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| Time | Nick | Message |
|---|---|---|
| 06:31 | egonw joined #bioclipse | |
| 06:41 | egonw_ joined #bioclipse | |
| 07:01 | masak joined #bioclipse | |
| 07:01 | masak | o/ |
| 07:01 | egonw | hi masak |
| 07:01 | masak | mornin'. |
| 08:01 | sneumann__ joined #bioclipse | |
| 08:12 | sneumann joined #bioclipse | |
| 08:21 | sneumann joined #bioclipse | |
| 08:36 | mgerlich joined #bioclipse | |
| 09:04 | jonalv joined #bioclipse | |
| 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 | it seems that both the reporter and the assigned person seem to agree it is a bug... | |
| 09:17 | (though they are both olas) | |
| 09:18 | masak: your referal to that article only says the report is badly formulated... | |
| 09:18 | masak: but I am sure the assigned person understand | |
| 09:18 | (though they are both olas) | |
| 09:19 | 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 | 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 | jonalv: tomorrow, thursdat | |
| 09:19 | 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 | 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 | 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 | 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 | 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 | |good | |
| 09:25 | masak | egonw: the ticket requested that we '*decide* on such an API'. |
| 09:25 | 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 | ? | |
| 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 | ? | |
| 09:26 | masak | dunno. probably had a bit of a bad day. |
| 09:26 | 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 | 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 | but if you cannot find it... than too bad | |
| 09:39 | legal matters | |
| 09:39 | jonalv | egonw: I guess I can keep looking... |
| 09:40 | egonw | no need, I guess |
| 09:40 | what was the bug number of PZ? | |
| 09:40 | @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 | [597] Properly synchronize the editor... http://tinyurl.com/b8rd5s | |
| 09:40 | [825] Write cdk.generateMissing2dCoor... http://tinyurl.com/ybpmpcz | |
| 09:40 | [1428] Wrong formula given http://tinyurl.com/yd24akx | |
| 09:40 | [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 | that's perfect! | |
| 09:48 | 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 | jonalv: what was your ID again? | |
| 10:11 | I have fails for: | |
| 10:11 | 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 | I'll explore these issues | |
| 10:13 | do you like to see the groovy script? | |
| 10:13 | jonalv | egonw: maybe I wrote it down in the bug report? |
| 10:13 | egonw: but it is reasonable to believe that it would be on of them... | |
| 10:14 | egonw | http://gist.github.com/255955 |
| 10:35 | jonalv: ping | |
| 10:36 | jonalv | egonw: yea? |
| 10:36 | egonw | did you see this bug report by Mark? : |
| 10:36 | 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 | 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 | https://sourceforge.net/tracke[…]50&group_id=20024 | |
| 10:37 | jonalv | egonw: hm what is wrong? |
| 10:38 | egonw | I'll forward Mark's latest email |
| 10:38 | basically comes down to this: | |
| 10:38 | 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 | you mean the 'piek' ? | |
| 10:39 | jonalv | http://www.ebi.ac.uk/chebi/sea[…]ebiId=CHEBI:51730 |
| 10:39 | zarah | jonalv's link is also http://tinyurl.com/ybqprbd |
| 10:39 | egonw | ah, yes... |
| 10:39 | look at the bottom bonds... | |
| 10:39 | the dots... | |
| 10:39 | 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 | think of it as a SMARTS query | |
| 10:40 | the MDL reader should fail on it, actually | |
| 10:40 | indicating that it cannot read such files | |
| 10:41 | jonalv | egonw: sry why should it not be able to read the file? |
| 10:41 | ah they are query bond types | |
| 10:42 | so maybe it's chebi that is wrong then? | |
| 10:42 | egonw | well... |
| 10:42 | there is nothing really that says that ChEBI contains just molecules | |
| 10:42 | so, mark asked if it is a feature or bug... | |
| 10:43 | I separately asked the ChEBI team this morning how I could filter out those entries | |
| 10:43 | because we cannot do this at a CDK level yet | |
| 10:43 | @pz CHEBI | |
| 10:43 | zarah | [1647] Properties view is buggy for M... http://tinyurl.com/yabxuzc |
| 10:43 | [1636] Wishlist: busy indicator for m... http://tinyurl.com/yctuyx9 | |
| 10:43 | 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 | 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 | 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 | egonw: it's nice if such a ticket is marked as a meta-ticket in some way, though. | |
| 12:12 | 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 | ;) | |
| 12:12 | masak | now wait a minute. |
| 12:13 | I'm about to reply to olass with approximately the same message you had. | |
| 12:13 | egonw | good |
| 13:19 | samuell joined #bioclipse | |
| 13:37 | jonalv | @pz sdf editor |
| 13:37 | zarah | [1333] 70 source files without copyri... http://tinyurl.com/nz9aff |
| 13:37 | [1612] NPE when reading virtual files... http://tinyurl.com/y9dn3wy | |
| 13:37 | [1326] Fix serialization/deserializat... http://tinyurl.com/msm3ak | |
| 13:37 | [303] MoleculesTable in CMLMultiEdito... http://tinyurl.com/dgjwj9 | |
| 13:37 | [1195] Calculate properties in moltab... http://tinyurl.com/y97vf8b | |
| 13:37 | Entire list (19) at http://tinyurl.com/yc7wdpo | |
| 14:05 | egonw_ joined #bioclipse | |
| 14:18 | jonalv | oh hai egonw_ |
| 14:18 | 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 | yes, sounds good | |
| 14:19 | masak | sounds intriguing. :) |
| 14:19 | 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 | masak: becasue the current state of jmol in Bioclsiep is just so sad | |
| 14:20 | masak | fairy 'nuff. |
| 14:26 | egonw_ joined #bioclipse | |
| 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: 03jonalv 07master * r7538989 10/ (2 files in 2 dirs): |
| 14:41 | bioclipse.structuredb: Just show all possible properties | |
| 14:41 | 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 | DEBUG - The feature: Pellet Feature version: 2.2.0.RC2 is not installed | |
| 14:54 | ...and the manager doesn't show up in the Bioclipse command line. | |
| 14:55 | (egonw_ , not egonw, I guess) | |
| 14:56 | egonw | :) |
| 14:56 | 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 | (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: 03Egon Willighagen 072.2.x * rb661455 10/ 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: 03Arvid Berg 07master * rdf92448 10/ (3 files in 2 dirs): |
| 15:14 | bioclipse.structuredb: Double-click opens MoleuclesEditor for labels | |
| 15:14 | bioclipse.structuredb: Solves bug #1642 | |
| 15:14 | 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 | (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 | egonw: if we remove the context menu from jmol then it is much harder to add that... | |
| 15:49 | or to activate that I eman | |
| 15:50 | my eyes are tired :) | |
| 15:50 | egonw | sorry? |
| 15:50 | 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 | but it was cool :) | |
| 15:56 | egonw | :) |
| 15:57 | 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 | 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 | 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... |
| 16:30 | sneumann joined #bioclipse | |
| 17:39 | sneumann_ joined #bioclipse | |
| 19:15 | miguelrojasch joined #bioclipse | |
| 21:52 | sneumann_ joined #bioclipse | |
| 22:05 | berry_ joined #bioclipse |
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