G'day,
>From where did you download the source? Was it the subversion repository? If so perhaps you just downloaded the src directory. All the required JARs (chemspider-api.jar) are in the lib directory. If you want to build MZmine from source then fetch everything from the trunk directory - you'll need all of it.
Regards,
Chris.
On 29/09/11 00:13, Chris Beecher wrote:
>From where did you download the source? Was it the subversion repository? If so perhaps you just downloaded the src directory. All the required JARs (chemspider-api.jar) are in the lib directory. If you want to build MZmine from source then fetch everything from the trunk directory - you'll need all of it.
Regards,
Chris.
On 29/09/11 00:13, Chris Beecher wrote:
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 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 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.
Regards,
Chris.
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