Audits #68
Merged
Audits #68
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
Contributor
sbreiff
commented
Jul 18, 2018
sbreiff
commented
- added 4 checks that are meant to replace fourfront audits
- fixed url for foursight dev in getting_started.md
Updated branch from master
chalicelib/checks/wrangler_checks.py
Outdated
| cell_line_types = ["primary cell", "primary cell line", "immortalized cell line", | ||
| "in vitro differentiated cells", "induced pluripotent stem cell line", | ||
| "stem cell", "stem cell derived cell line"] | ||
| biosources = ff_utils.search_metadata('search/?type=Biosource', ff_env=connection.ff_env, page_limit=200) |
There was a problem hiding this comment.
Could this be search/?type=Biosource&frame=object? Would be a bit more performant and it doesn't look like the check uses any embedded fields
chalicelib/checks/wrangler_checks.py
Outdated
| ''' | ||
| check = init_check_res(connection, 'external_expsets_without_pub') | ||
|
|
||
| ext = ff_utils.search_metadata('search/?award.project=External&type=ExperimentSet', |
There was a problem hiding this comment.
Same frame=object comment as above
There was a problem hiding this comment.
As an aside, page_limit=200 makes some pretty big search requests that have to go through Fourfront. I would recommend setting that value lower, especially if you're getting embedded experiment sets
chalicelib/checks/wrangler_checks.py
Outdated
| ''' | ||
| check = init_check_res(connection, 'expset_opfsets_unique_titles') | ||
|
|
||
| opf_expsets = ff_utils.search_metadata('search/?type=ExperimentSet&other_processed_files.files.uuid%21=No+value', |
There was a problem hiding this comment.
For this and the next check, page_limit on the search could be set to 20 or something else low
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.