Ben Soares [Wed, 28 Aug 2024 12:54:18 +0000 (13:54 +0100)]
JAL-3631 Allow use of ~/ for unixBinDir specified in response.varfile
Ben Soares [Wed, 28 Aug 2024 12:17:06 +0000 (13:17 +0100)]
JAL-3631 Allow unixBinDir (where a symbolic link gets made) to be set in response.varfile. If it's not set or empty then the usual (dynamic) default will be ascertained. Disallow reading in certain variables from the response.varfile that would just mess up the installation if changed.
Ben Soares [Wed, 28 Aug 2024 11:41:37 +0000 (12:41 +0100)]
JAL-3631 Configuration tweaks if using the response.varfile
Ben Soares [Wed, 28 Aug 2024 10:53:00 +0000 (11:53 +0100)]
JAL-3631 Adjustments to allow setting the Advanced options in the response.varfile. Also big improvement on setting sys.fileAssociation.launchers automatically so only sys.fileAssociation.extensions needs to be set in a response.varfile.
Ben Soares [Mon, 26 Aug 2024 18:36:56 +0000 (19:36 +0100)]
JAL-3631 Fix interpolatove quotation marks in grep in jalview.sh. Fix some folder name trailing slash checks in macos_install_jalview.sh, add ditto -v and more informative output.
Ben Soares [Mon, 26 Aug 2024 18:31:43 +0000 (19:31 +0100)]
JAL-3631 Fix interpolative quotation marks in new grep
Ben Soares [Mon, 26 Aug 2024 16:44:30 +0000 (17:44 +0100)]
JAL-3631 When appdir/jre can't be found, look for the installer.appdir found in installer.properties (if it exists) and use jre dir in installer.appdir
Ben Soares [Mon, 26 Aug 2024 16:43:29 +0000 (17:43 +0100)]
JAL-3631 Create an installer.properties file in the userappdir
Ben Soares [Mon, 19 Aug 2024 16:08:12 +0000 (17:08 +0100)]
JAL-3631 Change macos-install-jalview.sh to use ditto instead of Localise function vars.
Ben Soares [Fri, 16 Aug 2024 11:06:50 +0000 (12:06 +0100)]
JAL-3631 Fix EnvConfig.getUserAppdir() in getdown when running the getdown-launcher.jar update
Ben Soares [Thu, 15 Aug 2024 20:31:02 +0000 (21:31 +0100)]
JAL-3631 Create a jalview_x_update link in appdir/bin alongside jalview_x in install4j wizard
Ben Soares [Thu, 15 Aug 2024 20:18:52 +0000 (21:18 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Tue, 13 Aug 2024 17:50:44 +0000 (18:50 +0100)]
JAL-4111 Remove unnecessary dependency on gradle-imagemagick plugin, as causing problems in repo on Windows
Ben Soares [Mon, 12 Aug 2024 13:03:25 +0000 (14:03 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Thu, 8 Aug 2024 09:35:43 +0000 (10:35 +0100)]
JAL-3631 Better messaging and a root check on updating the --installation
Ben Soares [Thu, 8 Aug 2024 09:27:27 +0000 (10:27 +0100)]
JAL-3631 Change name of update link in DMGs. Correct wrong message in macos installer script. Adding build_properties and channel.props into hidden folder on DMG. I'm sure they will be useful!
Jim Procter [Wed, 7 Aug 2024 16:31:16 +0000 (17:31 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Tue, 6 Aug 2024 23:50:30 +0000 (00:50 +0100)]
JAL-3631 Made bespoke command line arguments for console or unattended installs only (i.e. not GUI install mode), and work consistently with macos-install-jalview.sh
Ben Soares [Tue, 6 Aug 2024 19:13:17 +0000 (20:13 +0100)]
JAL-3631 Added install4j installer command line options -a -u -U and -S to match the macos-install-jalview.sh script
Ben Soares [Tue, 6 Aug 2024 18:02:25 +0000 (19:02 +0100)]
JAL-3631 Important change to Execution Level in Windows. Some disabled attempts at File Association Reset.
Ben Soares [Tue, 6 Aug 2024 14:08:33 +0000 (15:08 +0100)]
JAL-3631 Short sleep added to 100% progress on installer wizard
Ben Soares [Tue, 6 Aug 2024 12:29:17 +0000 (13:29 +0100)]
JAL-3631 An attempt to add a Reset to defaults button on the File Associations screen, but no joy (yet). Useful changes to customizedIds left in
Ben Soares [Tue, 6 Aug 2024 11:05:37 +0000 (12:05 +0100)]
JAL-3631 Some small but important changes to run_other_script.ps1
Ben Soares [Mon, 5 Aug 2024 22:49:05 +0000 (23:49 +0100)]
JAL-3631 JAL-4444 Change way we add the jalview_x and jalview_x_update PS1 and BAT files, moved into build.gradle and removed from install4j. Add title icon to install4j.
Ben Soares [Mon, 5 Aug 2024 22:46:03 +0000 (23:46 +0100)]
JAL-3631 Icons for installer wizard title bar
Ben Soares [Mon, 5 Aug 2024 18:21:16 +0000 (19:21 +0100)]
JAL-3631 update.ps1 has fixed Readlink-f function, works across platforms
Ben Soares [Mon, 5 Aug 2024 18:20:46 +0000 (19:20 +0100)]
JAL-3631 Revert the Jalview installer icon back to the Jalview icon
Jim Procter [Mon, 5 Aug 2024 17:42:04 +0000 (18:42 +0100)]
JAL-1551 source formatting and header
Jim Procter [Mon, 5 Aug 2024 15:17:48 +0000 (16:17 +0100)]
JAL-1551 apply GPLv3 for source files
Jim Procter [Mon, 5 Aug 2024 15:14:37 +0000 (16:14 +0100)]
JAL-1551 gradle spotlessApply and doc tweaks
Ben Soares [Mon, 5 Aug 2024 14:40:17 +0000 (15:40 +0100)]
JAL-3631 Adjustment to wizard size (was too big in Windows) and add 'Administrator mode' label to installation progress screen
Jim Procter [Mon, 5 Aug 2024 11:48:39 +0000 (12:48 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Fri, 2 Aug 2024 16:49:18 +0000 (17:49 +0100)]
JAL-3631 made Readlink-f work in powershell. Need to test once more in Windows\!
Jim Procter [Fri, 2 Aug 2024 15:47:31 +0000 (16:47 +0100)]
JAL-4418 release note for JAL-3063 doc/jalview-projects.md
Jim Procter [Fri, 2 Aug 2024 15:41:03 +0000 (16:41 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Fri, 2 Aug 2024 15:06:22 +0000 (16:06 +0100)]
JAL-3631 update.sh script fixed to work in Windows (11)
Ben Soares [Thu, 1 Aug 2024 19:57:51 +0000 (20:57 +0100)]
JAL-3631 Administrator mode label on all screens of wizard
Ben Soares [Thu, 1 Aug 2024 16:24:00 +0000 (17:24 +0100)]
JAL-3631 Added a test for a specified update and a usage line. update.ps1 tested on macos
Ben Soares [Thu, 1 Aug 2024 15:34:01 +0000 (16:34 +0100)]
Merge branch 'develop' into feature/JAL-3631_allow_jalview_to_work_from_user-space_directory
Ben Soares [Thu, 1 Aug 2024 15:33:39 +0000 (16:33 +0100)]
JAL-3631 Small change to update.sh. update.ps1 NOT COMPLETED YET
Ben Soares [Thu, 1 Aug 2024 15:15:11 +0000 (16:15 +0100)]
JAL-3631 Remove a debug echo
Jim Procter [Thu, 1 Aug 2024 15:14:15 +0000 (16:14 +0100)]
JAL-4445 - increase the fileglob expected counts
Ben Soares [Thu, 1 Aug 2024 14:40:56 +0000 (15:40 +0100)]
JAL-3631 Convert both CLASSPATHS in update.sh
Ben Soares [Thu, 1 Aug 2024 14:30:15 +0000 (15:30 +0100)]
JAL-3631 Separated jalview.sh and update.sh, and included in install4j installer and macos DMG.
Jim Procter [Thu, 1 Aug 2024 13:57:32 +0000 (14:57 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Wed, 31 Jul 2024 15:38:42 +0000 (16:38 +0100)]
JAL-3631 Changes to bash launcher to allow headless updates to user-space or installation. Added some of this functionality to Powershell (work in progress). The update functionality is to be separated out to update.sh.
Ben Soares [Wed, 31 Jul 2024 15:37:17 +0000 (16:37 +0100)]
JAL-3631 Add a (by-passable) confirmation and improved output to the macos-install-jalview.sh script, with some corrections
Ben Soares [Wed, 31 Jul 2024 15:36:01 +0000 (16:36 +0100)]
JAL-3631 Changes to Getdown to call getdown-launcher.jar update without launching Jalview for both installation and user-space
Ben Soares [Wed, 31 Jul 2024 15:33:03 +0000 (16:33 +0100)]
JAL-3631 Correction to a comment in build.gradle
Ben Soares [Mon, 29 Jul 2024 18:44:49 +0000 (19:44 +0100)]
JAL-3631 Add --updateuser and --updateinstallation to the jalview.sh script: This runs getdown in headless mode to run update of either user or installation appdir without launching Jalview
Ben Soares [Mon, 29 Jul 2024 18:43:25 +0000 (19:43 +0100)]
JAL-3631 Small corrections
Ben Soares [Mon, 29 Jul 2024 18:42:47 +0000 (19:42 +0100)]
JAL-3631 Getdown acknowledges in output when only performing an update
Ben Soares [Mon, 29 Jul 2024 18:06:45 +0000 (19:06 +0100)]
JAL-3631 Ensure the DMG default vmoptions.txt has the commented properties
Ben Soares [Mon, 29 Jul 2024 18:04:49 +0000 (19:04 +0100)]
JAL-3631 Add PID to console info - only available in Java 9+
Jim Procter [Mon, 29 Jul 2024 16:35:38 +0000 (17:35 +0100)]
JAL-4443 patch out pasimap in GUI for JalviewJS and note some lines causing java2script issues
Ben Soares [Fri, 26 Jul 2024 16:50:10 +0000 (17:50 +0100)]
JAL-3631 Added an --update option to the jalview.sh launcher (does not launch, just updates). Combining the update script with this as there's a lot of work to make this shell script Linux/macOS/Cygwin/WSL compliant that doesn't need to be duplicated. PS1 still to do.
Jim Procter [Fri, 26 Jul 2024 16:02:24 +0000 (17:02 +0100)]
JAL-4418 updated release notes and release date to 13 august 2024
Jim Procter [Fri, 26 Jul 2024 15:25:34 +0000 (16:25 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Jim Procter [Fri, 26 Jul 2024 15:23:06 +0000 (16:23 +0100)]
Merge branch 'patch/JAL-4428_osx_codesigning_scripts' into develop
Ben Soares [Fri, 26 Jul 2024 14:39:41 +0000 (15:39 +0100)]
JAL-3631 Added verbose and quiet options, and matched vmoptions with installer. Provenance of options added.
Ben Soares [Fri, 26 Jul 2024 14:38:28 +0000 (15:38 +0100)]
JAL-3631 Some minor bugfixes to the install4j installer and word changes to match macos-install-jalview.sh
Ben Soares [Thu, 25 Jul 2024 16:35:57 +0000 (17:35 +0100)]
JAL-3631 Comprehensive install shell script for macos
Ben Soares [Thu, 25 Jul 2024 16:35:37 +0000 (17:35 +0100)]
JAL-3631 minor changes - spelling and comment spacing in install4j template
Jim Procter [Wed, 24 Jul 2024 14:27:28 +0000 (15:27 +0100)]
JAL-3063 added a brief description of how to update the jalview project POJO
Ben Soares [Wed, 24 Jul 2024 13:17:47 +0000 (14:17 +0100)]
JAL-3631 Correct some text to add the file separator which is being looked for too in substitutions
Ben Soares [Tue, 23 Jul 2024 16:03:43 +0000 (17:03 +0100)]
JAL-3631 Consolidated repeated code (mainly form verification). Added appdir hash routine. Wizard installer of .app bundle now deprecated, can't be used :(
Ben Soares [Mon, 22 Jul 2024 19:36:33 +0000 (20:36 +0100)]
JAL-3631 Minor fixes to the advanced options scripts
Ben Soares [Mon, 22 Jul 2024 17:08:36 +0000 (18:08 +0100)]
JAL-3631 Made both Advanced options into a group. Changed visibility scripts to minimum required. Added a Don't setUserAppdirPath comment.
Ben Soares [Sun, 21 Jul 2024 19:32:59 +0000 (20:32 +0100)]
JAL-3631 Improved tooltip on advanced options. Ensure empty box/border isn't displayed when no advanced options. Add message to clarify no Advanced options will be applied when checkbox not ticked.
Ben Soares [Sat, 20 Jul 2024 16:55:37 +0000 (17:55 +0100)]
JAL-3631 Group/box and simplify visibility of advanced options on additional tasks screen in the install4j installation wizard.
Ben Soares [Sat, 20 Jul 2024 08:52:28 +0000 (09:52 +0100)]
JAL-3631 Consistently and correctly enable/diable/hide elements on the additional tasks screen in the install4j installation wizard.
Ben Soares [Fri, 19 Jul 2024 17:47:35 +0000 (18:47 +0100)]
JAL-3631 Customise the user-space path in the install4j installation wizard. Not ready yet.
Ben Soares [Thu, 18 Jul 2024 16:21:58 +0000 (17:21 +0100)]
JAL-3631 Tweaks to getdown for updating and user appdir properties
Ben Soares [Thu, 18 Jul 2024 11:05:34 +0000 (12:05 +0100)]
JAL-3631 Allow override of appDataPath with property 'setuserappdirpath' substituting %h, %u and a leading ~/
Ben Soares [Wed, 17 Jul 2024 15:31:01 +0000 (16:31 +0100)]
JAL-3631 Extensive working of options in install4j for allowing/disabling user default appdir updates, and also allowing/disabling installation appdir updates. Appropriate guidance in tooltips and warnings when no updates will occur are given. A user-space install only allows disabling updates.
Jim Procter [Fri, 12 Jul 2024 16:58:43 +0000 (17:58 +0100)]
shorter hashes - just first seven characters.. like in git
Jim Procter [Fri, 12 Jul 2024 16:41:38 +0000 (17:41 +0100)]
JAL-3631 updated getdown jars
Jim Procter [Fri, 12 Jul 2024 16:40:46 +0000 (17:40 +0100)]
JAL-3631 - report that an additional flag might be needed if we didn't manage to get an appDir
Jim Procter [Fri, 12 Jul 2024 16:38:59 +0000 (17:38 +0100)]
JAL-3631 shorter digest string for the unique user app dir
Jim Procter [Fri, 12 Jul 2024 16:38:26 +0000 (17:38 +0100)]
JAL-3631 check we actually created EnvConfig!
Jim Procter [Fri, 12 Jul 2024 14:24:47 +0000 (15:24 +0100)]
JAL-3631 updated getdown jars
Jim Procter [Fri, 12 Jul 2024 13:17:35 +0000 (14:17 +0100)]
JAL-3631 insert digest of full path to installer.appdir in path for user appdir and add tests to verify nouserdefaultappdir clobbers userdefaultappdir
Jim Procter [Wed, 3 Jul 2024 19:56:00 +0000 (20:56 +0100)]
JAL-3631 rebuild getdown jars after merge to develop
Jim Procter [Wed, 3 Jul 2024 19:16:18 +0000 (20:16 +0100)]
Merge branch 'feature/JAL-3631_allow_jalview_to_work_from_user-space_directory' into develop
Ben Soares [Mon, 1 Jul 2024 01:05:40 +0000 (02:05 +0100)]
JAL-3631 Slightly larger wizard
Ben Soares [Mon, 1 Jul 2024 01:05:00 +0000 (02:05 +0100)]
JAL-3631 Harden defence against looping getdown relaunches. Null checked in HttpUtils. Remove unnecessary code in getdown
Ben Soares [Sat, 29 Jun 2024 21:53:27 +0000 (22:53 +0100)]
JAL-3631 JVL file with appbase now relaunches getdown
Ben Soares [Fri, 28 Jun 2024 17:18:51 +0000 (18:18 +0100)]
JAL-3631 Made an isAdmin flag to work in Windows Admin mode installation
Ben Soares [Fri, 28 Jun 2024 17:18:12 +0000 (18:18 +0100)]
JAL-3830 Added some quotation marks to jalview.bat for folders with spaces
Ben Soares [Fri, 28 Jun 2024 16:04:09 +0000 (17:04 +0100)]
JAL-3631 Remove the checkboxes from the Finish screen. Now moved to pre-install screen.
Ben Soares [Fri, 28 Jun 2024 15:53:52 +0000 (16:53 +0100)]
JAL-3631 Group USERSPACE and SYSTEMSPACE tasks (and other groups of tasks) together for neatness
Ben Soares [Fri, 28 Jun 2024 15:53:16 +0000 (16:53 +0100)]
JAL-3631 Change in user path for locally installed Jalview to avoid collision with old installation. Tidy a null check for Java Console output
Ben Soares [Fri, 28 Jun 2024 11:30:01 +0000 (12:30 +0100)]
JAL-3631 Change to Windows user-space default location, now same as default installation location
Ben Soares [Fri, 28 Jun 2024 11:04:50 +0000 (12:04 +0100)]
JAL-3631 Fixed a getdown Exception when launching Jalview in windows
Ben Soares [Fri, 28 Jun 2024 11:04:05 +0000 (12:04 +0100)]
JAL-3631 Adjustments to the Windows installer
Ben Soares [Thu, 27 Jun 2024 23:37:42 +0000 (00:37 +0100)]
JAL-3631 spelling correction
Ben Soares [Thu, 27 Jun 2024 21:15:41 +0000 (22:15 +0100)]
JAL-3631 Installers with separate actions for user/administrator installation
Ben Soares [Thu, 27 Jun 2024 21:14:58 +0000 (22:14 +0100)]
JAL-3631 Add property to let log4j know we're not running in a servlet (or it issues a warning which breaks cli headless output)
Ben Soares [Thu, 27 Jun 2024 16:46:47 +0000 (17:46 +0100)]
JAL-3631 Log4j logging to .jalview.log file when requested. Clean(ish) handover of log file from getdown to jalview.
Ben Soares [Tue, 25 Jun 2024 22:13:55 +0000 (23:13 +0100)]
JAL-3631 JAL-3384 Install4j launch now redirects STDOUT/STDERR to ~/.jalview_develop.log and passes the file on to getdown and Jalview which will also now log to this file. Single log file.