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Posted to dev@ctakes.apache.org by James Masanz <ma...@gmail.com> on 2017/10/03 21:56:12 UTC
building cTAKES (discussion transferred from CTAKES-445
A question was asked within JIRA issue CTAKES-445
<https://issues.apache.org/jira/browse/CTAKES-445> about building cTAKES
that is more general than the topic of CTAKES-445, so I'm transferring that
to this mailing list. It started with the following question
how someone is able to provide complete Apache cTakes 4.0 binaries @
http://archive.apache.org/dist/ctakes/ctakes-4.0.0/apache-ctakes-4.0.0-bin.tar.gz
while
we struggle to build it from official Apache repository because of issues
like this one [CTAKES-445 <https://issues.apache.org/jira/browse/CTAKES-445>
]
If you are trying to build a binary of cTAKES, I suggest you follow
instructions from the cTAKES 4.0 Developer Install Guide
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide>
to
get a copy of cTAKES from trunk, but when checking out the source, be sure
to specify the revision you are interested in. By checking out from trunk,
you will get pom files that have a SNAPSHOT version.
Then use the command line version of maven to do something like the
following
mvn clean install -DskipTests=true
You should find the binaries have been built somewhere under
ctakes-distribution
-- James
Re: building cTAKES (discussion transferred from CTAKES-445 [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
Alex,
I forgot to add: thanks for all your work on these changes and improvements.
regarding your email Sean,
I think a small non-umls custom dictionary for a pipeline test would be
great.
And test(s) with combined hsql and bsv would also be great. I don't know
they necessarily need to be outside a full pipeline, though that would be a
good start.
And I like the idea of using something like $JENKINS_HOME and/or
$BUILD_ID, if it can be done, to determine whether to run tests using UMLS
credentials if someone wants to look into it or knows how offhand.
On Fri, Oct 6, 2017 at 11:23 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Alex,
>
> I think that it goes against the umls license to have credentials
> available to the public. That might be what you were saying in a previous
> email:
> > Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> > succeed. But having some credentials in the Jenkins job (official)
> > doesn't make much sense.
>
> This might be a dumb question, but is it possible to disable a single test
> in Jenkins depending upon the run environment? Can something like
> $JENKINS_HOME and/or $BUILD_ID be used? If they are in the environment
> then it should be easy to check in a unit test and log a warning instead of
> running the test.
>
> One thing that we can do is use a small non-umls custom dictionary for a
> pipeline test.
>
> One thing that has long been on my plate is smaller hsql, bsv and combined
> component tests. They should be tests outside a full pipeline; just simple
> segment, sentence, pos and dictionary, and a created cas.
>
> What do you think? Anybody else?
>
> Sean
>
> -----Original Message-----
> From: Alexandru Zbarcea [mailto:alexz@apache.org]
> Sent: Friday, October 06, 2017 10:41 AM
> To: Apache cTAKES Dev
> Subject: Re: building cTAKES (discussion transferred from CTAKES-445
> [EXTERNAL]
>
> I started to look for ways to make the build stable. After applying patch
> for CTAKES-334, the only issue remains with:
>
> testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest):
> Initialization of CAS Processor with name "RegressionPipelineAggregateTes
> t"
> failed.
>
> which is caused by:
>
> ERROR UmlsUserApprover - User CHANGE_ME not allowed. It is a placeholder
> reminder.
>
> The first thought was to implement 2 profiles (in pom.xml), one *with*
> UMLS account and one *without*. A successful release would have to pass a
> test execution for both profiles though. That means, in the official
> Jenkins would have to be a reference for the UMLS credentials.
>
> What do you think?
>
> Alex
>
> On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org>
> wrote:
>
> > Hi James,
> >
> > I have been working on stabilizing the build for 4.0.0, and I
> > discovered the following:
> > * CTAKES-445 (commited)
> > * CTAKES-334 (patch provided - NOT committed by the community, but
> > ready,
> > tested)
> > * UMLS credential UTest (work-in-progress)
> >
> > Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> > succeed. But having some credentials in the Jenkins job (official)
> > doesn't make much sense.
> >
> > With all these patches, cTAKES would have a stable build, making it
> > closer to be releasable from official Apache repository.
> >
> > I also started cleaning up some WARNING(s): see CTAKES-463,
> > CTAKES-465, issues that would improve the quality of the binaries.
> >
> > I look forward to your feedback,
> > Alex
> >
> >
> >
> >
> >
> > On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com>
> > wrote:
> >
> >> A question was asked within JIRA issue CTAKES-445
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
> >> rg_jira_browse_CTAKES-2D445&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
> >> MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh
> >> 0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=3Z-jEPHYenjA6JszcDCLhiymi7al8J
> >> 5RcFbZTyy3XVY&e= > about building cTAKES that is more general than
> >> the topic of CTAKES-445, so I'm transferring that to this mailing
> >> list. It started with the following question
> >>
> >> how someone is able to provide complete Apache cTakes 4.0 binaries @
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.apache.or
> >> g_dist_ctakes_ctakes-2D4.0.0_apache-2D&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> >> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
> >> o&m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=oc8UopbX3fwk1z3oFmP
> >> UPyzdTYW5QW35NSfpB2T2rDA&e=
> >> ctakes-4.0.0-bin.tar.gz
> >> while
> >> we struggle to build it from official Apache repository because of
> >> issues like this one [CTAKES-445
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
> >> rg_jir&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
> >> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh0IADeKEvPAs2FfCE5JjPS
> >> wZ32r8Fw3DNV5FM&s=CXhGNBxrs_S7CFBpQMbtQ7ygcylD9lIq1bwElNx9BHA&e= >>
> >> a/browse/CTAKES-445> ]
> >>
> >>
> >> If you are trying to build a binary of cTAKES, I suggest you follow
> >> instructions from the cTAKES 4.0 Developer Install Guide
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> >> g_confluence_display_CTAKES_cTAKES-2B&d=DwIBaQ&c=qS4goWBT7poplM69zy_3
> >> xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
> >> &m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=RchFgtJIDpmC-PAgEW4z
> >> xd0a5hNtt8Yo3US-XtU5tiA&e= >> 4.0+Developer+Install+Guide> to get a
> copy of cTAKES from trunk, but when checking out the source, be sure to
> specify the revision you are interested in. By checking out from trunk, you
> will get pom files that have a SNAPSHOT version.
> >>
> >> Then use the command line version of maven to do something like the
> >> following mvn clean install -DskipTests=true You should find the
> >> binaries have been built somewhere under ctakes-distribution
> >>
> >> -- James
> >>
> >
> >
>
Re: building cTAKES (discussion transferred from CTAKES-445
[EXTERNAL]
Posted by Hadrian Zbarcea <hz...@gmail.com>.
Personally, I would prefer Sean's idea and I think it'd be easy to
implement using org.junit.Assume [1]. The drawback is that one *must*
remember to setup the umls credentials to run the tests during a
release, whereas the maven profiles enforce that. But either is fine.
My $0.02,
Hadrian
[1] http://junit.org/junit4/javadoc/4.12/org/junit/Assume.html
On 10/06/2017 02:47 PM, James Masanz wrote:
> Alex, I like the idea of "*2 profiles (in pom.xml), one *with* UMLS **account
> and one *without**". However, I would have just the one without the
> credentials be part of the Jenkins job and someone would manually run the
> other one as part of the release process (or whenever someone felt it was
> warranted).
>
>
> On Fri, Oct 6, 2017 at 11:23 AM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
>> Hi Alex,
>>
>> I think that it goes against the umls license to have credentials
>> available to the public. That might be what you were saying in a previous
>> email:
>>> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
>>> succeed. But having some credentials in the Jenkins job (official)
>>> doesn't make much sense.
>>
>> This might be a dumb question, but is it possible to disable a single test
>> in Jenkins depending upon the run environment? Can something like
>> $JENKINS_HOME and/or $BUILD_ID be used? If they are in the environment
>> then it should be easy to check in a unit test and log a warning instead of
>> running the test.
>>
>> One thing that we can do is use a small non-umls custom dictionary for a
>> pipeline test.
>>
>> One thing that has long been on my plate is smaller hsql, bsv and combined
>> component tests. They should be tests outside a full pipeline; just simple
>> segment, sentence, pos and dictionary, and a created cas.
>>
>> What do you think? Anybody else?
>>
>> Sean
>>
>> -----Original Message-----
>> From: Alexandru Zbarcea [mailto:alexz@apache.org]
>> Sent: Friday, October 06, 2017 10:41 AM
>> To: Apache cTAKES Dev
>> Subject: Re: building cTAKES (discussion transferred from CTAKES-445
>> [EXTERNAL]
>>
>> I started to look for ways to make the build stable. After applying patch
>> for CTAKES-334, the only issue remains with:
>>
>> testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest):
>> Initialization of CAS Processor with name "RegressionPipelineAggregateTes
>> t"
>> failed.
>>
>> which is caused by:
>>
>> ERROR UmlsUserApprover - User CHANGE_ME not allowed. It is a placeholder
>> reminder.
>>
>> The first thought was to implement 2 profiles (in pom.xml), one *with*
>> UMLS account and one *without*. A successful release would have to pass a
>> test execution for both profiles though. That means, in the official
>> Jenkins would have to be a reference for the UMLS credentials.
>>
>> What do you think?
>>
>> Alex
>>
>> On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org>
>> wrote:
>>
>>> Hi James,
>>>
>>> I have been working on stabilizing the build for 4.0.0, and I
>>> discovered the following:
>>> * CTAKES-445 (commited)
>>> * CTAKES-334 (patch provided - NOT committed by the community, but
>>> ready,
>>> tested)
>>> * UMLS credential UTest (work-in-progress)
>>>
>>> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
>>> succeed. But having some credentials in the Jenkins job (official)
>>> doesn't make much sense.
>>>
>>> With all these patches, cTAKES would have a stable build, making it
>>> closer to be releasable from official Apache repository.
>>>
>>> I also started cleaning up some WARNING(s): see CTAKES-463,
>>> CTAKES-465, issues that would improve the quality of the binaries.
>>>
>>> I look forward to your feedback,
>>> Alex
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com>
>>> wrote:
>>>
>>>> A question was asked within JIRA issue CTAKES-445
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
>>>> rg_jira_browse_CTAKES-2D445&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
>>>> MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh
>>>> 0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=3Z-jEPHYenjA6JszcDCLhiymi7al8J
>>>> 5RcFbZTyy3XVY&e= > about building cTAKES that is more general than
>>>> the topic of CTAKES-445, so I'm transferring that to this mailing
>>>> list. It started with the following question
>>>>
>>>> how someone is able to provide complete Apache cTakes 4.0 binaries @
>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.apache.or
>>>> g_dist_ctakes_ctakes-2D4.0.0_apache-2D&d=DwIBaQ&c=qS4goWBT7poplM69zy_
>>>> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>>>> o&m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=oc8UopbX3fwk1z3oFmP
>>>> UPyzdTYW5QW35NSfpB2T2rDA&e=
>>>> ctakes-4.0.0-bin.tar.gz
>>>> while
>>>> we struggle to build it from official Apache repository because of
>>>> issues like this one [CTAKES-445
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
>>>> rg_jir&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh0IADeKEvPAs2FfCE5JjPS
>>>> wZ32r8Fw3DNV5FM&s=CXhGNBxrs_S7CFBpQMbtQ7ygcylD9lIq1bwElNx9BHA&e= >>
>>>> a/browse/CTAKES-445> ]
>>>>
>>>>
>>>> If you are trying to build a binary of cTAKES, I suggest you follow
>>>> instructions from the cTAKES 4.0 Developer Install Guide
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
>>>> g_confluence_display_CTAKES_cTAKES-2B&d=DwIBaQ&c=qS4goWBT7poplM69zy_3
>>>> xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
>>>> &m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=RchFgtJIDpmC-PAgEW4z
>>>> xd0a5hNtt8Yo3US-XtU5tiA&e= >> 4.0+Developer+Install+Guide> to get a
>> copy of cTAKES from trunk, but when checking out the source, be sure to
>> specify the revision you are interested in. By checking out from trunk, you
>> will get pom files that have a SNAPSHOT version.
>>>>
>>>> Then use the command line version of maven to do something like the
>>>> following mvn clean install -DskipTests=true You should find the
>>>> binaries have been built somewhere under ctakes-distribution
>>>>
>>>> -- James
>>>>
>>>
>>>
>>
>
Re: building cTAKES (discussion transferred from CTAKES-445 [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
Alex, I like the idea of "*2 profiles (in pom.xml), one *with* UMLS **account
and one *without**". However, I would have just the one without the
credentials be part of the Jenkins job and someone would manually run the
other one as part of the release process (or whenever someone felt it was
warranted).
On Fri, Oct 6, 2017 at 11:23 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Alex,
>
> I think that it goes against the umls license to have credentials
> available to the public. That might be what you were saying in a previous
> email:
> > Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> > succeed. But having some credentials in the Jenkins job (official)
> > doesn't make much sense.
>
> This might be a dumb question, but is it possible to disable a single test
> in Jenkins depending upon the run environment? Can something like
> $JENKINS_HOME and/or $BUILD_ID be used? If they are in the environment
> then it should be easy to check in a unit test and log a warning instead of
> running the test.
>
> One thing that we can do is use a small non-umls custom dictionary for a
> pipeline test.
>
> One thing that has long been on my plate is smaller hsql, bsv and combined
> component tests. They should be tests outside a full pipeline; just simple
> segment, sentence, pos and dictionary, and a created cas.
>
> What do you think? Anybody else?
>
> Sean
>
> -----Original Message-----
> From: Alexandru Zbarcea [mailto:alexz@apache.org]
> Sent: Friday, October 06, 2017 10:41 AM
> To: Apache cTAKES Dev
> Subject: Re: building cTAKES (discussion transferred from CTAKES-445
> [EXTERNAL]
>
> I started to look for ways to make the build stable. After applying patch
> for CTAKES-334, the only issue remains with:
>
> testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest):
> Initialization of CAS Processor with name "RegressionPipelineAggregateTes
> t"
> failed.
>
> which is caused by:
>
> ERROR UmlsUserApprover - User CHANGE_ME not allowed. It is a placeholder
> reminder.
>
> The first thought was to implement 2 profiles (in pom.xml), one *with*
> UMLS account and one *without*. A successful release would have to pass a
> test execution for both profiles though. That means, in the official
> Jenkins would have to be a reference for the UMLS credentials.
>
> What do you think?
>
> Alex
>
> On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org>
> wrote:
>
> > Hi James,
> >
> > I have been working on stabilizing the build for 4.0.0, and I
> > discovered the following:
> > * CTAKES-445 (commited)
> > * CTAKES-334 (patch provided - NOT committed by the community, but
> > ready,
> > tested)
> > * UMLS credential UTest (work-in-progress)
> >
> > Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> > succeed. But having some credentials in the Jenkins job (official)
> > doesn't make much sense.
> >
> > With all these patches, cTAKES would have a stable build, making it
> > closer to be releasable from official Apache repository.
> >
> > I also started cleaning up some WARNING(s): see CTAKES-463,
> > CTAKES-465, issues that would improve the quality of the binaries.
> >
> > I look forward to your feedback,
> > Alex
> >
> >
> >
> >
> >
> > On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com>
> > wrote:
> >
> >> A question was asked within JIRA issue CTAKES-445
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
> >> rg_jira_browse_CTAKES-2D445&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
> >> MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh
> >> 0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=3Z-jEPHYenjA6JszcDCLhiymi7al8J
> >> 5RcFbZTyy3XVY&e= > about building cTAKES that is more general than
> >> the topic of CTAKES-445, so I'm transferring that to this mailing
> >> list. It started with the following question
> >>
> >> how someone is able to provide complete Apache cTakes 4.0 binaries @
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.apache.or
> >> g_dist_ctakes_ctakes-2D4.0.0_apache-2D&d=DwIBaQ&c=qS4goWBT7poplM69zy_
> >> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
> >> o&m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=oc8UopbX3fwk1z3oFmP
> >> UPyzdTYW5QW35NSfpB2T2rDA&e=
> >> ctakes-4.0.0-bin.tar.gz
> >> while
> >> we struggle to build it from official Apache repository because of
> >> issues like this one [CTAKES-445
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
> >> rg_jir&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
> >> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh0IADeKEvPAs2FfCE5JjPS
> >> wZ32r8Fw3DNV5FM&s=CXhGNBxrs_S7CFBpQMbtQ7ygcylD9lIq1bwElNx9BHA&e= >>
> >> a/browse/CTAKES-445> ]
> >>
> >>
> >> If you are trying to build a binary of cTAKES, I suggest you follow
> >> instructions from the cTAKES 4.0 Developer Install Guide
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
> >> g_confluence_display_CTAKES_cTAKES-2B&d=DwIBaQ&c=qS4goWBT7poplM69zy_3
> >> xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
> >> &m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=RchFgtJIDpmC-PAgEW4z
> >> xd0a5hNtt8Yo3US-XtU5tiA&e= >> 4.0+Developer+Install+Guide> to get a
> copy of cTAKES from trunk, but when checking out the source, be sure to
> specify the revision you are interested in. By checking out from trunk, you
> will get pom files that have a SNAPSHOT version.
> >>
> >> Then use the command line version of maven to do something like the
> >> following mvn clean install -DskipTests=true You should find the
> >> binaries have been built somewhere under ctakes-distribution
> >>
> >> -- James
> >>
> >
> >
>
RE: building cTAKES (discussion transferred from CTAKES-445
[EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Alex,
I think that it goes against the umls license to have credentials available to the public. That might be what you were saying in a previous email:
> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> succeed. But having some credentials in the Jenkins job (official)
> doesn't make much sense.
This might be a dumb question, but is it possible to disable a single test in Jenkins depending upon the run environment? Can something like $JENKINS_HOME and/or $BUILD_ID be used? If they are in the environment then it should be easy to check in a unit test and log a warning instead of running the test.
One thing that we can do is use a small non-umls custom dictionary for a pipeline test.
One thing that has long been on my plate is smaller hsql, bsv and combined component tests. They should be tests outside a full pipeline; just simple segment, sentence, pos and dictionary, and a created cas.
What do you think? Anybody else?
Sean
-----Original Message-----
From: Alexandru Zbarcea [mailto:alexz@apache.org]
Sent: Friday, October 06, 2017 10:41 AM
To: Apache cTAKES Dev
Subject: Re: building cTAKES (discussion transferred from CTAKES-445 [EXTERNAL]
I started to look for ways to make the build stable. After applying patch for CTAKES-334, the only issue remains with:
testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest):
Initialization of CAS Processor with name "RegressionPipelineAggregateTest"
failed.
which is caused by:
ERROR UmlsUserApprover - User CHANGE_ME not allowed. It is a placeholder
reminder.
The first thought was to implement 2 profiles (in pom.xml), one *with* UMLS account and one *without*. A successful release would have to pass a test execution for both profiles though. That means, in the official Jenkins would have to be a reference for the UMLS credentials.
What do you think?
Alex
On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org> wrote:
> Hi James,
>
> I have been working on stabilizing the build for 4.0.0, and I
> discovered the following:
> * CTAKES-445 (commited)
> * CTAKES-334 (patch provided - NOT committed by the community, but
> ready,
> tested)
> * UMLS credential UTest (work-in-progress)
>
> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> succeed. But having some credentials in the Jenkins job (official)
> doesn't make much sense.
>
> With all these patches, cTAKES would have a stable build, making it
> closer to be releasable from official Apache repository.
>
> I also started cleaning up some WARNING(s): see CTAKES-463,
> CTAKES-465, issues that would improve the quality of the binaries.
>
> I look forward to your feedback,
> Alex
>
>
>
>
>
> On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com>
> wrote:
>
>> A question was asked within JIRA issue CTAKES-445
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
>> rg_jira_browse_CTAKES-2D445&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
>> MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh
>> 0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=3Z-jEPHYenjA6JszcDCLhiymi7al8J
>> 5RcFbZTyy3XVY&e= > about building cTAKES that is more general than
>> the topic of CTAKES-445, so I'm transferring that to this mailing
>> list. It started with the following question
>>
>> how someone is able to provide complete Apache cTakes 4.0 binaries @
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.apache.or
>> g_dist_ctakes_ctakes-2D4.0.0_apache-2D&d=DwIBaQ&c=qS4goWBT7poplM69zy_
>> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTa
>> o&m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=oc8UopbX3fwk1z3oFmP
>> UPyzdTYW5QW35NSfpB2T2rDA&e=
>> ctakes-4.0.0-bin.tar.gz
>> while
>> we struggle to build it from official Apache repository because of
>> issues like this one [CTAKES-445
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.o
>> rg_jir&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bvLXDfh0IADeKEvPAs2FfCE5JjPS
>> wZ32r8Fw3DNV5FM&s=CXhGNBxrs_S7CFBpQMbtQ7ygcylD9lIq1bwElNx9BHA&e= >>
>> a/browse/CTAKES-445> ]
>>
>>
>> If you are trying to build a binary of cTAKES, I suggest you follow
>> instructions from the cTAKES 4.0 Developer Install Guide
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.or
>> g_confluence_display_CTAKES_cTAKES-2B&d=DwIBaQ&c=qS4goWBT7poplM69zy_3
>> xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao
>> &m=bvLXDfh0IADeKEvPAs2FfCE5JjPSwZ32r8Fw3DNV5FM&s=RchFgtJIDpmC-PAgEW4z
>> xd0a5hNtt8Yo3US-XtU5tiA&e= >> 4.0+Developer+Install+Guide> to get a copy of cTAKES from trunk, but when checking out the source, be sure to specify the revision you are interested in. By checking out from trunk, you will get pom files that have a SNAPSHOT version.
>>
>> Then use the command line version of maven to do something like the
>> following mvn clean install -DskipTests=true You should find the
>> binaries have been built somewhere under ctakes-distribution
>>
>> -- James
>>
>
>
Re: building cTAKES (discussion transferred from CTAKES-445
Posted by Alexandru Zbarcea <al...@apache.org>.
I started to look for ways to make the build stable. After applying patch
for CTAKES-334, the only issue remains with:
testCPE(org.apache.ctakes.regression.test.RegressionPipelineTest):
Initialization of CAS Processor with name "RegressionPipelineAggregateTest"
failed.
which is caused by:
ERROR UmlsUserApprover - User CHANGE_ME not allowed. It is a placeholder
reminder.
The first thought was to implement 2 profiles (in pom.xml), one *with* UMLS
account and one *without*. A successful release would have to pass a test
execution for both profiles though. That means, in the official Jenkins
would have to be a reference for the UMLS credentials.
What do you think?
Alex
On Thu, Oct 5, 2017 at 1:47 PM, Alexandru Zbarcea <al...@apache.org> wrote:
> Hi James,
>
> I have been working on stabilizing the build for 4.0.0, and I discovered
> the following:
> * CTAKES-445 (commited)
> * CTAKES-334 (patch provided - NOT committed by the community, but ready,
> tested)
> * UMLS credential UTest (work-in-progress)
>
> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> succeed. But having some credentials in the Jenkins job (official) doesn't
> make much sense.
>
> With all these patches, cTAKES would have a stable build, making it closer
> to be releasable from official Apache repository.
>
> I also started cleaning up some WARNING(s): see CTAKES-463, CTAKES-465,
> issues that would improve the quality of the binaries.
>
> I look forward to your feedback,
> Alex
>
>
>
>
>
> On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com>
> wrote:
>
>> A question was asked within JIRA issue CTAKES-445
>> <https://issues.apache.org/jira/browse/CTAKES-445> about building cTAKES
>> that is more general than the topic of CTAKES-445, so I'm transferring
>> that
>> to this mailing list. It started with the following question
>>
>> how someone is able to provide complete Apache cTakes 4.0 binaries @
>> http://archive.apache.org/dist/ctakes/ctakes-4.0.0/apache-
>> ctakes-4.0.0-bin.tar.gz
>> while
>> we struggle to build it from official Apache repository because of issues
>> like this one [CTAKES-445 <https://issues.apache.org/jir
>> a/browse/CTAKES-445>
>> ]
>>
>>
>> If you are trying to build a binary of cTAKES, I suggest you follow
>> instructions from the cTAKES 4.0 Developer Install Guide
>> <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+
>> 4.0+Developer+Install+Guide>
>> to
>> get a copy of cTAKES from trunk, but when checking out the source, be sure
>> to specify the revision you are interested in. By checking out from trunk,
>> you will get pom files that have a SNAPSHOT version.
>>
>> Then use the command line version of maven to do something like the
>> following
>> mvn clean install -DskipTests=true
>> You should find the binaries have been built somewhere under
>> ctakes-distribution
>>
>> -- James
>>
>
>
Re: building cTAKES (discussion transferred from CTAKES-445
Posted by Alexandru Zbarcea <al...@apache.org>.
Hi James,
I have been working on stabilizing the build for 4.0.0, and I discovered
the following:
* CTAKES-445 (commited)
* CTAKES-334 (patch provided - NOT committed by the community, but ready,
tested)
* UMLS credential UTest (work-in-progress)
Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build succeed.
But having some credentials in the Jenkins job (official) doesn't make much
sense.
With all these patches, cTAKES would have a stable build, making it closer
to be releasable from official Apache repository.
I also started cleaning up some WARNING(s): see CTAKES-463, CTAKES-465,
issues that would improve the quality of the binaries.
I look forward to your feedback,
Alex
On Tue, Oct 3, 2017 at 5:56 PM, James Masanz <ma...@gmail.com> wrote:
> A question was asked within JIRA issue CTAKES-445
> <https://issues.apache.org/jira/browse/CTAKES-445> about building cTAKES
> that is more general than the topic of CTAKES-445, so I'm transferring that
> to this mailing list. It started with the following question
>
> how someone is able to provide complete Apache cTakes 4.0 binaries @
> http://archive.apache.org/dist/ctakes/ctakes-4.0.0/
> apache-ctakes-4.0.0-bin.tar.gz
> while
> we struggle to build it from official Apache repository because of issues
> like this one [CTAKES-445 <https://issues.apache.org/
> jira/browse/CTAKES-445>
> ]
>
>
> If you are trying to build a binary of cTAKES, I suggest you follow
> instructions from the cTAKES 4.0 Developer Install Guide
> <https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+4.0+Developer+Install+Guide>
> to
> get a copy of cTAKES from trunk, but when checking out the source, be sure
> to specify the revision you are interested in. By checking out from trunk,
> you will get pom files that have a SNAPSHOT version.
>
> Then use the command line version of maven to do something like the
> following
> mvn clean install -DskipTests=true
> You should find the binaries have been built somewhere under
> ctakes-distribution
>
> -- James
>