| Age | Commit message (Expand) | Author |
|---|
| 2022-02-17 | Create client fixture for integration tests...Create a client fixture to help with the integration tests
| Frederick Muriuki Muriithi |
| 2022-02-17 | Use pytest's "mark" feature to categorise tests...Use pytest's `mark` feature to explicitly categorise the tests and run them
per category
| Frederick Muriuki Muriithi |
| 2022-02-17 | Add property tests for `dictify_by_samples`...Add property tests using pytest and hypothesis to test that the expected
properties hold for the
`gn3.computations.partial_correlations.dictify_by_samples`
function.
| Frederick Muriuki Muriithi |
| 2022-02-12 | Provide custom class to run tests | Frederick Muriuki Muriithi |
| 2022-02-11 | sql: Remove database mapping code....These tools have been greatly improved and moved to a new home at
https://git.genenetwork.org/arunisaac/dump-genenetwork-database
* sql/map-database.sh, sql/schema-from-in-db-documentation.org,
sql/schema-original.sql, sql/schema.png, sql/schema.sql, sql/schema.svg: New
files.
| Arun Isaac |
| 2022-02-11 | Add scaffolding to run different types of tests...Enable running commands:
- `python3 setup.py unit_check`: run the unit tests
- `python3 setup.py integration_check`: run integration tests
- `python3 setup.py performance_check`: run performance tests
| 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 |
| 2022-02-09 | github: Remove GitHub actions....We have our own laminar CI and no longer need GitHub actions.
* .github/workflows: Delete directory.
| Arun Isaac |
| 2022-02-09 | Remove obsolete `PublishFreeze` table | Frederick Muriuki Muriithi |
| 2022-02-08 | Merge iterations to remove unnecessary computations...Do all the work in a single iteration to avoid unnecessary iterations that
hamper performance.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Remove multiprocessing for stability...Web servers are long-running processes, and python is not very good at
cleaning up after itself especially in forked processes - this leads to memory
errors in the web-server after a while.
This commit removes the use of multiprocessing to avoid such failures.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Give sorting functions more descriptive names | Frederick Muriuki Muriithi |
| 2022-02-08 | Use multiprocessing to speed up computation...This commit refactors the code to make it possible to use multiprocessing to
speed up the computation of the partial correlations.
The major refactor is to move the `__compute_trait_info__` function to the
top-level of the module, and provide to it all the other necessary context via
the new args.
| Frederick Muriuki Muriithi |
| 2022-02-08 | Remove unnecessary computation...In Python3 when slicing,
seq[:min(some_val, len(seq))] == seq[:some_val]
because Python3 will just return a copy of the entire sequence if `some_val`
happens to be larger/greater than the length of the sequence.
This commit removes the unnecessary call to `min()`
| Frederick Muriuki Muriithi |
| 2022-02-08 | db: traits: Enable deletion of individual sample values...If a user replaces an individual value with an "x", delete that date entry
from the respective table. Deletion here is the only option since by default
the Nstrain, PublishData and PublishSE don't accept null values. Note that
deleting all 3 values is equivalent to removing the sample from the CSV file.
* gn3/db/traits.py (update_sample_data): If a value is "x", delete it from the
respective table.
| BonfaceKilz |
| 2022-02-08 | db: traits: Allow insertions of "0" in resp. sample values tables...When editing values from "x" to "0"(or any other value) when editing data, an
"update" statement was being run; thereby no new value was being inserted. To
the end user, modifying an "x" value to something else meant that no value was
being inserted. This commit fixes that by doing an insert whenever a change
from "x" to "0" is performed.
* gn3/db/traits.py (update_sample_data): Add insert statements whenever an
"update" statement returns a 0 row-count.
| BonfaceKilz |
| 2022-02-08 | db: traits: Insert "count" instead of "error" in "NStrain" table | BonfaceKilz |
| 2022-02-03 | db: Fetch correct sample data | BonfaceKilz |
| 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 PublishFreeze from retrieve_publish_trait_info query...The PublishFreeze table isn't necessary in phenotype queries, since
PublishFreeze.Id = InbredSet.Id (for the purposes of identifying traits,
at least)
| zsloan |
| 2022-02-02 | Fix bug where sample values of 0 were being treated as False...In line 91 of gn3/db/traits.py, there was an if statement "if
record[key] else 'x'" that was treating values of 0 as False, so I
changed it to explicitly check that values aren't None
| zsloan |
| 2022-02-02 | Fix retrieve_publish_trait_data query...The PublishFreeeze table is actually unnecessary for this query, since
the group ID (inbred_set_id) should be passed in and that ID is in the
PublishXRef table (so no neeed to join with PublishFreeze)
| zsloan |
| 2022-02-02 | response object error fix | Alexander Kabui |
| 2022-02-02 | pep8 formatting | Alexander Kabui |
| 2022-02-02 | remove comments | Alexander Kabui |
| 2022-02-02 | return 401 on request fail | Alexander Kabui |
| 2022-02-02 | refactor code for invoking ctl script | Alexander Kabui |
| 2022-02-02 | pep8 formatting | 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 |
| 2022-02-02 | fix comprehension list | Alexander Kabui |
| 2022-02-02 | Revert "Use guix shell shortcut with guix.scm file"...This reverts commit f676c291967f8a81836b73c5a5dcd3c65e02552c.
| BonfaceKilz |
| 2022-01-27 | Use guix shell shortcut with guix.scm file | jgart |
| 2022-01-24 | README: Add pylint and mypy CI badges....We now have separate CI jobs for the pylint and mypy tests.
* README.md: Add pylint and mypy CI badges.
| Arun Isaac |
| 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 | process ctl plot data img | Alexander Kabui |
| 2022-01-22 | generate ctl plots for each trait | Alexander Kabui |
| 2022-01-22 | read stdout data;handle exceptions | Alexander Kabui |
| 2022-01-22 | generate required json data for ctl api | Alexander Kabui |
| 2022-01-22 | fixes for ctl script:generate ctl ctl_significant json | Alexander Kabui |
| 2022-01-22 | bugfixes for script;create pheno and geno objects | Alexander Kabui |
| 2022-01-22 | add endpoint for ctl | Alexander Kabui |
| 2022-01-22 | init file to call ctl script | Alexander Kabui |
| 2022-01-22 | generate lineplot | Alexander Kabui |
| 2022-01-22 | minor fix:read input data from json file | Alexander Kabui |
