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Posted to dev@ctakes.apache.org by Murali Minnah <mm...@gmail.com> on 2016/12/05 18:26:21 UTC
cTAKES - 3.2.3 release
I wanted to check to see if there are objections to creating a 3.2.3
tag of trunk now to prepare for a 3.2.3-rc1?
Any comments from the participants/organizers on the success/lessons
learnt from the "hackathon" that the community can benefit from?
Best,
Murali
RE: cTAKES - 3.2.3 release
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Jeff,
Completely appropriate.
Thanks,
Sean
-----Original Message-----
From: Jeff Headley [mailto:jeffunf96@gmail.com]
Sent: Tuesday, December 06, 2016 11:21 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES - 3.2.3 release
I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
Jeff
On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
> In the past, the documentation on the website also shouldn’t hold up a release either.
>
> > On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
> >
> > Hi Murali,
> >
> > Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
> >
> > The primary takeaways from the hackathon were, not surprisingly:
> > 1. Installation of cTAKES is not as straightforward as we believe,
> > and 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
> > 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
> >
> > All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
> >
> > In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Murali Minnah [mailto:mminnah@gmail.com]
> > Sent: Monday, December 05, 2016 1:26 PM
> > To: dev@ctakes.apache.org
> > Subject: cTAKES - 3.2.3 release
> >
> > I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
> >
> > Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
> >
> > Best,
> > Murali
>
Re: cTAKES - 3.2.3 release
Posted by Pei Chen <ch...@apache.org>.
Thanks for the fix Murali and others!
I can confirm that 'mvn clean package' works from a fresh checkout of
trunk and doesn't throw the old failed test message. Others can
confirm and we can recreate the 3.2.3 branch in anticipation for any
release.
On Thu, Dec 15, 2016 at 10:00 PM, Murali Minnah <mm...@gmail.com> wrote:
> I already have the code base open and can commit the changes and
> delete/recreate the 3.2.3 branch.
>
> Best,
> Murali
>
> On Tue, Dec 6, 2016 at 11:57 AM, Pei Chen <pe...@wiredinformatics.com> wrote:
>> You’re welcome! I also compiled this same list last time and let several months elapse for any pending commits; feel free to check in any pending changes over the next few days- otherwise, let’s tag this Fri and prepare and push forward?
>>
>>> On Dec 6, 2016, at 11:52 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>
>>> Hi Pei,
>>>
>>> Thank you for starting step 1: compiling a list of tars and their status.
>>>
>>> Sean
>>>
>>> -----Original Message-----
>>> From: Pei Chen [mailto:pei.chen@wiredinformatics.com]
>>> Sent: Tuesday, December 06, 2016 11:44 AM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: cTAKES - 3.2.3 release
>>>
>>> I agree that a lot can be done to make cTAKES easier to use and there will always be room for improvement.
>>> However- I strongly disagree that we should delay releases for new features. We should release early and often. Folks can continue working off trunk; a tag/release does not stop anyone from to continue and work on enhancements.
>>>
>>> Considering it’s been almost 2 years since the last release; There are a lot of fixes that should justify a release.
>>> Sub-task
>>> [CTAKES-124 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D124&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vg40jDWGurWfAlOtiL-nInyy5wdq_jm13oDOnXHhXCk&e= >] - remove internal UIMA types from coreference Bug
>>> [CTAKES-76 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D76&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=h76FjI4WWu4LHulli161jAz527vnygd7e6T2DqyiMHg&e= >] - get third party dependencies into Maven Central
>>> [CTAKES-155 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D155&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Xj41oUWemrUSelkTZmm6UQddCs_LA11lruyU_5zCzR8&e= >] - SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters
>>> [CTAKES-178 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D178&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=dJVfIpgWukz1wFQ_H92mzzXXGK2-33JC2AedfAGeYSI&e= >] - parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)
>>> [CTAKES-213 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D213&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=a3DZ4QeENuzJBYd2mOYt75ALUWAGwq3ur8Y-otHbpLI&e= >] - ModifierExtractorAnnotator should produce XxxxModifier subtypes
>>> [CTAKES-275 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D275&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=kuusawQUbqYw40q_49bpslVhh9eXckc1VWykqcoXPW8&e= >] - some of the older junit tests don't have the right Project name in the run configurations
>>> [CTAKES-302 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D302&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=QqLaLVr9gwu1uNW4OrMwAGBaHbWQDPTJaiPwzhlIJ20&e= >] - Element type "hibernate-mapping" must be followed by either attribute specifications, ">" or "/>".
>>> [CTAKES-320 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D320&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Ar5W4F1ziHmni00PqBvX7NAJse3KWaJPjJaofcgShkA&e= >] - Methods used by getDefaultPipeline should be able to load reasonable defaults without expecting external files.
>>> [CTAKES-341 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D341&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ojjOCjbC-Wv8VLRPSwNfrORf2oKZvyYlf8PIxSuIYEM&e= >] - FractionFSM annotates incorrect span
>>> [CTAKES-364 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D364&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WmovdFOOKmxjpsxHF_oZj3Ws_P4vOfFsFOWJEgYwtJg&e= >] - Dictionary-Lookup-Fast will fail with URI is not Hierarchical
>>> [CTAKES-371 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D371&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EZl2YzPYv9kyhP3qtcxJ-z9ex80avSh3fYSALhua958&e= >] - update PTB tokenization logic in fast dictionary module
>>> [CTAKES-376 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D376&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=D3_dK6LFlkpGvNCcMelF2gUz6n7k3VkEjtP-63ta3xk&e= >] - ctakes-temporal throws NPE if LVG isn't run
>>> [CTAKES-379 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D379&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=wkOirnhGZRtWZW16Kc2cbGaOHJqkbQ9SRZjqZsWjAGU&e= >] - Placeholder - ISO Time Normalizer (wrapper)
>>> [CTAKES-389 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=UUvOh4qUdOhQEvfMv_WOhbnsr0xC3LMBqmZzmLLUmds&e= >] - cTAKES dictionary lookup missed word starting string bug
>>> [CTAKES-401 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D401&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vjr8h_J-Ss2ov1GNAM5c8iYKZmj095EBwH0B6m_5kOs&e= >] - License headers are JavaDoc comments but should be block comments Improvement
>>> [CTAKES-77 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D77&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ik8KjmPuw3_SmDeuV9J6dkvujHx6fxxvrAOQReFPrAg&e= >] - Update POSTagger Unit Tests
>>> [CTAKES-78 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D78&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q61CnLNqNUNwLKGPKMIejWQkOURg-4nMiHbDYEBilLM&e= >] - Update Chunker unit tests
>>> [CTAKES-122 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D122&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EVjs_Uj8_y1Jxan6l5drPalZFw47HHtIjifK925d-C8&e= >] - include LVG with a future version of cTAKES?
>>> [CTAKES-172 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D172&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=BTS35Jtbc4LDmXSn7jw68znfMhNTjjAlK6BMj7oCwsg&e= >] - relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator
>>> [CTAKES-295 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D295&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IY0H2klrJ6Y2tr3KR0GxSyoo0WpMKPxufu_aUqsA3o0&e= >] - Use UIMAFit-style configuration annotations
>>> [CTAKES-328 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D328&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sC9hzQGSRCkNSK0RVW3XB6ikk9eVw2gZuiUNq_1HQCc&e= >] - Clean up XML Annotator Descriptors
>>> [CTAKES-366 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D366&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=tadQy2cwyIgLuPCccfKNK5CDasCmEitr-77E1DnT1_g&e= >] - Add Cas Consumer that will save pretty human-readable annotations to file
>>> [CTAKES-367 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D367&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=A3jG_-BC6zblut37AlNN3I9svEJBskygYRT7njtFoaU&e= >] - FileLocator should output $CLASSPATH if file isn't found
>>> [CTAKES-368 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D368&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2QDfaT_dnp384pq-Xtov7f9H3vp2eqZ7b7WJiK2sutA&e= >] - Allow alternate CUI formats in fast dictionary lookup module
>>> [CTAKES-373 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D373&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q9UTv9kFrhTt5IPBRrF9frdexLd8OoR4sjFezLfhcN4&e= >] - MaxentParserWrapper can't handle section dividers: "=========="
>>> [CTAKES-380 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D380&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sW_XkXvYseK_Yzz42LZ15TPOY0uZ-C0kFvIUDZuZTFM&e= >] - Placeholder - New Sentence Detector
>>> [CTAKES-381 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D381&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eacLeerI11qVMGHVNCxzcO-GzvC2_mA3pXcpiaoiJIU&e= >] - Improved Location Of Model
>>> [CTAKES-385 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D385&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=CKTFvqZbJevxVi36-aVXP0ACLn3UEJSdArOAcEN86I8&e= >] - URI is not hierarchical when attempting to obtain lvg.properties within JAR
>>> [CTAKES-386 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D386&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=VQ3I-qmf_SVPsNP4hubSSWVHImtNjhZhCMmWy-zNTvM&e= >] - Remove all .classpath and.project files
>>> [CTAKES-387 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D387&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=TDB3-GZTDurRPNqAWE_YyRPlQjdM-6QjZGKzNTcyqrg&e= >] - Upgrade gov.nih.nlm.nls lvg artifact across the codebase
>>> [CTAKES-388 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D388&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=mOWKWmDTKkvAzH10vV9ansbFYPKpGWxG0uASseBlqy4&e= >] - URI is not hierarchical when attempting to obtain LookupDesc_Db.xml within JAR
>>> [CTAKES-399 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D399&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=9H7TNumGQg17tLnG6pIUhCpLCePTubQNr2s-8GT5i7c&e= >] - Add profile to pom.xml which permits build with JDK1.8 New Feature
>>> [CTAKES-314 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D314&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2UPU54d8kNVTSjC0FfpBWKWdSxq_7_0_wBs7FgLONYQ&e= >] - BigTop/Hadoop cTAKES integration
>>> [CTAKES-378 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D378&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IuYlnUhxS-jahucK8GzfMCzYmOBbBjMNcqkZsvuSAyk&e= >] - Fast Dictionary should be able to load custom codifications from db
>>> [CTAKES-382 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D382&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eq0O15eFRNk_YIsjhvlKCv4yHax4X8JOkITUifh-mys&e= >] - Add ability to easily add extension of UmlsConcept Type to jcas via dictionary lookup Task
>>> [CTAKES-74 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D74&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=o6JkmN2KMgyPJYDdsq0upy7S-mbT2LUfM5PGvw0afjI&e= >] - Tokenizer PennTreeBank breaks with certain apostrophes in tokens.
>>> [CTAKES-138 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D138&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=FKcIfK3Qjkbb02OjCm0yl6hKHJ3rGgkt3RsFtaumFC4&e= >] - Remove 3rd party jars from our SVN
>>> [CTAKES-232 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D232&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WE-LsxWpvhEVtVAi1tdjMeBbEFM1vU22JDmuU8MVc0M&e= >] - change concept type <>On Dec 6, 2016, at 11:20 AM, Jeff Headley <je...@gmail.com> wrote:
>>>>
>>>> I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
>>>>
>>>> Jeff
>>>>
>>>> On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
>>>>> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
>>>>> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
>>>>> In the past, the documentation on the website also shouldn’t hold up a release either.
>>>>>
>>>>>> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>>>>
>>>>>> Hi Murali,
>>>>>>
>>>>>> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>>>>>>
>>>>>> The primary takeaways from the hackathon were, not surprisingly:
>>>>>> 1. Installation of cTAKES is not as straightforward as we believe,
>>>>>> and 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
>>>>>> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>>>>>>
>>>>>> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>>>>>>
>>>>>> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>>>>>>
>>>>>> Sean
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Murali Minnah [mailto:mminnah@gmail.com]
>>>>>> Sent: Monday, December 05, 2016 1:26 PM
>>>>>> To: dev@ctakes.apache.org
>>>>>> Subject: cTAKES - 3.2.3 release
>>>>>>
>>>>>> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>>>>>>
>>>>>> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>>>>>>
>>>>>> Best,
>>>>>> Murali
>>>>>
>>>
>>
Re: cTAKES - 3.2.3 release
Posted by Murali Minnah <mm...@gmail.com>.
I already have the code base open and can commit the changes and
delete/recreate the 3.2.3 branch.
Best,
Murali
On Tue, Dec 6, 2016 at 11:57 AM, Pei Chen <pe...@wiredinformatics.com> wrote:
> You’re welcome! I also compiled this same list last time and let several months elapse for any pending commits; feel free to check in any pending changes over the next few days- otherwise, let’s tag this Fri and prepare and push forward?
>
>> On Dec 6, 2016, at 11:52 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>
>> Hi Pei,
>>
>> Thank you for starting step 1: compiling a list of tars and their status.
>>
>> Sean
>>
>> -----Original Message-----
>> From: Pei Chen [mailto:pei.chen@wiredinformatics.com]
>> Sent: Tuesday, December 06, 2016 11:44 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: cTAKES - 3.2.3 release
>>
>> I agree that a lot can be done to make cTAKES easier to use and there will always be room for improvement.
>> However- I strongly disagree that we should delay releases for new features. We should release early and often. Folks can continue working off trunk; a tag/release does not stop anyone from to continue and work on enhancements.
>>
>> Considering it’s been almost 2 years since the last release; There are a lot of fixes that should justify a release.
>> Sub-task
>> [CTAKES-124 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D124&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vg40jDWGurWfAlOtiL-nInyy5wdq_jm13oDOnXHhXCk&e= >] - remove internal UIMA types from coreference Bug
>> [CTAKES-76 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D76&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=h76FjI4WWu4LHulli161jAz527vnygd7e6T2DqyiMHg&e= >] - get third party dependencies into Maven Central
>> [CTAKES-155 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D155&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Xj41oUWemrUSelkTZmm6UQddCs_LA11lruyU_5zCzR8&e= >] - SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters
>> [CTAKES-178 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D178&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=dJVfIpgWukz1wFQ_H92mzzXXGK2-33JC2AedfAGeYSI&e= >] - parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)
>> [CTAKES-213 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D213&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=a3DZ4QeENuzJBYd2mOYt75ALUWAGwq3ur8Y-otHbpLI&e= >] - ModifierExtractorAnnotator should produce XxxxModifier subtypes
>> [CTAKES-275 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D275&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=kuusawQUbqYw40q_49bpslVhh9eXckc1VWykqcoXPW8&e= >] - some of the older junit tests don't have the right Project name in the run configurations
>> [CTAKES-302 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D302&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=QqLaLVr9gwu1uNW4OrMwAGBaHbWQDPTJaiPwzhlIJ20&e= >] - Element type "hibernate-mapping" must be followed by either attribute specifications, ">" or "/>".
>> [CTAKES-320 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D320&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Ar5W4F1ziHmni00PqBvX7NAJse3KWaJPjJaofcgShkA&e= >] - Methods used by getDefaultPipeline should be able to load reasonable defaults without expecting external files.
>> [CTAKES-341 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D341&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ojjOCjbC-Wv8VLRPSwNfrORf2oKZvyYlf8PIxSuIYEM&e= >] - FractionFSM annotates incorrect span
>> [CTAKES-364 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D364&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WmovdFOOKmxjpsxHF_oZj3Ws_P4vOfFsFOWJEgYwtJg&e= >] - Dictionary-Lookup-Fast will fail with URI is not Hierarchical
>> [CTAKES-371 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D371&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EZl2YzPYv9kyhP3qtcxJ-z9ex80avSh3fYSALhua958&e= >] - update PTB tokenization logic in fast dictionary module
>> [CTAKES-376 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D376&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=D3_dK6LFlkpGvNCcMelF2gUz6n7k3VkEjtP-63ta3xk&e= >] - ctakes-temporal throws NPE if LVG isn't run
>> [CTAKES-379 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D379&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=wkOirnhGZRtWZW16Kc2cbGaOHJqkbQ9SRZjqZsWjAGU&e= >] - Placeholder - ISO Time Normalizer (wrapper)
>> [CTAKES-389 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=UUvOh4qUdOhQEvfMv_WOhbnsr0xC3LMBqmZzmLLUmds&e= >] - cTAKES dictionary lookup missed word starting string bug
>> [CTAKES-401 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D401&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vjr8h_J-Ss2ov1GNAM5c8iYKZmj095EBwH0B6m_5kOs&e= >] - License headers are JavaDoc comments but should be block comments Improvement
>> [CTAKES-77 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D77&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ik8KjmPuw3_SmDeuV9J6dkvujHx6fxxvrAOQReFPrAg&e= >] - Update POSTagger Unit Tests
>> [CTAKES-78 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D78&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q61CnLNqNUNwLKGPKMIejWQkOURg-4nMiHbDYEBilLM&e= >] - Update Chunker unit tests
>> [CTAKES-122 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D122&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EVjs_Uj8_y1Jxan6l5drPalZFw47HHtIjifK925d-C8&e= >] - include LVG with a future version of cTAKES?
>> [CTAKES-172 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D172&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=BTS35Jtbc4LDmXSn7jw68znfMhNTjjAlK6BMj7oCwsg&e= >] - relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator
>> [CTAKES-295 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D295&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IY0H2klrJ6Y2tr3KR0GxSyoo0WpMKPxufu_aUqsA3o0&e= >] - Use UIMAFit-style configuration annotations
>> [CTAKES-328 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D328&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sC9hzQGSRCkNSK0RVW3XB6ikk9eVw2gZuiUNq_1HQCc&e= >] - Clean up XML Annotator Descriptors
>> [CTAKES-366 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D366&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=tadQy2cwyIgLuPCccfKNK5CDasCmEitr-77E1DnT1_g&e= >] - Add Cas Consumer that will save pretty human-readable annotations to file
>> [CTAKES-367 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D367&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=A3jG_-BC6zblut37AlNN3I9svEJBskygYRT7njtFoaU&e= >] - FileLocator should output $CLASSPATH if file isn't found
>> [CTAKES-368 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D368&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2QDfaT_dnp384pq-Xtov7f9H3vp2eqZ7b7WJiK2sutA&e= >] - Allow alternate CUI formats in fast dictionary lookup module
>> [CTAKES-373 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D373&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q9UTv9kFrhTt5IPBRrF9frdexLd8OoR4sjFezLfhcN4&e= >] - MaxentParserWrapper can't handle section dividers: "=========="
>> [CTAKES-380 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D380&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sW_XkXvYseK_Yzz42LZ15TPOY0uZ-C0kFvIUDZuZTFM&e= >] - Placeholder - New Sentence Detector
>> [CTAKES-381 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D381&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eacLeerI11qVMGHVNCxzcO-GzvC2_mA3pXcpiaoiJIU&e= >] - Improved Location Of Model
>> [CTAKES-385 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D385&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=CKTFvqZbJevxVi36-aVXP0ACLn3UEJSdArOAcEN86I8&e= >] - URI is not hierarchical when attempting to obtain lvg.properties within JAR
>> [CTAKES-386 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D386&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=VQ3I-qmf_SVPsNP4hubSSWVHImtNjhZhCMmWy-zNTvM&e= >] - Remove all .classpath and.project files
>> [CTAKES-387 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D387&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=TDB3-GZTDurRPNqAWE_YyRPlQjdM-6QjZGKzNTcyqrg&e= >] - Upgrade gov.nih.nlm.nls lvg artifact across the codebase
>> [CTAKES-388 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D388&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=mOWKWmDTKkvAzH10vV9ansbFYPKpGWxG0uASseBlqy4&e= >] - URI is not hierarchical when attempting to obtain LookupDesc_Db.xml within JAR
>> [CTAKES-399 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D399&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=9H7TNumGQg17tLnG6pIUhCpLCePTubQNr2s-8GT5i7c&e= >] - Add profile to pom.xml which permits build with JDK1.8 New Feature
>> [CTAKES-314 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D314&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2UPU54d8kNVTSjC0FfpBWKWdSxq_7_0_wBs7FgLONYQ&e= >] - BigTop/Hadoop cTAKES integration
>> [CTAKES-378 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D378&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IuYlnUhxS-jahucK8GzfMCzYmOBbBjMNcqkZsvuSAyk&e= >] - Fast Dictionary should be able to load custom codifications from db
>> [CTAKES-382 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D382&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eq0O15eFRNk_YIsjhvlKCv4yHax4X8JOkITUifh-mys&e= >] - Add ability to easily add extension of UmlsConcept Type to jcas via dictionary lookup Task
>> [CTAKES-74 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D74&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=o6JkmN2KMgyPJYDdsq0upy7S-mbT2LUfM5PGvw0afjI&e= >] - Tokenizer PennTreeBank breaks with certain apostrophes in tokens.
>> [CTAKES-138 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D138&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=FKcIfK3Qjkbb02OjCm0yl6hKHJ3rGgkt3RsFtaumFC4&e= >] - Remove 3rd party jars from our SVN
>> [CTAKES-232 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D232&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WE-LsxWpvhEVtVAi1tdjMeBbEFM1vU22JDmuU8MVc0M&e= >] - change concept type <>On Dec 6, 2016, at 11:20 AM, Jeff Headley <je...@gmail.com> wrote:
>>>
>>> I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
>>>
>>> Jeff
>>>
>>> On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
>>>> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
>>>> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
>>>> In the past, the documentation on the website also shouldn’t hold up a release either.
>>>>
>>>>> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>>>
>>>>> Hi Murali,
>>>>>
>>>>> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>>>>>
>>>>> The primary takeaways from the hackathon were, not surprisingly:
>>>>> 1. Installation of cTAKES is not as straightforward as we believe,
>>>>> and 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
>>>>> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>>>>>
>>>>> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>>>>>
>>>>> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>>>>>
>>>>> Sean
>>>>>
>>>>> -----Original Message-----
>>>>> From: Murali Minnah [mailto:mminnah@gmail.com]
>>>>> Sent: Monday, December 05, 2016 1:26 PM
>>>>> To: dev@ctakes.apache.org
>>>>> Subject: cTAKES - 3.2.3 release
>>>>>
>>>>> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>>>>>
>>>>> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>>>>>
>>>>> Best,
>>>>> Murali
>>>>
>>
>
Re: cTAKES - 3.2.3 release
Posted by Pei Chen <pe...@wiredinformatics.com>.
You’re welcome! I also compiled this same list last time and let several months elapse for any pending commits; feel free to check in any pending changes over the next few days- otherwise, let’s tag this Fri and prepare and push forward?
> On Dec 6, 2016, at 11:52 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Pei,
>
> Thank you for starting step 1: compiling a list of tars and their status.
>
> Sean
>
> -----Original Message-----
> From: Pei Chen [mailto:pei.chen@wiredinformatics.com]
> Sent: Tuesday, December 06, 2016 11:44 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES - 3.2.3 release
>
> I agree that a lot can be done to make cTAKES easier to use and there will always be room for improvement.
> However- I strongly disagree that we should delay releases for new features. We should release early and often. Folks can continue working off trunk; a tag/release does not stop anyone from to continue and work on enhancements.
>
> Considering it’s been almost 2 years since the last release; There are a lot of fixes that should justify a release.
> Sub-task
> [CTAKES-124 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D124&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vg40jDWGurWfAlOtiL-nInyy5wdq_jm13oDOnXHhXCk&e= >] - remove internal UIMA types from coreference Bug
> [CTAKES-76 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D76&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=h76FjI4WWu4LHulli161jAz527vnygd7e6T2DqyiMHg&e= >] - get third party dependencies into Maven Central
> [CTAKES-155 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D155&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Xj41oUWemrUSelkTZmm6UQddCs_LA11lruyU_5zCzR8&e= >] - SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters
> [CTAKES-178 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D178&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=dJVfIpgWukz1wFQ_H92mzzXXGK2-33JC2AedfAGeYSI&e= >] - parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)
> [CTAKES-213 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D213&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=a3DZ4QeENuzJBYd2mOYt75ALUWAGwq3ur8Y-otHbpLI&e= >] - ModifierExtractorAnnotator should produce XxxxModifier subtypes
> [CTAKES-275 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D275&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=kuusawQUbqYw40q_49bpslVhh9eXckc1VWykqcoXPW8&e= >] - some of the older junit tests don't have the right Project name in the run configurations
> [CTAKES-302 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D302&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=QqLaLVr9gwu1uNW4OrMwAGBaHbWQDPTJaiPwzhlIJ20&e= >] - Element type "hibernate-mapping" must be followed by either attribute specifications, ">" or "/>".
> [CTAKES-320 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D320&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Ar5W4F1ziHmni00PqBvX7NAJse3KWaJPjJaofcgShkA&e= >] - Methods used by getDefaultPipeline should be able to load reasonable defaults without expecting external files.
> [CTAKES-341 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D341&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ojjOCjbC-Wv8VLRPSwNfrORf2oKZvyYlf8PIxSuIYEM&e= >] - FractionFSM annotates incorrect span
> [CTAKES-364 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D364&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WmovdFOOKmxjpsxHF_oZj3Ws_P4vOfFsFOWJEgYwtJg&e= >] - Dictionary-Lookup-Fast will fail with URI is not Hierarchical
> [CTAKES-371 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D371&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EZl2YzPYv9kyhP3qtcxJ-z9ex80avSh3fYSALhua958&e= >] - update PTB tokenization logic in fast dictionary module
> [CTAKES-376 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D376&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=D3_dK6LFlkpGvNCcMelF2gUz6n7k3VkEjtP-63ta3xk&e= >] - ctakes-temporal throws NPE if LVG isn't run
> [CTAKES-379 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D379&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=wkOirnhGZRtWZW16Kc2cbGaOHJqkbQ9SRZjqZsWjAGU&e= >] - Placeholder - ISO Time Normalizer (wrapper)
> [CTAKES-389 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=UUvOh4qUdOhQEvfMv_WOhbnsr0xC3LMBqmZzmLLUmds&e= >] - cTAKES dictionary lookup missed word starting string bug
> [CTAKES-401 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D401&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vjr8h_J-Ss2ov1GNAM5c8iYKZmj095EBwH0B6m_5kOs&e= >] - License headers are JavaDoc comments but should be block comments Improvement
> [CTAKES-77 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D77&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ik8KjmPuw3_SmDeuV9J6dkvujHx6fxxvrAOQReFPrAg&e= >] - Update POSTagger Unit Tests
> [CTAKES-78 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D78&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q61CnLNqNUNwLKGPKMIejWQkOURg-4nMiHbDYEBilLM&e= >] - Update Chunker unit tests
> [CTAKES-122 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D122&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EVjs_Uj8_y1Jxan6l5drPalZFw47HHtIjifK925d-C8&e= >] - include LVG with a future version of cTAKES?
> [CTAKES-172 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D172&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=BTS35Jtbc4LDmXSn7jw68znfMhNTjjAlK6BMj7oCwsg&e= >] - relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator
> [CTAKES-295 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D295&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IY0H2klrJ6Y2tr3KR0GxSyoo0WpMKPxufu_aUqsA3o0&e= >] - Use UIMAFit-style configuration annotations
> [CTAKES-328 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D328&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sC9hzQGSRCkNSK0RVW3XB6ikk9eVw2gZuiUNq_1HQCc&e= >] - Clean up XML Annotator Descriptors
> [CTAKES-366 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D366&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=tadQy2cwyIgLuPCccfKNK5CDasCmEitr-77E1DnT1_g&e= >] - Add Cas Consumer that will save pretty human-readable annotations to file
> [CTAKES-367 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D367&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=A3jG_-BC6zblut37AlNN3I9svEJBskygYRT7njtFoaU&e= >] - FileLocator should output $CLASSPATH if file isn't found
> [CTAKES-368 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D368&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2QDfaT_dnp384pq-Xtov7f9H3vp2eqZ7b7WJiK2sutA&e= >] - Allow alternate CUI formats in fast dictionary lookup module
> [CTAKES-373 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D373&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q9UTv9kFrhTt5IPBRrF9frdexLd8OoR4sjFezLfhcN4&e= >] - MaxentParserWrapper can't handle section dividers: "=========="
> [CTAKES-380 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D380&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sW_XkXvYseK_Yzz42LZ15TPOY0uZ-C0kFvIUDZuZTFM&e= >] - Placeholder - New Sentence Detector
> [CTAKES-381 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D381&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eacLeerI11qVMGHVNCxzcO-GzvC2_mA3pXcpiaoiJIU&e= >] - Improved Location Of Model
> [CTAKES-385 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D385&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=CKTFvqZbJevxVi36-aVXP0ACLn3UEJSdArOAcEN86I8&e= >] - URI is not hierarchical when attempting to obtain lvg.properties within JAR
> [CTAKES-386 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D386&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=VQ3I-qmf_SVPsNP4hubSSWVHImtNjhZhCMmWy-zNTvM&e= >] - Remove all .classpath and.project files
> [CTAKES-387 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D387&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=TDB3-GZTDurRPNqAWE_YyRPlQjdM-6QjZGKzNTcyqrg&e= >] - Upgrade gov.nih.nlm.nls lvg artifact across the codebase
> [CTAKES-388 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D388&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=mOWKWmDTKkvAzH10vV9ansbFYPKpGWxG0uASseBlqy4&e= >] - URI is not hierarchical when attempting to obtain LookupDesc_Db.xml within JAR
> [CTAKES-399 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D399&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=9H7TNumGQg17tLnG6pIUhCpLCePTubQNr2s-8GT5i7c&e= >] - Add profile to pom.xml which permits build with JDK1.8 New Feature
> [CTAKES-314 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D314&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2UPU54d8kNVTSjC0FfpBWKWdSxq_7_0_wBs7FgLONYQ&e= >] - BigTop/Hadoop cTAKES integration
> [CTAKES-378 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D378&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IuYlnUhxS-jahucK8GzfMCzYmOBbBjMNcqkZsvuSAyk&e= >] - Fast Dictionary should be able to load custom codifications from db
> [CTAKES-382 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D382&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eq0O15eFRNk_YIsjhvlKCv4yHax4X8JOkITUifh-mys&e= >] - Add ability to easily add extension of UmlsConcept Type to jcas via dictionary lookup Task
> [CTAKES-74 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D74&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=o6JkmN2KMgyPJYDdsq0upy7S-mbT2LUfM5PGvw0afjI&e= >] - Tokenizer PennTreeBank breaks with certain apostrophes in tokens.
> [CTAKES-138 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D138&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=FKcIfK3Qjkbb02OjCm0yl6hKHJ3rGgkt3RsFtaumFC4&e= >] - Remove 3rd party jars from our SVN
> [CTAKES-232 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D232&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WE-LsxWpvhEVtVAi1tdjMeBbEFM1vU22JDmuU8MVc0M&e= >] - change concept type <>On Dec 6, 2016, at 11:20 AM, Jeff Headley <je...@gmail.com> wrote:
>>
>> I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
>>
>> Jeff
>>
>> On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
>>> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
>>> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
>>> In the past, the documentation on the website also shouldn’t hold up a release either.
>>>
>>>> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>>
>>>> Hi Murali,
>>>>
>>>> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>>>>
>>>> The primary takeaways from the hackathon were, not surprisingly:
>>>> 1. Installation of cTAKES is not as straightforward as we believe,
>>>> and 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
>>>> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>>>>
>>>> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>>>>
>>>> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>>>>
>>>> Sean
>>>>
>>>> -----Original Message-----
>>>> From: Murali Minnah [mailto:mminnah@gmail.com]
>>>> Sent: Monday, December 05, 2016 1:26 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: cTAKES - 3.2.3 release
>>>>
>>>> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>>>>
>>>> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>>>>
>>>> Best,
>>>> Murali
>>>
>
RE: cTAKES - 3.2.3 release
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Pei,
Thank you for starting step 1: compiling a list of tars and their status.
Sean
-----Original Message-----
From: Pei Chen [mailto:pei.chen@wiredinformatics.com]
Sent: Tuesday, December 06, 2016 11:44 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES - 3.2.3 release
I agree that a lot can be done to make cTAKES easier to use and there will always be room for improvement.
However- I strongly disagree that we should delay releases for new features. We should release early and often. Folks can continue working off trunk; a tag/release does not stop anyone from to continue and work on enhancements.
Considering it’s been almost 2 years since the last release; There are a lot of fixes that should justify a release.
Sub-task
[CTAKES-124 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D124&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vg40jDWGurWfAlOtiL-nInyy5wdq_jm13oDOnXHhXCk&e= >] - remove internal UIMA types from coreference Bug
[CTAKES-76 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D76&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=h76FjI4WWu4LHulli161jAz527vnygd7e6T2DqyiMHg&e= >] - get third party dependencies into Maven Central
[CTAKES-155 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D155&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Xj41oUWemrUSelkTZmm6UQddCs_LA11lruyU_5zCzR8&e= >] - SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters
[CTAKES-178 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D178&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=dJVfIpgWukz1wFQ_H92mzzXXGK2-33JC2AedfAGeYSI&e= >] - parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)
[CTAKES-213 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D213&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=a3DZ4QeENuzJBYd2mOYt75ALUWAGwq3ur8Y-otHbpLI&e= >] - ModifierExtractorAnnotator should produce XxxxModifier subtypes
[CTAKES-275 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D275&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=kuusawQUbqYw40q_49bpslVhh9eXckc1VWykqcoXPW8&e= >] - some of the older junit tests don't have the right Project name in the run configurations
[CTAKES-302 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D302&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=QqLaLVr9gwu1uNW4OrMwAGBaHbWQDPTJaiPwzhlIJ20&e= >] - Element type "hibernate-mapping" must be followed by either attribute specifications, ">" or "/>".
[CTAKES-320 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D320&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=Ar5W4F1ziHmni00PqBvX7NAJse3KWaJPjJaofcgShkA&e= >] - Methods used by getDefaultPipeline should be able to load reasonable defaults without expecting external files.
[CTAKES-341 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D341&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ojjOCjbC-Wv8VLRPSwNfrORf2oKZvyYlf8PIxSuIYEM&e= >] - FractionFSM annotates incorrect span
[CTAKES-364 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D364&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WmovdFOOKmxjpsxHF_oZj3Ws_P4vOfFsFOWJEgYwtJg&e= >] - Dictionary-Lookup-Fast will fail with URI is not Hierarchical
[CTAKES-371 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D371&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EZl2YzPYv9kyhP3qtcxJ-z9ex80avSh3fYSALhua958&e= >] - update PTB tokenization logic in fast dictionary module
[CTAKES-376 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D376&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=D3_dK6LFlkpGvNCcMelF2gUz6n7k3VkEjtP-63ta3xk&e= >] - ctakes-temporal throws NPE if LVG isn't run
[CTAKES-379 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D379&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=wkOirnhGZRtWZW16Kc2cbGaOHJqkbQ9SRZjqZsWjAGU&e= >] - Placeholder - ISO Time Normalizer (wrapper)
[CTAKES-389 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D389&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=UUvOh4qUdOhQEvfMv_WOhbnsr0xC3LMBqmZzmLLUmds&e= >] - cTAKES dictionary lookup missed word starting string bug
[CTAKES-401 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D401&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=vjr8h_J-Ss2ov1GNAM5c8iYKZmj095EBwH0B6m_5kOs&e= >] - License headers are JavaDoc comments but should be block comments Improvement
[CTAKES-77 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D77&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=ik8KjmPuw3_SmDeuV9J6dkvujHx6fxxvrAOQReFPrAg&e= >] - Update POSTagger Unit Tests
[CTAKES-78 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D78&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q61CnLNqNUNwLKGPKMIejWQkOURg-4nMiHbDYEBilLM&e= >] - Update Chunker unit tests
[CTAKES-122 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D122&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=EVjs_Uj8_y1Jxan6l5drPalZFw47HHtIjifK925d-C8&e= >] - include LVG with a future version of cTAKES?
[CTAKES-172 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D172&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=BTS35Jtbc4LDmXSn7jw68znfMhNTjjAlK6BMj7oCwsg&e= >] - relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator
[CTAKES-295 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D295&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IY0H2klrJ6Y2tr3KR0GxSyoo0WpMKPxufu_aUqsA3o0&e= >] - Use UIMAFit-style configuration annotations
[CTAKES-328 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D328&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sC9hzQGSRCkNSK0RVW3XB6ikk9eVw2gZuiUNq_1HQCc&e= >] - Clean up XML Annotator Descriptors
[CTAKES-366 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D366&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=tadQy2cwyIgLuPCccfKNK5CDasCmEitr-77E1DnT1_g&e= >] - Add Cas Consumer that will save pretty human-readable annotations to file
[CTAKES-367 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D367&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=A3jG_-BC6zblut37AlNN3I9svEJBskygYRT7njtFoaU&e= >] - FileLocator should output $CLASSPATH if file isn't found
[CTAKES-368 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D368&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2QDfaT_dnp384pq-Xtov7f9H3vp2eqZ7b7WJiK2sutA&e= >] - Allow alternate CUI formats in fast dictionary lookup module
[CTAKES-373 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D373&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=q9UTv9kFrhTt5IPBRrF9frdexLd8OoR4sjFezLfhcN4&e= >] - MaxentParserWrapper can't handle section dividers: "=========="
[CTAKES-380 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D380&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=sW_XkXvYseK_Yzz42LZ15TPOY0uZ-C0kFvIUDZuZTFM&e= >] - Placeholder - New Sentence Detector
[CTAKES-381 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D381&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eacLeerI11qVMGHVNCxzcO-GzvC2_mA3pXcpiaoiJIU&e= >] - Improved Location Of Model
[CTAKES-385 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D385&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=CKTFvqZbJevxVi36-aVXP0ACLn3UEJSdArOAcEN86I8&e= >] - URI is not hierarchical when attempting to obtain lvg.properties within JAR
[CTAKES-386 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D386&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=VQ3I-qmf_SVPsNP4hubSSWVHImtNjhZhCMmWy-zNTvM&e= >] - Remove all .classpath and.project files
[CTAKES-387 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D387&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=TDB3-GZTDurRPNqAWE_YyRPlQjdM-6QjZGKzNTcyqrg&e= >] - Upgrade gov.nih.nlm.nls lvg artifact across the codebase
[CTAKES-388 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D388&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=mOWKWmDTKkvAzH10vV9ansbFYPKpGWxG0uASseBlqy4&e= >] - URI is not hierarchical when attempting to obtain LookupDesc_Db.xml within JAR
[CTAKES-399 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D399&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=9H7TNumGQg17tLnG6pIUhCpLCePTubQNr2s-8GT5i7c&e= >] - Add profile to pom.xml which permits build with JDK1.8 New Feature
[CTAKES-314 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D314&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=2UPU54d8kNVTSjC0FfpBWKWdSxq_7_0_wBs7FgLONYQ&e= >] - BigTop/Hadoop cTAKES integration
[CTAKES-378 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D378&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=IuYlnUhxS-jahucK8GzfMCzYmOBbBjMNcqkZsvuSAyk&e= >] - Fast Dictionary should be able to load custom codifications from db
[CTAKES-382 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D382&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=eq0O15eFRNk_YIsjhvlKCv4yHax4X8JOkITUifh-mys&e= >] - Add ability to easily add extension of UmlsConcept Type to jcas via dictionary lookup Task
[CTAKES-74 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D74&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=o6JkmN2KMgyPJYDdsq0upy7S-mbT2LUfM5PGvw0afjI&e= >] - Tokenizer PennTreeBank breaks with certain apostrophes in tokens.
[CTAKES-138 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D138&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=FKcIfK3Qjkbb02OjCm0yl6hKHJ3rGgkt3RsFtaumFC4&e= >] - Remove 3rd party jars from our SVN
[CTAKES-232 <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D232&d=DgIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WE-LsxWpvhEVtVAi1tdjMeBbEFM1vU22JDmuU8MVc0M&e= >] - change concept type <>On Dec 6, 2016, at 11:20 AM, Jeff Headley <je...@gmail.com> wrote:
>
> I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
>
> Jeff
>
> On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
>> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
>> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
>> In the past, the documentation on the website also shouldn’t hold up a release either.
>>
>>> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>
>>> Hi Murali,
>>>
>>> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>>>
>>> The primary takeaways from the hackathon were, not surprisingly:
>>> 1. Installation of cTAKES is not as straightforward as we believe,
>>> and 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
>>> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>>>
>>> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>>>
>>> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>>>
>>> Sean
>>>
>>> -----Original Message-----
>>> From: Murali Minnah [mailto:mminnah@gmail.com]
>>> Sent: Monday, December 05, 2016 1:26 PM
>>> To: dev@ctakes.apache.org
>>> Subject: cTAKES - 3.2.3 release
>>>
>>> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>>>
>>> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>>>
>>> Best,
>>> Murali
>>
Re: cTAKES - 3.2.3 release
Posted by Pei Chen <pe...@wiredinformatics.com>.
I agree that a lot can be done to make cTAKES easier to use and there will always be room for improvement.
However- I strongly disagree that we should delay releases for new features. We should release early and often. Folks can continue working off trunk; a tag/release does not stop anyone from to continue and work on enhancements.
Considering it’s been almost 2 years since the last release; There are a lot of fixes that should justify a release.
Sub-task
[CTAKES-124 <https://issues.apache.org/jira/browse/CTAKES-124>] - remove internal UIMA types from coreference
Bug
[CTAKES-76 <https://issues.apache.org/jira/browse/CTAKES-76>] - get third party dependencies into Maven Central
[CTAKES-155 <https://issues.apache.org/jira/browse/CTAKES-155>] - SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters
[CTAKES-178 <https://issues.apache.org/jira/browse/CTAKES-178>] - parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)
[CTAKES-213 <https://issues.apache.org/jira/browse/CTAKES-213>] - ModifierExtractorAnnotator should produce XxxxModifier subtypes
[CTAKES-275 <https://issues.apache.org/jira/browse/CTAKES-275>] - some of the older junit tests don't have the right Project name in the run configurations
[CTAKES-302 <https://issues.apache.org/jira/browse/CTAKES-302>] - Element type "hibernate-mapping" must be followed by either attribute specifications, ">" or "/>".
[CTAKES-320 <https://issues.apache.org/jira/browse/CTAKES-320>] - Methods used by getDefaultPipeline should be able to load reasonable defaults without expecting external files.
[CTAKES-341 <https://issues.apache.org/jira/browse/CTAKES-341>] - FractionFSM annotates incorrect span
[CTAKES-364 <https://issues.apache.org/jira/browse/CTAKES-364>] - Dictionary-Lookup-Fast will fail with URI is not Hierarchical
[CTAKES-371 <https://issues.apache.org/jira/browse/CTAKES-371>] - update PTB tokenization logic in fast dictionary module
[CTAKES-376 <https://issues.apache.org/jira/browse/CTAKES-376>] - ctakes-temporal throws NPE if LVG isn't run
[CTAKES-379 <https://issues.apache.org/jira/browse/CTAKES-379>] - Placeholder - ISO Time Normalizer (wrapper)
[CTAKES-389 <https://issues.apache.org/jira/browse/CTAKES-389>] - cTAKES dictionary lookup missed word starting string bug
[CTAKES-401 <https://issues.apache.org/jira/browse/CTAKES-401>] - License headers are JavaDoc comments but should be block comments
Improvement
[CTAKES-77 <https://issues.apache.org/jira/browse/CTAKES-77>] - Update POSTagger Unit Tests
[CTAKES-78 <https://issues.apache.org/jira/browse/CTAKES-78>] - Update Chunker unit tests
[CTAKES-122 <https://issues.apache.org/jira/browse/CTAKES-122>] - include LVG with a future version of cTAKES?
[CTAKES-172 <https://issues.apache.org/jira/browse/CTAKES-172>] - relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator
[CTAKES-295 <https://issues.apache.org/jira/browse/CTAKES-295>] - Use UIMAFit-style configuration annotations
[CTAKES-328 <https://issues.apache.org/jira/browse/CTAKES-328>] - Clean up XML Annotator Descriptors
[CTAKES-366 <https://issues.apache.org/jira/browse/CTAKES-366>] - Add Cas Consumer that will save pretty human-readable annotations to file
[CTAKES-367 <https://issues.apache.org/jira/browse/CTAKES-367>] - FileLocator should output $CLASSPATH if file isn't found
[CTAKES-368 <https://issues.apache.org/jira/browse/CTAKES-368>] - Allow alternate CUI formats in fast dictionary lookup module
[CTAKES-373 <https://issues.apache.org/jira/browse/CTAKES-373>] - MaxentParserWrapper can't handle section dividers: "=========="
[CTAKES-380 <https://issues.apache.org/jira/browse/CTAKES-380>] - Placeholder - New Sentence Detector
[CTAKES-381 <https://issues.apache.org/jira/browse/CTAKES-381>] - Improved Location Of Model
[CTAKES-385 <https://issues.apache.org/jira/browse/CTAKES-385>] - URI is not hierarchical when attempting to obtain lvg.properties within JAR
[CTAKES-386 <https://issues.apache.org/jira/browse/CTAKES-386>] - Remove all .classpath and.project files
[CTAKES-387 <https://issues.apache.org/jira/browse/CTAKES-387>] - Upgrade gov.nih.nlm.nls lvg artifact across the codebase
[CTAKES-388 <https://issues.apache.org/jira/browse/CTAKES-388>] - URI is not hierarchical when attempting to obtain LookupDesc_Db.xml within JAR
[CTAKES-399 <https://issues.apache.org/jira/browse/CTAKES-399>] - Add profile to pom.xml which permits build with JDK1.8
New Feature
[CTAKES-314 <https://issues.apache.org/jira/browse/CTAKES-314>] - BigTop/Hadoop cTAKES integration
[CTAKES-378 <https://issues.apache.org/jira/browse/CTAKES-378>] - Fast Dictionary should be able to load custom codifications from db
[CTAKES-382 <https://issues.apache.org/jira/browse/CTAKES-382>] - Add ability to easily add extension of UmlsConcept Type to jcas via dictionary lookup
Task
[CTAKES-74 <https://issues.apache.org/jira/browse/CTAKES-74>] - Tokenizer PennTreeBank breaks with certain apostrophes in tokens.
[CTAKES-138 <https://issues.apache.org/jira/browse/CTAKES-138>] - Remove 3rd party jars from our SVN
[CTAKES-232 <https://issues.apache.org/jira/browse/CTAKES-232>] - change concept type
<>On Dec 6, 2016, at 11:20 AM, Jeff Headley <je...@gmail.com> wrote:
>
> I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
>
> Jeff
>
> On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
>> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
>> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
>> In the past, the documentation on the website also shouldn’t hold up a release either.
>>
>>> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>>>
>>> Hi Murali,
>>>
>>> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>>>
>>> The primary takeaways from the hackathon were, not surprisingly:
>>> 1. Installation of cTAKES is not as straightforward as we believe, and
>>> 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
>>> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>>>
>>> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>>>
>>> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>>>
>>> Sean
>>>
>>> -----Original Message-----
>>> From: Murali Minnah [mailto:mminnah@gmail.com]
>>> Sent: Monday, December 05, 2016 1:26 PM
>>> To: dev@ctakes.apache.org
>>> Subject: cTAKES - 3.2.3 release
>>>
>>> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>>>
>>> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>>>
>>> Best,
>>> Murali
>>
Re: cTAKES - 3.2.3 release
Posted by Jeff Headley <je...@gmail.com>.
I realize I’m not a committer and maybe I shouldn’t express an opinion. Apologies in advance if this is inappropriate. However as someone who has gone through the pain of trying to install, learn, and use ctakes; I strongly agree with Sean. I don’t inject myself into the situation lightly or to “vent”. I have been in software development since 1996 and a lot of that time in medical projects and using various open source frameworks like Spring, Seam, Hibernate, etc. Sean is right.
Jeff
On Dec 6, 2016, 10:00 AM -0500, Pei Chen <pe...@wiredinformatics.com>, wrote:
> Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
> I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
> In the past, the documentation on the website also shouldn’t hold up a release either.
>
> > On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
> >
> > Hi Murali,
> >
> > Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
> >
> > The primary takeaways from the hackathon were, not surprisingly:
> > 1. Installation of cTAKES is not as straightforward as we believe, and
> > 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
> > 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
> >
> > All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
> >
> > In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
> >
> > Sean
> >
> > -----Original Message-----
> > From: Murali Minnah [mailto:mminnah@gmail.com]
> > Sent: Monday, December 05, 2016 1:26 PM
> > To: dev@ctakes.apache.org
> > Subject: cTAKES - 3.2.3 release
> >
> > I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
> >
> > Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
> >
> > Best,
> > Murali
>
Re: cTAKES - 3.2.3 release
Posted by Pei Chen <pe...@wiredinformatics.com>.
Considering the amount of time since the release was created, we should not let any pending Jira’s or features hold up a release.
I suggest just we mark anything that hasn’t been fixed in Jira into the next release and push forward- I’ll volunteer to do that right now.
In the past, the documentation on the website also shouldn’t hold up a release either.
> On Dec 6, 2016, at 9:20 AM, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Murali,
>
> Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
>
> The primary takeaways from the hackathon were, not surprisingly:
> 1. Installation of cTAKES is not as straightforward as we believe, and
> 2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
> 3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
>
> All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
>
> In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
>
> Sean
>
> -----Original Message-----
> From: Murali Minnah [mailto:mminnah@gmail.com]
> Sent: Monday, December 05, 2016 1:26 PM
> To: dev@ctakes.apache.org
> Subject: cTAKES - 3.2.3 release
>
> I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
>
> Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
>
> Best,
> Murali
RE: cTAKES - 3.2.3 release
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Murali,
Before we make an rc, we must go through the list of currently open tars and requests. SOP. A list needs to be compiled of what should be closed as fixed or n/a plus another list of outstanding bugs that need to be dealt with and an estimate of effort. Then we should try to gather volunteers to handle said bugs. Can you take care of compiling those lists? I did this many months ago when rc 3.2.3 came up, and there were items on which no movement was made. If you can find my email that might be one place to start.
The primary takeaways from the hackathon were, not surprisingly:
1. Installation of cTAKES is not as straightforward as we believe, and
2. Getting started with cTAKES is extremely difficult (no good starting point) and scares off a large percentage of people who try.
3. Customization is next to impossible without diving into the code, which is more time consuming than anyone can stand.
All can be handled best by short and simple GUI tools and some "cTAKES for Beginners" documentation. We have some documentation that was used for the Hackathon that needs to be modified a bit, then posted on the main cTAKES website.
In my opinion these items should be worked upon before creating another release, otherwise the release is not as useful as it could be. I have started work on a simple pipeline builder gui that creates simple html or text output. I will check it into trunk soon, but as new functionality community testing will be required before a release.
Sean
-----Original Message-----
From: Murali Minnah [mailto:mminnah@gmail.com]
Sent: Monday, December 05, 2016 1:26 PM
To: dev@ctakes.apache.org
Subject: cTAKES - 3.2.3 release
I wanted to check to see if there are objections to creating a 3.2.3 tag of trunk now to prepare for a 3.2.3-rc1?
Any comments from the participants/organizers on the success/lessons learnt from the "hackathon" that the community can benefit from?
Best,
Murali