Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-11-02

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:48 egonw joined #bioclipse
06:46 sneumann__ joined #bioclipse
07:31 jonalv joined #bioclipse
07:55 egonw hi jonalv
07:56 sneumann__ joined #bioclipse
08:05 Gpox joined #bioclipse
08:18 mgerlich joined #bioclipse
08:20 edrin joined #bioclipse
08:21 edrin hi
08:21 zarah hi edrin
08:32 egonw edrin: did you get it working in the end?
08:33 egonw @pz webservices
08:33 zarah [1333] 70 source files without copyri... http://tinyurl.com/nz9aff
08:33 zarah [1688] net.bioclipse.webservices, whi... http://tinyurl.com/ye4c6p6
08:33 zarah [1658] Exceptions related to Virtual ... http://tinyurl.com/ygn8a73
08:33 zarah [960] Check if network connection fro... http://tinyurl.com/y85l2xv
08:33 zarah [1492] missing copyright headers         http://tinyurl.com/ygoj2hl
08:33 zarah Entire list at http://tinyurl.com/ye5mw2o
08:33 egonw @px #1688
08:33 egonw @pz #1688
08:33 edrin i filed two bug reports. but bc runs for me at least... just disabled some plugins i do not need
08:33 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1688
08:34 egonw great, thanx
08:34 edrin @pz net.bioclipse.xml
08:34 zarah [1689] net.bioclipse.xml wants xerces... http://tinyurl.com/yl4qjhc
08:34 zarah Entire list at http://tinyurl.com/ydsa484
08:34 egonw we now have to wait for Ola to wake up :)
08:41 jonalv egonw: hi can you help me
08:43 egonw I can try
08:43 egonw it is it not too bug
08:43 egonw very busy
08:46 jonalv egonw: what is the status of bioclispe.chemoinformatics? I get merge conflicts when I try to pull from you...
08:47 egonw oh, how come?
08:47 egonw are there still patches dangling in your master?
08:47 jonalv egonw: I don't know
08:48 jonalv egonw: how can I tell?
08:48 egonw if you have patches for me to pull from your fork, you can best put them in a branch
08:48 egonw jonalv: mom, let me check
08:51 egonw jonalv: yes, I think you have patches in your master that cause the conflict because I pulled them earlier
08:51 jonalv egonw: but this is not my master, it is my 2.2.x
08:51 egonw same story for that branch
08:52 jonalv I have conflicts with load append method in jmol manager
08:52 egonw I see three patches which I pulled in your 2.2.x
08:52 egonw right, that's one of those patches
08:52 jonalv egonw: but if you pulled them how come I get conflicts?
08:52 egonw not sure why the are not picked up as the same patch, though
08:52 egonw indeed... as said, not sure
08:52 jonalv I don't understand you now
08:54 jonalv egonw ?
08:55 egonw what bit particularly?
08:55 egonw I don't understand either why the patch equivalence is not recognized...
08:56 jonalv egonw: but what should I do?
08:56 jonalv egonw:  should I do the merge?
08:56 jonalv egonw: should I throw away my commits
08:56 egonw yes
08:56 jonalv egonw: which one?
08:56 egonw the last three, I think
08:56 egonw try this:
08:57 egonw git log egonw-master..master
08:57 egonw (assuming you have a branch for my master)
08:57 jonalv git log origin/master..master
08:57 jonalv gave me notheirng
08:57 jonalv ah no hang on
08:57 egonw but that's your origin, not?
08:58 jonalv yea just realised that
08:58 jonalv git log upstream/master..master
08:58 * egonw is pulling the NMRShiftDB into the SPARQL end point
08:58 jonalv gave me threee commits
08:58 egonw now with spectra shifts
08:59 egonw should boost the number of triples somewhat :)
08:59 egonw jonalv: sounds right
08:59 egonw delete those
08:59 jonalv egonw: oh 4 actually
08:59 egonw 4?
08:59 egonw http://github.com/jonalv/bioc​lipse.cheminformatics/network
08:59 jonalv egonw: but they are valid comits
08:59 zarah egonw's link is also http://tinyurl.com/yhvtlbm
08:59 egonw I see three there...
08:59 egonw d90b4
08:59 egonw 406038
09:00 egonw 7a8033
09:00 egonw 575a2 is arvid's and the last in common
09:00 egonw but maybe that graph is too outdated...
09:17 egonw jonalv: did you make progress?
09:17 jonalv egonw: no not really, I got disturbed by someone...
09:18 jonalv egonw: but I guess I should do the merge...
09:18 jonalv egonw: the patch that broke the ouline, did you apply it and then revert it?
09:20 egonw yes, because someone kindly asked me last week to just merge stuff
09:20 jonalv egonw: I am just checking
09:20 egonw and this person being persistent that I just did it, I did...
09:20 egonw bad mistake
09:20 egonw will make that very clear next time: I don't want to merge in patches blindly
09:21 jonalv egonw: I know I messed up. Keep on rubbing it if you want. But honestly if we are not allowed to make misstakes that I don't know if I want to keep working on jmol...
09:21 egonw could have saved me 3 hours of unproductivity
09:21 egonw jonalv: that I applied that patch was not your fault
09:21 egonw no, sorry... this is not a complaint against you
09:21 * jonalv does that merge operation now
09:22 egonw just annoyed that I just blindly applied patches without testing...
09:22 egonw bad patches always sneak in
09:22 egonw that's OK
09:22 egonw we need to try to minimize that chance
09:22 egonw and maximize the testing...
09:23 egonw nothing wrong with you having that patch written at all
09:31 jonalv egonw: you have copied the code from append(IFile) to append(IMolecule)
09:31 egonw indeed
09:32 egonw what's keeping olas...?
09:32 jonalv seems I mesed up the merge becasue I didn't manage to get the one taking the molecule after the merge
09:32 jonalv egonw: he had some stuff he had to do...
09:32 jonalv I will just copy your method takign a molecule into my version...
09:32 egonw well, I'll be around until 14h for talk about bug priority...
09:35 edrin are your it students interested in porting existing analysis algorithms to xmpp for fun in their spare time?
09:37 olass joined #bioclipse
09:37 olass moin
09:37 zarah ni hao olass
09:37 olass hola
09:37 zarah saluton olass
09:37 jonalv saluton olass
09:37 edrin hi olass
09:37 olass saluton compadres
09:52 egonw hi olass
09:52 olass hi egonw
09:54 olass egonw: did the context menu expressionwork?
09:54 egonw did not got around to that
09:55 egonw yet
10:03 * jonalv need help
10:03 jonalv I need to remove my 2.2.x branch on github and replace it by the new one I created from egonw's 'real' one
10:04 egonw git push origin :2.2.x
10:04 egonw that remove the branch from github
10:04 egonw note the :
10:04 jonalv but "git push origin :2.2.x" gives me:
10:04 jonalv /usr/local/bin/ssh-git-wrapper: line 3:  3641 Segmentation fault      /bin/sh -c "$SSH_ORIGINAL_COMMAND"
10:04 jonalv fatal: The remote end hung up unexpectedly
10:09 egonw hahah... a seg fault
10:09 egonw not good
10:09 egonw try updating your git installation
10:09 jonalv egonw: I give up. I am goign to send you two patches by mail
10:10 jonalv egonw: I need to start preparing for tomorrows lab
10:10 CIA-63 bioclipse.core: Ola Spjuth 2.2.x * rd0ae719 / (2 files in 2 dirs):
10:10 CIA-63 bioclipse.core: Fixed Birt exception on startup.
10:10 CIA-63 bioclipse.core: Birt 2.5.1 seems to require an explicit dependency to org.eclipse.birt.report.engine.script.javascript. I added this to the birt plugin and feature, which solves the problem. - http://bit.ly/1LVv6r
10:10 egonw jonalv: ack
10:14 jonalv olass++
11:08 olass egonw: could you apply jonalv's path so I can look at the jmol outline problem?
11:09 egonw yes
11:12 egonw jonalv: ping
11:12 egonw what's patch 0001 about?
11:12 egonw that looks like the patch I had to revert...
11:14 egonw jonalv: patch 0002 make patch 0001 only apply in case of append script?
11:16 egonw olass: I emailed you jonalv's patches...
11:23 samuell joined #bioclipse
11:23 egonw hi samuell
11:24 samuell hi egon
11:25 samuell I see your mails now... Nice! Will look into it.
11:58 samuell egonw: So, have I understood correctly, that there's currently no way to retreive single spectra, (i.e. through Sparql)?
11:58 samuell (I'm not sure about what Peter meant with blank nodes)
12:03 egonw joined #bioclipse
12:04 egonw seems I had a network issue...
12:04 egonw anything I missed?
12:05 samuell egonw: Maybe my question: egonw: So, have I understood correctly, that there's currently no way to retreive single spectra, (i.e. through Sparql)?
12:05 samuell (I'm not sure about what Peter meant with blank nodes)
12:05 egonw yes, missed that one...
12:07 egonw no, that should be possible
12:07 egonw hang on...
12:08 samuell (though I have to learn Sparql then... but I guess it's about time :) )
12:10 egonw samuell: http://gist.github.com/224118
12:11 samuell egonw: Thanks
12:22 samuell egonw: So, If running this sparql query from rdf.sparqlRemove, what URL do I specify? is http://www.nmrshiftdb.org/onto ?
12:22 zarah samuell's link is also http://tinyurl.com/yl5oet6
12:22 egonw no, of the sparql end point
12:22 egonw in this case:
12:22 egonw pele.farmbio.uu.se/nmrshiftdb/sparql
12:22 samuell egonw: Ah, IC
12:50 samuell egonw: When querying the sparql endpoint, I get data in this format: "[[177.0^^nmr:ppm], [^^nmr:ppm], [38.0^^nmr:ppm], [38.5^^nmr:ppm], ... " etc
12:50 samuell That isn't N-triples, no?
12:51 egonw it is, I think
12:51 egonw ^^ indicates the data type
12:51 samuell Ok
12:51 masak joined #bioclipse
12:52 samuell I'm trying to load it into and IRDF Strore and save to a file as RDF
12:52 samuell But I get this error: http://bioclipse.pastebin.com/m17ba1519
12:52 zarah samuell's link is also http://tinyurl.com/yao24ut
12:53 samuell It might of course be something with the file paths
12:54 samuell since I might not have this set up correctly.
12:54 egonw yeah, it seems to see that data as part of a file name
12:54 samuell Yes
12:55 samuell Ah!
12:55 samuell Of course. Stupid error.
12:56 samuell I switched the variables, calling rdf.saveRDFXML.
12:56 samuell Still getting errors though.
12:57 egonw message?
12:59 samuell I'm trying things.... will get back later if I still don't solve it.
13:01 egonw ok
13:08 samuell egonw: How do I turn the result from rdf.sparqlRemote into an IRDFStore? Can't seem to find methods for converting from NTriple?
13:08 egonw ah...
13:08 egonw good catch...
13:08 egonw google SPARQL CONSTRUCT
13:08 zarah egonw: http://www.snee.com/bobdc.blog/2009/0​9/appreciating-sparql-construct.html
13:08 egonw there is no convenience method yet...
13:09 egonw patch welcome :)
13:09 samuell Ah Ok :)
13:09 egonw but I am not sure there is a general solution...
13:09 egonw e.g. not sure how to catch difference in SPARQL query cleanly between SPARQL CONSTRUCT and other SPARQL...
13:09 egonw I guess Jena has a SPARQL parser...
13:09 egonw but have not had time to go into depth about that...
13:10 samuell Ok
13:13 samuell Ok, but is there currently any method to convert from NTriple/N3 to an IRDFStore?
13:14 egonw yes
13:14 egonw there is a read method
13:14 samuell importFile?
13:15 egonw right
13:15 egonw got to go now
13:15 egonw will be back tonight
13:16 samuell Yep
13:34 sneumann__ joined #bioclipse
13:53 masak Bioinformatics and the Semantic Web: http://blog.zacharyvoase.com/post/230672089
13:53 zarah masak's link is also http://tinyurl.com/y8hl768
14:23 masak Simple genome analysis with Arc: http://arcfn.com/2009/11/simple-​genome-analysis-with-arc-in.html
14:23 zarah masak's link is also http://tinyurl.com/yg6asy6
15:11 samuell all: In the Bioclipse console, can I save a string to a file, using ui.save? (then gotta convert the string to an inputstresm, which I don't know how to do in JS), Or do I have to do in another way?
15:12 masak samuell: hm. I don't think I've seen the feature you're describing.
15:12 samuell masak: Ok
16:45 sneumann__ joined #bioclipse
16:59 egonw joined #bioclipse
17:06 samuell egonw: Hi
17:06 egonw hi samuell
17:06 egonw edrin: ping
17:06 egonw edrin: I just realized that you are using master, correct?
17:09 samuell egonw: I'm a bit bewildered as to the format of the results I get from the sparql query from the bioclipse console. (I.e. "[[177.0^^nmr:ppm], [^^nmr:ppm], [38.0^^nmr:ppm]]"). Doesn't resemble at least the code examples on http://en.wikipedia.org/wiki/Notation_3 , http://en.wikipedia.org/wiki/N-Triples or http://en.wikipedia.org/wiki/Turtle_%28syntax%29
17:09 zarah samuell's link is also http://tinyurl.com/p85eq
17:09 egonw the quotes are missing
17:09 egonw moreover... note this entry:
17:09 egonw [^^nmr:ppm]
17:09 samuell Yep
17:09 egonw so, it should look like:
17:09 egonw "177.0"^^nmr:ppm
17:10 egonw and that problematic one would then more properly read like:
17:10 egonw ""^^nmr:ppm
17:11 samuell But I mean, the whole notation seem quite different from the default format, when running sparql from the web virtuoso interface: http://bioclipse.pastebin.com/m2d4e59a4
17:11 zarah samuell's link is also http://tinyurl.com/yfxqlbq
17:11 egonw oh, yes
17:12 egonw the sparqlRemote() returns a array of arrays
17:12 samuell Ah
17:12 egonw that's the brackets
17:12 samuell That makes sense.
17:13 samuell Ok, so, what I need to decide, is in what format I should receive these results in the blipkit plugin.
17:14 samuell I guess this "array of arrays" will be enough for testing
17:14 samuell but later on I guess I will want to have some more meta data as well... ?
17:16 egonw Gpox: ping
17:16 egonw samuell: yes, we can improve things when we find that required
17:16 Gpox egonw: pong
17:16 egonw Gpox: do you have those 4-5 cdk-externals patches also as patches against jchempaint-primary?
17:16 Gpox no
17:17 egonw mmm :(
17:17 egonw ok
17:17 samuell egonw: Yes, true.
17:17 egonw Gpox:
17:17 egonw Gpox: is that IGeneratorParameter<?> fine with the IGeneratorParameter<T> used?
17:18 * egonw feels rather novice and uncertain
17:18 * egonw is pleased to see Gpox using it though :)
17:19 Gpox ? means T can be of any type
17:19 egonw mmm... OK
17:19 * egonw will read that print out jonalv printed for him again
17:25 egonw dinner time
17:25 egonw bbl
17:42 edrin egonw: yes, I am using master
19:21 * samuell 's gotta go
20:06 edrin left #bioclipse
21:38 masak joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary