Camelia, the Perl 6 bug

IRC log for #cdk, 2009-12-11

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All times shown according to UTC.

Time Nick Message
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08:59 CIA-66 cdk: annulen * r15183 /jchempaint/trunk/src/main/org/ope​nscience/jchempaint/dialog/editor/ (7 files): i18n of *Editors
09:00 CIA-66 cdk: annulen * r15184 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/dialog/TemplateBrowser.java: Moved tabs in Templates Browser to the left (as in ChemSketch)
09:03 CIA-66 cdk: annulen * r15185 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (AbstractJChemPaintPanel.java JChemPaintPanel.java): API extended: transparentSnapshot, set/getAppTitle in AbstractJChemPaintPanel
09:20 CIA-66 cdk: annulen * r15186 /jchempaint/trunk/po/ (11 files): Updated keys.pot and all po-files; Russian
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11:18 CIA-66 cdk: shk3 * r15187 /jchempaint/trunk/ (11 files in 3 dirs): moved fest jars to libdevel dir and excluded from build
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11:32 PeterOdeus Bug or Feature? the "search" method of UniversalIsomorphismTester fails in my unit test when there is only one atom in the "second" molecule. The search method demands that the atom must be an IQueryAtom instance... maybe there is room for an if/else construct here?
11:36 egonw hi PeterOdeus
11:36 egonw PeterOdeus: there is a helper class to convert an IAtomContainer into a QueryAtomContainer
11:37 egonw QueryAtomContainerCreator
11:42 PeterOdeus Hi egonw, would the helper class be a temporary workaround? I'm asking because class UniversalIsomorphismTester has several instances of if/else constructs choosing between IQueryAtom and non-IQueryAtom. Why would the search method behave in another way? The javadoc still states that the second molecule _may_ be an IQueryAtomContainer...
11:42 egonw those if/else should only apply to the first passed atomcontainer...
11:43 egonw the second must always be a QueryAtomContainer
11:43 egonw oh wait
11:43 egonw now you got me confused...
11:43 PeterOdeus :-)
11:43 egonw this has been a while...
11:43 egonw one must be a QueryAtomContainer (to allows things like SMARTS)
11:44 egonw the second argument is the query
11:45 egonw and should be a QueryAtomContainer...
11:45 egonw I don't think the 'may' in the JavaDoc is correct...
11:46 egonw it seems the JavaDoc is matching the implementation
11:46 PeterOdeus How 'bout changing the method signatures if the QueryAtomContainer is mandatory?
11:46 egonw OK, going to reread your question now
11:46 egonw the if/else is about the second argument
11:46 egonw as you said
11:47 egonw OK...
11:47 egonw the one atom query is a special case
11:47 egonw because the UIT algorithm works with a three-bond minimum
11:48 egonw so, there are more special cases, really ...
11:48 egonw it seems that the special case is not properly implemented, by not allowing the second argument to be a IAtomContainer...
11:49 egonw PeterOdeus: can you contribute that unit test?
11:49 egonw as GNU FDL?
11:49 egonw otherwise, please send it me confidentially
11:49 egonw and I can pinpoint the code to fix
11:49 egonw I think you found a bug (inconsistency at least)
11:55 PeterOdeus seems that the inconsistency was introduced 2009-11-12
11:55 egonw got a commit hash?
11:56 PeterOdeus dfb28054f2124655cfdff963c3fabc1905a763b9 ???
11:57 PeterOdeus Junit test class is here: http://github.com/mp2D/TestProj/blob/master​/src/test/java/prototyping/InitialTest.java
11:57 zarah PeterOdeus's link is also http://tinyurl.com/y9tpa2m
11:57 egonw PeterOdeus: yes, that looks like the right hash :) thanx
11:59 egonw yes, that seems to be the right commit introducing the regression
12:00 PeterOdeus test case testReactantAndProductWithoutMCS brings a reaction id pointing at a reaction having only one product atom
12:00 egonw PeterOdeus: I need to fix a release blocker for BC 2.2 first... can you please file a bug report?
12:01 PeterOdeus sure. officially? where? how?
12:02 PeterOdeus ...and that single atom is a NNAtom instance which cannot be cast to an IQueryAtom instance.
12:02 egonw you have a SF account?
12:02 egonw PeterOdeus: yes, that cast is indeed that patch
12:02 egonw +          IQueryAtom queryAtom = (IQueryAtom) g2.getAtom(0);
12:03 egonw my bad...
12:03 egonw I approved that patch
12:04 PeterOdeus don't worry about it.
12:04 PeterOdeus re: SF... going there now
12:04 egonw the place would be around:
12:04 egonw sf.net/projects/cdk/develop
12:04 egonw under the Tracker menu/tab/thingy
12:05 PeterOdeus Bugs...
12:06 egonw yes
12:12 PeterOdeus seems like sf doesn't love me too much. I tried to create an account over a month ago, but I never got an initial email. It looks like they don't send an email this time either...
12:12 PeterOdeus File a bug anonymously? I'll try.
12:14 PeterOdeus no dice.
12:17 egonw :(
12:19 egonw OK, I will file a bug report then
12:19 egonw perhaps file a bug report against the SF project... alexander is the code name, I think
12:19 PeterOdeus and I'll try to beg sf for an account ;-)
12:19 egonw nope, but it's something like that :)
12:20 egonw see https://sourceforge.net/apps/​trac/sourceforge/wiki/Support
12:35 egonw PeterOdeus: https://sourceforge.net/tracker/?func=detail&amp​;aid=2912627&group_id=20024&atid=120024
12:47 sneumann PeterOdeus: try a different email adress, it could've been caught by a spamfilter.
12:52 PeterOdeus I tried a 2nd address but no luck. I am raising the issue at #sourceforge
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20:43 CIA-37 cdk: aherraez * r15188 /jchempaint/trunk/po/es.po: Spanish
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21:15 zarah oh hai jpansanel
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