def test_C_prostate(self):
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
print "\nStarting prostate.csv"
# columns start at 0
y = "1"
x = ""
csvFilename = "prostate.csv"
csvPathname = "logreg" + "/" + csvFilename
parseResult = h2i.import_parse(bucket="smalldata", path=csvPathname, hex_key=csvFilename + ".hex", schema="put")
for maxx in range(2, 6):
x = range(maxx)
x.remove(0) # 0 is member ID. not used
x.remove(1) # 1 is output
x = ",".join(map(str, x))
print "\nx:", x
print "y:", y
kwargs = {"x": x, "y": y, "n_folds": 5}
glm = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=15, **kwargs)
# ID,CAPSULE,AGE,RACE,DPROS,DCAPS,PSA,VOL,GLEASON
h2o_glm.simpleCheckGLM(self, glm, "AGE", **kwargs)
sys.stdout.write(".")
sys.stdout.flush()
# now redo it all thru the browser
# three times!
for i in range(3):
h2b.browseJsonHistoryAsUrl()
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
def test_B_benign(self):
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
print "\nStarting benign.csv"
csvFilename = "benign.csv"
csvPathname = "logreg" + "/" + csvFilename
parseResult = h2i.import_parse(bucket="smalldata", path=csvPathname, hex_key=csvFilename + ".hex", schema="put")
# columns start at 0
y = "3"
# cols 0-13. 3 is output
# no member id in this one
for maxx in range(11, 14):
x = range(maxx)
x.remove(3) # 3 is output
x = ",".join(map(str, x))
print "\nx:", x
print "y:", y
kwargs = {"x": x, "y": y}
glm = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=15, **kwargs)
# no longer look at STR?
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
sys.stdout.write(".")
sys.stdout.flush()
# now redo it all thru the browser
h2b.browseJsonHistoryAsUrl()
def test_B_benign(self):
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
print "\nStarting benign.csv"
csvFilename = "benign.csv"
csvPathname = 'logreg' + '/' + csvFilename
parseResult = h2i.import_parse(bucket='smalldata',
path=csvPathname,
hex_key=csvFilename + ".hex",
schema='put')
# columns start at 0
y = "3"
# cols 0-13. 3 is output
# no member id in this one
for maxx in range(11, 14):
x = range(maxx)
x.remove(3) # 3 is output
x = ",".join(map(str, x))
print "\nx:", x
print "y:", y
kwargs = {'x': x, 'y': y}
glm = h2o_cmd.runGLM(parseResult=parseResult,
timeoutSecs=15,
**kwargs)
# no longer look at STR?
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
sys.stdout.write('.')
sys.stdout.flush()
# now redo it all thru the browser
h2b.browseJsonHistoryAsUrl()
def test_rf_tnc3_fvec(self):
h2o.beta_features = True
csvPathname = 'tnc3.csv'
print "\n" + csvPathname
hex_key = "tnc3.hex"
### h2b.browseTheCloud()
parseResult = h2i.import_parse(bucket='smalldata', path=csvPathname, hex_key=hex_key, schema='put',
timeoutSecs=10, retryDelaySecs=0.25, header=1)
print "Parse result['Key']:", parseResult['destination_key']
inspect = h2o_cmd.runInspect(None, parseResult['destination_key'])
h2b.browseJsonHistoryAsUrlLastMatch("Inspect")
if 1==1:
lenNodes = len(h2o.nodes)
colResultList = h2e.exec_expr_list_across_cols(lenNodes, numExprList, hex_key, maxCol=10,
incrementingResult=False, timeoutSecs=10)
print "\ncolResultList after num swap", colResultList
if (1==1):
print "\nWe're not CM data getting back from RFView.json that we can check!. so look at the browser"
print 'The good case with ignore="boat,body"'
rfv = h2o_cmd.runRF(parseResult=parseResult, trees=5, timeoutSecs=10, retryDelaySecs=0.25,
ignored_cols_by_name="boat,body")
inspect = h2o_cmd.runInspect(None, parseResult['destination_key'])
### h2b.browseJsonHistoryAsUrlLastMatch("Inspect")
### time.sleep(3600)
h2b.browseJsonHistoryAsUrl(retryDelaySecs=0.5)
#******************
if 1==0:
colResultList = h2e.exec_expr_list_across_cols(lenNodes, charExprList, hex_key, maxCol=10,
incrementingResult=False, timeoutSecs=10, retryDelaySecs=0.25)
print "\ncolResultList after char swap", colResultList
if 1==1:
print "\nNow the bad case (no ignore)"
rfv = h2o_cmd.runRF(parseResult=parseResult, trees=5, timeoutSecs=10, retryDelaySecs=0.25)
inspect = h2o_cmd.runInspect(None, parseResult['destination_key'])
### h2b.browseJsonHistoryAsUrlLastMatch("Inspect")
### time.sleep(3600)
h2b.browseJsonHistoryAsUrl(retryDelaySecs=0.5)
def test_C_prostate(self):
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
print "\nStarting prostate.csv"
# columns start at 0
y = "1"
x = ""
csvFilename = "prostate.csv"
csvPathname = 'logreg' + '/' + csvFilename
parseResult = h2i.import_parse(bucket='smalldata',
path=csvPathname,
hex_key=csvFilename + ".hex",
schema='put')
for maxx in range(2, 6):
x = range(maxx)
x.remove(0) # 0 is member ID. not used
x.remove(1) # 1 is output
x = ",".join(map(str, x))
print "\nx:", x
print "y:", y
kwargs = {'x': x, 'y': y, 'n_folds': 5}
glm = h2o_cmd.runGLM(parseResult=parseResult,
timeoutSecs=15,
**kwargs)
# ID,CAPSULE,AGE,RACE,DPROS,DCAPS,PSA,VOL,GLEASON
h2o_glm.simpleCheckGLM(self, glm, 'AGE', **kwargs)
sys.stdout.write('.')
sys.stdout.flush()
# now redo it all thru the browser
# three times!
for i in range(3):
h2b.browseJsonHistoryAsUrl()
h2o.nodes[0].log_view()
namelist = h2o.nodes[0].log_download()
def test_GLM2_basic_browser(self):
h2b.browseTheCloud()
importFolderPath = "logreg"
csvFilename = 'prostate.csv'
csvPathname = importFolderPath + "/" + csvFilename
hex_key = csvFilename + ".hex"
parseResult = h2i.import_parse(bucket='smalldata', path=csvPathname, schema='local', hex_key=hex_key, timeoutSecs=180)
inspect = h2o_cmd.runInspect(None, parseResult['destination_key'])
print inspect
print "\n" + csvPathname, \
" numRows:", "{:,}".format(inspect['numRows']), \
" numCols:", "{:,}".format(inspect['numCols'])
x = 'ID'
y = 'CAPSULE'
family = 'binomial'
alpha = '0.5'
lambda_ = '1E-4'
nfolds = '0'
f = 'prostate'
modelKey = 'GLM_' + f
kwargs = { 'response' : y,
'ignored_cols' : x,
'family' : family,
'lambda' : lambda_,
'alpha' : alpha,
'n_folds' : nfolds, # passes if 0, fails otherwise
'destination_key' : modelKey,
}
timeoutSecs = 60
start = time.time()
glmResult = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=timeoutSecs, retryDelaySecs=0.25, pollTimeoutSecs=180, **kwargs)
# this stuff was left over from when we got the result after polling the jobs list
# okay to do it again
# GLM2: when it redirects to the model view, we no longer have the job_key! (unlike the first response and polling)
if 1==0:
job_key = glmResult['job_key']
# is the job finishing before polling would say it's done?
params = {'job_key': job_key, 'destination_key': modelKey}
glm = h2o.nodes[0].completion_redirect(jsonRequest="2/GLMProgressPage2.json", params=params)
print "GLM result from completion_redirect:", h2o.dump_json(a)
if 1==1:
glm = h2o.nodes[0].glm_view(_modelKey=modelKey)
### print "GLM result from glm_view:", h2o.dump_json(a)
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
glm_model = glm['glm_model']
_names = glm_model['_names']
coefficients_names = glm_model['coefficients_names']
submodels = glm_model['submodels'][0]
beta = submodels['beta']
norm_beta = submodels['norm_beta']
iteration = submodels['iteration']
validation = submodels['validation']
auc = validation['auc']
aic = validation['aic']
null_deviance = validation['null_deviance']
residual_deviance = validation['residual_deviance']
print '_names', _names
print 'coefficients_names', coefficients_names
# did beta get shortened? the simple check confirms names/beta/norm_beta are same length
print 'beta', beta
print 'iteration', iteration
print 'auc', auc
# now redo it all thru the browser
h2b.browseJsonHistoryAsUrl()
def test_GLM2_basic_browser(self):
h2b.browseTheCloud()
h2o.beta_features=True
importFolderPath = "logreg"
csvFilename = 'prostate.csv'
csvPathname = importFolderPath + "/" + csvFilename
hex_key = csvFilename + ".hex"
parseResult = h2i.import_parse(bucket='smalldata', path=csvPathname, schema='local', hex_key=hex_key, timeoutSecs=180)
inspect = h2o_cmd.runInspect(None, parseResult['destination_key'])
print inspect
print "\n" + csvPathname, \
" numRows:", "{:,}".format(inspect['numRows']), \
" numCols:", "{:,}".format(inspect['numCols'])
x = 'ID'
y = 'CAPSULE'
family = 'binomial'
alpha = '0.5'
lambda_ = '1E-4'
nfolds = '0'
f = 'prostate'
modelKey = 'GLM_' + f
kwargs = { 'response' : y,
'ignored_cols' : x,
'family' : family,
'lambda' : lambda_,
'alpha' : alpha,
'n_folds' : nfolds, # passes if 0, fails otherwise
'destination_key' : modelKey,
}
timeoutSecs = 60
start = time.time()
glmResult = h2o_cmd.runGLM(parseResult=parseResult, timeoutSecs=timeoutSecs, retryDelaySecs=0.25, pollTimeoutSecs=180, **kwargs)
# this stuff was left over from when we got the result after polling the jobs list
# okay to do it again
# GLM2: when it redirects to the model view, we no longer have the job_key! (unlike the first response and polling)
if 1==0:
job_key = glmResult['job_key']
# is the job finishing before polling would say it's done?
params = {'job_key': job_key, 'destination_key': modelKey}
glm = h2o.nodes[0].completion_redirect(jsonRequest="2/GLMProgressPage2.json", params=params)
print "GLM result from completion_redirect:", h2o.dump_json(a)
if 1==1:
glm = h2o.nodes[0].glm_view(_modelKey=modelKey)
### print "GLM result from glm_view:", h2o.dump_json(a)
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
glm_model = glm['glm_model']
_names = glm_model['_names']
coefficients_names = glm_model['coefficients_names']
submodels = glm_model['submodels'][0]
beta = submodels['beta']
norm_beta = submodels['norm_beta']
iteration = submodels['iteration']
validation = submodels['validation']
auc = validation['auc']
aic = validation['aic']
null_deviance = validation['null_deviance']
residual_deviance = validation['residual_deviance']
print '_names', _names
print 'coefficients_names', coefficients_names
# did beta get shortened? the simple check confirms names/beta/norm_beta are same length
print 'beta', beta
print 'iteration', iteration
print 'auc', auc
# now redo it all thru the browser
h2b.browseJsonHistoryAsUrl()
