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Posted to user@uima.apache.org by Mandy Neumann <ma...@th-koeln.de> on 2019/02/06 10:44:55 UTC
Issues with Ruta workbench (Permission Denied and wrong output view)
Hi all,
I'm just starting to get familiar with UIMA Ruta and the workbench, and
I'm having some strange issues.
I got a project from a co-worker who already prepared some scripts for
me to extend. The project has .html files in the input folder, and he
already provided a Ruta script to convert HTML markup into annotations.
The script is adapted from the Ruta manual:
> ENGINE utils.HtmlAnnotator;
> ENGINE utils.HtmlConverter;
> ENGINE HtmlViewWriter;
> TYPESYSTEM utils.HtmlTypeSystem;
> TYPESYSTEM utils.SourceDocumentInformation;
>
> Document{->CONFIGURE(HtmlAnnotator, "onlyContent"=true),
> EXEC(HtmlAnnotator, {TAG})};
>
> Document { -> CONFIGURE(HtmlConverter, "inputView" = "_InitialView",
> "outputView" = "plain", "expandOffsets"=false,
> "replaceLinebreaks"=true, "skipWhitespacs"=true,
> "linebreakReplacement"=" ", "processAll"=true),
> EXEC(HtmlConverter)};
>
> Document{ -> CONFIGURE(HtmlViewWriter, "inputView" = "plain",
> "outputView" = "_InitialView", "output" = "../converted"),
> EXEC(HtmlViewWriter)};
On my machine and with my settings, when I run this script, my console
get spammed with
org.apache.uima.analysis_engine.AnalysisEngineProcessExceptions caused
by java.io.FileNotFoundException
with the message "../converted (Permission denied)". I checked the
file permissions on this directory which were 775 - I even chmodded to
777 but still the same issue.
In spite of all these exceptions, the output still gets generated,
though. I would be fine with it if there weren't another issue -
although the script should write the annotations into _InitialView, I
need to change the view to "plain" in the editor to get plain text with
HTML annotations. The _InitialView still shows the html markup.
I think both issues are related. Any ideas?
Cheers,
Mandy
System Info: eclipse Oxygen.3a Release (4.7.3a), UIMA Ruta workbench
2.6.1, OS Kubuntu 18.04
Re: Issues with Ruta workbench (Permission Denied and wrong output
view)
Posted by Mandy Neumann <ma...@th-koeln.de>.
Hi Peter,
thanks for your answer. Now I see where my error in applying the script
was. I was already wondering why I need to specify an output location
both in the script and in the run configurations. What I did was to set
both to "converted". Now that I changed that, i.e. use "converted" as
output for the HtmlViewWriter, and set the output folder of the whole
script to "output", I can indeed see the difference you are mentioning.
Everything looks as expected now.
I hope I will make further progress now.
By the way, I would love to hear about doing the HTML conversion in
Java. Maybe this approach would also give me more flexibility on what
kind of html tags to convert to annotations?
Cheers,
Mandy
Am 06.02.19 um 16:42 schrieb Peter Klügl:
> Hi,
>
>
> does the plain vs _InitialView problem occur in the CASes in the output
> folder or in the converted folder?
>
>
> "output" should contain the result of the script processing. The
> _InitialView is set by the launcher, it's static and cannot be changed.
>
> "converted" should contain additional CASes where the plain view is
> copied to the _InitialView, which hasn't been set yet.
>
>
> (Although I think that I have written those rules as an example some
> time ago, I personally prefer to perform the HTML conversion in Java)
>
>
> Best,
>
>
> Peter
>
>
> Am 06.02.2019 um 16:18 schrieb Mandy Neumann:
>> Hi,
>>
>> after some additional digging I found this setting in the workbench
>> preferences where SourceDocumentInformation is used for the output
>> parameter. This seems to have fixed the permission issue, I get no
>> more exceptions.
>>
>> Unfortunately, the problem with plain vs. _InitialView still persists,
>> which is kind of annoying. Any ideas on that? (I'd like to also make
>> sure that this is not causing any further problems in my planned
>> workflow.)
>>
>> Best,
>>
>> Mandy
>>
>> Am 06.02.19 um 15:40 schrieb Marshall Schor:
>>> hi,
>>>
>>> I'm not an expert, but I'm guessing that there still is a permissions
>>> issue,
>>> perhaps on a different file or directory than the one you checked.
>>>
>>> Try having someone else take a look at your stack trace / error
>>> message, and
>>> your file system permissions. A second pair of eyes often is helpful
>>> (I speak
>>> from personal experience).
>>>
>>> Cheers. -Marshall
>>>
>>> On 2/6/2019 5:44 AM, Mandy Neumann wrote:
>>>> Hi all,
>>>>
>>>> I'm just starting to get familiar with UIMA Ruta and the workbench,
>>>> and I'm
>>>> having some strange issues.
>>>>
>>>> I got a project from a co-worker who already prepared some scripts
>>>> for me to
>>>> extend. The project has .html files in the input folder, and he already
>>>> provided a Ruta script to convert HTML markup into annotations. The
>>>> script is
>>>> adapted from the Ruta manual:
>>>>
>>>>> ENGINE utils.HtmlAnnotator;
>>>>> ENGINE utils.HtmlConverter;
>>>>> ENGINE HtmlViewWriter;
>>>>> TYPESYSTEM utils.HtmlTypeSystem;
>>>>> TYPESYSTEM utils.SourceDocumentInformation;
>>>>>
>>>>> Document{->CONFIGURE(HtmlAnnotator, "onlyContent"=true),
>>>>> EXEC(HtmlAnnotator,
>>>>> {TAG})};
>>>>>
>>>>> Document { -> CONFIGURE(HtmlConverter, "inputView" = "_InitialView",
>>>>> "outputView" = "plain", "expandOffsets"=false,
>>>>> "replaceLinebreaks"=true,
>>>>> "skipWhitespacs"=true, "linebreakReplacement"=" ", "processAll"=true),
>>>>> EXEC(HtmlConverter)};
>>>>>
>>>>> Document{ -> CONFIGURE(HtmlViewWriter, "inputView" = "plain",
>>>>> "outputView" = "_InitialView", "output" = "../converted"),
>>>>> EXEC(HtmlViewWriter)};
>>>> On my machine and with my settings, when I run this script, my
>>>> console get
>>>> spammed with
>>>> org.apache.uima.analysis_engine.AnalysisEngineProcessExceptions
>>>> caused by java.io.FileNotFoundException
>>>> with the message "../converted (Permission denied)". I checked the
>>>> file
>>>> permissions on this directory which were 775 - I even chmodded to
>>>> 777 but
>>>> still the same issue.
>>>>
>>>> In spite of all these exceptions, the output still gets generated,
>>>> though. I
>>>> would be fine with it if there weren't another issue - although the
>>>> script
>>>> should write the annotations into _InitialView, I need to change the
>>>> view to
>>>> "plain" in the editor to get plain text with HTML annotations. The
>>>> _InitialView still shows the html markup.
>>>>
>>>> I think both issues are related. Any ideas?
>>>>
>>>> Cheers,
>>>>
>>>> Mandy
>>>>
>>>>
>>>> System Info: eclipse Oxygen.3a Release (4.7.3a), UIMA Ruta workbench
>>>> 2.6.1, OS
>>>> Kubuntu 18.04
>>>>
>>>>
Re: Issues with Ruta workbench (Permission Denied and wrong output
view)
Posted by Peter Klügl <pe...@averbis.com>.
Hi,
does the plain vs _InitialView problem occur in the CASes in the output
folder or in the converted folder?
"output" should contain the result of the script processing. The
_InitialView is set by the launcher, it's static and cannot be changed.
"converted" should contain additional CASes where the plain view is
copied to the _InitialView, which hasn't been set yet.
(Although I think that I have written those rules as an example some
time ago, I personally prefer to perform the HTML conversion in Java)
Best,
Peter
Am 06.02.2019 um 16:18 schrieb Mandy Neumann:
> Hi,
>
> after some additional digging I found this setting in the workbench
> preferences where SourceDocumentInformation is used for the output
> parameter. This seems to have fixed the permission issue, I get no
> more exceptions.
>
> Unfortunately, the problem with plain vs. _InitialView still persists,
> which is kind of annoying. Any ideas on that? (I'd like to also make
> sure that this is not causing any further problems in my planned
> workflow.)
>
> Best,
>
> Mandy
>
> Am 06.02.19 um 15:40 schrieb Marshall Schor:
>> hi,
>>
>> I'm not an expert, but I'm guessing that there still is a permissions
>> issue,
>> perhaps on a different file or directory than the one you checked.
>>
>> Try having someone else take a look at your stack trace / error
>> message, and
>> your file system permissions. A second pair of eyes often is helpful
>> (I speak
>> from personal experience).
>>
>> Cheers. -Marshall
>>
>> On 2/6/2019 5:44 AM, Mandy Neumann wrote:
>>> Hi all,
>>>
>>> I'm just starting to get familiar with UIMA Ruta and the workbench,
>>> and I'm
>>> having some strange issues.
>>>
>>> I got a project from a co-worker who already prepared some scripts
>>> for me to
>>> extend. The project has .html files in the input folder, and he already
>>> provided a Ruta script to convert HTML markup into annotations. The
>>> script is
>>> adapted from the Ruta manual:
>>>
>>>> ENGINE utils.HtmlAnnotator;
>>>> ENGINE utils.HtmlConverter;
>>>> ENGINE HtmlViewWriter;
>>>> TYPESYSTEM utils.HtmlTypeSystem;
>>>> TYPESYSTEM utils.SourceDocumentInformation;
>>>>
>>>> Document{->CONFIGURE(HtmlAnnotator, "onlyContent"=true),
>>>> EXEC(HtmlAnnotator,
>>>> {TAG})};
>>>>
>>>> Document { -> CONFIGURE(HtmlConverter, "inputView" = "_InitialView",
>>>> "outputView" = "plain", "expandOffsets"=false,
>>>> "replaceLinebreaks"=true,
>>>> "skipWhitespacs"=true, "linebreakReplacement"=" ", "processAll"=true),
>>>> EXEC(HtmlConverter)};
>>>>
>>>> Document{ -> CONFIGURE(HtmlViewWriter, "inputView" = "plain",
>>>> "outputView" = "_InitialView", "output" = "../converted"),
>>>> EXEC(HtmlViewWriter)};
>>> On my machine and with my settings, when I run this script, my
>>> console get
>>> spammed with
>>> org.apache.uima.analysis_engine.AnalysisEngineProcessExceptions
>>> caused by java.io.FileNotFoundException
>>> with the message "../converted (Permission denied)". I checked the
>>> file
>>> permissions on this directory which were 775 - I even chmodded to
>>> 777 but
>>> still the same issue.
>>>
>>> In spite of all these exceptions, the output still gets generated,
>>> though. I
>>> would be fine with it if there weren't another issue - although the
>>> script
>>> should write the annotations into _InitialView, I need to change the
>>> view to
>>> "plain" in the editor to get plain text with HTML annotations. The
>>> _InitialView still shows the html markup.
>>>
>>> I think both issues are related. Any ideas?
>>>
>>> Cheers,
>>>
>>> Mandy
>>>
>>>
>>> System Info: eclipse Oxygen.3a Release (4.7.3a), UIMA Ruta workbench
>>> 2.6.1, OS
>>> Kubuntu 18.04
>>>
>>>
--
Dr. Peter Klügl
R&D Text Mining/Machine Learning
Averbis GmbH
Tennenbacher Str. 11
79106 Freiburg
Germany
Fon: +49 761 708 394 0
Fax: +49 761 708 394 10
Email: peter.kluegl@averbis.com
Web: https://averbis.com
Headquarters: Freiburg im Breisgau
Register Court: Amtsgericht Freiburg im Breisgau, HRB 701080
Managing Directors: Dr. med. Philipp Daumke, Dr. Kornél Markó
Re: Issues with Ruta workbench (Permission Denied and wrong output
view)
Posted by Mandy Neumann <ma...@th-koeln.de>.
Hi,
after some additional digging I found this setting in the workbench
preferences where SourceDocumentInformation is used for the output
parameter. This seems to have fixed the permission issue, I get no more
exceptions.
Unfortunately, the problem with plain vs. _InitialView still persists,
which is kind of annoying. Any ideas on that? (I'd like to also make
sure that this is not causing any further problems in my planned workflow.)
Best,
Mandy
Am 06.02.19 um 15:40 schrieb Marshall Schor:
> hi,
>
> I'm not an expert, but I'm guessing that there still is a permissions issue,
> perhaps on a different file or directory than the one you checked.
>
> Try having someone else take a look at your stack trace / error message, and
> your file system permissions. A second pair of eyes often is helpful (I speak
> from personal experience).
>
> Cheers. -Marshall
>
> On 2/6/2019 5:44 AM, Mandy Neumann wrote:
>> Hi all,
>>
>> I'm just starting to get familiar with UIMA Ruta and the workbench, and I'm
>> having some strange issues.
>>
>> I got a project from a co-worker who already prepared some scripts for me to
>> extend. The project has .html files in the input folder, and he already
>> provided a Ruta script to convert HTML markup into annotations. The script is
>> adapted from the Ruta manual:
>>
>>> ENGINE utils.HtmlAnnotator;
>>> ENGINE utils.HtmlConverter;
>>> ENGINE HtmlViewWriter;
>>> TYPESYSTEM utils.HtmlTypeSystem;
>>> TYPESYSTEM utils.SourceDocumentInformation;
>>>
>>> Document{->CONFIGURE(HtmlAnnotator, "onlyContent"=true), EXEC(HtmlAnnotator,
>>> {TAG})};
>>>
>>> Document { -> CONFIGURE(HtmlConverter, "inputView" = "_InitialView",
>>> "outputView" = "plain", "expandOffsets"=false, "replaceLinebreaks"=true,
>>> "skipWhitespacs"=true, "linebreakReplacement"=" ", "processAll"=true),
>>> EXEC(HtmlConverter)};
>>>
>>> Document{ -> CONFIGURE(HtmlViewWriter, "inputView" = "plain",
>>> "outputView" = "_InitialView", "output" = "../converted"),
>>> EXEC(HtmlViewWriter)};
>> On my machine and with my settings, when I run this script, my console get
>> spammed with org.apache.uima.analysis_engine.AnalysisEngineProcessExceptions
>> caused by java.io.FileNotFoundException
>> with the message "../converted (Permission denied)". I checked the file
>> permissions on this directory which were 775 - I even chmodded to 777 but
>> still the same issue.
>>
>> In spite of all these exceptions, the output still gets generated, though. I
>> would be fine with it if there weren't another issue - although the script
>> should write the annotations into _InitialView, I need to change the view to
>> "plain" in the editor to get plain text with HTML annotations. The
>> _InitialView still shows the html markup.
>>
>> I think both issues are related. Any ideas?
>>
>> Cheers,
>>
>> Mandy
>>
>>
>> System Info: eclipse Oxygen.3a Release (4.7.3a), UIMA Ruta workbench 2.6.1, OS
>> Kubuntu 18.04
>>
>>
Re: Issues with Ruta workbench (Permission Denied and wrong output
view)
Posted by Marshall Schor <ms...@schor.com>.
hi,
I'm not an expert, but I'm guessing that there still is a permissions issue,
perhaps on a different file or directory than the one you checked.
Try having someone else take a look at your stack trace / error message, and
your file system permissions. A second pair of eyes often is helpful (I speak
from personal experience).
Cheers. -Marshall
On 2/6/2019 5:44 AM, Mandy Neumann wrote:
> Hi all,
>
> I'm just starting to get familiar with UIMA Ruta and the workbench, and I'm
> having some strange issues.
>
> I got a project from a co-worker who already prepared some scripts for me to
> extend. The project has .html files in the input folder, and he already
> provided a Ruta script to convert HTML markup into annotations. The script is
> adapted from the Ruta manual:
>
>> ENGINE utils.HtmlAnnotator;
>> ENGINE utils.HtmlConverter;
>> ENGINE HtmlViewWriter;
>> TYPESYSTEM utils.HtmlTypeSystem;
>> TYPESYSTEM utils.SourceDocumentInformation;
>>
>> Document{->CONFIGURE(HtmlAnnotator, "onlyContent"=true), EXEC(HtmlAnnotator,
>> {TAG})};
>>
>> Document { -> CONFIGURE(HtmlConverter, "inputView" = "_InitialView",
>> "outputView" = "plain", "expandOffsets"=false, "replaceLinebreaks"=true,
>> "skipWhitespacs"=true, "linebreakReplacement"=" ", "processAll"=true),
>> EXEC(HtmlConverter)};
>>
>> Document{ -> CONFIGURE(HtmlViewWriter, "inputView" = "plain",
>> "outputView" = "_InitialView", "output" = "../converted"),
>> EXEC(HtmlViewWriter)};
>
> On my machine and with my settings, when I run this script, my console get
> spammed with org.apache.uima.analysis_engine.AnalysisEngineProcessExceptions
> caused by java.io.FileNotFoundException
> with the message "../converted (Permission denied)". I checked the file
> permissions on this directory which were 775 - I even chmodded to 777 but
> still the same issue.
>
> In spite of all these exceptions, the output still gets generated, though. I
> would be fine with it if there weren't another issue - although the script
> should write the annotations into _InitialView, I need to change the view to
> "plain" in the editor to get plain text with HTML annotations. The
> _InitialView still shows the html markup.
>
> I think both issues are related. Any ideas?
>
> Cheers,
>
> Mandy
>
>
> System Info: eclipse Oxygen.3a Release (4.7.3a), UIMA Ruta workbench 2.6.1, OS
> Kubuntu 18.04
>
>