Unable to get response

[Wickkey]

I get the following error:

[Errno 2] No such file or directory : './resources/GNormPlusJava/output/2ec5cc999ceefc8f5a83a423fe6db771ab7868adf7fb74598c36ccd.PubTator' -> ./resources/tmVarJava/input/2ec5cc999ceefc8f5a83a423fe6db771ab7868adf7fb74598c36ccd.PubTator.PubTator.Gene

does anyone can help me fix this?

I'm not able to get response when I call the rest api. Could someone please help?

[mjeensung]

Hi @Wickkey

Sorry for the late response. According to your log, it appears that external modules such as tmVar2.0 or GNormPlus are not running properly.

Could you please check if each program is running?

ps auxww | grep ner_server.py
ps auxww | grep GNormPlusServer.main.jar
ps auxww | grep tmVar2Server.main.jar 
ps auxww | grep disease_normalizer_21.jar 
ps auxww | grep gnormplus-normalization_21.jar 
ps auxww | grep server.py

[Crispae]

Hi @mjeensung I am also getting the similar error.

All the process are running fine. Can you please check it. Thanks

[mjeensung]

Hi,

Thanks for your patience.

It seems like the error is occurring due to the path. Could you please check whether the output folder exists?

[xuhaolei]

@mjeensung I encountered the same problem, and the folders all exist.

[xuhaolei]

@mjeensung The file with the suffix ".PubTator.PubTator.Gene" does not exist and appears to be unable to be created properly.

[mjeensung]

Thanks for reporting the issue!

@xuhaolei Could you please share what's in each log file so that I can find the reason for the issue?

• logs/nohup_multi_ner.out
• logs/nohup_gnormplus.out
• logs/nohup_tmvar.out
• logs/nohup_disease_normalize.out
• logs/nohup_gene_normalize.out
• logs/nohup_bern2.out

[xuhaolei]

@mjeensung Thank you for your reply. I temporarily resolved this issue last Sunday, commenting out all lines 373-442 in bern2.py will not cause this issue. The reason for the problem seems to be that this version of the program has not been finished yet, and the file paths on lines 328-341 have only been defined and not created. I have not found relevant functions that can affect these files in the future.

[mjeensung]

@xuhaolei Thanks for sharing the workaround. It will disable the normalization functionality, though.

If you still need the normalization of entities, could you please share some logs? I assume that these three logs are relevant to the issue.

• logs/nohup_gnormplus.out
• logs/nohup_tmvar.out
• logs/nohup_gene_normalize.out

[ChaeWoojin]

Actually, I'm suffering same problem.

The error message looks like below.

when I looked at some log, I could found something erroneous from nohup_multi_ner.out as follows.

Could you help me resolving this issue? Thanks a lot.