Thanks for the input.
So I am trying to use
the ClinicalPipelineFactory.getTokenProcessingPipeline which includes the
LVG which seems to be having the issue. But you say i can just replace the
LVG part with the DependencyParser in that pipeline? Can you elaborate a
bit on where I can find the DependencyParser?
On Wed, Aug 18, 2021 at 5:56 PM Peter Abramowitsch <pabramowit...@gmail.com>
wrote:
> Hi Benjamin,
>
> If what you're looking for are the lemmas of tokens, just use the
> DependencyParser instead of LVG
> I had another problem with LVG as well, but I think that it might be simply
> that all the needed resources are not being copied into the right place.
> This was done without the lvg
>
> {
> "_type": "ConllDependencyNode",
> "sofa": 1,
> "begin": 3,
> "end": 10,
> "id": 2,
> "form": "decided",
> "lemma": "decide",
> "cpostag": "VBD",
> "postag": "VBD",
> "feats": "_",
> "head": 137,
> "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 run?
> >
> > My second question is: Do you really need to use LVG?
> >
> > Sean
> > ________________________________________
> > From: Benjamin hansen <benjaminkakke...@gmail.com>
> > Sent: Wednesday, August 18, 2021 3:07 AM
> > To: dev@ctakes.apache.org
> > Subject: An exception occured 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.<init> (*File.java:420*)
> >
> > *at* org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load (
> > *LvgCmdApiResourceImpl.java:65*)
> >
> >
> > I found that this issue has already been reported 4 years ago here
> >
> >
> https://urldefense.com/v3/__https://issues.apache.org/jira/browse/CTAKES-445__;!!NZvER7FxgEiBAiR_!9HBmXkq30TUdwnSpuHc8_7iEVkoMAiJ3p_rSTXE5d90TARHEdioOMNukOUaL6eB5CboTRBMsOYI$
> >
> >
> > I am on MacOS which the workaround patched proposed in that thread does
> not
> > fix... And like the last comment in the thread says - the patch likely
> also
> > does not work on linux.
> >
> >
> > This seems to be quite a serious bug since both mac and linux would be
> > serious development and production platforms for ctakes users.
> >
> >
> > Is there no fix for this after 4 years?
> >
>
