Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-06

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All times shown according to UTC.

Time Nick Message
00:00 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r3c041a1 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Found problem for bug #1454: the format is not properly detected - http://bit.ly/rlBc5
00:00 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r3825bc6 / (3 files in 2 dirs): Added unit tests around bug #1454: PubChemXML not working with cdk.fromString() - http://bit.ly/11ahGB
00:00 zarah bug #1454 | http://tinyurl.com/n5xm3o
00:00 zarah bug #1454 | http://tinyurl.com/n5xm3o
05:05 sneumann joined #bioclipse
05:58 egonw joined #bioclipse
06:30 olass joined #bioclipse
06:39 Gpox joined #bioclipse
06:43 Gpoks joined #bioclipse
06:58 sneumann joined #bioclipse
07:03 egonw moin
07:03 zarah hi egonw
07:04 olass hi egonw
07:07 olass egonw: If a bug is marked "resolved later", should I close it then or leave it open?
07:08 egonw ummm...
07:08 egonw no clue
07:08 egonw what bug number
07:08 egonw ?
07:08 olass 825
07:10 olass egonw: I'm afraid that closing it is not right, but that it is forgotten in its present state
07:10 egonw no clue
07:10 olass IMO it should be reopened
07:10 egonw yeah, think so too
07:10 olass and for 2.2
07:10 olass ok
07:10 * olass does so
07:11 egonw the not throw ICDKException in the CDKManager...
07:11 egonw is that an important one?
07:11 egonw it does not show up in 1460, it seems
07:12 olass I removed it
07:12 olass not so important IMO
07:12 olass we have more urgent things
07:12 olass 1428 for example
07:13 olass if you could look at that I'd be happy
07:13 olass it is a crucial one
07:13 olass incorrect formula might mean a core error in cheminfo
07:14 egonw please add all important ones to 1460
07:14 olass yes
07:14 olass done so
07:14 olass (I think)
07:14 olass and will do so
07:14 olass (if I find new, going through bugs now)
07:14 egonw I only see:
07:14 egonw Depends on:  1454 1462 1463 1468 1469
07:15 olass ah, had forgotten to submit :(
07:15 olass 1428 now too
07:42 jonalv joined #bioclipse
07:46 egonw Gpox: I marked bug 1468 as blocker
07:47 egonw for bug #1428
07:58 jonalv CIA-63: ping?
08:03 egonw Gpox: ping
08:03 Gpox egonw: pong
08:03 egonw have you seen 1468 and 1469...
08:03 egonw can you plese comment on 1468...
08:03 Gpox yes
08:05 egonw I'm not sure I understand how updating the jcp code would make the jcp editor dirty...
08:06 egonw I guess something is different in the change event model...
08:08 shk3 joined #bioclipse
08:44 egonw olass: ping
08:44 egonw olass: please check bug report 1461
08:44 egonw I left a comment
08:44 egonw an important one
08:44 olass ok
08:55 olass egonw: let me know when you are finished
09:00 CIA-63 bioclipse.structuredb: jonalv master * r8ee625d / plugins/net.bioclipse.structuredb/src/net/b​ioclipse/structuredb/domain/DBMolecule.java : readded SMILES calculation which was accidentally outcommented in last commit - http://bit.ly/18spk5
09:00 jonalv CIA-63 is just so very fast (not)
09:04 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * reb01297 / (12 files in 3 dirs): Added test suite for the PubChem manager - http://bit.ly/14DEyR
09:04 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r92da271 / plugins/net.bioclipse.pubchem/META-INF/MANIFEST.MF : Added missing exports of two packages, needed by the manager test suite - http://bit.ly/4s9LUF
09:04 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r3daab9e / (3 files in 2 dirs): Added two methods to determine the CDK IChemFormat for a file and an inline String document + unit tests - http://bit.ly/sizNm
09:58 egonw jonalv: ping
09:58 egonw jonalv: I need a reminder...
09:59 egonw and not sure this is on the wiki page http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager#Manager_best_practices
09:59 zarah egonw's link is also http://tinyurl.com/dypvah
10:00 egonw making something a job is done by adding a method in the interface to eat IProgressMonitor, right?
10:03 jonalv egonw: I think so if I undesrtand what you mean with "eat" correctly
10:03 egonw :)
10:03 egonw yeah, lunch tim...
10:04 jonalv sure is
10:04 jonalv we are trying to figure out where to eat :)
10:06 * jonalv @ lunch
10:06 egonw Gpox++ (for the patches for 1468 and -69)
10:07 egonw Gpox: your pull request is not showing up in my fork queue... will apply manually though
10:08 CIA-63 bioclipse.cheminformatics: jonalv master * r185f2c4 / plugins/net.bioclipse.cdk.ui.sdfed​itor/src/net/bioclipse/cdk/ui/sdfe​ditor/editor/MoleculesEditor.java :
10:08 CIA-63 bioclipse.cheminformatics: Stuff needed in order to use the MoleculesEditor from Structuredb. Gpox++ wrote this...
10:08 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/LTSJT
10:08 egonw oh, cool
10:09 egonw GitHub web interface automatically added the Sign-off !
10:09 egonw GitHub++
10:10 olass egonw: have you pushed Gpox++ updates to cheminformatics or did he push himself? I want to verify 1468 and 1469 now works
10:15 egonw I have pushed jonalv's commit
10:16 egonw olass: hang on...
10:18 egonw Gpox: can you please rework your patches?
10:18 egonw http://github.com/goglepox/bioclipse.cheminformati​cs/commit/c0366eee9a32a49ff6725d3bb6061a0615cd60da
10:18 zarah egonw's link is also http://tinyurl.com/nbecpo
10:19 egonw please make that a patch http://pele.farmbio.uu.se/cgi-bin/git​web.cgi?p=jchempaint-primary.git;a=sh​ortlog;h=refs/heads/bioclipse-2.1.x
10:19 zarah egonw's link is also http://tinyurl.com/l72447
10:19 egonw Gpox: and split up http://github.com/goglepox/bioclipse.cheminformati​cs/commit/854ccd76bc37498ca16c08f435edd8ebc1f534fa
10:19 zarah egonw's link is also http://tinyurl.com/lzoml3
10:19 egonw in patch against the above jcpprim branch on pele
10:19 egonw and a patch again bioclipse.cheminfo
10:29 CIA-63 bioclipse.cheminformatics: Arvid Berg master * rdc9434e / (2 files in 2 dirs):
10:29 CIA-63 bioclipse.cheminformatics: Added call to Renderer.setup when changing model.
10:29 CIA-63 bioclipse.cheminformatics: It was also necessary to change the order in which
10:29 CIA-63 bioclipse.cheminformatics: the set methods was called to make sure
10:29 CIA-63 bioclipse.cheminformatics: Renderer.transform is initialized.
10:29 CIA-63 bioclipse.cheminformatics: fixes bug #1469
10:29 zarah bug #1469 | http://tinyurl.com/l75sfy
10:29 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/S8pVP
10:29 CIA-63 bioclipse.cheminformatics: Arvid Berg master * rcbc9c75 / (2 files):
10:29 CIA-63 bioclipse.cheminformatics: Implemented getEditOperation to return an IUndoRedoable
10:29 CIA-63 bioclipse.cheminformatics: that wrapps an IEdit.
10:29 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/8gvgc
10:33 egonw jonalv: and an example of partial returner I can find in the CDK manager?
10:37 egonw oh crap
10:37 egonw there is another 'how to make a manager' page :(
10:37 egonw http://wiki.bioclipse.net/index.p​hp?title=How_to_make_a_manager_2
10:37 zarah egonw's link is also http://tinyurl.com/ouun2r
10:37 egonw that one has more info!
10:42 egonw jonalv++ (for the well written docs!)
10:42 egonw jonalv-- (for not deleting the old wiki page :)
10:56 olass egonw: and the commit for 1468? Is that on the way or hidden inside the now pushed commits?
10:56 olass and what dows "Signed off by" means?
11:02 sneumann Guess that's taken from Linux Kernel world,
11:02 sneumann meaning who had a (second) look at the patch
11:03 olass but how is it implemented in git?
11:11 * jonalv is back and start to backlogg
11:13 jonalv egonw: "the old" page remains because not all plugins are using the way
11:13 jonalv |the new way
11:21 egonw olass: if you sign off a patch, you indicate that you support the patch, and take some responsibility for it
11:21 egonw sign off = approving
11:27 egonw jonalv: ping
11:27 jonalv egonw: pong
11:27 egonw jonalv: if I use BioclipseJobUpdateHook, there is no need to add IProgressMonitor too, correct?
11:27 * jonalv realises that he hasn't looked at this in a month
11:28 jonalv egonw: doesn't the documentation mention this situtation?
11:28 shk3 no, no need
11:29 jonalv egonw: I think you are wrong though. What makes you think that you suddenly don't need a progrssmonitor?
11:29 jonalv shk3: oh?
11:29 jonalv *lol*
11:29 shk3 well, I did it without and it works
11:29 shk3 like in the example in the doc
11:30 shk3 but that may be wrong
11:30 * jonalv is condufesd now.
11:30 shk3 it was me who wrote the doc and perhaps due my limited understanding
11:30 shk3 it is wrong
11:30 jonalv which example exactly are we talkign about?
11:30 shk3 http://wiki.bioclipse.net/index.php?title=​How_to_make_a_manager_2#Running_manager_me​thods_as_jobs_which_return_partial_results
11:30 zarah shk3's link is also http://tinyurl.com/ouun2r
11:31 shk3 that's what I am talking about
11:31 jonalv shk3: well if it works for you then I guess it works...
11:31 shk3 it works that way, yes
11:32 jonalv I have never done any use case with partial eturns so I am not 100% sure on expected behavior
11:32 jonalv do you want a progressmonitor that ticks up?
11:32 jonalv shk3: but that example is in the interface and in the call
11:32 shk3 but you need the monitor in the implementation
11:33 jonalv I still think you want the implemented method to have a progressmonitor though...
11:33 shk3 yes
11:33 jonalv okey then I think I missunderstood the question from egonw
11:33 shk3 see http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager_2#Running_manager_meth​ods_as_jobs_which_return_partial_results_2
11:33 zarah shk3's link is also http://tinyurl.com/ouun2r
11:33 jonalv NEVER any IPrpogressMonitors in the interface
11:33 shk3 oh, I might have misunderstood it
11:34 shk3 as well
11:34 shk3 but I think the examples make it clear
11:34 shk3 and they work
11:34 jonalv egonw: are you still there?
11:34 egonw yes, I am
11:34 shk3 egonw: if you have problems with understanding the examples, please report
11:34 jonalv egonw: does it make sence for you?
11:34 egonw ah, ok...
11:34 shk3 they might well be improved
11:34 egonw no IProgressMonitor in the IFooManager interface
11:34 shk3 yes
11:34 jonalv yes
11:35 egonw OK, but I see them here and there...
11:35 jonalv except if you really want to
11:35 jonalv then you may
11:35 shk3 really?
11:35 shk3 that's new for me
11:35 egonw jonalv: we really need unit tests...
11:35 jonalv but that is if you ned to call a manager method from within a job created from another manager method and want to use a subprogressmonitor for updating that...
11:35 egonw ok, so let's consider this method:
11:36 jonalv egonw: I thought we had unit tests...
11:36 egonw public List<IMolecule> download(List<Integer> cids);
11:36 egonw with jobs and progress monitoring that would look in the interface like:
11:36 egonw jonalv: not for the NWO yet
11:36 * shk3 is for lunch
11:36 jonalv shk3: et smaklig
11:37 jonalv (how do you spell that?)
11:37 egonw jonalv: well, you're the swedish dude here
11:37 jonalv egonw: was it that bad?
11:37 egonw I have no clue how to spell that in swedish
11:37 egonw oh
11:37 egonw you mean it is *not* swedish?
11:37 jonalv egonw: I wasn't aiming for swedish...
11:38 egonw hahahaha
11:38 egonw public BioclipseJob<IMolecule> download(List<Integer> cids, BioclipseJobUpdateHook<IMolecule> hook);
11:39 egonw is that right?
11:40 egonw or should the return type not be void here too?
11:41 jonalv egonw: uhm, I would go with returntype void here...
11:41 jonalv egonw: or no
11:41 jonalv you can off course return a BioclipseJob
11:41 jonalv sry I read wrong
11:42 egonw explanation?
11:42 jonalv egonw: olass wanted a BioclipseJob that he could join and wait for. (That solution is broken for other reasons though...) :(
11:43 egonw OK, will go for void now then...
11:43 egonw actually, I'll commit first without either...
11:43 jonalv egonw: I just hope it works with void there...
11:43 egonw so that olass can go ahead
11:43 olass egonw: thanks
11:43 * jonalv wonders why everything is broken...
11:44 * egonw is more interested in knowing why this did not trigger failing unit tests... ;)
11:47 jonalv that sounds like a good question
11:47 * jonalv is still wondering how to spell that btw...
12:01 CIA-63 bioclipse.core: jonalv master * r5eb7113 / plugins/net.bioclipse.core/src/net​/bioclipse/jobs/BioclipseJob.java : handle ugly case where the instance variable bioclipseManager might be null. This occurs with managers not built according to what is known as the Newest World Order... - http://bit.ly/yUTsZ
12:01 CIA-63 bioclipse.core: jonalv master * r9ce9544 / plugins/net.bioclipse.ui/src/net/bio​clipse/ui/jobs/CreateJobAdvice.java :
12:01 CIA-63 bioclipse.core: Handle exceptions from managers not in Newest World Order using the LogUtils.handleException method.
12:01 CIA-63 bioclipse.core: (Yes this means that Old World Order is going to swallow exceptions too but since I only know about Structuredb using this pattern still I think we can live with. At least for now...) - http://bit.ly/fQcCX
12:01 CIA-63 bioclipse.structuredb: jonalv master * rb49a466 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : layout - http://bit.ly/1YsvMR
12:01 CIA-63 bioclipse.structuredb: jonalv master * r7061422 / plugins/net.bioclipse.structuredb/src/​net/bioclipse/structuredb/internalbusi​ness/StructuredbInstanceManager.java :
12:01 CIA-63 bioclipse.structuredb: Removed method deleWithMolecules and just throw an exception "not yet Implemented" instead.
12:01 CIA-63 bioclipse.structuredb: Need to do this with one big (probably slow) SQL query instead. - http://bit.ly/j0BcO
12:10 jonalv olass, egonw: How much of your 300MB on GitHub are you guys using? We might have to start to pay for github some day...
12:10 egonw I'm around 300MB
12:11 olass hmm
12:11 olass 31.25MB / 300MB
12:11 olass sounds incorrect
12:11 jonalv I am at about 100
12:11 olass I think we'll do fine for a while longer
12:12 jonalv sounds like egonw mgiht not...
12:12 olass he could have 2 accounts
12:12 olass or priorotize things
12:12 egonw no, don't think that is allowed
12:12 olass well, up to you
12:12 egonw but we could consider buying a 'bioclipse' account
12:12 olass in time, yes
12:12 egonw when it becomes necessary
12:12 olass agreed
12:13 jonalv ho would that work and what would that do for good?
12:13 jonalv we don't all wanna be on the same Bioclipse account
12:13 jonalv then we loose track of who did what
12:13 olass jonalv: let's worry about that later
12:13 jonalv we loose the pullrequests
12:13 olass not now
12:13 jonalv :)
12:17 egonw OK, time to boot the pubchem manager
12:19 egonw > mol = cdk.fromString(pubchem.downloadAsString(176))
12:19 egonw CDKMolecule:C2H4O2
12:20 egonw > mol = pubchem.download(176)
12:20 egonw CDKMolecule:C2H4O2
12:20 olass jonalv, egonw: Jarl wanted to call our scripting language 'BSL'. He was quite firm on it. Is this OK with you?
12:21 egonw yes
12:21 olass good
12:21 egonw BC2.0 comes with BSL 1.0
12:21 olass Bioclipse Scripting Language
12:21 olass sounds good
12:21 olass BSL will change
12:21 egonw moreover, we'll have BSL in several languages
12:21 olass yes
12:21 egonw which we'll identify in detail as to as BSL-JS
12:22 egonw which we'll identify in detail as to as BSL-Groovy
12:22 olass sounds good
12:22 olass jonalv: agreed?
12:22 jonalv olass: you know what I think...
12:22 egonw and just BSL will refer to the JavaScript variant
12:22 olass jonalv: ?
12:22 egonw > mols = pubchem.download(pubchem.search("HIV"))
12:22 egonw [CDKMolecule:C17H31N3O4, CDKMolecule:C113H196N16O22S3,
12:22 egonw CDKMolecule:C111H183N19O23S3, CDKMolecule:C36H63N3O9,
12:22 egonw CDKMolecule:C205H277N107O49, CDKMolecule:C95H155N27O26S,
12:22 egonw CDKMolecule:C56H98N18O11S, CDKMolecule:C38H36F4N2O8, CDKMolecule:C38H36F4N2O8,
12:22 egonw CDKMolecule:C69H96N12O22, CDKMolecule:C34H50N4O6, CDKMolecule:C40H44N2O6,
12:22 egonw CDKMolecule:C64H114N10O14, CDKMolecule:C65H116N10O14,
12:22 olass nopaste!
12:22 egonw CDKMolecule:C259H408N70O84]
12:22 egonw olass: happy?
12:22 jonalv I don't like to call it a scripting language becasue it is not a language. It is an api
12:22 olass egonw++
12:23 olass egonw: help! jonalv is so not pragmatic
12:24 egonw jonalv: well... not entirely true, I think
12:24 egonw the managers are the API
12:24 jonalv egonw: explain yousrelf
12:24 egonw but the JS console converts this into a language
12:24 olass jonalv: OK if a calrify what we mean? It is a Domain Specific Language based on Javascript that we call BSL.
12:24 jonalv egonw: when we write in the JavaScript editor?
12:24 egonw jonalv: but you are correct that it does not define a new language
12:25 jonalv + we are going to enable other scripting languages except JavaScript to use the api
12:25 egonw jonalv: think of CML
12:25 olass hence BSL-JS
12:25 olass hence BSL-GROOVY
12:25 jonalv egonw: what about CML?
12:25 egonw jonalv: that also does not define a new language, not a new grammar
12:26 egonw jonalv: but just new words in that lamnguage
12:26 egonw likewise
12:26 egonw BSL defines new words in the JS/Groovy language
12:26 olass egonw++
12:26 egonw though not touching the grammar
12:26 jonalv I am not convinced
12:26 * olass is
12:26 * egonw is happy masak is not around :)
12:26 * olass too
12:26 egonw then again...
12:27 egonw he *might* agree with me too, instead of jonalv...
12:27 jonalv egonw: so you know that you are wrong but masak is not around to explain it for you...
12:27 egonw jonalv: I agree with you on a theoretical basis, but am happy with following customs in chem/bioinformatics
12:27 jonalv hence you keep pretending that you are not wrong...
12:27 olass well, if we just clarify what we mean with things then we should be OK. We can call things what we want, as long as we are clear what we define.
12:27 egonw jonalv: not sure I am really wrong...
12:28 egonw if two languages have the same grammar but have no word in common, are they the same?
12:28 * jonalv does not look forward to having to defend this decission every time he talks about this in the future
12:28 olass "BSL is a Domain Specific Language that extends Javascript with new commands in life science"
12:28 olass jonalv: ok?
12:28 egonw "BSL is a Domain Specific Language that extends existing scripting languages, such as JavaScript, with new commands in life science"
12:28 * jonalv feels like being in some Dilbert serie and being told by marketing what a language is although he knowd perfectly well what it really is...
12:28 olass egonw: I like your suggestion
12:28 egonw don't make fun of my pointy hair!
12:29 jonalv (and that is not what marketing tells him it is)
12:29 olass jonalv: so you agree with this last?
12:29 olass "BSL is a Domain Specific Language that extends existing scripting languages, such as JavaScript, with new commands in life science"
12:29 jonalv olass: what is it you think I agree with?
12:29 olass "BSL is a Domain Specific Language that extends existing scripting languages, such as JavaScript, with new commands in life science"
12:29 jonalv that sentence does not make sense
12:30 egonw fine, please suggest a fix
12:30 jonalv is _a_ language [...] that extends [...] _languages_
12:30 jonalv is it one lagunage or many langugaes? Make up your minds
12:30 olass [14:30] < egonw> fine, please suggest a fix < +1
12:30 olass jonalv: you just complain
12:31 olass be constructive
12:31 jonalv egonw: there is no fix becasuse the whole thing is based on the lie that we have created a new language
12:31 egonw extends <- sounds singular to me
12:31 olass jonalv: you just complain
12:31 olass be constructive
12:31 olass suggest something
12:31 jonalv okey call BAPI then
12:31 jonalv the Bioclipse API
12:31 olass absolutely not
12:31 jonalv that is what it is
12:31 * olass will probably ignore jonalv here
12:31 * jonalv is a very bad lier
12:32 olass egonw: glad to have your support
12:32 olass and Jarls
12:32 jonalv olass seems to be good at lieing however
12:32 jonalv lying
12:32 olass @slap jonalv
12:32 * zarah submits jonalv's email address to a dozen spam lists
12:32 jonalv *bah I can't spell)
12:32 egonw not sure if it is a DSL
12:32 egonw but more than happy to label our JS environemtn as BSL
12:32 jonalv egonw: what is a DSL?
12:32 olass masak and jonalv agreed to call it DSL
12:33 egonw http://en.wikipedia.org/wik​i/Domain-specific_language
12:33 zarah egonw's link is also http://tinyurl.com/3d9gng
12:33 olass last time we spoke
12:33 olass since DSL is so vague
12:33 jonalv egonw: that wikipedia oage does not cite any sources...
12:33 jonalv DSL is so vague that I would prefer to not use the word at all...
12:33 egonw at least 2!
12:33 olass jonalv: you agreed to it last time!!
12:33 olass you and masak!!
12:34 jonalv olass: yes we did
12:34 egonw and some 6 further reading
12:34 olass good. setlled.
12:34 jonalv olass: I still don't like this path though
12:34 egonw jonalv: is latex a langauge?
12:34 olass jonalv: noted
12:35 jonalv egonw: tex is a language. LaTeX is more of an extension to tex I think
12:35 egonw jonalv++
12:35 jonalv egonw: but I could be wrong
12:36 olass "Plugins can contribute functionality that is made available from a scripting language, for example Javascript. We call this BSL."
12:37 olass jonalv: better?
12:37 jonalv olass: yes except that I don't like the name BSL.
12:37 olass jonalv: I donät care
12:37 jonalv olass: I know
12:37 olass egonw: is this OK with you?
12:38 egonw guys... it's hot  inside...
12:38 egonw let's keep it cool here
12:38 olass egonw: is this OK with you?
12:38 egonw yes
12:38 olass good
12:38 olass settled
12:38 egonw BSL is also a nice title for a book
12:38 olass yes
12:39 olass in a few years...
12:39 olass generate the book from the manager docu + gists
12:39 * jonalv still think we are gonna run into trouble th day we add groovy or beanshell...
12:39 * olass thinks jonalv worries too much
12:39 jonalv olass: you might be right. I am the worrying kind...
12:40 olass we just adapt at that time, else we get nowhere
12:40 jonalv can't we just call it the Bioclipse libraries or something like that?
12:40 olass no
12:40 olass jonalv: stop now
12:40 olass it is settled
12:41 olass you agreed
12:41 olass leave it now
12:41 olass we need something we can advertize
12:41 jonalv olass: I won't leave this. I know that you have the final say but that doesn't stop me from sayingwhat I think or does it?
12:41 egonw and that reflects: 1. Bioclipse
12:41 egonw 2. Scripting
12:41 egonw 3. Something consistent and compact
12:42 olass jonalv: please...
12:42 olass we can go on forever then...
12:42 jonalv I am afraid so yes...
12:42 egonw olass: http://gist.github.com/163281
12:43 olass egonw: beautiful
12:43 jonalv egonw: that looks really nice
12:43 olass egonw++
12:44 olass egonw: one down
12:44 jonalv We should probably devlop some standards for how our managers should look.
12:44 jonalv method names and stuff
12:44 olass jonalv: indeed
12:44 olass soon we should have the meeting to organize/decisde BSL 2.0
12:44 olass BSL 1.0 is really undefined
12:45 jonalv so the question is will this be for Bioclispe 2.2 or later?
12:45 olass we'll see
12:46 egonw fuck
12:46 egonw forgot to rebase again
12:46 olass depends on if we need 2.2 out very soon or if it can wait a while
12:46 egonw another needless merge commit :(
12:46 olass egonw: relax
12:46 egonw ok, need to leave for some 15 minutes
12:46 olass jonalv does that all the time :)
12:46 jonalv I mean I know that masak is doing another naming shedule for the bioinformatics part of the API. ANd I am having trouble figureing out how to call my methods in StrucutreDB
12:47 olass jonalv: yes, I know the problem
12:47 egonw bbl
12:47 olass we need to harmonize things
12:47 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r01d116d / (3 files in 2 dirs): Extended the BSL with a few new pubchem.download() convenience methods (fixes #1461) - http://bit.ly/yhBmE
12:47 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * rfbb4780 / (5 files in 4 dirs): Merge branch 'master' of git@github.com:egonw/bioclipse.cheminformatics - http://bit.ly/5zewA
12:47 zarah bug #1461 | http://tinyurl.com/lfqffh
12:48 olass maybe we should schedule a day to start defining it quite soon
12:48 olass untile then: freedom!
12:55 jonalv olass: yes
12:56 olass we'll schedule a day that suits us all when people are back from holidays
13:08 jonalv shk3: around?
13:09 shk3 yes
13:09 shk3 always
13:09 shk3 well, almost always
13:09 jonalv shk3: did you create a dialog for picking a molecule somewhere in the workspace or have I dreamt that? :)
13:10 shk3 yes
13:10 shk3 mom
13:11 shk3 have a look at net.bioclipse.specmol
13:11 shk3 class net.bioclipse.specmol.wiza​rds.AddMoleculeWizardPage
13:11 shk3 it's a wizard page,
13:11 shk3 but it should be possible to make a dialog or whatever out of that.
13:11 jonalv shk3: ah, it seems that qsar has a wizard page like that as welll
13:11 shk3 sounds like a code duplication...
13:12 jonalv I was thinking that maybe we could use a gnereal standard dialog for just picking a molecule
13:12 shk3 sounds good
13:12 jonalv to avoid code duplication in this case at least...
13:12 shk3 yes
13:12 shk3 using the same wizardpage should not be a problem
13:12 shk3 given they do the same
13:12 shk3 of cours
13:12 jonalv shk3: yes it does sound like code duplication but I guess the qsar project and the specmol project are sort of working without talking to eachother about all they are doing...
13:13 shk3 it's a bit tricky to keep track of what's going on in general
13:13 jonalv yup :)
13:13 jonalv there is much going on :)
13:14 shk3 will you have a look?
13:14 shk3 am leaving soon and will not be here next week
13:14 shk3 I can't do it now
13:14 shk3 if you do not look at it, please file a bug report
13:14 jonalv shk3: look at what?
13:15 jonalv the code duplication?
13:15 shk3 yes
13:15 jonalv I can file a bug report...
13:15 shk3 plese do so
13:15 jonalv shk3: where can I find you code btw?
13:15 jonalv I could ha ve a look at it as well...
13:16 shk3 it's still in bioclipse svn
13:16 jonalv oh :(
13:16 shk3 I need to check out git,
13:16 shk3 make sure things work
13:16 shk3 and migrate
13:16 shk3 but there is so much to do
13:16 jonalv yup
13:16 jonalv know that feeling...
13:16 shk3 you may have heard of that situation
13:16 shk3 ah, you even had it yourself
13:17 shk3 then file the bug report and I will look at it
13:17 jonalv okey
13:17 shk3 your don't need to bother checking out stuff
13:17 shk3 oh, was that your question? the code duplication?
13:17 shk3 or were you actually looking for code to use yourself?
13:18 jonalv no I will file a bug for you to check if a common code can be used
13:18 jonalv I think olass might want to just ignore it though...
13:32 shk3 jonalv: which repository is the qsar plugin in?
13:32 jonalv bioclipse.qsar it's one of olass repos
13:34 shk3 ok
13:34 olass anyone called?
13:34 shk3 no
13:34 olass *pong*
13:35 olass ok
13:35 shk3 you were just mentioned
13:35 olass ok
13:35 * olass goes back into text editing mode
13:35 * jonalv is writing his first Dialog by hand
13:35 jonalv how can you people do this?
13:35 jonalv it's complicated stuff...
13:35 * olass has no problem with that
13:36 olass just do a grid layout
13:36 olass that is the key trick
13:36 * jonalv is copying pasteing and crossing his fingers...
13:54 jonalv Did edrins JavaScript edtior have a place of it's own?
13:59 shk3 egonw, olass: anybody can answer a few questions (one right now) on git checkout?
14:00 olass shk3: I am a novice, jonalv is probably better
14:00 olass but shoot
14:00 shk3 ok
14:00 shk3 jonalv
14:00 shk3 ok, so I checked out the core
14:00 shk3 some plugins have references to org.openscience.cdk plugins
14:01 shk3 is that ok?
14:01 shk3 for my understanding, core should not depend on that
14:01 jonalv shk3: aren't those plugins in core as well?
14:01 jonalv I think there are two or three org.openscience plguins in core
14:02 egonw two
14:02 egonw and that is fine
14:02 shk3 ah
14:02 shk3 that's in externals
14:02 egonw because they do not contain CDK specific code
14:02 shk3 ok, missed that
14:02 shk3 ah, 0 errors
14:03 shk3 now that looks promissing
14:03 shk3 clean and fast checkout
14:03 jonalv :)
14:04 shk3 I am trying "git clone http://github.com/egonw/bioclipse.cheminformatics"
14:04 zarah shk3's link is also http://tinyurl.com/nkbhqc
14:04 shk3 but get
14:04 shk3 Cannot get remote repository information.
14:04 shk3 Perhaps git-update-server-info needs to be run there?
14:04 shk3 anything wrong with that
14:04 shk3 ?
14:05 shk3 or must it be http://github.com/egonw/bio​clipse.cheminformatics.git?
14:05 zarah shk3's link is also http://tinyurl.com/krzfsy
14:05 shk3 ah, that's it
14:09 egonw shk3: yes, the grey box contains the Clone URLs
14:09 egonw check those
14:09 egonw shk3: BTW... there is also a Guides section on GitHub
14:09 egonw which I can very much recommend
14:10 egonw they are really good intros
14:10 sneumann joined #bioclipse
14:10 egonw the public clone for my bioclipse.cheminformatics is:
14:10 egonw git://github.com/egonw/bio​clipse.cheminformatics.git
14:11 egonw shk3: so, git:// instead of http://
14:11 egonw though git may be fine with either... never tried that
14:12 shk3 with http://, it's busy working for minutes and then giving up...
14:13 shk3 with git:// it's busy even longer, let's see if it gets a result in the end
14:22 jonalv can dialogs never be resized?
14:23 olass jonalv: pretty sure they can
14:24 jonalv olass: yea me tooo. BNut how do I make my dialog resiable? :)
14:24 olass @gg resize dialog swt
14:24 zarah olass: http://dev.eclipse.org/newslists/new​s.eclipse.platform.swt/msg30404.html
14:26 shk3 olass: the http://wiki.bioclipse.net/index.php?title=Instruc​tion_for_how_to_check_out_and_compile_Bioclipse_2 page
14:26 zarah shk3's link is also http://tinyurl.com/6nh6qk
14:26 shk3 still says bioclipse.product is in net.bioclipse.ui
14:26 shk3 this is wrong, isn't it?
14:26 olass yes
14:30 jonalv oh great, the dialog is resizable but the treeviewer insdie does not resize when I resize the dialog.
14:35 * jonalv is going to learn about the FormLayout. GridLayout seems to suck
14:36 jonalv (SWT and JFace book)++
14:40 CIA-63 bioclipse.cheminformatics: Arvid Berg master * ra1efb8b / (2 files in 2 dirs):
14:40 CIA-63 bioclipse.cheminformatics: Added check for if selection is null
14:40 CIA-63 bioclipse.cheminformatics: This code is exists in two places it should probably
14:40 CIA-63 bioclipse.cheminformatics: be reduced to only exist in one place.
14:40 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/ZLRPt
14:40 CIA-63 bioclipse.cheminformatics: Arvid Berg master * r28725e0 / cdk-externals/trunk/org.openscience.​cdk.controlbasic/src/org/openscience​/cdk/controller/ControllerHub.java :
14:40 CIA-63 bioclipse.cheminformatics: Commented out structureChanged() in setChemModel
14:40 CIA-63 bioclipse.cheminformatics: If there is need to get a event a new
14:40 CIA-63 bioclipse.cheminformatics: 'model changed' event should be added
14:40 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/2r1R9R
15:08 egonw wow!
15:08 egonw I canceled a javascript
15:09 egonw and am suggested to reboot Bioclipse??
15:19 jonalv egonw: yup
15:20 jonalv egonw: the JavaScript did no quit nicely within a time frame so we killed it for you. You go on runnign Bioclipse on your own responibility though becasue we have no idea what that Javacript was doing when we killed it...
15:20 egonw what's the time out?
15:21 egonw it was just downloading a file ...
15:26 olass @pz 1460
15:26 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1460
15:33 CIA-63 bioclipse.cheminformatics: egonw master * r14f8690 / cdk-externals/trunk/org.openscience.cdk.io/src​/org/openscience/cdk/io/cml/CMLCoreModule.java :
15:33 CIA-63 bioclipse.cheminformatics: Removed (too) early erasure of atom/bond data after storing data (see CDK bug #2817469)
15:33 CIA-63 bioclipse.cheminformatics: git-svn-id: https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@11614 fcb5ba71-d80d-0410-8237-ba3920747fcc - http://bit.ly/RyIGF
15:33 zarah bug #2817469 | http://tinyurl.com/mawweg
15:33 zarah bug #2817469 | http://tinyurl.com/lts4cx
15:40 egonw damn...
15:40 egonw I'm overflowing my URGENT .TOREPLY mail box
15:59 olass egonw: ping
15:59 egonw pong
15:59 olass cheminfo does not compile for me
15:59 egonw oh
16:00 olass abstractfiontmanager cannot be resolved
16:00 olass in ui.sdfeditor
16:00 olass a missing dep?
16:00 egonw did you add the new plugins?
16:00 olass will double check and refresh again
16:02 olass hmm
16:02 olass i cdk.jcp.view updated?
16:03 olass for me it complains on the import: import org.openscience.cdk.renderer.Renderer; etc
16:04 olass egonw: nope, does not compile
16:04 olass can you assist?
16:05 egonw I hope...
16:05 egonw please make sure you have in your workspace the plugin org.openscience.cdk.renderextra
16:06 olass yes
16:06 olass I have it
16:06 olass class: JChemPaintWidget
16:06 olass import org.openscience.cdk.renderer.Renderer; cannot be resolved
16:06 olass can you verify that this works with you?
16:07 olass egonw: ok, solved it
16:07 olass needed to do "clean"
16:07 olass why was that needed?
16:08 olass eclipse--
16:08 olass egonw: sorry to disturb
16:08 egonw ok, good
16:08 egonw need to eat pancakes now...
16:08 egonw bbl
16:08 olass egonw: about the script..
16:08 olass ok
16:08 olass cu later
16:08 * olass will be around
16:13 jonalv I am very close to gicing this up
16:13 jonalv |giving up
16:14 jonalv seems like you can't get a TitleAreaDialog resizable for real
16:23 CIA-63 bioclipse.structuredb: jonalv master * r9a57e5d / plugins/net.bioclipse.structuredb/s​rc/net/bioclipse/structuredb/dialog​s/CreateNewStructureDBDialog.java : removed unused imports - http://bit.ly/2jVln
16:23 CIA-63 bioclipse.structuredb: jonalv master * r88ae64b / (2 files in 2 dirs):
16:23 CIA-63 bioclipse.structuredb: started adding action for substructuresearch from the database view.
16:23 CIA-63 bioclipse.structuredb: It does not quite work yet but it's a start. Also we proabbly want the same functionality for Labels but there are no support for this in the manager yet. - http://bit.ly/BNdhv
16:45 jonalv -me gives up for today
18:00 olass egonw: ping
18:00 egonw pong
18:00 olass how are things?
18:01 egonw first test in the CDK seems to indicate that atom typing against implicit hydrogen count is no problem...
18:01 olass sounds good
18:01 * olass is working on exporting things
18:01 olass for devel release
18:03 egonw so, no clue on 1428 yet :(
18:03 egonw the incorrect hydrogen number
18:03 olass ack
18:05 egonw olass: the refs in the bioclipse app note do not have caps
18:05 egonw please add {} around the titles in the bibtex
18:05 egonw or can I?
18:05 olass well, I am using their style
18:06 egonw yeah, but this is not caused by the .bst
18:06 egonw but a bibtex thing
18:06 olass oh
18:06 olass ok so {} around the titles?
18:06 egonw I think you have:
18:06 olass I can do that
18:06 egonw title = "",
18:06 egonw etc
18:06 egonw make all into:
18:06 olass insted of?
18:06 egonw title = "{}",
18:06 olass ok
18:06 olass will do
18:07 egonw I will read it tonite
18:07 egonw and see if I have small comments
18:07 olass not true
18:07 olass Title = {Kalign--an accurate and fast multiple sequence alignment algorithm.},
18:07 olass I have {}
18:07 egonw then try adding the "'s
18:07 olass why care about this?
18:08 egonw because it now looks stupid
18:08 olass please explain
18:08 olass I think it looks good
18:09 egonw acronyms in lower case?
18:09 egonw no, that looks stupid
18:09 egonw and difficult to read
18:09 egonw because they look like words
18:09 egonw but are not
18:09 olass please explain
18:09 olass not all are acronyms
18:10 olass I downloaded the bibtex from pubmed and used it
18:10 egonw I'm not suggeting to convert everything in upper case
18:10 olass why bother changing it?
18:10 egonw because it looks stupid
18:10 egonw and you wrote it
18:10 olass nope
18:10 olass I did not
18:10 egonw so you're a crappy author
18:10 olass ??
18:10 egonw no one cares where you got your bibtex
18:11 olass so please explain how to fix it
18:11 egonw you wrote the paper
18:11 olass adding "" did not solve it
18:11 egonw where's the source?
18:11 olass I think this is their style
18:11 olass the source?
18:11 egonw svn right
18:11 egonw mom
18:11 olass nope
18:11 olass I can send it to you
18:12 olass if you like
18:12 olass mom
18:12 egonw please do
18:12 olass sent
18:13 egonw the whole thing, please
18:13 egonw cannot test with just a .bib
18:13 egonw and no .tex and style files
18:14 olass oh
18:14 olass I need to wrap all capital letters in {}
18:14 olass ok, I can do that
18:14 olass I did not understand you saying that
18:16 olass ok, I get it
18:16 olass you were thinking of Blue Obelisk for example
18:16 * olass is fixing things
18:17 egonw_ joined #bioclipse
18:17 egonw_ and I'm back
18:17 egonw_ olass: please see email
18:17 egonw_ it works for me
18:18 egonw_ trick seems to be:
18:18 egonw_ title = {{}}
18:18 egonw_ so, two brackets on both sides
18:18 olass ok
18:19 olass yes
18:19 olass I can confirm that works
18:19 olass would be nic ewith a regexp for this..
18:19 egonw_ lazy students nowadays....
18:19 olass :)
18:24 olass ok, fixed
18:24 olass will send you pdf to confirm
18:24 egonw_ thanx
18:28 egonw_ yeah, much better...
18:29 egonw_ being pedantic, I suggest EBI instead of Ebi now
18:29 egonw_ the request Chemistry Development Kit instead of the lower case one
18:29 egonw_ and Java instead of java
18:30 egonw_ btw, pubmed--
18:31 egonw_ ok, harry potter time
18:31 egonw_ bbl
18:31 egonw_ with new version numbers first
18:31 egonw_ does not seem 1428 will make the 2.1.0 release
19:42 olass egonw: did you see the updates to 1460?
19:43 egonw yes
19:43 egonw or did you make new ones?
19:43 olass well
19:43 olass not in 45 mins I guess
19:43 olass talking bout the versioning
19:44 egonw yes
20:10 CIA-63 bioclipse.core: Ola Spjuth master * r2335a9d / (18 files in 18 dirs): Updated version for 2.1.0 devel release. - http://bit.ly/rituq
20:14 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r42f2e2b / (17 files in 17 dirs): Updated version to 2.1.0.v20090807 - http://bit.ly/eIqdg
20:21 CIA-63 bioclipse.core: Ola Spjuth master * r368f6c1 / externals/org.openscience.cdk.a​nnotation/META-INF/MANIFEST.MF : set version to 1.3.0.0bioclipse2 - http://bit.ly/teG4B
20:22 egonw ah, right...
20:22 egonw cdk.annotation was not updated yet
20:22 egonw from 1.2 to 1.3
20:22 egonw but should not matter
20:22 egonw just two annotation classes
20:23 egonw olass: don't forget balloon
20:39 egonw olass: ping
20:39 egonw olass: that balloon line is not working either...
20:39 egonw expecting files
20:39 egonw right?
20:39 egonw are you working on that one?
20:44 olass have you pulled balloon?
20:44 egonw ah... sorry!
20:44 egonw damn
20:44 egonw still need to get used to the multiple repositories...
20:48 olass jonalv has a batch file for updating all
20:48 olass I think he put it on the wiki
20:48 olass I do it manually
20:48 egonw yeah, same here
20:48 egonw then I actually see what has happened...
20:48 egonw tired, I guess
20:49 egonw because my first thought should have been 'am I up to date'...
20:49 egonw it normally is...
20:49 egonw last nite I worked until 02:00 am
20:52 egonw running the unit tests
20:52 egonw testing subStructures()
20:57 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r548103d / (3 files in 2 dirs): Implemented subStructureMatches(List<ICDKMolecule>, ICDKMolecule subStructure) to return a list of matching molecules (implements #1462) - http://bit.ly/lCvso
21:05 olass egonw++
21:05 egonw WTF?!?
21:05 olass ?
21:05 egonw ChemSpider thinks the SMILES 'C1CNCC1' is pyrrole !
21:05 olass uhm..
21:06 olass when is the chemspider plugin coming for Bioclipse?
21:07 egonw yeah, good question
21:07 egonw last time I checked, you needed personal tokens to query via services...
21:10 olass well, royl chemistry in UK has taken over
21:10 olass maybe that imrpoves things
21:10 olass hear with duncan
21:10 olass they are pro openness afaiunderstand
21:11 olass how'd the gist coming along?
21:11 egonw getting there...
21:11 olass that bug 1428 is really nasty... makes me wonder if we have something serious broken in bioclipse..
21:11 olass what do you think?
21:11 olass is it minor?
21:12 olass I suppose it's not just the formula, and that it could affect other things
21:13 olass oh, so it's atom typing again?
21:13 * olass just read egonw's comment
21:14 egonw yes
21:14 egonw it's just in the feedback given
21:14 egonw which overcompensates for missing hydrogens
21:14 egonw the data is not affected, just the feedback bioclipse gives...
21:14 egonw should be fixed, though
21:14 olass oh ok
21:15 olass is it hard to fix?
21:15 olass can we get it in 2.1?
21:15 olass we have tomorrow on us as wel..
21:16 olass so is it the feedback you get in formula that is wrong?
21:16 * olass does not understand what egonw mean with 'bioclipse feedback'
21:18 egonw no, not easy to fix
21:18 egonw have not been able to find the exact cause yet
21:18 egonw yeah, formula feedback
21:19 egonw with cdk.molecularFormula()
21:19 egonw used by the props view
21:19 egonw and CDKMolecule.toString()
21:20 olass but no underlying chem affected?
21:20 olass please comment that in the bug
21:20 egonw correct
21:23 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r799a552 / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/ICDKManager.java : Fixed man page help: corrected type - http://bit.ly/10Sr9O
21:24 egonw olass: I'll assume the balloon command works
21:24 egonw leave that to you to check
21:25 egonw http://gist.github.com/163575
21:25 egonw feel free to remove line 5
21:26 egonw show integration with the BC ui
21:26 egonw ok, ok
21:26 egonw I removed that line
21:26 egonw check the first revision, if you like it
21:28 egonw leaving now
21:28 egonw cu tomorrow
21:37 olass bye

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