Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-17

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All times shown according to UTC.

Time Nick Message
06:29 egonw joined #bioclipse
06:57 annzi joined #bioclipse
07:15 egonw @olas: we'll have a power cut at home today, and I'll work offline for a shorter or longer period of the day (unsure yet how long)
07:15 egonw @tell olas we'll have a power cut at home today, and I'll work offline for a shorter or longer period of the day (unsure yet how long)
07:15 egonw @msg olas we'll have a power cut at home today, and I'll work offline for a shorter or longer period of the day (unsure yet how long)
07:15 egonw mmm...
07:24 olass joined #bioclipse
07:24 * egonw will be online until the power cut
07:24 olass hola
07:25 olass egonw: how long?
07:25 egonw dunno
07:25 olass what's teh cut for?
07:25 egonw work in a nearby barn
07:26 egonw guess, 2 hours
07:26 egonw starting soon
07:26 egonw thus should be back around lunch time
07:31 egonw do we have a screencast showing the mol table functionality?
07:31 olass egonw: no, but you could make one :)
07:31 olass don't forget to place it on bioclipse.net
07:32 egonw yeah
07:32 olass in the new Screencast sectio
07:33 masak joined #bioclipse
07:37 egonw joined #bioclipse
07:37 egonw and I'm back
07:37 egonw they are going to place a power meter in our house
07:39 masak Power meter? Watt's that? :P
07:49 egonw_ joined #bioclipse
07:49 egonw_ masak++
07:51 Gpox joined #bioclipse
07:51 sneumann joined #bioclipse
07:52 sneumann moin!
07:53 sneumann moin
07:53 sneumann hi
07:53 sneumann zarah ?
07:53 sneumann too early :-(
07:56 egonw zarah: awak?
07:56 egonw e
07:56 egonw masak: can you check up on zarah?
07:57 masak hm.
07:57 masak @ping
07:58 zarah joined #bioclipse
07:58 egonw moin zarah
08:03 CIA-60 bioclipse.core: Egon Willighagen master * rf4a9496 / (2 files): (log message trimmed)
08:03 CIA-60 bioclipse.core: Added Apache 2.0 licensed StAX 1.2.0.
08:03 CIA-60 bioclipse.core: Copied in jars from the Ubuntu package:
08:03 CIA-60 bioclipse.core: $ dpkg -l libstax-java
08:03 CIA-60 bioclipse.core: Desired=Unknown/Install/Remove/Purge/Hold
08:03 CIA-60 bioclipse.core: | Status=Not/Inst/Cfg-files/Unpacked/Fai​led-cfg/Half-inst/trig-aWait/Trig-pend
08:03 CIA-60 bioclipse.core: |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
08:03 CIA-60 bioclipse.core: Ola Spjuth master * rd413ef4 / plugins/net.bioclipse.scripting/src/n​et/bioclipse/scripting/JsThread.java : Merge branch 'master' of git@github.com:olas/bioclipse.core - http://bit.ly/a2egJK
08:03 CIA-60 bioclipse.core: Ola Spjuth master * ree90a1c / plugins/net.bioclipse.scripting/src/n​et/bioclipse/scripting/JsThread.java : Implemented waitUntilNotBusy (jonalv++). - http://bit.ly/bL1LSE
08:04 olass hola
08:04 zarah privet olass
08:04 olass hmm
08:04 olass egonw: ping
08:04 egonw pong
08:04 egonw still here :)
08:05 olass can you look at core commit rf4a9496 above?
08:05 olass seems I had not committed that yet
08:05 egonw what should I be looking for?
08:06 olass well.. I don't think that patch worked and I added the jars to rdf instead
08:06 olass could that be it?
08:06 olass did I not send you a pull request for it?
08:06 egonw yes, indeed
08:06 egonw sorry... head is clouded...
08:06 egonw I suggest reverting the patch then
08:06 egonw git revert f4a9496
08:07 olass ok
08:08 CIA-60 bioclipse.core: Ola Spjuth master * r7f06c19 / (2 files):
08:08 CIA-60 bioclipse.core: Revert "Added Apache 2.0 licensed StAX 1.2.0."
08:08 CIA-60 bioclipse.core: This reverts commit f4a949641015355c47b689abad0a8bf2d8b44cb9. - http://bit.ly/ag0XtN
08:08 olass thx
08:18 egonw I got a bloody headache
08:18 egonw a really bad one :(
08:34 masak headache--
08:40 olass (paracetamol + ibuprofen)++
08:48 egonw the sum is more than the components?
08:50 jkutzer joined #bioclipse
08:56 egonw @ask jonalv if he can perhaps write up a Cleaner Bioclipse manager code series, like http://chem-bla-ics.blogspot.com/2010/03/c​leaner-cdk-code-2-stringcontains-and.html
08:56 zarah egonw's link is also http://tinyurl.com/yawf3mo
08:56 zarah Consider it noted.
09:00 jonalv joined #bioclipse
09:22 * olass gets another cup of wonderful coffee
09:25 olass egonw: ping
09:26 olass I need to port some commits from master to 2.2.x branch, for example several QSAR commits and a few cheminfo and core commits
09:27 olass what would be the suggested way to do this?
09:27 olass masak: maybe you can advice?
09:27 masak 'advise' :)
09:27 olass gah
09:27 olass take them one by one using git cherry-pick?
09:27 * masak backlogs
09:27 olass is the order important?
09:28 masak olass: cherry-pick is probably the way to do that if you don't want all the commits. some kind of interactive rebase could work too, if you're feeling adventurous.
09:28 * olass is not feeling adventerous
09:28 masak olass: the order is important if later commits build upon earlier ones.
09:29 olass would it be possible to merge and then revert the undesired commits?
09:29 * egonw uses cherry-pick for these kind of things
09:29 egonw savest
09:29 olass if the number of commmits I want is much larger than the undesired ones I mean...
09:29 egonw full control then, not with merge, where everything gets in
09:30 egonw alternative:
09:30 olass can I remove a commit which is not latest?
09:30 masak olass: no, because a merge doesn't create new commits.
09:30 egonw git log for the list of commits
09:30 egonw for each patch you want copied you do:
09:30 egonw git format-patch -1 COMMIT_HASH
09:30 masak olass: you can go wild with the commit history (using rebase) as long as you didn't push.
09:30 egonw but then you loose order, as they will all start with 0001
09:31 egonw (you can increase the number with a command line option, though)
09:31 olass sounds like git cherry-pick is easiest
09:31 egonw masak: indeed...
09:31 egonw olass: that's a good option too...
09:31 egonw make a branch on 2.2.x
09:31 olass ok, will use this option
09:31 egonw apply all patches
09:31 egonw then use this:
09:31 egonw git rebase -i HEAD^6
09:31 egonw (adapt 6 to the number of patches you like to review)
09:32 egonw and then delete the lines in the editor you do not want to backport)
09:32 olass hmm, sounds interesting
09:32 egonw but, cherry-pick is clearer
09:32 olass yes
09:32 olass will try that
09:32 * olass likes cherries
09:33 * egonw is accepted to the "PhD Supervisor Training Course" :)
09:33 * egonw is happy
09:33 olass congrats
09:40 CIA-60 bioclipse.qsar: Ola Spjuth master * rb2d8291 / (4 files in 4 dirs): Wait for initialization of CDK on start using JsThread. - http://bit.ly/aq29Ga
09:50 olass egonw: might you cherry-pick commit 4e41b42765c42f580d04cf9ea80e942ec2bb483a from cheminfo master to 2.2.x and push this?
09:50 olass this makes SMI files appear in QSAR add.. dialog
09:50 egonw ack
09:51 CIA-60 bioclipse.cheminformatics: Arvid Berg master * r54c68a4 / plugins/net.bioclipse.cdk.ui.sdfeditor​/src/net/bioclipse/cdk/ui/sdfeditor/ed​itor/MoleculeTableContentProvider.java : Only cache visible rows. - http://bit.ly/c1ZfYG
09:51 CIA-60 bioclipse.cheminformatics: Arvid Berg master * r24055af / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Enabled test for bug 613 - http://bit.ly/dvIrBk
09:51 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rb016804 / (2 files in 2 dirs):
09:51 CIA-60 bioclipse.cheminformatics: Removed workaround for bug 613
09:51 CIA-60 bioclipse.cheminformatics: Solves bug 1926 - http://bit.ly/cWn8SM
09:51 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rd0e18f8 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java :
09:51 CIA-60 bioclipse.cheminformatics: Added checks to se if file exists before continuing test
09:51 CIA-60 bioclipse.cheminformatics: This makes the tests fail instead of throwing an exception - http://bit.ly/akJZ3x
09:51 zarah bug #0613 | http://tinyurl.com/cm84ht
09:51 zarah bug #0613 | http://tinyurl.com/cm84ht
09:51 zarah bug #1926 | http://tinyurl.com/y8e7jh9
09:53 CIA-60 bioclipse.cheminformatics: Ola Spjuth 2.2.x * r9ab9552 / plugins/net.bioclipse.chemoinformat​ics/src/net/bioclipse/chemoinformat​ics/util/ChemoinformaticUtils.java :
09:53 CIA-60 bioclipse.cheminformatics: Added smiles extension for QsarEditor Add... dialog
09:53 CIA-60 bioclipse.cheminformatics: (bug 1883). - http://bit.ly/9aO7so
09:53 zarah bug #1883 | http://tinyurl.com/yfzbn6y
11:02 samuell joined #bioclipse
12:09 jpansane1 joined #bioclipse
12:23 egonw_ joined #bioclipse
14:06 egonw olass: got your mail
14:06 egonw looking at it
14:06 olass ok
14:06 olass I hope it's a start for you
14:06 olass i am considering removing weightedPath descriptor in 2.2.x for now
14:07 egonw yes, please do that
14:07 olass the chiPath* are also very slow
14:07 egonw we can easily re-enable it later...
14:07 olass but seem to work at least
14:07 olass at least so far
14:07 olass seems to have stuck now too...
14:08 olass but the molecules I am testing on are form ChEMBL and really really large some
14:08 olass anyway, we should have a timeout
14:08 egonw yes
14:48 annzi joined #bioclipse
14:57 egonw reinstalling YourKit
15:02 annzi1 joined #bioclipse
15:08 annzi joined #bioclipse
15:48 CIA-60 bioclipse.cheminformatics: Ola Spjuth 2.2.x * rbfaff57 / (3 files in 2 dirs): Improved createMoleculeIterator to test format before returning an IteratingMDLReader. - http://bit.ly/9AQoTH
16:03 olass egonw: please apply to master as well
16:05 CIA-60 bioclipse.cheminformatics: Ola Spjuth master * r9ab9552 / plugins/net.bioclipse.chemoinformat​ics/src/net/bioclipse/chemoinformat​ics/util/ChemoinformaticUtils.java :
16:05 CIA-60 bioclipse.cheminformatics: Added smiles extension for QsarEditor Add... dialog
16:05 CIA-60 bioclipse.cheminformatics: (bug 1883). - http://bit.ly/9aO7so
16:05 CIA-60 bioclipse.cheminformatics: Ola Spjuth master * rbfaff57 / (3 files in 2 dirs): Improved createMoleculeIterator to test format before returning an IteratingMDLReader. - http://bit.ly/9AQoTH
16:05 CIA-60 bioclipse.cheminformatics: Egon Willighagen master * rbd3b410 / (3 files in 2 dirs): Merge remote branch 'origin/2.2.x' - http://bit.ly/bNHleW
16:05 zarah bug #1883 | http://tinyurl.com/yfzbn6y
17:06 olass egonw: ping
17:06 olass egonw: I get this SMILES generated with CDK: http://ws1.bmc.uu.se:8182/cdk/descriptor/org.ope​nscience.cdk.qsar.descriptors.molecular.RuleOfFi​veDescriptor/OC10CC(O)C7C(OC8(OC6CC(O)C5C(OC(C1C​CC(O)C(O)C1)C(O)C5(C4C(O)CC(O)C3C4(OC(C2CCC(O)C(​O)C2)C(O)C3)))C6C7C8(O))(C9CCC(O)C(O)C9))C10
17:06 zarah olass's link is also http://tinyurl.com/y9zhq7t
17:06 olass it contains % in it
17:07 olass and hence fails when called on URL
17:07 olass why does a % end up in there?
17:07 olass can I safely just remove all % in a SMILES String?
17:07 olass egonw: let me know what you think...
17:12 egonw no, %'s in SMILES are important
17:13 egonw don't see the % in the URL you pasted, but they are crucial to the SMILES meaning
17:13 egonw away for dinner
17:16 olass hmm
17:16 olass I wonder how I can escape them so that it is possible to use SMILES with the CDK REST services
17:16 olass egonw: do you know?
17:29 egonw http://www.december.com/html/spec/esccodes.html
17:29 zarah egonw's link is also http://tinyurl.com/9zofj
18:23 olass egonw: does this mean CDK REST re-escapes this?
18:28 olass sent mail to rajarshi to clarify this
18:29 olass egonw: ping
18:36 egonw pong
18:48 olass egonw: can you see anything wrong with this SMILES?
18:48 olass http://ws1.bmc.uu.se:8182/cdk/descriptor/or​g.openscience.cdk.qsar.descriptors.molecula​r.XLogPDescriptor/O=C1NC(=O)C(=C1)C5C2CCCCC​2N(C5(C3CCC4CCCCC4(C3)))CCCSC(N)=%5BN+%5D
18:48 zarah olass's link is also http://tinyurl.com/y9ruwfp
18:48 olass gah
18:48 olass mom
18:48 olass O=C1NC(=O)C(=C1)C5C2CCCCC2N(C5(​C3CCC4CCCCC4(C3)))CCCSC(N)=[N+]
18:49 olass ah
18:49 olass it is not escapd
18:49 olass sry
18:49 egonw nitrogen has an uncommon valency
18:49 egonw otherwise looks fine
18:49 egonw perhaps missing some double bonds
19:48 egonw_ joined #bioclipse
20:23 CIA-60 bioclipse.qsar: Ola Spjuth master * rd6fc6bb / (2 files in 2 dirs): Commented out weightDescriptor pending scaling investigation. - http://bit.ly/9Zhch9
20:23 CIA-60 bioclipse.qsar: Ola Spjuth master * r4e8d7b9 / plugins/net.bioclipse.qsar.ui/src/net/bioclipse/qs​ar/ui/wizards/MoleculePropertyContentProvider.java : Do not print exception to STDOUT for smiles files as they do not have an implemented iterator yet. - http://bit.ly/aNCoUX
20:24 CIA-60 bioclipse.qsar: Ola Spjuth master * r7e3c0a5 / plugins/net.bioclipse.cdk.qsar.rest/src/net/biocli​pse/cdk/qsar/rest/CdkRESTDescriptorCalculator.java : Handle the case when generated SMILES is null - http://bit.ly/axXvgl
20:24 CIA-60 bioclipse.qsar: Ola Spjuth master * rbb09ed0 / plugins/net.bioclipse.qsar.ui/src/net/bi​oclipse/qsar/ui/builder/QSARBuilder.java : Better handling of descriptor calculations with errors in results. - http://bit.ly/9usula
20:24 CIA-60 bioclipse.qsar: Ola Spjuth master * r6f27121 / plugins/net.bioclipse.cdk.qsar/src/net/bioclip​se/cdk/qsar/impl/CDKDescriptorCalculator.java : Added a missing error in descriptorresult if CDK descriptor calc failed. - http://bit.ly/c3mk4S
20:24 * olass is tired
20:31 egonw_ there are 45 mol descriptors
20:31 egonw_ in the CDK
20:31 egonw_ so, 44 is pretty accurate...
20:31 egonw_ not so much...
23:05 CIA-60 bioclipse.joelib: Egon Willighagen 2.2.x * rc07c28f / externals/net.sourceforge.joelib/src​/joelib2/feature/AbstractDouble.java : Fixed a bug: no abstract field, as that would mean one DescInfo for *all* descriptors - http://bit.ly/c84fwl
23:12 CIA-60 bioclipse.joelib: Egon Willighagen master * re136e91 / externals/net.sourceforge.joelib/src​/joelib2/feature/AbstractDouble.java : Fixed a bug: no abstract field, as that would mean one DescInfo for *all* descriptors - http://bit.ly/amOBVv

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