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Merge branch '43-implement-reporting-of-affected-compounds-and-featur…
…es-in-jobs' into 'master' Resolve "implement reporting of affected compounds and features in jobs and compute flag handling" Closes #37 and #43 See merge request bright-giant/sirius/sirius-frontend!15
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...in/java/de/unijena/bioinf/ms/frontend/subtools/projectspace/ImportFromMemoryWorkflow.java
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| /* | ||
| * | ||
| * This file is part of the SIRIUS library for analyzing MS and MS/MS data | ||
| * | ||
| * Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker, | ||
| * Chair of Bioinformatics, Friedrich-Schiller University. | ||
| * | ||
| * This library is free software; you can redistribute it and/or | ||
| * modify it under the terms of the GNU Lesser General Public | ||
| * License as published by the Free Software Foundation; either | ||
| * version 3 of the License, or (at your option) any later version. | ||
| * | ||
| * This library is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| * Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt> | ||
| */ | ||
|
|
||
| package de.unijena.bioinf.ms.frontend.subtools.projectspace; | ||
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| import de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment; | ||
| import de.unijena.bioinf.ChemistryBase.ms.SpectrumFileSource; | ||
| import de.unijena.bioinf.babelms.CloseableIterator; | ||
| import de.unijena.bioinf.babelms.GenericParser; | ||
| import de.unijena.bioinf.babelms.MsExperimentParser; | ||
| import de.unijena.bioinf.jjobs.JobProgressEvent; | ||
| import de.unijena.bioinf.jjobs.JobProgressEventListener; | ||
| import de.unijena.bioinf.jjobs.JobProgressMerger; | ||
| import de.unijena.bioinf.jjobs.ProgressSupport; | ||
| import de.unijena.bioinf.ms.frontend.workflow.Workflow; | ||
| import de.unijena.bioinf.projectspace.CompoundContainerId; | ||
| import de.unijena.bioinf.projectspace.Instance; | ||
| import de.unijena.bioinf.projectspace.ProjectSpaceManager; | ||
| import org.jetbrains.annotations.NotNull; | ||
|
|
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| import java.io.BufferedReader; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.function.Supplier; | ||
|
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| public class ImportFromMemoryWorkflow implements Workflow, ProgressSupport { | ||
| protected final JobProgressMerger progressSupport = new JobProgressMerger(this); | ||
| private List<CompoundContainerId> importedCompounds = null; | ||
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| public List<CompoundContainerId> getImportedCompounds() { | ||
| return importedCompounds; | ||
| } | ||
|
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| private ProjectSpaceManager<?> psm; | ||
|
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| private Supplier<BufferedReader> dataReaderProvide; | ||
|
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| private String sourceName; | ||
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| private String ext; | ||
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| public ImportFromMemoryWorkflow(ProjectSpaceManager<?> psm, Supplier<BufferedReader> dataReaderProvide, String sourceName, String ext) { | ||
| this.psm = psm; | ||
| this.dataReaderProvide = dataReaderProvide; | ||
| this.sourceName = sourceName; | ||
| this.ext = ext; | ||
| } | ||
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| @Override | ||
| public void updateProgress(long min, long max, long progress, String shortInfo) { | ||
| progressSupport.updateConnectedProgress(min, max, progress, shortInfo); | ||
| } | ||
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| @Override | ||
| public void addJobProgressListener(JobProgressEventListener listener) { | ||
| progressSupport.addPropertyChangeListener(listener); | ||
| } | ||
|
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| @Override | ||
| public void removeJobProgressListener(JobProgressEventListener listener) { | ||
| progressSupport.removeProgress(listener); | ||
| } | ||
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| @Override | ||
| public JobProgressEvent currentProgress() { | ||
| return progressSupport.currentConnectedProgress(); | ||
| } | ||
|
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| @Override | ||
| public JobProgressEvent currentCombinedProgress() { | ||
| return progressSupport.currentCombinedProgress(); | ||
| } | ||
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| @Override | ||
| public void run() { | ||
| importedCompounds = new ArrayList<>(); | ||
| GenericParser<Ms2Experiment> parser = new MsExperimentParser() | ||
| .getParserByExt(ext); | ||
|
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| int progress = 0; | ||
| try (BufferedReader bodyStream = dataReaderProvide.get()) { | ||
| updateProgress(0, -1, progress, "Data reader opened"); | ||
| try (CloseableIterator<Ms2Experiment> it = parser.parseIterator(bodyStream, null)) { | ||
| while (it.hasNext()) { | ||
| Ms2Experiment next = it.next(); | ||
| if (sourceName != null) // workaround to fake import file | ||
| next.setAnnotation(SpectrumFileSource.class, | ||
| new SpectrumFileSource( | ||
| new File("./" + (sourceName.endsWith(ext) ? sourceName : sourceName + "." + ext.toLowerCase())).toURI())); | ||
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| @NotNull Instance inst = psm.newCompoundWithUniqueId(next); | ||
| importedCompounds.add(inst.getID()); | ||
| updateProgress(0, -1, ++progress, "Imported: " + inst.getID().toString()); | ||
| } | ||
| } | ||
| } catch (IOException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| updateProgress(0, progress, progress, null); | ||
| } | ||
| } |
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