Logging and Reporting Bugs

From f47ded5b8b48d6372cd1ef8f49e1a630dcadfbdb Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 27 Aug 2020 15:53:02 +0100 Subject: [PATCH] JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs --- help/help/help.jhm | 1 + help/help/helpTOC.xml | 1 + help/help/html/logging.html | 65 +++++++++++++++++++++++++++++++++++++++---- 3 files changed, 61 insertions(+), 6 deletions(-) diff --git a/help/help/help.jhm b/help/help/help.jhm index 99d010d..7dbb76d 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -170,4 +170,5 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index a0c7fe6..c5660fe 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -156,6 +156,7 @@ + diff --git a/help/help/html/logging.html b/help/help/html/logging.html index 2993370..2393c61 100644 --- a/help/help/html/logging.html +++ b/help/help/html/logging.html @@ -20,12 +20,12 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Logging and Reporting Bugs +The Java Console, Logging and Reporting Bugs

- Logging and Reporting Bugs + The Java Console, Logging and Reporting Bugs

@@ -42,7 +42,7 @@

However, it is possible that some early logging information from when Jalview is initially launched, is not shown in the Java Console:
- If you are using a version of Jalview installed from one of our install4j installers, then Jalview's initial launch logging can be found in + If you are using a standard desktop version of Jalview installed from one of our install4j installers, then Jalview's initial launch logging can be found in

JALVIEW_APP_DIR/launcher.log

where JALVIEW_APP_DIR is the directory that Jalview's application was installed into.
@@ -53,14 +53,67 @@

In Linux and other Unix OSes this is ~/opt/jalview by default

- Whereas if you are using the Jalview executable jar file (also used by bioconda installations) then a minimised launcher will output logging information to STDOUT and STDERR. + Whereas if you are using the Jalview executable jar file (also used by bioconda installations) then the default run class (jalview.bin.Launcher -- a minimised launcher that will set memory and linux dpi settings before re-launching jalview.bin.Jalview), will output logging information to STDOUT and STDERR.

Java Console and Log Level

- - +

+ The Java Console is opened by selecting Tools → Show Java Console. This option is saved across Jalview sessions so you can start Jalview with the Java Console already open by previously quitting Jalview with the Java Console already opened. Selecting Show Java Console in the Tools menu a second time will deselect the option and close the window. Closing the window in your system's usual way will also deselect the option in the Tools menu. +

+ The Java Console's text display always shows information about your system and Jalview installation setup, which is followed by messages output from some of the processes that your Jalview session has performed since opening the console. +

+ You can control the detail of what appears as output by selecting a Log level using the drop-down list at the bottom left of the console. There are several levels of logging that you can choose from: in decreasing levels of verbosity they are: TRACE, DEBUG, INFO, WARN. By default the level initially chosen is INFO. +

+ Note! If you change the log level in the Java Console, this change will only persist for as long as the console is open. Once you close the console the log level will revert back to what it had been when you opened the console (usually INFO). +

+ You can change the default log level by editing the Jalview preferenecs file, .jalview_properties, found in your home directory, and setting the property logs.Jalview.level to the log level you prefer, e.g. +

+  logs.Jalview.level=DEBUG
+

+ You can also set this property to a log level not usually presented in the Java Console (though restricted to log levels used by Apache Log4j -- see Log4j Custom Log Levels for details of the standard log levels available). Jalview does not currently define any custom log levels.
+ If you do set the property with a log level that is normally not visible in the Java Console this should be respected and visibly selected when you open the console. +

+ The Clear button at the bottom of the console will clear all logging messages except for the initial system information which remains. +

+ The Copy to clipboard button at the bottom right of the console will copy all of the text in the console to your system clipboard, ready to paste into another application (e.g. email composer). +

Reporting Bugs

+ If you come across a problem in Jalview where something is not working as described, or how you think it should, you should first check the Jalview FAQ to see if this is a known problem and if there is a suggested workaround. +

+ If there is no FAQ answer covering your problem then you can submit a bug report on the Jalview Issue Tracker. It is good practice to search the issue tracker first to see if the issue has already been reported. If an issue already exists please continue to add your own comments to the issue which may well help narrow down the problem, if not then you can create an account and submit a new bug report: +

+ Make sure that you set Project to Jalview (JAL), and Issue Type to Bug or New Feature or Improvement appropriately.
+ Give a one line summary of the issue in the Summary. +
+ In the Environment text box you can describe the system you are using. This is usually most easily done by opening the Java Console, clicking the Clear button, and then immediately on the Copy to clipboard button, and then pasting the clipboard into the text box. +

+ You can then give more detailed information about how to recreate the problem in the Description text box. If you want to attach any screenshots or example alignment files that demonstrate the problem then you can drag them to the Create Issue dialog in your browser, or use the Attachment browse facility to locate them on your computer. +

+ +

+ To help the Jalview team with diagnosing a particular issue, it is really helpful if you can also add more detailed logs output whilst re-creating the problem. To do this, open the Java Console, click the Clear button and select TRACE in the Log level drop down list. +
+ Whilst leaving the console open, perform the task in Jalview that re-creates the problem. +
+ Then you can copy the debug information in the Java Console by clicking on the Copy to clipboard button and then paste that into the Description, or a Comment of your issue. +

+ +

For other queries or comments about Jalview, remember you can contact the Jalview team using email via the Jalview discussion list or on Twitter @Jalview! +

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