Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-05

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All times shown according to UTC.

Time Nick Message
07:02 olass joined #bioclipse
07:04 Gpox joined #bioclipse
07:45 masak joined #bioclipse
07:47 rojasm joined #bioclipse
07:50 CIA-40 bioclipse: ospjuth * r11055 /bioclipse2/trunk/plugins/n​et.bioclipse.ds/plugin.xml: Commented out DSPerspective from manifest since not yet implemented.
07:57 CIA-40 bioclipse: lc69 * r11056 /bioclipse2/trunk/plugins/net.biocli​pse.ds.signsig.bursi/src/net/bioclip​se/ds/signsig/bursi/SignSicHit.java: Changed the coloring to be red for positive predictions and green otherwise.
07:58 CIA-40 bioclipse: lc69 * r11057 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Added log statements to include the output of libsvm predictions.
07:59 zarah joined #bioclipse
08:03 olass hi
08:03 zarah ni hao olass
08:03 CIA-40 bioclipse: ospjuth * r11058 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Added exception for the case when ambiguous results in prediction and output these to TestsView.
08:09 shk3 joined #bioclipse
08:10 jonalv joined #bioclipse
08:11 shk3 hi jonalv
08:11 jonalv so pele is down_
08:11 shk3 are you alright up there in sweden?
08:11 jonalv ?
08:12 shk3 what was it yesterday?
08:12 masak shk3: yes.
08:12 shk3 earthquake?
08:12 shk3 flooding?
08:12 masak shk3: just a power outage.
08:12 shk3 hailstorms?
08:12 masak shk3: more likely general incompetence than weather.
08:12 masak it was raining, but not _that_ much.
08:12 shk3 glad to hear you survived
08:12 masak yeah.
08:13 masak people are squeamish though, going home just because there's no lighting and no net connection. :P
08:13 masak I remained for an hour or so, committing and surfing as usual. git++ Firefox++
08:14 jonalv masak: well call it what you want but without ne connection it's a bit hard to work...
08:14 shk3 yes. it really reminds you how dependant you are
08:15 Gpox How to use progress monitors http://henrik-eclipse.blogspot.com/20​09/05/progress-monitor-patterns.html
08:15 zarah Gpox's link is also http://tinyurl.com/r7nej6
08:15 jonalv hm a new one?
08:15 shk3 was the release done?
08:16 shk3 or was it a victim of power failure?
08:18 jonalv victim of power failure...
08:19 jonalv hard to make releases without net connection... :(
08:20 olass and a few last minute bugs
08:20 CIA-40 bioclipse: lc69 * r11059 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Changed the condition for the prediction ambiguity check.
08:20 shk3 ok
08:20 shk3 the speclipse update site is updated
08:21 shk3 I might redo this if necessary
08:23 olass RC1 release after lunch earliest
08:24 olass Gpox is working on important bugs until then
08:24 shk3 no problem
08:25 shk3 jonalv: you remember that "saveassd and open" problem?
08:25 jonalv shk3: not really no, remind me please
08:25 shk3 well, can't give you the bug number
08:25 shk3 if I save a file as sd file via manager
08:25 shk3 and then open it,
08:26 shk3 the save is done in background and open tries a non-existant or half empty file.
08:27 jonalv shk3: ah yes, there are a bunch of ways to solve this. We could go the Eclipse way and look the workspace during save. Or let the save method return a job which one can join. (not as good)
08:27 jonalv or only use BioclipseUIJobs
08:27 jonalv I think that probably the Eclipse way might be a good idea...
08:28 jonalv but I am not sure and maybe we should allow multiple variants?
08:28 shk3 can I use a bioclipseuijob?
08:28 jonalv shk3: I am not sure
08:28 shk3 the savesd method does not have one in icdkmanager
08:28 jonalv shk3: oh then I guess we could add one
08:34 jonalv shk3: which method seems to be the problem and is there a failing test?
08:35 shk3 well, the problem is, it's a bit erratic.
08:35 shk3 I try to find an example, mom
08:39 shk3 an example is tanimotoWizard l 113/114
08:39 shk3 sometimes the file opens correctly
08:39 shk3 sometimes it does not
08:39 shk3 but if I then close it and reopen it, it looks fine
08:39 shk3 my guess was this is because creation is done in background
08:39 shk3 can't see how to write a test for that
08:39 jonalv shk3: "l 113/114"?
08:40 shk3 because it's erratic
08:40 jonalv okey
08:40 shk3 and because the test can't test if the file looks ok on sdf editor
08:40 shk3 line 113 and line 114
08:40 jonalv ah
08:41 jonalv shk3: my TanimotoWizard file has 115 lines
08:42 jonalv shk3: l 113 is empty and 114 contains the clas closing }
08:42 shk3 updating...
08:42 shk3 it's the lines
08:42 shk3 cdkmanager.saveSDFile( sdfile, mols);
08:42 shk3 net.bioclipse.ui.business.Activa​tor.getDefault().getUIManager()
08:42 shk3 .open( sdfile );
08:42 shk3 anyway
08:44 jonalv shk3: yea BioclipseUIJObs should do the trick in that case
08:44 jonalv shk3: I will fix that
08:45 shk3 thanks
08:48 jonalv shk3: how do I testrun it? :)
08:49 shk3 choose a large number of molecule files, right click, choose tanimoto
08:49 shk3 choose compare molecule, go
08:50 jonalv works :)
08:51 jonalv shk3: was there a bug ticket number?
08:51 shk3 well, for me works sometimes
08:51 shk3 yes
08:51 * shk3 is going for coffee
08:51 shk3 will be back
08:51 jonalv shk3: no I amen I redid it with BioclispeUIJob and it work so hopefully it's fixed now
08:54 jonalv hey that ws easy. Anyone have more problems like that? :)
08:55 CIA-40 bioclipse: jonalv * r11060 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added method variant cdk.saveSDFile to ICDKManager that takes a BioclipseUIJob and made sure the TanimotoWizard uses it.
08:57 Gpox jonalv: you redid createSDFIndex to use IReturner, now I need  to call it from antoher method in the manager how should I do this? it is void now :(
08:57 jonalv Gpox: not sure I understand...
08:57 jonalv :)
08:58 Gpox in saveSDF i want to do SDFileIndex index = createSDFIndex(file,...) but this method is now void and takes an IReturner
08:58 jonalv Gpox: hm maybe the object should have a ref to it's proxy?
08:59 jonalv Gpox: you could use the IREturner but that is not very nice is it?
08:59 jonalv Gpox: what would you like to do?
08:59 jonalv or you could refactor out the code into a private method that both those two methods calls. That's probably the best solution
09:04 Gpox if i call a method with BioclipseUIJob or IReturner and it don't implement IReturner in the manager but it take a progress monitor it shoulb probably run as a job and fix ther return stuff.
09:05 jonalv Gpox: huh?
09:05 jonalv Gpox: that sounds complicated...
09:06 Gpox just an idea
09:06 * jonalv smiles and nods (always a good thing to do when you ahve no idea what someone just said)
09:07 jonalv Gpox: is it still the same problem? What was wrong with making an internal pricate method in the manager and just call it? The createSDFIndex method only does complete returns and not partial returns right?
09:07 masak jonalv: not always a good idea, no. :/
09:08 Gpox Object managerMethod(...,IProgressMonitor)  could be called with mangagetMethod(..., BioclipseUIJob) managerMethod(..., IReturner)
09:08 jonalv masak: probably better than loking angry and shaking the head...
09:08 Gpox yes i am doing it that way right now
09:08 masak well, that is the better response in some cases...
09:09 masak jonalv: you could shake your fist as well, for emphasis.
09:09 * jonalv angirly shakes his head (and fist as well (for emphasis))
09:09 jonalv LOL
09:10 Gpox Well i got a bug pending pelezilla's return about code examples for how you should do things
09:10 jonalv Gpox: yes that it a good idea...
09:11 Gpox right now my head hurts trying to figure out how the different interface -> manager transformations work
09:12 jonalv hm that is a problem yes. I was only trying to help...
09:14 jonalv Gpox: did you solve it?
09:15 Gpox yes using a private method and warping that in the IReturner one
09:15 jonalv okey good
09:17 shk3 jonalv: you fixed it? great!
09:17 jonalv shk3: anyhting else? :)
09:17 shk3 yes
09:17 jonalv o
09:17 shk3 tanimoto calculation in background
09:17 shk3 i tried it, but get wrong number of arguments
09:17 shk3 if you have time, i could commit that
09:17 shk3 and you could have a look
09:18 jonalv shk3: okey
09:18 CIA-40 bioclipse: ospjuth * r11061 /bioclipse2/trunk/plugins/​net.bioclipse.ds.dblookup/ (3 files in 2 dirs): Implemented NearestNeighbourTest and added check for required properties calculated on initialization of SDFmodel.
09:20 CIA-40 bioclipse: shk3 * r11062 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): tried to make tanimoto calculation using bioclipseuijob, but jonalv needs to look at it
09:21 jonalv so shk3 how do I test this one?
09:21 shk3 mom
09:21 shk3 conflict in tanimotowizard
09:23 shk3 ok, committed new tanimotowizard
09:23 CIA-40 bioclipse: shk3 * r11063 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/wizards/TanimotoWizard.java: tried to make tanimoto calculation using bioclipseuijob, but jonalv needs to look at it
09:23 shk3 there is now a bioclipseuijob in a bioclipseuijob
09:23 shk3 not sure about that
09:24 jonalv shk3: huh? :)
09:24 jonalv what does tht mean?
09:24 shk3 well, the calcuation is supposed to run as a job
09:24 shk3 (egonw filed bug report it blocks ui, which is right)
09:24 shk3 and this needs to trigger creation of sdfile, which needs to be in a job
09:24 shk3 or so
09:24 shk3 have a look
09:25 shk3 i did the "tanimoto in background" try before your fix for the sdfile saving
09:25 shk3 perhaps we should have done it together
09:25 shk3 but I suggest you have a look
09:25 jonalv shk3: how does it fail? Can I test run?
09:25 shk3 as before
09:26 shk3 choose mos, right click, tanimoto
09:26 shk3 mos=mols
09:27 jonalv not sure I understand what you ahve done...
09:29 shk3 sorry
09:29 jonalv hm never thougth of this but it would be nice if ot worked. I wonder what foes wrong...
09:29 jonalv |goes
09:29 shk3 there was a bug "tanimoto calculation blocks ui"
09:30 shk3 i thought a bioclipseuijob would be the solution
09:30 shk3 so i changed cdkmanager to be able to execute the calculateTanimoto method with a bioclipseuijob
09:30 shk3 once this method is finished, it needs to save to sdf and open the sdf
09:31 jonalv aha, well sounds reasonable
09:31 jonalv why does it fail then? :)
09:31 jonalv hm...
09:31 shk3 so the savesdf/open need to be in runInUI of calculateTanimoto
09:32 shk3 so you think my reasoning was reasonable?
09:33 jonalv shk3: yes
09:33 * jonalv is debugging now...
09:33 shk3 good
09:33 shk3 i get a wrong number of arguments
09:33 shk3 when calling calculateTanimoto
09:34 shk3 is that the error you get as well?
09:34 jonalv shk3: yes
09:34 jonalv it's missing the Ireturner for some reason
09:39 jonalv shk3: hm seems this situation has never been tested...
09:39 jonalv shk3++ seems to ahve found another corder case in the dispatcher
09:40 shk3 I got the wrong number of arguments also without your fix for "save and open"
09:40 shk3 so this is not related
09:40 shk3 (in case this wasn't clear)
09:41 jonalv shk3: no it seems the JavamanagermethodDispatcher does not handle Ireturners when executing in same thread. It's strage that it has gone unnoticed this long
09:41 jonalv but I guess all use cases has been jobs
09:41 jonalv I do wonder why this is run in the same thread though...
09:42 * shk3 is happy he could help with pointing out problems
09:42 jonalv shk3: the calculateTanimotot method returns a list
09:42 jonalv so maybe fix that instead of the error? :)
09:43 jonalv if I only could file bugs...
09:43 jonalv :(
09:44 shk3 i am confused
09:44 shk3 it needs to return a list
09:44 shk3 since there's a value for every input
09:44 shk3 no?
09:44 jonalv shk3: no that's what the IReturner is for...
09:44 jonalv or?
09:44 ilogger2 joined #bioclipse
09:45 * jonalv is gonna try andd get this to work first and then see how t make it run as a job
09:45 shk3 ah ok
09:47 shk3 so the method in the manager implementation needs to be void
09:47 shk3 and use
09:47 shk3 returner.completeReturn(mols)
09:47 shk3 for returning result?
09:52 jonalv shk3: yes...
09:52 shk3 ok
09:52 shk3 sorry for getting this wrong
09:53 jonalv no problem, I am gonna fix it.
09:53 jonalv shk3: Now that you know how to do things and what the pittfalls are, maybe you could write a little tutoprial on the wiki? For me everything is sort of obvious since I wrote it...
09:54 shk3 i could have a look at your "how to write a manager 2" document
09:54 shk3 I think this would be the place to have it?
09:56 jonalv shk3: yes
09:57 shk3 ok
09:57 shk3 i will try
09:58 shk3 should I add a new section like 1.1.7?
09:58 shk3 or somewhere else?
09:59 jonalv shk3: I don't know. Do waht you feel the best. trust the anarchy!
10:00 shk3 ok
10:00 shk3 do youdo the fix of the tanimoto method?
10:04 jonalv shk3: commiting now
10:05 shk3 ok
10:05 CIA-40 bioclipse: shk3 * r11064 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src​/net/bioclipse/seneca/editor/SenecaJobEditor.java: saving as sdf and opening is done using bioclipseuijob
10:06 CIA-40 bioclipse: jonalv * r11065 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java:
10:06 CIA-40 bioclipse: Made the JavaManagerMethodDispatcher handle returners when doing in same thread
10:06 CIA-40 bioclipse: excution. It's a strange corner case that shouldn't be used but nevertheless
10:06 CIA-40 bioclipse: it's evil to get an exception complaining about wrong number of paramaters much
10:06 CIA-40 bioclipse: better that it does what it's been told to do even if that is strange...
10:07 CIA-40 bioclipse: jonalv * r11066 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: calculateTanimoto takes an Ireturner so it should be void and return using the returner...
10:07 jonalv shk3: please test run now
10:09 shk3 great
10:09 shk3 jonalv++
10:14 * jonalv @ lunch
10:25 CIA-40 bioclipse: goglepox * r11067 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (3 files in 2 dirs):
10:25 CIA-40 bioclipse: Fixed saveSDF
10:25 CIA-40 bioclipse: saveSDF now succesfully save and renames the file.
10:25 CIA-40 bioclipse: Solves bug #1162, #1157
10:25 zarah bug #1162 | http://tinyurl.com/p75z32
10:29 olass Gpox++
10:31 olass to anyone:
10:31 olass any more commits that should go in RC1?
10:31 * olass will have lunch now and hopes all commits are made when he gets back
10:50 stain are you going for code freeze?
10:54 shk3 no
10:54 shk3 feature freeze
10:56 olass stain: it will be an RC1 which is forced due to political reasons
10:56 olass there will definitely be a RC2
10:57 olass but we need beta testers input
10:58 olass "release often"
11:02 stain mm
11:03 stain we have also got these lovely political reasons :-)
11:03 stain we want to release Taverna often, but we wanted to get it to a proper shape before we shipped what we called now beta 1
11:03 stain which meant we had internal release candidates of beta 1.. very confusing!
11:22 sneumann hey stain, you're one one of those taverna guys ?! Cool.
11:24 olass stain: I know exactly what you mean!
11:25 olass so this RC1 is sort of a pseudo-internal RC1
11:25 olass nevertheless, I will now build it
11:25 olass but first: a last update...
11:25 olass and coffee
11:35 CIA-40 bioclipse: ospjuth * r11068 /bioclipse2/trunk/features/net.bi​oclipse.sdk_feature/feature.xml: Updated copyright/license and version for RC1 of SDK feature.
12:05 rojas1 joined #bioclipse
12:10 shk3 jonalv: I had a go at the tutorial
12:10 jonalv shk3: okey cool
12:10 jonalv I will have a look
12:11 jonalv shk3: where is it?
12:11 shk3 How to make a manager 2
12:11 shk3 1.1.7
12:11 shk3 and 1.2.1
12:12 jonalv okey
12:12 shk3 the separation of 1.1
12:12 shk3 and 1.2 might be a bit artificial
12:12 shk3 not sure if 1.2 makes sense
12:12 shk3 or if it is better to integrate it into 1.1
12:12 jonalv aha yea that might be actually
12:13 jonalv but then again...
12:13 shk3 as I said, I am not sure
12:13 jonalv the interface and the class is two quite seperate hings for these managers
12:14 shk3 yes
12:14 shk3 indeed
12:16 jonalv this looks like a good addition
12:17 shk3 glad to hear that
12:19 shk3 have you time for another short question?
12:19 jonalv shk3: yes
12:19 shk3 btw, what about pele?
12:19 shk3 but the real question was:
12:19 shk3 egonw changed the spectrum manager to nwo
12:19 jonalv I am consdiering what to do with structuredb. Moving it into NWO is not trivial... :/
12:19 shk3 I am trying to adopt the tests to nwo
12:20 jonalv shk3: okey
12:20 shk3 now I saw that the manager as well as the interface have a loadSpectrum(IFile, IProgrssMonitor) method
12:20 shk3 which one of these do we need/should be there?
12:22 jonalv unless no other manager calls this method and want's to hand over an sub progressmonitor then the interface don't need to have a method taking a progressMonitor...
12:22 shk3 ok
12:23 shk3 and the implementation?
12:23 shk3 only with monitor, i believe?
12:24 jonalv shk3: yea that should be enough
12:24 jonalv unless something specially strange is going on there...
12:25 shk3 no, shouldn't
12:25 shk3 pretty standard
12:25 olass joined #bioclipse
12:26 olass eclipse is not behaving good today
12:36 jonalv hm net.bioclipse.services contains a servcies maanger which is never published as fa as I can see...
12:36 jonalv author olas, olass do you know anything about what condition it is in?
12:36 olass jonalv: in what feature is the services plugin in?
12:36 jonalv olass: structuredb
12:36 olass no idea
12:37 olass ok, so not in release
12:37 jonalv nope not yet :)
12:37 * olass will ignore it then
12:37 jonalv olass: I thought you were just waiting for Bioclipse to buiold an had tiem to answer some questions in the mean time..
12:37 jonalv hm "mean time"
12:38 jonalv why is it mean?
12:38 jonalv masak: any ideas? :)
12:38 olass nope
12:38 olass cruel time?
12:39 masak jonalv: 'mean' has a meaning 'middle', as in 'the mean value'. then it's easy to see why 'in the meantime' can mean 'between two given endpoints'.
12:39 masak that's a theory, at least. checking...
12:40 jonalv masak: sounds like a good theroy
12:40 masak jonalv: yup: [Middle English mene, middle, from Old French meien, from Latin mediānus, from medius; see  medhyo- in Indo-European roots.]
12:41 jonalv masak: oki
12:41 jonalv cool
12:43 jonalv uhm no it actually seems that hte services manager get's published
12:43 jonalv I wonder what it does :)
13:28 CIA-40 bioclipse: shk3 * r11069 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum.test/ (12 files in 3 dirs): updated spectrum tests to nwo
13:36 shk3 ah pele is back
13:36 shk3 uppsala++
13:36 CIA-40 bioclipse: shk3 * r11070 /bioclipse2/trunk/plugins/net.bioclipse.spe​ctrum/src/net/bioclipse/spectrum/business/ (ISpectrumManager.java SpectrumManager.java): removed methods which are no longer neede in nwo
14:26 shk3 jonalv: one more question?
14:26 jonalv shk3: yes?
14:26 shk3 i want to make the generate3dCoordinates method use an bioclipseuijob
14:26 shk3 now there are two of these, one calls the other.
14:27 shk3 how can I do this with bioclipseuijob?
14:27 shk3 simply pass on the returner?
14:27 jonalv shk3: what's the difference between them? I guess you could pass the returner...
14:28 shk3 one calculates for a list,
14:28 shk3 the other for one molecule
14:28 shk3 (by making a list and calling the other method)
14:33 edrin joined #bioclipse
14:35 edrin hi
14:37 shk3 hi
14:39 shk3 jonalv: what do you think?
14:40 * jonalv backlogs
14:41 jonalv shk3: ah, well I think it might be worth a try to pass on the returner but better is probably to like I told Gpox earlier today and refactor out a pricate method that both calls
14:42 jonalv that private method would return the old classic way...
14:42 shk3 i can do that
14:42 shk3 no problem
14:42 jonalv shk3: there are no partialreturns involved in this are there?
14:42 shk3 if you say this is the way to go
14:42 shk3 no
14:42 shk3 I wanted to get my bugs done first
14:42 shk3 then I will try partial return with seneca
14:42 jonalv shk3: It's the best solution I have come up with so far
14:42 shk3 (another thing i will bother you with)
14:43 shk3 ok, will do that
14:57 olass http://sourceforge.net/project/show​files.php?group_id=150681&packa​ge_id=286282&release_id=687593
14:57 olass please try
14:59 jonalv olass: well it seems to start at least :)
15:03 olass soudns good
15:03 olass shk3: please try you too
15:04 shk3 trying
15:04 shk3 btw, is update working from beta5 to rc1?
15:06 olass no
15:06 olass I am building the new update site now
15:07 olass and blogging :)
15:13 CIA-40 bioclipse: jonalv * r11071 /bioclipse2/trunk/ (16 files in 9 dirs): Attempt of getting rid of net.bioclipse.services from Structuredb feature. Create net.bioclipse.databases to containd the Databases view from the services plugin but it's not working at all yet... :(
15:13 jonalv olass: maybe you could help me iwth that next week?
15:15 olass sure
15:16 * jonalv thinks he might take weekend real-soon-now™
15:16 shk3 looks good
15:16 shk3 weekend? you disappoint me
15:18 jonalv :)
15:20 olass jonalv: try the update site
15:20 olass the experimental is not ready yet
15:20 olass still uploading
15:21 jonalv olass: oki
15:21 olass but the update2 can be tested
15:22 jonalv Network connection problems encountered during search.
15:22 jonalv Unable to access "http://update2.bioclipse.net".
15:22 jonalv Unable to access site: "http://update2.bioclipse.net" [Server returned HTTP response code: "404 Not Found" for URL: http://update2.bioclipse.net.]
15:22 jonalv Server returned HTTP response code: "404 Not Found" for URL: http://update2.bioclipse.net.
15:22 jonalv Unable to access site: "http://update2.bioclipse.net" [Server returned HTTP response code: "404 Not Found" for URL: http://update2.bioclipse.net.]
15:22 jonalv Server returned HTTP response code: "404 Not Found" for URL: http://update2.bioclipse.net.
15:22 jonalv
15:24 jonalv olass: I'z thinking is not working
15:24 jonalv anyone else?
15:24 olass ?
15:24 olass L'z ?
15:24 olass what is that?
15:24 jonalv I is
15:24 jonalv :)
15:24 jonalv lolspeal
15:24 olass ?
15:24 jonalv lolspeak
15:24 olass ?
15:24 jonalv nvm
15:24 olass english bitte
15:25 jonalv "bitte"? What is that?
15:25 jonalv olass: does it work 4 u?
15:26 olass let's wait until update2-experimental is finished
15:26 olass ah
15:26 olass try again
15:26 olass spelling error
15:26 olass my fault
15:27 jonalv better now
15:27 jonalv wow many things to download. what do I choose?
15:27 olass all?
15:28 jonalv hm oki the workshop tutorial needs qsar but I guess that's fine?
15:29 jonalv this is fun :)
15:31 olass ok, you can test experimental now
15:31 olass which contains the QSAR feature
15:32 * jonalv is still downloading the standard stuffs :)
15:32 olass jonalv: could you tag SVN for RC1?
15:32 olass 2.0.0.RC1
15:32 jonalv olass: I think that;s too late...
15:32 olass I don't know how to do that
15:32 olass no
15:32 olass never too late
15:33 olass please do
15:33 jonalv olass: okey what version shuld I tag?
15:33 olass 2.0.0.RC1
15:33 * jonalv is not sure about how to do it but how hard could it be?
15:33 olass thanks
15:33 jonalv olass: no which revision?
15:33 olass head
15:33 jonalv olass: but we have commited after you buildt I think..;
15:33 jonalv what rev did you build?
15:33 olass jonalv: please
15:33 olass tag head
15:34 olass it doesnät matter
15:34 olass the last commits are speclipse anyway
15:34 jonalv olass: uhm okey if you say so...
15:34 olass I say so
15:34 jonalv olass: and structuredb...
15:34 olass so?
15:35 * olass is trying to produce a nice screenshot for the release blog post
15:37 CIA-40 bioclipse: jonalv * r11072 /bioclipse2/tags/2.0.0.RC1/: made tag for 2.0.0.RC1
15:38 jonalv hm that was actually quite easy :)
15:49 jonalv olass: hm QSAR is not working... :(
15:49 olass ok, not tested that
15:49 olass what error do you get?
15:49 olass pastebin?
15:51 jonalv olass: http://gist.github.com/124340
15:52 olass hmm
15:52 olass yes, should have birt in another branch since it does not work anyway
15:52 olass will try to sort that out
15:52 olass thanks for spotting it
15:52 olass any other tings you stumble upon?
15:53 jonalv olass: no really
15:53 olass :)
15:53 jonalv |not
15:53 jonalv olass: I will fail bugs when I find em
15:53 jonalv |file
15:53 jonalv hag
15:53 jonalv |gah!
15:53 jonalv gah!
15:58 olass jonalv: had you installed the XML feature before trying the QSAR feature?
15:59 jonalv olass: no I tried em all at the same time
16:00 olass ok
16:00 jonalv uhm or xml which update site is that on?
16:03 olass no worries
16:03 olass I am sorting this error out
16:03 jonalv olass: what does the Generates view do?
16:03 olass oh
16:03 jonalv |Generators
16:03 olass that should have been removed :(
16:03 olass Gpox doing
16:03 olass damn
16:03 jonalv okey...
16:12 * jonalv gives up for today
16:18 edrin left #bioclipse
16:48 CIA-40 bioclipse: ospjuth * r11073 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Added dependencies for QSAR project on update site.
17:13 shk3 olass: do you know Gerard Kleywegt?
17:13 olass not really
17:13 olass he used to be here at BMC
17:13 olass but I think he moved to EBI
17:13 shk3 right
17:13 shk3 just read that
17:14 shk3 so I was curious
17:14 shk3 do you know anything about exceptions in nwo?
17:14 shk3 I want to catch an exception thrown in a manager method, but this seems not to work any longer
17:46 * shk3 is heading home
17:50 CIA-40 bioclipse: shk3 * r11074 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): this re-introduces explicit handling of NoSuchAtomException in modelbuilder3d, which was lost due to 1.2.x update.
18:45 edrin joined #bioclipse
18:45 edrin hi
18:59 sneumann_ joined #bioclipse
19:40 edrin olass still online?
19:40 olass sort of
19:40 olass and you?
19:41 edrin yeah
19:41 olass obviously ;)
19:41 edrin ;)
19:41 edrin working
21:02 zarah joined #bioclipse

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