Merge remote-tracking branch 'upstream/main' into decode-DOI-contains…

…-masked-characters#8787 * upstream/main: Add: Add test cases for non-default styles in CitationStyleTest (JabRef#8828) Open event log when clicking on collapsed notification (JabRef#8837) Fix right clicking a group and choosing "remove selected entries from this group" leads to error when Bibtex source tab is selected (JabRef#8821) Fix single identifier cannot be opened on click (JabRef#8838) Add Pubmed/Medline Query Transformer (JabRef#8818) adjust and add testcases for FileAnnotationViewModel (JabRef#8830) Append config instead of replacing (JabRef#8834) Fix eclipse config (JabRef#8835) Add Nemo file manager (JabRef#8831) Fix missing clear action on pressing esc within the "Filter groups" field (JabRef#8829) Update bouncycalse to new base version (JabRef#8827) add: add test cases for FileUtil (JabRef#8810) Restrict use of standard streams (JabRef#8816)
fly-ing-fish · May 22, 2022 · 51b77ba · 51b77ba
2 parents 5160bcf + 264357c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - Writing BibTeX data into a PDF (XMP) removes braces. [#8452](https://github.com/JabRef/jabref/issues/8452)
 - Writing BibTeX data into a PDF (XMP) does not write the `file` field.
 - Writing BibTeX data into a PDF (XMP) considers the configured keyword separator (and does not use "," as default any more)
+- The Medline/Pubmed search now also supports the [default fields and operators for searching](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax). [forum#3554](https://discourse.jabref.org/t/native-pubmed-search/3354)
 
 ### Fixed
 
@@ -30,6 +31,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where deprecated fields tab is shown when the fields don't contain any values. [#8396](https://github.com/JabRef/jabref/issues/8396)
 - We fixed an issue that there are exceptions for DOI search in case DOI contains masked characters. [#8787](https://github.com/JabRef/jabref/issues/8787)
 - We fixed an issue which allow us to select and open identifiers from a popup list in the maintable [#8758](https://github.com/JabRef/jabref/issues/8758), [8802](https://github.com/JabRef/jabref/issues/8802)
+- We fixed an issue where the escape button had no functionality within the "Filter groups" textfield. [koppor#562](https://github.com/koppor/jabref/issues/562)
+- We fixed an issue where right clicking a group and choose "remove selected entries from this group" leads to error when Bibtex source tab is selected. [#8012](https://github.com/JabRef/jabref/issues/8012)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -126,7 +126,7 @@ dependencies {
     implementation 'com.ibm.icu:icu4j-charset:71.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.70'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 

diff --git a/eclipse.gradle b/eclipse.gradle
@@ -25,11 +25,15 @@ eclipse {
                 }
 
                 def javafxcontrols = entries.find { isJavafxControls(it) };
-                javafxcontrols.entryAttributes['add-exports'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref';
+                javafxcontrols.entryAttributes['add-exports'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix';
                 javafxcontrols.entryAttributes['add-opens'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref:javafx.controls/javafx.scene.control.skin=org.controlsfx.controls';
 
                 def javafxgraphics = entries.find { isJavafxGraphics(it) };
                 javafxgraphics.entryAttributes['add-opens'] = 'javafx.graphics/javafx.scene=org.controlsfx.controls';
+                javafxgraphics.entryAttributes['add-exports'] = 'javafx.graphics/com.sun.javafx.stage=com.jfoenix';
+
+                def javafxbase = entries.find { isJavafxBase(it) };
+                javafxbase.entryAttributes['add-exports'] = 'javafx.base/com.sun.javafx.event=org.controlsfx.controls:';
 
                 def javafxfxml = entries.find { isJavafxFXML(it) };
                 javafxfxml.entryAttributes['add-opens'] = 'javafx.fxml/javafx.fxml=org.jabref';
@@ -61,6 +65,8 @@ boolean isJavafxControls(entry) { return entry.properties.path.contains('javafx-
 
 boolean isJavafxGraphics(entry) { return entry.properties.path.contains('javafx-graphics'); }
 
+boolean isJavafxBase(entry) { return entry.properties.path.contains('javafx-base'); }
+
 boolean isJavafxFXML(entry) { return entry.properties.path.contains('javafx-fxml'); }
 
 // add formatter and cleanup settings to Eclipse settings

diff --git a/src/main/java/org/jabref/architecture/AllowedToUseStandardStreams.java b/src/main/java/org/jabref/architecture/AllowedToUseStandardStreams.java
@@ -0,0 +1,10 @@
+package org.jabref.architecture;
+
+/**
+ * Annotation to indicate that this class can use System.Out.* instead of using the logging framework
+ */
+public @interface AllowedToUseStandardStreams {
+
+    // The rationale
+    String value();
+}
diff --git a/src/main/java/org/jabref/gui/JabRefDialogService.java b/src/main/java/org/jabref/gui/JabRefDialogService.java
@@ -35,6 +35,7 @@
 import javafx.stage.Window;
 import javafx.util.Duration;
 
+import org.jabref.gui.help.ErrorConsoleAction;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.gui.util.BackgroundTask;
@@ -343,9 +344,14 @@ public void notify(String message) {
                          .threshold(5,
                                  Notifications.create()
                                               .title(Localization.lang("Last notification"))
+                                              // TODO: Change to a notification overview instead of event log when that is available. The event log is not that user friendly (different purpose).
                                               .text(
                                                     "(" + Localization.lang("Check the event log to see all notifications") + ")"
-                                                     + "\n\n" + message))
+                                                     + "\n\n" + message)
+                                              .onAction((e)-> {
+                                                     ErrorConsoleAction ec = new ErrorConsoleAction();
+                                                     ec.execute();
+                                                 }))
                          .hideCloseButton()
                          .show();
         });

diff --git a/src/main/java/org/jabref/gui/JabRefMain.java b/src/main/java/org/jabref/gui/JabRefMain.java
@@ -80,7 +80,8 @@ private static void addLogToDisk() {
                 "writerFile.level", "info",
                 "writerFile.file", directory.resolve("log.txt").toString(),
                 "writerFile.charset", "UTF-8");
-        Configuration.replace(configuration);
+
+        configuration.entrySet().forEach(config -> Configuration.set(config.getKey(), config.getValue()));
         initializeLogger();
     }
 

diff --git a/src/main/java/org/jabref/gui/desktop/os/Linux.java b/src/main/java/org/jabref/gui/desktop/os/Linux.java
@@ -28,17 +28,17 @@ private void nativeOpenFile(String filePath) {
             try {
                 File file = new File(filePath);
                 Desktop.getDesktop().open(file);
-                System.out.println("Open file in default application with Desktop integration");
+                LOGGER.debug("Open file in default application with Desktop integration");
             } catch (IllegalArgumentException e) {
-                System.out.println("Fail back to xdg-open");
+                LOGGER.debug("Fail back to xdg-open");
                 try {
                     String[] cmd = {"xdg-open", filePath};
                     Runtime.getRuntime().exec(cmd);
                 } catch (Exception e2) {
-                    System.out.println("Open operation not successful: " + e2);
+                    LOGGER.warn("Open operation not successful: " + e2);
                 }
             } catch (IOException e) {
-                System.out.println("Native open operation not successful: " + e);
+                LOGGER.warn("Native open operation not successful: " + e);
             }
         });
     }
@@ -94,9 +94,13 @@ public void openFolderAndSelectFile(Path filePath) throws IOException {
         if (desktopSession != null) {
             desktopSession = desktopSession.toLowerCase(Locale.ROOT);
             if (desktopSession.contains("gnome")) {
-                cmd = "nautilus" + filePath.toString().replace(" ", "\\ ");
-            } else if (desktopSession.contains("kde")) {
+                cmd = "nautilus --select " + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("kde") || desktopSession.contains("plasma")) {
                 cmd = "dolphin --select " + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("mate")) {
+                cmd = "caja --select " + filePath.toString().replace(" ", "\\ ");
+            } else if (desktopSession.contains("cinnamon")) {
+                cmd = "nemo --select " + filePath.toString().replace(" ", "\\ ");
             }
         }
         Runtime.getRuntime().exec(cmd);

diff --git a/src/main/java/org/jabref/gui/entryeditor/SourceTab.java b/src/main/java/org/jabref/gui/entryeditor/SourceTab.java
@@ -306,7 +306,9 @@ private void storeSource(BibEntry outOfFocusEntry, String text) {
                     new FieldWriter(fieldWriterPreferences).write(fieldName, newValue);
 
                     compound.addEdit(new UndoableFieldChange(outOfFocusEntry, fieldName, oldValue, newValue));
-                    outOfFocusEntry.setField(fieldName, newValue);
+                    if (outOfFocusEntry.getField(fieldName).isPresent()) {
+                        outOfFocusEntry.setField(fieldName, newValue);
+                    }
                 }
             }
 

diff --git a/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java b/src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationViewModel.java
@@ -4,7 +4,6 @@
 import javafx.beans.property.StringProperty;
 
 import org.jabref.logic.formatter.bibtexfields.RemoveHyphenatedNewlinesFormatter;
-import org.jabref.logic.formatter.bibtexfields.RemoveNewlinesFormatter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.pdf.FileAnnotation;
 import org.jabref.model.pdf.FileAnnotationType;
@@ -33,22 +32,23 @@ private void setupContentProperties(FileAnnotation annotation) {
             String annotationContent = annotation.getContent();
             String illegibleTextMessage = Localization.lang("The marked area does not contain any legible text!");
             String markingContent = (annotationContent.isEmpty() ? illegibleTextMessage : annotationContent);
-            // remove newlines && hyphens before linebreaks
-            markingContent = markingContent.replaceAll("-" + NEWLINE, "");
-            new RemoveHyphenatedNewlinesFormatter().format(markingContent);
-            // remove new lines not preceded by '.' or ':'
-            markingContent = markingContent.replaceAll("(?<![.|:])" + NEWLINE, " ");
-            this.marking.set(markingContent);
+            this.marking.set(removePunctuationMark(markingContent));
         } else {
             String content = annotation.getContent();
-            // remove newlines && hyphens before linebreaks
-            content = new RemoveHyphenatedNewlinesFormatter().format(content);
-            content = new RemoveNewlinesFormatter().format(content);
-            this.content.set(content);
+            this.content.set(removePunctuationMark(content));
             this.marking.set("");
         }
     }
 
+    public String removePunctuationMark(String content) {
+        // remove newlines && hyphens before linebreaks
+        content = content.replaceAll("-" + NEWLINE, "");
+        content = new RemoveHyphenatedNewlinesFormatter().format(content);
+        // remove new lines not preceded by '.' or ':'
+        content = content.replaceAll("(?<![.|:])" + NEWLINE, " ");
+        return content;
+    }
+
     public String getAuthor() {
         return author.get();
     }

diff --git a/src/main/java/org/jabref/gui/keyboard/TextInputKeyBindings.java b/src/main/java/org/jabref/gui/keyboard/TextInputKeyBindings.java
@@ -90,6 +90,10 @@ public static void call(Scene scene, KeyEvent event) {
                         focusedTextField.positionCaret(res.caretPosition);
                         event.consume();
                     }
+                    case CLOSE -> {
+                        focusedTextField.clear();
+                        event.consume();
+                    }
                 }
             });
         }

diff --git a/src/main/java/org/jabref/gui/maintable/columns/LinkedIdentifierColumn.java b/src/main/java/org/jabref/gui/maintable/columns/LinkedIdentifierColumn.java
@@ -60,8 +60,9 @@ public LinkedIdentifierColumn(MainTableColumnModel model,
                 .withTooltip(this::createIdentifierTooltip)
                 .withMenu(this::createIdentifierMenu)
                 .withOnMouseClickedEvent((entry, linkedFiles) -> event -> {
-                    if ((event.getButton() == MouseButton.SECONDARY)) {
-                        new OpenUrlAction(dialogService, stateManager, preferences).execute();
+                    // If we only have one identifer, open directly
+                    if ((linkedFiles.size() == 1) && (event.getButton() == MouseButton.PRIMARY)) {
+                       new OpenUrlAction(dialogService, stateManager, preferences).execute();
                     }
                 })
                 .install(this);

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java
@@ -28,7 +28,7 @@
 import org.jabref.logic.importer.Parser;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.SearchBasedFetcher;
-import org.jabref.logic.importer.fetcher.transformers.DefaultQueryTransformer;
+import org.jabref.logic.importer.fetcher.transformers.MedlineQueryTransformer;
 import org.jabref.logic.importer.fileformat.MedlineImporter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
@@ -54,16 +54,6 @@ public class MedlineFetcher implements IdBasedParserFetcher, SearchBasedFetcher
 
     private int numberOfResultsFound;
 
-    /**
-     * Replaces all commas in a given string with " AND "
-     *
-     * @param query input to remove commas
-     * @return input without commas
-     */
-    private static String replaceCommaWithAND(String query) {
-        return query.replaceAll(", ", " AND ").replaceAll(",", " AND ");
-    }
-
     /**
      * When using 'esearch.fcgi?db=&lt;database>&term=&lt;query>' we will get a list of IDs matching the query.
      * Input: Any text query (&term)
@@ -164,7 +154,7 @@ private URL createSearchUrl(String query) throws URISyntaxException, MalformedUR
         uriBuilder.addParameter("db", "pubmed");
         uriBuilder.addParameter("sort", "relevance");
         uriBuilder.addParameter("retmax", String.valueOf(NUMBER_TO_FETCH));
-        uriBuilder.addParameter("term", replaceCommaWithAND(query));
+        uriBuilder.addParameter("term", query); // already lucene query
         return uriBuilder.build().toURL();
     }
 
@@ -200,7 +190,7 @@ private List<BibEntry> fetchMedline(List<String> ids) throws FetcherException {
     @Override
     public List<BibEntry> performSearch(QueryNode luceneQuery) throws FetcherException {
         List<BibEntry> entryList;
-        DefaultQueryTransformer transformer = new DefaultQueryTransformer();
+        MedlineQueryTransformer transformer = new MedlineQueryTransformer();
         Optional<String> transformedQuery = transformer.transformLuceneQuery(luceneQuery);
 
         if (transformedQuery.isEmpty() || transformedQuery.get().isBlank()) {

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/transformers/MedlineQueryTransformer.java b/src/main/java/org/jabref/logic/importer/fetcher/transformers/MedlineQueryTransformer.java
@@ -0,0 +1,54 @@
+package org.jabref.logic.importer.fetcher.transformers;
+
+/**
+ *
+ * Medline/Pubmed specific transformer which uses suffixes for searches
+ * see <a href="https://pubmed.ncbi.nlm.nih.gov/help/#search-tags">Pubmed help</a> for details
+ *
+ */
+public class MedlineQueryTransformer extends AbstractQueryTransformer {
+
+    @Override
+    protected String getLogicalAndOperator() {
+        return " AND ";
+    }
+
+    @Override
+    protected String getLogicalOrOperator() {
+        return " OR ";
+    }
+
+    @Override
+    protected String getLogicalNotOperator() {
+        return "NOT ";
+    }
+
+    @Override
+    protected String handleAuthor(String author) {
+        return author + "[au]";
+    }
+
+    @Override
+    protected String handleTitle(String title) {
+        return title + "[ti]";
+    }
+
+    @Override
+    protected String handleJournal(String journalTitle) {
+        return journalTitle + "[ta]";
+    }
+
+    @Override
+    protected String handleYear(String year) {
+        return year + "[dp]";
+    }
+
+    @Override
+    protected String handleYearRange(String yearRange) {
+        parseYearRange(yearRange);
+        if (endYear == Integer.MAX_VALUE) {
+            return yearRange;
+        }
+        return Integer.toString(startYear) + ":" + Integer.toString(endYear) + "[dp]";
+    }
+}
diff --git a/src/main/java/org/jabref/logic/util/io/XMLUtil.java b/src/main/java/org/jabref/logic/util/io/XMLUtil.java
@@ -14,6 +14,8 @@
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
+import org.jabref.architecture.AllowedToUseStandardStreams;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
@@ -25,6 +27,7 @@
 /**
  * Currently used for debugging only
  */
+@AllowedToUseStandardStreams("Used for debugging only")
 public class XMLUtil {
     private static final Logger LOGGER = LoggerFactory.getLogger(XMLUtil.class);
 

diff --git a/src/test/java/org/jabref/architecture/MainArchitectureTests.java b/src/test/java/org/jabref/architecture/MainArchitectureTests.java
@@ -6,6 +6,7 @@
 import com.tngtech.archunit.junit.AnalyzeClasses;
 import com.tngtech.archunit.junit.ArchIgnore;
 import com.tngtech.archunit.junit.ArchTest;
+import com.tngtech.archunit.library.GeneralCodingRules;
 
 import static com.tngtech.archunit.lang.syntax.ArchRuleDefinition.noClasses;
 import static com.tngtech.archunit.library.Architectures.layeredArchitecture;
@@ -20,6 +21,7 @@ class MainArchitectureTests {
     private static final String PACKAGE_ORG_JABREF_GUI = "org.jabref.gui..";
     private static final String PACKAGE_ORG_JABREF_LOGIC = "org.jabref.logic..";
     private static final String PACKAGE_ORG_JABREF_MODEL = "org.jabref.model..";
+    private static final String PACKAGE_ORG_JABREF_CLI = "org.jabref.cli..";
 
     @ArchTest
     public static void doNotUseApacheCommonsLang3(JavaClasses classes) {
@@ -92,7 +94,7 @@ public static void respectLayeredArchitecture(JavaClasses classes) {
                 .layer("Gui").definedBy(PACKAGE_ORG_JABREF_GUI)
                 .layer("Logic").definedBy(PACKAGE_ORG_JABREF_LOGIC)
                 .layer("Model").definedBy(PACKAGE_ORG_JABREF_MODEL)
-                .layer("Cli").definedBy("org.jabref.cli..")
+                .layer("Cli").definedBy(PACKAGE_ORG_JABREF_CLI)
                 .layer("Migrations").definedBy("org.jabref.migrations..") // TODO: Move to logic
                 .layer("Preferences").definedBy("org.jabref.preferences..")
                 .layer("Styletester").definedBy("org.jabref.styletester..")
@@ -135,4 +137,14 @@ public static void restrictUsagesInLogic(JavaClasses classes) {
                    .orShould().dependOnClassesThat().haveFullyQualifiedName(CLASS_ORG_JABREF_GLOBALS)
                    .check(classes);
     }
+
+    @ArchTest
+    public static void restrictStandardStreams(JavaClasses classes) {
+        noClasses().that().resideOutsideOfPackages(PACKAGE_ORG_JABREF_CLI)
+                   .and().resideOutsideOfPackages("org.jabref.gui.openoffice..") // Uses LibreOffice SDK
+                   .and().areNotAnnotatedWith(AllowedToUseStandardStreams.class)
+                   .should(GeneralCodingRules.ACCESS_STANDARD_STREAMS)
+                   .because("logging framework should be used instead or the class be marked explicitly as @AllowedToUseStandardStreams")
+                   .check(classes);
+    }
 }