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2022-04-07Create a new page to display case-attributes and their descriptionsBonfaceKilz
* wqflask/wqflask/metadata_edits.py: Import "gn3.db.sample_data.get_case_attributes". (show_case_attribute_columns): New function/ end-point to show case-attributes. * wqflask/tests/integration/wqflask/test_metadata_edits.py: New integration tests for the above. * wqflask/tests/integration/wqflask/__init__.py: New file. * wqflask/wqflask/templates/case_attributes.html: New template file to display the above.
2022-04-06Changed some styling for the edit_phenotype templatezsloan
2022-04-05Fix combined searches involving aliaseszsloan
The logic for building the SQL query wasn't working correctly when aliases were involved. The query also checks for a gene symbol's aliases in the DB, but this wasn't properly handling the AND/OR logic, leading to no results being shown when doing a "Get Combined" search involving a gene symbol. This also removed some unused code related to aliases.
2022-04-04Return None in load_json_from_redis when the item doesn't existzsloan
For some reason that isn't clear to me yet, a logged-in user session ID was set even when a user wasn't logged in, causing the user session code to attempt to fetch user information for a non-existent user ID
2022-04-04Change UserSession to properly remove user session ID when not logged inzsloan
It's not entirely clear to me exactly why the previous logic wasn't working correctly, but this change (that removes the user cookie when there's no user_session after the request and returns None if there aren't any user_details) appears to fix the issue. The main confusing part is why the user_cookie still exists even when not logged in
2022-04-01Fix the way database_connection was being called in 2 places inzsloan
metadata_edits.py For some reason there were two places where it wasn't being called as a function. Fixing this appears to have fixed the error
2022-03-31Add another check for >1 markers on a chromosome for interval mappingzsloan
There were two places this needed to be checked and I previously missed this one
2022-03-31Replace 'User Account Settings' with user's e-mail and add user_emailzsloan
property to user_session Also changed the order of the dropdowns to have Sign Out after the user drop-down, to more closely match NCBI's style
2022-03-31Fix the way database_connector is calledzsloan
The function returns a call to mdb.connect, which only returns the connection object. It was throwing an error due to trying to unpack multiple items. One thing I noticed while looking at this is that we should probably decide on a single way to create these connections. In some other files, we instead use database_connection from wqflask.database (instead of the gn3 database_connector from gn3.db_utils)
2022-03-30Merge pull request #690 from Alexanderlacuna/chore/ctl-wgcna-enhancementsAlexander Kabui
Chore/ctl wgcna enhancements
2022-03-30Remove double-encoding to jsonFrederick Muriuki Muriithi
Passing the data into `requests.post` as a `json=...` argument will automatically encode the data to JSON and set up the correct Content-Type header. The call `json.dumps(post_data)` was pre-encoding the data to a JSON string, that was the re-encoded to JSON yet again, which is not what we want. This commit fixes that.X
2022-03-25Fix Spearman Rank correlation appearing as 'r' instead of 'rho'zsloan
2022-03-25Fix issues that prevented genotype traits from being added to collectionszsloan
Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function
2022-03-24Check if there's only one coordinate for interval mappingzsloan
This is meant to deal with edge cases where there's only a single coordinate for a chromosome when doing interval mapping (which causes an error, since interval mapping requires that markers be linked within each chromosome)
2022-03-24Fix qtlreaper results sorting to deal with M as chromosome (should be at the ↵zsloan
end) Not sure how best to do this; I just had the sort algorithm change "M" to "z" (which will always be sorted last, behind X and Y)
2022-03-24code refactoringAlexander Kabui
2022-03-24display parametric values usedAlexander Kabui
2022-03-24rename template to gn3_wgcna_resultsAlexander Kabui
2022-03-22Fix logic for setting interval parameterzsloan
The parameter should never be interval if pair_scan is being run; not checking for this causes the --interval tag to pointlessly be included when running pair-scan, which also interferes with caching
2022-03-22Fix way pair_scan is checkedzsloan
Previously it would always register as True, due to being in the start_vars
2022-03-22Set pair_scan to false when using regular R/qtl mappingzsloan
2022-03-22Change d3panels CSS/JS to min fileszsloan
2022-03-22Merge remote-tracking branch 'origin/testing' into feature/add_rqtl_pairscanzsloan
2022-03-18add uniform font for titleAlexander Kabui
2022-03-18remove correlation test buttonAlexander Kabui
2022-03-18fixes for ImageButtonOptionsAlexander Kabui
2022-03-18code to fetch scree data from gn3Alexander Kabui
2022-03-18integrate scree plotAlexander Kabui
2022-03-18Merge pull request #671 from Alexanderlacuna/feature/gn3-pcaAlexander Kabui
Replace pca rpy2 code
2022-03-17Fix/change Authors column in phenotype search resultszsloan
- 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
2022-03-17Set min-width for table container, so the table never ends up so narrow it ↵zsloan
looks strange
2022-03-17Fix authentication for phenotype search resultszsloan
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"
2022-03-17Lint some test filesBonfaceKilz
2022-03-17Fix failing testBonfaceKilz
2022-03-17Create a db connection correctlyBonfaceKilz
* wqflask/maintenance/quantile_normalize.py: Fix how the cursor is created.
2022-03-17Skip unittestsBonfaceKilz
These tests touch on core data-structures in gn2; and there's a chance that refactoring said data-structures may break many things.
2022-03-17Replace "g.db" object with a proper database connectionBonfaceKilz
* 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.
2022-03-17Delete dead codeBonfaceKilz
2022-03-17Delete unused "logger" importBonfaceKilz
* wqflask/wqflask/snp_browser/snp_browser.py: Remove "getLogger".
2022-03-17Provide path to default settings/configuration file as a fallbackFrederick Muriuki Muriithi
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.
2022-03-16Remove unnecessary print statementzsloan
2022-03-16Replace top comment with docstringzsloan
2022-03-16Add code generating the new genotype fileszsloan
Also made a large number of other fixes that proved necessary during testing
2022-03-16Generate JSON file for target genotypeszsloan
Also store parents/type metadata from source genofiles
2022-03-16Fix the way target/source genofiles were being processed + some other changeszsloan
- 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
2022-03-16Add function for mapping strain to sample pos + begin creating ↵zsloan
generate_new_genofiles function
2022-03-16Add function for getting strain name from sample namezsloan
2022-03-16Change EOL from CRLF to LFzsloan
2022-03-16Minor changes/bug fixeszsloan
- 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
2022-03-16Add in-progress gen_ind_genofiles.pyzsloan
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