T032: filter_explore_activity_data error

[hamzaibrahim21]

When trying to run T032 locally to prepare for merge into master the following error occurred:

filter_explore_activity_data(PAPYRUS_VERSION, adenosine_receptors)

/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb Cell 46 in ()
      [3](vscode-notebook-cell:/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb#X63sZmlsZQ%3D%3D?line=2) print(DATA)
      [5](vscode-notebook-cell:/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb#X63sZmlsZQ%3D%3D?line=4) # Filter the Papyrus bioactivity dataset and plot the distribution of activity values for the targets of interest
----> [6](vscode-notebook-cell:/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb#X63sZmlsZQ%3D%3D?line=5) ar_dataset = filter_explore_activity_data(PAPYRUS_VERSION, adenosine_receptors)

/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb Cell 46 in filter_explore_activity_data(papyrus_version, targets)
     [17] # Read downloaded Papyrus dataset in chunks, as it does not fit in memory
     [18] CHUNKSIZE = 100000
---> [19] data = papyrus_scripts.read_papyrus(
     [20]     version=papyrus_version, chunksize=CHUNKSIZE, source_path=DATA
     [21] )
     [23](vscode-notebook-cell:/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb#X63sZmlsZQ%3D%3D?line=22) # Create filter for targets of interest
     [24](vscode-notebook-cell:/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/talktorial.ipynb#X63sZmlsZQ%3D%3D?line=23) target_accession_list = targets.values()

File [~/anaconda3/envs/teachopencadd_t032/lib/python3.8/site-packages/papyrus_scripts/reader.py:33](https://file+.vscode-resource.vscode-cdn.net/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/~/anaconda3/envs/teachopencadd_t032/lib/python3.8/site-packages/papyrus_scripts/reader.py:33), in read_papyrus(is3d, version, plusplus, chunksize, source_path)
     31 if source_path is not None:
     32     os.environ['PYSTOW_HOME'] = os.path.abspath(source_path)
---> 33 version = process_data_version(version=version, root_folder=source_path)
     34 source_path = pystow.module('papyrus', version)
     35 # Load data types

File [~/anaconda3/envs/teachopencadd_t032/lib/python3.8/site-packages/papyrus_scripts/utils/IO.py:179](https://file+.vscode-resource.vscode-cdn.net/home/hamza/Github/teachopencadd/teachopencadd/talktorials/T032_compound_activity_proteochemometrics/~/anaconda3/envs/teachopencadd_t032/lib/python3.8/site-packages/papyrus_scripts/utils/IO.py:179), in process_data_version(version, root_folder)
    173 """Confirm the version is available, downloaded and convert synonyms.
...
--> 179 available_versions = get_downloaded_versions(root_folder) + ['latest']
    180 if version not in available_versions:
    181     raise ValueError(f'version can only be one of [{", ".join(available_versions)}]')

TypeError: unsupported operand type(s) for +: 'dict' and 'list' 

To create the environment I used : conda env create -f T032_env.yml

Packages in the talktorial are installed successefully as well.

[AndreaVolkamer]

@gorostiolam and/or @jesperswillem we are preparing an update of the TOC master and wanted to include your notebook as well if possible, when running it locally, @hamzaibrahim21 came across the above issue, can you maybe help?

[gorostiolam]

Thanks for bringing it to my attention. This is an issue that arises when trying to read Papyrus data if it has not been downloaded. Was this cell run @hamzaibrahim21 ? And was the output successful?

%%time
papyrus_scripts.download_papyrus(
    outdir=DATA, version=PAPYRUS_VERSION, nostereo=True, stereo=False, descriptors=None
)
# If you want to download the latest version of the Papyrus dataset, change 'PAPYRUS_VERSION' to 'latest'

I have pulled and run the latest version of the talktorial with a freshly installed environment (conda env create -f T032_env.yml) and I have had no issues.

[hamzaibrahim21]

@gorostiolam It seems that I had a space issue that blocked data from being downloaded. It works now on my local machine. Thanks!