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2023-09-05Skip unittestMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace assertRegexpMatches with assertRegexMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Replace scipy.isnan with numpy.isnanMunyoki Kilyungi
* wqflask/wqflask/api/correlation.py (get_sample_r_and_p_values): Replace scipy.isnan with numpy.isnan. scipy.isnan is deprecated and will be removed in SciPy 2.0.0 Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-31Don't show decimal places when all values are integerszsloan
2023-08-31Update URL on tutorials pagezsloan
2023-08-31Use error-display utilityFrederick Muriuki Muriithi
Use the error-display utility to get rid of an unnecessary error-handling function.
2023-08-31Check for token expiryFrederick Muriuki Muriithi
Check whether a token has expired before attempting to use it. Clear the session if the token has expired.
2023-08-24Make download icon on search result page the same as other pageszsloan
2023-08-24Change order of options in mapping page + fix sort for 5th column of tablezsloan
2023-08-24Change inputs for pheno sample data CSV function + only fetch sample data ↵zsloan
for table when fewer than 2000 samples
2023-08-24Change URL for phenotype CSV download + only show sample table if fewer than ↵zsloan
2000 samples
2023-08-17Combine pheno/mrna update functions + add dataset_name parameter for ↵zsloan
fetching group name
2023-08-17Implement ProbeSet sample data editingzsloan
2023-08-17Increase the size of the field for editing phenotype sample data (so it can ↵zsloan
fit up to 6 digits)
2023-08-17Increase the size of the field for editing probe set sample data (so it can ↵zsloan
fit up to 6 digits)
2023-08-17Implement probeset sample data editing up until the approval stepzsloan
2023-08-17Fix probeset editing template to detect changes to sample valueszsloan
2023-08-17Fix probeset editing html to be the same as pheno editingzsloan
2023-08-17Change phenotype CSV endpoint to specify the type of traitzsloan
2023-08-11Revert "Auto-approve Publication Metadata Edit for phenotypes."Frederick Muriuki Muriithi
This reverts commit ce3568ce8e33a7ad1e722d42261913b5649df27f. It turns out we only ever save the approved commits in the database, so there is no point in adding the extra data to indicate that. This has been documented[^1] for the future. 1: https://github.com/genenetwork/gn-gemtext-threads/commit/4e016e43fd05202287730915d129daaed1a02efc
2023-08-11Auto-approve Publication Metadata Edit for phenotypes.Frederick Muriuki Muriithi
Mark all Publication metadata edits as automatically approved.
2023-08-10Set up defaults and check for mandatory settingsFrederick Muriuki Muriithi
Use etc/default_settings.py to setup defaults for the application. Check for mandatory settings and notify users if any of the mandatory settings are not defined.
2023-08-10Bug: Avoid repetition of data. Simplify UI.Frederick Muriuki Muriithi
2023-08-10Clean up data before attempting to persist.Frederick Muriuki Muriithi
2023-08-07Remove Twitter newsfeedzsloan
2023-08-04Remove use of deprecated, ORM-dependent `update` function.Frederick Muriuki Muriithi
2023-08-03Fix Submit Trait bugzsloan
2023-08-02Remove import of deleted `insert` function.Frederick Muriuki Muriithi
2023-08-02Remove import of deleted functions.Frederick Muriuki Muriithi
2023-08-02Fix Bug: Unchanged Values Were Being DeletedFrederick Muriuki Muriithi
The original code (using the homebrew ORM system) would simply ignore values that were `None` when doing updates - the new code using direct queries was not. My (fredmanglis) initial fix to provide a default for values in DB that did not accept NULL was incorrect; instead, I needed to remove any key-value pairs from the incoming data that were set to `None` to fix the bug. The fix still feels incorrect: maybe we should do direct comparisons for all old-new value pairs, and set the data to be updated based on the differences, rather than relying on `None`s.
2023-07-31Fix searches so they work with chromosomes X/Y and both including and not ↵zsloan
including 'chr' As far as I can tell, the regex from before wasn't necessary; it seems like a simple matter of extracting the 'chr' substring from the chromosome search term
2023-07-31Paginate resource data itemsFrederick Muriuki Muriithi
Provide a means to paginate the data items in the resources page.
2023-07-26bug: Fix bug where diffs were not computing correctly.Frederick Muriuki Muriithi
2023-07-26Fetch `metadata_audit` trails with direct queriesFrederick Muriuki Muriithi
Fetch the `metadata_audit` trails for phenotypes and probesets using direct queries rather than the ORM-dependent functions.
2023-07-26Create 'metadata_audit' trail: remove ORM-dependent functionFrederick Muriuki Muriithi
Create a 'metadata_audit' record with a direct query rather than using the ORM-dependent function to create it.
2023-07-26Avoid conflating `dataset_id` with `trait_name`.Frederick Muriuki Muriithi
2023-07-26Commit changes on success, rollback on failure.Frederick Muriuki Muriithi
Ensure that changes the database are committed if the query is successful, or rolled back if not.
2023-07-24Check user is logged in before checking privilegesFrederick Muriuki Muriithi
For editing, ensure the user is logged in before even attempting to check the authorisation privileges.
2023-07-24Display "Edit" button for all usersFrederick Muriuki Muriithi
Display the "Edit" button for all the users to ensure that they are aware of the feature.
2023-07-24Protect the "approve" and "reject" endpointsFrederick Muriuki Muriithi
Protect the actual "approve" or "reject" steps, rather than just the UI elements.
2023-07-24Fix bugsFrederick Muriuki Muriithi
* Add missing `.now()` * Provide defaults (not `None`) for required fields
2023-07-21Fetch and update publication with non-ORM functionsFrederick Muriuki Muriithi
Replace the ORM functions for fetching and updating the publication with non-ORM equivalents.
2023-07-19Replace ORM code with direct queries for ProbeSetsFrederick Muriuki Muriithi
2023-07-18Remove unused importzsloan
2023-07-18Fix issue where the full samplelist wasn't used in the values column for the ↵zsloan
traits export
2023-07-18Replace ORM calls with direct queriesFrederick Muriuki Muriithi
Avoid the use of the ORM code for fetching data from the database, and instead use direct queries that indicate easily what is being fetched from the database.
2023-07-18BugFix: Use reworked `retrieve_phenotype_group_name` functionFrederick Muriuki Muriithi
Use the reworked `retrieve_phenotype_group_name` to fetch the group name for phenotype datasets. == Bug Description == There was a subtle bug in the original calls to `retrieve_group_name` function where the `dataset_id` was passed in as an argument, rather than the group id. For some Datasets, the `group_id` and `dataset_id` share the same value, and would end up querying the correct values, but that was a fluke where doing the wrong thing ended up with the expected values. This commit fixes that by using the reworked function, which does the correct indirection from `dataset_id` to the appropriate `group_id`. See https://github.com/genenetwork/genenetwork3/commit/088b6181457ef4e528b7dcbf04b7aca29b274d1f for the reworked function.
2023-07-17Enable deletion of sample values.Frederick Muriuki Muriithi
2023-07-17Serialize to JSON with custom encoderFrederick Muriuki Muriithi
Serialize values to JSON using the custom encoder that is aware of data types the default encoder might not be aware of.
2023-07-17UI: Change input elementsFrederick Muriuki Muriithi
Change the input elements from all "<textarea ...>" to more closely adhere to the data that each element is concerned with.
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