Merge remote-tracking branch 'upstream/main' into jdk17

* upstream/main: (26 commits) Add unit test to four test classes (#7651) Fix IEEE test (#7852) New Crowdin updates (#7859) Fix markdown syntax of ADRs add missing l10n (#7857) New Crowdin updates (#7847) Bump mockito-core from 3.11.1 to 3.11.2 (#7856) Bump checkstyle from 8.43 to 8.44 (#7855) Fix for issue #4652: Add Find Unlinked Files Filter based on Date (#7846) Fix for entering a backslash in the custom entry preview dialog (#7851) Fixed INSPIREFetcherTest Fixed TitleFetcherTest Ignore baeldung.com and tldrlegal.com from out link checks New Crowdin updates (#7845) New Crowdin updates (#7843) Refactoring and addition of unit tests (#7597) CLI option to write XMP metadata to pdfs (#7814) Add query validation for web search (#7809) change eclipse default output dir (#7842) Bump lucene-queryparser from 8.8.2 to 8.9.0 (#7835) ...
JabRef · Jun 30, 2021 · 49757c8 · 49757c8
2 parents c25f8e8 + a01754c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a progress counter to the title bar in Possible Duplicates dialog window. [#7366](https://github.com/JabRef/jabref/issues/7366)
 - We added new "Customization" tab to the preferences which includes option to choose a custom address for DOI access. [#7337](https://github.com/JabRef/jabref/issues/7337)
 - We added zbmath to the public databases from which the bibliographic information of an existing entry can be updated. [#7437](https://github.com/JabRef/jabref/issues/7437)
+- We showed to the find Unlinked Files Dialog the date of the files' most recent modification. [#4652](https://github.com/JabRef/jabref/issues/4652)
+- We added to the find Unlinked Files function a filter to show only files based on date of last modification (Last Year, Last Month, Last Week, Last Day). [#4652](https://github.com/JabRef/jabref/issues/4652)
+- We added to the find Unlinked Files function a filter that sorts the files based on the date of last modification(Sort by Newest, Sort by Oldest First). [#4652](https://github.com/JabRef/jabref/issues/4652)
 - We added the possibility to add a new entry via its zbMath ID (zbMATH can be chosen as ID type in the "Select entry type" window). [#7202](https://github.com/JabRef/jabref/issues/7202)
 - We added the extension support and the external application support (For Texshow, Texmaker and LyX) to the flatpak [#7248](https://github.com/JabRef/jabref/pull/7248)
 - We added some symbols and keybindings to the context menu in the entry editor. [#7268](https://github.com/JabRef/jabref/pull/7268)
@@ -28,9 +31,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a select all button for the library import function. [#7786](https://github.com/JabRef/jabref/issues/7786)
 - We added a search feature for journal abbreviations. [#7804](https://github.com/JabRef/jabref/pull/7804)
 - We added auto-key-generation progress to the background task list. [#7267](https://github.com/JabRef/jabref/issues/72)
+- We added the option to write XMP metadata to pdfs from the CLI. [7814](https://github.com/JabRef/jabref/pull/7814)
 
 ### Changed
 
+- The export to MS Office XML now exports the author field as `Inventor` if the bibtex entry type is `patent` [#7830](https://github.com/JabRef/jabref/issues/7830)
 - We changed the EndNote importer to import the field `label` to the corresponding bibtex field `endnote-label` [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - The keywords added via "Manage content selectors" are now displayed in alphabetical order. [#3791](https://github.com/JabRef/jabref/issues/3791)
 - We improved the "Find unlinked files" dialog to show import results for each file. [#7209](https://github.com/JabRef/jabref/pull/7209)
@@ -53,6 +58,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an isuse where some texts (e.g. descriptionss) in dialogs could not be translated [#7854](https://github.com/JabRef/jabref/issues/7854)
 - We fixed an issue where import hangs for ris files with "ER - " [#7737](https://github.com/JabRef/jabref/issues/7737)
 - We fixed an issue where getting bibliograhpic data from DOI or another identifer did not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/6267)
 - We fixed an issue where importing entries would not respect the library mode (BibTeX/biblatex)[#1018](https://github.com/JabRef/jabref/issues/1018)
@@ -109,6 +115,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the RFC fetcher is not compatible with the draft [7305](https://github.com/JabRef/jabref/issues/7305)
 - We fixed an issue where duplicate files (both file names and contents are the same) is downloaded and add to linked files [#6197](https://github.com/JabRef/jabref/issues/6197)
 - We fixed an issue where changing the appearance of the preview tab did not trigger a restart warning. [#5464](https://github.com/JabRef/jabref/issues/5464)
+- We fixed an issue where editing "Custom preview style" triggers exception. [#7526](https://github.com/JabRef/jabref/issues/7526)
 - We fixed an issue where a title with multiple applied formattings in EndNote was not imported correctly [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - We fixed an issue where a `report` in EndNote was imported as `article` [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)
 - We fixed an issue where the field `publisher` in EndNote was not imported in JabRef [forum#2734](https://discourse.jabref.org/t/importing-endnote-label-field-to-jabref-from-xml-file/2734)

diff --git a/build.gradle b/build.gradle
@@ -130,8 +130,8 @@ dependencies {
 
     implementation 'commons-cli:commons-cli:1.4'
 
-    implementation 'org.libreoffice:libreoffice:7.1.3'
-    implementation 'org.libreoffice:unoloader:7.1.3'
+    implementation 'org.libreoffice:libreoffice:7.1.4'
+    implementation 'org.libreoffice:unoloader:7.1.4'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.10'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -142,18 +142,18 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.9.2'
     implementation 'org.antlr:antlr4-runtime:4.9.2'
 
-    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.8.2') {
+    implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.9.0') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
     }
 
-    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.11.1.202105131744-r'
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.12.0.202106070339-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.12.3'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.12.3'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.3'
 
-    implementation 'org.postgresql:postgresql:42.2.21'
+    implementation 'org.postgresql:postgresql:42.2.22'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -214,10 +214,10 @@ dependencies {
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.2'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.2'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.5'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.11.1'
+    testImplementation 'org.mockito:mockito-core:3.11.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.19.0'
@@ -226,7 +226,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.43'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.44'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
 }
 

diff --git a/docs/adr/0013-add-native-support-biblatex-software.md b/docs/adr/0013-add-native-support-biblatex-software.md
@@ -16,12 +16,12 @@ With citing software becoming fairly common, native support is helpful.
 ## Considered Options
 
 * Add the new entry types to the existing biblatex types
-* Add a divider with label Biblatex-Software under which the new entries are listed : Native support for Biblatex-Software
-* Support via customized entry types : A user can load a customized bib file
+* Add a divider with label Biblatex-Software under which the new entries are listed: Native support for Biblatex-Software
+* Support via customized entry types: A user can load a customized bib file
 
 ## Decision Outcome
 
-Chosen option: Add a new divider, because comes out best (see below).
+Chosen option: "Add a new divider", because comes out best (see below).
 
 ### Positive Consequences
 
@@ -33,15 +33,16 @@ Chosen option: Add a new divider, because comes out best (see below).
 
 ## Pros and Cons of the Options
 
-### Adding the new entry types to the existing biblatex types
+### Add the new entry types to the existing biblatex types
 
 * Good, because there is no need for a new category in the add entry pane
 
-### Add a divider with label Biblatex-Software with relevant types
+### Add a divider with label Biblatex-Software under which the new entries are listed: Native support for Biblatex-Software
 
 * Good, since this gives the user a bit more clarity
 
-### Support via customized entry types
+
+### Support via customized entry types: A user can load a customized bib file
 
 * Good, because no code needs to be changed
 * Bad, because documentation is needed

diff --git a/docs/adr/0018-use-regular-expression-to-split-multiple-sentence-titles.md b/docs/adr/0018-use-regular-expression-to-split-multiple-sentence-titles.md
@@ -23,4 +23,3 @@ Chosen option: "Regular expression", because we can use Java internal classes (P
 ### Negative Consequences
 
 * Regular expressions can never cover every case, therefore, splitting may not be accurate for every title
-
diff --git a/docs/adr/0019-implement-special-fields-as-seperate-fields.md b/docs/adr/0019-implement-special-fields-as-seperate-fields.md
@@ -49,7 +49,7 @@ keywords = {prio1, printed, read}
 
 * Good, because does not bloat the BibTeX file. Typically, 50% of the lines are special fields
 * Good, because the user can easily assign a special field. E.g, typing “, prio1” into keywords instead of “\n  priority = {prio1},”
-* Bad, because  they need to be synchronized to fields (because otherwise, the maintable cannot render it)
+* Bad, because they need to be synchronized to fields (because otherwise, the maintable cannot render it)
 * Bad, because keywords are related to the actual content
 * Bad, because some users want to keep publisher keywords
 
@@ -61,7 +61,7 @@ Example:
 jabrefspecial = {prio1, printed, red}
 ```
 
-* Good, because  typing effort
+* Good, because typing effort
 * Bad, because handling in table gets complicated → one field is now multiple columns
 
 ### Special fields as sub-feature of groups

diff --git a/docs/adr/0021-keep-study-as-a-dto.md b/docs/adr/0021-keep-study-as-a-dto.md
@@ -16,7 +16,7 @@ Chosen option: "Keep study as DTO and use transformators", because comes out bes
 
 ## Pros and Cons of the Options
 
-### Keep study as DTO and use transformators
+### Keep study as DTO and use transformers
 
 * Good, because no need for custom serialization
 * Good, because deactivated fetchers can be documented (important for traceable Searching (SLRs))

diff --git a/docs/adr/0022-remove-stop-words-during-query-transformation.md b/docs/adr/0022-remove-stop-words-during-query-transformation.md
@@ -0,0 +1,33 @@
+# Remove stop words during query transformation
+
+## Context and Problem Statement
+
+When quering for a title of a paper, the title might contain stop words such as "a", "for", "and". Some data providers return 0 results when querying for a stop word. When transforming a query to the lucene syntax, the default Boolean operator `and` is used. When using IEEE, this often leads to zero search results.
+
+## Decision Drivers
+
+* Consistent to the Google search engine
+* Allow reproducible searches
+* Avoid WTFs on the user's side
+
+## Considered Options
+
+* Remove stop words from the query
+* Automatically enclose in quotes if no Boolean operator is contained
+
+## Decision Outcome
+
+Chosen option: "Remove stop words from the query", because comes out best.
+
+## Pros and Cons of the Options
+
+### Remove stop words from the query
+
+* Good, because Good search results if no Boolean operators are used
+* Bad, because When using complex queries and stop words are used alone, they are silently removed
+
+### Automatically enclose in quotes if no Boolean operator is contained
+
+* Good, because Good search results if no Boolean operators are used
+* Bad, because Silently leads to different results
+* Bad, because Inconsistent to Google behavior
diff --git a/eclipse.gradle b/eclipse.gradle
@@ -40,7 +40,7 @@ eclipse {
             }
         }
 
-        defaultOutputDir = file('build')
+        defaultOutputDir = file('bin/main')
         downloadSources = true
         downloadJavadoc = true
     }

diff --git a/mlc_config.json b/mlc_config.json
@@ -1,5 +1,8 @@
 {
     "ignorePatterns": [
+        {
+            "pattern": "baeldung.com"
+        },
         {
             "pattern": "^CONTRIBUTING\\.md"
         },
@@ -21,6 +24,9 @@
         {
             "pattern": "^http://purl\\.org/net/bibteXMP"
         },
+        {
+            "pattern": "tldrlegal.com"
+        },
         {
             "pattern": "^https://www\\.slant\\.co/"
         },

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -2,13 +2,17 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Locale;
 import java.util.Optional;
 import java.util.Set;
+import java.util.Vector;
 import java.util.prefs.BackingStoreException;
 
 import org.jabref.gui.Globals;
@@ -24,6 +28,7 @@
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.exporter.TemplateExporter;
+import org.jabref.logic.exporter.XmpPdfExporter;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -49,6 +54,8 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.DummyFileUpdateMonitor;
+import org.jabref.model.util.FileHelper;
+import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.base.Throwables;
@@ -215,6 +222,12 @@ private List<ParserResult> processArguments() {
             automaticallySetFileLinks(loaded);
         }
 
+        if (cli.isWriteXMPtoPdf()) {
+            if (!loaded.isEmpty()) {
+                writeXMPtoPdf(loaded, cli.getWriteXMPtoPdf(), Globals.prefs.getDefaultEncoding(), Globals.prefs.getXmpPreferences(), Globals.prefs.getFilePreferences());
+            }
+        }
+
         if (cli.isFileExport()) {
             if (!loaded.isEmpty()) {
                 exportFile(loaded, cli.getFileExport().split(","));
@@ -239,6 +252,88 @@ private List<ParserResult> processArguments() {
         return loaded;
     }
 
+    private void writeXMPtoPdf(List<ParserResult> loaded, String filesAndCitekeys, Charset encoding, XmpPreferences xmpPreferences, FilePreferences filePreferences) {
+        if (loaded.isEmpty()) {
+            LOGGER.error("The write xmp option depends on a valid import option.");
+            return;
+        }
+        ParserResult pr = loaded.get(loaded.size() - 1);
+        BibDatabaseContext databaseContext = pr.getDatabaseContext();
+        BibDatabase dataBase = pr.getDatabase();
+
+        XmpPdfExporter xmpPdfExporter = new XmpPdfExporter(xmpPreferences);
+
+        if ("all".equals(filesAndCitekeys)) {
+            for (BibEntry entry : dataBase.getEntries()) {
+                writeXMPtoPDFsOfEntry(databaseContext, entry.getCitationKey().orElse("<no cite key defined>"), entry, encoding, filePreferences, xmpPdfExporter);
+            }
+            return;
+        }
+
+        Vector<String> citeKeys = new Vector<>();
+        Vector<String> pdfs = new Vector<>();
+        for (String fileOrCiteKey : filesAndCitekeys.split(",")) {
+            if (fileOrCiteKey.toLowerCase(Locale.ROOT).endsWith(".pdf")) {
+                pdfs.add(fileOrCiteKey);
+            } else {
+                citeKeys.add(fileOrCiteKey);
+            }
+        }
+
+        writeXMPtoPdfByCitekey(databaseContext, dataBase, citeKeys, encoding, filePreferences, xmpPdfExporter);
+        writeXMPtoPdfByFileNames(databaseContext, dataBase, pdfs, encoding, filePreferences, xmpPdfExporter);
+
+    }
+
+    private void writeXMPtoPDFsOfEntry(BibDatabaseContext databaseContext, String citeKey, BibEntry entry, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        try {
+            if (xmpPdfExporter.exportToAllFilesOfEntry(databaseContext, encoding, filePreferences, entry, Arrays.asList(entry))) {
+                LOGGER.info(String.format("Successfully written XMP metadata on at least one linked file of %s", citeKey));
+            } else {
+                LOGGER.error(String.format("Cannot write XMP metadata on any linked files of %s. Make sure there is at least one linked file and the path is correct.", citeKey));
+            }
+        } catch (Exception e) {
+            LOGGER.error(String.format("Failed writing XMP metadata on a linked file of %s.", citeKey));
+        }
+    }
+
+    private void writeXMPtoPdfByCitekey(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> citeKeys, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        for (String citeKey : citeKeys) {
+            List<BibEntry> bibEntryList = dataBase.getEntriesByCitationKey(citeKey);
+            if (bibEntryList.isEmpty()) {
+                LOGGER.error(String.format("Skipped - Cannot find %s in library.", citeKey));
+                continue;
+            }
+            for (BibEntry entry : bibEntryList) {
+                writeXMPtoPDFsOfEntry(databaseContext, citeKey, entry, encoding, filePreferences, xmpPdfExporter);
+            }
+        }
+    }
+
+    private void writeXMPtoPdfByFileNames(BibDatabaseContext databaseContext, BibDatabase dataBase, Vector<String> fileNames, Charset encoding, FilePreferences filePreferences, XmpPdfExporter xmpPdfExporter) {
+        for (String fileName : fileNames) {
+            Path filePath = Path.of(fileName);
+            if (!filePath.isAbsolute()) {
+                filePath = FileHelper.find(fileName, databaseContext.getFileDirectories(filePreferences)).orElse(FileHelper.find(fileName, Arrays.asList(Path.of("").toAbsolutePath())).orElse(filePath));
+            }
+            if (Files.exists(filePath)) {
+                try {
+                    if (xmpPdfExporter.exportToFileByPath(databaseContext, dataBase, encoding, filePreferences, filePath)) {
+                        LOGGER.info(String.format("Successfully written XMP metadata of at least one entry to %s", fileName));
+                    } else {
+                        LOGGER.error(String.format("File %s is not linked to any entry in database.", fileName));
+                    }
+                } catch (IOException e) {
+                    LOGGER.error("Error accessing files.", fileName);
+                } catch (Exception e) {
+                    LOGGER.error(String.format("Error writing entry to %s.", fileName));
+                }
+            } else {
+                LOGGER.error(String.format("Skipped - PDF %s does not exist", fileName));
+            }
+        }
+    }
+
     private boolean exportMatches(List<ParserResult> loaded) {
         String[] data = cli.getExportMatches().split(",");
         String searchTerm = data[0].replace("\\$", " "); // enables blanks within the search term:

diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -147,6 +147,14 @@ public boolean isAutomaticallySetFileLinks() {
         return cl.hasOption("automaticallySetFileLinks");
     }
 
+    public boolean isWriteXMPtoPdf() {
+        return cl.hasOption("writeXMPtoPdf");
+    }
+
+    public String getWriteXMPtoPdf() {
+        return cl.getOptionValue("writeXMPtoPdf");
+    }
+
     private static Options getOptions() {
         Options options = new Options();
 
@@ -242,6 +250,14 @@ private static Options getOptions() {
                 .argName("KEY1[,KEY2][,KEYn] | all")
                 .build());
 
+        options.addOption(Option
+                .builder("w")
+                .longOpt("writeXMPtoPdf")
+                .desc(String.format("%s: '%s'", Localization.lang("Write BibTeXEntry as XMP metadata to PDF."), "-w pathToMyOwnPaper.pdf"))
+                .hasArg()
+                .argName("CITEKEY1[,CITEKEY2][,CITEKEYn] | PDF1[,PDF2][,PDFn] | all")
+                .build());
+
         return options;
     }
 

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
@@ -1236,3 +1236,7 @@ TextFlow * {
 .fontsizeSpinner{
     -fx-pref-width: 5em;
 }
+
+.text-field:invalid {
+    -fx-background-color: rgba(240, 128, 128, 0.5);
+}