards", "Thomas_Perkins" ] for n in Names: SqlDataModel.Insert(sess, mCls.User(Name=n))
def AddDefaultSamplePreps(sess, mCls): Name = ["Standard_GelPurified"] Description = ["Amplified DNA, purified by gel electrophoresis," +\ "Bio-Rad Quantum freeze and squeeze, and (optionally)" +\ "Amicon 10K 0.5mL"] for n, desc in zip(Name, Description): SqlDataModel.Insert( sess, mCls.SamplePrep(Name=Name, Description=Description))
def AddDefaultTipPreps(sess, mCls): Description = "Standard As Of 2015/07" GoldEtchSec = 30 ChromEtchSec = 30 SqlDataModel.Insert( sess, mCls.TipPrep(Description=Description, Name="Standard", SecondsEtchGold=GoldEtchSec, SecondsEtchChromium=ChromEtchSec))
def AddDefaultRatings(sess, mCls): Ratings = [-1, 1, 2, 3, 4, 5] Names = [ "Unrated", "Very Low Quality, very high noise", "Low Quality or high noise", "Standard", "Great", "Paper-or Talk-Worthy" ] for rate, name in zip(Ratings, Names): # note that descriptions are the same as the names... SqlDataModel.Insert( sess, mCls.TraceRating(RatingValue=rate, Name=name, Description=name))
def AddDefaultMolecules(sess, mCls): # Add the families, molecule types, and samples FamilyNames = ["DNA", "RNA", "Protein"] Descriptions = [ "Deoxyribonucleic acid", "Oxyribonucleic acid", "A Polypeptide" ] dnaIndex = 0 nFamilies = len(FamilyNames) for i in range(nFamilies): mFam = mCls.MoleculeFamily(Name=FamilyNames[i], Description=Descriptions[i]) SqlDataModel.Insert(sess, mFam) # XXX magic number; 1 is the first thing in the database # add in the molecule type Description= "Mp13 plasmid with 1607F-DBCO and 3520R-Bio" +\ "primers with 12 nt complementary overhang: "+\ "GTG GTC CTA GTG" mFam = mCls.MolType(idMoleculeFamily=1, Name="CircularDNA", Description=Description, MolMass=0) SqlDataModel.Insert(sess, mFam)
def AddDefaultTipTypes(sess, mCls): # Add the tip types Names = [ "Biolever_Long", "Biolever_Mini", "BioLever_Fast", "FIB_Biolever_Fast", "FIB_BioLever_Mini" ] Descriptions = [ "Standard Olympus Biolever Long", "Standard Olympus Biolever Mini", "Standard Olympus Biolevel Fast", "Focused Ion Beam Modified Biolever Fast", "Focused Ion Beam Modified Biolevel Mini" ] nTypes = len(Names) i = 0 for i in range(nTypes): # POST: tmp is set up with the type and descriptions needed TipType = mCls.TipType(Name=Names[i], Description=Descriptions[i]) SqlDataModel.Insert(sess, TipType)
def AddDefaultTipManifests(sess, mCls): TimeMade = [ datetime.datetime(year=2015, month=6, day=16), datetime.datetime(year=2015, month=7, day=14) ] TipProtocol = [1, 1] TipTypes = [SQL_BOOT_CYPHER_LONG, SQL_BOOT_CYPHER_FIBMINI] TipPack = [1, 1] Name = ["BioLong6/16", "BioMini7/14"] PackPosition = ["Unknown", "Unknown"] for i in range(len(TimeMade)): timeMade = TimeMade[i] mTip = mCls.TipManifest(Name=Name[i], Description="", PackPosition=PackPosition[i], TimeMade=timeMade, TimeRinsed=timeMade, idTipPrep=TipProtocol[i], idTipPack=TipPack[i], idTipType=TipTypes[i]) SqlDataModel.Insert(sess, mTip)
def AddDefaultSamples(sess, mCls): DateSampleCreated = ["2015/6/04", "2015/6/04", "2015/6/30"] DateSampleDeposited = ["2015/6/16", "2015/7/4", "2015/7/6"] DateSampleRinsed = DateSampleDeposited concentration = 130 # ng/muL vol = 20 # uL loaded description = "Standard Circular DNA" MoleculeName = SQL_BOOT_CYPHER_DEF_SAMPLE_TYPE SamplePrep = SQL_BOOT_CYPHER_DEF_SAMPLE_PREP n = len(DateSampleCreated) for i in range(n): mSample = mCls.Sample(Name=description + str(i), DateCreated=DateSampleCreated[i], DateDeposited=DateSampleDeposited[i], DateRinsed=DateSampleRinsed[i], VolLoadedMuL=vol, ConcNanogMuL=concentration, idMolType=MoleculeName, idSamplePrep=SamplePrep, Description=description) SqlDataModel.Insert(sess, mSample)
def AddDefaultModels(sess, mCls): mModels = HighBandwidthModel.HighBandwidthModel() # add a couple of models to use... SqlDataModel.Insert(sess, mCls.Model(Name=mModels.ModelName(), Description=""))
def AddDefaultTipPack(sess, mCls): Name = "Unknown" Description = "Unkown Tip Pack" SqlDataModel.Insert(sess, mCls.TipPack(Name=Name, Description=Description))