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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: ctakes-vm.apache.org
Date Wed, 16 Apr 2014 16:17:05 GMT
Hi Andy,
Let me know if you're able to ssh -l -v to andymc@ctakes-vm.apache.org
I believe all you would need to do is run ssh-keygen and then copy your public key to id.apache.org.

James: 
opiekey is only required for sudo access.  I see you're able to log in successfully already.
Nethertheless, Jan reset opiekey so you can try again if needed.

https://issues.apache.org/jira/browse/INFRA-7451

--Pei

> -----Original Message-----
> From: andy mcmurry [mailto:mcmurry.andy@gmail.com]
> Sent: Monday, April 07, 2014 5:43 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes-vm.apache.org
> 
> On a mac here, also having trouble logging in to the VM.
> Looking more into the keys situation.
> 
> On mac, there is this problem: "no support for PKCS#11"
> Which I'm working to resolve.
> 
> 
> 
> 
> On Sat, Apr 5, 2014 at 12:15 PM, John Green
> <john.travis.green@gmail.com>wrote:
> 
> > Thanks Pei.
> >
> >
> >
> >
> > Sure, that would be great, add me.
> >
> >
> >
> >
> > Jg
> >
> > --
> > Sent from Mailbox for iPhone
> >
> > On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei
> > <Pei.Chen@childrens.harvard.edu
> > >
> > wrote:
> >
> > > John,
> > > You should have committer rights now... I would suggest opening a
> > > Jira
> > item just so that it can be tracked.
> > > But you should be able create a subdir within
> > https://svn.apache.org/repos/asf/ctakes/sandbox and do an svn commit.
> > > As a side note: ctakes-vm.apache.org has been created now.  John,
> > > let
> > me know if you would like to added as list of maintainers.
> > > We can use that machine to host any of the demo's.
> > > It requires passwordless ssh so you'll need to ssh-keygen and save
> > > them
> > via http://id.apache.org.
> > > --Pei
> > >> -----Original Message-----
> > >> From: John Green [mailto:john.travis.green@gmail.com]
> > >> Sent: Thursday, April 03, 2014 6:05 PM
> > >> To: dev@ctakes.apache.org
> > >> Cc: dev@ctakes.apache.org
> > >> Subject: RE: ctakes-vm.apache.org
> > >>
> > >> Would love to! Ive only submitted those example notes I did though
> > >> to a
> > jira
> > >> ticket. How do I push to the sandbox dir? Any special permissions I
> > need?
> > >>
> > >>
> > >>
> > >>
> > >> JG
> > >>
> > >> --
> > >> Sent from Mailbox for iPhone
> > >>
> > >> On Wed, Apr 2, 2014 at 10:51 PM, Chen, Pei
> > >> <Pei.Chen@childrens.harvard.edu>
> > >> wrote:
> > >>
> > >> > John,
> > >> > If there are no other objections, you can also put it directly in
> > >> > sandbox https://svn.apache.org/repos/asf/ctakes/sandbox/
> > >> > It may make it easier in the future if folks decided to integrate
> > >> > into
> > >> cTAKES... and possibly save any potential IP/License questions...
> > >> > --Pei
> > >> > ________________________________________
> > >> > From: John Green [john.travis.green@gmail.com]
> > >> > Sent: Wednesday, April 02, 2014 6:24 PM
> > >> > To: dev@ctakes.apache.org
> > >> > Subject: Re: ctakes-vm.apache.org Great!
> > >> > Let me clean it up this weekend and ill throw it out onto my github.
> > Will
> > >> post link soon; nlt cob this weekend.
> > >> > JG
> > >> > --
> > >> > Sent from Mailbox for iPhone
> > >> > On Wed, Apr 2, 2014 at 1:53 PM, andy mcmurry
> > >> <mcmurry.andy@gmail.com>
> > >> > wrote:
> > >> >> Yes! Impeccable timing. Where can we find the python source?
> > >> >> On Apr 2, 2014 8:33 AM, "John Green"
> > >> >> <john.travis.green@gmail.com>
> > >> wrote:
> > >> >>> Andy: this is very interesting and exciting.
> > >> >>>
> > >> >>>
> > >> >>>
> > >> >>>
> > >> >>> I hacked out a script that makes a visually appealing
> > >> >>> representation of the aggregate pipeline in d3js that, at
least
> > >> >>> for a clinician, is a nice overall summary of the meta data
generated
> from the pipeline.
> > >> >>> Its really no more than a parser of the xml through the type
> > >> >>> system spitted out into json, but when I was talking to my
> > >> >>> informatics department who didnt know much at all about ctakes,
> > >> >>> it was a great visual summary. Its in python. I dont know
if
> > >> >>> youd want it but it might be worth having the "demo site"
spit
> > >> >>> out a visually appealing graphic like this automatically.
If
> > >> >>> not in python it might be worth adapting it to whatever your
> > >> >>> using for a platform to spit out the
> > json for
> > >> the d3js graphic im using.
> > >> >>>
> > >> >>>
> > >> >>>
> > >> >>>
> > >> >>> John
> > >> >>>
> > >> >>> --
> > >> >>> Sent from Mailbox for iPhone
> > >> >>>
> > >> >>> On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry
> > >> >>> <mcmurry.andy@gmail.com>
> > >> >>> wrote:
> > >> >>>
> > >> >>> > Yes! I have been working full time on the "apt-get install"
> > >> >>> > task specific to medical genetics:
> > >> >>> > http://www.ncbi.nlm.nih.gov/medgen
> > >> >>> > Right now, millions of $$$ are invested in getting phenotype
> > >> >>> > concepts -- indications, diseases, problem lists -- linked
to
> > >> >>> > patient test results including DNA / RNA / etc. In industry,
> > >> >>> > most of the curation work is done manually because platforms
> > >> >>> > like cTAKES are not yet immediately
> > >> >>> accessible.
> > >> >>> > I have written code to
> > >> >>> > A) start automating the installer tasks for cTAKES on
Ubuntu
> > >> >>> > 13
> > >> >>> > B) install UMLS NLP tools metamap, semrep, semmed
> > >> >>> > C) mirror NLM content that extends UMLS annotation *SO
THAT :
> > >> >>> > * Mentions of diseases relationships -- SNOMED-CT, HPO,
OMIM,
> > >> >>> > GTR, UMLS -- reference the same semantic relationships
in
> > >> >>> > UMLS Clinical Terms and Genetic Test Reference. This
is
> > >> >>> > powerful and all credit to the NLM for creating MedGen
and
> > >> >>> > GTR, new crucial additions to the UMLS. To my knowledge,
> > >> >>> > these new sources have not been fully utilized by the
medical NLP
> community.
> > >> >>> > *I'm strongly advocating for a cTAKES VM that indexes
UMLS
> > >> >>> > concepts in
> > >> >>> the
> > >> >>> > same say that NCBI indexes UMLS linked Medical Genetics
> > >> >>> > terms.* Towards this goal, if other committers are
> > >> >>> > interested,  I'm 100% time committed to this problem.
> > >> >>> > *TL;DR*: at minimum, having a demo site makes cTAKES
more
> > >> >>> > accessible. We should demonstrate rather than explain
every
> > >> >>> > feature of cTAKES. I'm
> > >> >>> working
> > >> >>> > 100% on the Clinical Text +BioNLP problem. If that interests
> > >> >>> > you, let me know I'm convinced this area has huge,
> > >> >>> > understudied
> > potential.
> > >> >>> > --AndyMC
> > >> >>> > On Tue, Mar 18, 2014 at 8:15 AM, Pei Chen
> > >> >>> > <chenpei@apache.org>
> > >> wrote:
> > >> >>> >> FYI:
> > >> >>> >> ASF Infra is setting up our VM for demo purposes.
> > >> >>> >> INFRA-7451
> > >> >>> >>
> > >> >>> >> If you need access, feel free to let us now.
> > >> >>> >> Initial maintainers: james-masanz, andymc,chenpei
--Pei
> > >> >>> >>
> >

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