New model ready for testing!

github-actions[bot] commented 10 months ago

This model is ready for testing. If you are assigned to this issue, please try it out using the CLI, Google Colab and DockerHub and let us know if it works!

GemmaTuron commented 10 months ago

@emmakodes and @samuelmaina please test this model - no docker yet

emmakodes commented 10 months ago

CLI

👍 Model eos9sa2 fetched and make predictions successfully! eos9sa2_cli_log_output.txt eos9sa2Output.csv

Google Colab

Model fetched and makes predictions successfully eos9sa2_output.csv

samuelmaina commented 10 months ago

Google Colab
- Fetched and predicted successfully. colab_eos9sa2_fetch.log eos9sa2_eml_colab_predictions.csv

For CLI

Fetched successfully. eos9sa2_cli_fetch.log

I was not able to predict for eml_canonical.csv. I got this error.


results, output, model_id=self.model_id, api_name=self.api_name
File "/home/samuelmayna/miniconda3/envs/ersilia/lib/python3.7/site-packages/ersilia/io/output.py", line 301, in adapt
df = self._to_dataframe(result, model_id)
File "/home/samuelmayna/miniconda3/envs/ersilia/lib/python3.7/site-packages/ersilia/io/output.py", line 247, in _to_dataframe
output_keys_expanded = self.__expand_output_keys(vals, output_keys)
File "/home/samuelmayna/miniconda3/envs/ersilia/lib/python3.7/site-packages/ersilia/io/output.py", line 206, in __expand_output_keys
assert len(m) == len(v)
TypeError: object of type 'float' has no len()
``` . 
The whole error_log file can be viewed at 
[eos9sa2_cli_prediction_error.log](https://github.com/ersilia-os/eos9sa2/files/11780726/eos9sa2_cli_prediction_error.log)

samuelmaina commented 10 months ago

When I left the output file in run command I was able predict successfully. It is the same issue @HellenNamulinda was facing here https://github.com/ersilia-os/eos2r5a/issues/6

GemmaTuron commented 10 months ago

Hi @ZakiaYahya Please can you revise this?

ZakiaYahya commented 10 months ago

Hello @samuelmaina and @GemmaTuron I have run it again in my CLI with eml_canonical smiles and it is working fine inside ersilia with --repo_path. @samuelmaina can you try it again once more?? Meanwhile i'll try to figure it out why it's happening, as it also works for @emmakodes. Thanks.

ZakiaYahya commented 10 months ago

Hi @samuelmaina Did you test it again on CLI?? because its working fine on my side, i didn't get it why are you encountering this error. Try it again and let me know. Thanks.

samuelmaina commented 10 months ago

@ZakiaYahya ,I the error is resolved. eos9sa2_cli_eml_pred.csv

ZakiaYahya commented 10 months ago

Okay @samuelmaina, Thanks for testing it again. @GemmaTuron the model is working fine now. @emmakodes AND @samuelmaina, Can you please both test it on DockerHub as well. The model image is available on DcokerHub as well https://hub.docker.com/r/ersiliaos/eos9sa2 Thanks.

samuelmaina commented 10 months ago

@ZakiaYahya and @GemmaTuron Successfully predicted in docker .

^C^C
Aborted!
root@f6e4180166d3:/models# ersilia -v  run -i eml_canonical.csv -o eos9sa2_doc_eml_pred.csv
04:35:15 | DEBUG    | Getting session from /root/eos/session.json
04:35:15 | DEBUG    | Getting session from /root/eos/session.json
04:35:15 | WARNING  | Lake manager 'isaura' is not installed! We strongly recommend installing it to store calculations persistently
04:35:15 | ERROR    | Isaura is not installed! Calculations will be done without storing and reading from the lake, unfortunately.
04:35:16 | DEBUG    | Is fetched: True
04:35:16 | DEBUG    | Schema available in /root/eos/dest/eos9sa2/api_schema.json
04:35:16 | DEBUG    | Setting AutoService for eos9sa2
04:35:16 | INFO     | Service class provided
04:35:20 | DEBUG    | Reading card from eos9sa2
04:35:20 | DEBUG    | Reading shape from eos9sa2
04:35:20 | DEBUG    | Input Shape: Single
04:35:20 | DEBUG    | Input type is: compound
04:35:20 | DEBUG    | Input shape is: Single
04:35:20 | DEBUG    | Importing module: .types.compound
04:35:20 | DEBUG    | Checking RDKIT and other requirements necessary for compound inputs
04:35:20 | DEBUG    | InputShapeSingle shape: Single
04:35:20 | DEBUG    | Stopping sniffer for finding delimiter
04:35:20 | DEBUG    | Expected number: 1
04:35:20 | DEBUG    | Entity is list: False
04:35:20 | DEBUG    | Stopping sniffer for resolving column types
04:35:20 | DEBUG    | Has header True
04:35:20 | DEBUG    | Schema {'input': [1], 'key': None}
04:35:20 | DEBUG    | Standardizing input single
04:35:20 | DEBUG    | Reading standard file from /tmp/ersilia-t_505nf2/standard_input_file.csv
04:35:20 | DEBUG    | File has 443 lines
04:35:20 | DEBUG    | No file splitting necessary!
04:35:22 | DEBUG    | Reading card from eos9sa2
04:35:22 | DEBUG    | Reading shape from eos9sa2
04:35:22 | DEBUG    | Input Shape: Single
04:35:22 | DEBUG    | Input type is: compound
04:35:22 | DEBUG    | Input shape is: Single
04:35:22 | DEBUG    | Importing module: .types.compound
04:35:22 | DEBUG    | Checking RDKIT and other requirements necessary for compound inputs
04:35:22 | DEBUG    | InputShapeSingle shape: Single
04:35:22 | DEBUG    | API eos9sa2:run initialized at URL http://127.0.0.1:3000
04:35:22 | DEBUG    | Schema available in /root/eos/dest/eos9sa2/api_schema.json
04:35:22 | DEBUG    | Posting to run
04:35:22 | DEBUG    | Batch size 100
04:35:22 | DEBUG    | Stopping sniffer for finding delimiter
04:35:22 | DEBUG    | Expected number: 1
04:35:22 | DEBUG    | Entity is list: False
04:35:22 | DEBUG    | Stopping sniffer for resolving column types
04:35:22 | DEBUG    | Has header True
04:35:22 | DEBUG    | Schema {'input': [1], 'key': None}
04:35:22 | DEBUG    | Standardizing input single
04:35:22 | DEBUG    | Reading standard file from /tmp/ersilia-ko676u7b/standard_input_file.csv
04:35:23 | DEBUG    | Schema available in /root/eos/dest/eos9sa2/api_schema.json
04:35:54 | DEBUG    | Status code: 200
04:35:54 | DEBUG    | Schema available in /root/eos/dest/eos9sa2/api_schema.json
04:36:05 | DEBUG    | Status code: 200
04:36:20 | DEBUG    | Status code: 200
04:36:30 | DEBUG    | Status code: 200
04:36:38 | DEBUG    | Status code: 200
04:36:38 | DEBUG    | Done with unique posting
04:36:42 | DEBUG    | Data: outcome
04:36:42 | DEBUG    | Values: [0.3505815863609314]
04:36:42 | DEBUG    | Pure datatype: numeric_array
eos9sa2_doc_eml_pred.csv
root@f6e4180166d3:/models#

eos9sa2_doc_eml_pred.csv

GemmaTuron commented 10 months ago

Perfect, thanks all, we can close this issue !

ersilia-os / eos9sa2

New model ready for testing! #3

CLI

Google Colab