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Posted to user@uima.apache.org by Bonnie MacKellar <bk...@gmail.com> on 2016/01/17 20:34:27 UTC
examples of using maven with uima, uimaFit, ruta, etc?
Hi,
I had posted earlier asking about best practices for building a project
that uses uimaFit, Ruta, and the Metamap annotator. My current project,
while it works, is inordinately complex and I can't seem to figure out the
right way to structure it. I did get the advice to use Maven. I don't
normally use Maven, but I would if it gave some way to simplify this mess.
However, I can't find any mention of using Maven in the Uima tutorial, so I
am at a loss as to how to start. Are there instructions on the web that I
am just not finding? An example project?
thanks,
Bonnie MacKellar
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Peter Klügl <pe...@averbis.com>.
It's possible, I do it every day :-)
Let's see where the problem is...
Can you post the folder structure and the pom.xml (especially the
ruta-maven-plugin) of your project?
Can you describe the launch configuration of your script?
Is there an errer in your Eclispe installation (views->Error Log)
Best,
Peter
Am 18.01.2016 um 22:46 schrieb Bonnie MacKellar:
> Hi,
>
> Thanks. I had actually found these links 2 days ago. I sat with a friend
> who is very good with Maven, and we tried to figure it all out. I think we
> have gotten it to the point now where I can specify where to find the Ruta
> script file, meaning I can put it in src with the rest of the project. One
> problem though - I can't run the ruta script as a standalone, which makes
> it hard to test and develop. It isn't a Ruta project. But if I create my
> project as a Ruta project, then I get that default folder structure that I
> don't want. I am not sure how to correctly create a project so that it uses
> Maven, lets me put my script under the Src folder, and STILL lets me use
> the Workbench tools. Perhaps that just isn't possible?
>
> thanks,
> Bonnie MacKellar
>
> On Sun, Jan 17, 2016 at 4:34 PM, Peter Klügl <pe...@averbis.com>
> wrote:
>
>> Hi,
>>
>> first of all, sorry that I did not answer your last mail on Friday as I
>> said.
>>
>> There are some example/test projects for UIMA Ruta based on maven:
>>
>> http://home.apache.org/~pkluegl/examples/date-example.zip
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
>>
>> In the last four projects, the version needs to be set since they are
>> integration tests. To test the projects, siply download/ extract or
>> checkout the projects and import them as mexisting maven projects in
>> Eclipse.
>>
>> The documentation of the maven plugin for ruta can be found here:
>>
>>
>> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
>>
>>
>> I will try to provide a more information (also for your last mail)
>> tomorrow.
>>
>> Best,
>>
>> Peter
>>
>>
>>
>> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
>>
>>> Hi,
>>>
>>> I had posted earlier asking about best practices for building a project
>>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
>>> while it works, is inordinately complex and I can't seem to figure out the
>>> right way to structure it. I did get the advice to use Maven. I don't
>>> normally use Maven, but I would if it gave some way to simplify this mess.
>>> However, I can't find any mention of using Maven in the Uima tutorial, so
>>> I
>>> am at a loss as to how to start. Are there instructions on the web that I
>>> am just not finding? An example project?
>>>
>>> thanks,
>>> Bonnie MacKellar
>>>
>>>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Bonnie MacKellar <bk...@gmail.com>.
Hi,
Thanks. I had actually found these links 2 days ago. I sat with a friend
who is very good with Maven, and we tried to figure it all out. I think we
have gotten it to the point now where I can specify where to find the Ruta
script file, meaning I can put it in src with the rest of the project. One
problem though - I can't run the ruta script as a standalone, which makes
it hard to test and develop. It isn't a Ruta project. But if I create my
project as a Ruta project, then I get that default folder structure that I
don't want. I am not sure how to correctly create a project so that it uses
Maven, lets me put my script under the Src folder, and STILL lets me use
the Workbench tools. Perhaps that just isn't possible?
thanks,
Bonnie MacKellar
On Sun, Jan 17, 2016 at 4:34 PM, Peter Klügl <pe...@averbis.com>
wrote:
> Hi,
>
> first of all, sorry that I did not answer your last mail on Friday as I
> said.
>
> There are some example/test projects for UIMA Ruta based on maven:
>
> http://home.apache.org/~pkluegl/examples/date-example.zip
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
>
> In the last four projects, the version needs to be set since they are
> integration tests. To test the projects, siply download/ extract or
> checkout the projects and import them as mexisting maven projects in
> Eclipse.
>
> The documentation of the maven plugin for ruta can be found here:
>
>
> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
>
>
> I will try to provide a more information (also for your last mail)
> tomorrow.
>
> Best,
>
> Peter
>
>
>
> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
>
>> Hi,
>>
>> I had posted earlier asking about best practices for building a project
>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
>> while it works, is inordinately complex and I can't seem to figure out the
>> right way to structure it. I did get the advice to use Maven. I don't
>> normally use Maven, but I would if it gave some way to simplify this mess.
>> However, I can't find any mention of using Maven in the Uima tutorial, so
>> I
>> am at a loss as to how to start. Are there instructions on the web that I
>> am just not finding? An example project?
>>
>> thanks,
>> Bonnie MacKellar
>>
>>
>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Peter Klügl <pe...@averbis.com>.
Yes, exactly. addRutaNature needs to be set to true and the buildpath
needs to point ot the correct folder. Then all should work just fine.
Best,
Peter
Am 18.01.2016 um 22:49 schrieb Bonnie MacKellar:
> Thanks! I am also working with medical text but am bypassing ctakes for
> now. I think Metamap gives us what we need.
>
> In the cTAKES based project, I see this in the POM file
>
> <!-- Add UIMA Ruta nature to .project -->
> <!-- default value: false -->
> <addRutaNature>true</addRutaNature>
>
> <!-- Buildpath of the UIMA Ruta Workbench (IDE) for this
> project -->
> <!-- default value: none -->
> <buildPaths>
> <buildPath>script:src/main/ruta/</buildPath>
> <!--
> <buildPath>descriptor:target/generated-sources/ruta/descriptor/</buildPath>
> -->
> <!--
> <buildPath>resources:src/main/resources/wordlists</buildPath> -->
> </buildPaths>
>
>
> This looks useful. What is the effect of adding RutaNature in the POM file?
> If I add this snippet, will I be able to run Workbench with a script in a
> nonstandard location?
>
> thanks!
> Bonnie MacKellar
>
> On Mon, Jan 18, 2016 at 10:14 AM, Peter Klügl <pe...@averbis.com>
> wrote:
>
>> I missed the default example project:
>>
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/ruta-maven-example
>>
>> There is currently some effort to provide a ruta-based deidentification
>> of clinical notes in cTAKES. It's work in progress and not up-to-date
>> right now, but maybe also an example you can look at:
>>
>> https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid
>>
>> Let me know if these examples do help or if you need something else.
>>
>> Best,
>>
>> Peter
>>
>> Am 17.01.2016 um 22:42 schrieb Peter Klügl:
>>> and sorry for all the typos...
>>>
>>> Am 17.01.2016 um 22:34 schrieb Peter Klügl:
>>>> Hi,
>>>>
>>>> first of all, sorry that I did not answer your last mail on Friday as
>>>> I said.
>>>>
>>>> There are some example/test projects for UIMA Ruta based on maven:
>>>>
>>>> http://home.apache.org/~pkluegl/examples/date-example.zip
>>>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
>>>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
>>>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
>>>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
>>>>
>>>> In the last four projects, the version needs to be set since they are
>>>> integration tests. To test the projects, siply download/ extract or
>>>> checkout the projects and import them as mexisting maven projects in
>>>> Eclipse.
>>>>
>>>> The documentation of the maven plugin for ruta can be found here:
>>>>
>>>>
>> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
>>>>
>>>>
>>>> I will try to provide a more information (also for your last mail)
>>>> tomorrow.
>>>>
>>>> Best,
>>>>
>>>> Peter
>>>>
>>>>
>>>> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
>>>>> Hi,
>>>>>
>>>>> I had posted earlier asking about best practices for building a project
>>>>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
>>>>> while it works, is inordinately complex and I can't seem to figure
>>>>> out the
>>>>> right way to structure it. I did get the advice to use Maven. I don't
>>>>> normally use Maven, but I would if it gave some way to simplify this
>>>>> mess.
>>>>> However, I can't find any mention of using Maven in the Uima
>>>>> tutorial, so I
>>>>> am at a loss as to how to start. Are there instructions on the web
>>>>> that I
>>>>> am just not finding? An example project?
>>>>>
>>>>> thanks,
>>>>> Bonnie MacKellar
>>>>>
>>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Bonnie MacKellar <bk...@gmail.com>.
Thanks! I am also working with medical text but am bypassing ctakes for
now. I think Metamap gives us what we need.
In the cTAKES based project, I see this in the POM file
<!-- Add UIMA Ruta nature to .project -->
<!-- default value: false -->
<addRutaNature>true</addRutaNature>
<!-- Buildpath of the UIMA Ruta Workbench (IDE) for this
project -->
<!-- default value: none -->
<buildPaths>
<buildPath>script:src/main/ruta/</buildPath>
<!--
<buildPath>descriptor:target/generated-sources/ruta/descriptor/</buildPath>
-->
<!--
<buildPath>resources:src/main/resources/wordlists</buildPath> -->
</buildPaths>
This looks useful. What is the effect of adding RutaNature in the POM file?
If I add this snippet, will I be able to run Workbench with a script in a
nonstandard location?
thanks!
Bonnie MacKellar
On Mon, Jan 18, 2016 at 10:14 AM, Peter Klügl <pe...@averbis.com>
wrote:
> I missed the default example project:
>
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/ruta-maven-example
>
> There is currently some effort to provide a ruta-based deidentification
> of clinical notes in cTAKES. It's work in progress and not up-to-date
> right now, but maybe also an example you can look at:
>
> https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid
>
> Let me know if these examples do help or if you need something else.
>
> Best,
>
> Peter
>
> Am 17.01.2016 um 22:42 schrieb Peter Klügl:
> > and sorry for all the typos...
> >
> > Am 17.01.2016 um 22:34 schrieb Peter Klügl:
> >> Hi,
> >>
> >> first of all, sorry that I did not answer your last mail on Friday as
> >> I said.
> >>
> >> There are some example/test projects for UIMA Ruta based on maven:
> >>
> >> http://home.apache.org/~pkluegl/examples/date-example.zip
> >>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
> >>
> >>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
> >>
> >>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
> >>
> >>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
> >>
> >>
> >> In the last four projects, the version needs to be set since they are
> >> integration tests. To test the projects, siply download/ extract or
> >> checkout the projects and import them as mexisting maven projects in
> >> Eclipse.
> >>
> >> The documentation of the maven plugin for ruta can be found here:
> >>
> >>
> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
> >>
> >>
> >>
> >> I will try to provide a more information (also for your last mail)
> >> tomorrow.
> >>
> >> Best,
> >>
> >> Peter
> >>
> >>
> >> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
> >>> Hi,
> >>>
> >>> I had posted earlier asking about best practices for building a project
> >>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
> >>> while it works, is inordinately complex and I can't seem to figure
> >>> out the
> >>> right way to structure it. I did get the advice to use Maven. I don't
> >>> normally use Maven, but I would if it gave some way to simplify this
> >>> mess.
> >>> However, I can't find any mention of using Maven in the Uima
> >>> tutorial, so I
> >>> am at a loss as to how to start. Are there instructions on the web
> >>> that I
> >>> am just not finding? An example project?
> >>>
> >>> thanks,
> >>> Bonnie MacKellar
> >>>
> >>
> >
>
>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Peter Klügl <pe...@averbis.com>.
I missed the default example project:
https://svn.apache.org/repos/asf/uima/ruta/trunk/example-projects/ruta-maven-example
There is currently some effort to provide a ruta-based deidentification
of clinical notes in cTAKES. It's work in progress and not up-to-date
right now, but maybe also an example you can look at:
https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid
Let me know if these examples do help or if you need something else.
Best,
Peter
Am 17.01.2016 um 22:42 schrieb Peter Klügl:
> and sorry for all the typos...
>
> Am 17.01.2016 um 22:34 schrieb Peter Klügl:
>> Hi,
>>
>> first of all, sorry that I did not answer your last mail on Friday as
>> I said.
>>
>> There are some example/test projects for UIMA Ruta based on maven:
>>
>> http://home.apache.org/~pkluegl/examples/date-example.zip
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
>>
>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
>>
>>
>> In the last four projects, the version needs to be set since they are
>> integration tests. To test the projects, siply download/ extract or
>> checkout the projects and import them as mexisting maven projects in
>> Eclipse.
>>
>> The documentation of the maven plugin for ruta can be found here:
>>
>> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
>>
>>
>>
>> I will try to provide a more information (also for your last mail)
>> tomorrow.
>>
>> Best,
>>
>> Peter
>>
>>
>> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
>>> Hi,
>>>
>>> I had posted earlier asking about best practices for building a project
>>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
>>> while it works, is inordinately complex and I can't seem to figure
>>> out the
>>> right way to structure it. I did get the advice to use Maven. I don't
>>> normally use Maven, but I would if it gave some way to simplify this
>>> mess.
>>> However, I can't find any mention of using Maven in the Uima
>>> tutorial, so I
>>> am at a loss as to how to start. Are there instructions on the web
>>> that I
>>> am just not finding? An example project?
>>>
>>> thanks,
>>> Bonnie MacKellar
>>>
>>
>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Peter Klügl <pe...@averbis.com>.
and sorry for all the typos...
Am 17.01.2016 um 22:34 schrieb Peter Klügl:
> Hi,
>
> first of all, sorry that I did not answer your last mail on Friday as
> I said.
>
> There are some example/test projects for UIMA Ruta based on maven:
>
> http://home.apache.org/~pkluegl/examples/date-example.zip
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
>
> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
>
>
> In the last four projects, the version needs to be set since they are
> integration tests. To test the projects, siply download/ extract or
> checkout the projects and import them as mexisting maven projects in
> Eclipse.
>
> The documentation of the maven plugin for ruta can be found here:
>
> https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
>
>
>
> I will try to provide a more information (also for your last mail)
> tomorrow.
>
> Best,
>
> Peter
>
>
> Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
>> Hi,
>>
>> I had posted earlier asking about best practices for building a project
>> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
>> while it works, is inordinately complex and I can't seem to figure
>> out the
>> right way to structure it. I did get the advice to use Maven. I don't
>> normally use Maven, but I would if it gave some way to simplify this
>> mess.
>> However, I can't find any mention of using Maven in the Uima
>> tutorial, so I
>> am at a loss as to how to start. Are there instructions on the web
>> that I
>> am just not finding? An example project?
>>
>> thanks,
>> Bonnie MacKellar
>>
>
Re: examples of using maven with uima, uimaFit, ruta, etc?
Posted by Peter Klügl <pe...@averbis.com>.
Hi,
first of all, sorry that I did not answer your last mail on Friday as I
said.
There are some example/test projects for UIMA Ruta based on maven:
http://home.apache.org/~pkluegl/examples/date-example.zip
https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/conflictingShortName
https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/importByName
https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/multimodule
https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-maven-plugin/src/it/wordlists
In the last four projects, the version needs to be set since they are
integration tests. To test the projects, siply download/ extract or
checkout the projects and import them as mexisting maven projects in
Eclipse.
The documentation of the maven plugin for ruta can be found here:
https://uima.apache.org/d/ruta-current/tools.ruta.book.html#ugr.tools.ruta.maven
I will try to provide a more information (also for your last mail)
tomorrow.
Best,
Peter
Am 17.01.2016 um 20:34 schrieb Bonnie MacKellar:
> Hi,
>
> I had posted earlier asking about best practices for building a project
> that uses uimaFit, Ruta, and the Metamap annotator. My current project,
> while it works, is inordinately complex and I can't seem to figure out the
> right way to structure it. I did get the advice to use Maven. I don't
> normally use Maven, but I would if it gave some way to simplify this mess.
> However, I can't find any mention of using Maven in the Uima tutorial, so I
> am at a loss as to how to start. Are there instructions on the web that I
> am just not finding? An example project?
>
> thanks,
> Bonnie MacKellar
>