FileNotFoundError: [Errno 2] for local server POST

[starmpcc]

Hello. I installed BERN2 in my VM (Ubuntu 18.04 x64, 1 GPU).
It succesfully installed, however, if I run example post script on READAME.md, then the below error occured.
(Server console log)

[23/Mar/2022 06:02:40.831728] [550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d] GNormPlus 0.0001380443572998047 sec
Traceback (most recent call last):
  File "/home/vessl/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/home/vessl/BERN2/bern2/bern2.py", line 358, in tag_entities
    async_result = loop.run_until_complete(self.async_ner(arguments_for_coroutines))
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/home/vessl/BERN2/bern2/bern2.py", line 491, in async_ner
    result = await asyncio.gather(*coroutines)
  File "/home/vessl/BERN2/bern2/bern2.py", line 533, in _ner_wrap
    with open(output_mtner, 'r', encoding='utf-8') as f:
FileNotFoundError: [Errno 2] No such file or directory: './multi_ner/output/550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d.PubTator.json'

[2022-03-23 06:02:41,425] ERROR in app: Exception on /plain [POST]
Traceback (most recent call last):
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 2073, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1518, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1516, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1502, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/home/vessl/BERN2/app/__init__.py", line 85, in plain_api
    return Response(json.dumps({"error_message": result_dict["error_message"]}), status=404, content_type='application/json')
NameError: name 'Response' is not defined
127.0.0.1 - - [23/Mar/2022 06:02:41] "POST /plain HTTP/1.1" 500 -

nohup_multi_ner.out log

MTNER init_t 28.547 sec.
1it [00:00, 185.89it/s]
Prediction: 100%|██████████| 1/1 [00:00<00:00,  2.28it/s]
Traceback (most recent call last):
  File "multi_ner/ner_server.py", line 91, in <module>
    run_server(mt_ner, args)
  File "multi_ner/ner_server.py", line 63, in run_server
    mtner_recognize(model, dict_path, base_name, args)
  File "multi_ner/ner_server.py", line 47, in mtner_recognize
    with open(output_mt_ner, 'w', encoding='utf-8') as f:
PermissionError: [Errno 13] Permission denied: 'multi_ner/output/550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d.PubTator.json'

Thank you.

[mjeensung]

Hi, @starmpcc

Thanks for reaching out to us.

According to the error log, it seems like the output folder needs the write permission.

PermissionError: [Errno 13] Permission denied: 'multi_ner/output/550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d.PubTator.json'

I think there are two options.

1. Executing sudo ls and restarting BERN2.
2. Giving the write permission to the folder by executing chmod 755 multi_ner/output.

I hope this answer helps you.

[starmpcc]

Thank you!
As you expected, some of directories set as root permission so i executed chown -R USERNAME . and chgrp -R USERNAME .
However, the execution was failure with similiar error.

[23/Mar/2022 08:13:19.050116] [55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7] Multi-task NER 0.05367755889892578 sec, #entities: 2
Traceback (most recent call last):
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/shutil.py", line 566, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator' -> './resources/tmVarJava/input/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator.PubTator.Gene'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/vessl/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/home/vessl/BERN2/bern2/bern2.py", line 371, in tag_entities
    shutil.move(output_gnormplus, input_tmvar_gene)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/shutil.py", line 580, in move
    copy_function(src, real_dst)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/shutil.py", line 266, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator'

[2022-03-23 08:13:19,052] ERROR in app: Exception on /plain [POST]
Traceback (most recent call last):
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 2073, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1518, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1516, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1502, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/home/vessl/BERN2/app/__init__.py", line 85, in plain_api
    return Response(json.dumps({"error_message": result_dict["error_message"]}), status=404, content_type='application/json')
NameError: name 'Response' is not defined

Moreover, after failure and kill server, some of directories were changed to root. permission. I already checked all files and directories had user permission before execusion.
More precisely, the owner of multi_ner/output was changed from user to root.

(bern2) vessl@workspace-5fhfe79px43n-0:~/BERN2$ chown -R vessl .
chown: changing ownership of './resources/GNormPlusJava/input/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator': Operation not permitted
chown: changing ownership of './resources/tmVarJava/input/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator': Operation not permitted
chown: changing ownership of './multi_ner/output/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator.json': Operation not permitted
chown: changing ownership of './multi_ner/input/55a389534f6fe973b440b0c5bd0821aae7f7d339423b4cc486e1e0d7.PubTator.PubTator': Operation not permitted

I guess sudo in run_bern2.sh might caused the problem. However, delete that keyword didn't make change.

[ixalidamus]

similar error

File "/root/BERN2/app/result_parser.py", line 210, in parse_resultsorg_text = result_dict['text'] KeyError: 'text' [29/Mar/2022 09:28:50] "POST /senddata HTTP/1.1" 500 -

[lengluodefanhua]

similar error...

[mjeensung]

Hi @starmpcc @ixalidamus @lengluodefanhua

First of all, I removed sudo from run_bern2.sh after verifying that BERN2 can run without it.

It's most likely that the external modules (Multi-NER, tmVar, GNormPlus, etc.) are causing the issue. The reasons are various, so we need to check the logs.

The log files are saved in /logs so you can check them to see which module is causing the issue.

If you find anything suspicious in the logs, please share it with me so that I can help you.

[lengluodefanhua]

Hi @starmpcc @ixalidamus @lengluodefanhua

First of all, I removed sudo from run_bern2.sh after verifying that BERN2 can run without it.

It's most likely that the external modules (Multi-NER, tmVar, GNormPlus, etc.) are causing the issue. The reasons are various, so we need to check the logs.

The log files are saved in /logs so you can check them to see which module is causing the issue.

If you find anything suspicious in the logs, please share it with me so that I can help you.

The logs is below:

[Error] : CRF++ is loading fault. Please follow below instruction to re-install CRF++.
Execute "Installation.sh" to re-compile crf_test first.

$ sh Installation.sh

If failed by using Installation.sh, please reinstall CRF++ by below steps:

1. Download CRF++-0.58.tar.gz from https://drive.google.com/folderview?id=0B4y35FiV1wh7fngteFhHQUN2Y1B5eUJBNHZUemJYQV9VWlBUb3JlX0xBdWVZTWtSbVBneU0&usp=drive_web#list

2. Uncompress the file by

   $ tar -zxvf CRF++-0.58.tar.gz

3. Move all files and folders under CRF++-0.58 to the [CRF] folder.

4. Execute below instructions in CRF folder.
   $ ./configure
   $ make
   $ su
   $ make install

I've tried all of the following methods. It still doesn't work.

[mjeensung]

@lengluodefanhua

Thanks for sharing.

After installing CRF++ following the steps, do you still see the same error logs? Did you happen to come across any errors while installing the CRF++ module? Are you using Linux or Windows?

[shi4712shi]

@lengluodefanhua

Thanks for sharing.

After installing CRF++ following the steps, do you still see the same error logs? Did you happen to come across any errors while installing the CRF++ module? Are you using Linux or Windows?

Hi, @mjeensung:
I removed the resources directory and re-installed CRF++. And there is my situation:

After installing CRF++ following the steps, do you still see the same error logs?

Yes, following the steps, the error logs are the same as before.

Did you happen to come across any errors while installing the CRF++ module?

There is no error, except for a warning:
libtool: install: warning: remember to run libtool --finish /usr/local/lib'`.
And it's no help to run this command for this error.

Are you using Linux or Windows?

I am using Linux.

[minjiijnim]

Hi, I am getting the same error- the logs for [nohup_bern2.out] show:

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/mjkim/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/data/mjkim/BERN2/bern2/bern2.py", line 371, in tag_entities
    shutil.move(output_gnormplus, input_tmvar_gene)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 571, in move
    copy_function(src, real_dst)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 257, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/6df3ec056d96a405b8e2f77748f77716f089292e77672c761be974d6.PubTator'

and for [nohup_gnormplus.out] shows:

Starting GNormPlus Service at 127.0.1.1:18895
Loading Gene Dictionary : Processing ... 
Loading Gene Dictionary : Processing Time:9.087sec
Ready
java.io.IOException: Cannot run program "./CRF/crf_test": error=2, No such file or directory
Starting GNormPlus Service at 127.0.1.1:18895
Loading Gene Dictionary : Processing ... 
Loading Gene Dictionary : Processing Time:9.61sec
Ready
[Error] : CRF++ is loading fault. Please follow below instruction to re-install CRF++.
Execute "Installation.sh" to re-compile crf_test first.

	$ sh Installation.sh

If failed by using Installation.sh, please reinstall CRF++ by below steps:

1) Download CRF++-0.58.tar.gz from https://drive.google.com/folderview?id=0B4y35FiV1wh7fngteFhHQUN2Y1B5eUJBNHZUemJYQV9VWlBUb3JlX0xBdWVZTWtSbVBneU0&usp=drive_web#list
2) Uncompress the file by 

	$ tar -zxvf CRF++-0.58.tar.gz

3) Move all files and folders under CRF++-0.58 to the [CRF] folder.

4) Execute below instructions in CRF folder.
	$ ./configure 
	$ make
	$ su
	$ make install

I've tried removing and redownloading the resources file, and also have tried to reinstall CRF++ using the steps listed above. I am on linux, have also downloaded CRF as provided in the Readme file. How can I fix this error?

[mjeensung]

Hi @minjiijnim

Have you tried installing CRF++ following the steps on the readme?

# install CRF (Only for Linux/MacOS)
cd resources/GNormPlusJava/CRF
./configure --prefix="$HOME"
make
make install
cd ../../..

Can you find crf_test in ./resources/GNormPlusJava/CRF?

Other than that, what is the version of your C++ compiler?
According to https://taku910.github.io/crfpp/, C++ compiler (gcc 3.0 or higher) is required to install CRF++.

[minjiijnim]

Hi @minjiijnim

Have you tried installing CRF++ following the steps on the readme?

# install CRF (Only for Linux/MacOS)
cd resources/GNormPlusJava/CRF
./configure --prefix="$HOME"
make
make install
cd ../../..

Can you find crf_test in ./resources/GNormPlusJava/CRF?

Other than that, what is the version of your C++ compiler? According to https://taku910.github.io/crfpp/, C++ compiler (gcc 3.0 or higher) is required to install CRF++.

Hi! Thanks for the reply- I just checked the C++ complier and it is 5.4.0
Also, yes I have already installed CRF following the steps on Readme.
I also found 'crf test' in the path you mentioned.

Also, from running the program again, I noticed this:

[Errno 111] Connection refused
[20/Apr/2022 17:03:10.283182] [ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c] tmVar 2.0 0.0004878044128417969 sec
[20/Apr/2022 17:03:10.649087] [ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c] Multi-task NER 0.36307597160339355 sec, #entities: 2
[20/Apr/2022 17:03:11.132458] [ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c] GNormPlus 0.8491368293762207 sec
Traceback (most recent call last):
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 557, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c.PubTator' -> './resources/tmVarJava/input/ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c.PubTator.PubTator.Gene' 

I checked the tmVarJava/input file name and it don't seem to match with the name ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c.PubTator.PubTator.Gene but instead just has ba1482656d834f54ed08e197d6e59c6fbc65897952d38a5af448876c.PubTator (without the .PubTator.Gene at the end)

[mjeensung]

Hi @minjiijnim @lengluodefanhua @shi4712shi @starmpcc @ixalidamus

Greatly thanks for your patience.
I was finally able to reproduce the issue.

This issue is caused by the old crf_test file.
This file should be newly compiled depending on your server environments, which can be done by calling make install.
But, I found that when the file is already existing in the foler, compiling it is ignored.

So, the workaround for this issue is as follows:

1. Remove resources/GNormPlusJava/CRF
2. Download CRF++-0.58.tar.gz from https://drive.google.com/folderview?id=0B4y35FiV1wh7fngteFhHQUN2Y1B5eUJBNHZUemJYQV9VWlBUb3JlX0xBdWVZTWtSbVBneU0&usp=drive_web#list
3. Uncompress the file by
   $ tar -zxvf CRF++-0.58.tar.gz
4. Rename the folder [CRF++-0.58] to [CRF].
5. Execute below instructions in CRF folder.
   $ ./configure --prefix="$HOME"
   $ make
   $ make install

[minjiijnim]

@mjeensung

Thank you so much for the solution- the GNormPlusJava resource error seems to be fixed.
However, now there seems to be another error- this time with tmVarJava :'-)

Here is the error:

[29/Apr/2022 16:09:22.031069] id: 94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90
[Errno 111] Connection refused
[29/Apr/2022 16:09:22.033594] [94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90] tmVar 2.0 0.0004341602325439453 sec
[29/Apr/2022 16:09:22.433258] [94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90] GNormPlus 0.39952659606933594 sec
[29/Apr/2022 16:09:22.434386] [94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90] Multi-task NER 0.398362398147583 sec, #entities: 2
Traceback (most recent call last):
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 557, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: './resources/tmVarJava/output/94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90.PubTator.PubTator' -> './resources/tmVarJava/input/94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90.PubTator.PubTator'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/mjkim/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/data/mjkim/BERN2/bern2/bern2.py", line 372, in tag_entities
    shutil.move(output_tmvar_ner, input_tmvar_norm)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 571, in move
    copy_function(src, real_dst)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 257, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/data/mjkim/anaconda3/envs/bern/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: './resources/tmVarJava/output/94a2292b0aef74e2f32547207dd43d4f8f4ce65aba32f1fa0ab96d90.PubTator.PubTator'

Also, nohup_tmvar.out reads:

Starting tmVar 2.0 Service at 127.0.1.1:18896
Exception in thread "main" java.lang.NoClassDefFoundError: edu/stanford/nlp/tagger/maxent/MaxentTagger
	at kr.ac.korea.dmis.tmVar2.<init>(tmVar2.java:66)
	at kr.ac.korea.dmis.tmVar2Server.<init>(tmVar2Server.java:23)
	at kr.ac.korea.dmis.tmVar2Server.main(tmVar2Server.java:89)
Caused by: java.lang.ClassNotFoundException: edu.stanford.nlp.tagger.maxent.MaxentTagger
	at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
	... 3 more

(I've followed the steps for downloading and executing the new CRF folder as advised for resources/tmVarJava as well, but it doesn't seem to change the error.)

[mjeensung]

@minjiijnim

Thanks for sharing!

Can you check if there is this file resources/tmVarJava/stanford-corenlp-3.5.2.jar?

If you find it, could you compare the md5 checksum of it to mine?

$ md5sum stanford-corenlp-3.5.2.jar
>> c9827171f5badc07f475a66b2768c095 stanford-corenlp-3.5.2.jar