Troubles running locally, FileNotFoundError

[dmytrobabych]

I'm trying to run locally and following the steps described in README, I get this

[21/Jan/2022 11:56:35.780036] id: 7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05
[21/Jan/2022 11:56:36.632464] [7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05] tmVar 2.0 0.8203573226928711 sec
[21/Jan/2022 11:56:38.605409] [7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05] GNormPlus 2.742703914642334 sec
Traceback (most recent call last):
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 105, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 290, in tag_entities
    async_result = loop.run_until_complete(self.async_ner(arguments_for_coroutines))
  File "/Users/dima/opt/anaconda3/envs/bern2/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 417, in async_ner
    result = await asyncio.gather(*coroutines)
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 459, in _ner_wrap
    with open(output_mtner, 'r', encoding='utf-8') as f:
FileNotFoundError: [Errno 2] No such file or directory: './multi_ner/output/7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05.PubTator.json'

The only thing I've changed is removing transferring models to cuda, since I don't have GPU on my current machine.

[mjeensung]

Hi @dmytrobabych

Sorry for the inconvenience.
There seems to be a problem with the Multi-NER server.
Could you please share logs/nohup_multi_ner.out so that we can figure out what's causing the problem?

[dmytrobabych]

Thanks for the hint, I was able to fix the first problem by running script with sudo, it was a permission error. But now I have the same problem with tmVarJava:
FileNotFoundError: [Errno 2] No such file or directory: './resources/tmVarJava/output/0ee760de58f6bcfd46bd12453ebf632af84ef70592d5fb42d7ec5b61.PubTator.PubTator'
nohup_tmvar.out:

Starting tmVar 2.0 Service at 127.0.0.1:18896
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.PostME
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.PostME.ml
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.ME
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.PostME.data
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.data
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.output
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.PostME.output
Deleted a tmp file: tmp/a6d2905e425ecf265bd041fbc8edd80bd49582faa1d4049a16fa38be.PubTator.location
Reading POS tagger model from lib/taggers/english-left3words-distsim.tagger ... done [1.9 sec].
Loading tmVar : Processing Time:2.193sec
Ready
Exception in thread "main" java.lang.IllegalArgumentException: Empty command
	at java.lang.Runtime.exec(Runtime.java:445)
	at java.lang.Runtime.exec(Runtime.java:348)
	at tmVarlib.PostProcessing.toPostMEoutput(PostProcessing.java:1686)
	at kr.ac.korea.dmis.tmVar2.tag_ner(tmVar2.java:278)
	at kr.ac.korea.dmis.tmVar2Server.run(tmVar2Server.java:48)
	at kr.ac.korea.dmis.tmVar2Server.<init>(tmVar2Server.java:29)
	at kr.ac.korea.dmis.tmVar2Server.main(tmVar2Server.java:89)

[mjeensung]

Thanks for sharing.

tmVarJava checks OS type (e.g., Windows or Linux) and make command depending on it. Could you please let us know the OS you are using?

[dmytrobabych]

I'm on MacOS

[mjeensung]

Thank you for letting us know.

Unfortunately, tmVarJava currently does not support MacOS.
We'll get to work on it and get back to you as soon as it's finished.

[dmytrobabych]

Oh, thanks for the update
Regards

[mjeensung]

Hi, @dmytrobabych

Many thanks for your patience.
We've just released BERN2 v1.1 which supports MacOS.
Please follow the steps below to download the source code and resource files.

git clone -b v1.1.0 git@github.com:dmis-lab/BERN2.git
wget https://nlp.dmis.korea.edu/projects/bern2-sung-et-al-2022/resources_v1.1.tar.gz

[heweapon]

Hello, I’m encountering the same issue as described in this thread on my Windows system. Could you advise on how to resolve it?

Additionally, I initially intended to provide log details, but I found that the nohup_multi_ner.out file is empty. Unfortunately, I’m unable to share the log content. Apologies for the inconvenience.

Traceback (most recent call last):
  File "D:\dl_code\BERN2-main\bern2\bern2.py", line 107, in annotate_text
    output = self.tag_entities(text, base_name)
  File "D:\dl_code\BERN2-main\bern2\bern2.py", line 368, in tag_entities
    async_result = loop.run_until_complete(self.async_ner(arguments_for_coroutines))
  File "C:\Users\ustc\anaconda3\envs\bern2\lib\asyncio\base_events.py", line 587, in run_until_complete
    return future.result()
  File "D:\dl_code\BERN2-main\bern2\bern2.py", line 501, in async_ner
    result = await asyncio.gather(*coroutines)
  File "D:\dl_code\BERN2-main\bern2\bern2.py", line 543, in _ner_wrap
    with open(output_mtner, 'r', encoding='utf-8') as f:
FileNotFoundError: [Errno 2] No such file or directory: './multi_ner\\output\\5abc2ad6713f6307fcbaa2bcb6e4b9a3957f2a3bcc08ca77a51e0bf5.PubTator.json'```