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added commandline tool for easy selftest
(cherry picked from commit 9d64846)
1 parent ed7adb3 commit 6e3e302

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‎sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/selftest/SelfTestOptions.java‎

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package de.unijena.bioinf.ms.frontend.subtools.selftest;
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import de.unijena.bioinf.ms.frontend.subtools.Provide;
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import de.unijena.bioinf.ms.frontend.subtools.RootOptions;
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import de.unijena.bioinf.ms.frontend.subtools.StandaloneTool;
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import de.unijena.bioinf.ms.properties.ParameterConfig;
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import lombok.extern.slf4j.Slf4j;
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import picocli.CommandLine;
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@Slf4j
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@CommandLine.Command(name = "selftest", description = "<STANDALONE> Performs some basic tests to validate whether the application is working correctly independent from login, license and server connection. %n %n", versionProvider = Provide.Versions.class, mixinStandardHelpOptions = true, showDefaultValues = true, hidden = true)
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public class SelfTestOptions implements StandaloneTool<SelfTestWorkflow> {
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@Override
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public SelfTestWorkflow makeWorkflow(RootOptions<?> rootOptions, ParameterConfig config) {
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return new SelfTestWorkflow();
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}
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}

‎sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/subtools/selftest/SelfTestWorkflow.java‎

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package de.unijena.bioinf.ms.frontend.subtools.selftest;
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import de.unijena.bioinf.ChemistryBase.chem.MolecularFormula;
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import de.unijena.bioinf.ChemistryBase.chem.PrecursorIonType;
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import de.unijena.bioinf.ChemistryBase.jobs.SiriusJobs;
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import de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment;
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import de.unijena.bioinf.ChemistryBase.ms.MutableMs2Experiment;
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import de.unijena.bioinf.ChemistryBase.ms.ft.FTree;
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import de.unijena.bioinf.ChemistryBase.ms.ft.FragmentAnnotation;
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import de.unijena.bioinf.ChemistryBase.ms.ft.Score;
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import de.unijena.bioinf.ChemistryBase.ms.utils.SimpleSpectrum;
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import de.unijena.bioinf.FragmentationTreeConstruction.computation.FasterTreeComputationInstance;
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import de.unijena.bioinf.FragmentationTreeConstruction.computation.FragmentationPatternAnalysis;
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import de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilder;
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import de.unijena.bioinf.FragmentationTreeConstruction.computation.tree.TreeBuilderFactory;
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import de.unijena.bioinf.IsotopePatternAnalysis.ExtractedIsotopePattern;
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import de.unijena.bioinf.babelms.GenericParser;
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import de.unijena.bioinf.babelms.MsExperimentParser;
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import de.unijena.bioinf.jjobs.JJob;
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import de.unijena.bioinf.jjobs.JobManager;
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import de.unijena.bioinf.ms.frontend.core.ApplicationCore;
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import de.unijena.bioinf.ms.frontend.workflow.Workflow;
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import de.unijena.bioinf.sirius.Ms2Preprocessor;
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import de.unijena.bioinf.sirius.ProcessedInput;
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import de.unijena.bioinf.sirius.Sirius;
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import de.unijena.bioinf.sirius.annotations.DecompositionList;
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import it.unimi.dsi.fastutil.Pair;
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import lombok.extern.slf4j.Slf4j;
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import org.jetbrains.annotations.NotNull;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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@Slf4j
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public class SelfTestWorkflow implements Workflow {
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Sirius sirius = ApplicationCore.SIRIUS_PROVIDER.sirius();
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@Override
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public void run() {
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try {
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log.info("Checking ILP solvers using TreeBuilder.");
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for (TreeBuilderFactory.DefaultBuilder builderType : TreeBuilderFactory.DefaultBuilder.values()) {
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log.info("Checking solver: {}", builderType.name());
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TreeBuilder builder = TreeBuilderFactory.getInstance().getTreeBuilder(builderType);
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log.info("Checking solver '{}{}", builderType.name(), builder != null ? "' SUCCESSFUL." : "' FAILED!");
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}
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log.info("Checking ILP solvers SUCCESSFUL! At least one ILP solver is available.");
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log.info("Checking computing FragmentationTree...");
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testTreeComputation();
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log.info("FragmentationTree computation SUCCESSFUL!");
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log.info("Loading Test Data...");
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List<Pair<Ms2Experiment, MolecularFormula>> experiments = List.of(
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Pair.of(getStandardExample("/de.unijena.bioinf.ms.frontend.subtools.selftest/Kaempferol.ms"), MolecularFormula.parseOrThrow("C15H10O6")),
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Pair.of(getStandardExample("/de.unijena.bioinf.ms.frontend.subtools.selftest/Laudanosine.mgf"), MolecularFormula.parseOrThrow("C21H27NO4")),
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Pair.of(getStandardExample("/de.unijena.bioinf.ms.frontend.subtools.selftest/Valium.cef"), MolecularFormula.parseOrThrow("C16H13ClN2O")));
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log.info("Loading Test Data DONE!");
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for (Pair<Ms2Experiment, MolecularFormula> data : experiments) {
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testFormulaId(data.first(), data.second());
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}
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} catch (Exception e) {
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log.error("Self-test failed!", e);
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System.exit(99);
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}
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}
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public static MutableMs2Experiment getStandardExample(String resourcePath) throws IOException, URISyntaxException {
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MsExperimentParser parser = new MsExperimentParser();
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URL str = SelfTestOptions.class.getResource(resourcePath);
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BufferedReader buf = new BufferedReader(new InputStreamReader(str.openStream()));
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GenericParser<Ms2Experiment> p = parser.getParser(resourcePath);
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Ms2Experiment exp = p.parse(buf, str.toURI());
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return (MutableMs2Experiment) exp;
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}
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public void testTreeComputation() {
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final Ms2Experiment experiment = new MutableMs2Experiment(sirius.getMs2Experiment(368.113616943359d, PrecursorIonType.getPrecursorIonType("[M+H]+"),
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new SimpleSpectrum(
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new double[]{368.113616943359d, 369.116424560547d, 370.118530273438d, 371.121459960938d},
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new double[]{7.4298448E7d, 1.656387E7d, 2646426.25d, 296325.0625d }
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),
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Arrays.asList(
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new SimpleSpectrum(
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new double[]{100.3957290649414,109.0745849609375,110.39244079589844,116.84909057617188,119.04886627197266,124.55211639404297,138.5615692138672,139.62106323242188,149.0595703125,159.04342651367188,174.05429077148438,175.0388641357422,175.82968139648438,176.07041931152344,179.0346221923828,188.0712432861328,189.0785675048828,189.7934112548828,190.08619689941406,190.37754821777344,191.0943603515625,193.0496368408203,193.2034149169922,203.97384643554688,211.36386108398438,223.0755157470703,232.05950927734375,235.07550048828125,246.56312561035156,249.05589294433594,251.07077026367188,261.0544738769531,263.0704650878906,265.0871276855469,267.0630798339844,277.0498962402344,279.0650634765625,281.0810546875,289.0498352050781,291.0655822753906,292.0743713378906,293.08099365234375,295.0606384277344,297.0776672363281,297.3970947265625,302.46124267578125,303.0662841796875,305.08026123046875,305.6075134277344,306.0570373535156,306.45819091796875,306.8253479003906,307.0602111816406,307.2962951660156,307.5075988769531,307.66400146484375,308.0629577636719,309.07525634765625,318.4222412109375,318.80999755859375,319.0596923828125,319.3089599609375,319.70037841796875,320.06549072265625,321.0744323730469,322.1073913574219,325.07000732421875,326.0737609863281,332.0915222167969,333.0755310058594,335.0784606933594,337.0704040527344,338.0983581542969,339.0876159667969,350.1022033691406,353.0880432128906,366.08294677734375,367.3216247558594,368.11273193359375,368.216552734375,368.8077087402344,369.1158142089844,369.42626953125,369.91241455078125,},
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new double[]{4537.85205078125,4636.14208984375,4386.55224609375,4726.12646484375,9624.818359375,5201.5712890625,5279.810546875,4162.4697265625,177876.6875,6609.36865234375,10644.8896484375,13759.1005859375,4984.36572265625,151992.171875,12310.5283203125,25785.259765625,52822.25390625,14517.52734375,2420622.25,7693.88671875,55927.109375,12310.1162109375,5552.3896484375,5172.888671875,7269.5537109375,10368.4189453125,11730.9384765625,21044.888671875,4541.33251953125,11602.5078125,34444.68359375,46705.83984375,49155.7421875,27223.947265625,7353.82177734375,147195.140625,45302.55078125,62019.55859375,284616.4375,102046.0546875,35895.4609375,82949.75,69763.328125,8305.2294921875,6610.50537109375,7126.484375,47796.5703125,13488.21875,5194.052734375,7746.63916015625,36957.0703125,51496.2109375,7290191.5,30372.474609375,9119.17578125,28094.4296875,117144.4453125,70117.2421875,9554.611328125,11817.4228515625,1896174.375,8624.4208984375,8855.138671875,27861.388671875,37455.0078125,8466.224609375,333207.96875,6757.73486328125,70097.484375,37933.45703125,278163.8125,362786.59375,10204.8984375,17157.6484375,350741.3125,10007.03125,5503.0703125,6211.84912109375,1299435.75,6204.93994140625,10005.435546875,1837789.875,8296.6474609375,5625.576171875}
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))
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));
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final Ms2Preprocessor preprocessor = new Ms2Preprocessor();
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final ProcessedInput processedInput = preprocessor.preprocess(experiment);
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sirius.getMs1Analyzer().computeAndScoreIsotopePattern(processedInput);
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final FragmentationPatternAnalysis analysis = sirius.getMs2Analyzer();
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FasterTreeComputationInstance instance = new FasterTreeComputationInstance(analysis, processedInput);
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JobManager jobs = SiriusJobs.getGlobalJobManager();
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jobs.submitJob(instance);
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FasterTreeComputationInstance.FinalResult finalResult = instance.takeResult();
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final FTree top = finalResult.getResults().get(0);
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assert MolecularFormula.parseOrThrow("C20H17NO6").equals(top.getRoot().getFormula());
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// test ms1
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final FragmentAnnotation<Score> score = top.getFragmentAnnotationOrThrow(Score.class);
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assert (score.get(top.getRoot()).get("MS-Isotopes") > 0);
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// number of decompositions should be equal in MS1 and MSMS
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assert (processedInput.getAnnotationOrThrow(ExtractedIsotopePattern.class).getExplanations().size() == processedInput.getPeakAnnotationOrThrow(DecompositionList.class).get(processedInput.getParentPeak()).getDecompositions().size());
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}
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public void testFormulaId(@NotNull Ms2Experiment experiment, @NotNull MolecularFormula tophit) {
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log.info("Testing formulaID for '{}'...", experiment.getSource().toString());
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// for profiling
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final Ms2Preprocessor preprocessor = new Ms2Preprocessor();
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final ProcessedInput processedInput = preprocessor.preprocess(experiment);
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sirius.getMs1Analyzer().computeAndScoreIsotopePattern(processedInput);
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final FragmentationPatternAnalysis analysis = sirius.getMs2Analyzer();
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JobManager jobsManager = SiriusJobs.getGlobalJobManager();
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TreeBuilder builder = TreeBuilderFactory.getInstance().getTreeBuilder("clp");
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analysis.setTreeBuilder(builder);
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List<FasterTreeComputationInstance> jobs = new ArrayList<>();
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for (int i = 0; i < 20; ++i) {
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FasterTreeComputationInstance instance = new FasterTreeComputationInstance(analysis, processedInput);
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jobs.add(jobsManager.submitJob(instance));
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}
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jobs.forEach(JJob::takeResult);
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final FTree top = jobs.get(jobs.size() - 1).getResult().getResults().get(0);
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assert top.getRoot().getFormula().equals(tophit);
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log.info("Testing formulaID for '{}' SUCCESSFUL!", experiment.getSource().toString());
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}
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}

‎sirius_cli/src/main/java/de/unijena/bioinf/ms/frontend/workflow/WorkflowBuilder.java‎

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@@ -33,6 +33,7 @@
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import de.unijena.bioinf.ms.frontend.subtools.login.LoginOptions;
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import de.unijena.bioinf.ms.frontend.subtools.msnovelist.MsNovelistOptions;
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import de.unijena.bioinf.ms.frontend.subtools.project.ProjectOptions;
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import de.unijena.bioinf.ms.frontend.subtools.selftest.SelfTestOptions;
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import de.unijena.bioinf.ms.frontend.subtools.settings.SettingsOptions;
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import de.unijena.bioinf.ms.frontend.subtools.sirius.SiriusOptions;
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import de.unijena.bioinf.ms.frontend.subtools.spectra_search.SpectraSearchOptions;
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DefaultParameterConfigLoader configOptionLoader;
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//standalone tools
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public final SelfTestOptions selfTestOptions;
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public final CustomDBOptions customDBOptions;
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public final ProjectOptions projectOptions;
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@@ -149,6 +151,7 @@ CanopusOptions.class, new CanopusOptions(configOptionLoader),
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MsNovelistOptions.class, new MsNovelistOptions(configOptionLoader)
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);
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selfTestOptions = new SelfTestOptions();
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customDBOptions = new CustomDBOptions();
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projectOptions = new ProjectOptions();
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// similarityMatrixOptions = new SimilarityMatrixOptions(spaceManagerFactory);
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protected Object[] standaloneTools() {
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return Stream.concat(
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Stream.concat(
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Stream.of(customDBOptions, projectOptions, /*similarityMatrixOptions,*/ decompOptions, mgfExporterOptions, /*exportPredictions,*/ fingerprinterOptions/*, updateFingerprintOptions*/),
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Stream.of(customDBOptions, projectOptions, /*similarityMatrixOptions,*/ decompOptions, mgfExporterOptions, /*exportPredictions,*/ fingerprinterOptions/*, updateFingerprintOptions*/, selfTestOptions),
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additionalTools.stream()
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), Stream.of(loginOptions, settingsOptions, autocompleteOptions)
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).toArray(Object[]::new);

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