JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos...

diff --git a/build.gradle b/build.gradle
index 009b0c1..bea9951 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1573,7 +1573,7 @@ task getdownWebsite() {
       }
     }
     
-    def getdownWrapperScripts = [ getdown_mac_wrapper_script, getdown_unix_wrapper_script, getdown_windows_wrapper_script, getdown_powershell_wrapper_script ]
+    def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script ]
     getdownWrapperScripts.each{ script ->
       def s = file( "${jalviewDir}/utils/getdown/${script}" )
       if (s.exists()) {
@@ -1912,8 +1912,8 @@ task installers(type: com.install4j.gradle.Install4jTask) {
     'WINDOWS_APPLICATION_ID': install4jWinApplicationId,
     'MACOS_DMG_DS_STORE': install4jDMGDSStore,
     'MACOS_DMG_BG_IMAGE': install4jDMGBackgroundImage,
-    'MACOS_DMG_WRAPPER_LINK': install4j_dmg_wrapper_link,
-    'MACOS_WRAPPER_SCRIPT': getdown_mac_wrapper_script,
+    'MACOS_DMG_WRAPPER_LINK': getdown_bash_wrapper_script,
+    'MACOS_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
     'INSTALLER_NAME': install4jInstallerName,
     'INSTALL4J_UTILS_DIR': install4j_utils_dir,
     'GETDOWN_WEBSITE_DIR': getdown_website_dir,

diff --git a/gradle.properties b/gradle.properties
index d87a598..ba87a6c 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -133,10 +133,7 @@ install4j_png_icon_file = jalview_logo.png
 install4j_background = jalview_logo_background_fade-640x480.png
 install4j_dmg_background = jalview_dmg_background-NON-RELEASE.png
 install4j_dmg_ds_store = jalview_dmg_DS_Store
-install4j_dmg_wrapper_link = jalviewc
-getdown_mac_wrapper_script = jalviewc-macos
-getdown_unix_wrapper_script = jalviewc
-getdown_windows_wrapper_script = jalviewc-windows
+getdown_bash_wrapper_script = jalviewc
 getdown_powershell_wrapper_script = jalviewc.ps1
 
 OSX_KEYSTORE =

diff --git a/utils/getdown/jalviewc b/utils/getdown/jalviewc
index 4792a9c..29beb98 100755 (executable)
--- a/utils/getdown/jalviewc
+++ b/utils/getdown/jalviewc
@@ -1,33 +1,132 @@
 #!/usr/bin/env bash
 
+declare -a ARGS=("${@}")
 ARG1=$1
-DIR="$(dirname "$(readlink -f "$0")")"
 
-# check to see if $1 is set and is not start of other cli set args
-OPEN=""
-if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
- # first argument exists and does not start with a "-" and is not "open"
- OPEN="-open"
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+  FINDFILE="$1"
+  FILE="${FINDFILE}"
+  PREVFILE=""
+  C=0
+  MAX=100 # just in case we end up in a loop
+  FOUND=0
+  while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+    PREVFILE="${FILE}"
+    FILE="$(readlink "${FILE}")"
+    if [ -z "${FILE}" ]; then
+      # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+      FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+      FOUND=1
+    elif [ "${FILE#/}" = "${FILE}" ]; then
+      # FILE is not an absolute path link, we need to add the relative path to the previous dir
+      FILE="$(dirname "${PREVFILE}")/${FILE}"
+    fi
+    C=$((C+1))
+  done
+  if [ "${FOUND}" -ne 1 ]; then
+    echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+    exit 1
+  fi
+  echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+  ISMACOS=1
+fi
+
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+  DIR="$(dirname "$(readlinkf "$0")")"
+  APP="${DIR%.app/Contents/*}".app
+  if [ "${APP}" = "${APP%.app}" ]; then
+    echo "Could not find Jalview.app" >&2
+    exit 2
+  fi
+  APPDIR="${APP}/Contents/Resources/app"
+  JAVA="${APPDIR}/jre/Contents/Home/bin/java"
+  JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+else
+# NOT MACOS
+  DIR="$(dirname "$(readlink -f "$0")")"
+  APPDIR="${DIR}"
+  JAVA="${APPDIR}/jre/bin/java"
 fi
 
-APPDIR="${DIR}"
-JAVA="${APPDIR}/jre/bin/java"
+SYSJAVA=java
 GETDOWNTXT="${APPDIR}/getdown.txt"
+
 CLASSPATH=""
+# save an array of JAR paths in case we're in WSL (see later)
+declare -a JARPATHS=()
 if [ -e "${GETDOWNTXT}" ]; then
+  # always check grep and sed regexes on macos -- they're not the same
   for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
     [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
     CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
+    JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
   done
 else
   echo "Cannot find getdown.txt" >&2
   exit 3
 fi
 
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # macos doesn't like uname -o, best to avoid
+  if [ "$(uname -o)" = "Cygwin" ]; then
+  # CYGWIN
+    echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
+    CLASSPATH=$(cygpath -pw "${CLASSPATH}")
+    # now for some arg paths fun. only translating paths starting with './', '../' or '/'
+    ARGS=()
+    for ARG in "${@}"; do
+      if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
+        ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+      else
+        ARGS=( "${ARGS[@]}" "${ARG}" )
+      fi
+    done
+  elif uname -r | grep Microsoft >/dev/null; then
+  # WSL
+    echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
+    CLASSPATH=""
+    for JARPATH in "${JARPATHS[@]}"; do
+      [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
+      CLASSPATH="${CLASSPATH}$(wslpath -aw "${JARPATH}")"
+    done
+    ARGS=()
+    for ARG in "${@}"; do
+      if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
+        # annoyingly wslpath does not work if the file doesn't exist!
+        ARGBASENAME="$(basename "${ARG}")"
+        ARGDIRNAME="$(dirname "${ARG}")"
+        ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
+      else
+        ARGS=( "${ARGS[@]}" "${ARG}" )
+      fi
+    done
+    JAVA="${JAVA}.exe"
+    SYSJAVA="java.exe"
+  fi
+fi
+
+# Is there a bundled Java?  If not just try one in the PATH (do need .exe in WSL)
 if [ \! -e "${JAVA}" ]; then
-  echo "Cannot find bundled java, using system and hoping for the best!" >&2
-  JAVA=java
+  JAVA=$SYSJAVA
+  echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
+fi
+
+# check to see if $1 is set and is not start of other cli args
+OPEN=""
+if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
+ # first argument exists and does not start with a "-" and is not "open"
+ OPEN="-open"
 fi
 
-# don't quote $OPEN
-"${JAVA}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "$@"
+# don't quote $OPEN (don't want it accidentally mistaken as an empty string arg!)
+"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"

diff --git a/utils/getdown/jalviewc-macos b/utils/getdown/jalviewc-macos
deleted file mode 100755 (executable)
index e34685d..0000000
--- a/utils/getdown/jalviewc-macos
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env bash
-
-ARG1="$1"
-
-# this whole next part is because there's no readlink -f in Darwin
-function readlinkf() {
-  FINDFILE="$1"
-  FILE="${FINDFILE}"
-  PREVFILE=""
-  C=0
-  MAX=100 # just in case we end up in a loop
-  FOUND=0
-  while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
-    PREVFILE="${FILE}"
-    FILE="$(readlink "${FILE}")"
-    if [ -z "${FILE}" ]; then
-      # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
-      FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
-      FOUND=1
-    elif [ "${FILE#/}" = "${FILE}" ]; then
-      # FILE is not an absolute path link, we need to add the relative path to the previous dir
-      FILE="$(dirname "${PREVFILE}")/${FILE}"
-    fi
-    C=$((C+1))
-  done
-  if [ "${FOUND}" -ne 1 ]; then
-    echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
-    exit 1
-  fi
-  echo "${FILE}"
-}
-
-DIR="$(dirname "$(readlinkf "$0")")"
-APP="${DIR%.app/Contents/*}".app
-
-if [ "${APP}" = "${APP%.app}" ]; then
-  echo "Could not find Jalview.app dir" >&2
-  exit 2
-fi
-
-# check to see if $1 is set and is not start of other cli set args
-OPEN=""
-if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
- # first argument exists and does not start with a "-" and is not "open"
- OPEN="-open"
-fi
-
-APPDIR="${APP}/Contents/Resources/app"
-JAVA="${APPDIR}/jre/Contents/Home/bin/java"
-GETDOWNTXT="${APPDIR}/getdown.txt"
-CLASSPATH=""
-if [ -e "${GETDOWNTXT}" ]; then
-  # always check grep and sed regexes on macOS -- they're not the same
-  for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
-    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
-    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
-  done
-else
-  echo "Cannot find getdown.txt" >&2
-  exit 3
-fi
-
-if [ \! -e "${JAVA}" ]; then
-  echo "Cannot find bundled java, using system and hoping for the best!" >&2
-  JAVA=java
-fi
-
-# don't quote $OPEN
-"${JAVA}" -Xdock:icon="${APPDIR}"/resource/jalview_logo.png -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "$@"

diff --git a/utils/getdown/jalviewc-windows b/utils/getdown/jalviewc-windows
deleted file mode 100755 (executable)
index 2f0f968..0000000
--- a/utils/getdown/jalviewc-windows
+++ /dev/null
@@ -1,74 +0,0 @@
-#!/usr/bin/env bash
-
-ARG1=$1
-DIR="$(dirname "$(readlink -f "$0")")"
-
-# check to see if $1 is set and is not start of other cli set args
-OPEN=""
-if [ -n "${ARG1}" -a "${ARG1}" = "${ARG1#-}" -a "${ARG1}" != "open" ]; then
- # first argument exists and does not start with a "-" and is not "open"
- OPEN="-open"
-fi
-
-APPDIR="${DIR}"
-JAVA="${APPDIR}/jre/bin/java"
-GETDOWNTXT="${APPDIR}/getdown.txt"
-CLASSPATH=""
-if [ -e "${GETDOWNTXT}" ]; then
-  for JAR in $(grep -e '^code\s*=\s*' "${GETDOWNTXT}" | sed -e 's/^code\s*=\s*//;'); do
-    [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
-    CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
-  done
-else
-  echo "Cannot find getdown.txt" >&2
-  exit 3
-fi
-
-if [ \! -e "${JAVA}" ]; then
-  echo "Cannot find bundled java, using system and hoping for the best!" >&2
-  JAVA=java
-fi
-
-declare -a ARGS=("${@}")
-
-# change paths for Cygwin or Windows Subsystem for Linux (WSL)
-if [ "$(uname -o)" = "Cygwin" ]; then
-  echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
-  CLASSPATH=$(cygpath -pw "${CLASSPATH}")
-  # now for some arg paths fun. only translating paths starting with './', '../' or '/'
-  ARGS=()
-  for ARG in "${@}"; do
-    if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
-      ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
-    else
-      ARGS=( "${ARGS[@]}" "${ARG}" )
-    fi
-  done
-  JAVA="${JAVA}.exe"
-elif uname -r | grep Microsoft >/dev/null; then
-  echo "When using relative paths in args within WSL. please start with './' or '../'" >&2
-  WCLASSPATH=""
-  OLD_IFS="${IFS}"
-  IFS=":"
-  for JAR in $CLASSPATH; do
-    [ -n "${WCLASSPATH}" ] && WCLASSPATH="${WCLASSPATH};"
-    WCLASSPATH="${WCLASSPATH}$(wslpath -aw "${JAR}")"
-  done
-  CLASSPATH="${WCLASSPATH}"
-  IFS="${OLD_IFS}"
-  ARGS=()
-  for ARG in "${@}"; do
-    if [ "${ARG}" != "${ARG#./}" -o "${ARG}" != "${ARG#/}" -o "${ARG}" != "${ARG#../}" ]; then
-      # annoyingly wslpath does not work if the file doesn't exist!
-      ARGBASENAME="$(basename "${ARG}")"
-      ARGDIRNAME="$(dirname "${ARG}")"
-      ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
-    else
-      ARGS=( "${ARGS[@]}" "${ARG}" )
-    fi
-  done
-  JAVA="${JAVA}.exe"
-fi
-
-# don't quote $OPEN
-"${JAVA}" -cp "${CLASSPATH}" jalview.bin.Launcher ${OPEN} "${ARGS[@]}"

diff --git a/utils/install4j/install4j8_template.install4j b/utils/install4j/install4j8_template.install4j
index 0ab7fad..f81bab8 100644 (file)
--- a/utils/install4j/install4j8_template.install4j
+++ b/utils/install4j/install4j8_template.install4j
@@ -107,15 +107,11 @@
       <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files">
         <exclude>
           <entry location="jalviewc" />
-          <entry location="jalviewc-macos" />
-          <entry location="jalviewc-windows" />
           <entry location="jalviewc.ps1" />
         </exclude>
       </dirEntry>
       <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/examples" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="examples" />
       <fileEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/jalviewc" fileMode="755" overrideFileMode="true" />
-      <fileEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/jalviewc-macos" fileMode="755" overrideFileMode="true" />
-      <fileEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/jalviewc-windows" fileMode="755" overrideFileMode="true" />
       <fileEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_WEBSITE_DIR}/${compiler:JAVA_VERSION}/jalviewc.ps1" fileMode="755" overrideFileMode="true" />
       <dirEntry mountPoint="884" file="${compiler:MACOS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
       <dirEntry mountPoint="885" file="${compiler:WINDOWS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
@@ -717,7 +713,7 @@ return console.askYesNo(message, true);
               </action>
               <action id="1525" beanClass="com.install4j.runtime.beans.actions.files.DeleteFileAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
                 <serializedBean>
-                  <property name="files" type="array" class="java.io.File" length="44">
+                  <property name="files" type="array" class="java.io.File" length="40">
                     <element index="0">
                       <object class="java.io.File">
                         <string>jre</string>
@@ -905,39 +901,19 @@ return console.askYesNo(message, true);
                     </element>
                     <element index="37">
                       <object class="java.io.File">
-                        <string>jalviewc-macos</string>
-                      </object>
-                    </element>
-                    <element index="38">
-                      <object class="java.io.File">
                         <string>jalviewc.ps1</string>
                       </object>
                     </element>
-                    <element index="39">
+                    <element index="38">
                       <object class="java.io.File">
                         <string>jalviewcv</string>
                       </object>
                     </element>
-                    <element index="40">
-                      <object class="java.io.File">
-                        <string>jalviewc-macosv</string>
-                      </object>
-                    </element>
-                    <element index="41">
+                    <element index="39">
                       <object class="java.io.File">
                         <string>jalviewc.ps1v</string>
                       </object>
                     </element>
-                    <element index="42">
-                      <object class="java.io.File">
-                        <string>jalviewc-windows</string>
-                      </object>
-                    </element>
-                    <element index="43">
-                      <object class="java.io.File">
-                        <string>jalviewc-windowsv</string>
-                      </object>
-                    </element>
                   </property>
                   <property name="recursive" type="boolean" value="true" />
                 </serializedBean>