clickhouse.sql fixes #11577
Merged
clickhouse.sql fixes #11577
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
aaffb6c to
7036516
Compare
- add sql to "fix" sample_profile table with missing samples (in mutated case list but not represented in sample_profile) - add MUTATION_UNCALLED to excluded profiles (this profile type should not be included in genetic_alteration_derived) - include protein-encoding events (drop the filtering of off-panel genes from profiles) - whitespace in pom.xml standardized to two space indenting - add correction code for clickhouse import tests Co-authored-by: alisman <[email protected]> Co-authored-by: Robert Sheridan <[email protected]>
7036516 to
eeaa418
Compare
|
alisman
reviewed
Jun 10, 2025
| JOIN gene g ON ga.genetic_entity_id = g.genetic_entity_id | ||
| WHERE | ||
| gp.genetic_alteration_type NOT IN ('GENERIC_ASSAY', 'MUTATION_EXTENDED', 'STRUCTURAL_VARIANT')) | ||
| gp.genetic_alteration_type NOT IN ('GENERIC_ASSAY', 'MUTATION_EXTENDED', 'MUTATION_UNCALLED', 'STRUCTURAL_VARIANT')) |
There was a problem hiding this comment.
@sheridancbio this is intentional?
There was a problem hiding this comment.
Yes. The profile type "MUTATION_UNCALLED" is present in the public portal database and was not account for previously. These events should not be attempted to be put into genetic_alteration_derived.
|
Note: derived_table_schema version 1.0.1 was present in this PR, which is now superceeded and so will be closed: |
4 tasks
gulshan2052
pushed a commit
to gulshan2052/cbioportal
that referenced
this pull request
Jun 13, 2025
- add sql to "fix" sample_profile table with missing samples (in mutated case list but not represented in sample_profile) - add MUTATION_UNCALLED to excluded profiles (this profile type should not be included in genetic_alteration_derived) - include protein-encoding events (drop the filtering of off-panel genes from profiles) - whitespace in pom.xml standardized to two space indenting - add correction code for clickhouse import tests Co-authored-by: alisman <[email protected]>
forus
pushed a commit
that referenced
this pull request
Jun 17, 2025
- add sql to "fix" sample_profile table with missing samples (in mutated case list but not represented in sample_profile) - add MUTATION_UNCALLED to excluded profiles (this profile type should not be included in genetic_alteration_derived) - include protein-encoding events (drop the filtering of off-panel genes from profiles) - whitespace in pom.xml standardized to two space indenting - add correction code for clickhouse import tests Co-authored-by: alisman <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 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.
Describe changes proposed in this pull request:
Checks
Any screenshots or GIFs?
If this is a new visual feature please add a before/after screenshot or gif
here with e.g. Giphy CAPTURE or Peek
Notify reviewers
Read our Pull request merging
policy. It can help to figure out who worked on the
file before you. Please use
git blame <filename>to determine thatand notify them either through slack or by assigning them as a reviewer on the PR