Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-30

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Time Nick Message
05:25 jbrefort joined #cdk
06:15 Conrad joined #cdk
06:18 egonw_ joined #cdk
07:20 rojasm joined #cdk
07:45 egonw_ hi rojasm
07:50 rojas1 joined #cdk
08:04 rojas1 moin
08:04 egonw_ hi rojas1
08:05 rojas1 Hi egonw
08:05 rojas1 I will continue with the reaction after the seminar. I think I can finish today!
08:06 egonw_ ok, great
08:06 egonw_ you've started writing tests for the expected reaction products too?
08:07 rojas1 Yes!
08:07 egonw_ excellent
08:10 egonw_ Testcase: testCoverage(org.openscience.c​dk.test.FormulaCoverageTest):   FAILED
08:10 egonw_ The module is not fully tested! Missing number of method tests: 51 in number of classes: 15
08:10 egonw_ might you have a look at that too?
08:10 egonw_ in trunk/
08:10 rojas1 ja!
08:11 egonw_ let's do it like this:
08:11 egonw_ I'll write a class for these methods for the rules:
08:11 egonw_ testGetParameters
08:11 egonw_ testValidate_IMolecularFormula
08:11 egonw_ testSetParameters_arrayObject
08:11 egonw_ those are for all *Rule class tests
08:12 rojas1 ok, perfect
08:14 CIA-18 cdk: egonw * r9972 /trunk/cdk/src/META-INF/test-formula.cdkdepends: Added missing dependencies
08:14 egonw_ oh goodies...
08:14 egonw_ 28 commits left
08:34 masak joined #cdk
08:44 CIA-18 bioclipse: carl_masak * r4833 /trunk/plugins/net.bioclipse/src/net/​bioclipse/views/BioResourceView.java:
08:44 CIA-18 bioclipse: [BioResourceView.java]
08:44 CIA-18 bioclipse: * removed unused imports
08:44 CIA-18 bioclipse: * added generics and casts to remove warnings
08:52 jonalv joined #cdk
09:02 steinbeck joined #cdk
09:02 egonw_ hi steinbeck
09:02 steinbeck moin egonw
09:04 Annzi joined #cdk
09:17 CIA-18 cdk: egonw * r9973 /trunk/cdk/src/org/openscie​nce/cdk/test/formula/rules/ (6 files): Added missing tests for getParameter, setParameter and some default testing for validate
09:17 CIA-18 cdk: egonw * r9974 /trunk/cdk/src/org/openscience/cd​k/formula/rules/ChargeRule.java: Deal with the situation that a charge has not been set (aka NULL)
09:18 egonw_ rojas1: OK, back to you (when you get back from seminar :)
09:37 egonw__ joined #cdk
09:52 rojas1 egonw around?
09:53 egonw__ yes
09:53 rojas1 I am trying to solve the test formulaCoverageTest
09:53 egonw__ good
09:53 rojas1 But I don't know where to start
09:53 egonw__ run from the command line:
09:53 egonw__ ant clean dist-all test-dist-all
09:54 egonw__ ant -Dmodule=formula test-module
09:54 egonw__ more reports/result-formula.txt
09:54 egonw__ and fix them one by one
09:54 rojas1 perfect that was clear :)
09:54 rojas1 thanks
09:55 egonw_ I just used the nifty LaTeX package includepdf
09:56 egonw_ better: the command \includepdf from the package pdfpages
09:56 egonw_ very useful
10:09 rojasm joined #cdk
10:12 carsten joined #cdk
10:19 egonw_ carsten: what was that changelog page again?
10:19 egonw_ can't find it with google...
10:19 carsten There is an embargo on it anyway :-)
10:20 carsten http://www.kde.org/announcements/c​hangelogs/changelog4_0to4_0_1.php
10:20 carsten ah, already much longer, compared to yesterdayx
10:39 carsten egonw: and now with Kalziums three bugfixes as well :-)
10:44 egonw_ good
10:44 egonw_ only briefly checked it...
10:44 egonw_ should have given it a good testing...
10:44 egonw_ will do that after 4.0.1
10:46 egonw_ it's using the BODR data, right?
10:48 egonw_ the glossary is taken from Wikipedia?
10:48 carsten it is, yes
10:48 carsten but there are bug in bodr I found
10:48 carsten or at least issues
10:49 carsten I will report them soon
10:49 egonw_ please do
10:49 carsten cannot even remember them, need to diff  :-)
10:49 egonw_ indeed
10:50 egonw_ oi, just noticed that khelpcenter-kde4 is using htdig??
10:51 egonw_ I really had the impression the KDE4/Strigi integration was better than it really is...
10:51 egonw_ there is no integration :(
10:53 carsten yes
10:53 carsten strigisupport is at a minimum
10:54 egonw_ was just looking at the 'Atom Model'
10:54 egonw_ nice, but what it misses is some indication on how filled a shell is...
10:54 egonw_ I know the K shell only can hold 2 electrons...
10:55 egonw_ but maybe it would be an option to indicate unfilled shells with unfilled circles...
10:55 carsten wtf, Linux 2.6.25 has already 2000 (!) patches over 2.6.24...
10:55 carsten egonw: you mean the spdf stuff?
10:55 EskilA joined #cdk
10:55 egonw_ yes
10:56 carsten egonw_: the atom model is indeed not perfect...
10:56 carsten I need a graphical mockup
10:57 egonw_ ok, will think about that...
10:57 carsten egonw_: ok, found it. The density is not generated
10:57 egonw_ got to go now... pick up daughter from school
11:23 jbrefort joined #cdk
11:27 CIA-18 cdk: miguelrojasch * r9975 /trunk/cdk/src/org/openscience/cdk/ (11 files in 2 dirs): added name tests according the Junit4
11:34 egonw_ carsten: only shortly here...
11:34 egonw_ about to go for lunch
11:34 egonw_ but you were not registered as BODR developer...
11:34 carsten egonw_: mails
11:34 egonw_ will give you write access now
11:34 carsten I were not? ok :-)
11:34 egonw_ hang on...
11:34 * carsten just found a bug in your Perl-code
11:35 egonw_ cniehaus, right?
11:35 egonw_ you *were* developer for blueobelisk.sf.net
11:36 egonw_ but not yet for bodr.sf.net
11:36 carsten rigt
11:36 carsten +h
11:37 egonw_ ok, please try now
11:37 egonw_ bbl
11:37 egonw_ lunch first
11:59 egonw_ back
12:02 CIA-18 cdk: cniehaus * r7 /trunk/bodr/scripts/elements.pl:
12:02 CIA-18 cdk: This fixes several issues in the XML-generation.
12:02 CIA-18 cdk: * For one, we didn't skip comment lines.
12:02 CIA-18 cdk: * Second, we misgenerated lines with no discoverers.
12:10 CIA-18 cdk: cniehaus * r8 /trunk/bodr/scripts/elements.pl: Use a good regexp to skip comment lines. No difference in the output, just the right thing to do (tm)
12:20 CIA-18 bioclipse: carl_masak * r4834 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (5 files in 3 dirs):
12:20 CIA-18 bioclipse: * assays not in any specific experiment now end up in their own
12:20 CIA-18 bioclipse:  pseudo-experiment "Other assays"
12:58 CIA-18 bioclipse: carl_masak * r4835 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (7 files in 2 dirs):
12:58 CIA-18 bioclipse: * Database now loads all its descendants lazily
12:58 CIA-18 bioclipse: * coming up: more fine-grained lazy loading
13:06 CIA-18 bioclipse: carl_masak * r4836 /trunk/playground/plugins/net.bioclips​e.base2/src/net/bioclipse/base2/model/ (Database.java Project.java): * Projects now load lazily
13:13 carsten egonw_: mail
13:15 egonw_ replied
13:15 carsten thanks :)
13:18 CIA-18 cdk: cniehaus * r9 /trunk/bodr/elements/elements.xml: Regenerate the XML file.
13:18 CIA-18 bioclipse: Annzi * r4837 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.moss/src/net/bioclipse/moss/ (6 files in 2 dirs):
13:18 carsten egonw_: will update the CL in 10 minutes
13:22 egonw_ ack
13:22 carsten egonw_: what about the density...? Was there a reason we removed it?
13:23 CIA-18 cdk: miguelrojasch * r9976 /trunk/cdk/src/org/openscience/cdk/ (11 files in 4 dirs): Correction with name tests according Junit4. Solved all conflicts in Module formula.
13:23 egonw_ from the dictionary?
13:23 carsten density.txt is read in but not put our as XML
13:23 egonw_ mom
13:24 CIA-18 cdk: cniehaus * r10 /trunk/bodr/scripts/elements.pl: * Now using a RegExp to skip comment lines.
13:25 egonw_ ah, I remember
13:25 egonw_ see the ChangeLog:
13:25 egonw_ * scripts/elements.pl: Disabled density which is not an element property
13:25 egonw_ density is not an elemental property
13:25 egonw_ but a property of a compound
13:26 carsten ah
13:26 carsten ok
13:26 egonw_ e.g. carbon has at least three densities
13:26 carsten yes
13:26 egonw_ graphite, buckyball, diamond
13:26 carsten how do we solve this?
13:26 carsten no I cna remember...
13:27 carsten ok, is it ok to add the -1 for the elelments 112 to 116? (See patch)
13:27 egonw_ -1 on what?
13:27 CIA-18 cdk: cniehaus * r11 /trunk/bodr/ChangeLog: Updated
13:27 carsten In the given year the date has been described first. A "0" means that the element has always been known to mankind (for example Carbon). If the element is know but not officially accepted by the IUPAC the date will be "-1".
13:28 egonw_ mmm...
13:28 egonw_ was thinking about both...
13:28 egonw_ if known for mankind...
13:28 egonw_ not sure I like 0 and -1
13:29 egonw_ better use explicit semantice
13:29 egonw_ s
13:29 egonw_ instead
13:29 egonw_ 0 implies something...
13:29 egonw_ which we can express otherwise too...
13:29 egonw_ in a more semantic way
13:29 egonw_ e.g.
13:29 egonw_ iron is not know since mankind...
13:29 CIA-18 cdk: cniehaus * r12 /trunk/bodr/ (ChangeLog dicts/blueobelisk-dictionary.xml): adding doc for discoveryDate
13:29 egonw_ but only since the iron age
13:30 egonw_ and no idea when they discovered 'carbon'...
13:30 carsten egonw:^^^ that commit adds the info about the 0. That has been in BO since day one
13:30 egonw_ diamond may be around for some time...
13:30 egonw_ yeah, thanx for bringing it up...
13:30 carsten egonw: they never did, for example, graphite has always been known
13:30 egonw_ I don't think we have been doing this properly since day 0
13:30 carsten so has S
13:30 egonw_ so they knew about 'stone' too...
13:31 carsten egonw_ right, and fire
13:31 egonw_ the discovery date is about discovery of the element
13:31 egonw_ and that assumes 'element' was defined...
13:31 carsten there are dates for all elements but I think 16 like Cu, Fe, S and so on
13:31 egonw_ so post-Dalton I assume
13:31 carsten those 16 (?) have not really been discovered
13:31 egonw_ though Iron was elemental for much longer
13:31 carsten but just "relabeled" to "Element"
13:31 egonw_ quite so...
13:31 egonw_ in which case we should say:
13:32 carsten that is what the 0 describes
13:32 egonw_ "we have no idea when they discovered that"
13:32 egonw_ or
13:32 egonw_ "discovered in the iron-age"
13:32 egonw_ etc
13:32 carsten btw, I cannot svn log dates.txt to show you the 0 has always been in our database
13:32 carsten because:
13:32 carsten r2 | egonw | 2007-05-29 11:37:21 +0200 (Di, 29 Mai 2007) | 1 line
13:32 carsten Initial copy from the previous SVN machine at the CUBIC
13:33 egonw_ no worries
13:33 egonw_ I believe you that is was...
13:33 egonw_ never really thought about it
13:33 egonw_ but now that I do...
13:34 egonw_ I'd say '0' and '-1' is wrong
13:34 egonw_ that's all
13:34 egonw_ no blame, no whatever...
13:34 egonw_ I just think we can do better than that
13:35 carsten you are good @ XML, I suck there.
13:35 carsten Just tell me what to do ;-)
13:36 rojasm egow: question. is there some QueryAtomContaine which analyze all. I mean lonePair and single electrons ...!
13:36 carsten and also tell me what to do with density. I see two ways:
13:36 carsten a) Remove it completly
13:36 carsten b) Adding ALL "pure element" compounds (several Sulphurs, three Carbons and so on) (or at least more than just one)
13:37 egonw_ the date=0 should be remvoed
13:37 egonw_ and replaced in the XML, by something like:
13:37 CIA-18 bioclipse: carl_masak * r4838 /trunk/playground/plugins/net.bioclipse.base2/​src/net/bioclipse/base2/db/Base2Database.java:
13:37 CIA-18 bioclipse: [Base2Database.java]
13:37 CIA-18 bioclipse: * Better exception descriptions
13:38 rojasm egow: (sorry for interfering conversation) so I can know it the results of the reaction are correctly with what I expect
13:38 egonw_ <scalar dictRef="bo:discovery">iron age</scalar>
13:38 egonw_ about density...
13:38 CIA-18 bioclipse: jonalv * r4839 /branches/bioclipse2/ (17 files in 10 dirs): First code for making BioObjects recordable by proxies. Things may have gone broken. Please look for bugs and tell me.
13:38 egonw_ that requires a data base with structures...
13:38 carsten egonw_: which we ahbve
13:38 carsten egonw_: which we have
13:39 egonw_ bodr/elementalCrystals/crystals.xml ?
13:39 carsten no, jeroms
13:39 egonw_ rojasm: no, I don't think such a thing exists yet
13:40 rojasm could I implement in the QueryAtomContainerCreator class
13:40 egonw_ rojasm: absolutely
13:40 rojasm as QueryAtomContainerCreator.crea​teTotalQueryContainer(product)
13:40 rojasm good name?
13:41 egonw_ Total expects more, I guess
13:41 egonw_ to match every property
13:41 rojasm yes. May be better EveryQueryContainer
13:42 egonw_ LonePairAndSingleElectronQueryContainer?
13:43 rojasm ok, dat means indirect that it will be match the symbol and bonds?
13:43 rojasm sorry it was a question!
13:44 egonw_ no, not really
13:45 egonw_ just make sure the JavaDoc provide the details on what is matched
13:45 rojasm I mean that if we write only LPAndSE reflects that the method is only this checking
13:45 rojasm ok
13:47 CIA-18 bioclipse: jonalv * r4840 /branches/bioclipse2/ (4 files in 4 dirs): moved BioObjectList into core.domain
13:52 carsten egonw_: ok, I addressed the density-issue on the list. Perhaps we can continue the talk there, I need to go now
13:52 egonw_ ok
13:53 EskilA_ joined #cdk
13:53 carsten egonw_: and please don't CC me on mails, that breaks threading in KMail ;-)
13:54 egonw_ carsten: hehehehe
13:54 carsten the mails always end up in the inbox, not in the cdk-folder
13:55 CIA-18 bioclipse: carl_masak * r4841 /trunk/playground/plugins/net.bioclips​e.base2/src/net/bioclipse/base2/model/ (Experiment.java Project.java):
13:55 CIA-18 bioclipse: * Experiments now load lazily
13:55 CIA-18 bioclipse: * ...except if you expand "Other assays"
13:56 rojasm egonw: if I don't apply any QueryAtomContainer before applying the UniversalIsomorphismTester.isIsomorph that will mean that the isomorph method will compare any property of the IAtom and Bond, isn't it?
13:56 CIA-18 bioclipse: carl_masak * r4842 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/model/Database.java:
13:56 CIA-18 bioclipse: [Database.java]
13:56 CIA-18 bioclipse: * Removed unused imports
14:05 CIA-18 bioclipse: ospjuth * r4843 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (META-INF/MANIFEST.MF plugin.xml): Removed use of namespace EP and imported net.bioclipse.logging again.
14:06 CIA-18 bioclipse: ospjuth * r4844 /branches/bioclipse2/chemoinformatics/ne​t.bioclipse.cdk.ui/META-INF/MANIFEST.MF: Imported net.bioclipse.logging again.
14:07 CIA-18 bioclipse: ospjuth * r4845 /branches/bioclipse2/chemoinformatics/n​et.bioclipse.qsar/META-INF/MANIFEST.MF: Imported net.bioclipse.logging again.
14:08 steinbeck joined #cdk
14:10 CIA-18 bioclipse: carl_masak * r4846 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
14:10 CIA-18 bioclipse: [TreeView.java]
14:10 CIA-18 bioclipse: * added the mocked database alongside the real one
14:10 CIA-18 bioclipse: * still hardcoded, though
15:26 CIA-18 bioclipse: ospjuth * r4847 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (3 files in 3 dirs): Imported net.bioclipse.logging again and updated BioclipseException location.
15:31 CIA-18 cdk: miguelrojasch * r9977 /branches/miguelrojasch/react​ion/src/org/openscience/cdk/ (7 files in 3 dirs): Update the test to junit4. Solved errors in the test. RearrangementRadical* reactions
15:37 rojasm left #cdk
15:48 CIA-18 bioclipse: carl_masak * r4848 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (7 files in 3 dirs): * added new level to the data model: DataFile
15:50 CIA-18 bioclipse: ospjuth * r4849 /branches/bioclipse2/chemoinformati​cs/net.bioclipse.cdk.ui/plugin.xml: Use a contenttype instead of hardcoding file extensions into editor.
15:51 CIA-18 cdk: egonw * r9978 /branches/miguelrojasch/reactio​n/src/org/openscience/cdk/test/ (15 files in 2 dirs): A few compile fixes...
15:59 Annzi left #cdk
16:12 CIA-18 cdk: egonw * r9979 /branches/miguelrojasch/reactio​n/src/org/openscience/cdk/test/ (2 files in 2 dirs): Added some FIXMEs to clean up code
16:42 CIA-18 bioclipse: carl_masak * r4850 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
16:42 CIA-18 bioclipse: [ScriptingConsoleView.java]
16:42 CIA-18 bioclipse: * added TODO
16:42 CIA-18 bioclipse: * rebound HOME button to work as expected
17:31 Annzi joined #cdk
17:37 CIA-18 bioclipse: jonalv * r4851 /branches/bioclipse2/ (5 files in 3 dirs):
17:37 CIA-18 bioclipse: Removed ISequenceCollection. And made changes in sequenceContentprocider and
17:37 CIA-18 bioclipse: Sequencelabelprovider so that the objects in bioobjectlist only are retrieved
17:37 CIA-18 bioclipse: once. This is in order to get nicer recording. Perhaps we can figure out some
17:37 CIA-18 bioclipse: better way to do the recording/script generation because this restrictions feel
17:37 CIA-18 bioclipse: a bit sad...
17:37 CIA-18 bioclipse: olas: please check my changes since it was your code originally
18:00 dleidert joined #cdk
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19:14 CIA-18 jmol: aherraez * r8939 /trunk/Jmol/src/org/openscie​nce/jmol/app/About_nl.html: NL version of About copied from 11_4 branch
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