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OHNLP / Backbone

Provides backbone infrastructure elements for OHNLP toolsets.
Apache License 2.0
14 stars 7 forks source link

A few ques #13

Open mingust opened 2 months ago

mingust commented 2 months ago

Hi

I followed the readme to download the latest version of OHNLP but that points me to Backabone.zip but there is no longer any run_win.bat there. Please let me have some updated instructions.

Also the Covid19 folder under resources (Covid19 rules) had removed...

qqndrew commented 2 months ago

You are probably looking for the MedTagger project. I am unsure what instruction set you are following, there are several floating around out there depending on the project for which the instructions were created.

If you are actually intending to install backbone, please use the install script located at https://github.com/OHNLP/OHNLPTK_SETUP which will download/install everything at the correct location for you.

COVID-19 ruleset has been merged with PASC ruleset for the MedTagger project.

mingust commented 2 months ago

Thanks the info, will give it a go.

From the setup script seems you guy develop on Linux environment.. I should install on Linux also...sometimes it is a pain to adopt another environment that differs from the developers.

From: Andrew @.> Sent: Friday, August 16, 2024 10:29 AM To: OHNLP/Backbone @.> Cc: Ming Lo @.>; Author @.> Subject: Re: [OHNLP/Backbone] A few ques (Issue #13)

You are probably looking for the MedTagger project. I am unsure what instruction set you are following, there are several floating around out there depending on the project for which the instructions were created.

If you are actually intending to install backbone, please use the install script located at https://github.com/OHNLP/OHNLPTK_SETUP which will download/install everything at the correct location for you.

COVID-19 ruleset has been merged with PASC ruleset for the MedTagger project.

— Reply to this email directly, view it on GitHubhttps://github.com/OHNLP/Backbone/issues/13#issuecomment-2292619610, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATOFQALNBKFG6Q7DGA5DBI3ZRVPXVAVCNFSM6AAAAABMPXDEPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGYYTSNRRGA. You are receiving this because you authored the thread.Message ID: @.***>

qqndrew commented 2 months ago

For what it is worth, we do testing against all three major OSes and it works fine

Testing is done against Java 17 although anything Java 11+ should work (recommend 13 at a minimum though due to JDK11 being EOL and the modularization rework)

mingust commented 2 months ago

I think I installed ok.

When I run it (i.e. run_pipeline_local.sh), it list out 5 choices, what shall I do for a quick run (making sure it works).

From: Andrew @.> Sent: Friday, August 16, 2024 11:20 AM To: OHNLP/Backbone @.> Cc: Ming Lo @.>; Author @.> Subject: Re: [OHNLP/Backbone] A few ques (Issue #13)

For what it is worth, we do testing against all three major OSes and it works fine

Testing is done against Java 17 although anything Java 11+ should work (recommend 13 at a minimum though due to JDK11 being EOL and the modularization rework)

— Reply to this email directly, view it on GitHubhttps://github.com/OHNLP/Backbone/issues/13#issuecomment-2292658061, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATOFQAKNKARA2LY5XG3LSKTZRVVYHAVCNFSM6AAAAABMPXDEPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGY2TQMBWGE. You are receiving this because you authored the thread.Message ID: @.***>

qqndrew commented 2 months ago

So it really depends on what you are trying to do. You'll probably want to ./run_backbone_configurator.sh first and edit a pipeline. This repository (Backbone/OHNLPTK) is for setting up ETL pipelines (including NLP) at scale. If you are just wanting to run the NLP engine itself probably just run medtagger directly instead (see my response to your other issue instead)

mingust commented 2 months ago

Hi Andrew,

I tried to run_medtaggerunix_mac.sh ... Now I am working on Linux There is no error message (apart from Java messages) but no icon(or user menu) appears...?

From: Andrew @.> Sent: Friday, August 16, 2024 11:35 AM To: OHNLP/Backbone @.> Cc: Ming Lo @.>; Author @.> Subject: Re: [OHNLP/Backbone] A few ques (Issue #13)

So it really depends on what you are trying to do. You'll probably want to ./run_backbone_configurator.sh first and edit a pipeline. This repository (Backbone/OHNLPTK) is for setting up ETL pipelines (including NLP) at scale. If you are just wanting to run the NLP engine itself probably just run medtagger directly instead (see my response to your other issue instead)

— Reply to this email directly, view it on GitHubhttps://github.com/OHNLP/Backbone/issues/13#issuecomment-2292668400, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATOFQAK3TMU3D6UGRURCG3DZRVXRBAVCNFSM6AAAAABMPXDEPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJSGY3DQNBQGA. You are receiving this because you authored the thread.Message ID: @.***>

qqndrew commented 2 months ago

run_medtagger_unix_mac.sh is for a direct run via CLI using the supplied arguments and does not display a UI.

mingust commented 2 months ago

Hi Andrew,

Ok, I see. Now, I ran maven build successfully, finally ant dist seem outdated (recent ant version make changes).

On windows platform, shall I use an older version of ant (same as yours)? Or any alternatives?

Thanks again.

From: Andrew @.> Sent: Wednesday, August 21, 2024 1:11 AM To: OHNLP/Backbone @.> Cc: Ming Lo @.>; Author @.> Subject: Re: [OHNLP/Backbone] A few ques (Issue #13)

run_medtagger_unix_mac.sh is for a direct run via CLI using the supplied arguments and does not display a UI.

— Reply to this email directly, view it on GitHubhttps://github.com/OHNLP/Backbone/issues/13#issuecomment-2299349943, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATOFQAMIS3OP7EHUQB73F6TZSN2DNAVCNFSM6AAAAABMPXDEPCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJZGM2DSOJUGM. You are receiving this because you authored the thread.Message ID: @.***>

qqndrew commented 2 months ago

Ant should be up to date/is the same version that github actions uses. Is there any reason you are building from source instead of using the release? If you are not making code changes may be easier to just use the release compiled versions.