Hi Andy, Let me know if you're able to ssh -l -v to and...@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.a...@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.gr...@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.c...@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.gr...@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.c...@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.gr...@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.a...@gmail.com> > > >> > wrote: > > >> >> Yes! Impeccable timing. Where can we find the python source? > > >> >> On Apr 2, 2014 8:33 AM, "John Green" > > >> >> <john.travis.gr...@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.a...@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 > > >> >>> > <chen...@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 > > >> >>> >> > >
