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(s):
outDir = outDirBase + '_xy/'
opts = [
"--coordinates", coordDataFile, "--names", "layout", "--metric",
'spearman', "--scores", attsCodedFile, "--colormaps",
colorDataFile, "--directory", outDir, "--include-singletons",
"--no_layout_independent_stats", "--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
#check that it is mostly the same as the other files
util.compareActualVsExpectedDir(s,
expDir,
outDir,
excludeFiles=[
'log', 'mapMeta.json',
'assignments0.tab',
'neighbors_0.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_color(s):
outDir = outDirBase + '_xy_no_color/'
opts = [
"--coordinates", coordDataFile, "--scores", attsStringsFile,
"--names", "layout", "--directory", outDir, "--include-singletons",
"--no_layout_independent_stats", "--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(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_coordinates_layout_parms_renamed(s):
outDir = outDirBase + '_coordinates_layout_parms_renamed/'
opts = [
"--coordinates", coordDataFile, "--layoutName", "layout",
"--distanceMetric", 'spearman', "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
#check that it is mostly the same as the other files
util.compareActualVsExpectedDir(s,
expNoAttsDir,
outDir,
excludeFiles=[
'log', 'neighbors_0.tab',
'assignments0.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_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_group_meta_json_view_no_group_dir(s):
outDir = os.path.join(outDirBase, 'groupMetaCalcNoGroup/view/baseMap')
opts = [
"--layoutInputFile",
os.path.join(inDir, 'similarity.tab'), "--layoutInputFormat",
'sparseSimilarity', "--layoutName", "layout", "--role", "myRole",
"--outputDirectory", outDir, "--noLayoutIndependentStats",
"--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedFile(s, 'meta.json', expMetaDir, outDir)
def test_xy_no_atts(s):
outDir = outDirBase + '_xy_no_atts/'
opts = [
"--coordinates", coordDataFile, "--names", "layout", "--directory",
outDir, "--include-singletons", "--no_layout_independent_stats",
"--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(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_xy_no_atts(s):
outDir = outDirBase + 'xy_no_atts'
expDir = testDir + 'exp/layoutBasicNoAtts/'
#check that it is mostly the same as the other files
util.compareActualVsExpectedDir(s,
expDir,
outDir,
excludeFiles=[
'log', 'neighbors_0.tab',
'assignments0.tab', 'hexNames.tab',
'xyPreSquiggle_0.tab'
])
# These files for xy coords 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, '/neighbors_0.tab', expXyDir,
outDir)
util.compareActualVsExpectedFile(s, '/assignments0.tab', expXyDir,
outDir)
util.compareActualVsExpectedFile(s, '/xyPreSquiggle_0.tab', expXyDir,
outDir)
