From fbed1940c06bc4602d783aa8150efd32611e6f07 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 30 Oct 2019 17:10:47 +0000 Subject: [PATCH] JAL-3210 Fixed jalviewjs dependencies. Changed linkCheck to tee output to .out file. Tidying jalviewjs paths. --- .gitignore | 2 +- _j2sclasslist.txt | 959 ----------------------------------------------------- build.gradle | 175 +++++----- gradle.properties | 2 +- 4 files changed, 83 insertions(+), 1055 deletions(-) delete mode 100644 _j2sclasslist.txt diff --git a/.gitignore b/.gitignore index f313551..543fe0f 100644 --- a/.gitignore +++ b/.gitignore @@ -20,7 +20,7 @@ TESTNG /.gradle /build /local.properties -/utils/HelpLinksChecker.touch +/utils/HelpLinksChecker.out /getdown/website /getdown/full_app /getdown/files diff --git a/_j2sclasslist.txt b/_j2sclasslist.txt deleted file mode 100644 index 9a790a0..0000000 --- a/_j2sclasslist.txt +++ /dev/null @@ -1,959 +0,0 @@ -jalview/analysis/AAFrequency.js -jalview/analysis/AlignSeq.js -jalview/analysis/AlignmentAnnotationUtils.js -jalview/analysis/AlignmentUtils.js -jalview/analysis/AnnotationSorter.js -jalview/analysis/Conservation.js -jalview/analysis/CrossRef.js -jalview/analysis/NJTree.js -jalview/analysis/SeqsetUtils.js -jalview/analysis/TreeBuilder.js -jalview/analysis/TreeModel.js -jalview/analysis/scoremodels/DistanceScoreModel.js -jalview/analysis/scoremodels/FeatureDistanceModel.js -jalview/analysis/scoremodels/PIDModel.js -jalview/analysis/scoremodels/ScoreMatrix.js -jalview/analysis/scoremodels/ScoreModels.js -jalview/analysis/scoremodels/SimilarityParams.js -jalview/analysis/scoremodels/SimilarityScoreModel.js -jalview/api/AlignCalcManagerI.js -jalview/api/AlignCalcWorkerI.js -jalview/api/AlignViewControllerGuiI.js -jalview/api/AlignViewControllerI.js -jalview/api/AlignViewportI.js -jalview/api/AlignmentViewPanel.js -jalview/api/BuildDetailsI.js -jalview/api/FeatureColourI.js -jalview/api/FeatureRenderer.js -jalview/api/FeaturesDisplayedI.js -jalview/api/OOMHandlerI.js -jalview/api/SequenceRenderer.js -jalview/api/StructureSelectionManagerProvider.js -jalview/api/ViewStyleI.js -jalview/api/analysis/PairwiseScoreModelI.js -jalview/api/analysis/ScoreModelI.js -jalview/api/analysis/SimilarityParamsI.js -jalview/bin/ArgsParser.js -jalview/bin/BuildDetails.js -jalview/bin/Cache.js -jalview/bin/Jalview.js -jalview/bin/JalviewJS2.js -jalview/controller/AlignViewController.js -jalview/datamodel/ASequence.js -jalview/datamodel/ASequenceI.js -jalview/datamodel/Alignment.js -jalview/datamodel/AlignmentAnnotation.js -jalview/datamodel/AlignmentI.js -jalview/datamodel/AlignmentView.js -jalview/datamodel/AnnotatedCollectionI.js -jalview/datamodel/Annotation.js -jalview/datamodel/BinaryNode.js -jalview/datamodel/CigarArray.js -jalview/datamodel/CigarBase.js -jalview/datamodel/CigarSimple.js -jalview/datamodel/ColumnSelection.js -jalview/datamodel/ContiguousI.js -jalview/datamodel/DBRefSource.js -jalview/datamodel/HiddenColumns.js -jalview/datamodel/HiddenColumnsCursor.js -jalview/datamodel/HiddenCursorPosition.js -jalview/datamodel/HiddenSequences.js -jalview/datamodel/PDBEntry.js -jalview/datamodel/Profile.js -jalview/datamodel/ProfileI.js -jalview/datamodel/Profiles.js -jalview/datamodel/ProfilesI.js -jalview/datamodel/Range.js -jalview/datamodel/RangeIterator.js -jalview/datamodel/ResidueCount.js -jalview/datamodel/SearchResults.js -jalview/datamodel/SearchResultsI.js -jalview/datamodel/SeqCigar.js -jalview/datamodel/Sequence.js -jalview/datamodel/SequenceCollectionI.js -jalview/datamodel/SequenceCursor.js -jalview/datamodel/SequenceFeature.js -jalview/datamodel/SequenceGroup.js -jalview/datamodel/SequenceI.js -jalview/datamodel/SequenceNode.js -jalview/datamodel/features/FeatureLocationI.js -jalview/datamodel/features/FeatureMatcher.js -jalview/datamodel/features/FeatureMatcherI.js -jalview/datamodel/features/FeatureMatcherSet.js -jalview/datamodel/features/FeatureMatcherSetI.js -jalview/datamodel/features/FeatureStore.js -jalview/datamodel/features/RangeComparator.js -jalview/datamodel/features/SequenceFeatures.js -jalview/datamodel/features/SequenceFeaturesI.js -jalview/gui/AlignFrame.js -jalview/gui/AlignViewport.js -jalview/gui/AlignmentPanel.js -jalview/gui/AnnotationLabels.js -jalview/gui/AnnotationPanel.js -jalview/gui/CalculationChooser.js -jalview/gui/ColourMenuHelper.js -jalview/gui/ComboBoxTooltipRenderer.js -jalview/gui/Desktop.js -jalview/gui/FeatureRenderer.js -jalview/gui/IProgressIndicator.js -jalview/gui/IdCanvas.js -jalview/gui/IdPanel.js -jalview/gui/IdwidthAdjuster.js -jalview/gui/JalviewChangeSupport.js -jalview/gui/JvSwingUtils.js -jalview/gui/PaintRefresher.js -jalview/gui/PopupMenu.js -jalview/gui/Preferences.js -jalview/gui/ProgressBar.js -jalview/gui/ScalePanel.js -jalview/gui/SeqCanvas.js -jalview/gui/SeqPanel.js -jalview/gui/SequenceRenderer.js -jalview/gui/TreeCanvas.js -jalview/gui/TreePanel.js -jalview/gui/ViewSelectionMenu.js -jalview/io/AlignFile.js -jalview/io/AlignmentFileReaderI.js -jalview/io/AlignmentFileWriterI.js -jalview/io/AppletFormatAdapter.js -jalview/io/DataSourceType.js -jalview/io/FileFormat.js -jalview/io/FileFormatI.js -jalview/io/FileFormats.js -jalview/io/FileLoader.js -jalview/io/FileParse.js -jalview/io/IdentifyFile.js -jalview/io/PIRFile.js -jalview/io/ScoreMatrixFile.js -jalview/io/SequenceAnnotationReport.js -jalview/javascript/log4j/ConsoleAppender.js -jalview/javascript/log4j/Layout.js -jalview/javascript/log4j/Level.js -jalview/javascript/log4j/Logger.js -jalview/javascript/log4j/Priority.js -jalview/javascript/log4j/SimpleLayout.js -jalview/javascript/log4j/spi/OptionHandler.js -jalview/jbgui/GAlignFrame.js -jalview/jbgui/GAlignmentPanel.js -jalview/jbgui/GDesktop.js -jalview/jbgui/GPreferences.js -jalview/jbgui/GTreePanel.js -jalview/math/Matrix.js -jalview/math/MatrixI.js -jalview/project/Jalview2XML.js -jalview/renderer/AnnotationRenderer.js -jalview/renderer/AwtRenderPanelI.js -jalview/renderer/ResidueColourFinder.js -jalview/renderer/ResidueShader.js -jalview/renderer/ResidueShaderI.js -jalview/renderer/ScaleRenderer.js -jalview/renderer/seqfeatures/FeatureRenderer.js -jalview/schemes/Blosum62ColourScheme.js -jalview/schemes/BuriedColourScheme.js -jalview/schemes/ClustalxColourScheme.js -jalview/schemes/ColourSchemeI.js -jalview/schemes/ColourSchemeProperty.js -jalview/schemes/ColourSchemes.js -jalview/schemes/Consensus.js -jalview/schemes/FeatureColour.js -jalview/schemes/HelixColourScheme.js -jalview/schemes/HydrophobicColourScheme.js -jalview/schemes/JalviewColourScheme.js -jalview/schemes/NucleotideColourScheme.js -jalview/schemes/PIDColourScheme.js -jalview/schemes/PurinePyrimidineColourScheme.js -jalview/schemes/RNAHelicesColour.js -jalview/schemes/ResidueColourScheme.js -jalview/schemes/ResidueProperties.js -jalview/schemes/ScoreColourScheme.js -jalview/schemes/StrandColourScheme.js -jalview/schemes/TCoffeeColourScheme.js -jalview/schemes/TaylorColourScheme.js -jalview/schemes/TurnColourScheme.js -jalview/schemes/ZappoColourScheme.js -jalview/structure/CommandListener.js -jalview/structure/SelectionListener.js 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-javax/swing/event/InternalFrameAdapter.js -javax/swing/event/InternalFrameEvent.js -javax/swing/event/InternalFrameListener.js -javax/swing/event/ListDataListener.js -javax/swing/event/MenuKeyListener.js -javax/swing/event/MenuListener.js -javax/swing/event/TableModelListener.js -javax/swing/plaf/ActionMapUIResource.js -javax/swing/plaf/BorderUIResource.js -javax/swing/plaf/ColorUIResource.js -javax/swing/plaf/ComponentInputMapUIResource.js -javax/swing/plaf/ComponentUI.js -javax/swing/plaf/DimensionUIResource.js -javax/swing/plaf/FontUIResource.js -javax/swing/plaf/InsetsUIResource.js -javax/swing/plaf/UIResource.js -javax/swing/plaf/basic/BasicBorders.js -javax/swing/table/AbstractTableModel.js -javax/swing/table/TableModel.js -javax/xml/bind/ContextFinder.js -javax/xml/bind/GetPropertyAction.js -javax/xml/bind/JAXBContext.js -javax/xml/bind/JAXBContextFactory.js -javax/xml/bind/JAXBElement.js -javax/xml/bind/ModuleUtil.js -javax/xml/bind/ServiceLoaderUtil.js -javax/xml/bind/Unmarshaller.js -javax/xml/bind/ValidationEventHandler.js -javax/xml/bind/annotation/adapters/CollapsedStringAdapter.js -javax/xml/bind/annotation/adapters/XmlAdapter.js -javax/xml/bind/helpers/AbstractUnmarshallerImpl.js -javax/xml/bind/helpers/DefaultValidationEventHandler.js -javax/xml/datatype/XMLGregorianCalendar.js -javax/xml/namespace/QName.js -javax/xml/stream/XMLInputFactory.js -javax/xml/stream/XMLStreamReader.js -org/apache/xerces/jaxp/datatype/XMLGregorianCalendarImpl.js -org/json/simple/parser/JSONParser.js -org/json/simple/parser/ParseException.js -org/json/simple/parser/Yylex.js -org/xml/sax/AttributeList.js -org/xml/sax/Attributes.js -org/xml/sax/ContentHandler.js -org/xml/sax/InputSource.js -org/xml/sax/Parser.js -org/xml/sax/XMLReader.js -org/xml/sax/ext/Attributes2.js -sun/awt/AWTAccessor.js -sun/awt/AWTAutoShutdown.js -sun/awt/AppContext.js -sun/awt/CausedFocusEvent.js -sun/awt/ComponentFactory.js -sun/awt/EventQueueItem.js -sun/awt/KeyboardFocusManagerPeerProvider.js -sun/awt/MostRecentKeyValue.js -sun/awt/MostRecentThreadAppContext.js -sun/awt/PaintEventDispatcher.js -sun/awt/PostEventQueue.js -sun/awt/RequestFocusController.js -sun/awt/SunGraphicsCallback.js -sun/awt/SunToolkit.js -sun/awt/WindowClosingListener.js -sun/awt/WindowClosingSupport.js -sun/awt/image/DataStealer.js -sun/awt/image/IntegerComponentRaster.js -sun/awt/image/IntegerInterleavedRaster.js -sun/awt/image/SunWritableRaster.js -sun/font/FontDesignMetrics.js -sun/java2d/StateTrackable.js -sun/java2d/StateTrackableDelegate.js -sun/nio/cs/ArrayDecoder.js -sun/nio/cs/HistoricallyNamedCharset.js -sun/nio/cs/StandardCharsets.js -sun/nio/cs/ThreadLocalCoders.js -sun/nio/cs/UTF_8.js -sun/nio/cs/Unicode.js -sun/swing/DefaultLookup.js -sun/swing/SwingLazyValue.js -sun/swing/UIAction.js -sun/text/resources/FormatData.js -sun/text/resources/FormatData_en.js -sun/util/calendar/AbstractCalendar.js -sun/util/calendar/BaseCalendar.js -sun/util/calendar/CalendarDate.js -sun/util/calendar/CalendarSystem.js -sun/util/calendar/CalendarUtils.js -sun/util/calendar/Gregorian.js -sun/util/calendar/ZoneInfo.js -sun/util/resources/LocaleData.js -swingjs/JSApp.js -swingjs/JSApplet.js -swingjs/JSAppletThread.js -swingjs/JSAppletViewer.js -swingjs/JSCharSet.js -swingjs/JSFocusPeer.js -swingjs/JSFontMetrics.js -swingjs/JSFrameViewer.js -swingjs/JSGraphics2D.js -swingjs/JSGraphicsConfiguration.js -swingjs/JSGraphicsEnvironment.js -swingjs/JSKeyEvent.js -swingjs/JSMenuManager.js -swingjs/JSMouse.js -swingjs/JSScreenDevice.js -swingjs/JSThreadGroup.js -swingjs/JSToolkit.js -swingjs/JSUtil.js -swingjs/a2s/Dialog.js -swingjs/api/Interface.js -swingjs/api/js/DOMNode.js -swingjs/api/js/HTML5CanvasContext2D.js -swingjs/api/js/JSInterface.js -swingjs/jquery/JQueryUI.js -swingjs/jzlib/Adler32.js -swingjs/jzlib/CRC32.js -swingjs/jzlib/Checksum.js -swingjs/jzlib/InfBlocks.js -swingjs/jzlib/InfCodes.js -swingjs/jzlib/InfTree.js -swingjs/jzlib/Inflate.js -swingjs/jzlib/Inflater.js -swingjs/jzlib/InflaterInputStream.js -swingjs/jzlib/ZStream.js -swingjs/plaf/ButtonListener.js -swingjs/plaf/DefaultMenuLayout.js -swingjs/plaf/HTML5LookAndFeel.js -swingjs/plaf/JSAppletUI.js -swingjs/plaf/JSButtonUI.js -swingjs/plaf/JSCheckBoxMenuItemUI.js -swingjs/plaf/JSCheckBoxUI.js -swingjs/plaf/JSComboBoxUI.js -swingjs/plaf/JSComponentUI.js -swingjs/plaf/JSDesktopIconUI.js -swingjs/plaf/JSDesktopPaneUI.js -swingjs/plaf/JSEventHandler.js -swingjs/plaf/JSFrameUI.js -swingjs/plaf/JSGraphicsUtils.js -swingjs/plaf/JSInternalFrameUI.js -swingjs/plaf/JSLabelUI.js -swingjs/plaf/JSLayeredPaneUI.js -swingjs/plaf/JSLightweightUI.js -swingjs/plaf/JSMenuBarUI.js -swingjs/plaf/JSMenuItemUI.js -swingjs/plaf/JSMenuUI.js -swingjs/plaf/JSPanelUI.js -swingjs/plaf/JSPopupMenuSeparatorUI.js -swingjs/plaf/JSPopupMenuUI.js -swingjs/plaf/JSPopupUI.js -swingjs/plaf/JSProgressBarUI.js -swingjs/plaf/JSRadioButtonMenuItemUI.js -swingjs/plaf/JSRadioButtonUI.js -swingjs/plaf/JSRootPaneUI.js -swingjs/plaf/JSScrollBarUI.js -swingjs/plaf/JSScrollPaneUI.js -swingjs/plaf/JSSeparatorUI.js -swingjs/plaf/JSSliderUI.js -swingjs/plaf/JSTabbedPaneUI.js -swingjs/plaf/JSToolTipUI.js -swingjs/plaf/JSViewportUI.js -swingjs/plaf/JSWindowUI.js -swingjs/plaf/LazyActionMap.js -swingjs/plaf/Resizer.js -swingjs/xml/JSJAXBClass.js -swingjs/xml/JSJAXBContext.js -swingjs/xml/JSJAXBContextFactory.js -swingjs/xml/JSJAXBField.js -swingjs/xml/JSJAXBUnmarshaller.js -swingjs/xml/JSSAXAttributes.js -swingjs/xml/JSSAXParser.js -swingjs/xml/JSXMLGregorianCalendarImpl.js -swingjs/xml/JSXMLInputFactory.js -swingjs/xml/JSXMLStreamReader.js -intervalstore/api/IntervalI.js -intervalstore/api/IntervalStoreI.js -intervalstore/impl/BinarySearcher.js -intervalstore/impl/IntervalStore.js -jalview/analysis/GeneticCodeI.js -jalview/analysis/GeneticCodes.js -jalview/api/FeaturesSourceI.js -jalview/io/FastaFile.js -jalview/io/FeaturesFile.js -jalview/io/FormatAdapter.js -jalview/schemes/IdColourScheme.js -jalview/util/LinkedIdentityHashSet.js -jalview/util/ParseHtmlBodyAndLinks.js -java/util/function/Function.js -swingjs/a2s/A2SContainer.js - -jalview/fts/api/FTSData.js -jalview/fts/api/FTSDataColumnI.js -jalview/fts/api/FTSRestClientI.js -jalview/fts/core/DecimalFormatTableCellRenderer.js -jalview/fts/core/FTSDataColumnPreferences.js -jalview/fts/core/FTSRestClient.js -jalview/fts/core/FTSRestRequest.js -jalview/fts/core/FTSRestResponse.js -jalview/fts/service/pdb/PDBFTSRestClient.js -jalview/gui/StructureChooser.js -jalview/javascript/json/JSON.js -jalview/javascript/web/Client.js -jalview/javascript/web/ClientResponse.js -jalview/javascript/web/WebResource.js -jalview/jbgui/BackupFilesPresetEntry.js -jalview/jbgui/GStructureChooser.js -jalview/jbgui/IntKeyStringValueEntry.js -java/awt/CardLayout.js -java/awt/TextComponent.js -java/awt/image/ImageConsumer.js -java/io/ObjectStreamField.js -java/net/HttpsURLConnection.js -java/net/URI.js -java/util/ComparableTimSort.js -java/util/LinkedHashSet.js -java/util/WeakHashMap.js -javajs/util/Base64.js -javax/swing/CellRendererPane.js -javax/swing/DefaultListSelectionModel.js -javax/swing/DefaultRowSorter.js -javax/swing/DropMode.js -javax/swing/Icon.js -javax/swing/ImageIcon.js -javax/swing/JTable.js -javax/swing/JTextField.js -javax/swing/ListSelectionModel.js -javax/swing/RowSorter.js -javax/swing/SortOrder.js -javax/swing/event/CaretEvent.js -javax/swing/event/CaretListener.js -javax/swing/event/CellEditorListener.js -javax/swing/event/DocumentListener.js -javax/swing/event/ListSelectionEvent.js -javax/swing/event/ListSelectionListener.js -javax/swing/event/MouseInputListener.js -javax/swing/event/RowSorterEvent.js -javax/swing/event/RowSorterListener.js -javax/swing/event/SwingPropertyChangeSupport.js -javax/swing/event/TableColumnModelEvent.js -javax/swing/event/TableColumnModelListener.js -javax/swing/event/TableModelEvent.js -javax/swing/plaf/InputMapUIResource.js -javax/swing/table/DefaultTableCellRenderer.js -javax/swing/table/DefaultTableColumnModel.js -javax/swing/table/DefaultTableModel.js -javax/swing/table/JTableHeader.js -javax/swing/table/TableCellRenderer.js -javax/swing/table/TableColumn.js -javax/swing/table/TableColumnModel.js -javax/swing/table/TableRowSorter.js -javax/swing/text/Caret.js -javax/swing/text/DefaultCaret.js -javax/swing/text/DefaultEditorKit.js -javax/swing/text/Document.js -javax/swing/text/EditorKit.js -javax/swing/text/Element.js -javax/swing/text/JTextComponent.js -javax/swing/text/Position.js -javax/swing/text/TextAction.js -javax/swing/text/View.js -net/miginfocom/layout/AC.js -net/miginfocom/layout/AnimSpec.js -net/miginfocom/layout/BoundSize.js -net/miginfocom/layout/CC.js -net/miginfocom/layout/ComponentWrapper.js -net/miginfocom/layout/ConstraintParser.js -net/miginfocom/layout/ContainerWrapper.js -net/miginfocom/layout/DimConstraint.js -net/miginfocom/layout/Grid.js -net/miginfocom/layout/LC.js -net/miginfocom/layout/LayoutUtil.js -net/miginfocom/layout/LinkHandler.js -net/miginfocom/layout/PlatformDefaults.js -net/miginfocom/layout/ResizeConstraint.js -net/miginfocom/layout/UnitValue.js -net/miginfocom/swing/MigLayout.js -net/miginfocom/swing/SwingComponentWrapper.js -net/miginfocom/swing/SwingContainerWrapper.js -sun/swing/StringUIClientPropertyKey.js -sun/swing/SwingUtilities2.js -sun/swing/UIClientPropertyKey.js -sun/swing/table/DefaultTableCellHeaderRenderer.js -swingjs/JSAbstractDocument.js -swingjs/JSImage.js -swingjs/JSImagekit.js -swingjs/JSPlainDocument.js -swingjs/api/JSMinimalAbstractDocument.js -swingjs/json/JSON.js -swingjs/plaf/BasicHTML.js -swingjs/plaf/CellHolder.js -swingjs/plaf/JSTableHeaderUI.js -swingjs/plaf/JSTableUI.js -swingjs/plaf/JSTextFieldUI.js -swingjs/plaf/JSTextUI.js -swingjs/plaf/TextListener.js - -com/stevesoft/pat/Bracket.js -com/stevesoft/pat/CaseMgr.js -com/stevesoft/pat/FastMulti.js -com/stevesoft/pat/NUnicodeAlpha.js -com/stevesoft/pat/NUnicodeCurrency.js -com/stevesoft/pat/NUnicodeDigit.js -com/stevesoft/pat/NUnicodeMath.js -com/stevesoft/pat/NUnicodePunct.js -com/stevesoft/pat/NUnicodeW.js -com/stevesoft/pat/NUnicodeWhite.js -com/stevesoft/pat/NoPattern.js -com/stevesoft/pat/Or.js -com/stevesoft/pat/OrMark.js -com/stevesoft/pat/Pattern.js -com/stevesoft/pat/PatternSub.js -com/stevesoft/pat/Pthings.js -com/stevesoft/pat/Range.js -com/stevesoft/pat/RegOpt.js -com/stevesoft/pat/RegRes.js -com/stevesoft/pat/Regex.js -com/stevesoft/pat/Rthings.js -com/stevesoft/pat/StrPos.js -com/stevesoft/pat/StringLike.js -com/stevesoft/pat/SubMark.js -com/stevesoft/pat/UniValidator.js -com/stevesoft/pat/UnicodeAlpha.js -com/stevesoft/pat/UnicodeCurrency.js -com/stevesoft/pat/UnicodeDigit.js -com/stevesoft/pat/UnicodeLower.js -com/stevesoft/pat/UnicodeMath.js -com/stevesoft/pat/UnicodePunct.js -com/stevesoft/pat/UnicodeUpper.js -com/stevesoft/pat/UnicodeW.js -com/stevesoft/pat/UnicodeWhite.js -com/stevesoft/pat/Validator.js -com/stevesoft/pat/oneChar.js -com/stevesoft/pat/parsePerl.js -com/stevesoft/pat/patInt.js -com/stevesoft/pat/wrap/StringWrap.js - -jalview/api/DBRefEntryI.js -jalview/api/SequenceStructureBinding.js -jalview/api/structures/JalviewStructureDisplayI.js -jalview/datamodel/DBRefEntry.js -jalview/datamodel/Mapping.js -jalview/datamodel/features/FeatureAttributes.js diff --git a/build.gradle b/build.gradle index b7f2162..d45afa4 100644 --- a/build.gradle +++ b/build.gradle @@ -642,9 +642,9 @@ task copyHelp(type: Copy) { def outputDir = "${classes}/${helpDir}" from(inputDir) { exclude '**/*.gif' - exclude '**/*.jpg' - exclude '**/*.png' - filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) + exclude '**/*.jpg' + exclude '**/*.png' + filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")]) } from(inputDir) { include '**/*.gif' @@ -737,21 +737,27 @@ task compileLinkCheck(type: JavaCompile) { outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class") } -def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch") task linkCheck(type: JavaExec) { dependsOn prepare, compileLinkCheck + + def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out") classpath = files("${jalviewDir}/${utilsDir}") main = "HelpLinksChecker" workingDir = jalviewDir def help = "${classes}/${helpDir}" args = [ "${classes}/${helpDir}", "-nointernet" ] - doLast { - helplinkscheckertouchfile.createNewFile() - } + def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append + def errFOS = outFOS + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + outFOS, + standardOutput) + errorOutput = new org.apache.tools.ant.util.TeeOutputStream( + outFOS, + errorOutput) inputs.dir("${classes}/${helpDir}") - outputs.file(helplinkscheckertouchfile) + outputs.file(helpLinksCheckerOutFile) } // import the pubhtmlhelp target @@ -1265,11 +1271,7 @@ def jalviewjsTransferSiteDir task jalviewjsSitePath { def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath()) jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs" - if (jalviewjs_site_dir.startsWith('/')) { - jalviewjsSiteDir = jalviewjs_site_dir - } else { - jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" - } + jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}" jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site" } @@ -1283,12 +1285,13 @@ task jalviewjsSetEclipseWorkspace { propVal = System.getProperty("user.home") + propVal.substring(1) } } - def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" + def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}" + def propsFile = file(propsFileName) def eclipseWsDir = propVal def props = new Properties() - if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) { - def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}") + if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) { + def ins = new FileInputStream(propsFileName) props.load(ins) ins.close() if (props.getProperty(propKey, null) != null) { @@ -1296,30 +1299,32 @@ task jalviewjsSetEclipseWorkspace { } } + def writeProps = false if (eclipseWsDir == null || !file(eclipseWsDir).exists()) { def tempDir = File.createTempDir() eclipseWsDir = tempDir.getAbsolutePath() - props.setProperty(propKey, eclipseWsDir) - def propsFile = file(propsFileName) - propsFile.parentFile.mkdirs() - propsFile.createNewFile() // doesn't affect existing file - def outs = new FileOutputStream(propsFile, false) - props.store(outs, null) - outs.close() + writeProps = true } - eclipseWorkspace = file(eclipseWsDir) doFirst { + if (writeProps) { + props.setProperty(propKey, eclipseWsDir) + propsFile.parentFile.mkdirs() + def bytes = new ByteArrayOutputStream() + props.store(bytes, null) + def propertiesString = bytes.toString() + propsFile.text = propertiesString + } + println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath()) } + inputs.property(propKey, eclipseWsDir) outputs.file(propsFileName) } -def eclipseDropinsDir -def utilsDropinsDir def eclipseBinary def eclipseVersion def eclipseDebug = false @@ -1333,21 +1338,18 @@ task jalviewjsEclipsePaths { } if (OperatingSystem.current().isMacOsX()) { eclipseRoot += "/Eclipse.app" - eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins" eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse" eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct" } else if (OperatingSystem.current().isWindows()) { // check these paths!! if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } - eclipseDropinsDir = "${eclipseRoot}/dropins" eclipseBinary = "${eclipseRoot}/eclipse" eclipseProduct = "${eclipseRoot}/.eclipseproduct" } else { // linux or unix if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) { eclipseRoot += "/eclipse" } - eclipseDropinsDir = "${eclipseRoot}/dropins" eclipseBinary = "${eclipseRoot}/eclipse" eclipseProduct = "${eclipseRoot}/.eclipseproduct" } @@ -1371,16 +1373,15 @@ task jalviewjsEclipsePaths { } else { eclipseVersionSuffix = "_4.13" } - utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}${eclipseVersionSuffix}" */ - utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}" + def propKey = "eclipse_debug" eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true")) doFirst { if (!assumedVersion) { - println("ECLIPSE_VERSION=${eclipseVersion}") + println("ECLIPSE VERSION=${eclipseVersion}") } } } @@ -1395,9 +1396,9 @@ task eclipseSetup { task OLDjalviewjsEclipseCopyDropins { dependsOn jalviewjsEclipsePaths dependsOn jalviewjsCleanEclipse - def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar") + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") inputFiles += file(jalviewjs_j2s_plugin) - def outputDir = eclipseDropinsDir + def outputDir = "${buildDir}/jalviewjs inputs.files inputFiles inputFiles.each { file -> @@ -1419,15 +1420,12 @@ task OLDjalviewjsEclipseCopyDropins { task jalviewjsEclipseCopyDropins(type: Copy) { dependsOn jalviewjsEclipsePaths - from utilsDropinsDir - into eclipseDropinsDir + def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar") + inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}") + def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" - doLast { - copy { - from jalviewjs_j2s_plugin - into eclipseDropinsDir - } - } + from inputFiles + into outputDir } // this eclipse -clean doesn't actually work @@ -1448,10 +1446,6 @@ y """ def inputByteStream = new ByteArrayInputStream(inputString.getBytes()) standardInput = inputByteStream - - doFirst { - println("CLEAN ECLIPSE_DEBUG=${eclipseDebug}") - } } /* not really working yet jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse @@ -1486,14 +1480,14 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) { if (val != null) { if (prop == siteDirProperty) { if (!(val.startsWith('/') || val.startsWith("file://") )) { - val = "${jalviewjsTransferSiteDir}/${val}" + val = "${jalviewDir}/${jalviewjsTransferSiteDir}/${val}" } setSiteDir = true } property(prop,val) } if (!setSiteDir) { // default site location, don't override specifically set property - property(siteDirProperty,jalviewjsTransferSiteDir) + property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteDir}") } } inputs.properties(j2s_props) @@ -1555,14 +1549,9 @@ task jalviewjsProjectImport(type: Exec) { if (eclipseDebug) { args += "-debug" } - // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=utils/jalviewjs/eclipse/dropins"] here? (instead of copying plugins to eclipse dropins dir) - - doFirst { - println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}") - } + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] inputs.file("${jalviewDir}/.project") - outputs.dir(projdir) outputs.upToDateWhen { file(projdir).exists() } } @@ -1576,67 +1565,63 @@ task jalviewjsTranspile(type: Exec) { if (eclipseDebug) { args += "-debug" } - // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=swingjs"] here? (instead of copying plugins to eclipse dropins dir) + args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ] def stdout def stderr - stdout = new ByteArrayOutputStream() - stderr = new ByteArrayOutputStream() + doFirst { + stdout = new ByteArrayOutputStream() + stderr = new ByteArrayOutputStream() - def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}" - def logOutFile = file(logOutFileName) - logOutFile.createNewFile() - logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} + def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}" + def logOutFile = file(logOutFileName) + logOutFile.createNewFile() + logOutFile.text = """ROOT: ${jalviewjs_eclipse_root} BINARY: ${eclipseBinary} VERSION: ${eclipseVersion} WORKSPACE: ${eclipseWorkspace} DEBUG: ${eclipseDebug} ---- """ - def logOutFOS = new FileOutputStream(logOutFile, true) // true == append - //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}" - //def logErrFile = file(logFileName) - //logErrFile.createNewFile() - //def logErrFOS = new FileErrputStream(logErrFile, false) - // combine stdout and stderr - def logErrFOS = logOutFOS - - if (jalviewjs_j2s_to_console.equals("true")) { - standardOutput = new org.apache.tools.ant.util.TeeOutputStream( - new org.apache.tools.ant.util.TeeOutputStream( - logOutFOS, - stdout), - standardOutput) + def logOutFOS = new FileOutputStream(logOutFile, true) // true == append + //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}" + //def logErrFile = file(logFileName) + //logErrFile.createNewFile() + //def logErrFOS = new FileErrputStream(logErrFile, false) + // combine stdout and stderr + def logErrFOS = logOutFOS + + if (jalviewjs_j2s_to_console.equals("true")) { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout), + standardOutput) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr), errorOutput) - } else { - standardOutput = new org.apache.tools.ant.util.TeeOutputStream( - logOutFOS, - stdout) + } else { + standardOutput = new org.apache.tools.ant.util.TeeOutputStream( + logOutFOS, + stdout) errorOutput = new org.apache.tools.ant.util.TeeOutputStream( logErrFOS, stderr) + } } doLast { if (stdout.toString().contains("Error processing ")) { // j2s did not complete transpile - throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'") + throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'") } } - doFirst { - println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}") - } - inputs.dir("${jalviewDir}/${sourceDir}") - outputs.dir("${jalviewDir}/${eclipse_bin_dir}/main") outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}") - outputs.upToDateWhen { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } - + outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } ) } task jalviewjsCopyTransferSite(type: Copy) { @@ -1667,8 +1652,8 @@ task jalviewjsBuildSite { task cleanJalviewjsSite { doFirst { - delete jalviewjsTransferSiteDir - delete jalviewjsSiteDir + delete "${jalviewDir}/${jalviewjsTransferSiteDir}" + delete "${jalviewDir}/${jalviewjsSiteDir}" } } @@ -1685,10 +1670,10 @@ task jalviewjsSiteTar(type: Tar) { compression Compression.GZIP - from jalviewjsSiteDir + from "${jalviewDir}/${jalviewjsSiteDir}" into jalviewjs_site_dir // this is inside the tar file - inputs.dir(jalviewjsSiteDir) + inputs.dir("${jalviewDir}/${jalviewjsSiteDir}") } task jalviewjsServer { @@ -1736,13 +1721,15 @@ task cleanJalviewjsAll { dependsOn jalviewjsEclipsePaths doFirst { - delete jalviewjsBuildDir + delete "${jalviewDir}/${jalviewjsBuildDir}" delete "${jalviewDir}/${eclipse_bin_dir}" if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) { delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata") } delete "${jalviewDir}/${jalviewjs_j2s_settings}" } + + outputs.upToDateWhen( { false } ) } task jalviewjs { @@ -1753,8 +1740,8 @@ task jalviewjs { task jalviewjsIDECopyTransferSite(type: Copy) { - from jalviewjsTransferSiteDir - into jalviewjsSiteDir + from "${jalviewDir}/${jalviewjsTransferSiteDir}" + into "${jalviewDir}/${jalviewjsSiteDir}" } task jalviewjsIDEj2s { diff --git a/gradle.properties b/gradle.properties index 3cadc78..7569d00 100644 --- a/gradle.properties +++ b/gradle.properties @@ -150,7 +150,6 @@ eclipse_debug = false jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09 -jalviewjs_utils_dir = utils/jalviewjs jalviewjs_eclipse_dropins_dir = utils/jalviewjs/eclipse/dropins jalviewjs_swingjs_zip = swingjs/SwingJS-site.zip jalviewjs_j2s_plugin = swingjs/net.sf.j2s.core.jar @@ -159,6 +158,7 @@ jalviewjs_site_resource_dir = utils/jalviewjs/site-resources jalviewjs_j2s_settings = .j2s #jalviewjs_eclipse_workspace = ~/tmp/eclipse-workspace # these 3 files/dirs found in build/jalviewjs +jalviewjs_eclipse_tmp_dropins_dir = eclipse_dropins jalviewjs_eclipse_workspace_location_file = eclipse_workspace_location jalviewjs_site_dir = site jalviewjs_j2s_subdir = swingjs/j2s -- 1.7.10.2