Hello,
The deprecation warnings are harmless (I think) but the abundance issue is
real. My guess is that the problem is that your top-level XML file is
pointing to old chemElement (and no doubt also old chemComp, etc.) data.
(Once upon a time, I forget why, abundance was a percentage but now it is
a fraction.) The easiest way to change this is to edit the top-level XML
file. (So if your project is called Abc, then the file is Abc.xml.) In
that file you will need to change several of the Url entries, the ones
that have name = chemElementData, nmrExpPrototype, chemCompData and
nmrReferenceData (I hope that's all). They will have an incorrect path.
(Note, the update mechanism inside Analysis should -- hopefully -- avert
these problems since it automatically changes the name of the old ccpnmr
directory and calls the new one ccpnmr.)
Wayne
On Thu, 25 Jan 2007, Mark Pfuhl wrote:
> I used version 1.0.13 for the first time and it crashed with a project that
> has been fine with a previous version. This is the output in the shell:
>
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/XmlIO.py:
> [' target = getByKey(clazz,fullKey)\n']
> Deprecated: getByKey called with too short key
> from loadDelayedData line 1100 in /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memop
> ...
> this goes on and on and on and ends thus:
> ...
> Deprecated getResonanceGroups called from conv_ccp_Nmr_1_0_213 line 2025 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/Compatibility.py:
> [' for yy in headObject.resonanceGroups:\n']
> Deprecated getExperiments called from conv_ccp_Nmr_1_1_a2 line 2086 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/Compatibility.py:
> [' for x1 in headObject.experiments:\n']
> Deprecated getAxisTypes called from conv_ccpnmr_Analysis_1_1_a2 line 2564 in
> /usr/local/ccpnmr1.0.13/ccpnmr1.0/python/memops/format/xml/Compatibility.py:
> [' for x0 in headObject.axisTypes:\n']
> last xml element read:
> <Isotope _ID="_2" massNumber="169" gyroMagneticRatio="-22100000.0"
> mass="168.934211" abundance="100.0" receptivity="0.00056599999999999999"
> magneticMoment="-0.40000000000000002" spin="1/2">
>
>
> parser state was:
> reading
>
> ERROR loading xml ccp.molecule.ChemElement chemElements.xml
>
>
> In addition an error window pops up:
>
> Project invalid, please quit, fix and re-start:
> ccp.molecule.ChemElement.Isotope.setAbundance:FloatRatio
> constraint value_le_1 violated by value:100.0
>
> any suggestions?
> thanks,
> mark
>
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