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[bioontology-support] FW: BioPortal VM Image - access information

Paul R Alexander palexander at stanford.edu
Wed Dec 1 15:29:43 PST 2010


Sina,

The ncbo-appliance.ovf file does indeed have a different SHA1 hash than 
what is listed in the manifest. I'm not sure how this could be, but we 
haven't tested this on Windows so perhaps that is the cause.

Could you try replacing something in the manifest file for me? I've 
generated a new SHA1 hash based on the file you sent me, so switch:
SHA1(ncbo-appliance.ovf)= 63ff730146c82b6ad680e92e523b8c8d38bf298c
to
SHA1(ncbo-appliance.ovf)= db622f8777c9b0a0c458d78565baf5900f091fdc

And then run the utility again.

Sorry for the trouble.

Paul


On 12/1/10 2:40 PM, Madani,Sina wrote:
>
> Nope, I just deleted all files, unzipped the tar file (using 7-zip), 
> and re-ran the tool but got the same error. I am downloading the tar 
> file again just in case it's related to download.
>
> I attached my manifest and ovf file in case it helps to troubleshoot
>
> Sina
>
> *From:*Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Wednesday, December 01, 2010 4:34 PM
> *To:* Madani,Sina
> *Cc:* support at bioontology.org
> *Subject:* Re: [bioontology-support] FW: BioPortal VM Image - access 
> information
>
> Did you alter the ncbo-appliance.ovf file at all? This would result in 
> the hash not matching what is in the manifest (a security precaution). 
> You could try decompressing the archive from scratch to make sure 
> nothing was modified.
>
> Paul
>
>
> On 12/1/10 2:31 PM, Madani,Sina wrote:
>
> Hi Paul,
>
> I wasn't running ovftool in the unzip directory. So I copied all the 
> unzipped appliance zipped file in the ovf tool program folder and ran 
> it again. This time I got below error.
>
> The second screenshot shows ovf tool directory with all 3 disk images, 
> their sizes and the manifest file content. Is it an indication of a 
> bad download?
>
> Thanks for the help
>
> Sina
>
> *From:*Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Wednesday, December 01, 2010 4:17 PM
> *To:* Madani,Sina
> *Cc:* support at bioontology.org <mailto:support at bioontology.org>
> *Subject:* Re: [bioontology-support] FW: BioPortal VM Image - access 
> information
>
> Sina,
>
> The OVF file won't open directly in the VMWare Player (as you 
> discovered) so the recommended route is to convert, just as you tried 
> to do. I'm wondering if you can see the file 
> (ncbo-appliance-disk3.vmx) in the same directory that you're running 
> the ovftool? Also, there should be a manifest file (ncbo-appliance.mf) 
> and it looks like that is missing too. You need to run ovftool in the 
> same directory as all of the files that were in the archive that you 
> downloaded.
>
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal <http://bioportal.bioontology.org>
> Stanford Center for Biomedical Informatics Research
>
>
> On 12/1/10 1:08 PM, Madani,Sina wrote:
>
> Hi Trish,
>
> I downloaded and unzipped the appliance file. I tried to open the 
> ncbo-appliance ovf file using vmware player but got the error shown 
> below. Then I tried converting it into a vmx file using ovf tool but 
> got error again (last screenshot). Any hint?
>
> Thanks
>
> Sina
>
> *From:*Trish Whetzel [mailto:whetzel at stanford.edu]
> *Sent:* Tuesday, November 23, 2010 4:00 PM
> *To:* Madani,Sina
> *Subject:* BioPortal VM Image - access information
>
> Thank you for providing the user metrics information. The VM image can 
> be downloaded from:
>
> http://www.bioontology.org/ncbo-appliance/ncbo-appliance-v0.1.tar
> and the documentation is at:
> http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
> If you have any questions with the installation, please email 
> support at bioontology.org <x-msg://7/support@bioontology.org>.
>
> Trish
>
> On Nov 22, 2010, at 12:22 PM, Madani,Sina wrote:
>
>
>
>
>
> Hi Trish,
>
> We previously tested MetaMap for analyzing our dictated notes but when 
> Nigam presented his talk about Mgrep and the fact that it can process 
> text files more accurately we decided to launch a local version of it 
> because we didn't want to send our patient dictation files over the 
> net to Bioportal text analysis services.
>
> The intended user at this moment is only I &  possibly Mike Riben. I 
> anticipate to run the instance for text processing of at least 5 
> million clinical dictated notes.
>
> Sina
>
> *From:*Trish Whetzel [mailto:whetzel at stanford.edu]
> *Sent:*Monday, November 22, 2010 1:59 PM
> *To:*Madani,Sina
> *Cc:*Ray Fergerson
> *Subject:*Re: AMIA workshop
>
> Hi Sina,
>
> The support forum that Ray mentioned is our mailing 
> list:support at bioontology.org <mailto:support at bioontology.org>.  Can 
> you provide a short description on how you plan to use the VM image 
> and the expected number of users? We are collecting additional user 
> metrics in response to queries from our Advisory Board.
>
> Thanks!
>
> Trish
>
> On Nov 22, 2010, at 6:25 AM, Madani,Sina wrote:
>
>
>
>
>
>
> Thank you Ray.
>
> What is the url for support forum?
>
> Sina
>
> *From:*Ray Fergerson [mailto:ray.fergerson at stanford.edu]
> *Sent:*Friday, November 19, 2010 4:16 PM
> *To:*'Nigam Shah'; Madani,Sina
> *Cc:*'Trish Whetzel'
> *Subject:*RE: AMIA workshop
>
> Sina,
>
> Happy to hear you are interested in the VM instance. Trish (copied) is 
> responsible for collecting the necessary information and providing you 
> with the link. She also monitors the support mailing list where you 
> should send any help requests.
>
> Ray
>
> *From:*Nigam Shah [mailto:nigam at stanford.edu]
> *Sent:*Friday, November 19, 2010 10:15 AM
> *To:*Madani,Sina
> *Cc:*Ray Fergerson;support at bioontology.org 
> <mailto:support at bioontology.org>
> *Subject:*Re: AMIA workshop
>
> Hi Sina,
>
> It was good to meet you as well. I am copying Ray Fergerson, our 
> project manager, who can direct you to getting a VM instance.
>
> Regards,
>
> Nigam.
>
> ps: I will be leaving for a month long trip to my home country, from 
> Nov 26 - Dec 29 so might be unresponsive on email.
>
> On Fri, Nov 19, 2010 at 6:48 AM, Madani,Sina <AHMadani at mdanderson.org 
> <mailto:AHMadani at mdanderson.org>> wrote:
>
> Hi Nigam,
>
> It was very nice meeting you at AMIA. I really enjoyed your workshop 
> presentation. We talked briefly about the possibility of a VM instance 
> that Bioportal can provide for our institution note analysis purposes. 
> I appreciate your help on this.
>
> Thanks
>
> Sina
>
> Sina Madani, MD MS
>
> Data Integration & Modeling
>
> MD Anderson Cancer Center
>
> Phone : 713-563-1803
>
> Trish Whetzel, PhD
>
> Outreach Coordinator
>
> The National Center for Biomedical Ontology
>
> Ph: 650-721-2378
>
> whetzel at stanford.edu <mailto:whetzel at stanford.edu>
>
> http://www.bioontology.org <http://www.bioontology.org/>
>
>   
>   
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu  <mailto:bioontology-support at lists.stanford.edu>
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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