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benzoid
@benzoid
oops sorry -- one moment...
Jim Procter
@foreveremain
bit quiet round here. Happy Friday folks !
benzoid
@benzoid
It's so grey and rainy outside!! Garage roof has turned to weetabix already, but at least have a roofer arranged for two weeksish time :)
benzoid
@benzoid
I've been (Teams) chatting with Mateusz as after I recommended using the snap install of Eclipse on linux, he's spotted that you can't put the j2s jar into the dropins dir because snap installs it ro (in fact, MW says it mounts it ro). I gave him the recipe of command line args that the gradle build uses to add an external dropins dir and he reports that that does the trick. I've also tested that a snap installed eclipse works well with the gradle jalviewjs build itself (as an alternative to a ~buildtools installation). As it's RO it can't get messed up.
This info should definitely go in the building.md for JalviewJS, which I will keep in mind. I wonder about having a one line script in utils/jalviewjs too just as a helper script (as a workaround for system installed eclipse, or anyone who doesn't want to put a plugin directly into the dropins folder).
In which case I should probably make an issue to a) remind me and b) put the information somewhere.
benzoid
@benzoid
Jim Procter
@foreveremain
ta!
Jim Procter
@foreveremain
@/all just to let you know I'm doing some jira upgrades so issues.jalview.org is unavailable for a bit
Jim Procter
@foreveremain
@/all as you'll see - jira has been upgraded. There have been some other changes behind the scenes too so let me know ASAP if there are problems! @benzoid - we should catch up about this today :)
Mungo Carstairs
@gmungoc
Curious...example.org, example.com, example.net seem to have disappeared off DNS servers. example.edu is still there. I used example.org in HelpLinksChecker to test for internet connectivity.
@benzoid is it possible to add Gradle tasks to run this class and also MessageBundleChecker? Can't run directly from Eclipse since /utils is not a source folder.
Mungo Carstairs
@gmungoc
...ran HelpLinksChecker (hacked source path) and found this curiosity: help/index.html has a link to http://www-test.jalview.org/about/documentation which is now an invalid path (domain is there). I propose to remove the "-test" (added Nov 2012).
That is, the link from http://www.jalview.org/help.html to '.../about/documentation' is broken.
benzoid
@benzoid
I seemed to stay logged in through the upgrade -- cool :) @foreveremain Available all day (although a strict 6pm teatime!!)
Jim Procter
@foreveremain
chat now ?
benzoid
@benzoid
yep sure
Jim Procter
@foreveremain
(usual JalviewDevelopers place)
Mungo Carstairs
@gmungoc
If I click through from a JIRA issue to view commit diffs, they don't display.
Unable to get content for src/jalview/api/JalviewApp.java@7eea865f7a04c9dde807f907155f0e6e4c86f7b9
Error while communicating with VCS:
While executing: "git cat-file blob 0548c85fb1ca4de1eb4cc5d2f68da67b17cb28ef" in [/opt/homes/crucible/fisheye_data/var/cache/jalview/clone]
git could not be started
Cannot run program "git" (in directory "/opt/homes/crucible/fisheye_data/var/cache/jalview/clone"): error=2, No such file or directory
error=2, No such file or directory
3 replies
Mungo Carstairs
@gmungoc
Message bundles up to date on 2_11_1 and develop. Off to walk the doggie.
Jim Procter
@foreveremain
Thank you!
Jim Procter
@foreveremain
It's the crief symposium again today from 2pm, and I've had to schedule a call to discuss fellowships at 4pm. I'll post my update in the doc and suggest everyone else does the same. I can join around 4.30pm if you all want to meet from 4pm ?
Mungo Carstairs
@gmungoc
ok. Or I might be a little late myself if dropping boys off for their exercise (weather dependent).
Jim Procter
@foreveremain
OK - perhaps say we start at 4.30pm - I'll join when I can !
there's also 3.30-4pm but I think I need to have a break from continuous meetings today.
benzoid
@benzoid
Just to say all my expected emails from JIRA came through one by one overnight. Not sure if that was anything to do with the Junk Email->Safe Sender change or just stuck in the system.
benzoid
@benzoid
A crucible procedural question: once I've acted upon/replied to comments/issues raised in a code review, do I close it more or less straight away?
Mungo Carstairs
@gmungoc
I would say if you are confident you have resolved whatever is marked as needing resolving, you are empowered to close it. Most reviews should be fairly light touch - look you missed that, this could be coded more neatly - not big design debates.
Jim Procter
@foreveremain
yes - agree with that. If there are 'defects' still flagged then the person who raised them could take a look - particularly if you are closing the review without having resolved them, but for the most part code reviews are just to make sure others have taken a look at the code you committed to spot crazies and to see what new things you've brought in.
Jim Procter
@foreveremain
@warownia1 do you want to try merging feature/JAL-3686_slivka_client_js_update to alpha/merge_212_JalviewJS_2112 ? That's my prototype branch for evaluating JalviewJS 2.12. There are only minor conflicts as far as I can see.
1 reply
benzoid
@benzoid
@foreveremain When Preferences.java looks to see if USE_PROXY is true, if it isn't then it looks like Preferences.ok_actionPerformed actively removes values from the system properties http.proxyHost and http.proxyPort. These might have been passed in by user or getdown. What do we want to do here? Obviously if it's already set and saved in .jalview_properties then they will be used, but if they get set by a launching agent, disable? warn?
My suggestion is USE_PROXY should be false to allow external setting, and an info could go in the Java console if the properties are already set.
2 replies
Hmm, but in the case of a user turning it off then they need to be unset...
Jim Procter
@foreveremain
@/all there won't be a jalview developers meeting today since so many of us are on holiday or distracted by other work
Mungo Carstairs
@gmungoc
My last build (just now) failed https://builds.jalview.org/browse/JB-GDB191-JOB1-3/log
Not quite sure why but
_XSERVTransSocketUNIXCreateListener: ...SocketCreateListener() failed
20-Jul-2020 09:18:59 _XSERVTransMakeAllCOTSServerListeners: server already running
20-Jul-2020 09:18:59 (EE)
20-Jul-2020 09:18:59 Fatal server error:
20-Jul-2020 09:18:59 (EE) Cannot establish any listening sockets - Make sure an X server isn't already running(EE)
1 reply
Actually compile and test seems to have run ok. Error return code from Clover after this? :
/usr/bin/xvfb-run: line 186: kill: (499) - No such process
Mungo Carstairs
@gmungoc
@foreveremain @benzoid jitsi meet today? https://meet.jit.si/JalviewDevelopers
benzoid
@benzoid
on my way -- was in the SLS symposium poster sessions...
Jim Procter
@foreveremain
@gmungoc - I'm on jits now
Mateusz Warowny
@warownia1
I'm trying to get rid of busy loops in sequence annotation workers. Is it sufficient to refactor all classes extending AlignCalcWorker or is there more places that need to be changed as well?
19 replies
Jim Procter
@foreveremain
@benzoid - that was a mega branch name you pushed to bamboo last night.. are you working on the patch to fix the NPE in jalview.bin.Cache.loadProperties(..) ?
benzoid
@benzoid
NPE? I'm working in Cache, but not to do with loadProperties(). It was the proxy auth password prompt.
5 replies
The branch name is right but not right :( It stems from me having merged a lot of branches I'd been working on together to avoid clashes when merged onto the release branch.
i.e. it is a merge of all those issues, but JAL-3633 (the last of them) is open again.
Jim Procter
@foreveremain
@/all Jalview Development meeting back to normal time @2.30pm UK (8.30am Minnesota)
foreveremain @foreveremain waves
Jim Procter
@foreveremain
Just saying hi - I've been pushing docs/patches to releases/Release_2_11_1_Branch - will do a full review of the 2.11.1.1 patch release tomorrow but signing off for now.
benzoid
@benzoid
@foreveremain @gmungoc Whilst testing JAL-3509 I've found that drag and dropping an alignment file onto an alignment window stopped working in releases/Release_2_11_1_Branch which I have tracked down to commit db9f5c502 which was merging in my JAL-3609 and JAL-3608 branches (the behaviour changed to opening a new alignment window rather than appending the sequences into the existing alignment window). JAL-3609 and JAL-3608 were HiDPI (linux) and LaF changes, I don't think anything in jalview.gui changed, so I can't immediately think what has caused the problem -- any ideas where I should be looking?
8 replies
Jim Procter
@foreveremain
@/all jalview dev meeting today @2.30pm BST meet.ji.si/JalviewDevelopers
benzoid
@benzoid
Jim Procter
@foreveremain
:D
Adhitya
@kamakshidasan

@/all

Hi folks, I'm Adhitya, a visualization-user interfaces-data analyst guy. I really wanted to apply for the research engineer position, but it turns out that I just landed another job. Anyway, I would still like to contribute and learn more. I am generally free on the evenings/nights and weekends. So let me know if there any low-hanging fruits! :)

6 replies