Release/101 #260
Merged
Release/101 #260
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…e going to set old_server_uri
If we introduce new conservation-score types, we will review the DC
Otherwise, we should have been excluding more classes to make the filter accurate
…ams are running DC for release 1011 but we have not setup the metadata database yet. So instead the code will take whatever is current at the moment, this make sure that the test will run and be correct
Updated logic to use current version of the metadata. For example, te…
…lease 100. Extract the release number from the patch name for sorting.
Fix for sort - can't rely on an alphabetic sort...
…he database in the previous release - this is necessary to distinguish between species that are shared between Ensembl and EnsemblGenomes.
More robust sorting method for schema patches.
And we avoid another "Use of uninitialized value" warning
Add division condition to "old_db" metadata query...
Rename EPO_LOW_COVERAGE->EPO_EXTENDED in compara datacheck modules
Misc Compara changes
Revert "Also check when the assembly length is too long"
…ipelines can run to completion, and b) users get useful information on errors.
…h a single leading space.
… as a datacheck failure rather than dying.
Catch run-time errors and present them as test failures
…pt now extracts data for each species, not just the first one.
Update datachecks related to GO xrefs
…ther than before it - otherwise the TAP is not consistent, and is hard to parse.
…ult - print warning in such cases.
…ave multiple species with the same gene name.
…ross multiple datachecks.
…ded for gene tree highlighting. Not part of 'compara' group, because this data is reliant on the Protein Features pipeline having been run by the Production team.
…ude skip_tests for MLSS tag datachecks, and change group names to match those currently used.
…dna' table have a coord_system 'sequence_level' attribute.
Co-authored-by: CristiGuijarro <cristig@ebi.ac.uk>
New compara datachecks
Adding group for compara ancestral databases.
…to Core DBAdaptors
"ancestral_sequences" is what the Compara API uses to link GenomeDBs to Core DBAdaptors
james-monkeyshines
approved these changes
Jun 12, 2020
Pull Request Test Coverage Report for Build 1230
💛 - Coveralls |
|
There's already a JIRA ticket to address the drop in test coverage, due to the introduction of new compara test methods (https://www.ebi.ac.uk/panda/jira/browse/ENSPROD-5445). |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
11 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Merge 101 release before branching to 102