diff --git a/CHANGELOG.md b/CHANGELOG.md index fb03d68e..e1f1b7e7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ -## Version 0.3.0-SNAPSHOT -*In progress* +## Version 0.4.0 + +* Supports QuPath v0.5.0 +* Renamed to `qupath-extension-omero-web` + * To make way for a new OMERO extension soon... + + +## Version 0.3.0 * Now separated from QuPath in its own repository! * Log on/off OMERO servers with different credentials diff --git a/build.gradle b/build.gradle index 74dc8d1d..5dd09d64 100644 --- a/build.gradle +++ b/build.gradle @@ -1,18 +1,24 @@ plugins { id 'java-library' // To create a shadow/fat jar, including dependencies - id 'com.github.johnrengelman.shadow' version '7.0.0' - // Reduce JavaCPP dependencies - id 'org.bytedeco.gradle-javacpp-platform' version '1.5.7' + id 'com.github.johnrengelman.shadow' version '8.1.1' + id 'org.openjfx.javafxplugin' version '0.1.0' + // Version in settings.gradle + id 'org.bytedeco.gradle-javacpp-platform' } ext.moduleName = 'qupath.extension.omero' -archivesBaseName = 'qupath-extension-omero' -description = "QuPath extension to support image reading using OMERO's web API." -version = "0.3.1-SNAPSHOT" +ext.qupathVersion = gradle.ext.qupathVersion +ext.qupathJavaVersion = 17 + +base { + description = "QuPath extension to support image reading using OMERO's web API." + version = "0.4.0-SNAPSHOT" + group = "io.github.qupath" +} repositories { -// mavenLocal() + mavenCentral() maven { @@ -26,36 +32,59 @@ repositories { } dependencies { - implementation "org.apache.commons:commons-text:1.9" - - shadow "io.github.qupath:qupath-gui-fx:0.3.0" - shadow "org.slf4j:slf4j-api:1.7.30" + implementation libs.commons.text + shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}" + shadow libs.qupath.fxtras + + shadow libs.slf4j +} + +jar { + manifest { + attributes("Implementation-Title": project.name, + "Implementation-Version": archiveVersion, + "Automatic-Module-Name": moduleName) + } } processResources { - from ("${projectDir}/LICENSE.txt") { - into 'licenses/' - } + from ("${projectDir}/LICENSE") { + into 'licenses/' + } } tasks.register("copyDependencies", Copy) { - description "Copy dependencies into the output libs directory" - group "QuPath" - - from configurations.default - into 'build/libs' + description "Copy dependencies into the build directory for use elsewhere" + group "QuPath" + + from configurations.default + into 'build/libs' } java { - def version = project.findProperty('toolchain') - if (!version) - version = 11 - else if (version.strip() == 'skip') - version = null - if (version != null) { - logger.quiet("Setting toolchain to {}", version) - toolchain { - languageVersion = JavaLanguageVersion.of(version) - } + toolchain { + languageVersion = JavaLanguageVersion.of(qupathJavaVersion) } + withSourcesJar() + withJavadocJar() +} + +tasks.withType(Javadoc) { + options.encoding = 'UTF-8' + def strictJavadoc = findProperty('strictJavadoc') + if (!strictJavadoc) { + options.addStringOption('Xdoclint:none', '-quiet') + } +} + +tasks.named('compileJava') { + options.encoding = 'UTF-8' +} + +tasks.withType(org.gradle.jvm.tasks.Jar) { + duplicatesStrategy = DuplicatesStrategy.INCLUDE +} + +tasks.named('test') { + useJUnitPlatform() } diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 7454180f..41d9927a 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index aa991fce..a5952066 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index 744e882e..1b6c7873 100755 --- a/gradlew +++ b/gradlew @@ -1,7 +1,7 @@ -#!/usr/bin/env sh +#!/bin/sh # -# Copyright 2015 the original author or authors. +# Copyright © 2015-2021 the original authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -17,67 +17,101 @@ # ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +APP_BASE_NAME=${0##*/} # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MSYS* | MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar @@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -106,80 +140,95 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. # For Cygwin or MSYS, switch paths to Windows format before running java -if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=`expr $i + 1` + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - 0) set -- ;; - 1) set -- "$args0" ;; - 2) set -- "$args0" "$args1" ;; - 3) set -- "$args0" "$args1" "$args2" ;; - 4) set -- "$args0" "$args1" "$args2" "$args3" ;; - 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=`save "$@"` +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" diff --git a/settings.gradle b/settings.gradle index fc8a797c..e5666364 100644 --- a/settings.gradle +++ b/settings.gradle @@ -1 +1,31 @@ +pluginManagement { + plugins { + id 'org.bytedeco.gradle-javacpp-platform' version '1.5.9' + } +} + rootProject.name = 'qupath-extension-omero' + +gradle.ext.qupathVersion = "0.5.0" + +dependencyResolutionManagement { + versionCatalogs { + libs { + from("io.github.qupath:qupath-catalog:${gradle.ext.qupathVersion}") + } + } + + repositories { + + mavenCentral() + + maven { + url "https://maven.scijava.org/content/repositories/releases" + } + + maven { + url "https://maven.scijava.org/content/repositories/snapshots" + } + + } +} \ No newline at end of file diff --git a/src/main/java/qupath/lib/images/servers/omero/OmeroExtension.java b/src/main/java/qupath/lib/images/servers/omero/OmeroExtension.java index 6191cbec..46261dff 100644 --- a/src/main/java/qupath/lib/images/servers/omero/OmeroExtension.java +++ b/src/main/java/qupath/lib/images/servers/omero/OmeroExtension.java @@ -39,14 +39,14 @@ import javafx.scene.control.MenuItem; import javafx.scene.control.TextField; import javafx.scene.layout.GridPane; +import qupath.fx.dialogs.Dialogs; +import qupath.fx.utils.GridPaneUtils; import qupath.lib.common.Version; -import qupath.lib.gui.ActionTools; import qupath.lib.gui.QuPathGUI; -import qupath.lib.gui.dialogs.Dialogs; +import qupath.lib.gui.actions.ActionTools; import qupath.lib.gui.extensions.GitHubProject; import qupath.lib.gui.extensions.QuPathExtension; import qupath.lib.gui.tools.MenuTools; -import qupath.lib.gui.tools.PaneTools; /** * Extension to access images hosted on OMERO. @@ -131,8 +131,8 @@ private static Menu createServerListMenu(QuPathGUI qupath, Menu browseServerMenu gp.setVgap(5.0); TextField tf = new TextField(); tf.setPrefWidth(400); - PaneTools.addGridRow(gp, 0, 0, "Enter OMERO URL", new Label("Enter an OMERO server URL to browse (e.g. http://idr.openmicroscopy.org/):")); - PaneTools.addGridRow(gp, 1, 0, "Enter OMERO URL", tf, tf); + GridPaneUtils.addGridRow(gp, 0, 0, "Enter OMERO URL", new Label("Enter an OMERO server URL to browse (e.g. http://idr.openmicroscopy.org/):")); + GridPaneUtils.addGridRow(gp, 1, 0, "Enter OMERO URL", tf, tf); var confirm = Dialogs.showConfirmDialog("Enter OMERO URL", gp); if (!confirm) return; @@ -202,6 +202,6 @@ public GitHubRepo getRepository() { @Override public Version getQuPathVersion() { - return Version.parse("0.3.0-rc2"); + return Version.parse("0.5.0"); } } diff --git a/src/main/java/qupath/lib/images/servers/omero/OmeroWebClientsCommand.java b/src/main/java/qupath/lib/images/servers/omero/OmeroWebClientsCommand.java index 9c377f66..37d270e0 100644 --- a/src/main/java/qupath/lib/images/servers/omero/OmeroWebClientsCommand.java +++ b/src/main/java/qupath/lib/images/servers/omero/OmeroWebClientsCommand.java @@ -285,7 +285,7 @@ private GridPane createServerPane() { removeBtn.setOnMouseClicked(e -> { // Check if the webclient to delete is currently used in any viewer - if (qupath.getViewers().stream().anyMatch(viewer -> { + if (qupath.getAllViewers().stream().anyMatch(viewer -> { if (viewer.getServer() == null) return false; URI viewerURI = viewer.getServer().getURIs().iterator().next(); diff --git a/src/main/java/qupath/lib/images/servers/omero/OmeroWebImageServerBrowserCommand.java b/src/main/java/qupath/lib/images/servers/omero/OmeroWebImageServerBrowserCommand.java index 402d5da7..100dbbe0 100644 --- a/src/main/java/qupath/lib/images/servers/omero/OmeroWebImageServerBrowserCommand.java +++ b/src/main/java/qupath/lib/images/servers/omero/OmeroWebImageServerBrowserCommand.java @@ -49,6 +49,7 @@ import java.util.stream.Collectors; import java.util.stream.Stream; +import org.controlsfx.glyphfont.GlyphFontRegistry; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -348,8 +349,13 @@ public Owner fromString(String string) { if (e.getClickCount() == 2) { var selectedItem = tree.getSelectionModel().getSelectedItem(); if (selectedItem != null && selectedItem.getValue().getType() == OmeroObjectType.IMAGE && isSupported(selectedItem.getValue())) { - if (qupath.getProject() == null) - qupath.openImage(createObjectURI(selectedItem.getValue()), true, true); + if (qupath.getProject() == null) { + try { + qupath.openImage(qupath.getViewer(), createObjectURI(selectedItem.getValue()), true, true); + } catch (IOException ex) { + throw new RuntimeException(ex); + } + } else promptToImportOmeroImages(createObjectURI(selectedItem.getValue())); } @@ -376,7 +382,7 @@ public Owner fromString(String string) { Dialogs.showPlainMessage("Requesting orphaned folder", "Link to orphaned folder does not exist!"); return; } - QuPathGUI.launchBrowserWindow(createObjectURI(selected.get(0).getValue())); + QuPathGUI.openInBrowser(createObjectURI(selected.get(0).getValue())); } }); openBrowserItem.disableProperty().bind(tree.getSelectionModel().selectedItemProperty().isNull() @@ -611,8 +617,13 @@ else if (uri.getType() == OmeroObjectType.ORPHANED_FOLDER) return; } if (qupath.getProject() == null) { - if (validUris.length == 1) - qupath.openImage(validUris[0], true, true); + if (validUris.length == 1) { + try { + qupath.openImage(qupath.getViewer(), validUris[0], true, true); + } catch (IOException ex) { + throw new RuntimeException(ex); + } + } else Dialogs.showErrorMessage("Open OMERO images", "If you want to handle multiple images, you need to create a project first."); // Same as D&D for images return; @@ -1412,7 +1423,7 @@ private Node createAnnotationsPane(String title, OmeroAnnotations omeroAnnotatio } for (int i = 0; i < Math.round(rating/anns.size()); i++) - gp.add(IconFactory.createNode(QuPathGUI.TOOLBAR_ICON_SIZE, QuPathGUI.TOOLBAR_ICON_SIZE, IconFactory.PathIcons.STAR), i, 0); + gp.add(GlyphFontRegistry.font("icomoon").create("\u2605").size(QuPathGUI.TOOLBAR_ICON_SIZE).color(javafx.scene.paint.Color.GRAY), i, 0); gp.setHgap(10.0); break; default: @@ -1722,7 +1733,7 @@ protected void updateItem(SearchResult item, boolean empty) { return; } - button.setOnAction(e -> QuPathGUI.launchBrowserWindow(item.link.toString())); + button.setOnAction(e -> QuPathGUI.openInBrowser(item.link.toString())); setGraphic(button); } });