Cbioportal: "Checked DB schema version: (expected: 0)" in v1.11.x

[fedde-s]

When installing cBioPortal according to the instructions, configuring the server based on portal.properties.EXAMPLE, it's not possible to load any study data whatsoever. The cause of this is that commit c2dbde54054cc85c9a5dcb948d9d661f6adfd49b of pull request #3505 moved a property used by the data loading pipeline to a different file, without adjusting the code that looks for it in portal.properties.

[ersinciftci]

This is fixed in rc a few weeks ago.

[ersinciftci]

I guess this is a duplicated issue with https://github.com/cBioPortal/cbioportal/issues/3855

[fedde-s]

rc will not be released until the next major release though. It would be useful to rebase the fix and have a bugfix release for this, as it's still broken in 1.11.x. Unless 1.12.0 can be released today or tomorrow of course.

[fedde-s]

Either way, I integrated a workaround into the setup automation we use at The Hyve by re-introducing the properties to portal.properties, so it's no longer blocking me personally; I just thought it might be an unpleasant surprise to potential new contributors.

[pieterlukasse]

I agree it better if such fixes go via the new hotfix route (i.e. master) instead of rc. Was blocking for a while, but we found a workaround for now.

[romgrk]

@fedde-s I'm trying to install a new instance of the cBio portal and got stuck exactly at that point. Would you mind sharing a detailed explanation of what should be done to workaround this? Thanks!

[fedde-s]

@romgrk, until a bugfix is released, the workaround is to add these two lines to your portal.properties file before you (re-)run the mvn command that builds cBioPortal from source:

app.version=${timestamp}
db.version=${db.version}

[fedde-s]

I believe the fix for this has been released a while back now.