Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-12-14

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All times shown according to UTC.

Time Nick Message
06:31 egonw joined #bioclipse
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07:01 masak joined #bioclipse
07:01 masak o/
07:01 egonw hi masak
07:01 masak mornin'.
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09:16 egonw jonalv, masak: what is the point you are trying to make in pelezilla?!?!
09:16 jonalv egonw: I don't really understand you mail named "New bundlkes in bioclipse.core and bioclispe.rdf. Maybe it's just me but what do I need to do?
09:16 egonw what *are* you trying to achieve?
09:16 jonalv egonw: bugs that can be closed?
09:17 egonw why the hell are you taking over bugs that are not assigned to you?
09:17 egonw it seems that both the reporter and the assigned person seem to agree it is a bug...
09:17 egonw (though they are both olas)
09:18 egonw masak: your referal to that article only says the report is badly formulated...
09:18 egonw masak: but I am sure the assigned person understand
09:18 egonw (though they are both olas)
09:19 egonw jonalv, masak: it would really be more useful if you'd help refine the report then...
09:19 masak egonw: I can see that side of the argument.
09:19 egonw jonalv, masak: I'm sure you agree the BSL is inconsistent
09:19 egonw masak: what is my side precisely?
09:19 jonalv egonw: when are you goign to be on bmc?
09:19 egonw because I am lost on what you are trying to do
09:19 egonw jonalv: tomorrow, thursdat
09:19 egonw jonalv: wed perhaps
09:19 masak egonw: that imprecise bug tickets are OK if they're for yourself.
09:20 jonalv egonw: friday?
09:20 egonw masak: that makes your argument, that any badly reported bug should be closed without looking at it?
09:20 egonw jonalv: any special on friday?
09:20 jonalv egonw: you need to contact marine on 4301 when you are at bmc
09:21 egonw marine?
09:21 jonalv |Marina
09:21 egonw who is that?
09:21 jonalv tel 4301
09:21 jonalv she is standing in for Erica
09:21 masak egonw: a quick look revealed that it wasn't even a badly reported bug report. it was a TODO item.
09:21 egonw why does she not email me if it is important?
09:22 masak egonw: because she is a meatspace person, possibly.
09:22 masak some people are like that.
09:22 egonw masak: and since has it become policy that TODOs cannot be put in pelezilla?
09:22 jonalv egonw: you will have to ask her when you call her tomorrow...
09:22 egonw jonalv: thanx for relaying the message
09:22 masak egonw: I have always lived under such a policy.
09:22 jonalv egonw: np
09:23 masak egonw: I think we should reserve Bugzilla tickets to things related to flaws or feature requests in software.
09:23 jonalv egonw: on a totally different note. Where do I make that jumbno patch available?
09:23 egonw jonalv: anywhere public...
09:24 egonw but I suggest the bug ticket on SF for CDK
09:24 jonalv egonw: I mean I thought it would be incoperated in jumbo by now... I don\t really feel that I wanna fork jumbo...
09:24 egonw masak: so, what does the lack of consistent API in BSL not a flaw or feature request?
09:24 jonalv egonw: but just giving the patch there isn't really food enough is it?
09:25 jonalv |good
09:25 masak egonw: the ticket requested that we '*decide* on such an API'.
09:25 masak that's a near-meaningless ticket.
09:25 egonw ah, so why did you not request Ola to clarify what he meant with the bug report, instead of just closing it for him
09:25 egonw ?
09:25 masak because I didn't see a way to save it.
09:26 egonw ah, so why did you not request Ola to clarify what he meant with the bug report, instead of just closing it for him
09:26 egonw ?
09:26 masak dunno. probably had a bit of a bad day.
09:26 masak but looking at it now, and today is not a bad day, I still don't see the point of making a ticket for that.
09:26 egonw jonalv: you open those new bundles/plugins in your eclipse workspace
09:26 masak I think we should have a roadmap document or something, and put things in there.
09:27 jonalv egonw: as in importing them?
09:27 masak just as we shouldn't put important tickets on post-it notes on the wall instead of in Bugzilla, we shouldn't put TODO items in Bugzilla instead of in some TODO list managing software.
09:27 egonw masak: ok, please do feel free to bring this up... we should then also consistently remove the "Bioclipse 2.x has not been released" bugs, even though they seem to be damn convenient
09:27 masak or even a physical TODO list.
09:27 egonw jonalv: right
09:28 masak egonw: I do think that these are meaningless as well, yes.
09:28 masak egonw: especially since there is already a 'version' field in Bugzilla.
09:28 jonalv egonw: ah oki thanks, maybe that was obvious and I am jsut stupid today...
09:28 egonw ok, so please bring this up on bioclipse-devel so that it can be discussed
09:28 masak I will.
09:28 egonw and leave bug fixing, resolving to the assingnee ?
09:29 masak I'll try. :)
09:29 egonw (of coure you make still add comments to make your point too :)
09:29 masak goodie.
09:29 egonw :)
09:31 * egonw is running creation of CML on the ChEBI SD file (the copy I have here, at least, not the latest)
09:37 jonalv egonw: I don't think I can find that patch but why don't we just use the latest from jumbo. They ahve marked my bug report as fixced so they should have fixed it...
09:38 egonw we are using the latest CML
09:38 jonalv egonw: you lost me, what it the problem then?
09:38 egonw but have used the patched version at some time, so are required to release the source of that patch too...
09:39 egonw but if you cannot find it... than too bad
09:39 egonw legal matters
09:39 jonalv egonw: I guess I can keep looking...
09:40 egonw no need, I guess
09:40 egonw what was the bug number of PZ?
09:40 egonw @pz jumbo
09:40 zarah egonw: I couldn't find anything on 'jumbo' in the database.
09:40 egonw @pz cml
09:40 zarah [1776] Methods to work with labels in... http://tinyurl.com/y8fym9q
09:40 zarah [597] Properly synchronize the editor... http://tinyurl.com/b8rd5s
09:40 zarah [825] Write cdk.generateMissing2dCoor... http://tinyurl.com/ybpmpcz
09:40 zarah [1428] Wrong formula given               http://tinyurl.com/yd24akx
09:40 zarah [303] MoleculesTable in CMLMultiEdito... http://tinyurl.com/dgjwj9
09:40 jonalv egonw: I have the diff
09:40 zarah Entire list (21) at http://tinyurl.com/ye4geq7
09:40 egonw ah, great
09:40 egonw that's perfect!
09:48 egonw thanx!
10:05 * egonw wonders if olas is going to show up today
10:11 egonw jonalv: ok, it failed to convert 6 ChEBI entries to CML
10:11 egonw jonalv: what was your ID again?
10:11 egonw I have fails for:
10:11 egonw CHEBI:51642, CHEBI:51730, CHEBI:51736, CHEBI:52729, CHEBI:52748, and CHEBI:52749
10:12 jonalv egonw: uhm I can't remember
10:12 egonw no worries
10:12 egonw I'll explore these issues
10:13 egonw do you like to see the groovy script?
10:13 jonalv egonw: maybe I wrote it down in the bug report?
10:13 jonalv egonw: but it is reasonable to believe that it would be on of them...
10:14 egonw http://gist.github.com/255955
10:35 egonw jonalv: ping
10:36 jonalv egonw: yea?
10:36 egonw did you see this bug report by Mark? :
10:36 egonw working with JChempaint I noticed that some Chebi entries did not open properly. For example Chebi 51730. It turns out that its molfile contains a bond type > 4.
10:36 egonw that just happens to be one of the entries in the ChEBI I just parsed and failed to convert to CML
10:36 jonalv egonw: nope, is it related?
10:36 egonw yes, very much
10:37 egonw https://sourceforge.net/tracker/?func=detail&amp​;atid=120024&aid=2912050&group_id=20024
10:37 jonalv egonw: hm what is wrong?
10:38 egonw I'll forward Mark's latest email
10:38 egonw basically comes down to this:
10:38 egonw ChEBI does not just define molecules, but also fragments
10:38 jonalv egonw: what is that star intop of the christmus tree? :)
10:38 egonw huh?
10:39 egonw you mean the 'piek' ?
10:39 jonalv http://www.ebi.ac.uk/chebi/se​archId.do?chebiId=CHEBI:51730
10:39 zarah jonalv's link is also http://tinyurl.com/ybqprbd
10:39 egonw ah, yes...
10:39 egonw look at the bottom bonds...
10:39 egonw the dots...
10:39 egonw they are represented on MDL molfile level as "1 or aromatic" or "2 or aromatic"
10:39 jonalv yea I feel that my chmistry education did not include this... :)
10:40 egonw however, these are query bond types, but the CDK does not read queries as MDL molfile
10:40 egonw think of it as a SMARTS query
10:40 egonw the MDL reader should fail on it, actually
10:40 egonw indicating that it cannot read such files
10:41 jonalv egonw: sry why should it not be able to read the file?
10:41 jonalv ah they are query bond types
10:42 jonalv so maybe it's chebi that is wrong then?
10:42 egonw well...
10:42 egonw there is nothing really that says that ChEBI contains just molecules
10:42 egonw so, mark asked if it is a feature or bug...
10:43 egonw I separately asked the ChEBI team this morning how I could filter out those entries
10:43 egonw because we cannot do this at a CDK level yet
10:43 egonw @pz CHEBI
10:43 zarah [1647] Properties view is buggy for M... http://tinyurl.com/yabxuzc
10:43 zarah [1636] Wishlist: busy indicator for m... http://tinyurl.com/yctuyx9
10:43 zarah Entire list at http://tinyurl.com/ybrhtr2
10:43 jonalv egonw: hm so basically this all comes down to the fact that the sdf format does everything...
10:44 egonw yes, you could think of it like that
10:45 egonw it has some interesting features... the fact that they use query entries, does that make the whole file a set of query structures?
10:46 jonalv egonw: yea, intresting...
11:19 egonw masak: there is that hardly noticable sarcasm you tweeted about :)
11:19 masak egonw: where?
11:20 egonw right!
11:20 egonw masak++
12:10 masak egonw: "I don't: the observables are they child bug reports." -- what do you mean?
12:10 egonw a aggregation bug is fixed when all the childs are fixed
12:11 masak egonw: nod. I think that's an acceptable exception.
12:11 masak egonw: it's nice if such a ticket is marked as a meta-ticket in some way, though.
12:12 masak anyway, thanks for adding to my point by writing a short, ungrammatical retort. :P
12:12 egonw you're calling me a retard ?!?
12:12 egonw ;)
12:12 masak now wait a minute.
12:13 masak I'm about to reply to olass with approximately the same message you had.
12:13 egonw good
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13:37 jonalv @pz sdf editor
13:37 zarah [1333] 70 source files without copyri... http://tinyurl.com/nz9aff
13:37 zarah [1612] NPE when reading virtual files... http://tinyurl.com/y9dn3wy
13:37 zarah [1326] Fix serialization/deserializat... http://tinyurl.com/msm3ak
13:37 zarah [303] MoleculesTable in CMLMultiEdito... http://tinyurl.com/dgjwj9
13:37 zarah [1195] Calculate properties in moltab... http://tinyurl.com/y97vf8b
13:37 zarah Entire list (19) at http://tinyurl.com/yc7wdpo
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14:18 jonalv oh hai egonw_
14:18 jonalv egonw_: we need to plan a jmol hackathon and get gpox and masak and maybe olass in on it
14:19 egonw_ hi jonalv
14:19 egonw_ yes, sounds good
14:19 masak sounds intriguing. :)
14:19 masak why a Jmol hackathon?
14:19 jonalv I think we should take one week and just spend it on jmol all of us
14:19 jonalv masak: becasue the current state of jmol in Bioclsiep is just so sad
14:20 masak fairy 'nuff.
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14:28 jonalv egonw_: gilleain is not working on Bioclspe any longer right? Do you know if someone has taken over his bugs?
14:28 egonw_ on both questions: I do not know
14:31 jonalv egonw_: k
14:41 CIA-60 bioclipse.structuredb: jonalv master * r7538989 / (2 files in 2 dirs):
14:41 CIA-60 bioclipse.structuredb: Just show all possible properties
14:41 CIA-60 bioclipse.structuredb: Return all properties in the database instead of just the one that the molecules opened for the moment happend to have. - http://bit.ly/7MomfL
14:54 samuell egonw: On executing the pellet.product, I see in the log:
14:54 samuell DEBUG - The feature: Pellet Feature version: 2.2.0.RC2 is not installed
14:54 samuell ...and the manager doesn't show up in the Bioclipse command line.
14:55 samuell (egonw_ , not egonw, I guess)
14:56 egonw :)
14:56 egonw please put the full console output up somewhere
14:57 samuell egonw_: http://bioclipse.pastebin.com/m10395c5f
14:57 zarah samuell's link is also http://tinyurl.com/yaj5t5d
15:01 samuell It worked before the addition of TDB on friday
15:02 samuell (So maybe it is my patch that does something weird ... ?)
15:10 egonw samuell: nope... I forgot to commit all my changes
15:10 samuell Ok
15:11 CIA-60 bioclipse.rdf: Egon Willighagen 2.2.x * rb661455 / features/net.bioclipse.pellet_feature/feature.xml : Added missing plugin for TDB to feature - http://bit.ly/4oe3KT
15:13 egonw samuell: please try now
15:13 samuell Yep, so will I !
15:14 CIA-60 bioclipse.structuredb: Arvid Berg master * rdf92448 / (3 files in 2 dirs):
15:14 CIA-60 bioclipse.structuredb: Double-click opens MoleuclesEditor for labels
15:14 CIA-60 bioclipse.structuredb: Solves bug #1642
15:14 CIA-60 bioclipse.structuredb: Signed-off-by: jonalv <jonathan.alvarsson@gmail.com> - http://bit.ly/7hBNwT
15:14 zarah bug #1642 | http://tinyurl.com/y9sw633
15:15 jonalv gpox++
15:33 samuell egonw_: Do I have to do something special to get xerces installed (Xerxes imports don't resolve)
15:34 samuell (I have xerxes as a project in the workspace though)
15:37 egonw try updating classpath, reset platform, etc
15:43 * jonalv can haz 3d in Bioclispe
15:43 jonalv jmol++
15:46 egonw :)
15:48 jonalv steriographics is so cool
15:49 jonalv egonw: if we remove the context menu from jmol then it is much harder to add that...
15:49 jonalv or to activate that I eman
15:50 jonalv my eyes are tired :)
15:50 egonw sorry?
15:50 egonw I tried understanding your question, but did not see one
15:51 jonalv egonw: I found steriographics mode in the new jmol context menu so cool. But if we remove that context menu it is much harder to turn it on again... WE need to make a good jmol context menu that contains the parts from the orignal one that we want
15:52 egonw makes sense
15:52 jonalv aouch my eyes are really tired now :)
15:52 jonalv but it was cool :)
15:56 egonw :)
15:57 egonw but from you working on Jmol, I can assume StructureDB is ready for 2.2 Experimental ?
16:04 samuell egonw: Got it working now (after re-cloning the whole bioclipse.core et.c.)
16:04 jonalv egonw: I just took a check of all my bugs and I found a bunch jmol bugs and then I checked who had the rest of the jmol bugs wondering whether we should try and give all of them to the same person...
16:05 egonw jonalv: ah, you want to take over my Jmol bugs?
16:05 jonalv egonw: but yea I think structureDB is in 2.2 experimental
16:05 * samuell grabs coffee
16:05 jonalv egonw: well I was thinking maybe I could give mine to you... ;)
16:06 egonw jonalv: hahahaha
16:06 egonw samuell: ack
16:08 jonalv egonw: btw for cheminformatics, will there be a 2.4 branch soon or do we work against master or what is the plan?
16:08 egonw master, until the freeze
16:08 egonw so, make sure not to put anything in master that should not end up in 2.4
16:09 jonalv egonw: oki, I have a branch with a lot of worki going on both by me and by gpox should I rebase it interactively to squash down the number of commits in before you merge it in?
16:09 egonw yes, that always makes it easier to go through
16:10 * jonalv is not sure he should squash gpox's commits...
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