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_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_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_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_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_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_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_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_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_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_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_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 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_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_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)
import layout # # __MAIN__ # if __name__ == '__main__': print 'DB Check' initialize_curses_vars(True) bf = base_form() reset_terminal() layout.main() sys.exit(0) # # Meta Pwd # ask_meta_pwd() #dialog = test_dialog() #dialog.display() tab = table_window() tab.populate() tab.refresh() tab.display() tab.navigate()
del self.settings def main(): app = QtWidgets.QApplication(sys.argv) # app style app.setStyle("plastique") # app setting in general but specifically so that call to QSettings() uses meaningful path for settings app.setOrganizationName("jling_projects") app.setApplicationName("Time Machine") appWin = TimeMachineApp() # connect main window close and app close events app.aboutToQuit.connect(appWin.close) try: appWin.show() appWin.show_first_time() # disable resizing or stretching of main window appWin.setFixedSize(appWin.size()) except Exception as e: QtWidgets.QMessageBox.information("QCalendarWidget Date Selected", e) sys.exit(app.exec_()) if __name__ == '__main__': main()
pass import layout # # __MAIN__ # if __name__ == '__main__': print 'DB Check' initialize_curses_vars(True) bf = base_form() reset_terminal() layout.main() sys.exit(0) # # Meta Pwd # ask_meta_pwd() #dialog = test_dialog() #dialog.display() tab = table_window() tab.populate() tab.refresh() tab.display() tab.navigate()