Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-05-20

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All times shown according to UTC.

Time Nick Message
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05:12 egonw_ moin
05:12 zarah ni hao egonw_
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07:44 CIA-53 bioclipse.core: Arvid Berg 2.4.x * rfe37ba5 / (4 files): Added com.springsource.org.apache. xerces and xml to target.platform - http://bit.ly/bAEnhy
07:56 egonw_ Gpox: pin
07:56 egonw_ g
07:56 egonw_ Gpox: can you email me the patches for the nu.xom bundle?
07:56 Gpox egonw_: pon
07:56 Gpox g
07:57 egonw_ Mylyn does not seem to act as expected here...
07:57 Gpox net.bioclipse.target.platform/libs
07:58 egonw_ so, no patches for bioclipse.cheminformatics then?
07:59 Gpox nothing that is already there, I think
07:59 egonw_ is *not* already there?
07:59 egonw ok
07:59 egonw I was confused by the bug report
07:59 egonw @pz 1963
07:59 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1963
07:59 egonw which created an attachment
07:59 Gpox I thought it was for the org.openscience.cdk repo
08:00 egonw ok, will close the bug then
08:00 Gpox ok
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08:14 egonw annzi: I'm at BMC today
08:14 annzi egonw: ok
08:17 egonw let me know if I need to move plugins/features from bioclipse.rdf to another repository
08:17 egonw and if so, the complete list of plugins/features
08:17 egonw olass: I'm working on a patch for the InChI manager regarding the InChI issue
08:17 egonw olass: have been thinking about NestedVM again...
08:17 olass excellent!
08:17 egonw the main problem there is that it works with temporary files
08:18 egonw at least, the impl Mark made
08:28 egonw Gpox: what is the best to return in the inchi manager if the library does not load?
08:28 egonw well, others can comment too
08:28 egonw the method returns an InChI object
08:29 jonalv joined #bioclipse
08:29 egonw shall I instantiate a InChI.EMPTY or so?
08:29 egonw instead of returning null?
08:29 jonalv egonw, olass, Gpox: Do you know if there is a wiki page explaining how to include features and start from the bioclipse project?
08:29 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
08:30 olass jonalv: dunno
08:34 olass egonw: did you apply the patch I sent you about properties in CDKMolPropSource?
08:34 egonw no, not yet
08:34 egonw it's lined up...
08:34 olass ack
08:42 egonw olass: have you figured out how to turn off the osgi debug messaging tsunami?
08:44 egonw ok, will now commit a patch to introduce these two methods:
08:44 egonw inchi.load()
08:44 egonw which will return a String message, like "InChI library is loaded."
08:44 egonw inchi.isLoaded()
08:44 egonw should be clear, that one :)
08:45 egonw the patch also introduces two global manager boolean fields:
08:45 egonw loadingFailed, and isLoaded
08:45 egonw to allow generate() to fail early
08:50 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r926be02 / (3 files in 2 dirs):
08:50 CIA-53 bioclipse.cheminformatics: Introduced two new methods: inchi.load() and inchi.isLoaded(). Additionally, a manager instance now
08:50 CIA-53 bioclipse.cheminformatics: tracks the state of the library loading, failing early in generate() if loading failed. - http://bit.ly/9ONnUV
08:54 olass egonw: edit logback.xml in logback plugin
08:54 olass default for me is not OSGI
08:54 olass but format is longer than before
08:55 egonw should not be in git too?
08:55 olass (which you can configure as you like)
08:55 olass it is in git
08:55 egonw no, not outputting all that
08:55 olass outputting in git?
08:55 egonw we have had earlier discussions about too much debug info wrt to users
08:55 olass all that?
08:55 * olass does not see OSGI debugging
08:56 egonw not anymore?
08:56 olass nope
08:56 egonw is it not osgi but spring?
08:56 egonw olass: you lost me
08:56 olass ask Gpox, he's the master
08:56 egonw olass: looked at your patch...
08:56 egonw the PROPERT_* keys are not View specific,
08:57 olass took us 4 hours to find out how to fix that :(
08:57 egonw so, if the InChI is now in the file (e.g. PubChem downloaded files), they will be lost
08:57 egonw and not shown
08:57 egonw I don't think that is intended ... ?
08:57 olass we need a bioclipse.inchi property name
08:58 olass so we only treat our calculated this way
08:58 olass additional inchi should show up
08:58 olass but our calculated inchi should only be in General category
08:58 egonw true
08:58 olass not duplicated in Molecule Properties category
08:58 egonw but your patch will hide any InChI laoded from the fil
08:58 egonw e
08:59 olass please rename our inchi property
08:59 egonw ack
08:59 olass maybe to bioclipse.inchi?
08:59 egonw yeah, that's what I was thinking too
08:59 olass wanted to aks you about that before doing it
08:59 olass ok
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09:31 egonw Gpox: ping
09:31 egonw Gpox: some code uses different keys to set properties
09:31 egonw some use the PROPERTY_XX
09:32 egonw others uses CDKMOleculeUtils.MolProperty
09:32 masak Gpox is afk at the moment.
09:32 egonw can you comment?
10:13 CIA-53 bioclipse.cheminformatics: Ola Spjuth 2.4.x * rfcae1c4 / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Removed Inchi, InchiKey, and SMILES from "Molecular Properties" property category. They are already present in "General" category. Solves #1968. - http://bit.ly/a4Qd05
10:13 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r4365561 / plugins/net.bioclipse.cdk.business/src/n​et/bioclipse/cdk/domain/CDKMolecule.java : Renamed INCHI_KEY constant to reflect it is not the InChI Key, but the key for an InChI object; Removed the unused INCHIKEY_KEY constant - http://bit.ly/aEjt3G
10:13 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r10c9976 / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Use a long namespace (aka prefix) to ensure it does not overwrite InChI*, SMILES info that can be present in the file - http://bit.ly/brVNdu
10:13 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rf75d3f9 / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Ignore *anything* net.bioclipse namespaced, not just the stuff from the PropertySource - http://bit.ly/c0C2VH
10:13 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r9734ecc / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Removed two more sneaky, hidden uses of the MolProperty enumeration - http://bit.ly/aPNtSS
10:18 CIA-53 bioclipse.cheminformatics: Arvid Berg 2.4.x * r16af1c7 / plugins/net.bioclipse.cdk.jchempaint/src/net/bioc​lipse/cdk/jchempaint/editor/JChemPaintEditor.java :
10:18 CIA-53 bioclipse.cheminformatics: Added event for when model is loaded
10:18 CIA-53 bioclipse.cheminformatics: Also a method for seting property on the loaded molecule - http://bit.ly/coxo4I
11:27 CIA-53 bioclipse.moss: annzi master * ref6103c / plugins/net.bioclipse.moss.business/src/ne​t/bioclipse/moss/business/MossManager.java : New imports and variable declartions - http://bit.ly/drHHYE
11:27 CIA-53 bioclipse.moss: annzi master * rf50acb8 / plugins/net.bioclipse.moss.business/src/ne​t/bioclipse/moss/business/MossManager.java : Improved method for protein family querying - http://bit.ly/a1nk08
11:27 CIA-53 bioclipse.moss: annzi master * r75def29 / plugins/net.bioclipse.moss.business/plugin.xml : xml changed for moss-chembl wizard - http://bit.ly/c7PeLs
11:27 CIA-53 bioclipse.moss: annzi master * r874bcf4 / plugins/net.bioclipse.moss.b​usiness/META-INF/MANIFEST.MF : Dependency changes - http://bit.ly/dvRRpI
11:27 CIA-53 bioclipse.moss: annzi master * r9485ed2 / plugins/net.bioclipse.moss.business/src/net​/bioclipse/moss/business/IMossManager.java : Changed PublishedClass value - http://bit.ly/btvraV
11:27 CIA-53 bioclipse.moss: annzi master * r637c17c / plugins/net.bioclipse.moss.business/src/net​/bioclipse/moss/business/IMossManager.java : Added activity to parameters and changed method to IStringMatrix - http://bit.ly/aqrIAC
11:27 CIA-53 bioclipse.moss: annzi master * ra7a88e3 / plugins/net.bioclipse.moss​.business/icons/sample.gif : An icon map - http://bit.ly/bdAXv3
11:28 CIA-53 bioclipse.moss: annzi master * r4d1ae5d / (6 files): The moss-chembl wizard - http://bit.ly/9qtFRm
11:42 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r796ad68 / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Properly check if the InChI has already been calculated - http://bit.ly/arzlFK
11:46 olass egonw: http://paste2.org/p/840186
11:46 egonw tack
11:46 egonw ah, progress
11:46 egonw it's actually a NPE
11:46 egonw good :)
11:47 egonw ok, not sure if I can fix this one...
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12:14 masak egonw: was that you who restarted zarah?
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12:49 olass egonw: http://paste2.org/p/840248
12:56 jonalv egonw: have you tried update site on Ubuntu?
12:57 egonw masak: nope
12:57 egonw jonalv: what?
12:57 masak ok. prolly netsplit then.
12:57 jonalv egonw: remember I asked you if you could try accessing the Bioclipse update site from Ubuntu since Roland is having trouble (see the bioclipse-dev mailing list)
12:58 egonw masak: Dutch ni hiao: hallo of goede morgen (AM), goede middag (14-18), goede avond (other PM)
12:58 egonw ah...
12:58 egonw no, not yet
12:58 masak egonw: ah, cool.
13:01 egonw hi all... please vote: http://www.sciencebase.com/science-blog/whic​h-chemical-drawing-software-do-you-use.html
13:01 zarah egonw's link is also http://tinyurl.com/2dvl35t
13:07 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r65c776a / plugins/net.bioclipse.inchi/src/net/bio​clipse/inchi/business/InChIManager.java : Catch any exception, also the NPE you get when there is no native InChI lib available for your platform - http://bit.ly/cN8jLC
13:18 * olass is testing egonw's fix
13:20 olass egonw: http://paste2.org/p/840405
13:32 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r302febc / (3 files in 2 dirs): Added a convenience method inchi.isAvailable() allowing the CDKMolecule to fail early with InChI generation - http://bit.ly/bGvDw2
13:32 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * reb42a32 / plugins/net.bioclipse.inchi/src/net/bio​clipse/inchi/business/InChIManager.java : Used the new isAvailable() method - http://bit.ly/aU0enY
13:32 egonw olass: please try
13:32 egonw and let me know the results
14:05 egonw olass: ping
14:06 olass ok, testing your fix first
14:06 egonw excellent
14:07 olass egonw: http://paste2.org/p/840601
14:07 egonw I wish I could run OS/X in a VM
14:09 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r3a49ae5 / plugins/net.bioclipse.inchi/src/net/bio​clipse/inchi/business/InChIManager.java : OK, I give up. The above vars should do it, but the bottom line is factory being null - http://bit.ly/9Lesqr
14:12 olass egonw: you won't believe it - same problem!
14:12 egonw no, I don't believe it...
14:12 olass come here and set a breakpoint if you like
14:13 egonw cognatively I do believe you
14:13 egonw it's just that my body has objections
14:13 egonw kind of a WTF erlebnis
14:18 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r1b2a534 / plugins/net.bioclipse.inchi/src/net/bio​clipse/inchi/business/InChIManager.java : Arghh... OK, test for factory nullness here once more then :( - http://bit.ly/aUp7hm
14:23 olass egonw: http://paste2.org/p/840622
14:24 * olass hides
14:27 CIA-53 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r551fbf1 / plugins/net.bioclipse.inchi/src/net/bio​clipse/inchi/business/InChIManager.java : Fixed stupid code: completeReturn() does not return in the method :( Thanx to Ola for spotting it - http://bit.ly/dpTO17
14:35 olass egonw++ //works now
14:40 * egonw is heading to his Riskutbildning 1
14:40 egonw cu online tomorrow!
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15:33 olas hey
15:34 jonalv hey
15:34 jonalv what did I do?
15:34 olas joined #bioclipse
15:35 jonalv wb olas
15:36 olass left #bioclipse
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15:37 olass jonalv: ping
15:37 jonalv olass: pong
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