def removeVersion(endpoint):
va = sandVersion(endpoint)
vb = lastVersion(endpoint, -1)
if va == vb:
return (False, 'no more removable versions')
# check exposed version
if not checkOldSynthax(endpoint):
return (False, 'Unable to fix service-version.txt')
ndir = wkd + '/' + endpoint
if os.path.isfile(ndir + '/service-version.txt'):
versions = []
f = open(ndir + '/service-version.txt', 'r')
versions = f.readlines()
f.close()
del versions[-1]
f = open(ndir + '/service-version.txt', 'w')
for vi in versions:
f.write(vi)
f.close()
# remove directory
try:
shutil.rmtree(vb, ignore_errors=True)
except:
return (False, 'unable to remove ' + vb)
return (True, 'version ' + vb + ' removed OK')
def removeVersion (endpoint):
va = sandVersion (endpoint)
vb = lastVersion (endpoint,-1)
if va == vb:
return (False, 'no more removable versions')
# check exposed version
if not checkOldSynthax (endpoint):
return (False, 'Unable to fix service-version.txt')
ndir = wkd +'/'+endpoint
if os.path.isfile (ndir+'/service-version.txt'):
versions = []
f = open (ndir+'/service-version.txt','r')
versions = f.readlines()
f.close()
del versions[-1]
f = open (ndir+'/service-version.txt','w')
for vi in versions:
f.write (vi)
f.close()
# remove directory
try:
shutil.rmtree (vb, ignore_errors=True)
except:
return (False, 'unable to remove '+vb)
return (True,'version '+vb+' removed OK')
def get(endpoint, ver, piece):
if 'model' in piece:
piece_name = '/imodel.py'
elif 'series' in piece:
piece_name = '/training.sdf'
vb = lastVersion(endpoint, ver)
try:
shutil.copy(vb + piece_name, './')
except:
return (False, 'Unable to copy ' + piece_name)
return (True, 'File retrieved OK')
def get (endpoint, ver, piece):
if 'model' in piece:
piece_name = '/imodel.py'
elif 'series' in piece:
piece_name = '/training.sdf'
vb = lastVersion (endpoint,ver)
try:
shutil.copy(vb+piece_name,'./')
except:
return (False,'Unable to copy '+piece_name)
return (True, 'File retrieved OK')
def view(endpoint, molecules, verID, vtype, background, refname, refver):
"""Top level view function
molecules: SDFile containing the collection of 2D structures to be predicted
verID: version of the model that will be used. Value -1 means the last one
"""
if verID != -99:
va = lastVersion(endpoint, verID)
## if not molecules:
## molecules = va+'/training.sdf'
# load model
try:
sys.path.append(va)
from imodel import imodel
model = imodel(va)
except:
return (False, 'unable to load imodel')
if not model:
return (False, 'unable to load imodel')
# arguments of the call overwrite existing view settings of imodel.py
## viewMode = query or series
if vtype != None:
model.viewType = vtype
if background != None:
model.viewBackground = background
if molecules:
model.viewMode = 'query'
model.viewReferenceEndpoint = endpoint
model.viewReferenceVersion = verID
else:
model.viewMode = 'series'
if refname != None:
model.viewReferenceEndpoint = refname
if refver != None:
model.viewReferenceVersion = refver
result = model.viewWorkflow(molecules)
return (result)
def predict(endpoint,
molecules,
verID=-1,
api=0,
loc=-99,
detail=False,
progress=False,
extValid=False):
"""Top level prediction function
molecules: SDFile containing the collection of 2D structures to be predicted
verID: version of the model that will be used. Value -1 means the last one
detail: level of detail of the prediction. If True the structure of the
closest compond will be returned
"""
# web calls, we look for web exposed versions
if api in (1, 2, 5):
vpath = exposedVersion(endpoint)
if vpath == None:
return (False, 'no published model found')
else:
vpath = lastVersion(endpoint, verID) ## also for api==6 (API v3.0)
if not vpath:
return (False, "No versions directory found")
##print vpath
if loc != -99:
vpath += '/local%0.4d' % loc
sys.path.append(vpath)
from imodel import imodel
# load model
model = imodel(vpath)
# to maintain back-compatibility, the last parameter is only introduced when set to TRUE
# this is used only in command mode (-x flag) and therefore never set for web-based preditions
if extValid:
success, pred = model.predictWorkflow(molecules, detail, progress,
extValid)
else:
success, pred = model.predictWorkflow(molecules, detail, progress)
return (success, pred)
def predict (endpoint, molecules, verID=-1, api=0, loc=-99, detail=False, progress=False, extValid=False):
"""Top level prediction function
molecules: SDFile containing the collection of 2D structures to be predicted
verID: version of the model that will be used. Value -1 means the last one
detail: level of detail of the prediction. If True the structure of the
closest compond will be returned
"""
# web calls, we look for web exposed versions
if api in (1,2,5):
vpath = exposedVersion (endpoint)
if vpath == None:
return (False, 'no published model found')
else:
vpath = lastVersion (endpoint,verID) ## also for api==6 (API v3.0)
if not vpath:
return (False,"No versions directory found")
##print vpath
if loc != -99:
vpath += '/local%0.4d' % loc
sys.path.append(vpath)
from imodel import imodel
# load model
model = imodel(vpath)
# to maintain back-compatibility, the last parameter is only introduced when set to TRUE
# this is used only in command mode (-x flag) and therefore never set for web-based preditions
if extValid:
success, pred = model.predictWorkflow (molecules, detail, progress, extValid)
else:
success, pred = model.predictWorkflow (molecules, detail, progress)
return (success, pred)
def infoVersion(endpoint, ver, style, pubver):
vb = lastVersion(endpoint, ver)
unk = not os.path.isfile(vb + '/info.pkl')
##
## if :
## if ver == 0:
## print '* no model info available'
## else:
## print '%-4s no model info available'%ver
## return (True, 'OK')
##
## #return (False,'model information file not found')
if not unk:
modelInfo = open(vb + '/info.pkl', 'rb')
infoID = pickle.load(modelInfo)
infoSeries = pickle.load(modelInfo)
infoMD = pickle.load(modelInfo)
infoModel = pickle.load(modelInfo)
infoResult = pickle.load(modelInfo)
try:
infoNotes = pickle.load(modelInfo)
except:
infoNotes = []
modelInfo.close()
#print infoID, infoSeries, infoMD, infoModel, infoResult
if style in 'long':
if unk:
if ver == 0: print '*'
else: print '%-4s' % ver
#print ' web service :', isWS
if pubver > 0:
print ' public vers :', pubver
else:
print ' public vers : none'
print ' no model info available'
return (True, 'OK')
for i in infoID:
if 'version' in i: print i[1]
for i in infoID:
if not 'version' in i: print ' %-10s' % i[0], ' : ' + str(i[1])
#print " web service :", isWS
if pubver > 0:
print ' public vers :', pubver
else:
print ' public vers : none'
for i in infoSeries:
print ' %-10s' % i[0], ' : ' + str(i[1])
for i in infoMD:
print ' %-10s' % i[0], ' : ' + str(i[1])
for i in infoModel:
print ' %-10s' % i[0], ' : ' + str(i[1])
for i in infoResult:
print ' %-10s' % i[0], ' : ' + str(i[1])
for i in infoNotes:
print ' %-10s' % i[0], ' : ' + str(i[1])
print
def infoVersion(endpoint, ver, style, pubver):
vb = lastVersion(endpoint, ver)
unk = not os.path.isfile(vb + '/info.pkl')
##
## if :
## if ver == 0:
## print '* no model info available'
## else:
## print '%-4s no model info available'%ver
## return (True, 'OK')
##
## #return (False,'model information file not found')
if not unk:
modelInfo = open(vb + '/info.pkl', 'rb')
infoID = pickle.load(modelInfo)
infoSeries = pickle.load(modelInfo)
infoMD = pickle.load(modelInfo)
infoModel = pickle.load(modelInfo)
infoResult = pickle.load(modelInfo)
try:
infoNotes = pickle.load(modelInfo)
except:
infoNotes = []
modelInfo.close()
#print infoID, infoSeries, infoMD, infoModel, infoResult
if style in 'long':
if unk:
if ver == 0: print('*')
else: print('%-4s' % ver)
#print ' web service :', isWS
if pubver > 0:
print(' public vers :', pubver)
else:
print(' public vers : none')
print(' no model info available')
return (True, 'OK')
for i in infoID:
if 'version' in i: print(i[1])
for i in infoID:
if not 'version' in i: print(' %-10s' % i[0], ' : ' + str(i[1]))
#print " web service :", isWS
if pubver > 0:
print(' public vers :', pubver)
else:
print(' public vers : none')
for i in infoSeries:
print(' %-10s' % i[0], ' : ' + str(i[1]))
for i in infoMD:
print(' %-10s' % i[0], ' : ' + str(i[1]))
for i in infoModel:
print(' %-10s' % i[0], ' : ' + str(i[1]))
for i in infoResult:
print(' %-10s' % i[0], ' : ' + str(i[1]))
for i in infoNotes:
print(' %-10s' % i[0], ' : ' + str(i[1]))
print()
elif style in 'short':
iversion = 4 * ' '
iMD = 8 * ' '
imod = 16 * ' '
imol = isen = ispe = iMCC = ir2 = iq2 = isdep = iSSX = 4 * ' '
iconf = ''
if pubver == 0:
ws = ' '
else:
ws = ' %-2d' % pubver
## if isWS : ws = ' @ '
## else : ws = ' '
## if ver == 0: print '*'
## else : print '%-4s'%ver
if unk:
if ver == 0:
print('* ' + ws + 'no model info available')
else:
print('%-4s' % ver + ws + 'no model info available')
return (True, 'OK')
for i in infoID:
if 'version' == i[0]: iversion = '%-4s' % (i[1])
if 'confident' == i[0] and i[1] == 'True': iconf = ' confident'
for i in infoMD:
if 'MD' == i[0]: iMD = '%-8s' % (i[1])
for i in infoModel:
if 'model' == i[0]: imod = '%-16s' % (i[1])
for i in infoResult:
if 'nobj' == i[0]:
try:
imol = '%4d' % int(i[1])
except:
imol = ' 0'
elif 'sens' == i[0]:
try:
isen = '%4.2f' % (float(i[1]))
except:
isen = ' 0.00'
elif 'spec' == i[0]:
try:
ispe = '%4.2f' % (float(i[1]))
except:
ispe = ' 0.00'
elif 'MCC' == i[0]:
try:
iMCC = '%4.2f' % (float(i[1]))
except:
iMCC = ' 0.00'
elif 'R2' == i[0]:
try:
ir2 = '%4.2f' % (float(i[1]))
except:
ir2 = ' 0.00'
elif 'Q2' == i[0]:
try:
iq2 = '%4.2f' % (float(i[1]))
except:
iq2 = ' 0.00'
elif 'SDEP' == i[0]:
try:
isdep = '%4.2f' % (float(i[1]))
except:
isdep = ' 0.00'
elif 'SSX' == i[0]:
try:
iSSX = '%4.2f' % (float(i[1]))
except:
iSSX = ' 0.00'
#print '*'+str(iMCC)+'*'+str(iSSX)+'*'+str(ir2)+'*'
if iSSX != ' ': # PCA
print(iversion + ws + 'MD:' + iMD + ' mod:' + imod + ' mol:' +
imol + ' SSX:' + iSSX + iconf)
elif iMCC != ' ': # qualitative model / classifier
print(iversion + ws + 'MD:' + iMD + ' mod:' + imod + ' mol:' +
imol + ' sen:' + isen + ' spe:' + ispe + ' MCC:' + iMCC +
iconf)
elif ir2 != ' ':
cache = iversion + ws + 'MD:' + iMD + ' mod:' + imod + ' mol:' + imol + ' R2:' + ir2
if iq2 != ' ':
cache += ' Q2:' + iq2
if isdep != ' ':
cache += ' SDEP:' + isdep
cache += iconf
print(cache)
else:
print(iversion + ws + 'MD:' + iMD + ' mod:' + imod + ' mol:' +
imol + ' R2:' + ir2 + ' Q2:' + iq2 + ' SDEP:' + isdep +
iconf)
return (True, 'OK')
def infoVersion (endpoint,ver,style,pubver):
vb = lastVersion (endpoint,ver)
unk = not os.path.isfile (vb+'/info.pkl')
##
## if :
## if ver == 0:
## print '* no model info available'
## else:
## print '%-4s no model info available'%ver
## return (True, 'OK')
##
## #return (False,'model information file not found')
if not unk:
modelInfo = open (vb+'/info.pkl','rb')
infoID = pickle.load(modelInfo)
infoSeries = pickle.load(modelInfo)
infoMD = pickle.load(modelInfo)
infoModel = pickle.load(modelInfo)
infoResult = pickle.load(modelInfo)
try:
infoNotes = pickle.load(modelInfo)
except:
infoNotes = []
modelInfo.close()
#print infoID, infoSeries, infoMD, infoModel, infoResult
if style in 'long':
if unk :
if ver == 0: print '*'
else : print '%-4s'%ver
#print ' web service :', isWS
if pubver > 0 :
print ' public vers :', pubver
else:
print ' public vers : none'
print ' no model info available'
return (True, 'OK')
for i in infoID:
if 'version' in i: print i[1]
for i in infoID:
if not 'version' in i: print ' %-10s'%i[0],' : '+str(i[1])
#print " web service :", isWS
if pubver > 0 :
print ' public vers :', pubver
else:
print ' public vers : none'
for i in infoSeries:
print ' %-10s'%i[0],' : '+str(i[1])
for i in infoMD:
print ' %-10s'%i[0],' : '+str(i[1])
for i in infoModel:
print ' %-10s'%i[0],' : '+str(i[1])
for i in infoResult:
print ' %-10s'%i[0],' : '+str(i[1])
for i in infoNotes:
print ' %-10s'%i[0],' : '+str(i[1])
print