Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-09-19

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Time Nick Message
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07:48 olas morning everyone
07:48 jonalv morning
07:49 olas jonalv: forgot my security card today
07:49 olas fyi
07:49 jonalv oops
07:49 jonalv :)
08:41 jonalv joined #bioclipse
09:17 CIA-31 bioclipse: jonalv * r3773 /trunk/playground/plugins/ (7 files in 5 dirs):
09:17 CIA-31 bioclipse: The hsqldb server currently starts from the structuredb Activator and shuts down
09:17 CIA-31 bioclipse: from the stop method in the hsqldb Activator class. It probably won't be started
09:17 CIA-31 bioclipse: always when the strucutredb plugin is run but rather the structuredb plugin (and
09:17 CIA-31 bioclipse: any other plugins needing it) should start it when needed.
09:40 jonalv How do I callate smiles, smarts and fingerprints from an AtomContainer? It can't be too difficult?
09:40 jonalv s/callate/calculate
09:46 jonalv ping
10:03 CIA-31 bioclipse: jonalv * r3774 /trunk/playground/plugins/​net.bioclipse.structuredb/ (12 files in 8 dirs): Created domain objects. No references among them implemented yet.
10:04 EskilA joined #bioclipse
11:17 CIA-31 bioclipse: biocoder * r3775 /trunk/playground/plugins/net.bi​oclipse.chart/src/net/bioclipse/ (chart/ChartUtils.java plugins/views/ChartView.java): Added time series and code comments
12:23 CIA-31 bioclipse: biocoder * r3776 /trunk/playground/plugins/n​et.bioclipse.chart.testing/ (5 files in 2 dirs): The chart testing plugin can now test line plot, scatter plot, histogram and time series using sample data
12:36 rojasm joined #bioclipse
12:58 * olas is afk
13:01 CIA-31 bioclipse: jonalv * r3777 /trunk/playground/plugins/​net.bioclipse.structuredb/ (13 files in 7 dirs): created test cases for the domain class structure
13:02 jonalv egonw, You are good at loading files from the classpath aren't you? I can't get it to work... Do you think you could help me?
13:04 egonw did you try the code the CDK JUnit tests are using?
13:05 jonalv yes I did exactly like that
13:05 egonw did you include the files you want to load in the classpath at bin distrib and runtime?
13:05 jonalv At least I tried doing exactly like that... :/
13:05 jonalv yes runtime and bin build...
13:07 jonalv If you have the time maybe you could check out net.bioclipse.structuredb in playground and test running the tests. Then it will become obvious what isn't working...
13:07 egonw :)
13:07 egonw mom
13:08 jonalv more exactly the StructureTest
13:08 jonalv (which is the only test so far...)
13:10 egonw getting that plugin from svn now
13:13 egonw jonalv: please make sure to include copyright headers in all files you upload
13:13 jonalv egonw, copyright header? Interesting is there a wiki page where I can read more?
13:14 egonw just check any source file in net.bioclipse
13:14 jonalv ack
13:16 CIA-31 bioclipse: egonw * r3778 /trunk/playground/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: Fixed pointer to the HSQLDB plugin.
13:18 egonw jonalv: what's up with the HSQLDB stuff?
13:18 egonw you import HsqldbUtil...
13:18 egonw but that's not in net.bioclipse.database.hsqldb...
13:18 jonalv it is not?
13:19 jonalv net.bioclipse.hsqldb contains two classes Avtivator and HsqldbUtils. right?
13:20 egonw there is no such thing as net.bioclipse.hsqldb
13:20 egonw there is net.bioclipse.database.hsqldb
13:20 jonalv öööö hum wait
13:21 jonalv there is such a thing as net.bioclipse.database.hsqld?
13:21 egonw yes
13:21 egonw in trunk/plugins
13:21 jonalv then I probably shouldn't go creating a new plugin net.bioclipse.hsqldb
13:21 egonw correct
13:21 jonalv Didn't olas now about his?
13:21 egonw no idea
13:21 egonw he should have
13:21 jonalv me neither
13:21 egonw I demoed it when he was at CUBIC :)
13:21 jonalv Do you know what that plugin does?
13:22 jonalv you demoed it? Well you probably know...
13:22 jonalv :)
13:22 egonw demoed -> talked in a presentation about it
13:22 jonalv I mean if you demoed it than you know what it does
13:22 egonw HSQLDB is a backend for Hibernate
13:22 egonw (as any SQL db can be)
13:23 jonalv Well but that plugin doesn't have anything to do with Hibernate?
13:23 jonalv Does it start a hsqldb instance when needed and stop it when bioclipse is closed? Becasue that is what net.bioclipse.hsqldb does (which is in playground btw)
13:24 egonw yes, exactly
13:24 jonalv If it can do that that it is what I need.
13:24 egonw not sure if what Tobias wrote is using this backend
13:24 jonalv Who wrote this backend?
13:25 egonw I started that plugin, but Tobias might have hacked in it too...
13:25 egonw jonalv: email Tobias and ask for his PhD thesis...
13:25 egonw it should all described in that
13:25 jonalv okey so I will switch to using it instead
13:25 jonalv But if you could have a look at those tests I would be happy
13:25 egonw yes, once you fixed compilation
13:26 jonalv compilation of what exactly?
13:26 jonalv it compiles for me so I am somewhat at a loss...
13:28 jonalv egonw, does net.bioclipse.database.hsqld really do anything more but incapsulate hsqldb.jar?
13:28 egonw well, one thing is that net.bioclipse.hsqldb does not exist...
13:28 egonw jonalv: no
13:29 egonw so, you should upload those two classes into that plugin
13:29 jonalv and it contains a hibernate config file
13:29 jonalv That shouldn't be there
13:29 egonw sort of yes...
13:29 jonalv I want to use the database but not Hibernate
13:29 olas egonw: never seen the DB plugin in action
13:29 olas it doesn't work here at least
13:29 egonw olas: read Tobias' thesis
13:29 olas and since tobias is not around anymore
13:30 olas and we decided to skip hibernate
13:30 olas then it will require som additions
13:30 olas BUT
13:30 jonalv Should I simply move in and take over the net.bioclipse.database.hsqldb plugin instead of creating a new net.bioclipse.hsqldb?
13:30 olas in order not to screw up tobias stuff, I think it would be better with a new
13:30 olas if it relies on hibernate
13:30 olas (and I think it does)
13:30 olas but feel free to look into it
13:31 olas in fact, it would be good to clean it out if it's not working
13:31 olas I think it's quite unstable
13:31 olas with no docs
13:31 jonalv It doesn't look as if it does anything accept contain the hsqldb.jar file
13:31 olas then it's useless, stick with your impl
13:31 egonw there is a full thesis chapter about it!
13:31 jonalv and a Hibernate.cfg.xml_old file
13:31 egonw is that not docs enough?
13:32 olas where is this info?
13:32 olas URL please
13:32 olas and put the URL on the wiki
13:32 egonw olas: ask christoph
13:32 egonw anyway...
13:32 olas you see
13:32 olas there is no info
13:32 egonw jonalv's code does not compile here...
13:32 olas no?
13:32 egonw and he's writing a duplicate plugin
13:32 olas not duplicate
13:32 olas with ibatis instead of hibernate
13:32 egonw right
13:33 olas that's a BIG difference
13:33 egonw but that's not what is currently is
13:33 egonw it's now using hsqldb
13:33 olas but the jar itself is the same
13:33 olas ibatis is an ORM not a DB
13:33 jonalv The thing is that both plugins should use the same hsqldb.jar and probably comming from the same plugin
13:33 olas yes
13:33 olas agreed
13:33 olas but the jar is the only thing that can be shared, and possibly som preference page for the HSQLDB instance
13:34 jonalv egonw, could you be a bit more specific as to in what way the code doesn't compile?
13:34 olas or is it more, egonw?
13:34 olas it did compile here when I tried it...
13:34 egonw jonalv: again, net.bioclipse.hsqldb does not exist
13:34 egonw that's the compile error
13:34 olas ??
13:34 jonalv It can be checked out from playground
13:34 egonw jonalv: create a org.hsqldb plugin
13:34 egonw with just the jar
13:35 olas no
13:35 egonw and make net.bioclipse.database.hsqldb depend on that
13:35 olas we need a preference page too
13:35 egonw olas: then that goes into whatever...
13:35 egonw other plugin
13:35 olas why?
13:35 olas why do we need so many plugins?
13:35 olas If we want to use HSQLDB, we probably want a preference page for it, right?
13:36 jonalv That seems strange because it would be a prefrence page for hsqldb and not for what ever other plugins that would like to use it
13:36 olas agreed
13:36 egonw [15:35:45] <olas> why do we need so many plugins?
13:36 egonw that's the eclipse approach
13:37 olas not really
13:37 jonalv egonw, btw:  you shouldn't need hsqld to run the JUnit test StructureTest which I needed help with.
13:37 olas not TOO many plugins
13:37 egonw no, dependencies
13:37 olas and why split the jar and the preference page in two plugins?
13:37 egonw net.bioclipse.database.hsqldb does not need that pref page...
13:37 olas what possible use would that be?
13:37 olas maybe it should use it
13:38 olas because the user might want to set temporary spaces, change port numbers etc
13:38 jonalv We can do this, Actually that is more or less what we have already if I remove the jar from my plugin and reference net.bioclipse.database.hsqld instead. I would probably need to change name on my plugin aswell
13:38 olas really, do as you like
13:38 olas I don't care
13:39 egonw as long as it does not brake existing code
13:39 olas the database plugin is not stable
13:39 jonalv Then my question is: What shall I call my plugin which adds some gui stuff to the hsqld plugin and starts a database when needed and closeses it when Bioclispe is closed?
13:39 olas it is NOT in the release
13:39 olas hence not stable
13:39 egonw that's nonsense
13:39 olas is it?
13:39 egonw bioclipse is certainly not more stable than plugins in playground
13:40 egonw trunk/plugins is just the update server
13:40 olas well, that's how we defined it, right?
13:40 olas so plyground is no more stable?
13:40 olas I see...
13:40 jonalv the database.hsqldb doesn't really contain any code that can't be stable. It is just a small container plugin full of boilerplate code and a hibernate cfg file which shouldn't be there att all
13:40 olas leave it as it is
13:41 olas egonw: We talked about only bringing more stable plugins to the update server
13:41 jonalv leave everything as it is? But everything is strange...
13:41 olas jonalv: follow egonw's advice
13:42 jonalv which was?
13:42 olas don't change anything or you risk breaking tobias code
13:42 olas or you must set up tobias plugins and test them
13:42 egonw jonalv: database.hsqldb contains an extension
13:42 olas egonw: I don't like this approach at all..
13:42 jonalv Yes but what do I do with my code? We shouldn't have the hsqldb.jar at two places should we?
13:42 egonw olas, jonalv: make sure to get yourself of a copy of Tobias' thesis
13:42 olas How can we make sure other plugins don't break if we have no junit tests?
13:43 egonw then you actually know what your not using
13:43 egonw olas: run the code?
13:43 egonw jonalv: no, just one copy of hsqldb.jar please
13:43 olas And test every feature?
13:43 olas Every time I do something that could affect it?
13:43 jonalv olas, yes we need JUnit tests. I think we all know this. Right egonw?
13:44 olas yes
13:44 egonw yes, we need JUnit tests
13:44 olas but as it is now, it is impossible
13:44 olas it is really infeasible to test ALL plugins if you change something in net.bioclipse (a core dependency)
13:45 egonw olas: if you change the API or change the functionality behind an existing methods...
13:45 egonw then there are two options:
13:45 jonalv egonw, exactly one copy that's the idea. But can I go on calling my plugin net.bioclipse.hsqld and reference the jar file from the other plugin. I don't really need to change anything in it. (I hope)
13:45 egonw discuss that API change, so that others can update their code
13:45 egonw or
13:45 egonw fix the code yourself
13:45 olas true
13:45 egonw jonalv: the plugin name conventions prescribe that the name reflects dependencies...
13:46 olas but I don't think we should say that all plugins are "active"
13:46 egonw hence, you should rename your plugin to net.bioclipse.database.hsqldb.something
13:46 egonw olas: but that's not up to you to decide on your own...
13:46 olas the plugin does not rely only on hsqldb
13:46 jonalv egonw, good finally an answer to what I should do
13:46 jonalv actually that plugin does
13:47 olas structuredb?
13:47 olas egonw: I agree
13:47 jonalv The strucuredb plugin on the other hand depends on alot but it can't be named after all dependencies can it?
13:47 egonw olas: makring something as outdate should involve:
13:47 egonw 1. discussion on the mailing list
13:47 olas If we had "responsible person" then it would be easier
13:47 egonw 2. moving the plugin to trunk/outdated/pluings
13:47 egonw olas: that's de facto
13:48 jonalv olas, no not strucuredb but net.bioclipse.hsqldb
13:48 olas ok
13:48 egonw you don't mess with someone else's code
13:48 olas egonw: right
13:48 olas but playground seems like a place to play
13:48 egonw bad name indeed...
13:48 egonw some plugins are, others are not...
13:48 egonw we should differentiate there...
13:48 olas sounds good
13:49 egonw still... changes in net.bioclipse should be made only very sporadically
13:49 egonw *and* after discussion...
13:49 olas AND I'd prefer we have a responsible person for each plugin
13:49 egonw too many bugs in Bioclipse originate from undiscussed changes in functionality...
13:49 egonw to fix things, I am sure of that...
13:49 olas egonw: there are so many changes that need be done
13:49 egonw but still breaking existing code
13:50 egonw olas: no problem
13:50 egonw olas: that's what branches are for
13:50 olas yes
13:50 egonw I have no problem with 'svn move trunk/ branches/bioclipse-1.1.x/'
13:50 egonw OK, got to go now
13:50 egonw will be back later
13:50 olas see you egonw
13:51 jonalv see you
14:04 CIA-31 bioclipse: ospjuth * r3779 /trunk/playground/plugins/net.bioclipse.s​tructuredb/tests/testData/TestData.java: Soves classloading problem in Junit test
14:05 CIA-31 bioclipse: ospjuth * r3780 /trunk/playground/plugins/net.bioclip​se.structuredb/META-INF/MANIFEST.MF: Fixed manifest
14:14 CIA-31 bioclipse: biocoder * r3781 /trunk/playground/plugins/net.biocli​pse.chart/src/net/bioclipse/dialogs/ (. ChartDialog.java): Designing charting dialog
14:15 CIA-31 bioclipse: jonalv * r3782 /trunk/playground/plugins/ (net.bioclipse.database.hsqldb.runner/ net.bioclipse.hsqldb/): Renamed my hsqldb plugin. Next step will be to remove the hsqldb.jar and use the one in net.bioclipse.database.hsqldb instead
14:39 egonw rojasm: around?
14:39 rojasm yes
14:40 egonw I got quite far with the new atom types, but radicals are missing...
14:40 egonw and I had a question about F+
14:40 egonw which, I think, also comes from your work...
14:41 egonw I would very much learn how to update your code to use the new atom types...
14:41 rojasm I don't remenber exactly
14:41 egonw valency checking and hydrogen adding seems to work properly
14:41 jonalv egonw, what's up with this database plugin?
14:42 rojasm I have a look
14:42 egonw jonalv: as in?
14:42 jonalv Why is there Hibernate stuff everywhere?
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14:48 jonalv egonw,  I have problems here. This is not the way to do things. The net.bioclipse.database plugin is more like the net.bioclipse.hibernateMapper plugin or somethinlg like that. Which means that the net.bioclipse.database.hsqldb plugin is something like the net.bioclipse.hibernateMapper.hsqldbDatabase plugin which doesn't work for me since I don't want the hibernate mapper stuff only the hsqldb mapper stuff...
14:50 olas exactly what I tried explaining before :-)
14:50 olas I think we just have a naming error here
14:50 olas what tobias did was a hibernate-based DB
14:50 olas not a general DB
14:51 egonw jonalv: right, that's why I suggested a org.hsqldb with the hsqldb.jar
14:51 egonw olas: that's what I did at least...
14:51 olas sounds like a good idea, but can we really use their namespace?
14:51 egonw olas: I do not know of Tobias reused net.biclipse.database.hsqldb
14:52 olas I think we should use our namespace
14:52 olas net.bioclipse.something
14:53 olas what is wrong with net.bioclipse.hsqldb?
14:53 olas since net.bioclipse.database is already taken with hibernate-stuff
14:53 olas The original plan was to only use hibernate as it seemed good
14:53 olas BUT the wind has changed
14:53 olas we now think that Ibatis is promising
14:54 egonw ok, put the .jar in net.bioclipse.hsqldb
14:55 egonw make sure the version is the same... if you'll have net.bioclipse.database.hsqldb depend on it
14:55 olas I think the best would be to rename net.bioclipse.database to net.bioclipse.hibernate
14:55 olas and then make a GENERAL net.bioclipse.database
14:56 olas that does not rely on hibernate
14:56 olas and then create net.bioclipse.database.hsqldb
14:56 egonw sounds OK, if you apply, please announce on the mailing list and make the changes
15:00 jonalv egonw,  I am not that very good with SVN. Do you think that you could help me by making the move of net.bioclipse.database for me?
15:02 egonw no, not this week
15:02 jonalv Alright I'll have to give it a try myself then or continue using net.bioclipse.hsqld for now...
15:03 jonalv I think I will continue using net.bioclipse.hsqldb for now and then we can make this switch when you have the time?
15:03 egonw ack
15:04 egonw please email to the devel list in which you compare the versions differenctes for the jars
15:04 jonalv which jars and why?
15:05 egonw hsqldb.jar
15:05 egonw because of version incompatibilities
15:05 jonalv but we will not use the same ones will we?
15:06 egonw no idea
15:08 jonalv Okey you lost me. I think it is best to just leave the Hibernate stuff as it is for now and mess with it
15:08 jonalv just rename it and move it out of the way but so as little as possible
15:11 egonw ok
15:12 jonalv Why can't I revert my latest commit? Can someone try to revert my latest commit?
15:20 olas left #bioclipse
15:48 CIA-31 bioclipse: jonalv * r3783 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Made a fingerprint
15:55 CIA-31 bioclipse: jonalv * r3784 /trunk/playground/plugins/ (34 files in 9 dirs): reverted my renaming
16:00 CIA-31 bioclipse: jonalv * r3785 /trunk/playground/plugins/net.bioclipse.s​tructuredb/tests/testData/TestData.java: Spelling error on filename
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