bq query audit [VS-1396] #8847
Merged
bq query audit [VS-1396] #8847
Conversation
This file contains 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
|
Have you run an integration test? |
gbggrant
reviewed
May 28, 2024
mcovarr
commented
May 29, 2024
| NUMANRESULTS=$(awk 'END{print NR}' bq_an_output.csv) | ||
| NUMACRESULTS=$(awk 'END{print NR}' bq_ac_output.csv) | ||
|
|
||
|
|
||
| echo "false" > ~{pf_file} | ||
| # if the results of the queries have any rows, that means there are sites with mis-matched gvs_all_an or gvs_all_ac | ||
| if [[ $NUMANRESULTS != "0" ]]; then | ||
| echo "The VAT table ~{fq_vat_table} has mis-matched calculations for AC, and AC of subpopulations" > ~{results_file} | ||
| echo "The VAT table ~{fq_vat_table} has mis-matched calculations for AC, and AC of subpopulations, 100 rows max shown in results." 1>&2 |
There was a problem hiding this comment.
I'm not sure this is the very best way to handle the error message (suggestions please!), but the existing code was wrong: we wrote an error message to ~{results_file} and then immediately clobbered it with the CSV output from bq query. There's another pattern for this used above that I like even less so I'm reluctant to switch to that...
| cp bq_an_output.csv ~{results_file} | ||
| elif [[ $NUMACRESULTS != "0" ]]; then | ||
| echo "The VAT table ~{fq_vat_table} has mis-matched calculations for AN, and AN of subpopulations" > ~{results_file} | ||
| echo "The VAT table ~{fq_vat_table} has mis-matched calculations for AN, and AN of subpopulations, 100 rows max shown in results." 1>&2 |
There was a problem hiding this comment.
same situation as above
| @@ -395,7 +397,7 @@ task SpotCheckForExpectedTranscripts { | |||
| echo "The VAT table ~{fq_vat_table} only has the expected transcripts at the tested location ('IGFLR1' and 'AD000671.2' in chromosome 19, between positions 35,740,407 - 35,740,469)." > ~{results_file} | |||
| echo "true" > ~{pf_file} | |||
| else | |||
| echo "The VAT table ~{fq_vat_table} had unexpected transcripts at the tested location: [csv output follows] " > ~{results_file} | |||
| echo "The VAT table ~{fq_vat_table} had unexpected transcripts at the tested location: [csv output with 100 results max follows] " > ~{results_file} | |||
There was a problem hiding this comment.
Incidental finding: this is a bit strange, the result is a CSV with an extra line of error message at the top
There was a problem hiding this comment.
small lol that there are these issues with the VAT validation
| @@ -479,7 +482,7 @@ task SchemaNoNullRequiredFields { | |||
| echo "The VAT table ~{fq_vat_table} has no null values in required fields" > ~{results_file} | |||
| echo "true" > ~{pf_file} | |||
| else | |||
| echo "The VAT table ~{fq_vat_table} had null values in required fields: [csv output follows] " > ~{results_file} | |||
| echo "The VAT table ~{fq_vat_table} had null values in required fields: [csv output with 100 results max follows] " > ~{results_file} | |||
| @@ -597,7 +602,7 @@ task SchemaPrimaryKey { | |||
| echo "The VAT table ~{fq_vat_table} has all unique key combinations (vid+transcript)" > ~{results_file} | |||
| echo "true" > ~{pf_file} | |||
| else | |||
| echo "The VAT table ~{fq_vat_table} had repeating key combinations (vid+transcript): [csv output follows] " > ~{results_file} | |||
| echo "The VAT table ~{fq_vat_table} had repeating key combinations (vid+transcript): [csv output with 100 results max follows] " > ~{results_file} | |||
rsasch
reviewed
May 29, 2024
| @@ -117,7 +117,8 @@ task CoreStorageModelSizes { | |||
| local table_pattern="$1" | |||
| local output_file_name="$2" | |||
|
|
|||
| bq --apilog=false query --project_id='~{project_id}' --format=csv --use_legacy_sql=false \ | |||
| # bq query --max_rows check: explicitly set massive max rows as we expect there to be as many rows as there are superpartitions | |||
There was a problem hiding this comment.
isn't this going to always return one line because it's a sum()?
RoriCremer
approved these changes
May 29, 2024
RoriCremer
reviewed
May 29, 2024
| @@ -117,7 +117,8 @@ task CoreStorageModelSizes { | |||
| local table_pattern="$1" | |||
| local output_file_name="$2" | |||
|
|
|||
| bq --apilog=false query --project_id='~{project_id}' --format=csv --use_legacy_sql=false \ | |||
| # bq query --max_rows check: ok one row | |||
| bq --apilog=false query --max_rows 10000000 --project_id='~{project_id}' --format=csv --use_legacy_sql=false \ | |||
There was a problem hiding this comment.
do we eventually want the max_rows to be a param somewhere?
mcovarr
force-pushed
the
vs_1396_bq_query_audit
branch
from
6fcfb2a
to
afa1718
Compare
rsasch
approved these changes
May 29, 2024
|
Integration run here |
mcovarr
added a commit
that referenced
this pull request
May 31, 2024
mcovarr
added a commit
that referenced
this pull request
Jun 7, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
No description provided.