Fixed GitHub actions

.github/workflows/build_jar.yml

@@ -18,7 +18,9 @@
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
      - name: Grant execute permission for OMERO server setup script
-       run: chmod +x src/test/resources/qupath/ext/omero/setupOmeroServer.sh
+       run: chmod +x src/test/resources/omero-server/setup.sh
+     - name: Grant execute permission for OMERO web setup script
+       run: chmod +x src/test/resources/omero-web/setup.sh
      - name: Build with Gradle
        run: ./gradlew build -P toolchain=11
      - uses: actions/upload-artifact@v2

.github/workflows/gradle.yml

@@ -18,6 +18,8 @@
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
      - name: Grant execute permission for OMERO server setup script
-       run: chmod +x src/test/resources/qupath/ext/omero/setupOmeroServer.sh
+       run: chmod +x src/test/resources/omero-server/setup.sh
+     - name: Grant execute permission for OMERO web setup script
+       run: chmod +x src/test/resources/omero-web/setup.sh
      - name: Build with Gradle
        run: ./gradlew build -P toolchain=11

.gitignore

@@ -35,4 +35,3 @@ hs_err*.log
 *.swp
 *~.nib
 *thumbs.db
-bin/

src/test/resources/omero-web/omero-ms-pixel-buffer/bin/omero-ms-pixel-buffer

@@ -0,0 +1,243 @@
+#!/bin/sh
+
+#
+# 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.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+##############################################################################
+#
+#   omero-ms-pixel-buffer 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 omero-ms-pixel-buffer
+#
+#       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 OMERO_MS_PIXEL_BUFFER_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/HEAD/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
+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
+
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}.." && pwd -P ) || exit
+
+# Add default JVM options here. You can also use JAVA_OPTS and OMERO_MS_PIXEL_BUFFER_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Dvertx.logger-delegate-factory-class-name=io.vertx.core.logging.SLF4JLogDelegateFactory"'
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD=maximum
+
+warn () {
+    echo "$*"
+} >&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 ;;
+esac
+
+CLASSPATH=$APP_HOME/lib/omero-ms-pixel-buffer-0.6.3.jar:$APP_HOME/lib/simpleclient_vertx-0.6.0.jar:$APP_HOME/lib/omero-ms-core-0.7.0.jar:$APP_HOME/lib/brave-instrumentation-http-5.6.8.jar:$APP_HOME/lib/brave-5.6.8.jar:$APP_HOME/lib/brave-http-4.13.6.jar:$APP_HOME/lib/zipkin-sender-okhttp3-2.10.0.jar:$APP_HOME/lib/omero-blitz-5.6.2.jar:$APP_HOME/lib/omero-server-5.6.7.jar:$APP_HOME/lib/omero-renderer-5.5.12.jar:$APP_HOME/lib/omero-romio-5.7.2.jar:$APP_HOME/lib/omero-common-5.6.1.jar:$APP_HOME/lib/metrics-logback-3.0.2.jar:$APP_HOME/lib/logback-classic-1.2.11.jar:$APP_HOME/lib/log4j-over-slf4j-1.7.32.jar:$APP_HOME/lib/vertx-web-3.8.1.jar:$APP_HOME/lib/vertx-config-yaml-3.8.1.jar:$APP_HOME/lib/vertx-config-3.8.1.jar:$APP_HOME/lib/collector-0.12.0.jar:$APP_HOME/lib/simpleclient_hotspot-0.8.0.jar:$APP_HOME/lib/icegrid-3.6.5.jar:$APP_HOME/lib/simpleclient_common-0.6.0.jar:$APP_HOME/lib/simpleclient-0.8.0.jar:$APP_HOME/lib/brave-core-4.13.6.jar:$APP_HOME/lib/zipkin-reporter-2.10.0.jar:$APP_HOME/lib/zipkin-2.15.0.jar:$APP_HOME/lib/omero-model-5.6.10.jar:$APP_HOME/lib/formats-gpl-6.12.0.jar:$APP_HOME/lib/formats-bsd-6.12.0.jar:$APP_HOME/lib/formats-api-6.12.0.jar:$APP_HOME/lib/ome-xml-6.3.2.jar:$APP_HOME/lib/metakit-5.3.5.jar:$APP_HOME/lib/ome-poi-5.3.7.jar:$APP_HOME/lib/ome-codecs-0.4.4.jar:$APP_HOME/lib/ome-common-6.0.14.jar:$APP_HOME/lib/minio-5.0.2.jar:$APP_HOME/lib/okhttp-3.14.2.jar:$APP_HOME/lib/logback-core-1.2.11.jar:$APP_HOME/lib/calcite-core-1.20.0.jar:$APP_HOME/lib/spring-security-ldap-4.2.4.RELEASE.jar:$APP_HOME/lib/spring-ldap-core-2.3.2.RELEASE.jar:$APP_HOME/lib/avatica-core-1.15.0.jar:$APP_HOME/lib/json-path-2.4.0.jar:$APP_HOME/lib/avatica-metrics-1.15.0.jar:$APP_HOME/lib/metrics-graphite-3.0.2.jar:$APP_HOME/lib/metrics-jvm-3.0.2.jar:$APP_HOME/lib/metrics-core-3.0.2.jar:$APP_HOME/lib/hibernate-search-3.4.2.Final.jar:$APP_HOME/lib/hibernate-core-3.6.10.Final.jar:$APP_HOME/lib/bufr-3.0.jar:$APP_HOME/lib/hibernate-commons-annotations-3.2.0.Final.jar:$APP_HOME/lib/hibernate-search-analyzers-3.4.2.Final.jar:$APP_HOME/lib/cdm-core-5.3.3.jar:$APP_HOME/lib/jxrlib-all-0.2.4.jar:$APP_HOME/lib/native-lib-loader-2.1.4.jar:$APP_HOME/lib/httpservices-5.3.3.jar:$APP_HOME/lib/solr-analysis-extras-3.1.0.jar:$APP_HOME/lib/solr-core-3.1.0.jar:$APP_HOME/lib/solr-solrj-3.1.0.jar:$APP_HOME/lib/slf4j-api-1.7.32.jar:$APP_HOME/lib/lettuce-core-5.2.0.RELEASE.jar:$APP_HOME/lib/vertx-jdbc-client-3.8.1.jar:$APP_HOME/lib/kaitai-struct-runtime-0.8.jar:$APP_HOME/lib/aggdesigner-algorithm-6.0.jar:$APP_HOME/lib/commons-lang-2.6.jar:$APP_HOME/lib/vertx-web-common-3.8.1.jar:$APP_HOME/lib/vertx-auth-common-3.8.1.jar:$APP_HOME/lib/vertx-bridge-common-3.8.1.jar:$APP_HOME/lib/vertx-sql-common-3.8.1.jar:$APP_HOME/lib/vertx-core-3.8.1.jar:$APP_HOME/lib/jackson-databind-2.14.1.jar:$APP_HOME/lib/jackson-annotations-2.14.1.jar:$APP_HOME/lib/esri-geometry-api-2.2.0.jar:$APP_HOME/lib/jackson-core-2.14.1.jar:$APP_HOME/lib/jackson-dataformat-yaml-2.14.1.jar:$APP_HOME/lib/javax.activation-1.2.0.jar:$APP_HOME/lib/snakeyaml-1.33.jar:$APP_HOME/lib/okio-1.17.2.jar:$APP_HOME/lib/glacier2-3.6.5.jar:$APP_HOME/lib/ice-3.6.5.jar:$APP_HOME/lib/netty-handler-proxy-4.1.39.Final.jar:$APP_HOME/lib/netty-codec-http2-4.1.39.Final.jar:$APP_HOME/lib/netty-codec-http-4.1.39.Final.jar:$APP_HOME/lib/netty-handler-4.1.42.Final.jar:$APP_HOME/lib/netty-resolver-dns-4.1.39.Final.jar:$APP_HOME/lib/netty-codec-socks-4.1.39.Final.jar:$APP_HOME/lib/netty-codec-dns-4.1.39.Final.jar:$APP_HOME/lib/netty-codec-4.1.42.Final.jar:$APP_HOME/lib/netty-transport-4.1.42.Final.jar:$APP_HOME/lib/netty-buffer-4.1.42.Final.jar:$APP_HOME/lib/netty-resolver-4.1.42.Final.jar:$APP_HOME/lib/netty-common-4.1.42.Final.jar:$APP_HOME/lib/reactor-core-3.3.0.RELEASE.jar:$APP_HOME/lib/c3p0-0.9.5.4.jar:$APP_HOME/lib/spring-context-support-4.3.22.RELEASE.jar:$APP_HOME/lib/spring-jms-4.3.14.RELEASE.jar:$APP_HOME/lib/postgresql-42.2.1.jar:$APP_HOME/lib/btm-3.0.0-mk1.jar:$APP_HOME/lib/javax.mail-1.6.2.jar:$APP_HOME/lib/jhdf5-19.04.0.jar:$APP_HOME/lib/base-18.09.0.jar:$APP_HOME/lib/commons-io-2.7.jar:$APP_HOME/lib/reactive-streams-1.0.3.jar:$APP_HOME/lib/mchange-commons-java-0.2.15.jar:$APP_HOME/lib/spring-messaging-4.3.14.RELEASE.jar:$APP_HOME/lib/spring-orm-4.3.14.RELEASE.jar:$APP_HOME/lib/spring-jdbc-4.3.14.RELEASE.jar:$APP_HOME/lib/spring-tx-4.3.14.RELEASE.jar:$APP_HOME/lib/spring-security-core-4.2.4.RELEASE.jar:$APP_HOME/lib/spring-context-4.3.22.RELEASE.jar:$APP_HOME/lib/spring-aop-4.3.22.RELEASE.jar:$APP_HOME/lib/spring-beans-4.3.22.RELEASE.jar:$APP_HOME/lib/spring-expression-4.3.22.RELEASE.jar:$APP_HOME/lib/spring-core-4.3.22.RELEASE.jar:$APP_HOME/lib/calcite-linq4j-1.20.0.jar:$APP_HOME/lib/guava-29.0-jre.jar:$APP_HOME/lib/sketches-core-0.9.0.jar:$APP_HOME/lib/janino-3.0.11.jar:$APP_HOME/lib/commons-compiler-3.0.11.jar:$APP_HOME/lib/activation-1.1.jar:$APP_HOME/lib/commons-logging-1.2.jar:$APP_HOME/lib/aopalliance-1.0.jar:$APP_HOME/lib/protobuf-java-3.6.1.jar:$APP_HOME/lib/memory-0.9.0.jar:$APP_HOME/lib/udunits-4.5.5.jar:$APP_HOME/lib/antlr-2.7.6.jar:$APP_HOME/lib/commons-collections-3.1.jar:$APP_HOME/lib/dom4j-1.6.1.jar:$APP_HOME/lib/hibernate-jpa-2.0-api-1.0.1.Final.jar:$APP_HOME/lib/jta-1.1.jar:$APP_HOME/lib/lucene-smartcn-3.1.0.jar:$APP_HOME/lib/lucene-stempel-3.1.0.jar:$APP_HOME/lib/lucene-misc-3.1.0.jar:$APP_HOME/lib/lucene-spellchecker-3.1.0.jar:$APP_HOME/lib/lucene-analyzers-3.1.0.jar:$APP_HOME/lib/lucene-highlighter-3.1.0.jar:$APP_HOME/lib/lucene-memory-3.1.0.jar:$APP_HOME/lib/lucene-spatial-3.1.0.jar:$APP_HOME/lib/lucene-core-3.1.0.jar:$APP_HOME/lib/ome-mdbtools-5.3.2.jar:$APP_HOME/lib/JWlz-1.4.0.jar:$APP_HOME/lib/joda-time-2.10.3.jar:$APP_HOME/lib/kryo-4.0.2.jar:$APP_HOME/lib/json-20090211.jar:$APP_HOME/lib/sqlite-jdbc-3.28.0.jar:$APP_HOME/lib/jcip-annotations-1.0.jar:$APP_HOME/lib/specification-6.3.2.jar:$APP_HOME/lib/turbojpeg-6.12.0.jar:$APP_HOME/lib/jgoodies-forms-1.7.2.jar:$APP_HOME/lib/perf4j-0.9.16.jar:$APP_HOME/lib/xml-apis-1.4.01.jar:$APP_HOME/lib/re2j-1.3.jar:$APP_HOME/lib/reflectasm-1.11.3.jar:$APP_HOME/lib/minlog-1.3.0.jar:$APP_HOME/lib/objenesis-2.5.1.jar:$APP_HOME/lib/failureaccess-1.0.1.jar:$APP_HOME/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:$APP_HOME/lib/checker-qual-2.11.1.jar:$APP_HOME/lib/error_prone_annotations-2.3.4.jar:$APP_HOME/lib/j2objc-annotations-1.3.jar:$APP_HOME/lib/google-http-client-xml-1.20.0.jar:$APP_HOME/lib/ome-jai-0.1.3.jar:$APP_HOME/lib/aircompressor-0.21.jar:$APP_HOME/lib/jgoodies-common-1.7.0.jar:$APP_HOME/lib/asm-5.0.4.jar:$APP_HOME/lib/solr-commons-csv-3.1.0.jar:$APP_HOME/lib/google-http-client-1.20.0.jar:$APP_HOME/lib/xpp3-1.1.4c.jar
+
+
+# Determine the Java command to use to start the JVM.
+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=$JAVA_HOME/jre/sh/java
+    else
+        JAVACMD=$JAVA_HOME/bin/java
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD=java
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045 
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045 
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
+    esac
+fi
+
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and OMERO_MS_PIXEL_BUFFER_OPTS environment variables.
+
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$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
+    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
+        # 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
+fi
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $OMERO_MS_PIXEL_BUFFER_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        -classpath "$CLASSPATH" \
+        io.vertx.core.Launcher \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$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.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $OMERO_MS_PIXEL_BUFFER_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
+
+exec "$JAVACMD" "$@"