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))