From: Stefan K. <ste...@eb...> - 2008-06-30 18:47:21
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Hi all, today I had a look at the bug #1930029 and I added the test (org.os.cdk.io.cml.CMLCustomPropertyTest) to trunk and tried to fix the problems. But two problems remain: 1. In CMLCoreModule in line 608 and following there is code like bondCustomProperty.add(elementTitle); bondCustomProperty.add("true");//TODO here the value of the scalar must go in I must admit I have no idea how to read the value of the current element here. Or is this considered another element? Anybody an idea? 2. The test also contains a comparision of the input to the output after the roundtrip. This fail (I commented them out). Differences are things like isotopenumber given in output, but not in input explicitly. Even if one could fix e. g. the isotope stuff, it is still questionable if a verbatim comparision makes sense for cml. What do you think? Stefan |
From: Daniel Z. <zah...@dt...> - 2008-07-01 12:02:40
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On Jun 30, 2008, at 2:47 PM, Stefan Kuhn wrote: > Hi all, > today I had a look at the bug #1930029 and I added the test > (org.os.cdk.io.cml.CMLCustomPropertyTest) to trunk and tried to fix > the > problems. But two problems remain: > 1. In CMLCoreModule in line 608 and following there is code like > bondCustomProperty.add(elementTitle); > bondCustomProperty.add("true");//TODO here the value of the scalar > must go in > I must admit I have no idea how to read the value of the current > element here. > Or is this considered another element? Anybody an idea? > 2. The test also contains a comparision of the input to the output > after the > roundtrip. This fail (I commented them out). Differences are things > like > isotopenumber given in output, but not in input explicitly. Even if > one could > fix e. g. the isotope stuff, it is still questionable if a verbatim > comparision makes sense for cml. > What do you think? > I plan to work on this. I got Jim Downing to put together a Jumbo release so I could get the things I needed in Jumbo into an official release that could be synched up with CDK. That has happened, but I've had some other distractions over the last 4-6 weeks. I should be able to get some significant time to work on this starting early next week. DanZ /******************************************** Daniel Zaharevitz Chief, Information Technology Branch National Cancer Institute zah...@dt... ********************************************/ |
From: Egon W. <ego...@gm...> - 2008-07-01 12:06:43
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On Mon, Jun 30, 2008 at 8:47 PM, Stefan Kuhn <ste...@eb...> wrote: > today I had a look at the bug #1930029 and I added the test > (org.os.cdk.io.cml.CMLCustomPropertyTest) to trunk and tried to fix the > problems. Your attempts broke two existing unit tests: testPartialCharge(org.openscience.cdk.io.cml.CMLRoundTripTest) testDescriptorValue(org.openscience.cdk.io.cml.CMLRoundTripTest) As reported by Nightly... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Peter Murray-R. <pm...@ca...> - 2008-07-01 12:37:18
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Daniel Zaharevitz wrote: > > On Jun 30, 2008, at 2:47 PM, Stefan Kuhn wrote: > >> Hi all, >> today I had a look at the bug #1930029 and I added the test >> (org.os.cdk.io.cml.CMLCustomPropertyTest) to trunk and tried to fix the >> problems. But two problems remain: >> 1. In CMLCoreModule in line 608 and following there is code like >> bondCustomProperty.add(elementTitle); >> bondCustomProperty.add("true");//TODO here the value of the scalar >> must go in >> I must admit I have no idea how to read the value of the current >> element here. >> Or is this considered another element? Anybody an idea? >> 2. The test also contains a comparision of the input to the output >> after the >> roundtrip. This fail (I commented them out). Differences are things like >> isotopenumber given in output, but not in input explicitly. Even if >> one could >> fix e. g. the isotope stuff, it is still questionable if a verbatim >> comparision makes sense for cml. >> What do you think? >> > > I plan to work on this. I got Jim Downing to put together a Jumbo > release so I could get the things I needed in Jumbo into an official > release that could be synched up with CDK. That has happened, but I've > had some other distractions over the last 4-6 weeks. I should be able > to get some significant time to work on this starting early next week. > Thanks Dan and Stefan. We have frozen a JUMBO release and will try to fix bugs in it. If you are linking against JUMBO you should use Jim's release. I announced that there had been changes to the trunk so anyone developing against that should be aware that some methods have been changed. P. > DanZ > > /******************************************** > Daniel Zaharevitz > Chief, Information Technology Branch > National Cancer Institute > zah...@dt... <mailto:zah...@dt...> > ********************************************/ > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ------------------------------------------------------------------------ > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |
From: Egon W. <ego...@gm...> - 2008-07-01 12:38:54
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On Tue, Jul 1, 2008 at 2:37 PM, Peter Murray-Rust <pm...@ca...> wrote: > Thanks Dan and Stefan. We have frozen a JUMBO release and will try to > fix bugs in it. If you are linking against JUMBO you should use Jim's > release. I announced that there had been changes to the trunk so anyone > developing against that should be aware that some methods have been > changed. First step for the CDK would be to implement the matching CML Schema... Peter, what schema version matches this new Jumbo release? Egon -- ---- http://chem-bla-ics.blogspot.com/ |