Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-02-17

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All times shown according to UTC.

Time Nick Message
02:27 looper joined #bioclipse
08:28 egonw joined #bioclipse
09:01 egonw_ joined #bioclipse
09:23 jonalv joined #bioclipse
10:17 nina joined #bioclipse
10:18 egonw hi nina
10:18 egonw nina: you remember jonalv?
10:19 egonw mgerlich is from germany, cruttkie I am not sure...
10:19 nina hi egon
10:19 egonw looper I do not know, the rest are bots
10:20 looper I'm not a bot ;)
10:20 nina hi all
10:20 looper hehe hello
10:21 egonw hi looper
10:21 egonw ok, you're from lithuania
10:21 egonw same group as, umm, what's his name again...
10:22 egonw Sulev Sild ?
10:23 egonw nina: OK, I almost updated all my reposes
10:23 * egonw should really create that update script again :/
10:24 egonw nina: btw, branch details is here: http://wiki.bioclipse.net/inde​x.php?title=Branching_Strategy
10:31 egonw is the target platform setting working now?
10:32 nina no, i'm not sure what to tweak
10:33 egonw do you see the link now?
10:35 nina no, the target platform opens as a plain text file; guess eclipse setup is missing somethign
10:36 egonw darn, that is one of the worst youtube videos I have ever seen... http://www.youtube.com/watch?feature=​endscreen&NR=1&v=b9DMiy_DVok
10:36 egonw live footage of the 2004 tsunami...
10:37 egonw I was listening to music on youtube, when this showed up in the recommendations :(
10:38 egonw nina: I will try to add a time out preference field nos
10:38 egonw nina: I will try to add a time out preference field now
10:38 egonw let's see if I still have those powers :)
10:39 egonw yes, your eclipse is indeed missing something then...
10:39 egonw nina: install the Eclipse PDE
10:39 egonw short for Plugin-in Development Environment
10:58 nina ok, thanks
11:22 egonw nina: sorry, things are going really slow here...
11:22 egonw don't want to think about getting to work tomorrow again...
11:24 Gpox joined #bioclipse
11:25 egonw hi Gpox
11:36 egonw ok, I think I am back up to speed with prefs pages...
11:37 * egonw is hacking an OpenTox Network prefs page
11:39 egonw OK, I may have an empty prefs page now
11:53 commitbot joined #bioclipse
11:53 commitbot [bioclipse.opentox] egonw opened pull request #6: Typo fix. (master...1-typoFix)  http://git.io/0c8_5A
11:53 commitbot left #bioclipse
11:53 egonw lovely! :)
12:06 egonw OK, found the problem...
12:06 egonw I had a nasty ClassNotFoundException
12:07 egonw which showed up when I had added a new prefs class in an existing class :(
12:20 egonw nina: ping
12:20 egonw how should the search before create work practically?
12:20 egonw I guess we need a method first that adds an existing structure to the new dataset, or?
12:20 * egonw is looking at the time out...
12:20 egonw it seems that implementation is broken anyway...
12:20 egonw I don't think it even cancels after 20 secs...
12:21 egonw it just waits at most 20 seconds between attempts...
12:21 egonw the shortest is after 2 seconds...
12:21 egonw that's too soon, I guess
12:21 egonw and the longest should be how long?
12:22 egonw but it does *not* stop after 20 seconds...
12:22 egonw that's just the time between tries...
12:22 nina Egon, for now it is ok just to add the timeout
12:23 nina i mean don't bother with search for now.
12:23 egonw agreed :)
12:23 egonw I won't get that done anyway :)
12:23 nina When does bioclipse returns with "read timeout" ?
12:23 egonw just wondering...
12:23 egonw but just to get it clear...
12:23 egonw there is no current time out...
12:23 egonw well, not in the createDataSet()
12:24 egonw I guess what happens here is a time out on the HTTP connection...
12:24 nina otherwise you dont need to add structure to the dataset, just the uri of the structure and send it as argument to the model - thus you skip the uploading alltogether
12:24 egonw but that is more generic...
12:24 egonw yeah, we need to define an manager API for that set up
12:25 nina yes, and upload /search for the structure once not everytime a different tets is starting...
12:25 nina but let's figure out the timeout
12:25 nina but when you are waiting for the dataset to upload?
12:25 egonw when I get a Task returned
12:26 egonw the time out you get probably is from HttpClient
12:26 egonw not sure what the default is there...
12:27 nina it shouldn't be that quick by default
12:27 egonw so, the 20 secs it does do, is the time between pings to see what the state of the Task is
12:27 egonw the max...
12:28 egonw it starts with a 2secs between Task tests...
12:28 egonw then 4,6,8, and then 20, 20, 20, 20, ad infinitum
12:31 nina may be this ?method.getParams().setParam​eter("http.socket.timeout", new Integer(Activator.TIME_OUT));
12:33 nina 5 sec for the http connection is definitely not ok for the first requests
12:33 egonw yes, that looks good...
12:33 egonw for some apps it does...
12:33 egonw but not here...
12:33 egonw where is that?
12:34 egonw (I certainly needs that for Icebear...)
12:34 egonw nevermind... I'll find it...
12:34 egonw in fact... Icebear should not be using this TIME_OUT at all...
12:35 egonw it's in the OT Activator...
12:35 egonw OK, hang on...
12:35 egonw working on the prefs page...
12:35 egonw then you can set these network prefs
12:35 nina public class Activator extends AbstractUIPlugin {
12:36 nina just set it to something more for opentox. 50 would be good :)
12:38 nina my issue is the servlet does lazy loading , it doesn't initialize any classes before the first request. Hence the first request may take really long. You don't see this when on the public server, but if Bioclipse is sending the first request locally, then it hits
12:38 egonw I understand
12:41 nina anyway 5 sec is too low, responsive UI is considered below 8 sec :)
12:42 egonw yes, but that is different...
12:42 egonw the GUI response is done differently...
12:42 egonw anyways... hang on...
12:44 nina i meant a web page.  the default of apache httpd is 15 sec. anyway, good we know what it is
12:54 egonw argh...
12:54 egonw I do not do this things often enough to not have to use trial/error :(
13:09 egonw OK, I think I got it now
13:12 nina superb
13:28 egonw I really hate this stuff...
13:32 egonw ok, found the culprit
13:32 egonw and turns out that logger.debug does not have any effect in the develop branch :(
13:38 egonw OK, now trying to combine Ola's prefs work with mine...
13:46 egonw but really closing in now...
13:52 egonw OK, it looks OK now...
13:53 egonw the prefs page...
13:53 egonw values not used yet...
13:53 egonw that's up next...
13:55 egonw method.getParams().setParam​eter("http.socket.timeout",
13:55 egonw Activator.getDefault().getPreferenceStore​().getInt(OpenToxConstants.HTTP_TIMEOUT)
13:55 egonw );
13:56 egonw OK, let's see...
14:12 egonw ok, 50 seconds, not 50 milliseconds ... :)
14:14 egonw OK, seems to work
14:14 egonw sort of, anyway...
14:15 egonw also getting a lot of 500 for ambit services...
14:15 egonw unknown error
14:15 nina which service?
14:15 egonw many
14:15 egonw aqueous sol
14:15 egonw boiling point
14:15 egonw (both show up twice in the DS window
14:15 egonw )
14:16 egonw MP
14:16 egonw logKow
14:16 egonw many others work
14:16 nina mm, i don't see any errors here http://apps.ideaconsult.net​:8080/ambit2/task?max=1000
14:16 egonw e.g. http://ambit.uni-plovdiv.bg:8080/opentox/​task/6435e68b-82b7-4c76-9e12-339a96074fe0
14:17 nina ah, don't use plovdiv, it's read only!
14:17 egonw oh, empty content...
14:17 egonw ummm...
14:17 egonw OK... let me check
14:17 nina my fault, these are registered in the ontology service
14:17 egonw I think it comes from the onto serices...
14:17 egonw yes, right :)
14:18 nina cadaster models... but they changed the SOAP schema and only told me friday
14:18 egonw :/
14:18 nina so no way for these to work atm
14:19 egonw OK, that makes sense then :)
14:21 egonw but I think the settings are working now...
14:21 nina i removed all of cadaster models but one ; will fix them next week . The rest should work
14:22 egonw just trying to have the prefs page look a bit nicer
14:23 nina i am adding some warmup requests server side, so we may manage to fix the issue from both sides  :)
14:24 egonw I will try to find a few patches I wrote earlier...
14:24 egonw that may be very useful
14:31 commitbot joined #bioclipse
14:31 commitbot [bioclipse.opentox] egonw opened pull request #7: Fixed a small spelling error (develop...1-typoFix)  http://git.io/AJeJMA
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14:32 egonw (now the a request for bioclipse' develop branch)
14:34 egonw nina: ping
14:34 egonw nina: please try these patches: https://github.com/bioclips​e/bioclipse.opentox/pull/8
14:34 egonw two patches, to be precies
14:34 commitbot joined #bioclipse
14:34 commitbot [bioclipse.opentox] egonw opened pull request #8: Allow setting of custom network properties. Addressing bug #3487. (develop...2-networkPrefs)  http://git.io/hVEHng
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14:40 nina can i compile the plugin only and use it in an already installed bioclipse?
14:40 egonw theoretically, yes
14:40 egonw how? that I am not sure... :(
14:40 nina ok, how do i try the whole piece :)
14:40 egonw which kinda sucks indeed
14:41 egonw in the past, Jenkins would do that quickly...
14:41 egonw but since we now have a gate keeper :(
14:41 egonw yes...
14:41 egonw how to start Bioclipse from Eclipse...
14:42 nina command line compile is ok as well
14:42 egonw http://wiki.bioclipse.net/index.ph​p?title=Checking_out_Bioclipse_2.6​#Getting_ready_to_run_Bioclipse_2
14:42 egonw sorry, I don't know...
14:43 nina ok, will try getting eclipse intact
14:47 egonw I also have patches to add a local OT service as a plugin
14:47 egonw then you can simply install a plugin with a specific service
14:47 egonw e.g. TU Muenchen
14:48 nina TU Muenchen doesn't exist anymore (ok, that particular group )
14:48 nina best to remove that form available settings
14:49 egonw I think I only had that locally
14:50 egonw and in that patch, which I would not restore then
14:50 nina it appears in the release we've downloaded
14:51 nina or may be it is the OT plugin
14:52 egonw no, indeed...
14:52 egonw it's in the plugin
14:52 egonw I will try those the patches now, and send a pull request
14:55 egonw OK, these are the patches: 3-otServerAsAPlugin
14:55 egonw check my copy of bioclipse.opentox on GitHub
14:56 egonw seems to work for me :)
14:59 nina thanks :)
15:00 egonw well, auth is broken for me...
15:00 egonw but I need to talk with Klas about that, I guess
15:04 commitbot joined #bioclipse
15:04 commitbot [bioclipse.opentox] egonw opened pull request #9: Refactores the default OpenTox services, to have them as plugins (develop...3-otServerAsAPlugin)  http://git.io/Hwxxzg
15:04 commitbot left #bioclipse
15:04 egonw nina, can you comment on this bug report: http://pele.farmbio.uu.se/bu​gzilla/show_bug.cgi?id=3472
15:05 egonw I am checking for trailing /'s here and there, but apparently not enough...
15:05 egonw do you remember what call you were making?
15:06 egonw BTW, this is what I had when I had AMBIT2 running locally:
15:06 egonw <service
15:06 egonw id="net.bioclipse.opentox.localhost"
15:06 egonw name="Ambit2 - Localhost"
15:06 egonw serviceURL="http://localhost:8080/ambit2/"
15:06 egonw serviceSPARQL="http://localhost:8080/ontology/">
15:06 egonw </service>
15:07 egonw with that localhost plugin from the 3-otServerAsAPlugin branch
15:09 nina we hit this when the OT service in the preferences window was set without the flash. then saw in the tcpdump it tries to access /ambit2dataset instead of /ambit2/dataset
15:10 egonw yes, I understand that
15:10 egonw but some methods correct for that, while others do not
15:10 nina so the defaults might be fine, but one can enter anything in the ui
15:10 egonw so, I am trying to figure out where I forgot it :)
15:11 egonw I think I found them, though...
15:12 egonw https://github.com/egonw/bioclip​se.opentox/tree/4-trailingSlash
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15:13 commitbot [bioclipse.opentox] egonw opened pull request #10: Added missing trailing slashes on the fly (develop...4-trailingSlash)  http://git.io/kDRE9Q
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15:25 commitbot [bioclipse.opentox] egonw opened pull request #11: Stop trying multiple times; just once. (develop...5-onlyOneTry)  http://git.io/KccD3g
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15:40 commitbot [bioclipse.opentox] egonw opened pull request #12: When no data set was created, do not continue and return empty results (develop...6-onlyContinueWithDataSet)  http://git.io/Lczqiw
15:40 commitbot left #bioclipse
15:41 egonw OK, I'm done with BCOT hacking for today
15:41 egonw results: https://github.com/bioclip​se/bioclipse.opentox/pulls
15:42 nina egonw: thanks a lot!
15:42 egonw I hope they work well enough...
15:42 egonw I have done only minimal testing...
15:42 egonw and not all together either...
15:43 egonw these are most relevent to you:
15:43 egonw pull 8
15:43 egonw pull 10
15:43 egonw and pull 12
15:43 egonw but pull 9 is recommended too...
15:44 egonw regarding that one, please check the opentox.localhost plugin's plugin.xml and tune it to your needs
15:45 egonw OK, I need to do some other stuff now
15:46 egonw I hope this helps you continue
16:07 egonw nina: ping
16:08 nina yes
16:08 egonw what we kind of need is a AMBIT test server...
16:08 egonw with algorithms and models that always fail with the same error
16:09 nina yes - want one right now?
16:09 egonw or always succeed in a particular way
16:09 egonw no, not today :)
16:09 egonw but if you have one, please file me a BC bug report asking for BCOT unit tests using them
16:11 nina do you prefer hosting yourself or here?
16:11 egonw remote
16:12 egonw because then Jenkins can always run those unit tests
16:12 egonw does that also come with a test that takes 2 minutes?
16:12 egonw so that I can at least locally test progress monitoring with Task ?
16:12 egonw (we discussed that in the past)
16:12 nina ok
16:14 nina there is /algorithm/mockup with delay as a parameter
16:29 egonw full URI?
16:35 nina for example  curl -X POST http://apps.ideaconsult.net:​8080/ambit2/algorithm/mockup -d delay=50 -d dataset_uri=something -iv
16:37 egonw is that a model or a descriptor?
16:37 egonw well, not that it matters much...
16:38 jonalv joined #bioclipse
16:38 egonw hi jonalv
16:38 jonalv hi
16:39 egonw jonalv: how do I turn on debug logging in the develop branch?
16:39 egonw should be posted on the wiki ...
16:39 jonalv hm
16:39 jonalv there is a config file somewher
16:39 nina egonw: you could consider it a descriptor, it actually returns as a result whatever  string is submitted as dataset_uri; doesn't attempt to read the dataset
16:40 jonalv egonw: feel free to file a bug about updating the wiki...
16:42 jonalv egonw: net.bioclipse.logback/logback.xml looks promising
16:43 egonw that file is not in the repos
16:43 jonalv egonw: I am guessing line 28
16:43 egonw what content does it have
16:44 jonalv is it not?
16:44 jonalv Hang on
16:44 egonw ah... src/logback.xml
16:44 egonw $ git show 863bc33531c3875b7025fa52e07bf8ccc55a48cf
16:44 egonw commit 863bc33531c3875b7025fa52e07bf8ccc55a48cf
16:44 egonw Author: Arvid Berg <goglepox@gmail.com>
16:44 egonw Date:   Mon Nov 12 10:55:42 2012 +0100
16:44 egonw Updated log levels for release
16:44 egonw diff --git a/plugins/net.bioclipse.logback/src/logback.xml b/plugins/net.bioclipse.logback/src/logback.xml
16:44 egonw index e9b186c..22ff4d3 100644
16:44 egonw --- a/plugins/net.bioclipse.logback/src/logback.xml
16:44 egonw +++ b/plugins/net.bioclipse.logback/src/logback.xml
16:44 egonw @@ -25,7 +25,7 @@
16:44 egonw <logger name="org.eclipse" level="WARN" />
16:44 egonw <logger name="org.springframework" level="ERROR" />
16:44 egonw <logger name="org.hibernate" level="ERROR" />
16:44 egonw -       <logger name="net.bioclipse" level="DEBUG" />
16:44 egonw +       <logger name="net.bioclipse" level="INFO" />
16:44 egonw
16:44 egonw <root>
16:44 egonw <level value="INFO" />
16:44 egonw yeah, that looks very promising indeed
16:45 egonw oh, that's actually nice...
16:45 egonw because this way you can tune it to a particular java package...
16:46 egonw OK, hacking the wiki...
16:46 jonalv egonw++
16:49 egonw http://wiki.bioclipse.net/index.php?title=​Checking_out_Bioclipse_2.6#Debug_messages
16:49 egonw jonalv++ (for the pointer)
16:49 egonw nina++ (for hanging around here)
16:49 egonw @karma nina
16:49 egonw he??
16:49 egonw is zarah gone again :(
16:49 egonw what's she up to now??
16:50 jonalv I am thinking we need something that restarts here from time to time
16:50 zarah joined #bioclipse
16:50 jonalv zarah: welcome back
16:50 zarah jonalv: thank you. I feel like a new person! :)
16:51 jonalv egonw++
16:51 jonalv nina++
16:51 egonw @karma nina
16:51 zarah nina has a karma of 2
16:54 egonw OK, I will do those unit tests at some later point
16:54 egonw no quick hack
16:56 egonw bbl
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18:14 commitbot [bioclipse.cheminformatics] egonw opened pull request #21: Fixed @params of published methods (develop...2-paramFixes)  http://git.io/J2lgNw
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18:19 commitbot [bioclipse.cheminformatics] egonw opened pull request #22: Split the Jmol editors for small molecules and protein (develop...1-proteinSmallMolSplit)  http://git.io/VvWFpg
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18:30 egonw hi hybridivy
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18:43 commitbot [bioclipse.cheminformatics] egonw opened pull request #23: Updated OPSIN from 1.1 to 1.4 (develop...3-opsinUpdate)  http://git.io/AlvyeQ
18:43 commitbot left #bioclipse
18:59 hybridivy hi egonw
19:00 hybridivy i was just checking out how to creata a plugin for bioclipse
19:00 egonw depends on what the plugin is going to do
19:00 egonw the PV/Bioclipse integration project is certainly a hard one
19:01 hybridivy egonw: a demo one , and i was following your blog and could creata demo one checking out how things actually work
19:03 egonw there is a Eclipse new wizards extension: http://wiki.bioclipse.net/in​dex.php?title=Bioclipse_SDK
19:03 egonw but I have not tried that with Eclipse 4.2
19:04 egonw and you may want to keep an eye on this list: http://wiki.bioclipse.net/index.php?t​itle=Bioclipse2#Development_tutorials
19:04 egonw depending on what your demo will do
19:06 egonw for PV integration: http://wiki.bioclipse.net/index.​php?title=How_to_write_an_editor
19:07 egonw I got to reboot
19:07 hybridivy egonw: thanks for the links :)
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