cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Chen, Pei" <Pe...@childrens.harvard.edu>]

Thanks Andy for the feedback.
Examples are a good idea- Were you thinking of adding it to the README file or the confluence user guide?

Feel free to update the downloads page(s) (it uses Apache CMS) and the User Guides (Confluence wiki).  
Note: The release is still being replicated to all of the mirrors and may take up to 24 hrs, so I would wait until after the weekend before testing all of the mirror links.

--Pei
________________________________________
From: Andy McMurry [mcmurry.andy@gmail.com]
Sent: Friday, February 15, 2013 11:08 PM
To: ctakes-dev@incubator.apache.org
Subject: Re: [DISCUSS] Graduate cTAKES from Incubator

Clarifications

There isn't a last Apache release. But there are last previous NIH, Sourceforge, and Apache releases?
TODO: Project History Page (Simple, just the releases and times, ideally with JIRA generated release notes).

Suggestion: Demonstration > explanation. Use Examples !!

EXAMPLE 1 : Basic Pipeline (without UMLS)

** SHOW Before and after clinical text, demonstrates purpose
** LIST the 5 steps
** Most impressive demo would be the smoking status pipeline

EXAMPLE 2: Basic Pipeline (with UMLS)

** SHOW Before and after (input text -> output annotations)
** LIST the steps
** Most impressive demo would be a negation of a cancer diagnosis and NER of a medication (chemotherapuetic drug).

Thoughts?
--andy


On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com> wrote:

> Sure thing Pei.
>
> I dont think cTAKES is ready for attention grabbing release (humble opinion).
> And when you release you want to grab attention! ! cTAKES is awesome!!
>
> Suggestions (release blockers)
>
> (1) Downloads
> http://incubator.apache.org/ctakes/downloads.cgi
> ! Link to install instructions is not there but "Verifying signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> ! Last official release is blank because there isn't one, remove it
> ! First mirror I tried was a 404? (not sure which one). I changed the mirror then OK. Test all mirrors (script)
> ? Previous releases are VERY confusing.
> ? The NIH and SourceForge pages  should redirect to cTAKES, google "cTAKES download" and imagine how confused a beginner would be.
>
> (2) User Guide
> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> ? 3.0.0 : no list of new features from last stable release. Why would a user bother to upgrade to a beta?
> ! Would be better to have a bundled download with resources, if possible. Otherwise, make it clear to a newcomer what the benefit of getting UMLS / LVG is. (one sentence).
> ! Needs a very high level overview of the components in the context of using them to do a very basic task like.
> ! This is likely the most frequently accessed document for cTAKES. It has almost no pointers to where to find basic information.
>
> (3) OTHER
> * The NCI and SourceForge links are now highly confusing.
> * While I am downloading, I should be reading the recommended "Get Started" guide
>
> I'm still downloading the 2GB resources file.
> I'll try and get back to you about the install when that is done too.
>
> This constructive criticism is because I believe cTAKES is AWESOME.
> Hard to see how awesome it is given the current instructions.
>
> --Andy
>
>
> On Feb 15, 2013, at 5:02 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>
>> Hi Andy,
>> So much has changed in cTAKES since last year, if you have a chance- do you also want to try downloading the -bin and ensure at least the steps in the README are able to get you started?
>>
>> --Pei
>> ________________________________________
>> From: Andy McMurry [mcmurry.andy@gmail.com]
>> Sent: Friday, February 15, 2013 4:04 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>
>> Suggestion: can we get a good programmer with no cTAKES experience to kick the tires and tell us how long it took to get started?
>>
>> John Resig (jQuery founder) once told me "if it takes more than 15 minutes to get started, then that is way too long".
>>
>> "What is necessary is that enough investment be put into presentation that newcomers can get past the obstacle of unfamiliarity. …
>> Hactivation energy: the amount of energy a newcomer must put in before she starts getting something back"
>> -- From "Producing Open Source Software"
>>
>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hacktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9WGk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q=hacktivation%20energy&f=false
>>
>>
>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>>
>>> This is to open a discussion to graduate Apache cTAKES podling from the Apache Incubator.
>>>
>>> Apache cTAKES entered the Incubator in June of 2012. We have made significant progress with the project since moving over to Apache. We currently have 18 committers listed on our status page at [1] including over 10 which accepted after the podling was formed.
>>>
>>> During incubation, cTAKES has :
>>> * Produced 1 Release
>>> * Added 10 new Committer/PPMC members and shows constant community activities
>>> * Cleared IP on code
>>> * Developed Roadmap(s) for the next major and minor releases in a community process and started working on that [2]
>>> * The community of Apache cTAKES is active, healthy, and growing and has demonstrated the ability to self-govern using accepted Apache practices.
>>>
>>> [1] http://people.apache.org/committers-by-project.html#ctakes
>>> [2] https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassian.jira.plugin.system.project%3Aroadmap-panel
>>>
>>
>

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Masanz, James J." <Ma...@mayo.edu>]

+1 for examples. Thanks for volunteering to do those two.
cTAKES 2.5 had a testdata directory. I think we should get that added back into the binary distribution along with sample output, but I think that can wait for post-3.0.  I will update CTAKES-163 to be more general about that rather than about just one file.


Regards, 
James Masanz

> -----Original Message-----
> From: ctakes-dev-return-1256-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1256-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of andy mcmurry
> Sent: Tuesday, February 19, 2013 9:39 PM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> +1 nomination to graduate ctakes.
> +1 request to create examples
> 
> I'll attempt the smoking status and medication NER examples for after
> release (volunteer for task) On Feb 19, 2013 10:29 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu>
> wrote:
> 
> > I don't think ASF automatically makes any official press releases
> > about graduated projects other than the public resolutions.  But in
> > our announce to general@ about the release, I think we can explicitly
> > say that this is our first release in ASF and that it was primarily an
> > infra one just to make the move from SF to ASF.
> > (Essentially for us to learn the ropes here.)
> >
> > Also feel free to take a peek at:
> > https://issues.apache.org/jira/browse/CTAKES
> > There are plenty of items we could do to improve cTAKES for the
> > upcoming
> > release(s) [Hopefully we'll be able to follow the "Release Early,
> > Release Often" philosophy [1]] .  Will welcome any contributions
> > (especially yours regarding the end user experience which I think it's
> > extremely important) and also feel free to add to the Jira items...
> >
> > My point of view with OS is that if something sucks, you can usually
> > expect it to be fixed pretty fast as long as there is an mechanism for
> > accepting changes.  I believe ASF is much more about building a
> > diverse community and to have a framework in place for folks to make
> > contributions (so I actually don't necessary believe it is negative
> > that more people use cTAKES and therefore could be future
> contributors).
> >
> > [1] http://incubator.apache.org/guides/graduation.html#releases
> >
> > --Pei
> >
> > ________________________________________
> > From: andy mcmurry [mcmurry.andy@gmail.com]
> > Sent: Tuesday, February 19, 2013 8:42 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> > from Incubator
> >
> > Message received, and from that perspective I agree to graduate.
> >
> > Revised proposal to group:  no press advertisements about the release
> > until docs are ready.
> >
> > . If Apache does promotions for graduated incubators then we should
> > request holding off press releases until the docs are ready.
> >
> > My  battle scars from other open source projects remind me that if you
> > ask for attention be ready for lots of questions and short attention
> spans.
> > On Feb 19, 2013 6:13 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
> > wrote:
> >
> > > Andy,
> > > The purpose of this release is primarily infrastructural. There are
> > > a lot of tasks involved in the move to ASF and many reasons for
> > > separating his release. One of them is that it's probably not a
> > > great idea to have major code fixes/changes mixed in with just a
> refactoring change.
> > >
> > > Regarding ease of use- agree with all of the points.
> > > cTAKES has historically been a collection of annotators and reusing
> > UIMA's
> > > UI as examples and no real application built on top of it. However,
> > > there is a web GUI current in sandbox that should make things more
> intuitive.
> > > However, in order to produce releases efficiently and often, I
> > > believe we need graduate to a TLP (based on experience so far with
> the incubator).
> > We
> > > should be able to address those issues fairly quickly with
> > > incremental releases.
> > >
> > > The downloads page should work all the time as its pretty basic
> > > functionality; It's not good if its flaky. Could others recreate the
> > issue?
> > > Would be good if others could recreate it so we could get to the
> > > root of the issue.
> > > My 2 cents.
> > >
> > > -Pei
> > > Sent from my iPhone
> > >
> > > On Feb 19, 2013, at 5:47 PM, "andy mcmurry" <mc...@gmail.com>
> > > wrote:
> > >
> > > > Thank you Troy!
> > > >
> > > > *Summary: what is the purpose of the 3.0.0 release: changing the
> > license
> > > to
> > > > Apache or getting new users? *
> > > >
> > > > Releasing 3.0.0 without DOCS is OK so long as the expected user
> > > > base is CURRENT cTAKES users.
> > > > If that is the case and this transition is 100% about changing the
> > > license
> > > > to Apache, then OK.
> > > >
> > > > NEW users coming to cTAKES will probably be overwhelmed, for all
> > > > the reasons discussed.
> > > > We will likely "lose" these new users who will not come back when
> > > > the
> > > docs
> > > > are ready a month later.
> > > >
> > > > *Question for the group : who is the intended audience of the
> > > > 3.0.0 release? *
> > > >
> > > >
> > > > On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <
> > Bleeker.Troy@mayo.edu
> > > >wrote:
> > > >
> > > >> Summarizing where we are now ... completed items at the bottom of
> > > >> the
> > > list
> > > >> for reference only.
> > > >>
> > > >> The community decided to release cTAKES 3.0 without the doc being
> > > complete
> > > >> - these must be next:
> > > >> - The Developer Guide is not complete.
> > > >> [TODO] Dev Guide needs command line install instructions for UMLS
> > ID/pw
> > > >> and classpath. I'll work on this.
> > > >> - The User Guide has a caveat on the table at the bottom of the
> > > >> instructions because a similar set of examples was not
> > > >> distributed
> > like
> > > it
> > > >> was in 2.5. The instructions are longer as well since the user
> > > >> could
> > not
> > > >> just load and run existing samples.
> > > >> [TODO] Consider shipping test data resources from SourceForge in
> > > >> a ZIP file.
> > > >> - The Getting Started page needs to be written in context of all
> > future
> > > >> releases not just 3.0.
> > > >> [NEEDS REVIEW] A page was written. Is it as expected?
> > > >> - Previous releases list. We need to both point to the NCI sites
> > > >> for
> > 2.6
> > > >> and back plus create an archive for what will be the history of
> > > >> Apache releases. Needs work your right.
> > > >> [TODO] For now I removed 2 of the 3 links leaving only one that
> > > >> points back to NCI for 2.5 and back. Question is should we have a
> > > >> full
> > listing
> > > of
> > > >> the 2.5 and previous releases on the Apache site or simply point
> > > >> to
> > the
> > > NCI
> > > >> wiki. If point to NCI then there is no archive to be had yet
> > > >> since the
> > > only
> > > >> release in Apache is the current release.
> > > >> - Component Use Guide pages needing updates. There are items
> > > >> marked in reddish color that are incorrect or in need of updates
> on these pages:
> > > >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+C
> > > >> ore
> > > >>
> > > >>
> > >
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Depend
> > ency+Parser+and+Semantic+Role+Labeler
> > > >>
> > > >>
> > >
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+N
> > amed+Entity+Recognition
> > > >>
> > >
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Con
> > texts
> > > >>
> > > >>
> > >
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Te
> > rm+Spotter
> > > >>
> > >
> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Ta
> > gger
> > > >> [TODO] Component knowledgeable people must update these pages.
> > > >>
> > > >> Potential priorities after that:
> > > >> - The examples, as described by Andy, would be more than a readme
> > should
> > > >> have. This would be great for a how-to guide. The Developer Guide
> > > >> and
> > > User
> > > >> Guide have historically been install guides not how-to guides. I
> > > >> don't think a how-to guide should be incorporated into these but
> > > >> should be
> > its
> > > >> own document.
> > > >> [TODO] Should the current user and dev guides be renamed?
> > > >> - cTAKES has never had a how-to guide that I know of. Making one
> > > >> would
> > > be
> > > >> great and as you say should include things like 1) pointers to
> > > >> where
> > to
> > > >> find basic information 2) very high level overview of the
> > > >> components
> > in
> > > the
> > > >> context of using them to do a very basic task like 3) I think it
> > > >> was suggested that the Getting Started page might be something
> > > >> like this
> > in
> > > >> very short form. If we did that then it would point to a more
> > > comprehensive
> > > >> how-to guide.
> > > >> [TODO] Decide if we are going to do this.
> > > >> - Project history page of all cTAKES releases placed on Apache
> > > >> sites somewhere. Good plan if short. I would not copy readmes
> > > >> there but have links to them.
> > > >> [TODO] This was done in the past but removed from the bottom of
> > > >> the downloads page. This page exists now but is not linked to
> > > >> from the
> > > Apache
> > > >> cTAKES site. Here is a direct link:
> > > >> http://incubator.apache.org/ctakes/roadmap.html  It would need
> > > >> 3.0
> > info
> > > >> added if we decide to use it.
> > > >> - Creating a single download for a newcomer.
> > > >> [LATER] This has been discussed and tabled by the community for
> > > >> the
> > time
> > > >> being in order to get the 3.0 release done and out the door. We
> > > >> need
> > to
> > > >> come back to this in order to make the best first impression.
> > > >>
> > > >> Completed:
> > > >> - The downloads page must work. It now seems to function alright
> > > ***IF***
> > > >> you refresh the page or select a mirror and click the Change
> button.
> > If
> > > you
> > > >> do neither and try to download you get this error: "The requested
> > > >> URL
> > > >>
> > >
> > /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin
> > .tar.gz
> > > >> was not found on this server." Anyone have time to fix this?
> > > >> [WORK-AROUND] Seems intermittent. Tried 5 different machines.
> > > >> James
> > and
> > > >> Troy changed the downloads page to tell the user to select the
> > > >> Change button when they have issues. It should work if they do
> > > >> that. Best
> > > guess -
> > > >> the randomly selected mirror sites do not all work. Also,
> > > >> selecting a
> > > site
> > > >> in the drop-down and pressing the Change button does not set the
> > mirror
> > > >> site to the one you selected. Next best guess - other Apache
> > > >> sites
> > have
> > > a
> > > >> double // in the URL just after the mirror domain in the file
> > > >> download link. Maybe this is required. Tried this too.
> > > >> - Adding a link to the install instructions makes it obvious
> > > >> (which I
> > > have
> > > >> done to the page) but it was there in a sense.
> > > >> [DONE] Link added.
> > > >> - "Last official release" was held until now. Since 3.0 is going
> > > >> to be officially announced, 3.0 will go there. I made that change
> as well.
> > > >> [DONE] Reworked the page.
> > > >> - A list of changed features has not been high priority since the
> > > original
> > > >> goal was to make a 3.0 in Apache that pretty much matched the
> > > >> function
> > > of
> > > >> 2.5. The only thing that changed was how the product is built and
> > > shipped.
> > > >> Nevertheless we need to state at least that somewhere.
> > > >> [DONE] That was wrong, there is new function. Relation Extractor
> > > >> now documented on the downloads page.
> > > >> - The resources file is 1.1 GB not 2 right?
> > > >> [DONE] Andy said it in an email. The web site lists it fine.
> > > >> - There are still 3.0 developer and user guide pages on the
> > > >> cTAKES
> > home
> > > >> site that should be removed so no one stumbles on to them.
> > > >> [DONE] Removed.
> > > >> - Where would a newcomer hit first? Internet search for "ctakes"
> > > >> or "ctakes 3.0" is probably first. Top hits on those lists should
> > > >> be
> > > modified
> > > >> to point to the best Apache cTAKES landing page.
> > > >> [DONE] James and Troy made changes to the top hit pages and other
> > places
> > > >> that made sense.
> > > >> - The current guides are still not complete.
> > > >> [DONE] User Guide James and Troy went through.
> > > >>
> > > >> Thanks
> > > >> Troy
> > > >>
> > > >> -----Original Message-----
> > > >> From: ctakes-dev-return-1250-Bleeker.Troy=
> > mayo.edu@incubator.apache.org
> > > [mailto:
> > > >> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org
> > > >> ] On Behalf Of Masanz, James J.
> > > >> Sent: Tuesday, February 19, 2013 10:10 AM
> > > >> To: 'ctakes-dev@incubator.apache.org'
> > > >> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate
> > > >> cTAKES
> > > from
> > > >> Incubator
> > > >>
> > > >>
> > > >>> - The resources file is 1.1 GB not 2 right?
> > > >>
> > > >> I agree. But I don't see it listed as 2GB on the download page.
> > > >> If you tell me where you saw it listed as 2GB I will update that
> page.
> > > >>
> > > >>> - A list of changed features has not been high priority since
> > > >> I will update the downloads page right now stating the relation
> > > extractor
> > > >> is new for 3.0
> > > >>
> > > >>
> > > >>> - Where would a newcomer hit first? Internet search for "ctakes"
> > > >>> or "ctakes 3.0" is probably first. Top hits on those lists
> > > >>> should be modified to point to the best Apache cTAKES landing
> page.
> > > >>
> > > >> I modified the following pages to have a link to Apache cTAKES
> > > >> home
> > page
> > > >>
> > > >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
> > > >> https://sourceforge.net/projects/ohnlp/files/cTAKES/
> > > >> https://sourceforge.net/projects/ohnlp/
> > > >> http://ohnlp.sourceforge.net/
> > > >>
> > > >> The update to the last one is not appearing yet, but it was
> updated.
> > > >>
> > > >>> - The Getting Started page needs to be written in context of all
> > future
> > > >>> releases not just 3.0.
> > > >>
> > > >> Looks like you updated that page, thanks.
> > > >>
> > > >>> - The current guides are still not complete.
> > > >>
> > > >> I took a quick run through the User Guide on the Wiki and made
> > > >> some updates.
> > > >>
> > > >> -- James Masanz
> > > >>
> > > >>
> > > >>> -----Original Message-----
> > > >>> From: ctakes-dev-return-1239-Masanz.James=
> > > mayo.edu@incubator.apache.org
> > > >>> [mailto:ctakes-dev-return-1239-
> > > >>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of
> > > >>> Bleeker,
> > Troy
> > > >>> C.
> > > >>> Sent: Monday, February 18, 2013 10:58 AM
> > > >>> To: ctakes-dev@incubator.apache.org
> > > >>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate
> > > >>> cTAKES from Incubator
> > > >>>
> > > >>> All the suggestions and discussion are good. There's a lot here,
> > sorry
> > > >>> for the long summary. First things first:
> > > >>>
> > > >>> - The downloads page must work. It now seems to function alright
> > > >>> ***IF*** you refresh the page or select a mirror and click the
> > > >>> Change button. If you do neither and try to download you get
> this error:
> > "The
> > > >>> requested URL
> > /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> > > >>> incubating-bin.tar.gz was not found on this server." Anyone have
> > > >>> time
> > > to
> > > >>> fix this?
> > > >>> - Adding a link to the install instructions makes it obvious
> > > >>> (which I have done to the page) but it was there in a sense. The
> > > >>> page said
> > "Use
> > > >>> the Developer and User Guides to direct you through the
> > > >>> installation process." and the links to those were just to the
> > > >>> left in the
> > > hierarchy.
> > > >>> - "Last official release" was held until now. Since 3.0 is going
> > > >>> to
> > be
> > > >>> officially announced, 3.0 will go there. I made that change as
> well.
> > > >>> - A list of changed features has not been high priority since
> > > >>> the original goal was to make a 3.0 in Apache that pretty much
> > > >>> matched
> > the
> > > >>> function of 2.5. The only thing that changed was how the product
> > > >>> is built and shipped. Nevertheless we need to state at least
> > > >>> that somewhere.
> > > >>> - The resources file is 1.1 GB not 2 right?
> > > >>>
> > > >>> Keep in mind that the community decided to release cTAKES 3.0
> > > >>> without the doc being complete, but these must be next:
> > > >>> - The current guides are still not complete. I made it through
> > > >>> the developer guide but the user guide still has problems. I get
> > > >>> errors after installing and running scripts. I have not been
> > > >>> able to try the comparison test that was available previously.
> > > >>> The table at the
> > bottom
> > > I
> > > >>> have not got to yet.
> > > >>> - We have 2 sites now 1) cTAKES home
> > > http://incubator.apache.org/ctakes/
> > > >>> 2) cTAKES doc
> https://cwiki.apache.org/confluence/display/CTAKES.
> > I've
> > > >>> done my best to minimize a user going back and forth. We have it
> > > >>> this way because a useful guide is not easy (IMHO or even
> > > >>> possible) with markdown text in the cTAKES home pages. There are
> > > >>> still 3.0 developer and user guide pages on the cTAKES home site
> > > >>> that should be removed
> > so
> > > >>> no one stumbles on to them.
> > > >>> - The Getting Started page needs to be written in context of all
> > future
> > > >>> releases not just 3.0.
> > > >>> - Previous releases list. We need to both point to the NCI sites
> > > >>> for
> > > 2.6
> > > >>> and back plus create an archive for what will be the history of
> > Apache
> > > >>> releases. Needs work your right.
> > > >>>
> > > >>> Potential priorities after that:
> > > >>> - The examples, as described by Andy, would be more than a
> > > >>> readme
> > > should
> > > >>> have. This would be great for a how-to guide.
> > > >>> - The Developer Guide and User Guide have historically been
> > > >>> install guides not how-to guides. I don't think a how-to guide
> > > >>> should be incorporated into these but should be its own
> document.
> > > >>> - cTAKES has never had a how-to guide that I know of. Making one
> > would
> > > >>> be great and as you say should include things like 1) pointers
> > > >>> to
> > where
> > > >>> to find basic information 2) very high level overview of the
> > components
> > > >>> in the context of using them to do a very basic task like 3) I
> > > >>> think
> > it
> > > >>> was suggested that the Getting Started page might be something
> > > >>> like
> > > this
> > > >>> in very short form. If we did that then it would point to a more
> > > >>> comprehensive how-to guide.
> > > >>> - Project history page of all cTAKES releases placed on Apache
> > > >>> sites somewhere. Good plan if short. I would not copy readmes
> > > >>> there but
> > have
> > > >>> links to them.
> > > >>> I already did this for cTAKES 2.5 and past:
> > > >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> > > >>> Move this page to Apache? Have a page on Apache that continues
> > > >>> this
> > and
> > > >>> points back to what already exists?
> > > >>> Also, I had this project history on the Apache cTAKES downloads
> > > >>> page
> > > but
> > > >>> that section was removed when 3.0 was placed on there. If you
> > > >>> can
> > find
> > > >>> the history of changes to that page you may find something
> > > >>> already
> > done
> > > >>> in markdown format.
> > > >>> - Creating a single download for a newcomer. This has been
> > > >>> discussed
> > > and
> > > >>> tabled by the community for the time being in order to get the
> > > >>> 3.0 release done and out the door. We need to come back to this
> > > >>> in order
> > to
> > > >>> make the best first impression.
> > > >>>
> > > >>> Troy
> > > >>>
> > > >>> -----Original Message-----
> > > >>> From: ctakes-dev-return-1230-Bleeker.Troy=
> > > mayo.edu@incubator.apache.org
> > > >>> [mailto:ctakes-dev-return-1230-
> > > >>> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen,
> > > >>> Pei
> > > >>> Sent: Friday, February 15, 2013 10:17 PM
> > > >>> To: ctakes-dev@incubator.apache.org
> > > >>> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate
> > > >>> cTAKES
> > from
> > > >>> Incubator
> > > >>>
> > > >>> Thanks Andy for the feedback.
> > > >>> Examples are a good idea- Were you thinking of adding it to the
> > README
> > > >>> file or the confluence user guide?
> > > >>>
> > > >>> Feel free to update the downloads page(s) (it uses Apache CMS)
> > > >>> and
> > the
> > > >>> User Guides (Confluence wiki).
> > > >>> Note: The release is still being replicated to all of the
> > > >>> mirrors and may take up to 24 hrs, so I would wait until after
> > > >>> the weekend before testing all of the mirror links.
> > > >>>
> > > >>> --Pei
> > > >>> ________________________________________
> > > >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> > > >>> Sent: Friday, February 15, 2013 11:08 PM
> > > >>> To: ctakes-dev@incubator.apache.org
> > > >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> > > >>>
> > > >>> Clarifications
> > > >>>
> > > >>> There isn't a last Apache release. But there are last previous
> > > >>> NIH, Sourceforge, and Apache releases?
> > > >>> TODO: Project History Page (Simple, just the releases and times,
> > > ideally
> > > >>> with JIRA generated release notes).
> > > >>>
> > > >>> Suggestion: Demonstration > explanation. Use Examples !!
> > > >>>
> > > >>> EXAMPLE 1 : Basic Pipeline (without UMLS)
> > > >>>
> > > >>> ** SHOW Before and after clinical text, demonstrates purpose
> > > >>> ** LIST the 5 steps
> > > >>> ** Most impressive demo would be the smoking status pipeline
> > > >>>
> > > >>> EXAMPLE 2: Basic Pipeline (with UMLS)
> > > >>>
> > > >>> ** SHOW Before and after (input text -> output annotations)
> > > >>> ** LIST the steps
> > > >>> ** Most impressive demo would be a negation of a cancer
> > > >>> diagnosis and NER of a medication (chemotherapuetic drug).
> > > >>>
> > > >>> Thoughts?
> > > >>> --andy
> > > >>>
> > > >>>
> > > >>> On Feb 15, 2013, at 7:36 PM, Andy McMurry
> > > >>> <mc...@gmail.com>
> > > >>> wrote:
> > > >>>
> > > >>>> Sure thing Pei.
> > > >>>>
> > > >>>> I dont think cTAKES is ready for attention grabbing release
> > > >>>> (humble
> > > >>> opinion).
> > > >>>> And when you release you want to grab attention! ! cTAKES is
> > awesome!!
> > > >>>>
> > > >>>> Suggestions (release blockers)
> > > >>>>
> > > >>>> (1) Downloads
> > > >>>> http://incubator.apache.org/ctakes/downloads.cgi
> > > >>>> ! Link to install instructions is not there but "Verifying
> > signatures"
> > > >>> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL
> > INSTRUCTIONS.
> > > >>>> ! Last official release is blank because there isn't one,
> > > >>>> remove it
> > !
> > > >>>> First mirror I tried was a 404? (not sure which one). I changed
> > > >>>> the mirror then OK. Test all mirrors (script) ? Previous
> > > >>>> releases are
> > VERY
> > > >>> confusing.
> > > >>>> ? The NIH and SourceForge pages  should redirect to cTAKES,
> > > >>>> google
> > > >>> "cTAKES download" and imagine how confused a beginner would be.
> > > >>>>
> > > >>>> (2) User Guide
> > > >>>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > > >>>> ? 3.0.0 : no list of new features from last stable release. Why
> > would
> > > >>> a user bother to upgrade to a beta?
> > > >>>> ! Would be better to have a bundled download with resources, if
> > > >>> possible. Otherwise, make it clear to a newcomer what the
> > > >>> benefit of getting UMLS / LVG is. (one sentence).
> > > >>>> ! Needs a very high level overview of the components in the
> > > >>>> context
> > of
> > > >>> using them to do a very basic task like.
> > > >>>> ! This is likely the most frequently accessed document for
> cTAKES.
> > It
> > > >>> has almost no pointers to where to find basic information.
> > > >>>>
> > > >>>> (3) OTHER
> > > >>>> * The NCI and SourceForge links are now highly confusing.
> > > >>>> * While I am downloading, I should be reading the recommended
> > > >>>> "Get Started" guide
> > > >>>>
> > > >>>> I'm still downloading the 2GB resources file.
> > > >>>> I'll try and get back to you about the install when that is
> > > >>>> done
> > too.
> > > >>>>
> > > >>>> This constructive criticism is because I believe cTAKES is
> AWESOME.
> > > >>>> Hard to see how awesome it is given the current instructions.
> > > >>>>
> > > >>>> --Andy
> > > >>>>
> > > >>>>
> > > >>>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> > > >>> <Pe...@childrens.harvard.edu> wrote:
> > > >>>>
> > > >>>>> Hi Andy,
> > > >>>>> So much has changed in cTAKES since last year, if you have a
> > chance-
> > > >>> do you also want to try downloading the -bin and ensure at least
> > > >>> the steps in the README are able to get you started?
> > > >>>>>
> > > >>>>> --Pei
> > > >>>>> ________________________________________
> > > >>>>> From: Andy McMurry [mcmurry.andy@gmail.com]
> > > >>>>> Sent: Friday, February 15, 2013 4:04 PM
> > > >>>>> To: ctakes-dev@incubator.apache.org
> > > >>>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> > > >>>>>
> > > >>>>> Suggestion: can we get a good programmer with no cTAKES
> > > >>>>> experience
> > to
> > > >>> kick the tires and tell us how long it took to get started?
> > > >>>>>
> > > >>>>> John Resig (jQuery founder) once told me "if it takes more
> > > >>>>> than 15
> > > >>> minutes to get started, then that is way too long".
> > > >>>>>
> > > >>>>> "What is necessary is that enough investment be put into
> > presentation
> > > >>>>> that newcomers can get past the obstacle of unfamiliarity. ...
> > > >>> Hactivation energy: the amount of energy a newcomer must put in
> > before
> > > >>> she starts getting something back"
> > > >>>>> -- From "Producing Open Source Software"
> > > >>>>>
> > > >>>>>
> > > http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=ha
> > > c
> > > >>>>>
> > ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> > > >>>>>
> > Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> > > >>>>> =hacktivation%20energy&f=false
> > > >>>>>
> > > >>>>>
> > > >>>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> > > >>> <Pe...@childrens.harvard.edu> wrote:
> > > >>>>>
> > > >>>>>> This is to open a discussion to graduate Apache cTAKES
> > > >>>>>> podling
> > from
> > > >>> the Apache Incubator.
> > > >>>>>>
> > > >>>>>> Apache cTAKES entered the Incubator in June of 2012. We have
> > > >>>>>> made
> > > >>> significant progress with the project since moving over to
> > > >>> Apache. We currently have 18 committers listed on our status
> > > >>> page at [1]
> > including
> > > >>> over 10 which accepted after the podling was formed.
> > > >>>>>>
> > > >>>>>> During incubation, cTAKES has :
> > > >>>>>> * Produced 1 Release
> > > >>>>>> * Added 10 new Committer/PPMC members and shows constant
> > > >>>>>> community activities
> > > >>>>>> * Cleared IP on code
> > > >>>>>> * Developed Roadmap(s) for the next major and minor releases
> > > >>>>>> in a community process and started working on that [2]
> > > >>>>>> * The community of Apache cTAKES is active, healthy, and
> > > >>>>>> growing
> > and
> > > >>> has demonstrated the ability to self-govern using accepted
> > > >>> Apache practices.
> > > >>>>>>
> > > >>>>>> [1]
> > > >>>>>> http://people.apache.org/committers-by-project.html#ctakes
> > > >>>>>> [2]
> > > >>>>>>
> > > https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> > > >>>>>> an.jira.plugin.system.project%3Aroadmap-panel
> > > >>
> > > >>
> > >
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

[andy mcmurry <mc...@gmail.com>]

+1 nomination to graduate ctakes.
+1 request to create examples

I'll attempt the smoking status and medication NER examples for after
release (volunteer for task)
On Feb 19, 2013 10:29 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
wrote:

> I don't think ASF automatically makes any official press releases about
> graduated projects other than the public resolutions.  But in our announce
> to general@ about the release, I think we can explicitly say that this is
> our first release in ASF and that it was primarily an infra one just to
> make the move from SF to ASF.
> (Essentially for us to learn the ropes here.)
>
> Also feel free to take a peek at:
> https://issues.apache.org/jira/browse/CTAKES
> There are plenty of items we could do to improve cTAKES for the upcoming
> release(s) [Hopefully we'll be able to follow the "Release Early, Release
> Often" philosophy [1]] .  Will welcome any contributions (especially yours
> regarding the end user experience which I think it's extremely important)
> and also feel free to add to the Jira items...
>
> My point of view with OS is that if something sucks, you can usually
> expect it to be fixed pretty fast as long as there is an mechanism for
> accepting changes.  I believe ASF is much more about building a diverse
> community and to have a framework in place for folks to make contributions
> (so I actually don't necessary believe it is negative that more people use
> cTAKES and therefore could be future contributors).
>
> [1] http://incubator.apache.org/guides/graduation.html#releases
>
> --Pei
>
> ________________________________________
> From: andy mcmurry [mcmurry.andy@gmail.com]
> Sent: Tuesday, February 19, 2013 8:42 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> Incubator
>
> Message received, and from that perspective I agree to graduate.
>
> Revised proposal to group:  no press advertisements about the release until
> docs are ready.
>
> . If Apache does promotions for graduated incubators then we should request
> holding off press releases until the docs are ready.
>
> My  battle scars from other open source projects remind me that if you ask
> for attention be ready for lots of questions and short attention spans.
> On Feb 19, 2013 6:13 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
> wrote:
>
> > Andy,
> > The purpose of this release is primarily infrastructural. There are a lot
> > of tasks involved in the move to ASF and many reasons for separating his
> > release. One of them is that it's probably not a great idea to have major
> > code fixes/changes mixed in with just a refactoring change.
> >
> > Regarding ease of use- agree with all of the points.
> > cTAKES has historically been a collection of annotators and reusing
> UIMA's
> > UI as examples and no real application built on top of it. However, there
> > is a web GUI current in sandbox that should make things more intuitive.
> > However, in order to produce releases efficiently and often, I believe we
> > need graduate to a TLP (based on experience so far with the incubator).
> We
> > should be able to address those issues fairly quickly with incremental
> > releases.
> >
> > The downloads page should work all the time as its pretty basic
> > functionality; It's not good if its flaky. Could others recreate the
> issue?
> > Would be good if others could recreate it so we could get to the root of
> > the issue.
> > My 2 cents.
> >
> > -Pei
> > Sent from my iPhone
> >
> > On Feb 19, 2013, at 5:47 PM, "andy mcmurry" <mc...@gmail.com>
> > wrote:
> >
> > > Thank you Troy!
> > >
> > > *Summary: what is the purpose of the 3.0.0 release: changing the
> license
> > to
> > > Apache or getting new users? *
> > >
> > > Releasing 3.0.0 without DOCS is OK so long as the expected user base is
> > > CURRENT cTAKES users.
> > > If that is the case and this transition is 100% about changing the
> > license
> > > to Apache, then OK.
> > >
> > > NEW users coming to cTAKES will probably be overwhelmed, for all the
> > > reasons discussed.
> > > We will likely "lose" these new users who will not come back when the
> > docs
> > > are ready a month later.
> > >
> > > *Question for the group : who is the intended audience of the 3.0.0
> > > release? *
> > >
> > >
> > > On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <
> Bleeker.Troy@mayo.edu
> > >wrote:
> > >
> > >> Summarizing where we are now ... completed items at the bottom of the
> > list
> > >> for reference only.
> > >>
> > >> The community decided to release cTAKES 3.0 without the doc being
> > complete
> > >> - these must be next:
> > >> - The Developer Guide is not complete.
> > >> [TODO] Dev Guide needs command line install instructions for UMLS
> ID/pw
> > >> and classpath. I'll work on this.
> > >> - The User Guide has a caveat on the table at the bottom of the
> > >> instructions because a similar set of examples was not distributed
> like
> > it
> > >> was in 2.5. The instructions are longer as well since the user could
> not
> > >> just load and run existing samples.
> > >> [TODO] Consider shipping test data resources from SourceForge in a ZIP
> > >> file.
> > >> - The Getting Started page needs to be written in context of all
> future
> > >> releases not just 3.0.
> > >> [NEEDS REVIEW] A page was written. Is it as expected?
> > >> - Previous releases list. We need to both point to the NCI sites for
> 2.6
> > >> and back plus create an archive for what will be the history of Apache
> > >> releases. Needs work your right.
> > >> [TODO] For now I removed 2 of the 3 links leaving only one that points
> > >> back to NCI for 2.5 and back. Question is should we have a full
> listing
> > of
> > >> the 2.5 and previous releases on the Apache site or simply point to
> the
> > NCI
> > >> wiki. If point to NCI then there is no archive to be had yet since the
> > only
> > >> release in Apache is the current release.
> > >> - Component Use Guide pages needing updates. There are items marked in
> > >> reddish color that are incorrect or in need of updates on these pages:
> > >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
> > >>
> > >>
> >
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
> > >>
> > >>
> >
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
> > >>
> >
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
> > >>
> > >>
> >
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
> > >>
> >
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
> > >> [TODO] Component knowledgeable people must update these pages.
> > >>
> > >> Potential priorities after that:
> > >> - The examples, as described by Andy, would be more than a readme
> should
> > >> have. This would be great for a how-to guide. The Developer Guide and
> > User
> > >> Guide have historically been install guides not how-to guides. I don't
> > >> think a how-to guide should be incorporated into these but should be
> its
> > >> own document.
> > >> [TODO] Should the current user and dev guides be renamed?
> > >> - cTAKES has never had a how-to guide that I know of. Making one would
> > be
> > >> great and as you say should include things like 1) pointers to where
> to
> > >> find basic information 2) very high level overview of the components
> in
> > the
> > >> context of using them to do a very basic task like 3) I think it was
> > >> suggested that the Getting Started page might be something like this
> in
> > >> very short form. If we did that then it would point to a more
> > comprehensive
> > >> how-to guide.
> > >> [TODO] Decide if we are going to do this.
> > >> - Project history page of all cTAKES releases placed on Apache sites
> > >> somewhere. Good plan if short. I would not copy readmes there but have
> > >> links to them.
> > >> [TODO] This was done in the past but removed from the bottom of the
> > >> downloads page. This page exists now but is not linked to from the
> > Apache
> > >> cTAKES site. Here is a direct link:
> > >> http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0
> info
> > >> added if we decide to use it.
> > >> - Creating a single download for a newcomer.
> > >> [LATER] This has been discussed and tabled by the community for the
> time
> > >> being in order to get the 3.0 release done and out the door. We need
> to
> > >> come back to this in order to make the best first impression.
> > >>
> > >> Completed:
> > >> - The downloads page must work. It now seems to function alright
> > ***IF***
> > >> you refresh the page or select a mirror and click the Change button.
> If
> > you
> > >> do neither and try to download you get this error: "The requested URL
> > >>
> >
> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz
> > >> was not found on this server." Anyone have time to fix this?
> > >> [WORK-AROUND] Seems intermittent. Tried 5 different machines. James
> and
> > >> Troy changed the downloads page to tell the user to select the Change
> > >> button when they have issues. It should work if they do that. Best
> > guess -
> > >> the randomly selected mirror sites do not all work. Also, selecting a
> > site
> > >> in the drop-down and pressing the Change button does not set the
> mirror
> > >> site to the one you selected. Next best guess - other Apache sites
> have
> > a
> > >> double // in the URL just after the mirror domain in the file download
> > >> link. Maybe this is required. Tried this too.
> > >> - Adding a link to the install instructions makes it obvious (which I
> > have
> > >> done to the page) but it was there in a sense.
> > >> [DONE] Link added.
> > >> - "Last official release" was held until now. Since 3.0 is going to be
> > >> officially announced, 3.0 will go there. I made that change as well.
> > >> [DONE] Reworked the page.
> > >> - A list of changed features has not been high priority since the
> > original
> > >> goal was to make a 3.0 in Apache that pretty much matched the function
> > of
> > >> 2.5. The only thing that changed was how the product is built and
> > shipped.
> > >> Nevertheless we need to state at least that somewhere.
> > >> [DONE] That was wrong, there is new function. Relation Extractor now
> > >> documented on the downloads page.
> > >> - The resources file is 1.1 GB not 2 right?
> > >> [DONE] Andy said it in an email. The web site lists it fine.
> > >> - There are still 3.0 developer and user guide pages on the cTAKES
> home
> > >> site that should be removed so no one stumbles on to them.
> > >> [DONE] Removed.
> > >> - Where would a newcomer hit first? Internet search for "ctakes" or
> > >> "ctakes 3.0" is probably first. Top hits on those lists should be
> > modified
> > >> to point to the best Apache cTAKES landing page.
> > >> [DONE] James and Troy made changes to the top hit pages and other
> places
> > >> that made sense.
> > >> - The current guides are still not complete.
> > >> [DONE] User Guide James and Troy went through.
> > >>
> > >> Thanks
> > >> Troy
> > >>
> > >> -----Original Message-----
> > >> From: ctakes-dev-return-1250-Bleeker.Troy=
> mayo.edu@incubator.apache.org
> > [mailto:
> > >> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On
> > >> Behalf Of Masanz, James J.
> > >> Sent: Tuesday, February 19, 2013 10:10 AM
> > >> To: 'ctakes-dev@incubator.apache.org'
> > >> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> > from
> > >> Incubator
> > >>
> > >>
> > >>> - The resources file is 1.1 GB not 2 right?
> > >>
> > >> I agree. But I don't see it listed as 2GB on the download page. If you
> > >> tell me where you saw it listed as 2GB I will update that page.
> > >>
> > >>> - A list of changed features has not been high priority since
> > >> I will update the downloads page right now stating the relation
> > extractor
> > >> is new for 3.0
> > >>
> > >>
> > >>> - Where would a newcomer hit first? Internet search for "ctakes" or
> > >>> "ctakes 3.0" is probably first. Top hits on those lists should be
> > >>> modified to point to the best Apache cTAKES landing page.
> > >>
> > >> I modified the following pages to have a link to Apache cTAKES home
> page
> > >>
> > >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
> > >> https://sourceforge.net/projects/ohnlp/files/cTAKES/
> > >> https://sourceforge.net/projects/ohnlp/
> > >> http://ohnlp.sourceforge.net/
> > >>
> > >> The update to the last one is not appearing yet, but it was updated.
> > >>
> > >>> - The Getting Started page needs to be written in context of all
> future
> > >>> releases not just 3.0.
> > >>
> > >> Looks like you updated that page, thanks.
> > >>
> > >>> - The current guides are still not complete.
> > >>
> > >> I took a quick run through the User Guide on the Wiki and made some
> > >> updates.
> > >>
> > >> -- James Masanz
> > >>
> > >>
> > >>> -----Original Message-----
> > >>> From: ctakes-dev-return-1239-Masanz.James=
> > mayo.edu@incubator.apache.org
> > >>> [mailto:ctakes-dev-return-1239-
> > >>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker,
> Troy
> > >>> C.
> > >>> Sent: Monday, February 18, 2013 10:58 AM
> > >>> To: ctakes-dev@incubator.apache.org
> > >>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> > >>> from Incubator
> > >>>
> > >>> All the suggestions and discussion are good. There's a lot here,
> sorry
> > >>> for the long summary. First things first:
> > >>>
> > >>> - The downloads page must work. It now seems to function alright
> > >>> ***IF*** you refresh the page or select a mirror and click the Change
> > >>> button. If you do neither and try to download you get this error:
> "The
> > >>> requested URL
> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> > >>> incubating-bin.tar.gz was not found on this server." Anyone have time
> > to
> > >>> fix this?
> > >>> - Adding a link to the install instructions makes it obvious (which I
> > >>> have done to the page) but it was there in a sense. The page said
> "Use
> > >>> the Developer and User Guides to direct you through the installation
> > >>> process." and the links to those were just to the left in the
> > hierarchy.
> > >>> - "Last official release" was held until now. Since 3.0 is going to
> be
> > >>> officially announced, 3.0 will go there. I made that change as well.
> > >>> - A list of changed features has not been high priority since the
> > >>> original goal was to make a 3.0 in Apache that pretty much matched
> the
> > >>> function of 2.5. The only thing that changed was how the product is
> > >>> built and shipped. Nevertheless we need to state at least that
> > >>> somewhere.
> > >>> - The resources file is 1.1 GB not 2 right?
> > >>>
> > >>> Keep in mind that the community decided to release cTAKES 3.0 without
> > >>> the doc being complete, but these must be next:
> > >>> - The current guides are still not complete. I made it through the
> > >>> developer guide but the user guide still has problems. I get errors
> > >>> after installing and running scripts. I have not been able to try the
> > >>> comparison test that was available previously. The table at the
> bottom
> > I
> > >>> have not got to yet.
> > >>> - We have 2 sites now 1) cTAKES home
> > http://incubator.apache.org/ctakes/
> > >>> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES.
> I've
> > >>> done my best to minimize a user going back and forth. We have it this
> > >>> way because a useful guide is not easy (IMHO or even possible) with
> > >>> markdown text in the cTAKES home pages. There are still 3.0 developer
> > >>> and user guide pages on the cTAKES home site that should be removed
> so
> > >>> no one stumbles on to them.
> > >>> - The Getting Started page needs to be written in context of all
> future
> > >>> releases not just 3.0.
> > >>> - Previous releases list. We need to both point to the NCI sites for
> > 2.6
> > >>> and back plus create an archive for what will be the history of
> Apache
> > >>> releases. Needs work your right.
> > >>>
> > >>> Potential priorities after that:
> > >>> - The examples, as described by Andy, would be more than a readme
> > should
> > >>> have. This would be great for a how-to guide.
> > >>> - The Developer Guide and User Guide have historically been install
> > >>> guides not how-to guides. I don't think a how-to guide should be
> > >>> incorporated into these but should be its own document.
> > >>> - cTAKES has never had a how-to guide that I know of. Making one
> would
> > >>> be great and as you say should include things like 1) pointers to
> where
> > >>> to find basic information 2) very high level overview of the
> components
> > >>> in the context of using them to do a very basic task like 3) I think
> it
> > >>> was suggested that the Getting Started page might be something like
> > this
> > >>> in very short form. If we did that then it would point to a more
> > >>> comprehensive how-to guide.
> > >>> - Project history page of all cTAKES releases placed on Apache sites
> > >>> somewhere. Good plan if short. I would not copy readmes there but
> have
> > >>> links to them.
> > >>> I already did this for cTAKES 2.5 and past:
> > >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> > >>> Move this page to Apache? Have a page on Apache that continues this
> and
> > >>> points back to what already exists?
> > >>> Also, I had this project history on the Apache cTAKES downloads page
> > but
> > >>> that section was removed when 3.0 was placed on there. If you can
> find
> > >>> the history of changes to that page you may find something already
> done
> > >>> in markdown format.
> > >>> - Creating a single download for a newcomer. This has been discussed
> > and
> > >>> tabled by the community for the time being in order to get the 3.0
> > >>> release done and out the door. We need to come back to this in order
> to
> > >>> make the best first impression.
> > >>>
> > >>> Troy
> > >>>
> > >>> -----Original Message-----
> > >>> From: ctakes-dev-return-1230-Bleeker.Troy=
> > mayo.edu@incubator.apache.org
> > >>> [mailto:ctakes-dev-return-1230-
> > >>> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> > >>> Sent: Friday, February 15, 2013 10:17 PM
> > >>> To: ctakes-dev@incubator.apache.org
> > >>> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from
> > >>> Incubator
> > >>>
> > >>> Thanks Andy for the feedback.
> > >>> Examples are a good idea- Were you thinking of adding it to the
> README
> > >>> file or the confluence user guide?
> > >>>
> > >>> Feel free to update the downloads page(s) (it uses Apache CMS) and
> the
> > >>> User Guides (Confluence wiki).
> > >>> Note: The release is still being replicated to all of the mirrors and
> > >>> may take up to 24 hrs, so I would wait until after the weekend before
> > >>> testing all of the mirror links.
> > >>>
> > >>> --Pei
> > >>> ________________________________________
> > >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> > >>> Sent: Friday, February 15, 2013 11:08 PM
> > >>> To: ctakes-dev@incubator.apache.org
> > >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> > >>>
> > >>> Clarifications
> > >>>
> > >>> There isn't a last Apache release. But there are last previous NIH,
> > >>> Sourceforge, and Apache releases?
> > >>> TODO: Project History Page (Simple, just the releases and times,
> > ideally
> > >>> with JIRA generated release notes).
> > >>>
> > >>> Suggestion: Demonstration > explanation. Use Examples !!
> > >>>
> > >>> EXAMPLE 1 : Basic Pipeline (without UMLS)
> > >>>
> > >>> ** SHOW Before and after clinical text, demonstrates purpose
> > >>> ** LIST the 5 steps
> > >>> ** Most impressive demo would be the smoking status pipeline
> > >>>
> > >>> EXAMPLE 2: Basic Pipeline (with UMLS)
> > >>>
> > >>> ** SHOW Before and after (input text -> output annotations)
> > >>> ** LIST the steps
> > >>> ** Most impressive demo would be a negation of a cancer diagnosis and
> > >>> NER of a medication (chemotherapuetic drug).
> > >>>
> > >>> Thoughts?
> > >>> --andy
> > >>>
> > >>>
> > >>> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> > >>> wrote:
> > >>>
> > >>>> Sure thing Pei.
> > >>>>
> > >>>> I dont think cTAKES is ready for attention grabbing release (humble
> > >>> opinion).
> > >>>> And when you release you want to grab attention! ! cTAKES is
> awesome!!
> > >>>>
> > >>>> Suggestions (release blockers)
> > >>>>
> > >>>> (1) Downloads
> > >>>> http://incubator.apache.org/ctakes/downloads.cgi
> > >>>> ! Link to install instructions is not there but "Verifying
> signatures"
> > >>> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL
> INSTRUCTIONS.
> > >>>> ! Last official release is blank because there isn't one, remove it
> !
> > >>>> First mirror I tried was a 404? (not sure which one). I changed the
> > >>>> mirror then OK. Test all mirrors (script) ? Previous releases are
> VERY
> > >>> confusing.
> > >>>> ? The NIH and SourceForge pages  should redirect to cTAKES, google
> > >>> "cTAKES download" and imagine how confused a beginner would be.
> > >>>>
> > >>>> (2) User Guide
> > >>>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > >>>> ? 3.0.0 : no list of new features from last stable release. Why
> would
> > >>> a user bother to upgrade to a beta?
> > >>>> ! Would be better to have a bundled download with resources, if
> > >>> possible. Otherwise, make it clear to a newcomer what the benefit of
> > >>> getting UMLS / LVG is. (one sentence).
> > >>>> ! Needs a very high level overview of the components in the context
> of
> > >>> using them to do a very basic task like.
> > >>>> ! This is likely the most frequently accessed document for cTAKES.
> It
> > >>> has almost no pointers to where to find basic information.
> > >>>>
> > >>>> (3) OTHER
> > >>>> * The NCI and SourceForge links are now highly confusing.
> > >>>> * While I am downloading, I should be reading the recommended "Get
> > >>>> Started" guide
> > >>>>
> > >>>> I'm still downloading the 2GB resources file.
> > >>>> I'll try and get back to you about the install when that is done
> too.
> > >>>>
> > >>>> This constructive criticism is because I believe cTAKES is AWESOME.
> > >>>> Hard to see how awesome it is given the current instructions.
> > >>>>
> > >>>> --Andy
> > >>>>
> > >>>>
> > >>>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> > >>> <Pe...@childrens.harvard.edu> wrote:
> > >>>>
> > >>>>> Hi Andy,
> > >>>>> So much has changed in cTAKES since last year, if you have a
> chance-
> > >>> do you also want to try downloading the -bin and ensure at least the
> > >>> steps in the README are able to get you started?
> > >>>>>
> > >>>>> --Pei
> > >>>>> ________________________________________
> > >>>>> From: Andy McMurry [mcmurry.andy@gmail.com]
> > >>>>> Sent: Friday, February 15, 2013 4:04 PM
> > >>>>> To: ctakes-dev@incubator.apache.org
> > >>>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> > >>>>>
> > >>>>> Suggestion: can we get a good programmer with no cTAKES experience
> to
> > >>> kick the tires and tell us how long it took to get started?
> > >>>>>
> > >>>>> John Resig (jQuery founder) once told me "if it takes more than 15
> > >>> minutes to get started, then that is way too long".
> > >>>>>
> > >>>>> "What is necessary is that enough investment be put into
> presentation
> > >>>>> that newcomers can get past the obstacle of unfamiliarity. ...
> > >>> Hactivation energy: the amount of energy a newcomer must put in
> before
> > >>> she starts getting something back"
> > >>>>> -- From "Producing Open Source Software"
> > >>>>>
> > >>>>>
> > http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> > >>>>>
> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> > >>>>>
> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> > >>>>> =hacktivation%20energy&f=false
> > >>>>>
> > >>>>>
> > >>>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> > >>> <Pe...@childrens.harvard.edu> wrote:
> > >>>>>
> > >>>>>> This is to open a discussion to graduate Apache cTAKES podling
> from
> > >>> the Apache Incubator.
> > >>>>>>
> > >>>>>> Apache cTAKES entered the Incubator in June of 2012. We have made
> > >>> significant progress with the project since moving over to Apache. We
> > >>> currently have 18 committers listed on our status page at [1]
> including
> > >>> over 10 which accepted after the podling was formed.
> > >>>>>>
> > >>>>>> During incubation, cTAKES has :
> > >>>>>> * Produced 1 Release
> > >>>>>> * Added 10 new Committer/PPMC members and shows constant community
> > >>>>>> activities
> > >>>>>> * Cleared IP on code
> > >>>>>> * Developed Roadmap(s) for the next major and minor releases in a
> > >>>>>> community process and started working on that [2]
> > >>>>>> * The community of Apache cTAKES is active, healthy, and growing
> and
> > >>> has demonstrated the ability to self-govern using accepted Apache
> > >>> practices.
> > >>>>>>
> > >>>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
> > >>>>>> [2]
> > >>>>>>
> > https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> > >>>>>> an.jira.plugin.system.project%3Aroadmap-panel
> > >>
> > >>
> >
>

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Chen, Pei" <Pe...@childrens.harvard.edu>]

I don't think ASF automatically makes any official press releases about graduated projects other than the public resolutions.  But in our announce to general@ about the release, I think we can explicitly say that this is our first release in ASF and that it was primarily an infra one just to make the move from SF to ASF.  
(Essentially for us to learn the ropes here.)

Also feel free to take a peek at:
https://issues.apache.org/jira/browse/CTAKES
There are plenty of items we could do to improve cTAKES for the upcoming release(s) [Hopefully we'll be able to follow the "Release Early, Release Often" philosophy [1]] .  Will welcome any contributions (especially yours regarding the end user experience which I think it's extremely important) and also feel free to add to the Jira items...

My point of view with OS is that if something sucks, you can usually expect it to be fixed pretty fast as long as there is an mechanism for accepting changes.  I believe ASF is much more about building a diverse community and to have a framework in place for folks to make contributions (so I actually don't necessary believe it is negative that more people use cTAKES and therefore could be future contributors).

[1] http://incubator.apache.org/guides/graduation.html#releases

--Pei

________________________________________
From: andy mcmurry [mcmurry.andy@gmail.com]
Sent: Tuesday, February 19, 2013 8:42 PM
To: ctakes-dev@incubator.apache.org
Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

Message received, and from that perspective I agree to graduate.

Revised proposal to group:  no press advertisements about the release until
docs are ready.

. If Apache does promotions for graduated incubators then we should request
holding off press releases until the docs are ready.

My  battle scars from other open source projects remind me that if you ask
for attention be ready for lots of questions and short attention spans.
On Feb 19, 2013 6:13 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:

> Andy,
> The purpose of this release is primarily infrastructural. There are a lot
> of tasks involved in the move to ASF and many reasons for separating his
> release. One of them is that it's probably not a great idea to have major
> code fixes/changes mixed in with just a refactoring change.
>
> Regarding ease of use- agree with all of the points.
> cTAKES has historically been a collection of annotators and reusing UIMA's
> UI as examples and no real application built on top of it. However, there
> is a web GUI current in sandbox that should make things more intuitive.
> However, in order to produce releases efficiently and often, I believe we
> need graduate to a TLP (based on experience so far with the incubator). We
> should be able to address those issues fairly quickly with incremental
> releases.
>
> The downloads page should work all the time as its pretty basic
> functionality; It's not good if its flaky. Could others recreate the issue?
> Would be good if others could recreate it so we could get to the root of
> the issue.
> My 2 cents.
>
> -Pei
> Sent from my iPhone
>
> On Feb 19, 2013, at 5:47 PM, "andy mcmurry" <mc...@gmail.com>
> wrote:
>
> > Thank you Troy!
> >
> > *Summary: what is the purpose of the 3.0.0 release: changing the license
> to
> > Apache or getting new users? *
> >
> > Releasing 3.0.0 without DOCS is OK so long as the expected user base is
> > CURRENT cTAKES users.
> > If that is the case and this transition is 100% about changing the
> license
> > to Apache, then OK.
> >
> > NEW users coming to cTAKES will probably be overwhelmed, for all the
> > reasons discussed.
> > We will likely "lose" these new users who will not come back when the
> docs
> > are ready a month later.
> >
> > *Question for the group : who is the intended audience of the 3.0.0
> > release? *
> >
> >
> > On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <Bleeker.Troy@mayo.edu
> >wrote:
> >
> >> Summarizing where we are now ... completed items at the bottom of the
> list
> >> for reference only.
> >>
> >> The community decided to release cTAKES 3.0 without the doc being
> complete
> >> - these must be next:
> >> - The Developer Guide is not complete.
> >> [TODO] Dev Guide needs command line install instructions for UMLS ID/pw
> >> and classpath. I'll work on this.
> >> - The User Guide has a caveat on the table at the bottom of the
> >> instructions because a similar set of examples was not distributed like
> it
> >> was in 2.5. The instructions are longer as well since the user could not
> >> just load and run existing samples.
> >> [TODO] Consider shipping test data resources from SourceForge in a ZIP
> >> file.
> >> - The Getting Started page needs to be written in context of all future
> >> releases not just 3.0.
> >> [NEEDS REVIEW] A page was written. Is it as expected?
> >> - Previous releases list. We need to both point to the NCI sites for 2.6
> >> and back plus create an archive for what will be the history of Apache
> >> releases. Needs work your right.
> >> [TODO] For now I removed 2 of the 3 links leaving only one that points
> >> back to NCI for 2.5 and back. Question is should we have a full listing
> of
> >> the 2.5 and previous releases on the Apache site or simply point to the
> NCI
> >> wiki. If point to NCI then there is no archive to be had yet since the
> only
> >> release in Apache is the current release.
> >> - Component Use Guide pages needing updates. There are items marked in
> >> reddish color that are incorrect or in need of updates on these pages:
> >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
> >> [TODO] Component knowledgeable people must update these pages.
> >>
> >> Potential priorities after that:
> >> - The examples, as described by Andy, would be more than a readme should
> >> have. This would be great for a how-to guide. The Developer Guide and
> User
> >> Guide have historically been install guides not how-to guides. I don't
> >> think a how-to guide should be incorporated into these but should be its
> >> own document.
> >> [TODO] Should the current user and dev guides be renamed?
> >> - cTAKES has never had a how-to guide that I know of. Making one would
> be
> >> great and as you say should include things like 1) pointers to where to
> >> find basic information 2) very high level overview of the components in
> the
> >> context of using them to do a very basic task like 3) I think it was
> >> suggested that the Getting Started page might be something like this in
> >> very short form. If we did that then it would point to a more
> comprehensive
> >> how-to guide.
> >> [TODO] Decide if we are going to do this.
> >> - Project history page of all cTAKES releases placed on Apache sites
> >> somewhere. Good plan if short. I would not copy readmes there but have
> >> links to them.
> >> [TODO] This was done in the past but removed from the bottom of the
> >> downloads page. This page exists now but is not linked to from the
> Apache
> >> cTAKES site. Here is a direct link:
> >> http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0 info
> >> added if we decide to use it.
> >> - Creating a single download for a newcomer.
> >> [LATER] This has been discussed and tabled by the community for the time
> >> being in order to get the 3.0 release done and out the door. We need to
> >> come back to this in order to make the best first impression.
> >>
> >> Completed:
> >> - The downloads page must work. It now seems to function alright
> ***IF***
> >> you refresh the page or select a mirror and click the Change button. If
> you
> >> do neither and try to download you get this error: "The requested URL
> >>
> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz
> >> was not found on this server." Anyone have time to fix this?
> >> [WORK-AROUND] Seems intermittent. Tried 5 different machines. James and
> >> Troy changed the downloads page to tell the user to select the Change
> >> button when they have issues. It should work if they do that. Best
> guess -
> >> the randomly selected mirror sites do not all work. Also, selecting a
> site
> >> in the drop-down and pressing the Change button does not set the mirror
> >> site to the one you selected. Next best guess - other Apache sites have
> a
> >> double // in the URL just after the mirror domain in the file download
> >> link. Maybe this is required. Tried this too.
> >> - Adding a link to the install instructions makes it obvious (which I
> have
> >> done to the page) but it was there in a sense.
> >> [DONE] Link added.
> >> - "Last official release" was held until now. Since 3.0 is going to be
> >> officially announced, 3.0 will go there. I made that change as well.
> >> [DONE] Reworked the page.
> >> - A list of changed features has not been high priority since the
> original
> >> goal was to make a 3.0 in Apache that pretty much matched the function
> of
> >> 2.5. The only thing that changed was how the product is built and
> shipped.
> >> Nevertheless we need to state at least that somewhere.
> >> [DONE] That was wrong, there is new function. Relation Extractor now
> >> documented on the downloads page.
> >> - The resources file is 1.1 GB not 2 right?
> >> [DONE] Andy said it in an email. The web site lists it fine.
> >> - There are still 3.0 developer and user guide pages on the cTAKES home
> >> site that should be removed so no one stumbles on to them.
> >> [DONE] Removed.
> >> - Where would a newcomer hit first? Internet search for "ctakes" or
> >> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified
> >> to point to the best Apache cTAKES landing page.
> >> [DONE] James and Troy made changes to the top hit pages and other places
> >> that made sense.
> >> - The current guides are still not complete.
> >> [DONE] User Guide James and Troy went through.
> >>
> >> Thanks
> >> Troy
> >>
> >> -----Original Message-----
> >> From: ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:
> >> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On
> >> Behalf Of Masanz, James J.
> >> Sent: Tuesday, February 19, 2013 10:10 AM
> >> To: 'ctakes-dev@incubator.apache.org'
> >> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from
> >> Incubator
> >>
> >>
> >>> - The resources file is 1.1 GB not 2 right?
> >>
> >> I agree. But I don't see it listed as 2GB on the download page. If you
> >> tell me where you saw it listed as 2GB I will update that page.
> >>
> >>> - A list of changed features has not been high priority since
> >> I will update the downloads page right now stating the relation
> extractor
> >> is new for 3.0
> >>
> >>
> >>> - Where would a newcomer hit first? Internet search for "ctakes" or
> >>> "ctakes 3.0" is probably first. Top hits on those lists should be
> >>> modified to point to the best Apache cTAKES landing page.
> >>
> >> I modified the following pages to have a link to Apache cTAKES home page
> >>
> >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
> >> https://sourceforge.net/projects/ohnlp/files/cTAKES/
> >> https://sourceforge.net/projects/ohnlp/
> >> http://ohnlp.sourceforge.net/
> >>
> >> The update to the last one is not appearing yet, but it was updated.
> >>
> >>> - The Getting Started page needs to be written in context of all future
> >>> releases not just 3.0.
> >>
> >> Looks like you updated that page, thanks.
> >>
> >>> - The current guides are still not complete.
> >>
> >> I took a quick run through the User Guide on the Wiki and made some
> >> updates.
> >>
> >> -- James Masanz
> >>
> >>
> >>> -----Original Message-----
> >>> From: ctakes-dev-return-1239-Masanz.James=
> mayo.edu@incubator.apache.org
> >>> [mailto:ctakes-dev-return-1239-
> >>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> >>> C.
> >>> Sent: Monday, February 18, 2013 10:58 AM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> >>> from Incubator
> >>>
> >>> All the suggestions and discussion are good. There's a lot here, sorry
> >>> for the long summary. First things first:
> >>>
> >>> - The downloads page must work. It now seems to function alright
> >>> ***IF*** you refresh the page or select a mirror and click the Change
> >>> button. If you do neither and try to download you get this error: "The
> >>> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> >>> incubating-bin.tar.gz was not found on this server." Anyone have time
> to
> >>> fix this?
> >>> - Adding a link to the install instructions makes it obvious (which I
> >>> have done to the page) but it was there in a sense. The page said "Use
> >>> the Developer and User Guides to direct you through the installation
> >>> process." and the links to those were just to the left in the
> hierarchy.
> >>> - "Last official release" was held until now. Since 3.0 is going to be
> >>> officially announced, 3.0 will go there. I made that change as well.
> >>> - A list of changed features has not been high priority since the
> >>> original goal was to make a 3.0 in Apache that pretty much matched the
> >>> function of 2.5. The only thing that changed was how the product is
> >>> built and shipped. Nevertheless we need to state at least that
> >>> somewhere.
> >>> - The resources file is 1.1 GB not 2 right?
> >>>
> >>> Keep in mind that the community decided to release cTAKES 3.0 without
> >>> the doc being complete, but these must be next:
> >>> - The current guides are still not complete. I made it through the
> >>> developer guide but the user guide still has problems. I get errors
> >>> after installing and running scripts. I have not been able to try the
> >>> comparison test that was available previously. The table at the bottom
> I
> >>> have not got to yet.
> >>> - We have 2 sites now 1) cTAKES home
> http://incubator.apache.org/ctakes/
> >>> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> >>> done my best to minimize a user going back and forth. We have it this
> >>> way because a useful guide is not easy (IMHO or even possible) with
> >>> markdown text in the cTAKES home pages. There are still 3.0 developer
> >>> and user guide pages on the cTAKES home site that should be removed so
> >>> no one stumbles on to them.
> >>> - The Getting Started page needs to be written in context of all future
> >>> releases not just 3.0.
> >>> - Previous releases list. We need to both point to the NCI sites for
> 2.6
> >>> and back plus create an archive for what will be the history of Apache
> >>> releases. Needs work your right.
> >>>
> >>> Potential priorities after that:
> >>> - The examples, as described by Andy, would be more than a readme
> should
> >>> have. This would be great for a how-to guide.
> >>> - The Developer Guide and User Guide have historically been install
> >>> guides not how-to guides. I don't think a how-to guide should be
> >>> incorporated into these but should be its own document.
> >>> - cTAKES has never had a how-to guide that I know of. Making one would
> >>> be great and as you say should include things like 1) pointers to where
> >>> to find basic information 2) very high level overview of the components
> >>> in the context of using them to do a very basic task like 3) I think it
> >>> was suggested that the Getting Started page might be something like
> this
> >>> in very short form. If we did that then it would point to a more
> >>> comprehensive how-to guide.
> >>> - Project history page of all cTAKES releases placed on Apache sites
> >>> somewhere. Good plan if short. I would not copy readmes there but have
> >>> links to them.
> >>> I already did this for cTAKES 2.5 and past:
> >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> >>> Move this page to Apache? Have a page on Apache that continues this and
> >>> points back to what already exists?
> >>> Also, I had this project history on the Apache cTAKES downloads page
> but
> >>> that section was removed when 3.0 was placed on there. If you can find
> >>> the history of changes to that page you may find something already done
> >>> in markdown format.
> >>> - Creating a single download for a newcomer. This has been discussed
> and
> >>> tabled by the community for the time being in order to get the 3.0
> >>> release done and out the door. We need to come back to this in order to
> >>> make the best first impression.
> >>>
> >>> Troy
> >>>
> >>> -----Original Message-----
> >>> From: ctakes-dev-return-1230-Bleeker.Troy=
> mayo.edu@incubator.apache.org
> >>> [mailto:ctakes-dev-return-1230-
> >>> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> >>> Sent: Friday, February 15, 2013 10:17 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> >>> Incubator
> >>>
> >>> Thanks Andy for the feedback.
> >>> Examples are a good idea- Were you thinking of adding it to the README
> >>> file or the confluence user guide?
> >>>
> >>> Feel free to update the downloads page(s) (it uses Apache CMS) and the
> >>> User Guides (Confluence wiki).
> >>> Note: The release is still being replicated to all of the mirrors and
> >>> may take up to 24 hrs, so I would wait until after the weekend before
> >>> testing all of the mirror links.
> >>>
> >>> --Pei
> >>> ________________________________________
> >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>> Sent: Friday, February 15, 2013 11:08 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>
> >>> Clarifications
> >>>
> >>> There isn't a last Apache release. But there are last previous NIH,
> >>> Sourceforge, and Apache releases?
> >>> TODO: Project History Page (Simple, just the releases and times,
> ideally
> >>> with JIRA generated release notes).
> >>>
> >>> Suggestion: Demonstration > explanation. Use Examples !!
> >>>
> >>> EXAMPLE 1 : Basic Pipeline (without UMLS)
> >>>
> >>> ** SHOW Before and after clinical text, demonstrates purpose
> >>> ** LIST the 5 steps
> >>> ** Most impressive demo would be the smoking status pipeline
> >>>
> >>> EXAMPLE 2: Basic Pipeline (with UMLS)
> >>>
> >>> ** SHOW Before and after (input text -> output annotations)
> >>> ** LIST the steps
> >>> ** Most impressive demo would be a negation of a cancer diagnosis and
> >>> NER of a medication (chemotherapuetic drug).
> >>>
> >>> Thoughts?
> >>> --andy
> >>>
> >>>
> >>> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> >>> wrote:
> >>>
> >>>> Sure thing Pei.
> >>>>
> >>>> I dont think cTAKES is ready for attention grabbing release (humble
> >>> opinion).
> >>>> And when you release you want to grab attention! ! cTAKES is awesome!!
> >>>>
> >>>> Suggestions (release blockers)
> >>>>
> >>>> (1) Downloads
> >>>> http://incubator.apache.org/ctakes/downloads.cgi
> >>>> ! Link to install instructions is not there but "Verifying signatures"
> >>> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> >>>> ! Last official release is blank because there isn't one, remove it !
> >>>> First mirror I tried was a 404? (not sure which one). I changed the
> >>>> mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> >>> confusing.
> >>>> ? The NIH and SourceForge pages  should redirect to cTAKES, google
> >>> "cTAKES download" and imagine how confused a beginner would be.
> >>>>
> >>>> (2) User Guide
> >>>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> >>>> ? 3.0.0 : no list of new features from last stable release. Why would
> >>> a user bother to upgrade to a beta?
> >>>> ! Would be better to have a bundled download with resources, if
> >>> possible. Otherwise, make it clear to a newcomer what the benefit of
> >>> getting UMLS / LVG is. (one sentence).
> >>>> ! Needs a very high level overview of the components in the context of
> >>> using them to do a very basic task like.
> >>>> ! This is likely the most frequently accessed document for cTAKES. It
> >>> has almost no pointers to where to find basic information.
> >>>>
> >>>> (3) OTHER
> >>>> * The NCI and SourceForge links are now highly confusing.
> >>>> * While I am downloading, I should be reading the recommended "Get
> >>>> Started" guide
> >>>>
> >>>> I'm still downloading the 2GB resources file.
> >>>> I'll try and get back to you about the install when that is done too.
> >>>>
> >>>> This constructive criticism is because I believe cTAKES is AWESOME.
> >>>> Hard to see how awesome it is given the current instructions.
> >>>>
> >>>> --Andy
> >>>>
> >>>>
> >>>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> >>> <Pe...@childrens.harvard.edu> wrote:
> >>>>
> >>>>> Hi Andy,
> >>>>> So much has changed in cTAKES since last year, if you have a chance-
> >>> do you also want to try downloading the -bin and ensure at least the
> >>> steps in the README are able to get you started?
> >>>>>
> >>>>> --Pei
> >>>>> ________________________________________
> >>>>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>>>> Sent: Friday, February 15, 2013 4:04 PM
> >>>>> To: ctakes-dev@incubator.apache.org
> >>>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>>>
> >>>>> Suggestion: can we get a good programmer with no cTAKES experience to
> >>> kick the tires and tell us how long it took to get started?
> >>>>>
> >>>>> John Resig (jQuery founder) once told me "if it takes more than 15
> >>> minutes to get started, then that is way too long".
> >>>>>
> >>>>> "What is necessary is that enough investment be put into presentation
> >>>>> that newcomers can get past the obstacle of unfamiliarity. ...
> >>> Hactivation energy: the amount of energy a newcomer must put in before
> >>> she starts getting something back"
> >>>>> -- From "Producing Open Source Software"
> >>>>>
> >>>>>
> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> >>>>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> >>>>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> >>>>> =hacktivation%20energy&f=false
> >>>>>
> >>>>>
> >>>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> >>> <Pe...@childrens.harvard.edu> wrote:
> >>>>>
> >>>>>> This is to open a discussion to graduate Apache cTAKES podling from
> >>> the Apache Incubator.
> >>>>>>
> >>>>>> Apache cTAKES entered the Incubator in June of 2012. We have made
> >>> significant progress with the project since moving over to Apache. We
> >>> currently have 18 committers listed on our status page at [1] including
> >>> over 10 which accepted after the podling was formed.
> >>>>>>
> >>>>>> During incubation, cTAKES has :
> >>>>>> * Produced 1 Release
> >>>>>> * Added 10 new Committer/PPMC members and shows constant community
> >>>>>> activities
> >>>>>> * Cleared IP on code
> >>>>>> * Developed Roadmap(s) for the next major and minor releases in a
> >>>>>> community process and started working on that [2]
> >>>>>> * The community of Apache cTAKES is active, healthy, and growing and
> >>> has demonstrated the ability to self-govern using accepted Apache
> >>> practices.
> >>>>>>
> >>>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>>>>> [2]
> >>>>>>
> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> >>>>>> an.jira.plugin.system.project%3Aroadmap-panel
> >>
> >>
>

Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

[andy mcmurry <mc...@gmail.com>]

Message received, and from that perspective I agree to graduate.

Revised proposal to group:  no press advertisements about the release until
docs are ready.

. If Apache does promotions for graduated incubators then we should request
holding off press releases until the docs are ready.

My  battle scars from other open source projects remind me that if you ask
for attention be ready for lots of questions and short attention spans.
On Feb 19, 2013 6:13 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:

> Andy,
> The purpose of this release is primarily infrastructural. There are a lot
> of tasks involved in the move to ASF and many reasons for separating his
> release. One of them is that it's probably not a great idea to have major
> code fixes/changes mixed in with just a refactoring change.
>
> Regarding ease of use- agree with all of the points.
> cTAKES has historically been a collection of annotators and reusing UIMA's
> UI as examples and no real application built on top of it. However, there
> is a web GUI current in sandbox that should make things more intuitive.
> However, in order to produce releases efficiently and often, I believe we
> need graduate to a TLP (based on experience so far with the incubator). We
> should be able to address those issues fairly quickly with incremental
> releases.
>
> The downloads page should work all the time as its pretty basic
> functionality; It's not good if its flaky. Could others recreate the issue?
> Would be good if others could recreate it so we could get to the root of
> the issue.
> My 2 cents.
>
> -Pei
> Sent from my iPhone
>
> On Feb 19, 2013, at 5:47 PM, "andy mcmurry" <mc...@gmail.com>
> wrote:
>
> > Thank you Troy!
> >
> > *Summary: what is the purpose of the 3.0.0 release: changing the license
> to
> > Apache or getting new users? *
> >
> > Releasing 3.0.0 without DOCS is OK so long as the expected user base is
> > CURRENT cTAKES users.
> > If that is the case and this transition is 100% about changing the
> license
> > to Apache, then OK.
> >
> > NEW users coming to cTAKES will probably be overwhelmed, for all the
> > reasons discussed.
> > We will likely "lose" these new users who will not come back when the
> docs
> > are ready a month later.
> >
> > *Question for the group : who is the intended audience of the 3.0.0
> > release? *
> >
> >
> > On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <Bleeker.Troy@mayo.edu
> >wrote:
> >
> >> Summarizing where we are now ... completed items at the bottom of the
> list
> >> for reference only.
> >>
> >> The community decided to release cTAKES 3.0 without the doc being
> complete
> >> - these must be next:
> >> - The Developer Guide is not complete.
> >> [TODO] Dev Guide needs command line install instructions for UMLS ID/pw
> >> and classpath. I'll work on this.
> >> - The User Guide has a caveat on the table at the bottom of the
> >> instructions because a similar set of examples was not distributed like
> it
> >> was in 2.5. The instructions are longer as well since the user could not
> >> just load and run existing samples.
> >> [TODO] Consider shipping test data resources from SourceForge in a ZIP
> >> file.
> >> - The Getting Started page needs to be written in context of all future
> >> releases not just 3.0.
> >> [NEEDS REVIEW] A page was written. Is it as expected?
> >> - Previous releases list. We need to both point to the NCI sites for 2.6
> >> and back plus create an archive for what will be the history of Apache
> >> releases. Needs work your right.
> >> [TODO] For now I removed 2 of the 3 links leaving only one that points
> >> back to NCI for 2.5 and back. Question is should we have a full listing
> of
> >> the 2.5 and previous releases on the Apache site or simply point to the
> NCI
> >> wiki. If point to NCI then there is no archive to be had yet since the
> only
> >> release in Apache is the current release.
> >> - Component Use Guide pages needing updates. There are items marked in
> >> reddish color that are incorrect or in need of updates on these pages:
> >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
> >>
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
> >>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
> >> [TODO] Component knowledgeable people must update these pages.
> >>
> >> Potential priorities after that:
> >> - The examples, as described by Andy, would be more than a readme should
> >> have. This would be great for a how-to guide. The Developer Guide and
> User
> >> Guide have historically been install guides not how-to guides. I don't
> >> think a how-to guide should be incorporated into these but should be its
> >> own document.
> >> [TODO] Should the current user and dev guides be renamed?
> >> - cTAKES has never had a how-to guide that I know of. Making one would
> be
> >> great and as you say should include things like 1) pointers to where to
> >> find basic information 2) very high level overview of the components in
> the
> >> context of using them to do a very basic task like 3) I think it was
> >> suggested that the Getting Started page might be something like this in
> >> very short form. If we did that then it would point to a more
> comprehensive
> >> how-to guide.
> >> [TODO] Decide if we are going to do this.
> >> - Project history page of all cTAKES releases placed on Apache sites
> >> somewhere. Good plan if short. I would not copy readmes there but have
> >> links to them.
> >> [TODO] This was done in the past but removed from the bottom of the
> >> downloads page. This page exists now but is not linked to from the
> Apache
> >> cTAKES site. Here is a direct link:
> >> http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0 info
> >> added if we decide to use it.
> >> - Creating a single download for a newcomer.
> >> [LATER] This has been discussed and tabled by the community for the time
> >> being in order to get the 3.0 release done and out the door. We need to
> >> come back to this in order to make the best first impression.
> >>
> >> Completed:
> >> - The downloads page must work. It now seems to function alright
> ***IF***
> >> you refresh the page or select a mirror and click the Change button. If
> you
> >> do neither and try to download you get this error: "The requested URL
> >>
> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz
> >> was not found on this server." Anyone have time to fix this?
> >> [WORK-AROUND] Seems intermittent. Tried 5 different machines. James and
> >> Troy changed the downloads page to tell the user to select the Change
> >> button when they have issues. It should work if they do that. Best
> guess -
> >> the randomly selected mirror sites do not all work. Also, selecting a
> site
> >> in the drop-down and pressing the Change button does not set the mirror
> >> site to the one you selected. Next best guess - other Apache sites have
> a
> >> double // in the URL just after the mirror domain in the file download
> >> link. Maybe this is required. Tried this too.
> >> - Adding a link to the install instructions makes it obvious (which I
> have
> >> done to the page) but it was there in a sense.
> >> [DONE] Link added.
> >> - "Last official release" was held until now. Since 3.0 is going to be
> >> officially announced, 3.0 will go there. I made that change as well.
> >> [DONE] Reworked the page.
> >> - A list of changed features has not been high priority since the
> original
> >> goal was to make a 3.0 in Apache that pretty much matched the function
> of
> >> 2.5. The only thing that changed was how the product is built and
> shipped.
> >> Nevertheless we need to state at least that somewhere.
> >> [DONE] That was wrong, there is new function. Relation Extractor now
> >> documented on the downloads page.
> >> - The resources file is 1.1 GB not 2 right?
> >> [DONE] Andy said it in an email. The web site lists it fine.
> >> - There are still 3.0 developer and user guide pages on the cTAKES home
> >> site that should be removed so no one stumbles on to them.
> >> [DONE] Removed.
> >> - Where would a newcomer hit first? Internet search for "ctakes" or
> >> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified
> >> to point to the best Apache cTAKES landing page.
> >> [DONE] James and Troy made changes to the top hit pages and other places
> >> that made sense.
> >> - The current guides are still not complete.
> >> [DONE] User Guide James and Troy went through.
> >>
> >> Thanks
> >> Troy
> >>
> >> -----Original Message-----
> >> From: ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:
> >> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On
> >> Behalf Of Masanz, James J.
> >> Sent: Tuesday, February 19, 2013 10:10 AM
> >> To: 'ctakes-dev@incubator.apache.org'
> >> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from
> >> Incubator
> >>
> >>
> >>> - The resources file is 1.1 GB not 2 right?
> >>
> >> I agree. But I don't see it listed as 2GB on the download page. If you
> >> tell me where you saw it listed as 2GB I will update that page.
> >>
> >>> - A list of changed features has not been high priority since
> >> I will update the downloads page right now stating the relation
> extractor
> >> is new for 3.0
> >>
> >>
> >>> - Where would a newcomer hit first? Internet search for "ctakes" or
> >>> "ctakes 3.0" is probably first. Top hits on those lists should be
> >>> modified to point to the best Apache cTAKES landing page.
> >>
> >> I modified the following pages to have a link to Apache cTAKES home page
> >>
> >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
> >> https://sourceforge.net/projects/ohnlp/files/cTAKES/
> >> https://sourceforge.net/projects/ohnlp/
> >> http://ohnlp.sourceforge.net/
> >>
> >> The update to the last one is not appearing yet, but it was updated.
> >>
> >>> - The Getting Started page needs to be written in context of all future
> >>> releases not just 3.0.
> >>
> >> Looks like you updated that page, thanks.
> >>
> >>> - The current guides are still not complete.
> >>
> >> I took a quick run through the User Guide on the Wiki and made some
> >> updates.
> >>
> >> -- James Masanz
> >>
> >>
> >>> -----Original Message-----
> >>> From: ctakes-dev-return-1239-Masanz.James=
> mayo.edu@incubator.apache.org
> >>> [mailto:ctakes-dev-return-1239-
> >>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> >>> C.
> >>> Sent: Monday, February 18, 2013 10:58 AM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> >>> from Incubator
> >>>
> >>> All the suggestions and discussion are good. There's a lot here, sorry
> >>> for the long summary. First things first:
> >>>
> >>> - The downloads page must work. It now seems to function alright
> >>> ***IF*** you refresh the page or select a mirror and click the Change
> >>> button. If you do neither and try to download you get this error: "The
> >>> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> >>> incubating-bin.tar.gz was not found on this server." Anyone have time
> to
> >>> fix this?
> >>> - Adding a link to the install instructions makes it obvious (which I
> >>> have done to the page) but it was there in a sense. The page said "Use
> >>> the Developer and User Guides to direct you through the installation
> >>> process." and the links to those were just to the left in the
> hierarchy.
> >>> - "Last official release" was held until now. Since 3.0 is going to be
> >>> officially announced, 3.0 will go there. I made that change as well.
> >>> - A list of changed features has not been high priority since the
> >>> original goal was to make a 3.0 in Apache that pretty much matched the
> >>> function of 2.5. The only thing that changed was how the product is
> >>> built and shipped. Nevertheless we need to state at least that
> >>> somewhere.
> >>> - The resources file is 1.1 GB not 2 right?
> >>>
> >>> Keep in mind that the community decided to release cTAKES 3.0 without
> >>> the doc being complete, but these must be next:
> >>> - The current guides are still not complete. I made it through the
> >>> developer guide but the user guide still has problems. I get errors
> >>> after installing and running scripts. I have not been able to try the
> >>> comparison test that was available previously. The table at the bottom
> I
> >>> have not got to yet.
> >>> - We have 2 sites now 1) cTAKES home
> http://incubator.apache.org/ctakes/
> >>> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> >>> done my best to minimize a user going back and forth. We have it this
> >>> way because a useful guide is not easy (IMHO or even possible) with
> >>> markdown text in the cTAKES home pages. There are still 3.0 developer
> >>> and user guide pages on the cTAKES home site that should be removed so
> >>> no one stumbles on to them.
> >>> - The Getting Started page needs to be written in context of all future
> >>> releases not just 3.0.
> >>> - Previous releases list. We need to both point to the NCI sites for
> 2.6
> >>> and back plus create an archive for what will be the history of Apache
> >>> releases. Needs work your right.
> >>>
> >>> Potential priorities after that:
> >>> - The examples, as described by Andy, would be more than a readme
> should
> >>> have. This would be great for a how-to guide.
> >>> - The Developer Guide and User Guide have historically been install
> >>> guides not how-to guides. I don't think a how-to guide should be
> >>> incorporated into these but should be its own document.
> >>> - cTAKES has never had a how-to guide that I know of. Making one would
> >>> be great and as you say should include things like 1) pointers to where
> >>> to find basic information 2) very high level overview of the components
> >>> in the context of using them to do a very basic task like 3) I think it
> >>> was suggested that the Getting Started page might be something like
> this
> >>> in very short form. If we did that then it would point to a more
> >>> comprehensive how-to guide.
> >>> - Project history page of all cTAKES releases placed on Apache sites
> >>> somewhere. Good plan if short. I would not copy readmes there but have
> >>> links to them.
> >>> I already did this for cTAKES 2.5 and past:
> >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> >>> Move this page to Apache? Have a page on Apache that continues this and
> >>> points back to what already exists?
> >>> Also, I had this project history on the Apache cTAKES downloads page
> but
> >>> that section was removed when 3.0 was placed on there. If you can find
> >>> the history of changes to that page you may find something already done
> >>> in markdown format.
> >>> - Creating a single download for a newcomer. This has been discussed
> and
> >>> tabled by the community for the time being in order to get the 3.0
> >>> release done and out the door. We need to come back to this in order to
> >>> make the best first impression.
> >>>
> >>> Troy
> >>>
> >>> -----Original Message-----
> >>> From: ctakes-dev-return-1230-Bleeker.Troy=
> mayo.edu@incubator.apache.org
> >>> [mailto:ctakes-dev-return-1230-
> >>> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> >>> Sent: Friday, February 15, 2013 10:17 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> >>> Incubator
> >>>
> >>> Thanks Andy for the feedback.
> >>> Examples are a good idea- Were you thinking of adding it to the README
> >>> file or the confluence user guide?
> >>>
> >>> Feel free to update the downloads page(s) (it uses Apache CMS) and the
> >>> User Guides (Confluence wiki).
> >>> Note: The release is still being replicated to all of the mirrors and
> >>> may take up to 24 hrs, so I would wait until after the weekend before
> >>> testing all of the mirror links.
> >>>
> >>> --Pei
> >>> ________________________________________
> >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>> Sent: Friday, February 15, 2013 11:08 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>
> >>> Clarifications
> >>>
> >>> There isn't a last Apache release. But there are last previous NIH,
> >>> Sourceforge, and Apache releases?
> >>> TODO: Project History Page (Simple, just the releases and times,
> ideally
> >>> with JIRA generated release notes).
> >>>
> >>> Suggestion: Demonstration > explanation. Use Examples !!
> >>>
> >>> EXAMPLE 1 : Basic Pipeline (without UMLS)
> >>>
> >>> ** SHOW Before and after clinical text, demonstrates purpose
> >>> ** LIST the 5 steps
> >>> ** Most impressive demo would be the smoking status pipeline
> >>>
> >>> EXAMPLE 2: Basic Pipeline (with UMLS)
> >>>
> >>> ** SHOW Before and after (input text -> output annotations)
> >>> ** LIST the steps
> >>> ** Most impressive demo would be a negation of a cancer diagnosis and
> >>> NER of a medication (chemotherapuetic drug).
> >>>
> >>> Thoughts?
> >>> --andy
> >>>
> >>>
> >>> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> >>> wrote:
> >>>
> >>>> Sure thing Pei.
> >>>>
> >>>> I dont think cTAKES is ready for attention grabbing release (humble
> >>> opinion).
> >>>> And when you release you want to grab attention! ! cTAKES is awesome!!
> >>>>
> >>>> Suggestions (release blockers)
> >>>>
> >>>> (1) Downloads
> >>>> http://incubator.apache.org/ctakes/downloads.cgi
> >>>> ! Link to install instructions is not there but "Verifying signatures"
> >>> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> >>>> ! Last official release is blank because there isn't one, remove it !
> >>>> First mirror I tried was a 404? (not sure which one). I changed the
> >>>> mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> >>> confusing.
> >>>> ? The NIH and SourceForge pages  should redirect to cTAKES, google
> >>> "cTAKES download" and imagine how confused a beginner would be.
> >>>>
> >>>> (2) User Guide
> >>>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> >>>> ? 3.0.0 : no list of new features from last stable release. Why would
> >>> a user bother to upgrade to a beta?
> >>>> ! Would be better to have a bundled download with resources, if
> >>> possible. Otherwise, make it clear to a newcomer what the benefit of
> >>> getting UMLS / LVG is. (one sentence).
> >>>> ! Needs a very high level overview of the components in the context of
> >>> using them to do a very basic task like.
> >>>> ! This is likely the most frequently accessed document for cTAKES. It
> >>> has almost no pointers to where to find basic information.
> >>>>
> >>>> (3) OTHER
> >>>> * The NCI and SourceForge links are now highly confusing.
> >>>> * While I am downloading, I should be reading the recommended "Get
> >>>> Started" guide
> >>>>
> >>>> I'm still downloading the 2GB resources file.
> >>>> I'll try and get back to you about the install when that is done too.
> >>>>
> >>>> This constructive criticism is because I believe cTAKES is AWESOME.
> >>>> Hard to see how awesome it is given the current instructions.
> >>>>
> >>>> --Andy
> >>>>
> >>>>
> >>>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> >>> <Pe...@childrens.harvard.edu> wrote:
> >>>>
> >>>>> Hi Andy,
> >>>>> So much has changed in cTAKES since last year, if you have a chance-
> >>> do you also want to try downloading the -bin and ensure at least the
> >>> steps in the README are able to get you started?
> >>>>>
> >>>>> --Pei
> >>>>> ________________________________________
> >>>>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>>>> Sent: Friday, February 15, 2013 4:04 PM
> >>>>> To: ctakes-dev@incubator.apache.org
> >>>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>>>
> >>>>> Suggestion: can we get a good programmer with no cTAKES experience to
> >>> kick the tires and tell us how long it took to get started?
> >>>>>
> >>>>> John Resig (jQuery founder) once told me "if it takes more than 15
> >>> minutes to get started, then that is way too long".
> >>>>>
> >>>>> "What is necessary is that enough investment be put into presentation
> >>>>> that newcomers can get past the obstacle of unfamiliarity. ...
> >>> Hactivation energy: the amount of energy a newcomer must put in before
> >>> she starts getting something back"
> >>>>> -- From "Producing Open Source Software"
> >>>>>
> >>>>>
> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> >>>>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> >>>>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> >>>>> =hacktivation%20energy&f=false
> >>>>>
> >>>>>
> >>>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> >>> <Pe...@childrens.harvard.edu> wrote:
> >>>>>
> >>>>>> This is to open a discussion to graduate Apache cTAKES podling from
> >>> the Apache Incubator.
> >>>>>>
> >>>>>> Apache cTAKES entered the Incubator in June of 2012. We have made
> >>> significant progress with the project since moving over to Apache. We
> >>> currently have 18 committers listed on our status page at [1] including
> >>> over 10 which accepted after the podling was formed.
> >>>>>>
> >>>>>> During incubation, cTAKES has :
> >>>>>> * Produced 1 Release
> >>>>>> * Added 10 new Committer/PPMC members and shows constant community
> >>>>>> activities
> >>>>>> * Cleared IP on code
> >>>>>> * Developed Roadmap(s) for the next major and minor releases in a
> >>>>>> community process and started working on that [2]
> >>>>>> * The community of Apache cTAKES is active, healthy, and growing and
> >>> has demonstrated the ability to self-govern using accepted Apache
> >>> practices.
> >>>>>>
> >>>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>>>>> [2]
> >>>>>>
> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> >>>>>> an.jira.plugin.system.project%3Aroadmap-panel
> >>
> >>
>

Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Chen, Pei" <Pe...@childrens.harvard.edu>]

Andy,
The purpose of this release is primarily infrastructural. There are a lot of tasks involved in the move to ASF and many reasons for separating his release. One of them is that it's probably not a great idea to have major code fixes/changes mixed in with just a refactoring change. 

Regarding ease of use- agree with all of the points. 
cTAKES has historically been a collection of annotators and reusing UIMA's UI as examples and no real application built on top of it. However, there is a web GUI current in sandbox that should make things more intuitive. However, in order to produce releases efficiently and often, I believe we need graduate to a TLP (based on experience so far with the incubator). We should be able to address those issues fairly quickly with incremental releases. 

The downloads page should work all the time as its pretty basic functionality; It's not good if its flaky. Could others recreate the issue? Would be good if others could recreate it so we could get to the root of the issue.
My 2 cents. 

-Pei
Sent from my iPhone

On Feb 19, 2013, at 5:47 PM, "andy mcmurry" <mc...@gmail.com> wrote:

> Thank you Troy!
> 
> *Summary: what is the purpose of the 3.0.0 release: changing the license to
> Apache or getting new users? *
> 
> Releasing 3.0.0 without DOCS is OK so long as the expected user base is
> CURRENT cTAKES users.
> If that is the case and this transition is 100% about changing the license
> to Apache, then OK.
> 
> NEW users coming to cTAKES will probably be overwhelmed, for all the
> reasons discussed.
> We will likely "lose" these new users who will not come back when the docs
> are ready a month later.
> 
> *Question for the group : who is the intended audience of the 3.0.0
> release? *
> 
> 
> On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <Bl...@mayo.edu>wrote:
> 
>> Summarizing where we are now ... completed items at the bottom of the list
>> for reference only.
>> 
>> The community decided to release cTAKES 3.0 without the doc being complete
>> - these must be next:
>> - The Developer Guide is not complete.
>> [TODO] Dev Guide needs command line install instructions for UMLS ID/pw
>> and classpath. I'll work on this.
>> - The User Guide has a caveat on the table at the bottom of the
>> instructions because a similar set of examples was not distributed like it
>> was in 2.5. The instructions are longer as well since the user could not
>> just load and run existing samples.
>> [TODO] Consider shipping test data resources from SourceForge in a ZIP
>> file.
>> - The Getting Started page needs to be written in context of all future
>> releases not just 3.0.
>> [NEEDS REVIEW] A page was written. Is it as expected?
>> - Previous releases list. We need to both point to the NCI sites for 2.6
>> and back plus create an archive for what will be the history of Apache
>> releases. Needs work your right.
>> [TODO] For now I removed 2 of the 3 links leaving only one that points
>> back to NCI for 2.5 and back. Question is should we have a full listing of
>> the 2.5 and previous releases on the Apache site or simply point to the NCI
>> wiki. If point to NCI then there is no archive to be had yet since the only
>> release in Apache is the current release.
>> - Component Use Guide pages needing updates. There are items marked in
>> reddish color that are incorrect or in need of updates on these pages:
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
>> 
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
>> 
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
>> 
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
>> [TODO] Component knowledgeable people must update these pages.
>> 
>> Potential priorities after that:
>> - The examples, as described by Andy, would be more than a readme should
>> have. This would be great for a how-to guide. The Developer Guide and User
>> Guide have historically been install guides not how-to guides. I don't
>> think a how-to guide should be incorporated into these but should be its
>> own document.
>> [TODO] Should the current user and dev guides be renamed?
>> - cTAKES has never had a how-to guide that I know of. Making one would be
>> great and as you say should include things like 1) pointers to where to
>> find basic information 2) very high level overview of the components in the
>> context of using them to do a very basic task like 3) I think it was
>> suggested that the Getting Started page might be something like this in
>> very short form. If we did that then it would point to a more comprehensive
>> how-to guide.
>> [TODO] Decide if we are going to do this.
>> - Project history page of all cTAKES releases placed on Apache sites
>> somewhere. Good plan if short. I would not copy readmes there but have
>> links to them.
>> [TODO] This was done in the past but removed from the bottom of the
>> downloads page. This page exists now but is not linked to from the Apache
>> cTAKES site. Here is a direct link:
>> http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0 info
>> added if we decide to use it.
>> - Creating a single download for a newcomer.
>> [LATER] This has been discussed and tabled by the community for the time
>> being in order to get the 3.0 release done and out the door. We need to
>> come back to this in order to make the best first impression.
>> 
>> Completed:
>> - The downloads page must work. It now seems to function alright ***IF***
>> you refresh the page or select a mirror and click the Change button. If you
>> do neither and try to download you get this error: "The requested URL
>> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz
>> was not found on this server." Anyone have time to fix this?
>> [WORK-AROUND] Seems intermittent. Tried 5 different machines. James and
>> Troy changed the downloads page to tell the user to select the Change
>> button when they have issues. It should work if they do that. Best guess -
>> the randomly selected mirror sites do not all work. Also, selecting a site
>> in the drop-down and pressing the Change button does not set the mirror
>> site to the one you selected. Next best guess - other Apache sites have a
>> double // in the URL just after the mirror domain in the file download
>> link. Maybe this is required. Tried this too.
>> - Adding a link to the install instructions makes it obvious (which I have
>> done to the page) but it was there in a sense.
>> [DONE] Link added.
>> - "Last official release" was held until now. Since 3.0 is going to be
>> officially announced, 3.0 will go there. I made that change as well.
>> [DONE] Reworked the page.
>> - A list of changed features has not been high priority since the original
>> goal was to make a 3.0 in Apache that pretty much matched the function of
>> 2.5. The only thing that changed was how the product is built and shipped.
>> Nevertheless we need to state at least that somewhere.
>> [DONE] That was wrong, there is new function. Relation Extractor now
>> documented on the downloads page.
>> - The resources file is 1.1 GB not 2 right?
>> [DONE] Andy said it in an email. The web site lists it fine.
>> - There are still 3.0 developer and user guide pages on the cTAKES home
>> site that should be removed so no one stumbles on to them.
>> [DONE] Removed.
>> - Where would a newcomer hit first? Internet search for "ctakes" or
>> "ctakes 3.0" is probably first. Top hits on those lists should be modified
>> to point to the best Apache cTAKES landing page.
>> [DONE] James and Troy made changes to the top hit pages and other places
>> that made sense.
>> - The current guides are still not complete.
>> [DONE] User Guide James and Troy went through.
>> 
>> Thanks
>> Troy
>> 
>> -----Original Message-----
>> From: ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org[mailto:
>> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On
>> Behalf Of Masanz, James J.
>> Sent: Tuesday, February 19, 2013 10:10 AM
>> To: 'ctakes-dev@incubator.apache.org'
>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
>> Incubator
>> 
>> 
>>> - The resources file is 1.1 GB not 2 right?
>> 
>> I agree. But I don't see it listed as 2GB on the download page. If you
>> tell me where you saw it listed as 2GB I will update that page.
>> 
>>> - A list of changed features has not been high priority since
>> I will update the downloads page right now stating the relation extractor
>> is new for 3.0
>> 
>> 
>>> - Where would a newcomer hit first? Internet search for "ctakes" or
>>> "ctakes 3.0" is probably first. Top hits on those lists should be
>>> modified to point to the best Apache cTAKES landing page.
>> 
>> I modified the following pages to have a link to Apache cTAKES home page
>> 
>> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
>> https://sourceforge.net/projects/ohnlp/files/cTAKES/
>> https://sourceforge.net/projects/ohnlp/
>> http://ohnlp.sourceforge.net/
>> 
>> The update to the last one is not appearing yet, but it was updated.
>> 
>>> - The Getting Started page needs to be written in context of all future
>>> releases not just 3.0.
>> 
>> Looks like you updated that page, thanks.
>> 
>>> - The current guides are still not complete.
>> 
>> I took a quick run through the User Guide on the Wiki and made some
>> updates.
>> 
>> -- James Masanz
>> 
>> 
>>> -----Original Message-----
>>> From: ctakes-dev-return-1239-Masanz.James=mayo.edu@incubator.apache.org
>>> [mailto:ctakes-dev-return-1239-
>>> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
>>> C.
>>> Sent: Monday, February 18, 2013 10:58 AM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
>>> from Incubator
>>> 
>>> All the suggestions and discussion are good. There's a lot here, sorry
>>> for the long summary. First things first:
>>> 
>>> - The downloads page must work. It now seems to function alright
>>> ***IF*** you refresh the page or select a mirror and click the Change
>>> button. If you do neither and try to download you get this error: "The
>>> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
>>> incubating-bin.tar.gz was not found on this server." Anyone have time to
>>> fix this?
>>> - Adding a link to the install instructions makes it obvious (which I
>>> have done to the page) but it was there in a sense. The page said "Use
>>> the Developer and User Guides to direct you through the installation
>>> process." and the links to those were just to the left in the hierarchy.
>>> - "Last official release" was held until now. Since 3.0 is going to be
>>> officially announced, 3.0 will go there. I made that change as well.
>>> - A list of changed features has not been high priority since the
>>> original goal was to make a 3.0 in Apache that pretty much matched the
>>> function of 2.5. The only thing that changed was how the product is
>>> built and shipped. Nevertheless we need to state at least that
>>> somewhere.
>>> - The resources file is 1.1 GB not 2 right?
>>> 
>>> Keep in mind that the community decided to release cTAKES 3.0 without
>>> the doc being complete, but these must be next:
>>> - The current guides are still not complete. I made it through the
>>> developer guide but the user guide still has problems. I get errors
>>> after installing and running scripts. I have not been able to try the
>>> comparison test that was available previously. The table at the bottom I
>>> have not got to yet.
>>> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/
>>> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
>>> done my best to minimize a user going back and forth. We have it this
>>> way because a useful guide is not easy (IMHO or even possible) with
>>> markdown text in the cTAKES home pages. There are still 3.0 developer
>>> and user guide pages on the cTAKES home site that should be removed so
>>> no one stumbles on to them.
>>> - The Getting Started page needs to be written in context of all future
>>> releases not just 3.0.
>>> - Previous releases list. We need to both point to the NCI sites for 2.6
>>> and back plus create an archive for what will be the history of Apache
>>> releases. Needs work your right.
>>> 
>>> Potential priorities after that:
>>> - The examples, as described by Andy, would be more than a readme should
>>> have. This would be great for a how-to guide.
>>> - The Developer Guide and User Guide have historically been install
>>> guides not how-to guides. I don't think a how-to guide should be
>>> incorporated into these but should be its own document.
>>> - cTAKES has never had a how-to guide that I know of. Making one would
>>> be great and as you say should include things like 1) pointers to where
>>> to find basic information 2) very high level overview of the components
>>> in the context of using them to do a very basic task like 3) I think it
>>> was suggested that the Getting Started page might be something like this
>>> in very short form. If we did that then it would point to a more
>>> comprehensive how-to guide.
>>> - Project history page of all cTAKES releases placed on Apache sites
>>> somewhere. Good plan if short. I would not copy readmes there but have
>>> links to them.
>>> I already did this for cTAKES 2.5 and past:
>>> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
>>> Move this page to Apache? Have a page on Apache that continues this and
>>> points back to what already exists?
>>> Also, I had this project history on the Apache cTAKES downloads page but
>>> that section was removed when 3.0 was placed on there. If you can find
>>> the history of changes to that page you may find something already done
>>> in markdown format.
>>> - Creating a single download for a newcomer. This has been discussed and
>>> tabled by the community for the time being in order to get the 3.0
>>> release done and out the door. We need to come back to this in order to
>>> make the best first impression.
>>> 
>>> Troy
>>> 
>>> -----Original Message-----
>>> From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
>>> [mailto:ctakes-dev-return-1230-
>>> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
>>> Sent: Friday, February 15, 2013 10:17 PM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
>>> Incubator
>>> 
>>> Thanks Andy for the feedback.
>>> Examples are a good idea- Were you thinking of adding it to the README
>>> file or the confluence user guide?
>>> 
>>> Feel free to update the downloads page(s) (it uses Apache CMS) and the
>>> User Guides (Confluence wiki).
>>> Note: The release is still being replicated to all of the mirrors and
>>> may take up to 24 hrs, so I would wait until after the weekend before
>>> testing all of the mirror links.
>>> 
>>> --Pei
>>> ________________________________________
>>> From: Andy McMurry [mcmurry.andy@gmail.com]
>>> Sent: Friday, February 15, 2013 11:08 PM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>> 
>>> Clarifications
>>> 
>>> There isn't a last Apache release. But there are last previous NIH,
>>> Sourceforge, and Apache releases?
>>> TODO: Project History Page (Simple, just the releases and times, ideally
>>> with JIRA generated release notes).
>>> 
>>> Suggestion: Demonstration > explanation. Use Examples !!
>>> 
>>> EXAMPLE 1 : Basic Pipeline (without UMLS)
>>> 
>>> ** SHOW Before and after clinical text, demonstrates purpose
>>> ** LIST the 5 steps
>>> ** Most impressive demo would be the smoking status pipeline
>>> 
>>> EXAMPLE 2: Basic Pipeline (with UMLS)
>>> 
>>> ** SHOW Before and after (input text -> output annotations)
>>> ** LIST the steps
>>> ** Most impressive demo would be a negation of a cancer diagnosis and
>>> NER of a medication (chemotherapuetic drug).
>>> 
>>> Thoughts?
>>> --andy
>>> 
>>> 
>>> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
>>> wrote:
>>> 
>>>> Sure thing Pei.
>>>> 
>>>> I dont think cTAKES is ready for attention grabbing release (humble
>>> opinion).
>>>> And when you release you want to grab attention! ! cTAKES is awesome!!
>>>> 
>>>> Suggestions (release blockers)
>>>> 
>>>> (1) Downloads
>>>> http://incubator.apache.org/ctakes/downloads.cgi
>>>> ! Link to install instructions is not there but "Verifying signatures"
>>> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
>>>> ! Last official release is blank because there isn't one, remove it !
>>>> First mirror I tried was a 404? (not sure which one). I changed the
>>>> mirror then OK. Test all mirrors (script) ? Previous releases are VERY
>>> confusing.
>>>> ? The NIH and SourceForge pages  should redirect to cTAKES, google
>>> "cTAKES download" and imagine how confused a beginner would be.
>>>> 
>>>> (2) User Guide
>>>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
>>>> ? 3.0.0 : no list of new features from last stable release. Why would
>>> a user bother to upgrade to a beta?
>>>> ! Would be better to have a bundled download with resources, if
>>> possible. Otherwise, make it clear to a newcomer what the benefit of
>>> getting UMLS / LVG is. (one sentence).
>>>> ! Needs a very high level overview of the components in the context of
>>> using them to do a very basic task like.
>>>> ! This is likely the most frequently accessed document for cTAKES. It
>>> has almost no pointers to where to find basic information.
>>>> 
>>>> (3) OTHER
>>>> * The NCI and SourceForge links are now highly confusing.
>>>> * While I am downloading, I should be reading the recommended "Get
>>>> Started" guide
>>>> 
>>>> I'm still downloading the 2GB resources file.
>>>> I'll try and get back to you about the install when that is done too.
>>>> 
>>>> This constructive criticism is because I believe cTAKES is AWESOME.
>>>> Hard to see how awesome it is given the current instructions.
>>>> 
>>>> --Andy
>>>> 
>>>> 
>>>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
>>> <Pe...@childrens.harvard.edu> wrote:
>>>> 
>>>>> Hi Andy,
>>>>> So much has changed in cTAKES since last year, if you have a chance-
>>> do you also want to try downloading the -bin and ensure at least the
>>> steps in the README are able to get you started?
>>>>> 
>>>>> --Pei
>>>>> ________________________________________
>>>>> From: Andy McMurry [mcmurry.andy@gmail.com]
>>>>> Sent: Friday, February 15, 2013 4:04 PM
>>>>> To: ctakes-dev@incubator.apache.org
>>>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>>>> 
>>>>> Suggestion: can we get a good programmer with no cTAKES experience to
>>> kick the tires and tell us how long it took to get started?
>>>>> 
>>>>> John Resig (jQuery founder) once told me "if it takes more than 15
>>> minutes to get started, then that is way too long".
>>>>> 
>>>>> "What is necessary is that enough investment be put into presentation
>>>>> that newcomers can get past the obstacle of unfamiliarity. ...
>>> Hactivation energy: the amount of energy a newcomer must put in before
>>> she starts getting something back"
>>>>> -- From "Producing Open Source Software"
>>>>> 
>>>>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
>>>>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
>>>>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
>>>>> =hacktivation%20energy&f=false
>>>>> 
>>>>> 
>>>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
>>> <Pe...@childrens.harvard.edu> wrote:
>>>>> 
>>>>>> This is to open a discussion to graduate Apache cTAKES podling from
>>> the Apache Incubator.
>>>>>> 
>>>>>> Apache cTAKES entered the Incubator in June of 2012. We have made
>>> significant progress with the project since moving over to Apache. We
>>> currently have 18 committers listed on our status page at [1] including
>>> over 10 which accepted after the podling was formed.
>>>>>> 
>>>>>> During incubation, cTAKES has :
>>>>>> * Produced 1 Release
>>>>>> * Added 10 new Committer/PPMC members and shows constant community
>>>>>> activities
>>>>>> * Cleared IP on code
>>>>>> * Developed Roadmap(s) for the next major and minor releases in a
>>>>>> community process and started working on that [2]
>>>>>> * The community of Apache cTAKES is active, healthy, and growing and
>>> has demonstrated the ability to self-govern using accepted Apache
>>> practices.
>>>>>> 
>>>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
>>>>>> [2]
>>>>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
>>>>>> an.jira.plugin.system.project%3Aroadmap-panel
>> 
>> 

Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

[andy mcmurry <mc...@gmail.com>]

Thank you Troy!

*Summary: what is the purpose of the 3.0.0 release: changing the license to
Apache or getting new users? *

Releasing 3.0.0 without DOCS is OK so long as the expected user base is
CURRENT cTAKES users.
If that is the case and this transition is 100% about changing the license
to Apache, then OK.

NEW users coming to cTAKES will probably be overwhelmed, for all the
reasons discussed.
We will likely "lose" these new users who will not come back when the docs
are ready a month later.

*Question for the group : who is the intended audience of the 3.0.0
release? *


On Tue, Feb 19, 2013 at 5:11 PM, Bleeker, Troy C. <Bl...@mayo.edu>wrote:

> Summarizing where we are now ... completed items at the bottom of the list
> for reference only.
>
> The community decided to release cTAKES 3.0 without the doc being complete
> - these must be next:
> - The Developer Guide is not complete.
> [TODO] Dev Guide needs command line install instructions for UMLS ID/pw
> and classpath. I'll work on this.
> - The User Guide has a caveat on the table at the bottom of the
> instructions because a similar set of examples was not distributed like it
> was in 2.5. The instructions are longer as well since the user could not
> just load and run existing samples.
> [TODO] Consider shipping test data resources from SourceForge in a ZIP
> file.
> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.
> [NEEDS REVIEW] A page was written. Is it as expected?
> - Previous releases list. We need to both point to the NCI sites for 2.6
> and back plus create an archive for what will be the history of Apache
> releases. Needs work your right.
> [TODO] For now I removed 2 of the 3 links leaving only one that points
> back to NCI for 2.5 and back. Question is should we have a full listing of
> the 2.5 and previous releases on the Apache site or simply point to the NCI
> wiki. If point to NCI then there is no archive to be had yet since the only
> release in Apache is the current release.
> - Component Use Guide pages needing updates. There are items marked in
> reddish color that are incorrect or in need of updates on these pages:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
> [TODO] Component knowledgeable people must update these pages.
>
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should
> have. This would be great for a how-to guide. The Developer Guide and User
> Guide have historically been install guides not how-to guides. I don't
> think a how-to guide should be incorporated into these but should be its
> own document.
> [TODO] Should the current user and dev guides be renamed?
> - cTAKES has never had a how-to guide that I know of. Making one would be
> great and as you say should include things like 1) pointers to where to
> find basic information 2) very high level overview of the components in the
> context of using them to do a very basic task like 3) I think it was
> suggested that the Getting Started page might be something like this in
> very short form. If we did that then it would point to a more comprehensive
> how-to guide.
> [TODO] Decide if we are going to do this.
> - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have
> links to them.
> [TODO] This was done in the past but removed from the bottom of the
> downloads page. This page exists now but is not linked to from the Apache
> cTAKES site. Here is a direct link:
> http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0 info
> added if we decide to use it.
> - Creating a single download for a newcomer.
> [LATER] This has been discussed and tabled by the community for the time
> being in order to get the 3.0 release done and out the door. We need to
> come back to this in order to make the best first impression.
>
> Completed:
> - The downloads page must work. It now seems to function alright ***IF***
> you refresh the page or select a mirror and click the Change button. If you
> do neither and try to download you get this error: "The requested URL
> /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz
> was not found on this server." Anyone have time to fix this?
> [WORK-AROUND] Seems intermittent. Tried 5 different machines. James and
> Troy changed the downloads page to tell the user to select the Change
> button when they have issues. It should work if they do that. Best guess -
> the randomly selected mirror sites do not all work. Also, selecting a site
> in the drop-down and pressing the Change button does not set the mirror
> site to the one you selected. Next best guess - other Apache sites have a
> double // in the URL just after the mirror domain in the file download
> link. Maybe this is required. Tried this too.
> - Adding a link to the install instructions makes it obvious (which I have
> done to the page) but it was there in a sense.
> [DONE] Link added.
> - "Last official release" was held until now. Since 3.0 is going to be
> officially announced, 3.0 will go there. I made that change as well.
> [DONE] Reworked the page.
> - A list of changed features has not been high priority since the original
> goal was to make a 3.0 in Apache that pretty much matched the function of
> 2.5. The only thing that changed was how the product is built and shipped.
> Nevertheless we need to state at least that somewhere.
> [DONE] That was wrong, there is new function. Relation Extractor now
> documented on the downloads page.
> - The resources file is 1.1 GB not 2 right?
>  [DONE] Andy said it in an email. The web site lists it fine.
> - There are still 3.0 developer and user guide pages on the cTAKES home
> site that should be removed so no one stumbles on to them.
> [DONE] Removed.
> - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be modified
> to point to the best Apache cTAKES landing page.
> [DONE] James and Troy made changes to the top hit pages and other places
> that made sense.
> - The current guides are still not complete.
> [DONE] User Guide James and Troy went through.
>
> Thanks
> Troy
>
> -----Original Message-----
> From: ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org[mailto:
> ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On
> Behalf Of Masanz, James J.
> Sent: Tuesday, February 19, 2013 10:10 AM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> Incubator
>
>
> > - The resources file is 1.1 GB not 2 right?
>
> I agree. But I don't see it listed as 2GB on the download page. If you
> tell me where you saw it listed as 2GB I will update that page.
>
> > - A list of changed features has not been high priority since
> I will update the downloads page right now stating the relation extractor
> is new for 3.0
>
>
> > - Where would a newcomer hit first? Internet search for "ctakes" or
> > "ctakes 3.0" is probably first. Top hits on those lists should be
> > modified to point to the best Apache cTAKES landing page.
>
> I modified the following pages to have a link to Apache cTAKES home page
>
> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
> https://sourceforge.net/projects/ohnlp/files/cTAKES/
> https://sourceforge.net/projects/ohnlp/
> http://ohnlp.sourceforge.net/
>
> The update to the last one is not appearing yet, but it was updated.
>
> > - The Getting Started page needs to be written in context of all future
> > releases not just 3.0.
>
> Looks like you updated that page, thanks.
>
> > - The current guides are still not complete.
>
> I took a quick run through the User Guide on the Wiki and made some
> updates.
>
> -- James Masanz
>
>
> > -----Original Message-----
> > From: ctakes-dev-return-1239-Masanz.James=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1239-
> > Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> > C.
> > Sent: Monday, February 18, 2013 10:58 AM
> > To: ctakes-dev@incubator.apache.org
> > Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> > from Incubator
> >
> > All the suggestions and discussion are good. There's a lot here, sorry
> > for the long summary. First things first:
> >
> > - The downloads page must work. It now seems to function alright
> > ***IF*** you refresh the page or select a mirror and click the Change
> > button. If you do neither and try to download you get this error: "The
> > requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> > incubating-bin.tar.gz was not found on this server." Anyone have time to
> > fix this?
> > - Adding a link to the install instructions makes it obvious (which I
> > have done to the page) but it was there in a sense. The page said "Use
> > the Developer and User Guides to direct you through the installation
> > process." and the links to those were just to the left in the hierarchy.
> > - "Last official release" was held until now. Since 3.0 is going to be
> > officially announced, 3.0 will go there. I made that change as well.
> > - A list of changed features has not been high priority since the
> > original goal was to make a 3.0 in Apache that pretty much matched the
> > function of 2.5. The only thing that changed was how the product is
> > built and shipped. Nevertheless we need to state at least that
> > somewhere.
> > - The resources file is 1.1 GB not 2 right?
> >
> > Keep in mind that the community decided to release cTAKES 3.0 without
> > the doc being complete, but these must be next:
> > - The current guides are still not complete. I made it through the
> > developer guide but the user guide still has problems. I get errors
> > after installing and running scripts. I have not been able to try the
> > comparison test that was available previously. The table at the bottom I
> > have not got to yet.
> > - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/
> > 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> > done my best to minimize a user going back and forth. We have it this
> > way because a useful guide is not easy (IMHO or even possible) with
> > markdown text in the cTAKES home pages. There are still 3.0 developer
> > and user guide pages on the cTAKES home site that should be removed so
> > no one stumbles on to them.
> > - The Getting Started page needs to be written in context of all future
> > releases not just 3.0.
> > - Previous releases list. We need to both point to the NCI sites for 2.6
> > and back plus create an archive for what will be the history of Apache
> > releases. Needs work your right.
> >
> > Potential priorities after that:
> > - The examples, as described by Andy, would be more than a readme should
> > have. This would be great for a how-to guide.
> > - The Developer Guide and User Guide have historically been install
> > guides not how-to guides. I don't think a how-to guide should be
> > incorporated into these but should be its own document.
> > - cTAKES has never had a how-to guide that I know of. Making one would
> > be great and as you say should include things like 1) pointers to where
> > to find basic information 2) very high level overview of the components
> > in the context of using them to do a very basic task like 3) I think it
> > was suggested that the Getting Started page might be something like this
> > in very short form. If we did that then it would point to a more
> > comprehensive how-to guide.
> > - Project history page of all cTAKES releases placed on Apache sites
> > somewhere. Good plan if short. I would not copy readmes there but have
> > links to them.
> > I already did this for cTAKES 2.5 and past:
> > https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> > Move this page to Apache? Have a page on Apache that continues this and
> > points back to what already exists?
> > Also, I had this project history on the Apache cTAKES downloads page but
> > that section was removed when 3.0 was placed on there. If you can find
> > the history of changes to that page you may find something already done
> > in markdown format.
> > - Creating a single download for a newcomer. This has been discussed and
> > tabled by the community for the time being in order to get the 3.0
> > release done and out the door. We need to come back to this in order to
> > make the best first impression.
> >
> > Troy
> >
> > -----Original Message-----
> > From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1230-
> > Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> > Sent: Friday, February 15, 2013 10:17 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> > Incubator
> >
> > Thanks Andy for the feedback.
> > Examples are a good idea- Were you thinking of adding it to the README
> > file or the confluence user guide?
> >
> > Feel free to update the downloads page(s) (it uses Apache CMS) and the
> > User Guides (Confluence wiki).
> > Note: The release is still being replicated to all of the mirrors and
> > may take up to 24 hrs, so I would wait until after the weekend before
> > testing all of the mirror links.
> >
> > --Pei
> > ________________________________________
> > From: Andy McMurry [mcmurry.andy@gmail.com]
> > Sent: Friday, February 15, 2013 11:08 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >
> > Clarifications
> >
> > There isn't a last Apache release. But there are last previous NIH,
> > Sourceforge, and Apache releases?
> > TODO: Project History Page (Simple, just the releases and times, ideally
> > with JIRA generated release notes).
> >
> > Suggestion: Demonstration > explanation. Use Examples !!
> >
> > EXAMPLE 1 : Basic Pipeline (without UMLS)
> >
> > ** SHOW Before and after clinical text, demonstrates purpose
> > ** LIST the 5 steps
> > ** Most impressive demo would be the smoking status pipeline
> >
> > EXAMPLE 2: Basic Pipeline (with UMLS)
> >
> > ** SHOW Before and after (input text -> output annotations)
> > ** LIST the steps
> > ** Most impressive demo would be a negation of a cancer diagnosis and
> > NER of a medication (chemotherapuetic drug).
> >
> > Thoughts?
> > --andy
> >
> >
> > On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> > wrote:
> >
> > > Sure thing Pei.
> > >
> > > I dont think cTAKES is ready for attention grabbing release (humble
> > opinion).
> > > And when you release you want to grab attention! ! cTAKES is awesome!!
> > >
> > > Suggestions (release blockers)
> > >
> > > (1) Downloads
> > > http://incubator.apache.org/ctakes/downloads.cgi
> > > ! Link to install instructions is not there but "Verifying signatures"
> > takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> > > ! Last official release is blank because there isn't one, remove it !
> > > First mirror I tried was a 404? (not sure which one). I changed the
> > > mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> > confusing.
> > > ? The NIH and SourceForge pages  should redirect to cTAKES, google
> > "cTAKES download" and imagine how confused a beginner would be.
> > >
> > > (2) User Guide
> > > http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > > ? 3.0.0 : no list of new features from last stable release. Why would
> > a user bother to upgrade to a beta?
> > > ! Would be better to have a bundled download with resources, if
> > possible. Otherwise, make it clear to a newcomer what the benefit of
> > getting UMLS / LVG is. (one sentence).
> > > ! Needs a very high level overview of the components in the context of
> > using them to do a very basic task like.
> > > ! This is likely the most frequently accessed document for cTAKES. It
> > has almost no pointers to where to find basic information.
> > >
> > > (3) OTHER
> > > * The NCI and SourceForge links are now highly confusing.
> > > * While I am downloading, I should be reading the recommended "Get
> > > Started" guide
> > >
> > > I'm still downloading the 2GB resources file.
> > > I'll try and get back to you about the install when that is done too.
> > >
> > > This constructive criticism is because I believe cTAKES is AWESOME.
> > > Hard to see how awesome it is given the current instructions.
> > >
> > > --Andy
> > >
> > >
> > > On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> > <Pe...@childrens.harvard.edu> wrote:
> > >
> > >> Hi Andy,
> > >> So much has changed in cTAKES since last year, if you have a chance-
> > do you also want to try downloading the -bin and ensure at least the
> > steps in the README are able to get you started?
> > >>
> > >> --Pei
> > >> ________________________________________
> > >> From: Andy McMurry [mcmurry.andy@gmail.com]
> > >> Sent: Friday, February 15, 2013 4:04 PM
> > >> To: ctakes-dev@incubator.apache.org
> > >> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> > >>
> > >> Suggestion: can we get a good programmer with no cTAKES experience to
> > kick the tires and tell us how long it took to get started?
> > >>
> > >> John Resig (jQuery founder) once told me "if it takes more than 15
> > minutes to get started, then that is way too long".
> > >>
> > >> "What is necessary is that enough investment be put into presentation
> > >> that newcomers can get past the obstacle of unfamiliarity. ...
> > Hactivation energy: the amount of energy a newcomer must put in before
> > she starts getting something back"
> > >> -- From "Producing Open Source Software"
> > >>
> > >> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> > >> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> > >> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> > >> =hacktivation%20energy&f=false
> > >>
> > >>
> > >> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> > <Pe...@childrens.harvard.edu> wrote:
> > >>
> > >>> This is to open a discussion to graduate Apache cTAKES podling from
> > the Apache Incubator.
> > >>>
> > >>> Apache cTAKES entered the Incubator in June of 2012. We have made
> > significant progress with the project since moving over to Apache. We
> > currently have 18 committers listed on our status page at [1] including
> > over 10 which accepted after the podling was formed.
> > >>>
> > >>> During incubation, cTAKES has :
> > >>> * Produced 1 Release
> > >>> * Added 10 new Committer/PPMC members and shows constant community
> > >>> activities
> > >>> * Cleared IP on code
> > >>> * Developed Roadmap(s) for the next major and minor releases in a
> > >>> community process and started working on that [2]
> > >>> * The community of Apache cTAKES is active, healthy, and growing and
> > has demonstrated the ability to self-govern using accepted Apache
> > practices.
> > >>>
> > >>> [1] http://people.apache.org/committers-by-project.html#ctakes
> > >>> [2]
> > >>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> > >>> an.jira.plugin.system.project%3Aroadmap-panel
> > >>>
> > >>
> > >
>
>

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Bleeker, Troy C." <Bl...@mayo.edu>]

Summarizing where we are now ... completed items at the bottom of the list for reference only.

The community decided to release cTAKES 3.0 without the doc being complete - these must be next:
- The Developer Guide is not complete.
[TODO] Dev Guide needs command line install instructions for UMLS ID/pw and classpath. I'll work on this.
- The User Guide has a caveat on the table at the bottom of the instructions because a similar set of examples was not distributed like it was in 2.5. The instructions are longer as well since the user could not just load and run existing samples.
[TODO] Consider shipping test data resources from SourceForge in a ZIP file.
- The Getting Started page needs to be written in context of all future releases not just 3.0.
[NEEDS REVIEW] A page was written. Is it as expected?
- Previous releases list. We need to both point to the NCI sites for 2.6 and back plus create an archive for what will be the history of Apache releases. Needs work your right.
[TODO] For now I removed 2 of the 3 links leaving only one that points back to NCI for 2.5 and back. Question is should we have a full listing of the 2.5 and previous releases on the Apache site or simply point to the NCI wiki. If point to NCI then there is no archive to be had yet since the only release in Apache is the current release.
- Component Use Guide pages needing updates. There are items marked in reddish color that are incorrect or in need of updates on these pages:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Core
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dependency+Parser+and+Semantic+Role+Labeler
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Drug+Named+Entity+Recognition
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+NE+Contexts
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+PAD+Term+Spotter
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+POS+Tagger
[TODO] Component knowledgeable people must update these pages. 

Potential priorities after that:
- The examples, as described by Andy, would be more than a readme should have. This would be great for a how-to guide. The Developer Guide and User Guide have historically been install guides not how-to guides. I don't think a how-to guide should be incorporated into these but should be its own document.
[TODO] Should the current user and dev guides be renamed?
- cTAKES has never had a how-to guide that I know of. Making one would be great and as you say should include things like 1) pointers to where to find basic information 2) very high level overview of the components in the context of using them to do a very basic task like 3) I think it was suggested that the Getting Started page might be something like this in very short form. If we did that then it would point to a more comprehensive how-to guide.
[TODO] Decide if we are going to do this.
- Project history page of all cTAKES releases placed on Apache sites somewhere. Good plan if short. I would not copy readmes there but have links to them.
[TODO] This was done in the past but removed from the bottom of the downloads page. This page exists now but is not linked to from the Apache cTAKES site. Here is a direct link: http://incubator.apache.org/ctakes/roadmap.html  It would need 3.0 info added if we decide to use it.
- Creating a single download for a newcomer.
[LATER] This has been discussed and tabled by the community for the time being in order to get the 3.0 release done and out the door. We need to come back to this in order to make the best first impression.

Completed:
- The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button. If you do neither and try to download you get this error: "The requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz was not found on this server." Anyone have time to fix this?
[WORK-AROUND] Seems intermittent. Tried 5 different machines. James and Troy changed the downloads page to tell the user to select the Change button when they have issues. It should work if they do that. Best guess - the randomly selected mirror sites do not all work. Also, selecting a site in the drop-down and pressing the Change button does not set the mirror site to the one you selected. Next best guess - other Apache sites have a double // in the URL just after the mirror domain in the file download link. Maybe this is required. Tried this too.
- Adding a link to the install instructions makes it obvious (which I have done to the page) but it was there in a sense. 
[DONE] Link added.
- "Last official release" was held until now. Since 3.0 is going to be officially announced, 3.0 will go there. I made that change as well.
[DONE] Reworked the page.
- A list of changed features has not been high priority since the original goal was to make a 3.0 in Apache that pretty much matched the function of 2.5. The only thing that changed was how the product is built and shipped. Nevertheless we need to state at least that somewhere.
[DONE] That was wrong, there is new function. Relation Extractor now documented on the downloads page.
- The resources file is 1.1 GB not 2 right?
 [DONE] Andy said it in an email. The web site lists it fine.
- There are still 3.0 developer and user guide pages on the cTAKES home site that should be removed so no one stumbles on to them.
[DONE] Removed.
- Where would a newcomer hit first? Internet search for "ctakes" or "ctakes 3.0" is probably first. Top hits on those lists should be modified to point to the best Apache cTAKES landing page.
[DONE] James and Troy made changes to the top hit pages and other places that made sense.
- The current guides are still not complete. 
[DONE] User Guide James and Troy went through.

Thanks
Troy

-----Original Message-----
From: ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1250-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Masanz, James J.
Sent: Tuesday, February 19, 2013 10:10 AM
To: 'ctakes-dev@incubator.apache.org'
Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator


> - The resources file is 1.1 GB not 2 right?

I agree. But I don't see it listed as 2GB on the download page. If you tell me where you saw it listed as 2GB I will update that page.

> - A list of changed features has not been high priority since 
I will update the downloads page right now stating the relation extractor is new for 3.0


> - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified to point to the best Apache cTAKES landing page.

I modified the following pages to have a link to Apache cTAKES home page

https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
https://sourceforge.net/projects/ohnlp/files/cTAKES/
https://sourceforge.net/projects/ohnlp/
http://ohnlp.sourceforge.net/

The update to the last one is not appearing yet, but it was updated.

> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.

Looks like you updated that page, thanks.

> - The current guides are still not complete.

I took a quick run through the User Guide on the Wiki and made some updates.

-- James Masanz


> -----Original Message-----
> From: ctakes-dev-return-1239-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1239-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> C.
> Sent: Monday, February 18, 2013 10:58 AM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> All the suggestions and discussion are good. There's a lot here, sorry
> for the long summary. First things first:
> 
> - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change
> button. If you do neither and try to download you get this error: "The
> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> incubating-bin.tar.gz was not found on this server." Anyone have time to
> fix this?
> - Adding a link to the install instructions makes it obvious (which I
> have done to the page) but it was there in a sense. The page said "Use
> the Developer and User Guides to direct you through the installation
> process." and the links to those were just to the left in the hierarchy.
> - "Last official release" was held until now. Since 3.0 is going to be
> officially announced, 3.0 will go there. I made that change as well.
> - A list of changed features has not been high priority since the
> original goal was to make a 3.0 in Apache that pretty much matched the
> function of 2.5. The only thing that changed was how the product is
> built and shipped. Nevertheless we need to state at least that
> somewhere.
> - The resources file is 1.1 GB not 2 right?
> 
> Keep in mind that the community decided to release cTAKES 3.0 without
> the doc being complete, but these must be next:
> - The current guides are still not complete. I made it through the
> developer guide but the user guide still has problems. I get errors
> after installing and running scripts. I have not been able to try the
> comparison test that was available previously. The table at the bottom I
> have not got to yet.
> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/
> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> done my best to minimize a user going back and forth. We have it this
> way because a useful guide is not easy (IMHO or even possible) with
> markdown text in the cTAKES home pages. There are still 3.0 developer
> and user guide pages on the cTAKES home site that should be removed so
> no one stumbles on to them.
> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.
> - Previous releases list. We need to both point to the NCI sites for 2.6
> and back plus create an archive for what will be the history of Apache
> releases. Needs work your right.
> 
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should
> have. This would be great for a how-to guide.
> - The Developer Guide and User Guide have historically been install
> guides not how-to guides. I don't think a how-to guide should be
> incorporated into these but should be its own document.
> - cTAKES has never had a how-to guide that I know of. Making one would
> be great and as you say should include things like 1) pointers to where
> to find basic information 2) very high level overview of the components
> in the context of using them to do a very basic task like 3) I think it
> was suggested that the Getting Started page might be something like this
> in very short form. If we did that then it would point to a more
> comprehensive how-to guide.
> - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have
> links to them.
> I already did this for cTAKES 2.5 and past:
> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> Move this page to Apache? Have a page on Apache that continues this and
> points back to what already exists?
> Also, I had this project history on the Apache cTAKES downloads page but
> that section was removed when 3.0 was placed on there. If you can find
> the history of changes to that page you may find something already done
> in markdown format.
> - Creating a single download for a newcomer. This has been discussed and
> tabled by the community for the time being in order to get the 3.0
> release done and out the door. We need to come back to this in order to
> make the best first impression.
> 
> Troy
> 
> -----Original Message-----
> From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1230-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 10:17 PM
> To: ctakes-dev@incubator.apache.org
> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> Incubator
> 
> Thanks Andy for the feedback.
> Examples are a good idea- Were you thinking of adding it to the README
> file or the confluence user guide?
> 
> Feel free to update the downloads page(s) (it uses Apache CMS) and the
> User Guides (Confluence wiki).
> Note: The release is still being replicated to all of the mirrors and
> may take up to 24 hrs, so I would wait until after the weekend before
> testing all of the mirror links.
> 
> --Pei
> ________________________________________
> From: Andy McMurry [mcmurry.andy@gmail.com]
> Sent: Friday, February 15, 2013 11:08 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> 
> Clarifications
> 
> There isn't a last Apache release. But there are last previous NIH,
> Sourceforge, and Apache releases?
> TODO: Project History Page (Simple, just the releases and times, ideally
> with JIRA generated release notes).
> 
> Suggestion: Demonstration > explanation. Use Examples !!
> 
> EXAMPLE 1 : Basic Pipeline (without UMLS)
> 
> ** SHOW Before and after clinical text, demonstrates purpose
> ** LIST the 5 steps
> ** Most impressive demo would be the smoking status pipeline
> 
> EXAMPLE 2: Basic Pipeline (with UMLS)
> 
> ** SHOW Before and after (input text -> output annotations)
> ** LIST the steps
> ** Most impressive demo would be a negation of a cancer diagnosis and
> NER of a medication (chemotherapuetic drug).
> 
> Thoughts?
> --andy
> 
> 
> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> wrote:
> 
> > Sure thing Pei.
> >
> > I dont think cTAKES is ready for attention grabbing release (humble
> opinion).
> > And when you release you want to grab attention! ! cTAKES is awesome!!
> >
> > Suggestions (release blockers)
> >
> > (1) Downloads
> > http://incubator.apache.org/ctakes/downloads.cgi
> > ! Link to install instructions is not there but "Verifying signatures"
> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> > ! Last official release is blank because there isn't one, remove it !
> > First mirror I tried was a 404? (not sure which one). I changed the
> > mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> confusing.
> > ? The NIH and SourceForge pages  should redirect to cTAKES, google
> "cTAKES download" and imagine how confused a beginner would be.
> >
> > (2) User Guide
> > http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > ? 3.0.0 : no list of new features from last stable release. Why would
> a user bother to upgrade to a beta?
> > ! Would be better to have a bundled download with resources, if
> possible. Otherwise, make it clear to a newcomer what the benefit of
> getting UMLS / LVG is. (one sentence).
> > ! Needs a very high level overview of the components in the context of
> using them to do a very basic task like.
> > ! This is likely the most frequently accessed document for cTAKES. It
> has almost no pointers to where to find basic information.
> >
> > (3) OTHER
> > * The NCI and SourceForge links are now highly confusing.
> > * While I am downloading, I should be reading the recommended "Get
> > Started" guide
> >
> > I'm still downloading the 2GB resources file.
> > I'll try and get back to you about the install when that is done too.
> >
> > This constructive criticism is because I believe cTAKES is AWESOME.
> > Hard to see how awesome it is given the current instructions.
> >
> > --Andy
> >
> >
> > On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >
> >> Hi Andy,
> >> So much has changed in cTAKES since last year, if you have a chance-
> do you also want to try downloading the -bin and ensure at least the
> steps in the README are able to get you started?
> >>
> >> --Pei
> >> ________________________________________
> >> From: Andy McMurry [mcmurry.andy@gmail.com]
> >> Sent: Friday, February 15, 2013 4:04 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>
> >> Suggestion: can we get a good programmer with no cTAKES experience to
> kick the tires and tell us how long it took to get started?
> >>
> >> John Resig (jQuery founder) once told me "if it takes more than 15
> minutes to get started, then that is way too long".
> >>
> >> "What is necessary is that enough investment be put into presentation
> >> that newcomers can get past the obstacle of unfamiliarity. ...
> Hactivation energy: the amount of energy a newcomer must put in before
> she starts getting something back"
> >> -- From "Producing Open Source Software"
> >>
> >> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> >> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> >> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> >> =hacktivation%20energy&f=false
> >>
> >>
> >> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>
> >>> This is to open a discussion to graduate Apache cTAKES podling from
> the Apache Incubator.
> >>>
> >>> Apache cTAKES entered the Incubator in June of 2012. We have made
> significant progress with the project since moving over to Apache. We
> currently have 18 committers listed on our status page at [1] including
> over 10 which accepted after the podling was formed.
> >>>
> >>> During incubation, cTAKES has :
> >>> * Produced 1 Release
> >>> * Added 10 new Committer/PPMC members and shows constant community
> >>> activities
> >>> * Cleared IP on code
> >>> * Developed Roadmap(s) for the next major and minor releases in a
> >>> community process and started working on that [2]
> >>> * The community of Apache cTAKES is active, healthy, and growing and
> has demonstrated the ability to self-govern using accepted Apache
> practices.
> >>>
> >>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>> [2]
> >>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> >>> an.jira.plugin.system.project%3Aroadmap-panel
> >>>
> >>
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Masanz, James J." <Ma...@mayo.edu>]

> - The resources file is 1.1 GB not 2 right?

I agree. But I don't see it listed as 2GB on the download page. If you tell me where you saw it listed as 2GB I will update that page.

> - A list of changed features has not been high priority since 
I will update the downloads page right now stating the relation extractor is new for 3.0


> - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified to point to the best Apache cTAKES landing page.

I modified the following pages to have a link to Apache cTAKES home page

https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5
https://sourceforge.net/projects/ohnlp/files/cTAKES/
https://sourceforge.net/projects/ohnlp/
http://ohnlp.sourceforge.net/

The update to the last one is not appearing yet, but it was updated.

> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.

Looks like you updated that page, thanks.

> - The current guides are still not complete.

I took a quick run through the User Guide on the Wiki and made some updates.

-- James Masanz


> -----Original Message-----
> From: ctakes-dev-return-1239-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1239-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> C.
> Sent: Monday, February 18, 2013 10:58 AM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> All the suggestions and discussion are good. There's a lot here, sorry
> for the long summary. First things first:
> 
> - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change
> button. If you do neither and try to download you get this error: "The
> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> incubating-bin.tar.gz was not found on this server." Anyone have time to
> fix this?
> - Adding a link to the install instructions makes it obvious (which I
> have done to the page) but it was there in a sense. The page said "Use
> the Developer and User Guides to direct you through the installation
> process." and the links to those were just to the left in the hierarchy.
> - "Last official release" was held until now. Since 3.0 is going to be
> officially announced, 3.0 will go there. I made that change as well.
> - A list of changed features has not been high priority since the
> original goal was to make a 3.0 in Apache that pretty much matched the
> function of 2.5. The only thing that changed was how the product is
> built and shipped. Nevertheless we need to state at least that
> somewhere.
> - The resources file is 1.1 GB not 2 right?
> 
> Keep in mind that the community decided to release cTAKES 3.0 without
> the doc being complete, but these must be next:
> - The current guides are still not complete. I made it through the
> developer guide but the user guide still has problems. I get errors
> after installing and running scripts. I have not been able to try the
> comparison test that was available previously. The table at the bottom I
> have not got to yet.
> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/
> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> done my best to minimize a user going back and forth. We have it this
> way because a useful guide is not easy (IMHO or even possible) with
> markdown text in the cTAKES home pages. There are still 3.0 developer
> and user guide pages on the cTAKES home site that should be removed so
> no one stumbles on to them.
> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.
> - Previous releases list. We need to both point to the NCI sites for 2.6
> and back plus create an archive for what will be the history of Apache
> releases. Needs work your right.
> 
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should
> have. This would be great for a how-to guide.
> - The Developer Guide and User Guide have historically been install
> guides not how-to guides. I don't think a how-to guide should be
> incorporated into these but should be its own document.
> - cTAKES has never had a how-to guide that I know of. Making one would
> be great and as you say should include things like 1) pointers to where
> to find basic information 2) very high level overview of the components
> in the context of using them to do a very basic task like 3) I think it
> was suggested that the Getting Started page might be something like this
> in very short form. If we did that then it would point to a more
> comprehensive how-to guide.
> - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have
> links to them.
> I already did this for cTAKES 2.5 and past:
> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> Move this page to Apache? Have a page on Apache that continues this and
> points back to what already exists?
> Also, I had this project history on the Apache cTAKES downloads page but
> that section was removed when 3.0 was placed on there. If you can find
> the history of changes to that page you may find something already done
> in markdown format.
> - Creating a single download for a newcomer. This has been discussed and
> tabled by the community for the time being in order to get the 3.0
> release done and out the door. We need to come back to this in order to
> make the best first impression.
> 
> Troy
> 
> -----Original Message-----
> From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1230-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 10:17 PM
> To: ctakes-dev@incubator.apache.org
> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> Incubator
> 
> Thanks Andy for the feedback.
> Examples are a good idea- Were you thinking of adding it to the README
> file or the confluence user guide?
> 
> Feel free to update the downloads page(s) (it uses Apache CMS) and the
> User Guides (Confluence wiki).
> Note: The release is still being replicated to all of the mirrors and
> may take up to 24 hrs, so I would wait until after the weekend before
> testing all of the mirror links.
> 
> --Pei
> ________________________________________
> From: Andy McMurry [mcmurry.andy@gmail.com]
> Sent: Friday, February 15, 2013 11:08 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> 
> Clarifications
> 
> There isn't a last Apache release. But there are last previous NIH,
> Sourceforge, and Apache releases?
> TODO: Project History Page (Simple, just the releases and times, ideally
> with JIRA generated release notes).
> 
> Suggestion: Demonstration > explanation. Use Examples !!
> 
> EXAMPLE 1 : Basic Pipeline (without UMLS)
> 
> ** SHOW Before and after clinical text, demonstrates purpose
> ** LIST the 5 steps
> ** Most impressive demo would be the smoking status pipeline
> 
> EXAMPLE 2: Basic Pipeline (with UMLS)
> 
> ** SHOW Before and after (input text -> output annotations)
> ** LIST the steps
> ** Most impressive demo would be a negation of a cancer diagnosis and
> NER of a medication (chemotherapuetic drug).
> 
> Thoughts?
> --andy
> 
> 
> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> wrote:
> 
> > Sure thing Pei.
> >
> > I dont think cTAKES is ready for attention grabbing release (humble
> opinion).
> > And when you release you want to grab attention! ! cTAKES is awesome!!
> >
> > Suggestions (release blockers)
> >
> > (1) Downloads
> > http://incubator.apache.org/ctakes/downloads.cgi
> > ! Link to install instructions is not there but "Verifying signatures"
> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> > ! Last official release is blank because there isn't one, remove it !
> > First mirror I tried was a 404? (not sure which one). I changed the
> > mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> confusing.
> > ? The NIH and SourceForge pages  should redirect to cTAKES, google
> "cTAKES download" and imagine how confused a beginner would be.
> >
> > (2) User Guide
> > http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > ? 3.0.0 : no list of new features from last stable release. Why would
> a user bother to upgrade to a beta?
> > ! Would be better to have a bundled download with resources, if
> possible. Otherwise, make it clear to a newcomer what the benefit of
> getting UMLS / LVG is. (one sentence).
> > ! Needs a very high level overview of the components in the context of
> using them to do a very basic task like.
> > ! This is likely the most frequently accessed document for cTAKES. It
> has almost no pointers to where to find basic information.
> >
> > (3) OTHER
> > * The NCI and SourceForge links are now highly confusing.
> > * While I am downloading, I should be reading the recommended "Get
> > Started" guide
> >
> > I'm still downloading the 2GB resources file.
> > I'll try and get back to you about the install when that is done too.
> >
> > This constructive criticism is because I believe cTAKES is AWESOME.
> > Hard to see how awesome it is given the current instructions.
> >
> > --Andy
> >
> >
> > On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >
> >> Hi Andy,
> >> So much has changed in cTAKES since last year, if you have a chance-
> do you also want to try downloading the -bin and ensure at least the
> steps in the README are able to get you started?
> >>
> >> --Pei
> >> ________________________________________
> >> From: Andy McMurry [mcmurry.andy@gmail.com]
> >> Sent: Friday, February 15, 2013 4:04 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>
> >> Suggestion: can we get a good programmer with no cTAKES experience to
> kick the tires and tell us how long it took to get started?
> >>
> >> John Resig (jQuery founder) once told me "if it takes more than 15
> minutes to get started, then that is way too long".
> >>
> >> "What is necessary is that enough investment be put into presentation
> >> that newcomers can get past the obstacle of unfamiliarity. ...
> Hactivation energy: the amount of energy a newcomer must put in before
> she starts getting something back"
> >> -- From "Producing Open Source Software"
> >>
> >> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> >> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> >> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> >> =hacktivation%20energy&f=false
> >>
> >>
> >> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>
> >>> This is to open a discussion to graduate Apache cTAKES podling from
> the Apache Incubator.
> >>>
> >>> Apache cTAKES entered the Incubator in June of 2012. We have made
> significant progress with the project since moving over to Apache. We
> currently have 18 committers listed on our status page at [1] including
> over 10 which accepted after the podling was formed.
> >>>
> >>> During incubation, cTAKES has :
> >>> * Produced 1 Release
> >>> * Added 10 new Committer/PPMC members and shows constant community
> >>> activities
> >>> * Cleared IP on code
> >>> * Developed Roadmap(s) for the next major and minor releases in a
> >>> community process and started working on that [2]
> >>> * The community of Apache cTAKES is active, healthy, and growing and
> has demonstrated the ability to self-govern using accepted Apache
> practices.
> >>>
> >>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>> [2]
> >>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> >>> an.jira.plugin.system.project%3Aroadmap-panel
> >>>
> >>
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Bleeker, Troy C." <Bl...@mayo.edu>]

Very odd. I tried another Windows machine
FF works
IE fails (and it does show a mirror is selected) Before the error would only happen if the mirror name showed up as [preferred].

Tried on officemate's mac and windows.
Mac with FF fails.
Windows with IE works.

Thanks
Troy

-----Original Message-----
From: ctakes-dev-return-1248-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1248-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Masanz, James J.
Sent: Tuesday, February 19, 2013 9:43 AM
To: '<ct...@incubator.apache.org>'
Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

Odd, I just went to a different computer to test fresh and here is what I see for this page:

http://incubator.apache.org/ctakes/downloads.cgi

If I click on one of file names in the "File" column of the table, I get prompted to download (or a download starts) in all of these :

FF 18.0.1
IE 8
Chrome

Could it be a clearing cache problem on your machine Troy?
Could you try a different PC?

-- James

> -----Original Message-----
> From: 
> ctakes-dev-return-1247-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1247-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy 
> C.
> Sent: Tuesday, February 19, 2013 9:29 AM
> To: <ct...@incubator.apache.org>
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES 
> from Incubator
> 
> I just open the downloads page again this morning. If the first thing 
> I do is click a downloadable file I get the error.
> I'm using FF 18.02. I also tried IE 8, same thing.
> In both cases pressing the Change button makes it work.
> 
> Thanks
> Troy
> -----Original Message-----
> From: 
> ctakes-dev-return-1246-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1246-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Tuesday, February 19, 2013 8:45 AM
> To: <ct...@incubator.apache.org>
> Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES 
> from Incubator
> 
> > - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change 
> button.
> 
> Hi Troy,
> I think this was fixed. Links (sidenav) were updated to use 
> downloads.cgi instead of html.  Could you confirm?
> 
> On Feb 18, 2013, at 11:58 AM, "Bleeker, Troy C." 
> <Bl...@mayo.edu>
> wrote:
> 
> > All the suggestions and discussion are good. There's a lot here, 
> > sorry
> for the long summary. First things first:
> >
> > - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change 
> button. If you do neither and try to download you get this error: "The 
> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> incubating-bin.tar.gz was not found on this server." Anyone have time 
> to fix this?
> > - Adding a link to the install instructions makes it obvious (which 
> > I
> have done to the page) but it was there in a sense. The page said "Use 
> the Developer and User Guides to direct you through the installation 
> process." and the links to those were just to the left in the hierarchy.
> > - "Last official release" was held until now. Since 3.0 is going to 
> > be
> officially announced, 3.0 will go there. I made that change as well.
> > - A list of changed features has not been high priority since the
> original goal was to make a 3.0 in Apache that pretty much matched the 
> function of 2.5. The only thing that changed was how the product is 
> built and shipped. Nevertheless we need to state at least that 
> somewhere.
> > - The resources file is 1.1 GB not 2 right?
> >
> > Keep in mind that the community decided to release cTAKES 3.0 
> > without
> the doc being complete, but these must be next:
> > - The current guides are still not complete. I made it through the
> developer guide but the user guide still has problems. I get errors 
> after installing and running scripts. I have not been able to try the 
> comparison test that was available previously. The table at the bottom 
> I have not got to yet.
> > - We have 2 sites now 1) cTAKES home
> http://incubator.apache.org/ctakes/ 2) cTAKES doc 
> https://cwiki.apache.org/confluence/display/CTAKES. I've done my best 
> to minimize a user going back and forth. We have it this way because a 
> useful guide is not easy (IMHO or even possible) with markdown text in 
> the cTAKES home pages. There are still 3.0 developer and user guide 
> pages on the cTAKES home site that should be removed so no one 
> stumbles on to them.
> > - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be 
> modified to point to the best Apache cTAKES landing page.
> > - The Getting Started page needs to be written in context of all
> future releases not just 3.0.
> > - Previous releases list. We need to both point to the NCI sites for
> 2.6 and back plus create an archive for what will be the history of 
> Apache releases. Needs work your right.
> >
> > Potential priorities after that:
> > - The examples, as described by Andy, would be more than a readme
> should have. This would be great for a how-to guide.
> > - The Developer Guide and User Guide have historically been install
> guides not how-to guides. I don't think a how-to guide should be 
> incorporated into these but should be its own document.
> > - cTAKES has never had a how-to guide that I know of. Making one 
> > would be great and as you say should include things like 1) pointers 
> > to
> where to find basic information 2) very high level overview of the 
> components in the context of using them to do a very basic task like 
> 3) I think it was suggested that the Getting Started page might be 
> something like this in very short form. If we did that then it would 
> point to a more comprehensive how-to guide.
> > - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have 
> links to them.
> > I already did this for cTAKES 2.5 and past:
> > https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> > Move this page to Apache? Have a page on Apache that continues this
> and points back to what already exists?
> > Also, I had this project history on the Apache cTAKES downloads page
> but that section was removed when 3.0 was placed on there. If you can 
> find the history of changes to that page you may find something 
> already done in markdown format.
> > - Creating a single download for a newcomer. This has been discussed
> and tabled by the community for the time being in order to get the 3.0 
> release done and out the door. We need to come back to this in order 
> to make the best first impression.
> >
> > Troy
> >
> > -----Original Message-----
> > From:
> > ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.
> > org] On Behalf Of Chen, Pei
> > Sent: Friday, February 15, 2013 10:17 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES 
> > from Incubator
> >
> > Thanks Andy for the feedback.
> > Examples are a good idea- Were you thinking of adding it to the 
> > README
> file or the confluence user guide?
> >
> > Feel free to update the downloads page(s) (it uses Apache CMS) and 
> > the
> User Guides (Confluence wiki).
> > Note: The release is still being replicated to all of the mirrors 
> > and
> may take up to 24 hrs, so I would wait until after the weekend before 
> testing all of the mirror links.
> >
> > --Pei
> > ________________________________________
> > From: Andy McMurry [mcmurry.andy@gmail.com]
> > Sent: Friday, February 15, 2013 11:08 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >
> > Clarifications
> >
> > There isn't a last Apache release. But there are last previous NIH,
> Sourceforge, and Apache releases?
> > TODO: Project History Page (Simple, just the releases and times,
> ideally with JIRA generated release notes).
> >
> > Suggestion: Demonstration > explanation. Use Examples !!
> >
> > EXAMPLE 1 : Basic Pipeline (without UMLS)
> >
> > ** SHOW Before and after clinical text, demonstrates purpose
> > ** LIST the 5 steps
> > ** Most impressive demo would be the smoking status pipeline
> >
> > EXAMPLE 2: Basic Pipeline (with UMLS)
> >
> > ** SHOW Before and after (input text -> output annotations)
> > ** LIST the steps
> > ** Most impressive demo would be a negation of a cancer diagnosis 
> > and
> NER of a medication (chemotherapuetic drug).
> >
> > Thoughts?
> > --andy
> >
> >
> > On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> wrote:
> >
> >> Sure thing Pei.
> >>
> >> I dont think cTAKES is ready for attention grabbing release (humble
> opinion).
> >> And when you release you want to grab attention! ! cTAKES is
> awesome!!
> >>
> >> Suggestions (release blockers)
> >>
> >> (1) Downloads
> >> http://incubator.apache.org/ctakes/downloads.cgi
> >> ! Link to install instructions is not there but "Verifying
> signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL 
> INSTRUCTIONS.
> >> ! Last official release is blank because there isn't one, remove it !
> >> First mirror I tried was a 404? (not sure which one). I changed the 
> >> mirror then OK. Test all mirrors (script) ? Previous releases are
> VERY confusing.
> >> ? The NIH and SourceForge pages  should redirect to cTAKES, google
> "cTAKES download" and imagine how confused a beginner would be.
> >>
> >> (2) User Guide
> >> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> >> ? 3.0.0 : no list of new features from last stable release. Why 
> >> would
> a user bother to upgrade to a beta?
> >> ! Would be better to have a bundled download with resources, if
> possible. Otherwise, make it clear to a newcomer what the benefit of 
> getting UMLS / LVG is. (one sentence).
> >> ! Needs a very high level overview of the components in the context
> of using them to do a very basic task like.
> >> ! This is likely the most frequently accessed document for cTAKES. 
> >> It
> has almost no pointers to where to find basic information.
> >>
> >> (3) OTHER
> >> * The NCI and SourceForge links are now highly confusing.
> >> * While I am downloading, I should be reading the recommended "Get 
> >> Started" guide
> >>
> >> I'm still downloading the 2GB resources file.
> >> I'll try and get back to you about the install when that is done too.
> >>
> >> This constructive criticism is because I believe cTAKES is AWESOME.
> >> Hard to see how awesome it is given the current instructions.
> >>
> >> --Andy
> >>
> >>
> >> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>
> >>> Hi Andy,
> >>> So much has changed in cTAKES since last year, if you have a 
> >>> chance-
> do you also want to try downloading the -bin and ensure at least the 
> steps in the README are able to get you started?
> >>>
> >>> --Pei
> >>> ________________________________________
> >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>> Sent: Friday, February 15, 2013 4:04 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>
> >>> Suggestion: can we get a good programmer with no cTAKES experience
> to kick the tires and tell us how long it took to get started?
> >>>
> >>> John Resig (jQuery founder) once told me "if it takes more than 15
> minutes to get started, then that is way too long".
> >>>
> >>> "What is necessary is that enough investment be put into 
> >>> presentation that newcomers can get past the obstacle of
> unfamiliarity. ... Hactivation energy: the amount of energy a newcomer 
> must put in before she starts getting something back"
> >>> -- From "Producing Open Source Software"
> >>>
> >>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=
> >>> ha
> >>> c
> >>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210
> >>> ktivation+D9
> >>> ktivation+W
> >>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepag
> >>> e&
> >>> q
> >>> =hacktivation%20energy&f=false
> >>>
> >>>
> >>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>>
> >>>> This is to open a discussion to graduate Apache cTAKES podling 
> >>>> from
> the Apache Incubator.
> >>>>
> >>>> Apache cTAKES entered the Incubator in June of 2012. We have made
> significant progress with the project since moving over to Apache. We 
> currently have 18 committers listed on our status page at [1] 
> including over 10 which accepted after the podling was formed.
> >>>>
> >>>> During incubation, cTAKES has :
> >>>> * Produced 1 Release
> >>>> * Added 10 new Committer/PPMC members and shows constant 
> >>>> community activities
> >>>> * Cleared IP on code
> >>>> * Developed Roadmap(s) for the next major and minor releases in a 
> >>>> community process and started working on that [2]
> >>>> * The community of Apache cTAKES is active, healthy, and growing
> and has demonstrated the ability to self-govern using accepted Apache 
> practices.
> >>>>
> >>>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>>> [2]
> >>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atla
> >>>> ss i an.jira.plugin.system.project%3Aroadmap-panel
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Masanz, James J." <Ma...@mayo.edu>]

Odd, I just went to a different computer to test fresh and here is what I see for this page:

http://incubator.apache.org/ctakes/downloads.cgi

If I click on one of file names in the "File" column of the table, I get prompted to download (or a download starts) in all of these :

FF 18.0.1
IE 8
Chrome

Could it be a clearing cache problem on your machine Troy?
Could you try a different PC?

-- James

> -----Original Message-----
> From: ctakes-dev-return-1247-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1247-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> C.
> Sent: Tuesday, February 19, 2013 9:29 AM
> To: <ct...@incubator.apache.org>
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> I just open the downloads page again this morning. If the first thing I
> do is click a downloadable file I get the error.
> I'm using FF 18.02. I also tried IE 8, same thing.
> In both cases pressing the Change button makes it work.
> 
> Thanks
> Troy
> -----Original Message-----
> From: ctakes-dev-return-1246-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1246-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Tuesday, February 19, 2013 8:45 AM
> To: <ct...@incubator.apache.org>
> Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> > - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change
> button.
> 
> Hi Troy,
> I think this was fixed. Links (sidenav) were updated to use
> downloads.cgi instead of html.  Could you confirm?
> 
> On Feb 18, 2013, at 11:58 AM, "Bleeker, Troy C." <Bl...@mayo.edu>
> wrote:
> 
> > All the suggestions and discussion are good. There's a lot here, sorry
> for the long summary. First things first:
> >
> > - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change
> button. If you do neither and try to download you get this error: "The
> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> incubating-bin.tar.gz was not found on this server." Anyone have time to
> fix this?
> > - Adding a link to the install instructions makes it obvious (which I
> have done to the page) but it was there in a sense. The page said "Use
> the Developer and User Guides to direct you through the installation
> process." and the links to those were just to the left in the hierarchy.
> > - "Last official release" was held until now. Since 3.0 is going to be
> officially announced, 3.0 will go there. I made that change as well.
> > - A list of changed features has not been high priority since the
> original goal was to make a 3.0 in Apache that pretty much matched the
> function of 2.5. The only thing that changed was how the product is
> built and shipped. Nevertheless we need to state at least that
> somewhere.
> > - The resources file is 1.1 GB not 2 right?
> >
> > Keep in mind that the community decided to release cTAKES 3.0 without
> the doc being complete, but these must be next:
> > - The current guides are still not complete. I made it through the
> developer guide but the user guide still has problems. I get errors
> after installing and running scripts. I have not been able to try the
> comparison test that was available previously. The table at the bottom I
> have not got to yet.
> > - We have 2 sites now 1) cTAKES home
> http://incubator.apache.org/ctakes/ 2) cTAKES doc
> https://cwiki.apache.org/confluence/display/CTAKES. I've done my best to
> minimize a user going back and forth. We have it this way because a
> useful guide is not easy (IMHO or even possible) with markdown text in
> the cTAKES home pages. There are still 3.0 developer and user guide
> pages on the cTAKES home site that should be removed so no one stumbles
> on to them.
> > - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified to point to the best Apache cTAKES landing page.
> > - The Getting Started page needs to be written in context of all
> future releases not just 3.0.
> > - Previous releases list. We need to both point to the NCI sites for
> 2.6 and back plus create an archive for what will be the history of
> Apache releases. Needs work your right.
> >
> > Potential priorities after that:
> > - The examples, as described by Andy, would be more than a readme
> should have. This would be great for a how-to guide.
> > - The Developer Guide and User Guide have historically been install
> guides not how-to guides. I don't think a how-to guide should be
> incorporated into these but should be its own document.
> > - cTAKES has never had a how-to guide that I know of. Making one would
> > be great and as you say should include things like 1) pointers to
> where to find basic information 2) very high level overview of the
> components in the context of using them to do a very basic task like 3)
> I think it was suggested that the Getting Started page might be
> something like this in very short form. If we did that then it would
> point to a more comprehensive how-to guide.
> > - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have
> links to them.
> > I already did this for cTAKES 2.5 and past:
> > https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> > Move this page to Apache? Have a page on Apache that continues this
> and points back to what already exists?
> > Also, I had this project history on the Apache cTAKES downloads page
> but that section was removed when 3.0 was placed on there. If you can
> find the history of changes to that page you may find something already
> done in markdown format.
> > - Creating a single download for a newcomer. This has been discussed
> and tabled by the community for the time being in order to get the 3.0
> release done and out the door. We need to come back to this in order to
> make the best first impression.
> >
> > Troy
> >
> > -----Original Message-----
> > From:
> > ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.
> > org] On Behalf Of Chen, Pei
> > Sent: Friday, February 15, 2013 10:17 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> > Incubator
> >
> > Thanks Andy for the feedback.
> > Examples are a good idea- Were you thinking of adding it to the README
> file or the confluence user guide?
> >
> > Feel free to update the downloads page(s) (it uses Apache CMS) and the
> User Guides (Confluence wiki).
> > Note: The release is still being replicated to all of the mirrors and
> may take up to 24 hrs, so I would wait until after the weekend before
> testing all of the mirror links.
> >
> > --Pei
> > ________________________________________
> > From: Andy McMurry [mcmurry.andy@gmail.com]
> > Sent: Friday, February 15, 2013 11:08 PM
> > To: ctakes-dev@incubator.apache.org
> > Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >
> > Clarifications
> >
> > There isn't a last Apache release. But there are last previous NIH,
> Sourceforge, and Apache releases?
> > TODO: Project History Page (Simple, just the releases and times,
> ideally with JIRA generated release notes).
> >
> > Suggestion: Demonstration > explanation. Use Examples !!
> >
> > EXAMPLE 1 : Basic Pipeline (without UMLS)
> >
> > ** SHOW Before and after clinical text, demonstrates purpose
> > ** LIST the 5 steps
> > ** Most impressive demo would be the smoking status pipeline
> >
> > EXAMPLE 2: Basic Pipeline (with UMLS)
> >
> > ** SHOW Before and after (input text -> output annotations)
> > ** LIST the steps
> > ** Most impressive demo would be a negation of a cancer diagnosis and
> NER of a medication (chemotherapuetic drug).
> >
> > Thoughts?
> > --andy
> >
> >
> > On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> wrote:
> >
> >> Sure thing Pei.
> >>
> >> I dont think cTAKES is ready for attention grabbing release (humble
> opinion).
> >> And when you release you want to grab attention! ! cTAKES is
> awesome!!
> >>
> >> Suggestions (release blockers)
> >>
> >> (1) Downloads
> >> http://incubator.apache.org/ctakes/downloads.cgi
> >> ! Link to install instructions is not there but "Verifying
> signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL
> INSTRUCTIONS.
> >> ! Last official release is blank because there isn't one, remove it !
> >> First mirror I tried was a 404? (not sure which one). I changed the
> >> mirror then OK. Test all mirrors (script) ? Previous releases are
> VERY confusing.
> >> ? The NIH and SourceForge pages  should redirect to cTAKES, google
> "cTAKES download" and imagine how confused a beginner would be.
> >>
> >> (2) User Guide
> >> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> >> ? 3.0.0 : no list of new features from last stable release. Why would
> a user bother to upgrade to a beta?
> >> ! Would be better to have a bundled download with resources, if
> possible. Otherwise, make it clear to a newcomer what the benefit of
> getting UMLS / LVG is. (one sentence).
> >> ! Needs a very high level overview of the components in the context
> of using them to do a very basic task like.
> >> ! This is likely the most frequently accessed document for cTAKES. It
> has almost no pointers to where to find basic information.
> >>
> >> (3) OTHER
> >> * The NCI and SourceForge links are now highly confusing.
> >> * While I am downloading, I should be reading the recommended "Get
> >> Started" guide
> >>
> >> I'm still downloading the 2GB resources file.
> >> I'll try and get back to you about the install when that is done too.
> >>
> >> This constructive criticism is because I believe cTAKES is AWESOME.
> >> Hard to see how awesome it is given the current instructions.
> >>
> >> --Andy
> >>
> >>
> >> On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>
> >>> Hi Andy,
> >>> So much has changed in cTAKES since last year, if you have a chance-
> do you also want to try downloading the -bin and ensure at least the
> steps in the README are able to get you started?
> >>>
> >>> --Pei
> >>> ________________________________________
> >>> From: Andy McMurry [mcmurry.andy@gmail.com]
> >>> Sent: Friday, February 15, 2013 4:04 PM
> >>> To: ctakes-dev@incubator.apache.org
> >>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>>
> >>> Suggestion: can we get a good programmer with no cTAKES experience
> to kick the tires and tell us how long it took to get started?
> >>>
> >>> John Resig (jQuery founder) once told me "if it takes more than 15
> minutes to get started, then that is way too long".
> >>>
> >>> "What is necessary is that enough investment be put into
> >>> presentation that newcomers can get past the obstacle of
> unfamiliarity. ... Hactivation energy: the amount of energy a newcomer
> must put in before she starts getting something back"
> >>> -- From "Producing Open Source Software"
> >>>
> >>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=ha
> >>> c
> >>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9
> >>> ktivation+W
> >>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&
> >>> q
> >>> =hacktivation%20energy&f=false
> >>>
> >>>
> >>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>>
> >>>> This is to open a discussion to graduate Apache cTAKES podling from
> the Apache Incubator.
> >>>>
> >>>> Apache cTAKES entered the Incubator in June of 2012. We have made
> significant progress with the project since moving over to Apache. We
> currently have 18 committers listed on our status page at [1] including
> over 10 which accepted after the podling was formed.
> >>>>
> >>>> During incubation, cTAKES has :
> >>>> * Produced 1 Release
> >>>> * Added 10 new Committer/PPMC members and shows constant community
> >>>> activities
> >>>> * Cleared IP on code
> >>>> * Developed Roadmap(s) for the next major and minor releases in a
> >>>> community process and started working on that [2]
> >>>> * The community of Apache cTAKES is active, healthy, and growing
> and has demonstrated the ability to self-govern using accepted Apache
> practices.
> >>>>
> >>>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>>> [2]
> >>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlass
> >>>> i an.jira.plugin.system.project%3Aroadmap-panel
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Bleeker, Troy C." <Bl...@mayo.edu>]

I just open the downloads page again this morning. If the first thing I do is click a downloadable file I get the error.
I'm using FF 18.02. I also tried IE 8, same thing.
In both cases pressing the Change button makes it work.

Thanks
Troy
-----Original Message-----
From: ctakes-dev-return-1246-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1246-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Tuesday, February 19, 2013 8:45 AM
To: <ct...@incubator.apache.org>
Subject: Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

> - The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button.

Hi Troy,
I think this was fixed. Links (sidenav) were updated to use downloads.cgi instead of html.  Could you confirm?

On Feb 18, 2013, at 11:58 AM, "Bleeker, Troy C." <Bl...@mayo.edu> wrote:

> All the suggestions and discussion are good. There's a lot here, sorry for the long summary. First things first:
> 
> - The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button. If you do neither and try to download you get this error: "The requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz was not found on this server." Anyone have time to fix this?
> - Adding a link to the install instructions makes it obvious (which I have done to the page) but it was there in a sense. The page said "Use the Developer and User Guides to direct you through the installation process." and the links to those were just to the left in the hierarchy.
> - "Last official release" was held until now. Since 3.0 is going to be officially announced, 3.0 will go there. I made that change as well.
> - A list of changed features has not been high priority since the original goal was to make a 3.0 in Apache that pretty much matched the function of 2.5. The only thing that changed was how the product is built and shipped. Nevertheless we need to state at least that somewhere.
> - The resources file is 1.1 GB not 2 right?
> 
> Keep in mind that the community decided to release cTAKES 3.0 without the doc being complete, but these must be next:
> - The current guides are still not complete. I made it through the developer guide but the user guide still has problems. I get errors after installing and running scripts. I have not been able to try the comparison test that was available previously. The table at the bottom I have not got to yet.
> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/ 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've done my best to minimize a user going back and forth. We have it this way because a useful guide is not easy (IMHO or even possible) with markdown text in the cTAKES home pages. There are still 3.0 developer and user guide pages on the cTAKES home site that should be removed so no one stumbles on to them.
> - Where would a newcomer hit first? Internet search for "ctakes" or "ctakes 3.0" is probably first. Top hits on those lists should be modified to point to the best Apache cTAKES landing page.
> - The Getting Started page needs to be written in context of all future releases not just 3.0.
> - Previous releases list. We need to both point to the NCI sites for 2.6 and back plus create an archive for what will be the history of Apache releases. Needs work your right.
> 
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should have. This would be great for a how-to guide.
> - The Developer Guide and User Guide have historically been install guides not how-to guides. I don't think a how-to guide should be incorporated into these but should be its own document.
> - cTAKES has never had a how-to guide that I know of. Making one would 
> be great and as you say should include things like 1) pointers to where to find basic information 2) very high level overview of the components in the context of using them to do a very basic task like 3) I think it was suggested that the Getting Started page might be something like this in very short form. If we did that then it would point to a more comprehensive how-to guide.
> - Project history page of all cTAKES releases placed on Apache sites somewhere. Good plan if short. I would not copy readmes there but have links to them.
> I already did this for cTAKES 2.5 and past: 
> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> Move this page to Apache? Have a page on Apache that continues this and points back to what already exists?
> Also, I had this project history on the Apache cTAKES downloads page but that section was removed when 3.0 was placed on there. If you can find the history of changes to that page you may find something already done in markdown format.
> - Creating a single download for a newcomer. This has been discussed and tabled by the community for the time being in order to get the 3.0 release done and out the door. We need to come back to this in order to make the best first impression.
> 
> Troy
> 
> -----Original Message-----
> From: 
> ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org 
> [mailto:ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.
> org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 10:17 PM
> To: ctakes-dev@incubator.apache.org
> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from 
> Incubator
> 
> Thanks Andy for the feedback.
> Examples are a good idea- Were you thinking of adding it to the README file or the confluence user guide?
> 
> Feel free to update the downloads page(s) (it uses Apache CMS) and the User Guides (Confluence wiki).  
> Note: The release is still being replicated to all of the mirrors and may take up to 24 hrs, so I would wait until after the weekend before testing all of the mirror links.
> 
> --Pei
> ________________________________________
> From: Andy McMurry [mcmurry.andy@gmail.com]
> Sent: Friday, February 15, 2013 11:08 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> 
> Clarifications
> 
> There isn't a last Apache release. But there are last previous NIH, Sourceforge, and Apache releases?
> TODO: Project History Page (Simple, just the releases and times, ideally with JIRA generated release notes).
> 
> Suggestion: Demonstration > explanation. Use Examples !!
> 
> EXAMPLE 1 : Basic Pipeline (without UMLS)
> 
> ** SHOW Before and after clinical text, demonstrates purpose
> ** LIST the 5 steps
> ** Most impressive demo would be the smoking status pipeline
> 
> EXAMPLE 2: Basic Pipeline (with UMLS)
> 
> ** SHOW Before and after (input text -> output annotations)
> ** LIST the steps
> ** Most impressive demo would be a negation of a cancer diagnosis and NER of a medication (chemotherapuetic drug).
> 
> Thoughts?
> --andy
> 
> 
> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com> wrote:
> 
>> Sure thing Pei.
>> 
>> I dont think cTAKES is ready for attention grabbing release (humble opinion).
>> And when you release you want to grab attention! ! cTAKES is awesome!!
>> 
>> Suggestions (release blockers)
>> 
>> (1) Downloads
>> http://incubator.apache.org/ctakes/downloads.cgi
>> ! Link to install instructions is not there but "Verifying signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
>> ! Last official release is blank because there isn't one, remove it ! 
>> First mirror I tried was a 404? (not sure which one). I changed the 
>> mirror then OK. Test all mirrors (script) ? Previous releases are VERY confusing.
>> ? The NIH and SourceForge pages  should redirect to cTAKES, google "cTAKES download" and imagine how confused a beginner would be.
>> 
>> (2) User Guide
>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
>> ? 3.0.0 : no list of new features from last stable release. Why would a user bother to upgrade to a beta?
>> ! Would be better to have a bundled download with resources, if possible. Otherwise, make it clear to a newcomer what the benefit of getting UMLS / LVG is. (one sentence).
>> ! Needs a very high level overview of the components in the context of using them to do a very basic task like.
>> ! This is likely the most frequently accessed document for cTAKES. It has almost no pointers to where to find basic information.
>> 
>> (3) OTHER
>> * The NCI and SourceForge links are now highly confusing.
>> * While I am downloading, I should be reading the recommended "Get 
>> Started" guide
>> 
>> I'm still downloading the 2GB resources file.
>> I'll try and get back to you about the install when that is done too.
>> 
>> This constructive criticism is because I believe cTAKES is AWESOME.
>> Hard to see how awesome it is given the current instructions.
>> 
>> --Andy
>> 
>> 
>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>> 
>>> Hi Andy,
>>> So much has changed in cTAKES since last year, if you have a chance- do you also want to try downloading the -bin and ensure at least the steps in the README are able to get you started?
>>> 
>>> --Pei
>>> ________________________________________
>>> From: Andy McMurry [mcmurry.andy@gmail.com]
>>> Sent: Friday, February 15, 2013 4:04 PM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>> 
>>> Suggestion: can we get a good programmer with no cTAKES experience to kick the tires and tell us how long it took to get started?
>>> 
>>> John Resig (jQuery founder) once told me "if it takes more than 15 minutes to get started, then that is way too long".
>>> 
>>> "What is necessary is that enough investment be put into 
>>> presentation that newcomers can get past the obstacle of unfamiliarity. ... Hactivation energy: the amount of energy a newcomer must put in before she starts getting something back"
>>> -- From "Producing Open Source Software"
>>> 
>>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=ha
>>> c
>>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9
>>> ktivation+W
>>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&
>>> q
>>> =hacktivation%20energy&f=false
>>> 
>>> 
>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>>> 
>>>> This is to open a discussion to graduate Apache cTAKES podling from the Apache Incubator.
>>>> 
>>>> Apache cTAKES entered the Incubator in June of 2012. We have made significant progress with the project since moving over to Apache. We currently have 18 committers listed on our status page at [1] including over 10 which accepted after the podling was formed.
>>>> 
>>>> During incubation, cTAKES has :
>>>> * Produced 1 Release
>>>> * Added 10 new Committer/PPMC members and shows constant community 
>>>> activities
>>>> * Cleared IP on code
>>>> * Developed Roadmap(s) for the next major and minor releases in a 
>>>> community process and started working on that [2]
>>>> * The community of Apache cTAKES is active, healthy, and growing and has demonstrated the ability to self-govern using accepted Apache practices.
>>>> 
>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
>>>> [2]
>>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlass
>>>> i an.jira.plugin.system.project%3Aroadmap-panel
> 

Re: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Chen, Pei" <Pe...@childrens.harvard.edu>]

> - The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button.

Hi Troy,
I think this was fixed. Links (sidenav) were updated to use downloads.cgi instead of html.  Could you confirm?

On Feb 18, 2013, at 11:58 AM, "Bleeker, Troy C." <Bl...@mayo.edu> wrote:

> All the suggestions and discussion are good. There's a lot here, sorry for the long summary. First things first:
> 
> - The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button. If you do neither and try to download you get this error: "The requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz was not found on this server." Anyone have time to fix this?
> - Adding a link to the install instructions makes it obvious (which I have done to the page) but it was there in a sense. The page said "Use the Developer and User Guides to direct you through the installation process." and the links to those were just to the left in the hierarchy.
> - "Last official release" was held until now. Since 3.0 is going to be officially announced, 3.0 will go there. I made that change as well.
> - A list of changed features has not been high priority since the original goal was to make a 3.0 in Apache that pretty much matched the function of 2.5. The only thing that changed was how the product is built and shipped. Nevertheless we need to state at least that somewhere.
> - The resources file is 1.1 GB not 2 right?
> 
> Keep in mind that the community decided to release cTAKES 3.0 without the doc being complete, but these must be next:
> - The current guides are still not complete. I made it through the developer guide but the user guide still has problems. I get errors after installing and running scripts. I have not been able to try the comparison test that was available previously. The table at the bottom I have not got to yet.
> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/ 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've done my best to minimize a user going back and forth. We have it this way because a useful guide is not easy (IMHO or even possible) with markdown text in the cTAKES home pages. There are still 3.0 developer and user guide pages on the cTAKES home site that should be removed so no one stumbles on to them.
> - Where would a newcomer hit first? Internet search for "ctakes" or "ctakes 3.0" is probably first. Top hits on those lists should be modified to point to the best Apache cTAKES landing page.
> - The Getting Started page needs to be written in context of all future releases not just 3.0.
> - Previous releases list. We need to both point to the NCI sites for 2.6 and back plus create an archive for what will be the history of Apache releases. Needs work your right.
> 
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should have. This would be great for a how-to guide.
> - The Developer Guide and User Guide have historically been install guides not how-to guides. I don't think a how-to guide should be incorporated into these but should be its own document.
> - cTAKES has never had a how-to guide that I know of. Making one would be great and as you say should include things like 1) pointers to where to find basic information 2) very high level overview of the components in the context of using them to do a very basic task like 3) 
> I think it was suggested that the Getting Started page might be something like this in very short form. If we did that then it would point to a more comprehensive how-to guide.
> - Project history page of all cTAKES releases placed on Apache sites somewhere. Good plan if short. I would not copy readmes there but have links to them.
> I already did this for cTAKES 2.5 and past: https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> Move this page to Apache? Have a page on Apache that continues this and points back to what already exists?
> Also, I had this project history on the Apache cTAKES downloads page but that section was removed when 3.0 was placed on there. If you can find the history of changes to that page you may find something already done in markdown format.
> - Creating a single download for a newcomer. This has been discussed and tabled by the community for the time being in order to get the 3.0 release done and out the door. We need to come back to this in order to make the best first impression.
> 
> Troy
> 
> -----Original Message-----
> From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 10:17 PM
> To: ctakes-dev@incubator.apache.org
> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator
> 
> Thanks Andy for the feedback.
> Examples are a good idea- Were you thinking of adding it to the README file or the confluence user guide?
> 
> Feel free to update the downloads page(s) (it uses Apache CMS) and the User Guides (Confluence wiki).  
> Note: The release is still being replicated to all of the mirrors and may take up to 24 hrs, so I would wait until after the weekend before testing all of the mirror links.
> 
> --Pei
> ________________________________________
> From: Andy McMurry [mcmurry.andy@gmail.com]
> Sent: Friday, February 15, 2013 11:08 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> 
> Clarifications
> 
> There isn't a last Apache release. But there are last previous NIH, Sourceforge, and Apache releases?
> TODO: Project History Page (Simple, just the releases and times, ideally with JIRA generated release notes).
> 
> Suggestion: Demonstration > explanation. Use Examples !!
> 
> EXAMPLE 1 : Basic Pipeline (without UMLS)
> 
> ** SHOW Before and after clinical text, demonstrates purpose
> ** LIST the 5 steps
> ** Most impressive demo would be the smoking status pipeline
> 
> EXAMPLE 2: Basic Pipeline (with UMLS)
> 
> ** SHOW Before and after (input text -> output annotations)
> ** LIST the steps
> ** Most impressive demo would be a negation of a cancer diagnosis and NER of a medication (chemotherapuetic drug).
> 
> Thoughts?
> --andy
> 
> 
> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com> wrote:
> 
>> Sure thing Pei.
>> 
>> I dont think cTAKES is ready for attention grabbing release (humble opinion).
>> And when you release you want to grab attention! ! cTAKES is awesome!!
>> 
>> Suggestions (release blockers)
>> 
>> (1) Downloads
>> http://incubator.apache.org/ctakes/downloads.cgi
>> ! Link to install instructions is not there but "Verifying signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
>> ! Last official release is blank because there isn't one, remove it ! 
>> First mirror I tried was a 404? (not sure which one). I changed the 
>> mirror then OK. Test all mirrors (script) ? Previous releases are VERY confusing.
>> ? The NIH and SourceForge pages  should redirect to cTAKES, google "cTAKES download" and imagine how confused a beginner would be.
>> 
>> (2) User Guide
>> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
>> ? 3.0.0 : no list of new features from last stable release. Why would a user bother to upgrade to a beta?
>> ! Would be better to have a bundled download with resources, if possible. Otherwise, make it clear to a newcomer what the benefit of getting UMLS / LVG is. (one sentence).
>> ! Needs a very high level overview of the components in the context of using them to do a very basic task like.
>> ! This is likely the most frequently accessed document for cTAKES. It has almost no pointers to where to find basic information.
>> 
>> (3) OTHER
>> * The NCI and SourceForge links are now highly confusing.
>> * While I am downloading, I should be reading the recommended "Get 
>> Started" guide
>> 
>> I'm still downloading the 2GB resources file.
>> I'll try and get back to you about the install when that is done too.
>> 
>> This constructive criticism is because I believe cTAKES is AWESOME.
>> Hard to see how awesome it is given the current instructions.
>> 
>> --Andy
>> 
>> 
>> On Feb 15, 2013, at 5:02 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>> 
>>> Hi Andy,
>>> So much has changed in cTAKES since last year, if you have a chance- do you also want to try downloading the -bin and ensure at least the steps in the README are able to get you started?
>>> 
>>> --Pei
>>> ________________________________________
>>> From: Andy McMurry [mcmurry.andy@gmail.com]
>>> Sent: Friday, February 15, 2013 4:04 PM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>> 
>>> Suggestion: can we get a good programmer with no cTAKES experience to kick the tires and tell us how long it took to get started?
>>> 
>>> John Resig (jQuery founder) once told me "if it takes more than 15 minutes to get started, then that is way too long".
>>> 
>>> "What is necessary is that enough investment be put into presentation 
>>> that newcomers can get past the obstacle of unfamiliarity. ... Hactivation energy: the amount of energy a newcomer must put in before she starts getting something back"
>>> -- From "Producing Open Source Software"
>>> 
>>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
>>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
>>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
>>> =hacktivation%20energy&f=false
>>> 
>>> 
>>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>>> 
>>>> This is to open a discussion to graduate Apache cTAKES podling from the Apache Incubator.
>>>> 
>>>> Apache cTAKES entered the Incubator in June of 2012. We have made significant progress with the project since moving over to Apache. We currently have 18 committers listed on our status page at [1] including over 10 which accepted after the podling was formed.
>>>> 
>>>> During incubation, cTAKES has :
>>>> * Produced 1 Release
>>>> * Added 10 new Committer/PPMC members and shows constant community 
>>>> activities
>>>> * Cleared IP on code
>>>> * Developed Roadmap(s) for the next major and minor releases in a 
>>>> community process and started working on that [2]
>>>> * The community of Apache cTAKES is active, healthy, and growing and has demonstrated the ability to self-govern using accepted Apache practices.
>>>> 
>>>> [1] http://people.apache.org/committers-by-project.html#ctakes
>>>> [2] 
>>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
>>>> an.jira.plugin.system.project%3Aroadmap-panel
> 

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Masanz, James J." <Ma...@mayo.edu>]

A few quick things

2.6 release was cancelled so no need to refer to it anymore.

3.0.0 does have new function since 2.6 was never released. 3.0 contains the relation extractor.

I made some changes to pages on the nci wiki to point people to the apache cTAKES mailing lists and to also point people to the Apache cTAKES (incubating) pages so that if someone goes to the 2.5 pages they will know there is a newer release.

Pages I updated include:
https://wiki.nci.nih.gov/pages/viewpage.action?pageId=65733244
https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5


Regards, 
James Masanz

> -----Original Message-----
> From: ctakes-dev-return-1239-Masanz.James=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1239-
> Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Bleeker, Troy
> C.
> Sent: Monday, February 18, 2013 10:58 AM
> To: ctakes-dev@incubator.apache.org
> Subject: RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES
> from Incubator
> 
> All the suggestions and discussion are good. There's a lot here, sorry
> for the long summary. First things first:
> 
> - The downloads page must work. It now seems to function alright
> ***IF*** you refresh the page or select a mirror and click the Change
> button. If you do neither and try to download you get this error: "The
> requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-
> incubating-bin.tar.gz was not found on this server." Anyone have time to
> fix this?
> - Adding a link to the install instructions makes it obvious (which I
> have done to the page) but it was there in a sense. The page said "Use
> the Developer and User Guides to direct you through the installation
> process." and the links to those were just to the left in the hierarchy.
> - "Last official release" was held until now. Since 3.0 is going to be
> officially announced, 3.0 will go there. I made that change as well.
> - A list of changed features has not been high priority since the
> original goal was to make a 3.0 in Apache that pretty much matched the
> function of 2.5. The only thing that changed was how the product is
> built and shipped. Nevertheless we need to state at least that
> somewhere.
> - The resources file is 1.1 GB not 2 right?
> 
> Keep in mind that the community decided to release cTAKES 3.0 without
> the doc being complete, but these must be next:
> - The current guides are still not complete. I made it through the
> developer guide but the user guide still has problems. I get errors
> after installing and running scripts. I have not been able to try the
> comparison test that was available previously. The table at the bottom I
> have not got to yet.
> - We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/
> 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've
> done my best to minimize a user going back and forth. We have it this
> way because a useful guide is not easy (IMHO or even possible) with
> markdown text in the cTAKES home pages. There are still 3.0 developer
> and user guide pages on the cTAKES home site that should be removed so
> no one stumbles on to them.
> - Where would a newcomer hit first? Internet search for "ctakes" or
> "ctakes 3.0" is probably first. Top hits on those lists should be
> modified to point to the best Apache cTAKES landing page.
> - The Getting Started page needs to be written in context of all future
> releases not just 3.0.
> - Previous releases list. We need to both point to the NCI sites for 2.6
> and back plus create an archive for what will be the history of Apache
> releases. Needs work your right.
> 
> Potential priorities after that:
> - The examples, as described by Andy, would be more than a readme should
> have. This would be great for a how-to guide.
> - The Developer Guide and User Guide have historically been install
> guides not how-to guides. I don't think a how-to guide should be
> incorporated into these but should be its own document.
> - cTAKES has never had a how-to guide that I know of. Making one would
> be great and as you say should include things like 1) pointers to where
> to find basic information 2) very high level overview of the components
> in the context of using them to do a very basic task like 3) I think it
> was suggested that the Getting Started page might be something like this
> in very short form. If we did that then it would point to a more
> comprehensive how-to guide.
> - Project history page of all cTAKES releases placed on Apache sites
> somewhere. Good plan if short. I would not copy readmes there but have
> links to them.
> I already did this for cTAKES 2.5 and past:
> https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
> Move this page to Apache? Have a page on Apache that continues this and
> points back to what already exists?
> Also, I had this project history on the Apache cTAKES downloads page but
> that section was removed when 3.0 was placed on there. If you can find
> the history of changes to that page you may find something already done
> in markdown format.
> - Creating a single download for a newcomer. This has been discussed and
> tabled by the community for the time being in order to get the 3.0
> release done and out the door. We need to come back to this in order to
> make the best first impression.
> 
> Troy
> 
> -----Original Message-----
> From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org
> [mailto:ctakes-dev-return-1230-
> Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Friday, February 15, 2013 10:17 PM
> To: ctakes-dev@incubator.apache.org
> Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from
> Incubator
> 
> Thanks Andy for the feedback.
> Examples are a good idea- Were you thinking of adding it to the README
> file or the confluence user guide?
> 
> Feel free to update the downloads page(s) (it uses Apache CMS) and the
> User Guides (Confluence wiki).
> Note: The release is still being replicated to all of the mirrors and
> may take up to 24 hrs, so I would wait until after the weekend before
> testing all of the mirror links.
> 
> --Pei
> ________________________________________
> From: Andy McMurry [mcmurry.andy@gmail.com]
> Sent: Friday, February 15, 2013 11:08 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> 
> Clarifications
> 
> There isn't a last Apache release. But there are last previous NIH,
> Sourceforge, and Apache releases?
> TODO: Project History Page (Simple, just the releases and times, ideally
> with JIRA generated release notes).
> 
> Suggestion: Demonstration > explanation. Use Examples !!
> 
> EXAMPLE 1 : Basic Pipeline (without UMLS)
> 
> ** SHOW Before and after clinical text, demonstrates purpose
> ** LIST the 5 steps
> ** Most impressive demo would be the smoking status pipeline
> 
> EXAMPLE 2: Basic Pipeline (with UMLS)
> 
> ** SHOW Before and after (input text -> output annotations)
> ** LIST the steps
> ** Most impressive demo would be a negation of a cancer diagnosis and
> NER of a medication (chemotherapuetic drug).
> 
> Thoughts?
> --andy
> 
> 
> On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com>
> wrote:
> 
> > Sure thing Pei.
> >
> > I dont think cTAKES is ready for attention grabbing release (humble
> opinion).
> > And when you release you want to grab attention! ! cTAKES is awesome!!
> >
> > Suggestions (release blockers)
> >
> > (1) Downloads
> > http://incubator.apache.org/ctakes/downloads.cgi
> > ! Link to install instructions is not there but "Verifying signatures"
> takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> > ! Last official release is blank because there isn't one, remove it !
> > First mirror I tried was a 404? (not sure which one). I changed the
> > mirror then OK. Test all mirrors (script) ? Previous releases are VERY
> confusing.
> > ? The NIH and SourceForge pages  should redirect to cTAKES, google
> "cTAKES download" and imagine how confused a beginner would be.
> >
> > (2) User Guide
> > http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> > ? 3.0.0 : no list of new features from last stable release. Why would
> a user bother to upgrade to a beta?
> > ! Would be better to have a bundled download with resources, if
> possible. Otherwise, make it clear to a newcomer what the benefit of
> getting UMLS / LVG is. (one sentence).
> > ! Needs a very high level overview of the components in the context of
> using them to do a very basic task like.
> > ! This is likely the most frequently accessed document for cTAKES. It
> has almost no pointers to where to find basic information.
> >
> > (3) OTHER
> > * The NCI and SourceForge links are now highly confusing.
> > * While I am downloading, I should be reading the recommended "Get
> > Started" guide
> >
> > I'm still downloading the 2GB resources file.
> > I'll try and get back to you about the install when that is done too.
> >
> > This constructive criticism is because I believe cTAKES is AWESOME.
> > Hard to see how awesome it is given the current instructions.
> >
> > --Andy
> >
> >
> > On Feb 15, 2013, at 5:02 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >
> >> Hi Andy,
> >> So much has changed in cTAKES since last year, if you have a chance-
> do you also want to try downloading the -bin and ensure at least the
> steps in the README are able to get you started?
> >>
> >> --Pei
> >> ________________________________________
> >> From: Andy McMurry [mcmurry.andy@gmail.com]
> >> Sent: Friday, February 15, 2013 4:04 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
> >>
> >> Suggestion: can we get a good programmer with no cTAKES experience to
> kick the tires and tell us how long it took to get started?
> >>
> >> John Resig (jQuery founder) once told me "if it takes more than 15
> minutes to get started, then that is way too long".
> >>
> >> "What is necessary is that enough investment be put into presentation
> >> that newcomers can get past the obstacle of unfamiliarity. ...
> Hactivation energy: the amount of energy a newcomer must put in before
> she starts getting something back"
> >> -- From "Producing Open Source Software"
> >>
> >> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
> >> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
> >> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
> >> =hacktivation%20energy&f=false
> >>
> >>
> >> On Feb 15, 2013, at 12:55 PM, "Chen, Pei"
> <Pe...@childrens.harvard.edu> wrote:
> >>
> >>> This is to open a discussion to graduate Apache cTAKES podling from
> the Apache Incubator.
> >>>
> >>> Apache cTAKES entered the Incubator in June of 2012. We have made
> significant progress with the project since moving over to Apache. We
> currently have 18 committers listed on our status page at [1] including
> over 10 which accepted after the podling was formed.
> >>>
> >>> During incubation, cTAKES has :
> >>> * Produced 1 Release
> >>> * Added 10 new Committer/PPMC members and shows constant community
> >>> activities
> >>> * Cleared IP on code
> >>> * Developed Roadmap(s) for the next major and minor releases in a
> >>> community process and started working on that [2]
> >>> * The community of Apache cTAKES is active, healthy, and growing and
> has demonstrated the ability to self-govern using accepted Apache
> practices.
> >>>
> >>> [1] http://people.apache.org/committers-by-project.html#ctakes
> >>> [2]
> >>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
> >>> an.jira.plugin.system.project%3Aroadmap-panel
> >>>
> >>
> >

RE: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

["Bleeker, Troy C." <Bl...@mayo.edu>]

All the suggestions and discussion are good. There's a lot here, sorry for the long summary. First things first:

- The downloads page must work. It now seems to function alright ***IF*** you refresh the page or select a mirror and click the Change button. If you do neither and try to download you get this error: "The requested URL /ctakes/[preferred]incubator/ctakes/apache-ctakes-3.0.0-incubating-bin.tar.gz was not found on this server." Anyone have time to fix this?
- Adding a link to the install instructions makes it obvious (which I have done to the page) but it was there in a sense. The page said "Use the Developer and User Guides to direct you through the installation process." and the links to those were just to the left in the hierarchy.
- "Last official release" was held until now. Since 3.0 is going to be officially announced, 3.0 will go there. I made that change as well.
- A list of changed features has not been high priority since the original goal was to make a 3.0 in Apache that pretty much matched the function of 2.5. The only thing that changed was how the product is built and shipped. Nevertheless we need to state at least that somewhere.
- The resources file is 1.1 GB not 2 right?

Keep in mind that the community decided to release cTAKES 3.0 without the doc being complete, but these must be next:
- The current guides are still not complete. I made it through the developer guide but the user guide still has problems. I get errors after installing and running scripts. I have not been able to try the comparison test that was available previously. The table at the bottom I have not got to yet.
- We have 2 sites now 1) cTAKES home http://incubator.apache.org/ctakes/ 2) cTAKES doc https://cwiki.apache.org/confluence/display/CTAKES. I've done my best to minimize a user going back and forth. We have it this way because a useful guide is not easy (IMHO or even possible) with markdown text in the cTAKES home pages. There are still 3.0 developer and user guide pages on the cTAKES home site that should be removed so no one stumbles on to them.
- Where would a newcomer hit first? Internet search for "ctakes" or "ctakes 3.0" is probably first. Top hits on those lists should be modified to point to the best Apache cTAKES landing page.
- The Getting Started page needs to be written in context of all future releases not just 3.0.
- Previous releases list. We need to both point to the NCI sites for 2.6 and back plus create an archive for what will be the history of Apache releases. Needs work your right.

Potential priorities after that:
- The examples, as described by Andy, would be more than a readme should have. This would be great for a how-to guide.
- The Developer Guide and User Guide have historically been install guides not how-to guides. I don't think a how-to guide should be incorporated into these but should be its own document.
- cTAKES has never had a how-to guide that I know of. Making one would be great and as you say should include things like 1) pointers to where to find basic information 2) very high level overview of the components in the context of using them to do a very basic task like 3) 
I think it was suggested that the Getting Started page might be something like this in very short form. If we did that then it would point to a more comprehensive how-to guide.
- Project history page of all cTAKES releases placed on Apache sites somewhere. Good plan if short. I would not copy readmes there but have links to them.
I already did this for cTAKES 2.5 and past: https://wiki.nci.nih.gov/display/VKC/cTAKES+Roadmap
Move this page to Apache? Have a page on Apache that continues this and points back to what already exists?
Also, I had this project history on the Apache cTAKES downloads page but that section was removed when 3.0 was placed on there. If you can find the history of changes to that page you may find something already done in markdown format.
- Creating a single download for a newcomer. This has been discussed and tabled by the community for the time being in order to get the 3.0 release done and out the door. We need to come back to this in order to make the best first impression.

Troy

-----Original Message-----
From: ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1230-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Friday, February 15, 2013 10:17 PM
To: ctakes-dev@incubator.apache.org
Subject: cTAKES 3.0.0 Feedback Was: RE: [DISCUSS] Graduate cTAKES from Incubator

Thanks Andy for the feedback.
Examples are a good idea- Were you thinking of adding it to the README file or the confluence user guide?

Feel free to update the downloads page(s) (it uses Apache CMS) and the User Guides (Confluence wiki).  
Note: The release is still being replicated to all of the mirrors and may take up to 24 hrs, so I would wait until after the weekend before testing all of the mirror links.

--Pei
________________________________________
From: Andy McMurry [mcmurry.andy@gmail.com]
Sent: Friday, February 15, 2013 11:08 PM
To: ctakes-dev@incubator.apache.org
Subject: Re: [DISCUSS] Graduate cTAKES from Incubator

Clarifications

There isn't a last Apache release. But there are last previous NIH, Sourceforge, and Apache releases?
TODO: Project History Page (Simple, just the releases and times, ideally with JIRA generated release notes).

Suggestion: Demonstration > explanation. Use Examples !!

EXAMPLE 1 : Basic Pipeline (without UMLS)

** SHOW Before and after clinical text, demonstrates purpose
** LIST the 5 steps
** Most impressive demo would be the smoking status pipeline

EXAMPLE 2: Basic Pipeline (with UMLS)

** SHOW Before and after (input text -> output annotations)
** LIST the steps
** Most impressive demo would be a negation of a cancer diagnosis and NER of a medication (chemotherapuetic drug).

Thoughts?
--andy


On Feb 15, 2013, at 7:36 PM, Andy McMurry <mc...@gmail.com> wrote:

> Sure thing Pei.
>
> I dont think cTAKES is ready for attention grabbing release (humble opinion).
> And when you release you want to grab attention! ! cTAKES is awesome!!
>
> Suggestions (release blockers)
>
> (1) Downloads
> http://incubator.apache.org/ctakes/downloads.cgi
> ! Link to install instructions is not there but "Verifying signatures" takes up 20% of the page. NEEDS OBVIOUS LINK TO  INSTALL INSTRUCTIONS.
> ! Last official release is blank because there isn't one, remove it ! 
> First mirror I tried was a 404? (not sure which one). I changed the 
> mirror then OK. Test all mirrors (script) ? Previous releases are VERY confusing.
> ? The NIH and SourceForge pages  should redirect to cTAKES, google "cTAKES download" and imagine how confused a beginner would be.
>
> (2) User Guide
> http://incubator.apache.org/ctakes/3.0.0/user-guide-3.0
> ? 3.0.0 : no list of new features from last stable release. Why would a user bother to upgrade to a beta?
> ! Would be better to have a bundled download with resources, if possible. Otherwise, make it clear to a newcomer what the benefit of getting UMLS / LVG is. (one sentence).
> ! Needs a very high level overview of the components in the context of using them to do a very basic task like.
> ! This is likely the most frequently accessed document for cTAKES. It has almost no pointers to where to find basic information.
>
> (3) OTHER
> * The NCI and SourceForge links are now highly confusing.
> * While I am downloading, I should be reading the recommended "Get 
> Started" guide
>
> I'm still downloading the 2GB resources file.
> I'll try and get back to you about the install when that is done too.
>
> This constructive criticism is because I believe cTAKES is AWESOME.
> Hard to see how awesome it is given the current instructions.
>
> --Andy
>
>
> On Feb 15, 2013, at 5:02 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>
>> Hi Andy,
>> So much has changed in cTAKES since last year, if you have a chance- do you also want to try downloading the -bin and ensure at least the steps in the README are able to get you started?
>>
>> --Pei
>> ________________________________________
>> From: Andy McMurry [mcmurry.andy@gmail.com]
>> Sent: Friday, February 15, 2013 4:04 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: [DISCUSS] Graduate cTAKES from Incubator
>>
>> Suggestion: can we get a good programmer with no cTAKES experience to kick the tires and tell us how long it took to get started?
>>
>> John Resig (jQuery founder) once told me "if it takes more than 15 minutes to get started, then that is way too long".
>>
>> "What is necessary is that enough investment be put into presentation 
>> that newcomers can get past the obstacle of unfamiliarity. ... Hactivation energy: the amount of energy a newcomer must put in before she starts getting something back"
>> -- From "Producing Open Source Software"
>>
>> http://books.google.com/books?id=0vbr7xvvzjgC&pg=PA21&lpg=PA21&dq=hac
>> ktivation+energy&source=bl&ots=D0hP85ndwz&sig=G5HO-7GbLqQPwLaI6210D9W
>> Gk2E&hl=en&sa=X&ei=N6EeUZXVHMHhiALq3YG4BQ&ved=0CDoQ6AEwAQ#v=onepage&q
>> =hacktivation%20energy&f=false
>>
>>
>> On Feb 15, 2013, at 12:55 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>>
>>> This is to open a discussion to graduate Apache cTAKES podling from the Apache Incubator.
>>>
>>> Apache cTAKES entered the Incubator in June of 2012. We have made significant progress with the project since moving over to Apache. We currently have 18 committers listed on our status page at [1] including over 10 which accepted after the podling was formed.
>>>
>>> During incubation, cTAKES has :
>>> * Produced 1 Release
>>> * Added 10 new Committer/PPMC members and shows constant community 
>>> activities
>>> * Cleared IP on code
>>> * Developed Roadmap(s) for the next major and minor releases in a 
>>> community process and started working on that [2]
>>> * The community of Apache cTAKES is active, healthy, and growing and has demonstrated the ability to self-govern using accepted Apache practices.
>>>
>>> [1] http://people.apache.org/committers-by-project.html#ctakes
>>> [2] 
>>> https://issues.apache.org/jira/browse/CTAKES#selectedTab=com.atlassi
>>> an.jira.plugin.system.project%3Aroadmap-panel
>>>
>>
>