search

sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
171 stars 65 forks source link

cBioPortal legacy API is shut down #1434

Closed kkaris closed 3 months ago

kkaris commented 7 months ago

It looks like cBioPortal has shut down their legacy API at http://www.cbioportal.org/webservice.do that we use in the cbio client.

There are alternatives documented at https://docs.cbioportal.org/web-api-and-clients/, one is to use their new rest API: https://www.cbioportal.org/api/swagger-ui/index.html another is to use the Python client: https://docs.cbioportal.org/web-api-and-clients/#python-client

bgyori commented 7 months ago

I started implementing a new client on a branch, the endpoints and nomenclature have changed a lot so each functionality needs to be investigated to figure out how to reproduce.

bgyori commented 3 months ago

Done in #1435