Thanks Chris,
Your pointer is to the executable bundle. I had downloaded the source,
loaded it into eclipse and searched for the jar through google, but could
never find the chemspider jar alone. (so the error messages were in
eclipse, jar not found, not at run time.)
Thank you. I have now gotten it. Should it be made available from some
source as a standalone jar? Would Chemspider want to offer it for other
java programmers? I think it is probably quite universally handy.
Best wishes,
Chris
On Tue, Sep 27, 2011 at 11:48 PM, Pudney Chris (ext) GBJH <
chris.pud...@syngenta.com> wrote:
> G'day,
>
> I just downloaded
> MZmine-2.3<http://sourceforge.net/projects/mzmine/files/mzmine2/2.3/>and the
> JAR file is present.
>
> After unzipping it's in MZmine-2.3/lib/chemspider-api.jar
>
> I tested this version and was able to search ChemSpider without problems.
>
> When you say that the ChemSpider search isn't working, are you seeing error
> messages?
>
> Are you running on Linux/Windows/MacOS, and are you using the startMZmine
> script to run the program?
>
> Regards,
> Chris.
>
> P.S. CC'd mzmine-devel mailing list
>
> On 27/09/11 22:12, Chris Beecher wrote:
>
> Thanks Chris,
>
> This helps a lot. Is the jar available from anywhere? It is not part of
> the distribution and I have searched high and low to find it.
>
> I did read the Axis/WSDL2Java, but am not sure I fully understand how to
> create one myself. I am running MZmine 2.3 and like it quite a bit. All
> the bits to work (except the chemspider link) and I have begun making small
> tweaks to optimize MZmine for my particular problem. If the jar is not
> available I will put this on the list of things to do and thank you for the
> advice when I get to it. If it is available somewhere I would like to use
> it.
>
> Best wishes,
>
> Chris Beecher
>
> Director, Metabolomics Facility
> University of Michigan Medical School
>
> On Mon, Sep 26, 2011 at 11:08 PM, Pudney Chris (ext) GBJH <
> chris.pud...@syngenta.com> wrote:
>
>> G'day,
>>
>> Apologies for the delay in responding, I've been busy with other projects.
>>
>> Yes, I wrote the ChemSpider module for MZmine.
>>
>> The JAR file for the ChemSpider is lib/chemspider-api.jar. It was
>> automatically generated using
>> WSDL2Java<https://ws.apache.org/axis/java/user-guide.html#WSDL2JavaBuildingStubsSkeletonsAndDataTypesFromWSDL>from
>> the WSDL for the Mass Spec and Search APIs
>>
>> http://www.chemspider.com/MassSpecAPI.asmx?WSDL
>> http://www.chemspider.com/Search.asmx?WSDL
>>
>> I tested the ChemSpider search module today (on the latest release of
>> MZmine v2.3) and it works fine for me.
>>
>> What errors are you seeing when you try to run ChemSpider searches from
>> MZmine? Are you using the latest version?
>>
>> There have been periods when the service was down. Also MZmine has
>> recently been undergoing active development and for a period some on-line
>> database searches were broken - perhaps you had downloaded such a version?
>>
>> Please try the latest MZmine v2.3.
>>
>> If you experience any issues (with ChemSpider or other features) then
>> please post them to the mzmine-devel mailing
>> list<http://sourceforge.net/mailarchive/forum.php?forum_name=mzmine-devel>
>> .
>>
>> Regards,
>> Chris.
>>
>
>
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