| Age | Commit message (Expand) | Author |
|---|
| 2023-06-02 | auth: Increase limit to 100K records | Frederick Muriuki Muriithi |
| 2023-06-02 | auth: Add delay between DB inserts...Add delays to avoid overwhelming the DB server.
| Frederick Muriuki Muriithi |
| 2023-06-02 | Auth: Bug: Display all admins before taking choice | Frederick Muriuki Muriithi |
| 2023-05-31 | scripts: Write table checksums into index....* scripts/index-genenetwork (main): Write table checksums into index.
| Arun Isaac |
| 2023-05-31 | scripts: Introduce SQLTableClause....* scripts/index-genenetwork (SQLTableClause): New variable.
(genes_query, phenotypes_query): Express tables using SQLTableClause.
(serialize_sql): Serialize SQLTableClause.
| Arun Isaac |
| 2023-05-31 | scripts: Fold long lines....* scripts/index-genenetwork (write_document, index_query): Fold long lines.
| Arun Isaac |
| 2023-05-31 | scripts: Ensure only one indexing job may run at a time....* scripts/index-genenetwork (main): Ensure no other indexing job is running.
| Arun Isaac |
| 2023-05-30 | Fix linting errors and failing tests...* scripts/register_sys_admin.py: fix linting error
* tests/unit/auth/fixtures/oauth2_client_fixtures.py: hash client secret in
database. The code expects it hashed in the database.
| Frederick Muriuki Muriithi |
| 2023-05-30 | Enable registering sys-admin on CLI...To ease registration of system-admin user, provide a CLI script to register
the user and mark them as sys admin in one go.
| Frederick Muriuki Muriithi |
| 2023-05-26 | Document CLI Utility Commands...Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.
| Frederick Muriuki Muriithi |
| 2023-05-25 | Add some error checks. | Frederick Muriuki Muriithi |
| 2023-05-25 | Script to assign existing data to publicly-visible resources...A script to assign existing data not assigned to any group to publicly-visible
resources.
| Frederick Muriuki Muriithi |
| 2023-05-22 | Make directory at "path" and all intermediate ones....Make the directory at the given path, and any intermediate ones to avoid
errors in the indexing code when the directory, or its parent(s) do not exist.
| Frederick Muriuki Muriithi |
| 2023-04-19 | oauth2: Link the phenotype traits to user groups. | Frederick Muriuki Muriithi |
| 2023-04-19 | Fix minor linting and typing issues | Frederick Muriuki Muriithi |
| 2023-04-19 | auth: Setup selected traits correctly...Fix bugs with setting up of the selected traits for use while filtering the
search results.
| Frederick Muriuki Muriithi |
| 2023-04-18 | auth: Consistently JSON encode values....Consistently encode all values for the top-level keys stored in redis to avoid
issues with json encode/decode
| Frederick Muriuki Muriithi |
| 2023-04-17 | Hook up code to use external search script for phenotypes | Frederick Muriuki Muriithi |
| 2023-04-14 | auth: Add external script to search for phenotypes...We need a search through the available phenotype traits in the database when
linking the traits to user groups. Unfortunately, the Xapian Search indexes do
not (and should not) include the internal identifiers we use to disambiguate
the traits.
On the other hand, we do not want to present the user with traits that have
already been linked to any user group within the search results.
The script in this commit, together with the modified queries for fetching the
phenotype data form a "hack" of sorts to wrap around the way the search works
while ensuring we do not present the user with "non-actionable" (linked)
traits in the search results.
| Frederick Muriuki Muriithi |
| 2023-04-06 | Remove deprecated `gn3.db_utils.database_connector` function...Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
| Frederick Muriuki Muriithi |
| 2023-04-05 | Enable use of `database_connection` in scripts without current_app...There is need to run external scripts using the same configurations as the
application but without the need to couple the script to the application.
In this case, we provide the needed configuration directly in the CLI, and
modify the existing `gn3.db_utils.database_connection` function to allow it to
work coupled to the app or otherwise.
| Frederick Muriuki Muriithi |
| 2023-02-13 | scripts: Fallback to 1 worker when indexing....* scripts/index-genenetwork (worker_queue): Set default number of workers to 1
if the number of CPUs cannot be determined.
| Arun Isaac |
| 2023-02-13 | scripts: Type hint xapian indexing script....* scripts/index-genenetwork: Import Callable, Generator, Iterable and List
from typing. Type hint all functions.
| Arun Isaac |
| 2022-10-18 | Add xapian indexing script....* scripts/index-genenetwork: New file.
* setup.py (install_requires): Add click, pymonad and xapian-bindings.
(scripts): Add scripts/index-genenetwork.
| Arun Isaac |
| 2022-07-29 | New script to run sample correlations...* README.md: update mypy's invocation
* scripts/argparse_actions.py: new file - implement custom FileCheck action
for argparse
* scripts/sample_correlations.py: new file - implement new script to run
sample correlations in an external process
| Frederick Muriuki Muriithi |
| 2022-06-28 | Parse the method from UI before passing it to external process...To reduce the chances of the system failing due to the external process being
launched with the wrong parameters, add a parsing stage that converts the
method from the UI into a form acceptable by the CLI script.
* gn3/commands.py: parse the method from UI
* scripts/partial_correlations.py: simplify the acceptable methods
| Frederick Muriuki Muriithi |
| 2022-06-20 | Restrict partial correlation method choices...- Have "Pearson's r" and "Spearman's rho" as the only valid choices for the
partial correlations
| Frederick Muriuki Muriithi |
| 2022-05-24 | Run partial correlations with external script...Use new external script to run the partial correlations for both cases,
i.e.
- against an entire dataset, or
- against selected traits
| Frederick Muriuki Muriithi |
| 2022-05-24 | New script to compute partial correlations...* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
| Frederick Muriuki Muriithi |
| 2022-05-05 | Extract common error checking. Rename function....* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
| Frederick Muriuki Muriithi |
| 2022-03-22 | Merge branch 'feature/add_rqtl_pairscan' of https://github.com/zsloan/genenet... | zsloan |
| 2022-03-22 | Change order of if statements for running genoprob command...Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)
Also added a couple more verbose prints
| zsloan |
| 2022-03-22 | Updated rqtl_wrapper to also return a map file when doing a pair-scan (since ... | zsloan |
| 2022-03-22 | Added line priting pair-scan results to CSV and changed the default step-size... | zsloan |
| 2022-03-22 | - Added scan_func function that determines whether scanone or scantwo...(pairscan) is used
- For pairscan default to using step 20 (subject to change, but some
step is required during calc.genoprob to make it run fast enough)
- Added some new verbose prints
| zsloan |
| 2022-03-22 | Added option for running pairscan to rqtl_wrapper.R | zsloan |
| 2022-03-08 | Create database connections within context managers...Use the `with` context manager to open database connections, so as to ensure
that those connections are closed once the call is completed. This hopefully
avoids the 'too many connections' error
| Frederick Muriuki Muriithi |
| 2022-03-03 | Run partial correlations in an external process...Run the partial correlations code in an external python process decoupling it
from the server and making it asynchronous.
Summary of changes:
* gn3/api/correlation.py:
- Remove response processing code
- Queue partial corrs processing
- Create new endpoint to get results
* gn3/commands.py
- Compose the pcorrs command to be run in an external process
- Enable running of subprocess commands with list args
* gn3/responses/__init__.py: new module indicator file
* gn3/responses/pcorrs_responses.py: Hold response processing code extracted
from ~gn3.api.correlations.py~ file
* scripts/partial_correlations.py: CLI script to process the pcorrs
* sheepdog/worker.py:
- Add the *genenetwork3* path at the beginning of the ~sys.path~ list to
override any GN3 in the site-packages
- Add any environment variables to be set for the command to be run
| Frederick Muriuki Muriithi |
| 2022-02-11 | Quote shell variables to prevent globbing...Quote the shell variables to prevent globbing and word splitting.
Deactivate this check for the specific lines that require intentional word
splitting
| Frederick Muriuki Muriithi |
| 2022-02-02 | Fix R/qtl covar bug...The rqtl_wrapper script was throwing an error when only a single
categorical covariate was used. This is apparently because "covars[,name]"
throws an error in such a situation. Using just "covars" in such a
situation prevents the error. So I just added an if statement checking
the number of covariates. There might be some better way to deal with
this in R, but this is the best I could come up with.
| zsloan |
| 2022-02-02 | remove comments | Alexander Kabui |
| 2022-02-02 | match case string input to boolean | Alexander Kabui |
| 2022-02-02 | fix for parametric input | Alexander Kabui |
| 2022-02-02 | use user input significance | Alexander Kabui |
| 2022-02-02 | new line fix | Alexander Kabui |
| 2022-02-02 | add new json output | Alexander Kabui |
| 2022-01-22 | minor refactoring | Alexander Kabui |
| 2022-01-22 | function override:fix target specific output file for network | Alexander Kabui |
| 2022-01-22 | generate network | Alexander Kabui |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui |
