def test_parms_renaming_deprecated_parms(s):
outDir = outDirBase + '_renamingDeprecatedParms/'
opts = [
# parms renaming deprecated parms
"--outputDirectory",
outDir,
"--firstAttribute",
"mutated/not",
"--layoutName",
"layout",
"--noLayoutIndependentStats",
"--noLayoutAwareStats",
"--distanceMetric",
"cosine",
"--outputTar",
os.path.join(outDir, 'tar.tar'),
"--outputZip",
os.path.join(outDir, 'zip.zip'),
"--authGroup",
"myRole",
"--colorAttributeFile",
attsStringsFile,
"--neighborCount",
"9",
"--feature_space",
rawDataFile
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(
s, expParmDir, outDir,
['log', 'meta.json', 'mapMeta.json', 'tar.tar', 'zip.zip'])
def test_sim6Layout_check(s):
'''
This test insures that if you start from the same data,
the output does not depend on the input form
'''
outDir = outDirBase + '_top6/'
#opts for compute sparse to create a sparse top 6 spearman
optsSparsSim = [
'--in_file', rawDataFile,
'--metric', 'spearman',
'--output_type', 'SPARSE',
'--top', '6',
'--out_file', outSim6File,
'--num_jobs', '2'
]
compute_sparse_matrix.main(optsSparsSim)
optsLayoutSparse = [
"--similarity", outSim6File,
"--names", "layout",
"--scores", attsCodedFile,
"--colormaps", colorDataFile,
"--directory", outDir,
"--include-singletons",
"--no_layout_independent_stats",
"--no_layout_aware_stats"]
util.removeOldOutFiles(outDir)
layout.main(optsLayoutSparse)
util.compareActualVsExpectedDir(s, expDir, 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(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_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_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_deprecated_parms_renamed(s):
outDir = outDirBase + '_deprecatedParmsRenamed/'
opts = [
# parms deprecated in favor of new names
"--directory",
outDir,
"--first_attribute",
"mutated/not",
"--names",
"layout",
"--no_layout_independent_stats",
"--no_layout_aware_stats",
"--metric",
"cosine",
"--output_tar",
os.path.join(outDir, 'tar.tar'),
"--output_zip",
os.path.join(outDir, 'zip.zip'),
"--role",
"myRole",
"--scores",
attsStringsFile,
"--truncation_edges",
"9",
"--feature_space",
rawDataFile
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(
s, expParmDir, outDir,
['log', 'meta.json', 'mapMeta.json', 'tar.tar', 'zip.zip'])
def test_raw_no_atts(s):
outDir = outDirBase + '_raw_no_atts/'
opts = [
"--feature_space", rawDataFile, "--names", "layout", "--metric",
'spearman', "--directory", outDir, "--include-singletons",
"--no_layout_independent_stats", "--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, 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_top6_no_color(s):
outDir = outDirBase + '_top6_no_color/'
opts = [
"--scores", attsStringsFile, "--similarity", top6SimDataFile,
"--names", "layout", "--directory", outDir, "--include-singletons",
"--no_layout_independent_stats", "--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoColorDir, outDir)
def test_raw_layout_parms_renamed(s):
outDir = outDirBase + '_raw_layout_parms_renamed/'
opts = [
"--feature_space", rawDataFile, "--layoutName", "layout",
"--distanceMetric", 'spearman', "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, outDir)
def test_parms_renaming_full_layout(s):
outDir = outDirBase + 'parms_renaming_full_layout/'
opts = [
"--layoutInputFile", fullSimDataFile, "--layoutInputFormat",
"fullSimilarity", "--layoutName", "layout", "--distanceMetric",
'spearman', "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, 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_renaming_2_raw_layout(s):
outDir = outDirBase + '_renaming_2_raw_layout/'
opts = [
"--layoutInputFile", rawDataFile, "--layoutInputFile",
rawDataFile_2, "--layoutInputFormat", 'clusterData',
"--layoutName", "layout", "--layoutName", "layout_2",
"--distanceMetric", 'spearman', "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoAtts2Dir, 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_map_meta_json_non_standard(s):
outDir = os.path.join(outDirBase, 'mapMetaCalcNonStandard')
opts = [
"--layoutInputFile",
os.path.join(inDir, 'full_matrix.tab'), "--layoutInputFile",
os.path.join(inDir, 'full_matrix_2.tab'), "--layoutInputFormat",
'clusterData', "--layoutName", "layout", "--layoutName",
"layout_2", "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedFile2(
s, os.path.join(expMetaDir, 'mapMetaEmpty.json'),
os.path.join(outDir, 'mapMeta.json'))
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_no_feature_file(s):
outDir = outDirBase + '_junk/'
opts = [
"--names", "layout", "--metric", 'spearman', "--directory", outDir,
"--include-singletons", "--no_layout_independent_stats",
"--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
try:
rc = 0
rc = layout.main(opts)
s.assertTrue(rc, 'this should have failed')
except ValueError as e:
s.assertTrue(e, e)
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_map_meta_json_standard_simple(s):
inDir = os.path.join(testDir, 'in/dataRoot/featureSpace/simpleMapName')
outDir = os.path.join(outDirBase, 'mapMetaCalcStandardSimple')
opts = [
"--layoutInputFile",
os.path.join(inDir, 'full_matrix.tab'), "--layoutInputFile",
os.path.join(inDir, 'full_matrix_2.tab'), "--layoutInputFormat",
'clusterData', "--layoutName", "layout", "--layoutName",
"layout_2", "--outputDirectory", outDir,
"--noLayoutIndependentStats", "--noLayoutAwareStats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedFile2(
s, os.path.join(expMetaDir, 'mapMetaSimple.json'),
os.path.join(outDir, 'mapMeta.json'))
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_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 test_full(s):
outDir = outDirBase + '_full/'
#opts for compute sparse to create a full spearman
opts = [
'--in_file', rawDataFile, '--metric', 'spearman', '--output_type',
'full', '--out_file', fullSimDataFile, '--num_jobs', '2'
]
compute_sparse_matrix.main(opts)
#options for different layout.py executions
opts = [
"--similarity_full", fullSimDataFile, "--names", "layout",
"--scores", attsCodedFile, "--colormaps", colorDataFile,
"--directory", outDir, "--include-singletons",
"--no_layout_independent_stats", "--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expDir, outDir)
def test_constants_replacing_deprecated_parms(s):
outDir = outDirBase + '_constantsReplacingdeprecatedParms/'
opts = [
# deprecated parms replaced with constant values
#"--directed_graph",
#"--include-singletons",
#"--window_size", "9999",
# unchanged parms:
"--feature_space",
rawDataFile,
"--names",
"layout",
"--directory",
outDir,
"--no_layout_independent_stats",
"--no_layout_aware_stats"
]
util.removeOldOutFiles(outDir)
layout.main(opts)
util.compareActualVsExpectedDir(s, expNoAttsDir, outDir)
def runPy(s):
# Build the parms to be passed to layout.py
opts = [
'--similarity',
inDir + 'artificial_sparse.tab',
'--names',
'mRNA',
'--scores',
inDir + 'attributes.tabstringed',
'--colormaps',
inDir + 'colormaps.tab',
'--first_attribute',
'Subtype',
'--directory',
outDir,
]
#clear output directory
util.removeOldOutFiles(outDir)
# Run the layout
layout.main(opts)
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)
