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* test/requests/test-website.py: Delete "from wqflask import
app". This has the undesired effect of starting an instance of
Genenetwork2.
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Document the configurations for the service, and how to use them when
invoking the service.
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- Limit number of full names to 2 followed by "et al."
- Fix wrong logic that was using the full length of the authors string instead of the truncated length when determining the width of the column, resulting in it always being at least 500px wide
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looks strange
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Previously authentication didn't work correctly if users had "edit" privileges, because the code specifically looked for just "view"; this changes it to check for either "view" or "edit"
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* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is
created.
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These tests touch on core data-structures in gn2; and there's a chance
that refactoring said data-structures may break many things.
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* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper
database connection instead of the db connection attached at "g.db".
* wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto.
* wqflask/wqflask/api/correlation.py: Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
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* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger".
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Add documentation on how to run the tests - this was no clear from the
existing documentation up to this point.
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If the GN2_SETTINGS environment variable, is for some reason, not set,
and the application actually ever tries to get a connection to the
database, then use the default settings/configuration file.
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Also made a large number of other fixes that proved necessary during
testing
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Also store parents/type metadata from source genofiles
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- I was mixing up source/target genofiles previously; the JSON file is for the source genofiles
- references to the app context are removed in favor of just taking input as arguments or environment variables
- Updated example commands
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generate_new_genofiles function
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- Removed some unused code
- Strip marker genotype to avoid newline character at end
- Convert zip to list for marker genotypes
- Add typing to group_samples
- Rename strain_genofile to source_genofile
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gen_ind_genofiles.py is a command line script to generate genotype files for groups of
individuals/samples, taking a source .geno or .json file and a target 'dummy' .geno file as input
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* .github/ISSUE_TEMPLATE/: Delete this directory.
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We have moved to Laminar. See: <https://penguin2.genenetwork.org/>
* .github/workflows/main.yml: Delete it.
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* wqflask/wqflask/metadata_edits.py: Import "extract_invalid_csv_headers"
and "get_allowable_sampledata_headers".
(display_phenotype_metadata): Pass the allowable headers to the
template.
(update_phenotype): If a user uploads data with a column header that's
not in the db, don't upload the file, and send a warning message.
* wqflask/wqflask/templates/edit_phenotype.html: List the allowable
headers in the template.
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This is a WIP.
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Using "database_connection" within a context-manager makes sure that
the SQL connection that is created is closed.
* wqflask/wqflask/metadata_edits.py (display_probeset_metadata):
Connect to the db within a context-manager.
(update_phenotype): Ditto.
(update_probeset): Ditto.
(approve_data): Ditto.
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* wqflask/wqflask/metadata_edits.py (approve_data): Explicitly close a
connection after it is used.
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* wqflask/wqflask/metadata_edits.py (approve_data): Update query
strings.
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* wqflask/wqflask/metadata_edits.py: Replace imports that start with
`db.traits` with `db.sample_data`.
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* wqflask/wqflask/metadata_edits (update_phenotype): The logic was for
generating csv_diff and removing insignificant values in the edits was
moved to gn3; use those functions instead of the manual way.
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* doc/database.org: Also join on StrainId for case-attribute data.
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