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ersilia-os / ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
https://ersilia.io
GNU General Public License v3.0
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✍️ Contribution period: <Zakia Yahya> #616

Closed ZakiaYahya closed 1 year ago

ZakiaYahya commented 1 year ago

Week 1 - Get to know the community

Week 2 - Install and run an ML model

Week 3 - Propose new models

Week 4 - Prepare your final application

ZakiaYahya commented 1 year ago

Bug: Error Occurs while Fetching Model: Ersilia exception class: ModelPackageInstallError. Hello @GemmaTuron I have installed Ersilia successfully on my system(Window 10 pro , WLS ubuntu 18.04), i have verified it by running ersilia --help and ersilia -catalog commands and it run successfully as well. But when i tries to fetch model eos3b5e, it throughs exception error i.e. ModelPackageInstallError. Here's the error

⬇️ Fetching model eos3b5e: molecular-weight 0%| | 0/8 [00:00<?, ?it/s]17:34:58 | INFO | GitHub CLI is not installed. Ersilia can work without it, but we highy recommend that you install this tool. 17:34:58 | DEBUG | Git LFS is installed Updated Git hooks. Git LFS initialized. 17:34:59 | DEBUG | Git LFS has been activated 17:34:59 | DEBUG | Connected to the internet 17:34:59 | DEBUG | Conda is installed 17:34:59 | DEBUG | EOS Home path exists Checking setup: 1.328s 12%|██████████▋ | 1/8 [00:01<00:09, 1.33s/it]17:34:59 | INFO | Starting delete of model eos3b5e 17:34:59 | INFO | Removing folder /home/zakia/eos/dest/eos3b5e 17:35:06 | INFO | Deleting conda environment eos3b5e

Remove all packages in environment /home/zakia/miniconda3/envs/eos3b5e:

17:35:21 | DEBUG | Deleting /home/zakia/eos/isaura/lake/eos3b5e_local.h5 17:35:21 | DEBUG | Deleting /home/zakia/eos/isaura/lake/eos3b5e_public.h5 17:35:21 | INFO | Removing docker images and stopping containers related to eos3b5e 17:35:21 | DEBUG | Model entry eos3b5e was not available in the fetched models registry 17:35:21 | SUCCESS | Model eos3b5e deleted successfully Preparing model: 21.638407945632935s 25%|█████████████████████▎ | 2/8 [00:22<01:19, 13.28s/it]17:35:35 | DEBUG | Cloning from github to /home/zakia/eos/dest/eos3b5e Cloning into 'eos3b5e'... remote: Enumerating objects: 47, done. remote: Counting objects: 100% (47/47), done. remote: Compressing objects: 100% (41/41), done. remote: Total 47 (delta 15), reused 17 (delta 4), pack-reused 0 Unpacking objects: 100% (47/47), done. rm: cannot remove '/tmp/ersilia-7iu95iie': Is a directory 17:35:39 | INFO | 🚀 Model starting... 17:35:39 | DEBUG | {'version': '0.11.0', 'slim': False, 'python': 'py37'} Getting model: 17.42978000640869s 38%|███████████████████████████████▉ | 3/8 [00:40<01:15, 15.17s/it]17:35:39 | DEBUG | Check if model can be run with vanilla (system) code (i.e. dockerfile has no installs) 17:35:39 | DEBUG | Check bentoml and python version 17:35:39 | INFO | BentoML version {'version': '0.11.0', 'slim': False, 'python': 'py37'} 17:35:39 | DEBUG | Custom Ersilia BentoML is used, no need for modifying protobuf version 17:35:39 | DEBUG | Model needs some installs 17:35:39 | DEBUG | Checking if only python/conda install will be sufficient 17:35:39 | DEBUG | Mode: conda 17:35:39 | DEBUG | Trying to remove path: /home/zakia/bentoml/repository/eos3b5e 17:35:39 | DEBUG | ...successfully 17:35:39 | DEBUG | ...but path did not exist! 17:35:39 | DEBUG | Initializing conda packer 17:35:39 | DEBUG | Packing model with Conda 17:35:39 | DEBUG | Writing install commands 17:35:39 | DEBUG | Run commands: ['pip install rdkit-pypi'] 17:35:39 | DEBUG | Writing install commands in /home/zakia/eos/dest/eos3b5e/model_install_commands.sh 17:35:39 | DEBUG | Setting up 17:35:39 | DEBUG | Installs file /home/zakia/eos/dest/eos3b5e/model_install_commands.sh 17:35:39 | DEBUG | Conda environment eos3b5e 17:35:41 | DEBUG | Environment eos3b5e does not exist 17:35:43 | INFO | Cloning base conda environment and adding model dependencies Source: /home/zakia/miniconda3/envs/eosbase-bentoml-0.11.0-py37 Destination: /home/zakia/miniconda3/envs/eos3b5e Packages: 20 Files: 0

Downloading and Extracting Packages

Downloading and Extracting Packages

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate eos3b5e

#

To deactivate an active environment, use

#

$ conda deactivate

17:36:14 | DEBUG | Run commandlines on eos3b5e 17:36:14 | DEBUG | python -m pip --disable-pip-version-check install rdkit-pypi python -m pip --disable-pip-version-check install git+https://github.com/ersilia-os/bentoml-ersilia.git

17:36:16 | DEBUG | Activating base environment 17:36:16 | DEBUG | Current working directory: /home/zakia/eos/dest/eos3b5e 17:36:17 | DEBUG | Running bash /tmp/ersilia-vmrkqgxb/script.sh > /tmp/ersilia-t_hk034w/command_outputs.log 2>&1 17:36:50 | DEBUG | # conda environments: # base /home/zakia/miniconda3 eos3b5e * /home/zakia/miniconda3/envs/eos3b5e eosbase-bentoml-0.11.0-py37 /home/zakia/miniconda3/envs/eosbase-bentoml-0.11.0-py37 ersilia /home/zakia/miniconda3/envs/ersilia

WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f076abedc10>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f076abedb10>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f076abd9c10>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f076a53b350>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f076a53b6d0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ ERROR: Could not find a version that satisfies the requirement rdkit-pypi (from versions: none) ERROR: No matching distribution found for rdkit-pypi Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-wyt6xppq Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-wyt6xppq Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit a0f0040a1198e8f1704f0395e5d9ce328aaecf71 Installing build dependencies: started Installing build dependencies: finished with status 'error' error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [8 lines of output] WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdcce7e03d0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdcce7bfb10>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdcce7e0950>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdcce7e0c90>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdcce7e0fd0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ ERROR: Could not find a version that satisfies the requirement setuptools>=40.8.0 (from versions: none) ERROR: No matching distribution found for setuptools>=40.8.0 WARNING: There was an error checking the latest version of pip. [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

17:36:50 | DEBUG | Error occurred while running: bash /tmp/ersilia-vmrkqgxb/script.sh > /tmp/ersilia-t_hk034w/command_outputs.log 2>&1 17:36:50 | ERROR | Ersilia exception class: ModelPackageInstallError

Detailed error: Error occured while installing package by running "bash /tmp/ersilia-vmrkqgxb/script.sh > /tmp/ersilia-t_hk034w/command_outputs.log 2>&1" command

Hints: Try to manually activate the model environment and install package manually. If this does not work, please report the error at:

🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨

Error message:

Ersilia exception class: ModelPackageInstallError

Detailed error: Error occured while installing package by running "bash /tmp/ersilia-vmrkqgxb/script.sh > /tmp/ersilia-t_hk034w/command_outputs.log 2>&1" command

Hints: Try to manually activate the model environment and install package manually. If this does not work, please report the error at:

If this error message is not helpful, open an issue at:

If you haven't, try to run your command in verbose mode (-v in the CLI)

GemmaTuron commented 1 year ago

Hi @ZakiaYahya !

Welcome to the Outreachy contribution period. It seems you are encountering a network problem, make sure there is no firewall or whether your are using a VPN for example... more pointers here: https://stackoverflow.com/questions/45576930/python-requests-newconnectionerror

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya !

Welcome to the Outreachy contribution period. It seems you are encountering a network problem, make sure there is no firewall or whether your are using a VPN for example... more pointers here: https://stackoverflow.com/questions/45576930/python-requests-newconnectionerror

Thanks @GemmaTuron. I have some connectivity issues in my area rightnow, so i'm waiting for connection stability, once it's established; i'll try it again and will let you know.

Isaakkamau commented 1 year ago

Hello, @ZakiaYahya also check whether you have activated your model environment conda activate <your environment>

ZakiaYahya commented 1 year ago

Hello, @ZakiaYahya also check whether you have activated your model environment conda activate <your environment>

Hi @Isaakkamau yes i did.

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya ! Welcome to the Outreachy contribution period. It seems you are encountering a network problem, make sure there is no firewall or whether your are using a VPN for example... more pointers here: https://stackoverflow.com/questions/45576930/python-requests-newconnectionerror

Thanks @GemmaTuron. I have some connectivity issues in my area rightnow, so i'm waiting for connection stability, once it's established; i'll try it again and will let you know.

Hello @GemmaTuron i have switched to other network, disable firefox as well as proxy but didn't able to fetch the model. Getting same error, i have checked my connection stability by running "ping google.com" on terminal and it works well. Any other solution?

GemmaTuron commented 1 year ago

Hi @ZakiaYahya

As I pointed in the issue #613 , it seems you are not having the same error as Adedeji . Please:

  1. Collect the most recent log file and paste it here
  2. Read through the log file error to identify what is the source of the problem
  3. If it still is a connection error, read this issue: https://github.com/ersilia-os/ersilia/issues/605 and try to use a VPN

Hope this helps!

ZakiaYahya commented 1 year ago

Hello @GemmaTuron. Here's the error log,

_ersilia -v fetch eos3b5e ⬇️ Fetching model eos3b5e: molecular-weight 0%| | 0/8 [00:00<?, ?it/s]17:45:14 | INFO | GitHub CLI is not installed. Ersilia can work without it, but we highy recommend that you install this tool. 17:45:14 | DEBUG | Git LFS is installed Updated Git hooks. Git LFS initialized. 17:45:14 | DEBUG | Git LFS has been activated 17:45:15 | DEBUG | Connected to the internet 17:45:15 | DEBUG | Conda is installed 17:45:15 | DEBUG | EOS Home path exists Checking setup: 1.385s
12%|████████████▎ | 1/8 [00:01<00:09, 1.38s/it]17:45:15 | INFO | Starting delete of model eos3b5e 17:45:15 | INFO | Removing folder /home/zakia/eos/dest/eos3b5e 17:45:21 | INFO | Deleting conda environment eos3b5e

Remove all packages in environment /home/zakia/miniconda3/envs/eos3b5e:

17:45:43 | DEBUG | Deleting /home/zakia/eos/isaura/lake/eos3b5e_local.h5 17:45:43 | DEBUG | Deleting /home/zakia/eos/isaura/lake/eos3b5e_public.h5 17:45:43 | INFO | Removing docker images and stopping containers related to eos3b5e 17:45:43 | DEBUG | Model entry eos3b5e was not available in the fetched models registry 17:45:43 | SUCCESS | Model eos3b5e deleted successfully Preparing model: 28.444167613983154s
25%|████████████████████████▌ | 2/8 [00:29<01:43, 17.30s/it]17:46:05 | DEBUG | Cloning from github to /home/zakia/eos/dest/eos3b5e Cloning into 'eos3b5e'... remote: Enumerating objects: 47, done. remote: Counting objects: 100% (47/47), done. remote: Compressing objects: 100% (41/41), done. remote: Total 47 (delta 15), reused 17 (delta 4), pack-reused 0 Unpacking objects: 100% (47/47), done. rm: cannot remove '/tmp/ersilia-g6g0mfrt': Is a directory 17:46:08 | INFO | 🚀 Model starting... 17:46:08 | DEBUG | {'version': '0.11.0', 'slim': False, 'python': 'py37'} Getting model: 24.91094660758972s
38%|████████████████████████████████████▊ | 3/8 [00:54<01:43, 20.78s/it]17:46:08 | DEBUG | Check if model can be run with vanilla (system) code (i.e. dockerfile has no installs) 17:46:08 | DEBUG | Check bentoml and python version 17:46:08 | INFO | BentoML version {'version': '0.11.0', 'slim': False, 'python': 'py37'} 17:46:08 | DEBUG | Custom Ersilia BentoML is used, no need for modifying protobuf version 17:46:08 | DEBUG | Model needs some installs 17:46:08 | DEBUG | Checking if only python/conda install will be sufficient 17:46:08 | DEBUG | Mode: conda 17:46:08 | DEBUG | Trying to remove path: /home/zakia/bentoml/repository/eos3b5e 17:46:08 | DEBUG | ...successfully 17:46:08 | DEBUG | ...but path did not exist! 17:46:08 | DEBUG | Initializing conda packer 17:46:08 | DEBUG | Packing model with Conda 17:46:08 | DEBUG | Writing install commands 17:46:08 | DEBUG | Run commands: ['pip install rdkit-pypi'] 17:46:08 | DEBUG | Writing install commands in /home/zakia/eos/dest/eos3b5e/model_install_commands.sh 17:46:08 | DEBUG | Setting up 17:46:08 | DEBUG | Installs file /home/zakia/eos/dest/eos3b5e/model_install_commands.sh 17:46:08 | DEBUG | Conda environment eos3b5e 17:46:11 | DEBUG | Environment eos3b5e does not exist 17:46:14 | INFO | Cloning base conda environment and adding model dependencies Source: /home/zakia/miniconda3/envs/eosbase-bentoml-0.11.0-py37 Destination: /home/zakia/miniconda3/envs/eos3b5e Packages: 20 Files: 0

Downloading and Extracting Packages

Downloading and Extracting Packages

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate eos3b5e

#

To deactivate an active environment, use

#

$ conda deactivate

17:47:03 | DEBUG | Run commandlines on eos3b5e 17:47:03 | DEBUG | python -m pip --disable-pip-version-check install rdkit-pypi python -m pip --disable-pip-version-check install git+https://github.com/ersilia-os/bentoml-ersilia.git

17:47:06 | DEBUG | Activating base environment 17:47:06 | DEBUG | Current working directory: /home/zakia/eos/dest/eos3b5e 17:47:06 | DEBUG | Running bash /tmp/ersilia-tdmt6yfc/script.sh > /tmp/ersilia-7r03i_jk/command_outputs.log 2>&1 17:47:37 | DEBUG | # conda environments: # base /home/zakia/miniconda3 eos157v /home/zakia/miniconda3/envs/eos157v eos3b5e * /home/zakia/miniconda3/envs/eos3b5e eos8h6g /home/zakia/miniconda3/envs/eos8h6g eosbase-bentoml-0.11.0-py37 /home/zakia/miniconda3/envs/eosbase-bentoml-0.11.0-py37 ersilia /home/zakia/miniconda3/envs/ersilia

WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f04cbc4ed50>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f04cbc4ef90>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f04cb595290>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f04cb595610>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f04cb595950>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/rdkit-pypi/ ERROR: Could not find a version that satisfies the requirement rdkit-pypi (from versions: none) ERROR: No matching distribution found for rdkit-pypi Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-3ekvjhyj Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-3ekvjhyj Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit a0f0040a1198e8f1704f0395e5d9ce328aaecf71 Installing build dependencies: started Installing build dependencies: finished with status 'error' error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [8 lines of output] WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f640843c5d0>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f640843c350>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f640843ca50>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f640843cd90>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f6407d85110>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/setuptools/ ERROR: Could not find a version that satisfies the requirement setuptools>=40.8.0 (from versions: none) ERROR: No matching distribution found for setuptools>=40.8.0 WARNING: There was an error checking the latest version of pip. [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

17:47:37 | DEBUG | Error occurred while running: bash /tmp/ersilia-tdmt6yfc/script.sh > /tmp/ersilia-7r03i_jk/command_outputs.log 2>&1 17:47:37 | ERROR | Ersilia exception class: ModelPackageInstallError

Detailed error: Error occured while installing package by running "bash /tmp/ersilia-tdmt6yfc/script.sh > /tmp/ersilia-7r03i_jk/command_outputs.log 2>&1" command

Hints: Try to manually activate the model environment and install package manually. If this does not work, please report the error at:

🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨

Error message:

Ersilia exception class: ModelPackageInstallError

Detailed error: Error occured while installing package by running "bash /tmp/ersilia-tdmt6yfc/script.sh > /tmp/ersilia-7r03i_jk/command_outputs.log 2>&1" command

Hints: Try to manually activate the model environment and install package manually. If this does not work, please report the error at:

If this error message is not helpful, open an issue at:

If you haven't, try to run your command in verbose mode (-v in the CLI)

ZakiaYahya commented 1 year ago

@GemmaTuron, I have see the error log in detail and found some information about the error i.e.

(1) ERROR: Could not find a version that satisfies the requirement setuptools>=40.8.0 (from versions: none) ERROR: No matching distribution found for setuptools>=40.8.0 WARNING: There was an error checking the latest version of pip.

(2) ERROR: Could not find a version that satisfies the requirement rdkit-pypi (from versions: none) ERROR: No matching distribution found for rdkit-pypi

I have manually install that packages with required versions, upgraded the pip as well. Conda environment detected thet packages as installed as well but i'm still getting the same error again and again.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors.

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors. Hello @GemmaTuron, i'm attaching the log file here. Kindly have a look. Thanks Error.txt

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors.

@GemmaTuron, I even switched to different networks and even used VPN but the same error occurred.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya

I know you managed to run Ersilia successfully in the past, so we must figure out what might have changed since then. Can you please delete any old installations of Ersilia / Isaura / Conda that you have and start anew?

ZakiaYahya commented 1 year ago

Hi @GemmaTuron, Yes, i deleted ersilia after asking you and installed it freshly. But something is still missing that causes this error to occur. I'm again deleted all ersilia related packages and conda envs again today and doing installation again. once it done i'll let you know. Many thanks.

GemmaTuron commented 1 year ago

Thanks @ZakiaYahya

Please paste the log files here so we can help you out.

Zainab-ik commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors. Hello @GemmaTuron, i'm attaching the log file here. Kindly have a look. Thanks Error.txt

@GemmaTuron This is the log file

Zainab-ik commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors. Hello @GemmaTuron, i'm attaching the log file here. Kindly have a look. Thanks Error.txt

@ZakiaYahya From this log file, I can deduce a connection error. Try changing the connection and check the connection speed at fast.com

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya Thanks for this, pelase provide the error as a log file so I can point out the lines of code that are probably the cause of the errors. Hello @GemmaTuron, i'm attaching the log file here. Kindly have a look. Thanks Error.txt

@ZakiaYahya From this log file, I can deduce a connection error. Try changing the connection and check the connection speed at [fast.com](

Thanks @Zainab-ik, but i don't think so it's a network problem because i have checked it by using my mobile 4G, with wingle, with wifi and even used VPN but the same error occurs. I have installed all dependancies manually that are showing problem in error log but no gain. I have delete all ersilia related files and did fresh installation a well but still facing the same error. Still trying :(.

ZakiaYahya commented 1 year ago

Thanks @ZakiaYahya

Please paste the log files here so we can help you out.

Hello @GemmaTuron, i have successfully fetch, serve and predict the test model eos3b5e on my system. The error wasn't due to "ConnectionError", it seems like some packages got corrupted, i deleted all the ersilia setup and other dependancies, disable ubuntu from WSL and upgrade WSL to WSL2 and finally able to fetch the model.

ZakiaYahya commented 1 year ago

My Motivation to work at Ersilia:

Hi, my name is Zakia Yahya, and I completed my degree in 2018. After graduation, I secured a job in a research lab where I worked on various ML/AI models. One of my research projects during my job was accepted in the IEEE journal and my thesis work was accepted in IEEE conference. Unfortunately, I had to resign from the job due to severe gender-discrimination. I am currently a housewife and cannot leave the house to work outside. I began looking for freelance work, but due to a three-year gap i found it challenging to secure a job. A friend of mine introduced me to Outreachy, and fortunately, applications for the next round were open. I applied immediately, as Outreachy appears to be an excellent platform for me to re-learn and refresh my concepts.

Upon receiving the congratulatory email from Outreachy, I felt thrilled and eager to begin my contribution and learning journey. As I went through the list of available projects, one project in particular caught my attention - the Ersilia project. Although there were two other projects that I also found interesting, the unique aspect of Ersilia that stood out to me was their goal of supporting researchers in low-resourced settings and providing access to tools for underdeveloped countries that may not have the financial means to afford expensive equipment was especially compelling as I also belong to low-sourced country. Additionally, their focus on enhancing the research capacity for infectious and neglected diseases through the development and implementation of innovative AI and machine learning tools caught my eye. I extensively worked on similar kind of projects in which I used different python tools such as keras and pytorch etc. and google colab to work on different build-in ML/AI models and different kind of datasets (videos, images and 1-D datasets) both in my Master's-Thesis and in my Research-based job as well. So, I have a basic knowledge of the python language and its tools, I have hands-on experience with different kinds of datasets, I have a basic knowledge of how to train models for classification purposes.

As this project involves Python programming and work with Machine learning models, that I am very passionate about, I would really like to be a part of ersilia that helps low-sourced countries and different institutes including universities and hospitals where ML and bioinformatic expertise are difficult to obtain.

GemmaTuron commented 1 year ago

Hello @ZakiaYahya

Thanks for your interest in Ersilia. While we wait to start the contributions for week 2, please head over https://github.com/ersilia-os/eos1bba/issues/4 and test if the model is working. Masroor has also been assigned to this model, please collaborate if you find any problems! Many thanks

ZakiaYahya commented 1 year ago

Hello @ZakiaYahya

Thanks for your interest in Ersilia. While we wait to start the contributions for week 2, please head over ersilia-os/eos1bba#4 and test if the model is working. Masroor has also been assigned to this model, please collaborate if you find any problems! Many thanks

Sure @GemmaTuron. I'm working on it. Thanks.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya Thansk for testing the model eos1bba, we'll let you know when it is ready for checking again!

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya Thansk for testing the model eos1bba, we'll let you know when it is ready for checking again!

Okay @GemmaTuron. I'm waiting for karthikjetty response, once he's done, I'll test it again. Thanks.

ZakiaYahya commented 1 year ago

WEEK 2: Run an ML model: select a model:

Hello @GemmaTuron, For my Week-2 Task, I want to choose the STOUT model (SMILES to IUPAC) and work on it. Firstly, I'm motivated to select this model because I appreciate the idea of assigning clear and understandable nomenclature to chemical compounds/chemical strings especially for documentation purpose. Although working with strings is convenient when working with models, but documenting it in a way that is comprehensible to those with limited knowledge is difficult. With the help of STRING to IUPAC name conversion one can better understand the chemical compound he/she working with. Secondly, this model uses a deep-learning neural machine translation approach to generate the IUPAC name for a given molecule from its SMILES string as well as the reverse translation. And i have a background working with deep learning neural networks. Thank you.

Kindly let me know, can i proceed??

ZakiaYahya commented 1 year ago

Hello @GemmaTuron, I have successfully installed and run STOUT model from their original repository. I have encountered following error "FileExistsError: [Errno 17] JVM DLL not found: Define/path/or/set/JAVA_HOME/variable/properly" you can find the whole error log here stout_Error.txt

I resolved that issue by installing OpenJDK manually using "sudo apt install default-jre" command.

I am able to run Original stout on my system and using ersilia Model Hub. But for now i have just checked it with single smile. The ouputs are attached here;

Output of Original STOUT on my system: output.txt

Output of Ersilia Model Hub: stout_ersilia.txt

Now i'm trying to run it for whole EML file. Thanks.

ZakiaYahya commented 1 year ago

Hello @GemmaTuron, I have run prediction using Original STOUT model and Ersilia smiles2iupac model on whole EML file. It took around 8-9 hours to do predictions for all smiles in the EML file. I'm attaching the output files here,

Output of Original STOUT: stout_output_ALL.csv

Output of Ersilia smiles2iupac Model: Ersilia_smiles2iupac_output.csv

Kindly check it. Thanks.

ZakiaYahya commented 1 year ago

Hello @GemmaTuron, can you please explain a little bit about "Compare results with the Ersilia Model Hub implementation". Is it meant to be one to one comparison or we have to used some metric to do this. I'm confused in this? Thanks.

AhmedYusuff commented 1 year ago

Hi @ZakiaYahya , there's this resource you can use to compare two CSV files for differences.

https://pypi.org/project/csv-diff/

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya , there's this resource you can use to compare two CSV files for differences.

https://pypi.org/project/csv-diff/

Hello @AhmedYusuff, Thanks for sharing.

ZakiaYahya commented 1 year ago

Hello @GemmaTuron, i'm done with STOUT, can you please assign me another model for working as you said in slack channel. Waiting for your response. Thanks.

GemmaTuron commented 1 year ago

Hi @ZakiaYahya !

Thanks, very good work. Can I ask you, like I did to Masroor, to try out the NCATS models? In your case, could you start by the solubility model? comparing the NCATS original model with the Ersilia model output

Many thanks!

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya !

Thanks, very good work. Can I ask you, like I did to Masroor, to try out the NCATS models? In your case, could you start by the solubility model? comparing the NCATS original model with the Ersilia model output

Many thanks!

Thanks @GemmaTuron. Yeah sure, i'll start working on it and will let you know. Can you please mention the ersilia model too it's slug or identifier? Thanks.

ZakiaYahya commented 1 year ago

Hello @GemmaTuron and @pauline-banye I successfully fetch and serve NCATS based ersilia model eos74bo. I tried executing run api on single smile and it's giving me output perfectly i.e.

{ "input": { "key": "POLCUAVZOMRGSN-UHFFFAOYSA-N", "input": "CCCOCCC", "text": "CCCOCCC" }, "output": { "outcome": [ 0.002611332107335329 ] } }

But when i tries to execute 'run' api on whole EML file it gave me "assert len(m) == len(v) TypeError: object of type 'float' has no len()" , log file is attached here, eos74bo_log.log

I tries to convert float to str before getting it's len but then it throws an AssertionError. Kindly suggests me something. Thanks.

GemmaTuron commented 1 year ago

Thanks @ZakiaYahya !

Can you try passing a shorter list? Like, 20 SMILES, in CSV format, and see if this also reproduces the same error

ZakiaYahya commented 1 year ago

Thanks @ZakiaYahya !

Can you try passing a shorter list? Like, 20 SMILES, in CSV format, and see if this also reproduces the same error

Hello @GemmaTuron, i have tried passing a csv file comprising 20 smiles string but same error occurred , then i passed a csv file having a single smile string and same error occurred , although without passing a csv file , passing just a single smile directly on CLI produces the ouput, i still don't understand why this is happening.

GemmaTuron commented 1 year ago

@pauline-banye Canyou please provide guidance on that? if I recall correctly the model should work with .csv files

ZakiaYahya commented 1 year ago

Hello @GemmaTuron and @pauline-banye I'm getting an error while calling python app.py using the original NCATS repo,

"Using TensorFlow backend. Loading RLM random forest model rf_morgan_all_data.pkl: 305B [00:00, 377kB/s] Traceback (most recent call last): File "app.py", line 20, in from predictors.rlm.rlm_predictor import RLMPredictior File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 168, in rlm_rf_model = load_rlm_rf_model() File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 47, in load_rlm_rf_model rlm_rf_model = pickle.load(rlm_rf_pkl_file) _pickle.UnpicklingError: invalid load key, '<'.

i go through several forums and they suggests downloading and reinstalling the repo again due to some corrupt files and i did reinstalling the repo but issue didn't resolved. And it took around 6 hours in my case just to create yaml env, so it's not possible to delete and reinstall the whole thing again and again. Any idea? @masroor07 did you encountered this problem while running app.py??

masroor07 commented 1 year ago

Hello @GemmaTuron and @pauline-banye I'm getting an error while calling python app.py using the original NCATS repo,

"Using TensorFlow backend. Loading RLM random forest model rf_morgan_all_data.pkl: 305B [00:00, 377kB/s] Traceback (most recent call last): File "app.py", line 20, in from predictors.rlm.rlm_predictor import RLMPredictior File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 168, in rlm_rf_model = load_rlm_rf_model() File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 47, in load_rlm_rf_model rlm_rf_model = pickle.load(rlm_rf_pkl_file) _pickle.UnpicklingError: invalid load key, '<'.

i go through several forums and they suggests downloading and reinstalling the repo again due to some corrupt files and i did reinstalling the repo but issue didn't resolved. And it took around 6 hours in my case just to create yaml env, so it's not possible to delete and reinstall the whole thing again and again. Any idea? @masroor07 did you encountered this problem while running app.py??

Just finished my college! had to reset my system, some config files were corrupted during the process. I will try setting up the environment again in a while and get back at it. Will let you know if i fave the same issue.

masroor07 commented 1 year ago

Hello @GemmaTuron and @pauline-banye I'm getting an error while calling python app.py using the original NCATS repo,

"Using TensorFlow backend. Loading RLM random forest model rf_morgan_all_data.pkl: 305B [00:00, 377kB/s] Traceback (most recent call last): File "app.py", line 20, in from predictors.rlm.rlm_predictor import RLMPredictior File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 168, in rlm_rf_model = load_rlm_rf_model() File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 47, in load_rlm_rf_model rlm_rf_model = pickle.load(rlm_rf_pkl_file) _pickle.UnpicklingError: invalid load key, '<'.

i go through several forums and they suggests downloading and reinstalling the repo again due to some corrupt files and i did reinstalling the repo but issue didn't resolved. And it took around 6 hours in my case just to create yaml env, so it's not possible to delete and reinstall the whole thing again and again. Any idea? @masroor07 did you encountered this problem while running app.py??

the tensorflow issue! try uninstalling and reinstalling it. That solved my problem

ZakiaYahya commented 1 year ago

Hello @GemmaTuron and @pauline-banye I'm getting an error while calling python app.py using the original NCATS repo, "Using TensorFlow backend. Loading RLM random forest model rf_morgan_all_data.pkl: 305B [00:00, 377kB/s] Traceback (most recent call last): File "app.py", line 20, in from predictors.rlm.rlm_predictor import RLMPredictior File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 168, in rlm_rf_model = load_rlm_rf_model() File "/home/zakia/ncats-adme/server/predictors/rlm/init.py", line 47, in load_rlm_rf_model rlm_rf_model = pickle.load(rlm_rf_pkl_file) _pickle.UnpicklingError: invalid load key, '<'. i go through several forums and they suggests downloading and reinstalling the repo again due to some corrupt files and i did reinstalling the repo but issue didn't resolved. And it took around 6 hours in my case just to create yaml env, so it's not possible to delete and reinstall the whole thing again and again. Any idea? @masroor07 did you encountered this problem while running app.py??

Just finished my college! had to reset my system, some config files were corrupted during the process. I will try setting up the environment again in a while and get back at itWill let you know if i fave the same issue.

Hi @masroor07, no it's not the tensorflow problem, i already tried uninstalling and reinstalling tensorflow. It seems like error is caused by pytorch "File "/home/zakia/ncats-adme/server/env/lib/python3.8/site-packages/torch/serialization.py" but couldn't find the solution yet, trying from last 3 hours.

Pradnya2203 commented 1 year ago

Hey @ZakiaYahya I've been facing the exact same issue and I tried to update both tensorflow and pytorch but nothing seems to work. Could you find a way around it?

GemmaTuron commented 1 year ago

Hi @ZakiaYahya

The model is not able to load, did you download the right model manually and added it to the folder as per the instructions? Pretrained models need to be manually downloaded

GemmaTuron commented 1 year ago

@pauline-banye can you check the issue with .csv files mentioned by @ZakiaYahya above?

ZakiaYahya commented 1 year ago

Hi @ZakiaYahya

The model is not able to load, did you download the right model manually and added it to the folder as per the instructions? Pretrained models need to be manually downloaded

Alright @GemmaTuron, no i didn't downloaded it manually, i used "git clone --recursive https://github.com/ncats/ncats-adme.git" command to download the repo. I just downloaded the ncats-adme model from repo manually, now trying to create the environment which takes upto 5-6 hours, once it done i will let you know. Thanks.

ZakiaYahya commented 1 year ago

Hey @ZakiaYahya I've been facing the exact same issue and I tried to update both tensorflow and pytorch but nothing seems to work. Could you find a way around it?

Hi @Pradnya2203 no not yet but Gemma suggested to download the repo manually instead of clonning, so i'm trying that way if that works i'll let you know.

ZakiaYahya commented 1 year ago

@pauline-banye can you check the issue with .csv files mentioned by @ZakiaYahya above?

Yes please check it @pauline, it's not working on CLI, i'm trying to run it on Colab.

ZakiaYahya commented 1 year ago

@pauline-banye can you check the issue with .csv files mentioned by @ZakiaYahya above?

Yes please check it @pauline, it's not working on CLI, i'm trying to run it on Colab

Hello @GemmaTuron and @pauline-banye, model NCAT solubility based ersilia eos74bo is working perfectly fine on Colab, it gave me output too, i'm attaching the output file here eos74bo_ersilia_colab.csv

but it continuously giving me error when pass whole csv file while executing "run" api. Although, it works fine too when passing single smile string on CLI.

paulinebanye commented 1 year ago

@pauline-banye can you check the issue with .csv files mentioned by @ZakiaYahya above?

Yes please check it @pauline, it's not working on CLI, i'm trying to run it on Colab

Hello @GemmaTuron and @pauline-banye, model NCAT solubility based ersilia eos74bo is working perfectly fine on Colab, it gave me output too, i'm attaching the output file here eos74bo_ersilia_colab.csv

but it continuously giving me error when pass whole csv file while executing "run" api. Although, it works fine too when passing single smile string on CLI.

@ZakiaYahya Oh I'm sorry for the late response, just saw your message. could you share the command you're running?

Did it fetch successfully?I am currently testing the model as well.

Could you also share the log file of the error you received?

ZakiaYahya commented 1 year ago

@pauline-banye can you check the issue with .csv files mentioned by @ZakiaYahya above?

Yes please check it @pauline, it's not working on CLI, i'm trying to run it on Colab

Hello @GemmaTuron and @pauline-banye, model NCAT solubility based ersilia eos74bo is working perfectly fine on Colab, it gave me output too, i'm attaching the output file here eos74bo_ersilia_colab.csv but it continuously giving me error when pass whole csv file while executing "run" api. Although, it works fine too when passing single smile string on CLI.

Oh I'm sorry for the late response, just saw your message. could you share the command you're running?

Did it fetch successfully?I am currently testing the model as well.

Could you also share the log file of the error you received?

Yes sure @pauline, yes it fetch and serve successfully after granting user priviledge. I'm running this command on CLI "ersilia -v api run -i "eml_canonical.csv" -o "eos74bo_output.csv" > eos74bo_log.log 2>&1" and it's giving me error: "TypeError: object of type 'float' has no len()" . I'm attaching the Error log here too eos74bo_log.log. Kindly have a look, Thanks.