Opentargets installation

[areyesromero]

Dear all,

I wanted to report that it is not possible to install opentargets neither with pip install nor with conda -c bioconda.

If I try to use pip I get the following message.

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

with conda

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

[andrewhercules]

Hello @areyesromero!

With the launch of the next-gen Platform in April 2021, the opentargets-py package has been deprecated. The underlying REST API has been replaced with our GraphQL API that is optimised for a single target, disease, phenotype, drug, or target-disease association.

For more information on how to use our data, please check out our Platform data access documentation.

Cheers,

~ Andrew 🙂

[cthoyt]

Dear @andrewhercules, there's a big difference between deprecation and pulling the code from PyPI. Lots of people will be having the same issue and it's now pretty non-obvious since https://pypi.org/project/opentargets/ has simply disappeared.

[andrewhercules]

Hi @cthoyt!

Thank you for getting in touch and raising this to my attention. My apologies for the frustration caused by the removal of the opentargets package.

I removed the package from PyPi in early October after consulting with my team and users that contacted our help desk. It was removed from PyPi because the underlying REST API has not been available since June 2021 and the underlying data that powered the REST API was last updated in February 2021. Even though the opentargets package could be used against a REST API that powers a private internal instance of the Platform, our data model and pipeline processes have significantly changed. And thus, even for an internal API, it would no longer be advisable to use the package as the data would be different when compared to the data available from the GraphQL API, BigQuery, or our dataset downloads.

I will work with our team to restore a stub package that explains the situation and provides links to the other options for accessing our data.

Again, my apologies about this and I will post updates in your ticket #42 when available.

~ Andrew 🙂

CC: @areyesromero and @laurendelong21