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76 changes: 76 additions & 0 deletions
76
...o/github/mzmine/modules/visualization/projectmetadata/io/ProjectMetadataExportModule.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| /* | ||
| * Copyright (c) 2004-2024 The mzmine Development Team | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person | ||
| * obtaining a copy of this software and associated documentation | ||
| * files (the "Software"), to deal in the Software without | ||
| * restriction, including without limitation the rights to use, | ||
| * copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the | ||
| * Software is furnished to do so, subject to the following | ||
| * conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be | ||
| * included in all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, | ||
| * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES | ||
| * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND | ||
| * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT | ||
| * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | ||
| * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | ||
| * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR | ||
| * OTHER DEALINGS IN THE SOFTWARE. | ||
| */ | ||
|
|
||
| package io.github.mzmine.modules.visualization.projectmetadata.io; | ||
|
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| import io.github.mzmine.datamodel.MZmineProject; | ||
| import io.github.mzmine.modules.MZmineModuleCategory; | ||
| import io.github.mzmine.modules.MZmineProcessingModule; | ||
| import io.github.mzmine.parameters.ParameterSet; | ||
| import io.github.mzmine.taskcontrol.Task; | ||
| import io.github.mzmine.util.ExitCode; | ||
| import java.time.Instant; | ||
| import java.util.Collection; | ||
| import java.util.logging.Logger; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.jetbrains.annotations.Nullable; | ||
|
|
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| public class ProjectMetadataExportModule implements MZmineProcessingModule { | ||
|
|
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| private static final Logger logger = Logger.getLogger( | ||
| ProjectMetadataExportModule.class.getName()); | ||
|
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| private static final String MODULE_NAME = "Project metadata export"; | ||
| private static final String MODULE_DESCRIPTION = "This module exports metadata to .tsv or .csv-format."; | ||
|
|
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| @Override | ||
| public @NotNull String getName() { | ||
| return MODULE_NAME; | ||
| } | ||
|
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| @Override | ||
| public @NotNull String getDescription() { | ||
| return MODULE_DESCRIPTION; | ||
| } | ||
|
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| @Override | ||
| public @Nullable Class<? extends ParameterSet> getParameterSetClass() { | ||
| return ProjectMetadataImportParameters.class; | ||
| } | ||
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| @Override | ||
| public @NotNull MZmineModuleCategory getModuleCategory() { | ||
| return MZmineModuleCategory.PROJECTMETADATA; | ||
| } | ||
|
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| @Override | ||
| public @NotNull ExitCode runModule(@NotNull MZmineProject project, | ||
| @NotNull ParameterSet parameters, @NotNull Collection<Task> tasks, | ||
| @NotNull Instant moduleCallDate) { | ||
| tasks.add(new ProjectMetadataExportTask(moduleCallDate, parameters)); | ||
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| return ExitCode.OK; | ||
| } | ||
| } |
77 changes: 77 additions & 0 deletions
77
...thub/mzmine/modules/visualization/projectmetadata/io/ProjectMetadataExportParameters.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| /* | ||
| * Copyright (c) 2004-2024 The mzmine Development Team | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person | ||
| * obtaining a copy of this software and associated documentation | ||
| * files (the "Software"), to deal in the Software without | ||
| * restriction, including without limitation the rights to use, | ||
| * copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the | ||
| * Software is furnished to do so, subject to the following | ||
| * conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be | ||
| * included in all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, | ||
| * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES | ||
| * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND | ||
| * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT | ||
| * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | ||
| * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | ||
| * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR | ||
| * OTHER DEALINGS IN THE SOFTWARE. | ||
| */ | ||
|
|
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| package io.github.mzmine.modules.visualization.projectmetadata.io; | ||
|
|
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| import io.github.mzmine.parameters.ParameterSet; | ||
| import io.github.mzmine.parameters.impl.SimpleParameterSet; | ||
| import io.github.mzmine.parameters.parametertypes.ComboParameter; | ||
| import io.github.mzmine.parameters.parametertypes.filenames.FileNameParameter; | ||
| import io.github.mzmine.parameters.parametertypes.filenames.FileSelectionType; | ||
| import io.github.mzmine.util.files.ExtensionFilters; | ||
| import java.io.File; | ||
|
|
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| public class ProjectMetadataExportParameters extends SimpleParameterSet { | ||
|
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| public enum MetadataFileFormat { | ||
| DEFAULT, | ||
| /** | ||
| * Adds additional headers for data types | ||
| */ | ||
| MZMINE_INTERNAL, | ||
| /** | ||
| * GNPS requires Filename and then all other columns with ATTRIBUTE_ prefix | ||
| */ | ||
| GNPS; | ||
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| @Override | ||
| public String toString() { | ||
| return switch (this) { | ||
| case DEFAULT -> "Default"; | ||
| case MZMINE_INTERNAL -> "mzmine internal"; | ||
| case GNPS -> "GNPS"; | ||
| }; | ||
| } | ||
| } | ||
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| public static final FileNameParameter fileName = new FileNameParameter("Metadata file", """ | ||
| CSV or TSV file to save metadata to.""", ExtensionFilters.CSV_TSV_EXPORT, | ||
| FileSelectionType.SAVE); | ||
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| public static final ComboParameter<MetadataFileFormat> format = new ComboParameter<>("Format", | ||
| "Format to export the metadata in", MetadataFileFormat.values(), MetadataFileFormat.DEFAULT); | ||
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| public ProjectMetadataExportParameters() { | ||
| super(fileName, format); | ||
| } | ||
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| public static ParameterSet create(final File file, final MetadataFileFormat mFormat) { | ||
| ParameterSet params = new ProjectMetadataExportParameters().cloneParameterSet(); | ||
| params.setParameter(fileName, file); | ||
| params.setParameter(format, mFormat); | ||
| return params; | ||
| } | ||
|
|
||
| } |
66 changes: 66 additions & 0 deletions
66
.../io/github/mzmine/modules/visualization/projectmetadata/io/ProjectMetadataExportTask.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,66 @@ | ||
| /* | ||
| * Copyright (c) 2004-2024 The mzmine Development Team | ||
| * | ||
| * Permission is hereby granted, free of charge, to any person | ||
| * obtaining a copy of this software and associated documentation | ||
| * files (the "Software"), to deal in the Software without | ||
| * restriction, including without limitation the rights to use, | ||
| * copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| * copies of the Software, and to permit persons to whom the | ||
| * Software is furnished to do so, subject to the following | ||
| * conditions: | ||
| * | ||
| * The above copyright notice and this permission notice shall be | ||
| * included in all copies or substantial portions of the Software. | ||
| * | ||
| * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, | ||
| * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES | ||
| * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND | ||
| * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT | ||
| * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, | ||
| * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | ||
| * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR | ||
| * OTHER DEALINGS IN THE SOFTWARE. | ||
| */ | ||
|
|
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| package io.github.mzmine.modules.visualization.projectmetadata.io; | ||
|
|
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| import io.github.mzmine.modules.visualization.projectmetadata.io.ProjectMetadataExportParameters.MetadataFileFormat; | ||
| import io.github.mzmine.modules.visualization.projectmetadata.table.MetadataTable; | ||
| import io.github.mzmine.parameters.ParameterSet; | ||
| import io.github.mzmine.project.ProjectService; | ||
| import io.github.mzmine.taskcontrol.AbstractSimpleToolTask; | ||
| import java.io.File; | ||
| import java.time.Instant; | ||
| import org.jetbrains.annotations.NotNull; | ||
|
|
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| public class ProjectMetadataExportTask extends AbstractSimpleToolTask { | ||
|
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| private final File file; | ||
| private final MetadataFileFormat format; | ||
|
|
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| /** | ||
| * @param moduleCallDate the call date of module to order execution order | ||
| */ | ||
| public ProjectMetadataExportTask(final @NotNull Instant moduleCallDate, | ||
| @NotNull final ParameterSet parameters) { | ||
| super(moduleCallDate, parameters); | ||
| file = parameters.getValue(ProjectMetadataExportParameters.fileName); | ||
| format = parameters.getValue(ProjectMetadataExportParameters.format); | ||
| } | ||
|
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| @Override | ||
| protected void process() { | ||
| MetadataTable metadata = ProjectService.getProject().getProjectMetadata(); | ||
| ProjectMetadataWriter writer = new ProjectMetadataWriter(metadata, format); | ||
| if (!writer.exportTo(file)) { | ||
| error("Error during metadata file export"); | ||
| return; | ||
| } | ||
| } | ||
|
|
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| @Override | ||
| public String getTaskDescription() { | ||
| return "Exporting project metadata to file"; | ||
| } | ||
| } |
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