Release notes: https://docs.targetvalidation.org/release-notes
Updated documentation (https://github.com/opentargets/data_pipeline/blob/19.04.5/README.md) improvements to clarify essential gene plugins and evidence json schema versioning
Replace external API with frozen files to improve reproducibility https://github.com/opentargets/platform/issues/325
Use pypeln (https://cgarciae.github.io/pypeln/) for multiprocessing instead of Redis https://github.com/opentargets/platform/issues/361 for improved reliability
many other improvements to improve reliability and performance of using multiple threads & processes
externalize url source to separate python package https://github.com/opentargets/platform/issues/416
reduce default logging to info, and various minor logging improvements
remove delay between stages in Makefile which is a very minor performance improvement
new gene plugin to handle safety data
Updated documentation (https://github.com/opentargets/rest_api/blob/19.04.5/README.md) particularly using docker and SSL, and proxy
update swagger documentation to new platform API URL (https://platform-api.opentargets.io/v3/platform/docs/swagger-ui). Note, configuring the API URL used by swagger is still open
minor configuration change to support crispr evidence
Option to auto expand certain data types e.g. for private data https://github.com/opentargets/platform/issues/566
Customization of "new" icon on panels https://github.com/opentargets/platform/issues/511
Customization of CSS styling and updated documentation on custom styling (https://github.com/opentargets/webapp/blob/3.12.0/README.md)
Target safety data on the target profile page https://github.com/opentargets/platform/issues/460 - this is implemented directly on the page and not as a plugin (like all the other sections) as it is displayed only when there is relevant data.
New CRISPR cancer cell line data table on evidence page https://github.com/opentargets/platform/issues/466 - tables under “Pathways & systems biology” show when relevant.
Release notes now live in docs (so those in the app are now deprecated)
now separate schema all in one at: https://raw.githubusercontent.com/opentargets/json_schema/1.5.0/opentargets.json - *should* be backwards compatible, no evidence string changes needed
now baked into the REST API docker image
New infrastructure associated with the 19.02 release
Because of the changes to the proxy above, `proxy.opentargets.io` should become `platform-api.opentargets.io/proxy`. The cause is that the Nginx proxy is included in the `rest_api` docker image instead of being separate, which is easier for us to maintain and for partners to use.
Note: Eventually (approx. 6 months), `proxy.opentargets.io` will be decommissioned so anyone running pre-19.02 releases will need to update them.
now configurable from two files - ops and data
data config file will be in public google bucket, can use for pipeline or download & customise
ops config can be on command line, or environment variable, or config file (in decreasing priority)
Example of ops config: https://github.com/opentargets/data_pipeline/blob/19.02.1/mrtarget.ops.yml
including docker, make, config.
incorporates information from data_release wiki, which is now deprecated https://github.com/opentargets/platform/issues/259
PyPI cleanup (Python packaging infrastructure - where client is downloaded from)
packages now have common "opentargets" prefix in the name (except ontoma, working on it!) https://github.com/opentargets/platform/issues/233
Pipeline technical improvements
better handling of --val threads https://github.com/opentargets/platform/issues/350
better handling of --gen exceptions
better handling of remote resources
replace redis queue with pypeln in --hpa https://github.com/opentargets/platform/issues/360
remove unused code (PRs 426-432, 434-436)
fix and improve elasticsearch bulk indexing
cleanup and improve ontology loading and lookup table construction