t;: "_"
> > > }
> > >
> > > On Wed, Aug 18, 2021 at 7:29 AM Finan, Sean <
> > > sean.fi...@childrens.harvard.edu> wrote:
> > >
> > > > Hi Benjamin,
> > > >
> > > > My first question is: what pipeline a
"_"
> > }
> >
> > On Wed, Aug 18, 2021 at 7:29 AM Finan, Sean <
> > sean.fi...@childrens.harvard.edu> wrote:
> >
> > > Hi Benjamin,
> > >
> > > My first question is: what pipeline are you trying to run?
> &g
;,
>> "pdeprel": "_"
>> }
>>
>> On Wed, Aug 18, 2021 at 7:29 AM Finan, Sean <
>> sean.fi...@childrens.harvard.edu> wrote:
>>
>> > Hi Benjamin,
>> >
>> > My first question is: what pipeline are you tryi
"deprel": "root",
> "pdeprel": "_"
> }
>
> On Wed, Aug 18, 2021 at 7:29 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Benjamin,
> >
> > My first question is: what pipeline are you trying to
> Hi Benjamin,
>
> My first question is: what pipeline are you trying to run?
>
> My second question is: Do you really need to use LVG?
>
> Sean
>
> From: Benjamin hansen
> Sent: Wednesday,
while executing the Java class. URI is not
hierarchical [EXTERNAL]
* External Email - Caution *
While working at a simple pipeline example I got this error:
*java.lang.IllegalArgumentException*: *URI is not hierarchical*
*at* java.io.File. (*File.java:420*)
*at
While working at a simple pipeline example I got this error:
*java.lang.IllegalArgumentException*: *URI is not hierarchical*
*at* java.io.File. (*File.java:420*)
*at* org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load (
*LvgCmdApiResourceImpl.java:65*)
I found that this issue
, I
understand that there may be some push back against a manual download.
Sean
-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Tuesday, May 02, 2017 11:14 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Where I'm at with avoiding "
Where I'm at with avoiding "URI is not hierarchical" caused by ctakes-lvg
when using ctakes as maven dependency (not installing the convenience
binary)
LVG documentation indicates it needs the LVG HSQLDB to not be in a jar, but
something that can be accessed by a java File object.
unless someone
> else beats me to it before then.
>
>
> FYI, to test this workaround, before I did the copy, I was seeing
>
> java.lang.IllegalArgumentException: URI is not hierarchical
>at java.io.File.(File.java:418)
>at org.apache.ctakes.lvg.resourc
Ok thanks, I found the problem and checked in a fix.
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Saturday, April 29, 2017 10:59 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Attached is a snippet of the console messages
On Sat, Apr 29, 2017 at 9:18 AM, Finan
ust copy the
> > lvg.properties file for this workaround, you have to copy the entire
> > subtree, or it will create an empty lvg database.
> >
> >
> > I'll check out the StringIndexOutOfBoundsException on Monday unless
> someone
> > else beats me to it
.
>
>
> I'll check out the StringIndexOutOfBoundsException on Monday unless someone
> else beats me to it before then.
>
>
> FYI, to test this workaround, before I did the copy, I was seeing
>
> java.lang.Illegal
t;I couldn't
> find it here or there or the other place ..." and then thrown a
> FileNotFoundException.
>
>
>
> -Original Message-
> From: James Masanz [mailto:masanz.ja...@gmail.com]
> Sent: Saturday, April 29, 2017 2:00 AM
> To: dev@ctakes.apache.org
&
-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Saturday, April 29, 2017 2:00 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
what revision of trunk are you using? I'm getting an error you weren't seeing
so I'm guessing it's because I c
se.
I'll check out the StringIndexOutOfBoundsException on Monday unless someone
else beats me to it before then.
FYI, to test this workaround, before I did the copy, I was seeing
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.(
nto a subdirectory called ctakes-misc, and I updated my
> local
> > copy of the main pom.xml for ctakes to include ctakes-misc.
> >
> > I am able to reproduce getting URI is not hierarchical just by letting
> > tests run during "mvn clean install":
> >
> >
rom your
> ctakes-misc into a subdirectory called ctakes-misc, and I updated my local
> copy of the main pom.xml for ctakes to include ctakes-misc.
>
> I am able to reproduce getting URI is not hierarchical just by letting
> tests run during "mvn cle
[mailto:masanz.ja...@gmail.com]
Sent: Friday, April 28, 2017 5:31 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
Just to let you know I am taking a look at this. More later, if not today,
then tomorrow. FYI here is where I'm at so far.
I checked out a fresh copy
main pom.xml for ctakes to include ctakes-misc.
I am able to reproduce getting URI is not hierarchical just by letting
tests run during "mvn clean install":
Tests in error:
testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
URI is not hierarchica
x27;t take too much kludge. Flw.
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Friday, April 28, 2017 1:52 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
My goal is just to run the pipelines in ctakes-misc on a remote server. I
irst of all, a huge thank you for taking time to debug this issue. I
>> really appreciate your help.
>>
>> Second, I think my main message somehow got lost in translation
>> (sorry, I should’ve included it for clarity with my recent ema
[mailto:masanz.ja...@gmail.com]
Sent: Friday, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing
lvg.properties
as being within a jar
14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing
lvg.properties as being within a jar
14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
=file:/home/dima/.m2/repository/net/s
t emails). I never had any
> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> error only happens when I run it from command line.
>
> I run it using the following maven command:
>
> mvn exec:java
> -Dexec.mainClass="org.apache.ctakes.pipelines.Um
Eclipse. The “URI is not hierarchical” error
only happens when I run it from command line.
I run it using the following maven command:
mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
-Dexec.args="" -Dctakes.umlsuser= -Dctakes.umlspw=
As I said
sn't doing anything.
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:46 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
I am definitely still seeing the “URI is not hierarchical” issue. Here’s a
piece of informa
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:18 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
As I said in my previous email, the piper approach looks very promising.
However many of us probably still have lots of
I am definitely still seeing the “URI is not hierarchical” issue. Here’s a
piece of information that might help you figure out what the problem is:
It only happens if the pipeline includes dictionary lookup. For instance, this
one fails:
https://github.com/dmitriydligach/ctakes-misc/blob
du]
> Sent: Wednesday, April 26, 2017 12:16 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Hi Sean,
>
>
>
> Thanks again for providing this information — the piper approach looks very
> promising.
>
>
>
> So I gave it a
Hi again Dima,
The piper files are not meant to replace uimafit. Uimafit is great for many
purposes.
As for that annoying old "URI is not hierarchical" bug, a while back I checked
in a fix that worked for me. Since then I cannot duplicate it.
Sean
-Original Message-
Fro
directory and what is your classpath?
Thanks,
Sean
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, April 26, 2017 12:16 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
Thanks again for providing this information — the piper
As I said in my previous email, the piper approach looks very promising.
However many of us probably still have lots of existing uimaFIT pipelines and
it would be nice to be able to run them from command line.
So, are there any plans to finally fix this old “URI is not hierarchical”
problem
n on piper files in the wiki.
>
> https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
>
>
> -----Original Message-
> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> Sent: Friday, April 14, 2017 12:17 PM
> To: cTAKES Developer list
> Subject: URI is not h
Ok, thanks. For your original question:
>it fails with “URI is not hierarchical” when the dictionary lookup is enabled.
> I believe this is an old issue, so are there any plans for fixing it in the
> new release?
I thought that I had already fixed it. So much for my thorough test
the runPiperFile script in the bin/ directory.
>
> I am in the process of writing documentation on piper files in the wiki.
>
> https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
&g
: RE: URI is not hierarchical [SUSPICIOUS]
Hi Dima,
Where did you get that class? I don't have UmlsLookupPipeline or the package
org.apache.ctakes.pipelines.
If you want to run from command-line I highly recommend that you use the
PiperFileRunner class in core.pipeline.
To ru
bject: URI is not hierarchical
Dear cTAKES developers,
I am trying to run a simple pipeline that involves dictionary lookup:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_UmlsLookupPipeline.j
=“org.apache.ctakes.pipelines.UmlsLookupPipeline”
It runs fine if the dictionary lookup related fragmented is commented out, but
it fails with “URI is not hierarchical” when the dictionary lookup is enabled.
I believe this is an old issue, so are there any plans for fixing it in the new
release? In the
On second thought... This might be useful
http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical
On 6/28/16, 9:24 AM, "Abramowitsch, Peter"
wrote:
>Dima
>
>Although I'm not an expert, I don't think Ctakes relies on any Environment
>varia
;d=Cw
>>>>>IGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5
>>>>>Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkern
>>>>>B6S3FhhH1RYXhU7RpzHFREfscxk&e=
>
>>>>>
. It runs fine when in
>>>>> Eclipse, but when I run it from command line:
>>>>>
>>>>> mvn exec:java
>>>>> -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineW
run but then crashes. I am including the error messages
>>>> below. Any clues?
>>>>
>>>> Thank you in advance,
>>>>
>>>> Dima
>>>>
>>>> ava.lang.refl
essages below.
>>> Any clues?
>>>
>>> Thank you in advance,
>>>
>>> Dima
>>>
>>> ava.lang.reflect.InvocationTargetException
>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>> at
>>> sun.reflect.Nativ
earch the mailing list for
> additional discussion on this issue.
>
> Thanks,
> Brandon
>
> -Original Message-
> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> Sent: Tuesday, June 28, 2016 10:45 AM
> To: cTAKES Developer list
> Subject: URI is not hie
orImpl.java:62)
>> at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:497)
>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>&g
ssorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:497)
> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
> at java.lang.Thread.run(Thread.java:745)
>Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
> at java.io.File.(File.java:418
andon
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Tuesday, June 28, 2016 10:45 AM
To: cTAKES Developer list
Subject: URI is not hierarchical
Dear cTAKES developers,
I am looking for a simple cTAKEs pipeline that can be run from command line to
introduce a gro
)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.(File.java:418
peline code along with cTAKES dependencies and some
resources packaged into an uber jar which I am utilizing within my Spark driver
code. When I submit this to the Spark cluster I get a nasty stack trace [0]
with the following being important
* Caused by: java.lang.IllegalArgumentExc
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