def test_NA_fill(s):
"""Cluster data with Na present and zeroReplace
flag should pass.
"""
opts = Namespace(
layoutInputFormat = "clusterData",
layoutInputFile = [mat_with_na],
names = ["layout"],
metric = 'spearman',
directory = "out/nas",
singletons = True,
clumpinessStats = True,
mutualinfo = True,
associations = True,
zeroReplace = True
)
try:
layout.makeMapUIfiles(opts)
passed = True
except ValueError:
passed = False
s.assertTrue(passed)
def test_xy(s):
outDir = outDirBase + '_xy/'
opts = Namespace(
layoutInputFile= [coordDataFile],
names= ["layout"],
metric= 'spearman',
scores= [attsCodedFile],
colormaps= colorDataFile,
directory= outDir,
singletons=True,
clumpinessStats=False,
mutualinfo=False,
associations=False
)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
#check that it is mostly the same as the other files
util.compareActualVsExpectedDir(s,expDir, outDir,
excludeFiles = ['log',
'mapMeta.json',
'neighbors_0.tab',
'assignments0.tab',
'hexNames.tab',
'xyPreSquiggle_0.tab']
)
util.compareActualVsExpectedFile(s,'assignments0.tab',expXyDir,outDir)
util.compareActualVsExpectedFile(s,'xyPreSquiggle_0.tab',expXyDir,outDir)
def test_xy_no_colorMakeMapUIfiles(s):
outDir = outDirBase + '_xy_no_color/'
opts = Namespace(coordinates=[coordDataFile],
scores=[attsStringsFile],
names=["layout"],
directory=outDir,
singletons=True,
clumpinessStats=False,
mutualinfo=False,
associations=False)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
#check that it is mostly the same as the other files
util.compareActualVsExpectedDir(s,
expNoColorDir,
outDir,
excludeFiles=[
'log', 'assignments0.tab',
'neighbors_0.tab', 'hexNames.tab',
'xyPreSquiggle_0.tab'
])
#theese files are not expected to be the same as other runs,
# but to make sure they are correct we have but previous runs in a different
# expected directory.
util.compareActualVsExpectedFile(s, 'assignments0.tab', expXyDir,
outDir)
util.compareActualVsExpectedFile(s, 'xyPreSquiggle_0.tab', expXyDir,
outDir)
def test_xy_no_attsfromMakeUI(s):
outDir = outDirBase + '_xy_no_atts/'
opts = Namespace(coordinates=[coordDataFile],
names=["layout"],
directory=outDir,
singletons=True,
clumpinessStats=True,
mutualinfo=True,
associations=True)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s,
expNoAttsDir,
outDir,
excludeFiles=[
'log', 'mapMeta.json',
'neighbors_0.tab',
'assignments0.tab', 'hexNames.tab',
'xyPreSquiggle_0.tab'
])
util.compareActualVsExpectedFile(s, 'assignments0.tab', expXyDir,
outDir)
util.compareActualVsExpectedFile(s, 'xyPreSquiggle_0.tab', expXyDir,
outDir)
def test_top6_no_attsfromMakeUIfiles(s):
outDir = outDirBase + '_top6_no_atts/'
opts = Namespace(similarity=[top6SimDataFile],
names=["layout"],
directory=outDir,
singletons=True,
clumpinessStats=True,
mutualinfo=True,
associations=True)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, outDir)
def test_raw_no_attsfromMakeUIfiles(s):
outDir = outDirBase + '_raw_no_atts/'
opts = Namespace(feature_space=[rawDataFile],
names=["layout"],
metric='spearman',
directory=outDir,
singletons=True,
clumpinessStats=True,
mutualinfo=True,
associations=True)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, outDir)
def test_full_no_colorfromMakeUIfiles(s):
outDir = outDirBase + '_full_no_color/'
opts = Namespace(similarity_full=[fullSimDataFile],
names=["layout"],
scores=[attsStringsFile],
directory=outDir,
singletons=True,
clumpinessStats=False,
mutualinfo=False,
associations=False)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expNoColorDir, outDir)
def test_top6fromMakeUIfiles(s):
outDir = outDirBase + '_top6/'
opts = Namespace(similarity=[top6SimDataFile],
names=["layout"],
scores=[attsCodedFile],
colormaps=colorDataFile,
directory=outDir,
singletons=True,
clumpinessStats=False,
mutualinfo=False,
associations=False)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expDir, outDir)
def test_rawfromMakeUIfiles(s):
outDir = outDirBase + '_raw/'
opts = Namespace(feature_space=[rawDataFile],
names=["layout"],
metric='spearman',
scores=[attsCodedFile],
colormaps=colorDataFile,
directory=outDir,
singletons=True,
clumpinessStats=False,
mutualinfo=False,
associations=False)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expDir, outDir)
def test_fullfromMakeUIfiles(s):
outDir = outDirBase + '_full/'
#options for different layout.py executions
opts = Namespace(
layoutInputFile = [fullSimDataFile],
names = ["layout"],
scores = [attsCodedFile],
colormaps = colorDataFile,
directory = outDir,
singletons = True,
clumpinessStats=False,
mutualinfo=False,
associations=False
)
util.removeOldOutFiles(outDir)
layout.makeMapUIfiles(opts)
util.compareActualVsExpectedDir(s, expDir, outDir)
def calcMain(parms, ctx):
# The main process in which the job executes.
# Use standard exceptions here to report errors.
# @param parms: the parameters for the operation
# @param ctx: the job context
# @returns: (status, result) where the status is 'Success' or 'Error'
# and the result depends on the status:
# Success: a dict like:
# {
# 'status': 'Success',
# 'url': 'https://tumormap.ucsc.edu/?p=myMap',
# 'logFile': <logFileName>
# }
# Error: a dict containing one of the below:
# {'error': <message>}
# {'error': <message>, 'stackTrace': <trace>}
# Fix up relative paths and map any newer parm names to old parm names
# that are expected by the calc function. If we want this to become a public
# API, we need to accept the new names only.
opts = Namespace()
# layoutInput is required: accept either a file location relative to the
# data root, or a URL.
ctx.layoutInputUrls = []
if 'layoutInputDataId' in parms:
opts.layoutInputFile = \
[path.join(ctx.app.dataRoot, parms['layoutInputDataId'])]
ctx.layoutInputUrls.append(ctx.app.dataServer + '/data/' +
parms['layoutInputDataId'])
elif 'layoutInputUrl' in parms:
opts.layoutInputFile = [parms['layoutInputUrl']]
ctx.layoutInputUrls.append(parms['layoutInputUrl'])
# names and directory are required
opts.names = [parms['layoutInputName']]
opts.directory = path.join(ctx.app.dataRoot, parms['outputDirectory'])
# colorAttribute is optional: accept either a file location relative to the
# data root, or a URL.
ctx.colorAttributeUrls = []
if 'colorAttributeDataId' in parms:
opts.scores = \
[path.join(ctx.app.dataRoot, parms['colorAttributeDataId'])]
ctx.colorAttributeUrls.append(ctx.app.dataServer + '/data/' +
parms['colorAttributeDataId'])
elif 'colorAttributeUrl' in parms:
opts.scores = [parms['colorAttributeUrl']]
ctx.colorAttributeUrls.append(parms['colorAttributeUrl'])
# The rest of these are optional.
if 'zeroReplace' in parms:
opts.zeroReplace = parms['zeroReplace']
if 'noLayoutIndependentStats' in parms:
opts.associations = not parms['noLayoutIndependentStats']
if 'noLayoutAwareStats' in parms:
opts.mutualinfo = not parms['noLayoutAwareStats']
# Call the calc function.
result = {
'logFile': layout.makeMapUIfiles(opts),
}
# Check the calc log for success.
checkLog(result, ctx)
# Save the url to access the new map.
if 'viewServer' in parms:
viewServer = parms['viewServer']
else:
viewServer = ctx.app.viewServer
result['url'] = viewServer + '/?p=' + ctx.map
return "Success", result
