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| # Journal Abbreviations | ||
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| ## Preparation | ||
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| - Ensure that `buildres/abbrv.jabref.org` contains data. Otherwise, the submodules were not configured correctly. | ||
| - Ensure that `build/resources/main/journals/journal-list.mv` exists. It is generated by gradle task `generateJournalListMV`, which uses `org.jabref.cli.JournalListMvGenerator`. | ||
|
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| ## Where does the data come from? | ||
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| The generator uses all `.csv` files from <https://github.com/JabRef/abbrv.jabref.org/tree/main/journals>, but ignores following ones: | ||
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| ```java | ||
| Set<String> ignoredNames = Set.of( | ||
| // remove all lists without dot in them: | ||
| // we use abbreviation lists containing dots in them only (to be consistent) | ||
| "journal_abbreviations_entrez.csv", | ||
| "journal_abbreviations_medicus.csv", | ||
| "journal_abbreviations_webofscience-dotless.csv", | ||
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| // we currently do not have good support for BibTeX strings | ||
| "journal_abbreviations_ieee_strings.csv" | ||
| ); | ||
| ``` | ||
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| ## Future work | ||
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| See <https://github.com/JabRef/jabref-issue-melting-pot/issues/41> |
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docs/decisions/0043-show-merge-dialog-when-importing-a-single-pdf.md
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| --- | ||
| nav_order: 43 | ||
| parent: Decision Records | ||
| --- | ||
| # Show merge dialog when importing a single PDF | ||
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| ## Context and Problem Statement | ||
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| PDF files are one of the main format for transferring various documents, especially scientific papers. However, by itself, | ||
| PDF is like a picture, it contains commands solely for displaying the human-readable text, but it might not contain | ||
| computer-readable metadata. | ||
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| To overcome these problems various heuristics and AI models are used to "convert" a PDF into a BibTeX entry. However, it | ||
| also introduces a level of problems, as heuristics are not ideal: sometimes it works perfectly, but on others it generates | ||
| random output. | ||
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| PDF importing in JabRef is done via `PdfImporter` abstract class and its descendants, and via `PdfMergeMetadataImporter`. | ||
| `PdfImporter` is typically a single heuristics or method of extracting a `BibEntry` from PDF. `PdfMergeMetadataImporter` | ||
| collects `BibEntry` candidates from all `PdfImporter`s and merges them automatically into a single `BibEntry`. | ||
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| The specific problem JabRef has: should JabRef automate all heuristics (automatically merge all `BibEntry`ies from | ||
| several `PdfImporter`s) when importing PDF files or should every file be analysed thoroughly by users? | ||
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| ## Decision Drivers | ||
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| * Option should provide a good-enough quality. | ||
| * It is desired to have a fine-grained controls of PDF importing for power-users. | ||
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| ## Considered Options | ||
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| * Automatically merge all `BibEntry` candidates from `PdfImporters`. | ||
| * Open a merge dialog with all candidates. | ||
| * Open a merge dialog with all candidates if a single PDF is imported. | ||
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| ## Decision Outcome | ||
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| Chosen option: "Open a merge dialog with all candidates if a single PDF is imported", because comes out best (see below). | ||
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| ## Pros and Cons of the Options | ||
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| ### Automatically merge all `BibEntry` candidates from `PdfImporters` | ||
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| * Good, because minimal user interaction and disruption of flow. It also allows batch-processing. | ||
| * Bad, because heuristics are not ideal, and it is even harder to develop a "smarter" merging algorithm. | ||
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| ### Open a merge dialog with all candidates | ||
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| * Good, because allows for fine-grained import. Some correct field may be overridden by a wrong field from other importer, | ||
| which is undesirable for power-users. | ||
| * Bad, because it is a dialog. If lots of PDFs are imported, then there will be lots of dialogs, which might be | ||
| too daunting to process manually. | ||
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| ### Open a merge dialog with all candidates if a single PDF is imported | ||
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| Explanation: | ||
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| - If a single PDF is imported, then open a merge dialog. | ||
| - If several PDFs are imported, merge candidates for each PDF automatically. | ||
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| Outcomes: | ||
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| * Good, because it combines the best of the other two options: Allow both for PDF batch-processing and for fine-grained control. | ||
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| <!-- markdownlint-disable-file MD004 --> |
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src/main/java/org/jabref/gui/externalfiles/PdfMergeDialog.java
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| package org.jabref.gui.externalfiles; | ||
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| import java.io.IOException; | ||
| import java.nio.file.Path; | ||
| import java.util.function.Supplier; | ||
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| import org.jabref.gui.mergeentries.MultiMergeEntriesView; | ||
| import org.jabref.gui.preferences.GuiPreferences; | ||
| import org.jabref.logic.importer.Importer; | ||
| import org.jabref.logic.importer.ParserResult; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfContentImporter; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfEmbeddedBibFileImporter; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfGrobidImporter; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfImporter; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfVerbatimBibtexImporter; | ||
| import org.jabref.logic.importer.fileformat.pdf.PdfXmpImporter; | ||
| import org.jabref.logic.l10n.Localization; | ||
| import org.jabref.logic.util.TaskExecutor; | ||
| import org.jabref.model.entry.BibEntry; | ||
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| public class PdfMergeDialog { | ||
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| /** | ||
| * Constructs a merge dialog for a PDF file. This dialog calls various {@link PdfImporter}s, collects the results, and lets the user choose between them. | ||
| * <p> | ||
| * {@link PdfImporter}s try to extract a {@link BibEntry} out of a PDF file, | ||
| * but it does not perform this 100% perfectly, it is only a set of heuristics that in some cases might work, in others not. | ||
| * Thus, JabRef provides this merge dialog that collects the results of all {@link PdfImporter}s | ||
| * and gives user a choice between field values. | ||
| * | ||
| * @param entry the entry to merge with | ||
| * @param filePath the path to the PDF file. This PDF is used as the source for the {@link PdfImporter}s. | ||
| * @param preferences the preferences to use. Full preference object is required, because of current implementation of {@link MultiMergeEntriesView}. | ||
| * @param taskExecutor the task executor to use when the multi merge dialog executes the importers. | ||
| */ | ||
| public static MultiMergeEntriesView createMergeDialog(BibEntry entry, Path filePath, GuiPreferences preferences, TaskExecutor taskExecutor) { | ||
| MultiMergeEntriesView dialog = new MultiMergeEntriesView(preferences, taskExecutor); | ||
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| dialog.setTitle(Localization.lang("Merge PDF metadata")); | ||
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| dialog.addSource(Localization.lang("Entry"), entry); | ||
| dialog.addSource(Localization.lang("Verbatim"), wrapImporterToSupplier(new PdfVerbatimBibtexImporter(preferences.getImportFormatPreferences()), filePath)); | ||
| dialog.addSource(Localization.lang("Embedded"), wrapImporterToSupplier(new PdfEmbeddedBibFileImporter(preferences.getImportFormatPreferences()), filePath)); | ||
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| if (preferences.getGrobidPreferences().isGrobidEnabled()) { | ||
| dialog.addSource("Grobid", wrapImporterToSupplier(new PdfGrobidImporter(preferences.getImportFormatPreferences()), filePath)); | ||
| } | ||
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| dialog.addSource(Localization.lang("XMP metadata"), wrapImporterToSupplier(new PdfXmpImporter(preferences.getXmpPreferences()), filePath)); | ||
| dialog.addSource(Localization.lang("Content"), wrapImporterToSupplier(new PdfContentImporter(), filePath)); | ||
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| return dialog; | ||
| } | ||
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| private static Supplier<BibEntry> wrapImporterToSupplier(Importer importer, Path filePath) { | ||
| return () -> { | ||
| try { | ||
| ParserResult parserResult = importer.importDatabase(filePath); | ||
| if (parserResult.isInvalid() || parserResult.isEmpty() || !parserResult.getDatabase().hasEntries()) { | ||
| return null; | ||
| } | ||
| return parserResult.getDatabase().getEntries().getFirst(); | ||
| } catch (IOException e) { | ||
| return null; | ||
| } | ||
| }; | ||
| } | ||
| } |
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