| Age | Commit message (Expand) | Author |
|---|
| 2023-04-18 | oauth2: update UI and js to display initial search results. | Frederick Muriuki Muriithi |
| 2023-04-17 | Add a link to the GN2 GeneWiki page...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-17 | Add genewiki page...* wqflask/wqflask/templates/generif.html: New template.
* wqflask/wqflask/views.py (display_diffs_users): New route.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-17 | oauth2: Build code to do search...At this point, the code fails with a 404, despite the appropriate
endpoint existing. Will need further debugging.
| Frederick Muriuki Muriithi |
| 2023-04-15 | Revert "Fix the way database_connection() is called"...This reverts commit b8b62aea1c7924e2ee7455c6fe8b34eee7cb8e74.
We do need to decouple the entire `gn3.db_utils` from the
`flask.current_app` object, and as such, the use of `SQL_URI` from the
`utility.tools` module in GN2 was on purpose. This is also to help
towards fixing issue
https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
| Frederick Muriuki Muriithi |
| 2023-04-14 | Handle errors for group consistent with the UI. | Frederick Muriuki Muriithi |
| 2023-04-12 | oauth2: Generalise JS code to work for both mRNA and Genotype datasets. | Frederick Muriuki Muriithi |
| 2023-04-12 | delete dead code | Alexander_Kabui |
| 2023-04-12 | add code to store metadata in files | Alexander_Kabui |
| 2023-04-11 | Fix bug where publication years had links even when there's no PMID...This was just caused by the correlation code not directly being passed the PMID (and instead only being passed the link and the text), so the logic in the table code needed to be changed to check for the link instead of the PMID
| zsloan |
| 2023-04-11 | Fix the way database_connection() is called...I think it now gets the SQL_URI from settings
| zsloan |
| 2023-04-11 | Fix indentation for conn.commit() | zsloan |
| 2023-04-11 | modify default textfile path | Alexander_Kabui |
| 2023-04-10 | Add UI for searching and linking mRNA Assay datasets. | Frederick Muriuki Muriithi |
| 2023-04-10 | Do search. Filter out selected datasets....Enable search when user types in search box. Filter out any selected
datasets.
| Frederick Muriuki Muriithi |
| 2023-04-08 | oauth2: Link the Genotype datasets. | Frederick Muriuki Muriithi |
| 2023-04-07 | Move JS to external file. Generalise functions....Move the javascript to an external file to ease development.
Generalise some functions to make it easier to reuse the code down the line.
| Frederick Muriuki Muriithi |
| 2023-04-06 | Commit updates for phenotype/publication metadata | zsloan |
| 2023-04-06 | `flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`...Genenetwork2 configs are a tad weird, and instead of using the configs
in `flask.current_app`, we need to use those in `utility.tools`.
| Frederick Muriuki Muriithi |
| 2023-04-06 | correlations: Provide more output to enable debug of errors. | Frederick Muriuki Muriithi |
| 2023-04-06 | Remove use of deprecated `gn3.db_utils.database_connector` function....Remove use of deprecated function and fix a myriad of bugs that rise
from its removal.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
| Frederick Muriuki Muriithi |
| 2023-04-06 | oauth2: UI - Enable auto-selection of datasets to be linked...When a user selects a dataset in the search table, automatically add
it to the link table and remove it from the search table.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - Retain look and feel without using jQuery DataTables...Simplify the implementation by dropping the use of the jQuery
DataTables plugin - this avoids a lot of arising bugs while retaining
the UI look and feel until we have something working.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - Autoselect on user click...Try auto-selecting datasets on user click: not successful at this
point.
There are some weird bugs with the DataTables that I have not been
able to resolve yet.
| Frederick Muriuki Muriithi |
| 2023-04-05 | oauth2: UI - retain data in table attributes...Since the table data could change depending on user input, save the
state in the `data-*` attributes to enable update of tables on
changes.
| Frederick Muriuki Muriithi |
| 2023-04-04 | oauth2: Provide UI for linking genotype datasets. | Frederick Muriuki Muriithi |
| 2023-04-03 | Add conn.commit() for metadata edits | zsloan |
| 2023-03-28 | Re-add md5.min.js to search result template | zsloan |
| 2023-03-28 | Only include 'cytochrome AND P450' as part of the placeholder text | zsloan |
| 2023-03-25 | oauth2: Add UI to use to link data | Frederick Muriuki Muriithi |
| 2023-03-24 | oauth2: data: setup search as user types...Filter out data as the user types, with a short delay to prevent
searching on each and every character.
| Frederick Muriuki Muriithi |
| 2023-03-23 | oauth2: data: Provide a UI for linking data, with search....Provide a UI for the phenotype datasets with a search
interface (currently inactive) that is eventually going to allow for
linking the traits to user groups.
| Frederick Muriuki Muriithi |
| 2023-03-22 | Fix search result table width | zsloan |
| 2023-03-21 | The mean deaults to 'N/A' for phenotypes...The previous code caused an error when the mean was N/A (when trying to
take the float() of it)
| zsloan |
| 2023-03-21 | Remove session['user_details'] references since they seem to cause an error | zsloan |
| 2023-03-21 | Replace twitter-post-fetcher with Twitter's provided timeline link | zsloan |
| 2023-03-20 | Add link to diff page when sample-data is updated...* wqflask/wqflask/metadata_edits.py (update_phenotype): Add url to
diff page in flash message.
* wqflask/wqflask/templates/edit_phenotype.html: Render flash message
with HTML.
| Munyoki Kilyungi |
| 2023-03-20 | Fix minor pep-8 issues...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-03-20 | Disable editing case-attributes...ATM, editing case-attributes is very buggy.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Delete.
* wqflask/wqflask/decorators.py: Remove:
gn3.authentication.get_groups_by_user_uid import.
(case_attributes_edit_access): Delete.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Remove
wqflask.decorators.case_attributes_edit_access,
gn3.db.case_attributes.get_case_attributes,
gn3.db.case_attributes.get_unreviewed_diffs,
gn3.db.case_attributes.insert_case_attribute_audit,
gn3.db.case_attributes.reject_case_attribute and
gn3.db.case_attributes.approve_case_attribute.
(display_phenotype_metadata): Remove headers arg when rendering
template.
(update_phenotype): Remove case attribute headers list when updating a
phenotype.
(show_case_attribute_columns, update_case_attributes): Delete.
(reject_case_attribute_data, approve_case_attribute_data): Ditto.
* wqflask/wqflask/templates/edit_phenotype.html: Remove link that
shows all the listed case-attributes.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-03-20 | oauth2: Load menu and populate dropdown...In order to enable searching through the existing datasets for linking
with the auth system, we need a way to filter the data.
In this commit, I load the menu and load it onto a dropdown box as a
proof of concept to give an idea of some of the filters I can use down
the road to fetch the data.
This commit breaks the data-linking code. I will need to rework the
data-linking code entirely to get it working again.
| Frederick Muriuki Muriithi |
| 2023-03-20 | oauth2: Pass the offset in the query | Frederick Muriuki Muriithi |
| 2023-03-20 | oauth2: phenotypes: list/link at trait level...List/link the phenotypes at the trait level rather than at the dataset level.
| Frederick Muriuki Muriithi |
| 2023-03-20 | corrs: Handle JSONDecodeError...In the case that the JSON output from the correlations computation is
malformed, we capture that into a new exception an re-raise it to help
with debugging and fixing issues.
| Frederick Muriuki Muriithi |
| 2023-03-18 | oauth2: resources: toggle whether a resource is public or not. | Frederick Muriuki Muriithi |
| 2023-03-18 | oauth2: resources: Disallow duplicate resource names. | Frederick Muriuki Muriithi |
| 2023-03-17 | Fix correlation bug caused by a NULL UPDATE_TIME in the DB | zsloan |
| 2023-03-16 | Make the two Submit Change buttons consistent | zsloan |
| 2023-03-16 | Edit dataset dropdown JS to handle Species sub-categories | zsloan |
| 2023-03-16 | Change the UI for the phenotype editing page...Edit Sample Data and Edit Metadata are now two separate sections, and Edit Sample Data appears first
| zsloan |
| 2023-03-15 | minor globalsearch enhancement | Alexander_Kabui |
