| Age | Commit message (Expand) | Author |
|---|
| 2023-10-10 | Check whether there's changes before queuing the diff. | Frederick Muriuki Muriithi |
| 2023-10-10 | Process Edit data. Fix bugs and typos....Process the edit data into a CSV form for diff generation.
Fix bug in:
* processing of original data into a CSV
* variable passed to DictWriter
* arguments to functions
| Frederick Muriuki Muriithi |
| 2023-10-10 | Retrieve InbredSet Group's samples/strains...Retrieve the samples/strains that relate to a particular InbredSet group.
| Frederick Muriuki Muriithi |
| 2023-10-10 | Retrieve InbredSet group details. | Frederick Muriuki Muriithi |
| 2023-10-10 | Clean-up original data, and case-attribute names...For diff-generation purposes, this commit processes the data into a form that
is useful for generation of the CSV files to be used for the diffs.
| Frederick Muriuki Muriithi |
| 2023-10-10 | Implement computing of diffs | Frederick Muriuki Muriithi |
| 2023-10-10 | Extract fetching of case-attribute names...Extract the fetching of case-attribute names into a separate function that can
be used elsewhere.
| Frederick Muriuki Muriithi |
| 2023-10-10 | Rename function: Make it clearer what function does. | Frederick Muriuki Muriithi |
| 2023-10-10 | Bug: Fix missing cursor object. | Frederick Muriuki Muriithi |
| 2023-10-10 | Add scaffolding for add/delete endpoints. | Frederick Muriuki Muriithi |
| 2023-10-10 | Add scaffolding for case-attribute editing logic. | Frederick Muriuki Muriithi |
| 2023-10-10 | Extract fetching of case-attributes by InbredSetId | Frederick Muriuki Muriithi |
| 2023-10-10 | Editing: Retrieve case-attribute values for an InbredSet group. | Frederick Muriuki Muriithi |
| 2023-10-10 | Editing: Retrieve case attributes by the related InbredSet | Frederick Muriuki Muriithi |
| 2023-10-10 | Remove authentication from GN3...Authentication should be handled by the auth server (gn-auth) and thus, this
commit removes code handling user authentication from the GN3 system.
| Frederick Muriuki Muriithi |
| 2023-10-06 | pylint: fix variable name. | Frederick Muriuki Muriithi |
| 2023-10-06 | Make argument mandatory...Make the `base_dir` argument mandatory to force it to be passed in from the
point the function is called.
| Frederick Muriuki Muriithi |
| 2023-10-06 | Get `CORRELATION_COMMAND` from current_app not `gn3.settings`...The default settings in `gn3.settings` are meant to be overridden thus the
code should not be importing the setting from there, rather, the code should
get its configurations settings from `flask.current_app.config`.
| Frederick Muriuki Muriithi |
| 2023-10-06 | Provide keyword argument. | Frederick Muriuki Muriithi |
| 2023-10-06 | Pass in configs/settings as function arguments...To avoid reliance of `flask.current_app.config` or on `gn3.settings` modules
globally, this commit passes in the appropriate configurations as arguments to
the relevant functions.
| Frederick Muriuki Muriithi |
| 2023-10-06 | Settings: Add note to discourage importing directly from defaults | Frederick Muriuki Muriithi |
| 2023-09-21 | Fix query in update_cross_reference | zsloan |
| 2023-09-05 | Delete un-used import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary ellipsis...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary string concatenation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove pylint skip...* gn3/auth/authentication/oauth2/models/oauth2token.py
(introspect_token, check_permission): Delete "pylint:
disable=[no-self-use]". R0022: Useless option value for 'disable',
'no-self-use' was moved to an optional extension, see
https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers.
* gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py
(delete_authorization_code): Ditto.
* tests/unit/test_heatmaps.py (test_cluster_traits):
Delete "pylint: disable=R0201". R0022: Useless option value for
'disable', 'no-self-use' was moved to an optional extension, see
https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers.
* tests/unit/computations/test_partial_correlations.py
(test_tissue_correlation): Ditto.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Replace "escape_string" with safe-query parameters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove type annotations for "none_case_attrs" variables...* gn3/db/sample_data.py (update_sample_data, delete_sample_data,
insert_sample_data): Remove type hints for "none_case_attrs".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-08-24 | Change get_pheno_csv_sample_data to use group ID instead of phenotype ID | zsloan |
| 2023-08-18 | Commit on success, rollback on error. | Frederick Muriuki Muriithi |
| 2023-08-17 | Fix query for fetching DataId when inserting ProbeSet data | zsloan |
| 2023-08-17 | Fix a couple remaining issues with function parameters | zsloan |
| 2023-08-17 | Combine pheno/mrna update functions + some other fixes | zsloan |
| 2023-08-17 | Fix queries for fetching group names | zsloan |
| 2023-08-17 | Fix fetch_trait query for phenotypes | zsloan |
| 2023-08-17 | Fix a few misnamed tables in mrna delete/insert functions | zsloan |
| 2023-08-17 | Implement ProbeSet sample data editing...Currently there's a lot of duplicated code, so I need to ask how best to simplify it later
| zsloan |
| 2023-08-17 | Fix probeset sample data and CSV sample data functions | zsloan |
| 2023-08-17 | Fix query for retrieving mrna dataset group name | zsloan |
| 2023-08-17 | Fix get_mrna_sample_data query | zsloan |
| 2023-08-17 | Fix mrna group name query | zsloan |
| 2023-08-17 | Remove Id select from probeset metadata query, since it's included in cols | zsloan |
| 2023-08-17 | Add function for retrieving mRNA Assay group name | zsloan |
| 2023-08-17 | Make several sample_data fetching functions specific to phenotype or mrna ass... | zsloan |
| 2023-08-04 | Remove the ORM-dependent `update` function. | Frederick Muriuki Muriithi |
| 2023-08-02 | Add deprecation notice to ORM-dependent `update` function...Add a deprecation notice to discourage other devs from using the deprecated
`update` function.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `insert` function...Remove the object-relation-mapping dependent `insert` function to prevent it
being used in the code down the line.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Remove ORM-dependent `fetchall` and `fetchone` functions...Remove Object-Relational Mapping dependent function, `fetchall` and `fetchone`
so as to prevent theirs use in the code moving forward.
| Frederick Muriuki Muriithi |
| 2023-08-02 | Integrate Temp traits to Auth...Temporary traits are not saved to the database, and have no attached
resource (at this time). As such, make them all simply public-read to enable
access for users.
This might change after more information on usage of temporary traits is
collected and considered.
| Frederick Muriuki Muriithi |
