Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-23

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Time Nick Message
04:08 jpansane1 joined #bioclipse
04:45 egonw joined #bioclipse
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05:45 annzi joined #bioclipse
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07:05 Gpox joined #bioclipse
07:17 olass joined #bioclipse
07:35 egonw moin
07:35 zarah ni hao egonw
08:13 egonw damn
08:14 CIA-71 bioclipse.core: jonalv 2.4.x * r935217c / features/net.bioclipse.pla​tform_feature/feature.xml : set version RC2_1 - http://bit.ly/dBQsLx
08:17 egonw annzi: editing...
08:18 annzi egonw: :)
08:18 egonw mmm... chat does not work in Gdocs... :(
08:19 annzi I know :(
08:49 egonw annzi: OK, please read it through... I made some small changes here and there...
08:50 egonw when you are done, we copy in Jarl, as will want to see it too before it will hit the blog
08:50 egonw annzi: if you can please give it a quick check, we can send it to Jarl around 11am
08:50 annzi egonw: ok will look at it right away
08:53 annzi egonw: I see that you have experience :)
09:00 masak joined #bioclipse
09:01 annzi egonw: what do you want to say with
09:01 annzi "and will many other applications for integrating the chEMBL data with other databases and other applications."
09:01 annzi in the end of the taxt
09:01 annzi text
09:03 egonw how about now?
09:05 annzi egonw: much better
09:05 annzi I think I like it now
09:08 annzi egonw: what do you think?
09:09 egonw I sent it to Jarl now then
09:10 annzi great
09:12 egonw OK, added a few more words:
09:12 egonw "Sounds interesting, or like to give us feedback?"
09:12 egonw email to Jarl sent
09:13 egonw btw, regarding wizard 1... the 'save all' button... should that not be better labeled 'select all' or so?
09:13 egonw also, it is not clear how a single item is selected...
09:13 egonw I am also confused about the role of the 'Select all' checkbox
09:16 annzi when the button 'save all' is pushed they automatically end up in the 'save table' thought that would be representative label
09:16 annzi a single item is selected with drag and drop
09:17 annzi how do I make someone understand that?
09:20 egonw "save all" sounds very definite...
09:20 egonw DnD is something they will have to learn...
09:20 egonw "saving" is not what the users are doing at that step...
09:21 egonw I would it find more clear if the bottom table was called: "Selected items"
09:21 egonw you also use two types of methods to select things...
09:21 egonw normal select in top table... check boxes in the below
09:22 egonw are those used for the same task (moving up and down items)? then inconsistent
09:31 egonw ok, something else...
09:31 egonw for whom are SMILES automatically updated when you edit in the JCP editor?
09:31 egonw Gpox: can you please check
09:32 egonw for me, neither InChI nor SMILES are updated...
09:36 Gpox it is not updated for me
09:38 egonw :(
09:38 egonw I cannot test in RC1
09:50 egonw downloading RC1
09:51 egonw confirmation in 2.2.x would be very useful
09:58 jonalv joined #bioclipse
09:59 egonw Gpox: problem confirmed in RC1 too...
10:00 egonw Gpox: that's before the CDK and JCP upgrade :(
10:00 egonw jonalv: serious new problem found
10:00 * jonalv puts finger in ear and goes *lalala*
10:00 jonalv egonw: okey seriously, what?
10:00 jonalv bug tickets?
10:00 egonw no ticket yet
10:00 egonw exploring aspects
10:00 jonalv okey
10:01 jonalv I hae to leave for lunch
10:01 * jonalv afk
10:11 egonw Gpox: problems exists in 2.0 too
10:12 egonw 2.2.0 that is
10:12 egonw wondering if this has anything to do with it:
10:12 egonw WARN - inchi.generate is not void or returning a BioclipseJob. But implementation takes a progress monitor. Can not run as Job. Running in same thread. This message will not be repeated withing the next 120 seconds
10:12 egonw WARN - The MonitorContainer could not find a monitor connected to current thread so returning a NullProgressMonitor. This warning will not be repeated withing the comming 120seconds for thread with id: .26
10:12 egonw WARN - cdk.calculateSMILES is not void or returning a BioclipseJob. But implementation takes a progress monitor. Can not run as Job. Running in same thread. This
10:14 egonw mmm... and my bioclipse 2.0 no longer boots ...
10:14 egonw olass: ping
10:14 egonw Gpox: ping
10:15 egonw olass, Gpox: can you confirm that 2.0 was automatically updating SMILES and InChI when editing something in JChemPaint?
10:21 olass egonw: pong
10:21 egonw olass: please backtrace
10:21 egonw is this a blocker or not?
10:22 olass egonw: yes, that worked
10:22 egonw I confirmed it was already present in 2.0
10:22 olass in 2.2
10:22 egonw well, not for me
10:22 egonw modifying the molecule did *not* update the SMILES or InChI
10:22 egonw that's with an official release
10:22 olass please file as blocker for 2.4.0
10:22 olass that _must_ work
10:22 egonw yes, I think so too
10:23 egonw it amazes me that I have not noticed it before...
10:23 * olass neither
10:23 egonw says something about how often I use that functionality :)
10:23 egonw olass: can you test something for me?
10:23 egonw I don't have OS/X
10:23 egonw cannot test myself
10:24 olass sure
10:24 egonw I don't want to push to the main branch
10:24 egonw please download this:
10:24 egonw http://sourceforge.net/projects/jni-inch​i/files/jni-inchi/0.6-std/jni-inchi-0.6-​std-jar-with-dependencies.jar/download
10:24 zarah egonw's link is also http://tinyurl.com/264pbem
10:24 egonw save the jar to replace the current 0.7 inchi jar
10:24 olass ok
10:24 egonw the one which has the OS/X .xlib(?) in METAINF
10:24 egonw and see if that works
10:24 egonw thanx
10:24 olass ok
10:28 * olass is testing
10:29 olass egonw: same problem
10:30 olass net.sf.jnati.deploy.resolver​.ArtefactNotFoundException: Artefact not found: jniinchi-1.7-std-MAC-X86_64
10:30 olass egonw: how about making it a source plugin (unjar the jar) so it can be debugged?
10:30 * olass will get a haircut now and will be afk for an hour
10:31 egonw olass: sounds interesting, but I do not have time for that... not for 2.4.0 anyway...
10:31 olass ok
10:31 egonw but I now have enough info to email Sam
10:31 olass great
10:32 * olass is afk
10:37 samuell joined #bioclipse
10:45 egonw olass: ping
10:45 egonw olass: the bug is know with sam:
10:45 egonw http://sourceforge.net/tracker/?func=detail&​aid=2958920&group_id=173262&atid=864778
10:45 zarah egonw's link is also http://tinyurl.com/25k8t2z
11:17 * jonalv is back
11:24 egonw jonalv: please see @px 2016
11:24 egonw @pz 2016
11:24 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=2016
11:25 jonalv egonw: yea I have commented on it
11:25 egonw ah, good... had not seen that yet
11:26 egonw jonalv: didn't 2.0 update InChI and SMILES then when we edited in JChemPaint?
11:26 * jonalv has no idea
11:26 egonw jonalv: do you have a running 2.0 version on your machine?
11:26 jonalv should be easy to test right?
11:26 egonw can you please test, if so? that would be useful info
11:26 egonw yes
11:27 jonalv just download one from sf and test?
11:30 jonalv egonw: yes 2.0 did actually update it
11:31 egonw ok, please add that as comment
11:31 egonw it's a regression that sneaked in before 2.2 and no one ever noticed
11:32 jonalv yup
11:32 jonalv didn't Gpox remake the properties things for 2.2.?
11:34 egonw yeah, and didn't jonalv change the manager API?
11:34 egonw and who did they quality assurance of the 2.2 release again?
11:34 egonw as the world turns
11:41 edrin joined #bioclipse
11:42 edrin egonw: olass thank you for the xmpp related mail. I think the ws1 xmpp server is simply down, thus the clients cannot connect
11:44 egonw ok, the machine seems online, so the server is down
11:44 egonw olass: can you have a short look a that later?
11:59 olass egonw: I'm back (with much less hair)
11:59 egonw oh no... what happened?
11:59 * olass tries to start ws1 ejabberd
11:59 egonw the battery of your mac exploded?
11:59 olass hah
12:04 olass egonw. edrin: I restarted ejabberd
12:04 olass I can now connect
12:04 olass services should restart in a matter of minutes
12:04 olass 15 maybe?
12:04 * olass does not remember the interval in the cron job
12:05 olass ok, some services have already restarted
12:11 egonw dunno how often my crontab runs, but will let you know if I still have problem when emails come in
12:34 egonw @pz 1944
12:34 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1944
12:35 egonw ok, once more going to trust on Arvid...
13:11 olass (trust Arvid)++
13:14 egonw olass: updated gdoc
13:14 olass great
13:26 CIA-71 org.openscience.cdk: Arvid Berg bioclipse2.4 * r167989e / plugins/org.openscience.cdk.contro​lbasic/src/org/openscience/cdk/con​troller/AlterBondStereoModule.java :
13:26 CIA-71 org.openscience.cdk: Enables AlterBondStereoModule to cycle between different stereo modes
13:26 CIA-71 org.openscience.cdk: UP->UP_INVERTED->NONE->UP...
13:26 CIA-71 org.openscience.cdk: DOWN->DOWN_INVERTED->NONE->DOWN... - http://bit.ly/bQ0Hm8
14:13 olass egonw: ping
14:13 egonw pong
14:13 olass my org.opens.cdk does not compile
14:13 olass complains about xmlcml..
14:13 olass any changes I might have missed?
14:13 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rc6ac8f5 / plugins/net.bioclipse.cdk.business/src/n​et/bioclipse/cdk/domain/CDKMolecule.java : Do not calculate new SMILES and InChI if there chemistry is not correct (addresses #2015) - http://bit.ly/9iCdFP
14:13 zarah bug #2015 | http://tinyurl.com/37mb522
14:13 CIA-71 bioclipse.cheminformatics: Arvid Berg 2.4.x * r2d381f9 / plugins/net.bioclipse.cdk.jchempaint/src/net/bioc​lipse/cdk/jchempaint/editor/JChemPaintEditor.java : Changed getAdapter to work for IMolecule aswell. - http://bit.ly/c75Ubz
14:13 CIA-71 bioclipse.cheminformatics: Arvid Berg 2.4.x * re8449f4 / plugins/net.bioclipse.cdk.jchempaint.view/src/net/​bioclipse/cdk/jchempaint/view/JChemPaintView.java :
14:13 CIA-71 bioclipse.cheminformatics: Re-factored reactOnSelection method to run coordinate creation in a background job.
14:13 CIA-71 bioclipse.cheminformatics: Solves bug 1944 - http://bit.ly/alhRFS
14:13 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r53abeb4 / plugins/net.bioclipse.cdk.jchempain​t/src/net/bioclipse/cdk/jchempaint/​widgets/JChemPaintEditorWidget.java : Remove dangling hydrogens. ie. those not connected to anything else (addresses #950) - http://bit.ly/bxMA8q
14:13 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rd96166f / plugins/net.bioclipse.cdk.jchempaint​/src/net/bioclipse/cdk/jchempaint/pr​eferences/PreferenceInitializer.java : A better default; still a dirty hack, but this will get fixed when CDK-JChemPaint moves to value relative to the bond length - http://bit.ly/d47qYy
14:14 zarah bug #1944 | http://tinyurl.com/33xg4wq
14:14 zarah bug #0950 | http://tinyurl.com/mxcd5l
14:14 egonw olass: mom
14:15 egonw olass: check your target platform
14:15 egonw in libs/ you should have the cmlxom
14:15 olass ok
14:15 olass ah
14:15 olass so removed from org.op.cdk repo?
14:15 egonw yes
14:15 olass thx
14:15 egonw ask Gpox for the details...
14:16 egonw it was needed to get hudson working
14:16 olass is the entire externals fodler removed?
14:16 olass folder
14:16 egonw no, don't think so
14:17 * olass resets TP
14:19 olass ok, fixes most issues
14:19 egonw what is left?
14:22 olass egonw: how do I abandon all in a repo and get latest HEAD?
14:23 egonw git fetch upstream branch
14:23 egonw git reset upstream/branch
14:23 egonw masak had an oneliner alternative... but forgot what it was...
14:23 * masak too
14:23 olass no
14:24 masak pull --rebase isn't it in this case.
14:24 olass still leaves me with things
14:24 olass unstaged changes
14:24 olass I mean COMPLETELY abandon everything
14:24 masak olass: clone a new repo?
14:24 masak seem easiest.
14:24 olass ok
14:25 egonw olass: what's the state of your clone?
14:25 egonw you have uncommited stuff?
14:25 olass no idea
14:25 olass nope
14:25 Gpox git reset --hard upstream/branch
14:25 olass diverged
14:25 olass ok.
14:25 egonw Gpox++
14:26 olass Gpox++ //Solved it
14:32 masak Gpox++ # ah, so that's how
14:32 masak I'd only used git-reset for local commits before.
14:37 egonw Gpox: ping
14:37 egonw Gpox: how do the popup actions work?
14:37 Gpox pong
14:37 egonw I'm looking at the 'Add explicit Hydrogensä
14:37 egonw I'm looking at the 'Add explicit Hydrogens'
14:37 egonw looking at the plugin.xml it causes
14:38 egonw a JCHmePaintManager call
14:38 egonw of addExplicitHydrogens
14:38 egonw but
14:38 egonw that method does not do atom type perpection
14:38 egonw yet that happens
14:38 masak olass: this tutorial that I'm following -- http://wiki.eclipse.org/index.php/GMF_Tutorial -- did you try it?
14:38 zarah masak's link is also http://tinyurl.com/yoom9u
14:38 egonw where is the action wrapping the manager call
14:38 egonw ?
14:39 olass masak: don't remember
14:39 olass seems updated
14:39 olass how come?
14:40 masak many links in there are broken, and the instructions aren't very clear.
14:40 Gpox ManagerHandler
14:40 egonw Gpox: ok, thanx
14:41 egonw Gpox: mmm... the recalculating of atom types is not there either :(
14:41 egonw must be JCPEditorWidget.structureChanged() then...
14:41 masak olass: you know how when one has gotten stuck at about ten different small things and switch into a mode wherein the tutorial becomes a challenge more than a learning process? I'm at that stage. not sure whether it's just me.
14:42 Gpox JChemPaintEditorWidget.updateAtomTypesAndHCounts
14:42 egonw Gpox: indeed
14:42 egonw and I see the reason...
14:42 egonw line 744
14:42 masak olass: last week, I submitted four different bugs about the tutorial. this week, I've stopped bothering.
14:42 egonw this is a pain...
14:42 egonw there just is no general solution to cheminformatics :(
14:49 olass masak: sorry to hear this
14:49 olass I don't seem to remember doing that tutorial
14:49 olass but I might have done the previous version of it
14:50 olass sorry I cannot help
14:50 masak I understand.
14:50 masak olass: I think I'll borrow jonalv for a while tomorrow and see if masak+jonalv has an easier time with the tutorial than just masak. :)
14:50 olass :)
14:51 masak I'm a bit tired of being stuck in this tutorial, frankly.
14:51 masak GMF seems to be a fine, though complex, tool.
14:52 jonalv masak: I am going to be at the hospital tomorrow too
14:53 masak oh, ok.
14:57 masak well, mek_ will be here tomorrow. maybe he wants to give it a try.
14:58 egonw what is GMF?
14:58 egonw I know what GEF is
14:58 egonw and EMF
14:58 masak GMF combines the two, IIUC.
14:59 masak kind of appropriate, since its acronym is halfway between the other two's :)
15:14 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r8bfc9e2 / plugins/net.bioclipse.cdk.ui/src/net/biocli​pse/cdk/ui/wizards/NewFromSMILESWizard.java : Use the DeduceBondSystemTool to do a best job as we currently can in dealing with the SMILES organic subset lower-case formalism (fixes #1627) - http://bit.ly/9jC422
15:14 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r5453860 / (2 files): Fixed the 'Next' button going active when there is a valid SMILES: there is not next page :( - http://bit.ly/9qOmjG
15:14 zarah bug #1627 | http://tinyurl.com/32b5w2t
16:15 sneumann joined #bioclipse
16:58 egonw joined #bioclipse
17:08 egonw olass: is there an easy way to ask if a feature is installed programmatically?
17:08 egonw olass: using the feature ID would be fine
17:09 egonw olass: I am thinking here about bioclipse.requireFeature("ne​t.bioclipse.joelib_feature")
17:28 egonw joined #bioclipse
17:40 CIA-71 bioclipse.social: Egon Willighagen 2.4.x * r569d312 / (2 files): Added a method to list all BSL scripts - http://bit.ly/a0fZN5
18:30 olass egonw: about requireFeature: not sure
18:30 olass proibably
18:30 olass hmm, pretty sure there is
18:30 egonw so bloody difficult to google for these kind of things
18:31 olass hmm, I think I know
18:31 olass file me a bug, or reassign to me with 2.4.0
18:31 olass need to cook dinner now
18:31 egonw will google a bit more
18:31 olass and watch the World cup :)
18:31 egonw what game?
18:31 egonw who are playing tonight?
18:31 egonw tomorrow I'm on again :)
18:38 sneumann_ joined #bioclipse
18:58 egonw olass: http://www.myexperiment.org/workflows/1354
18:58 zarah egonw's link is also http://tinyurl.com/2eofvr3
18:58 egonw @tell jonalv http://www.myexperiment.org/workflows/1354
18:58 zarah egonw's link is also http://tinyurl.com/2eofvr3
18:58 zarah Consider it noted.
20:24 egonw @pz chemspider
20:24 zarah egonw: I couldn't find anything on 'chemspider' in the database.
20:27 CIA-71 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r38cf36f / (13 files in 6 dirs): Added ChemSpider InChIKey resolution functionality - http://bit.ly/aQXxDC
20:56 egonw_ joined #bioclipse
21:00 CIA-71 bioclipse.core: Egon Willighagen 2.4.x * rc50d15d / (2 files): Implemented bioclipse.assumeOnline() (implements #1940) - http://bit.ly/blzxdv

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