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_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_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_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 = [ "--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_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_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_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_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_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_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_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_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_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_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_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_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)
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 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_stats(s): s.runPy() util.compareActualVsExpectedDir(s, expDir, outDir)
def test_top6_no_atts(s): outDir = outDirBase + 'top6_no_atts' expDir = testDir + 'exp/layoutBasicNoAtts/' util.compareActualVsExpectedDir(s, expDir, outDir)
def test_raw_no_colors(s): outDir = outDirBase + 'raw_no_colors' expDir = testDir + 'exp/layoutBasicNoColor/' util.compareActualVsExpectedDir(s, expDir, outDir)