| Age | Commit message (Expand) | Author |
|---|
| 2025-05-19 | Provide missing URI to the MariaDB database to the script. | Frederick Muriuki Muriithi |
| 2025-05-19 | Cross-reference phenotypes, publications, and data. | Frederick Muriuki Muriithi |
| 2025-05-19 | Retrieve publication first. | Frederick Muriuki Muriithi |
| 2025-05-19 | Simplify handling of publications: Assume a maximum of one.•••Adding publication details in the R/qtl2 bundle might not be an easy
thing, so for now, assume all the phenotypes uploaded in a particular
session are all published in one publication.
| Frederick Muriuki Muriithi |
| 2025-05-19 | Add placeholder stub to be implemented later. | Frederick Muriuki Muriithi |
| 2025-05-19 | Add some notes for later. | Frederick Muriuki Muriithi |
| 2025-05-19 | Save numeric/computational data for phenotypes. | Frederick Muriuki Muriithi |
| 2025-05-19 | Retrieve samples' details from the database. | Frederick Muriuki Muriithi |
| 2025-05-19 | Add function to save the numerical data for phenotypes. | Frederick Muriuki Muriithi |
| 2025-05-19 | Use correct files for basic phenotypes data. Add notes to self.•••The basic phenotype data will be in files under the key
"gn-metadata" -> "pheno". We support the possibility of having some
descriptions in the "phenocovar" files, since that can happen also.
| Frederick Muriuki Muriithi |
| 2025-05-19 | Rework order of execution of potential steps. | Frederick Muriuki Muriithi |
| 2025-05-19 | Cleanup function call. | Frederick Muriuki Muriithi |
| 2025-05-19 | Fetch next available PublishXRef.DataId value for the phenotypes. | Frederick Muriuki Muriithi |
| 2025-05-19 | Save the basic phenotypes data into the database. | Frederick Muriuki Muriithi |
| 2025-05-19 | Read headers from a CSV file, whether transposed or not. | Frederick Muriuki Muriithi |
| 2025-05-19 | Pass Connection rather than Cursor: Transaction is maintained.•••The idea is that all the data is saved to the database in a single
transaction, rather than in bits that could lead to data
inconsistencies.
As it were, simply passing the connection object, and letting each
function create its own cursor will still allow the transaction to be
maintained and will not necessitate the refactor of multiple already
existing functions.
| Frederick Muriuki Muriithi |
| 2025-05-19 | Initialise function to save publications•••Do a rudimentary save of the publications: this is incomplete and
probably very buggy.
| Frederick Muriuki Muriithi |
| 2025-05-19 | Setup log format for the application. | Frederick Muriuki Muriithi |
| 2025-05-12 | Wireframe saving the data into the database. | Frederick Muriuki Muriithi |
| 2025-05-12 | Print out progress to STDOUT. | Frederick Muriuki Muriithi |
| 2025-05-12 | Use builtin functions to compute log level. | Frederick Muriuki Muriithi |
| 2025-05-12 | Pass in the logger, rather than the name of the logger. | Frederick Muriuki Muriithi |
| 2025-05-12 | Handle exceptions within the `with` to prevent silent failure•••One, or both of the context managers is "swallowing" exceptions,
leading to silent failures. This change manually handles the
exceptions within the context manager to avoid such silent failures.
| Frederick Muriuki Muriithi |
| 2025-05-12 | Break "merge file" race-condition•••Multiple requests/threads were attempting to merge the same file,
leading to race conditions, and sometimes, rarely, it would lead to
actual data corruption.
| Frederick Muriuki Muriithi |
| 2025-05-12 | Allow lowercase versions of the log-level choices. | Frederick Muriuki Muriithi |
| 2025-05-12 | BugFix: Don't scroll to top of page on clicking "Browse" buttons.•••This fixes the behaviour where clicking the "Browse" buttons on any of
the resumable elements, the viewport would scroll to the top of the page.
| Frederick Muriuki Muriithi |
| 2025-05-09 | Use more of the screen width for content on smaller screens.•••Display only the links and main content on screens smaller than 20 CSS
inches — the idea is that laptop screens and smaller will only display
the links and the main content, leaving the sidebar content hidden.
| Frederick Muriuki Muriithi |
| 2025-05-05 | Init setup and script for async job to load phenotypes into database | Frederick Muriuki Muriithi |
| 2025-05-05 | Save/Create new phenotypes in the database. | Frederick Muriuki Muriithi |
| 2025-05-05 | Provide endpoint for loading data after QC is successful. | Frederick Muriuki Muriithi |
| 2025-05-05 | Require that the publication is present. | Frederick Muriuki Muriithi |
| 2025-05-05 | Move previews below each item rather than being in the sidebar. | Frederick Muriuki Muriithi |
| 2025-05-05 | Include the publication when provided. | Frederick Muriuki Muriithi |
| 2025-05-05 | Allow plain text files too. | Frederick Muriuki Muriithi |
| 2025-05-02 | Mark directories as packages to make modules unique. | Frederick Muriuki Muriithi |
| 2025-05-02 | PoC: Use independent module-level loggers with application•••Using flask.current_app.logger for logging in modules leads to the
modules requiring an app context, even when the module itself could be
used outside of the application.
This commit provides a proof-of-concept (really, me finally putting in
the effort to figure out logging) for how we could allow independent
loggers at the module level, that can then be hooked up to the main
logging in the system in question.
| Frederick Muriuki Muriithi |
| 2025-05-02 | Format abstracts a little better. | Frederick Muriuki Muriithi |
| 2025-04-28 | Provide correct redirection uri, and data. | Frederick Muriuki Muriithi |
| 2025-04-28 | Encode data to UTF-8 to prevent persistence errors. | Frederick Muriuki Muriithi |
| 2025-04-28 | Search for radio was slow for some reason. | Frederick Muriuki Muriithi |
| 2025-04-28 | Allow selection from existing publications. | Frederick Muriuki Muriithi |
| 2025-04-28 | Do not auto-update publication details on conflict•••Auto-update of a publication's details on an "insert conflict" would
lead to a bug where publications could be overwritten with the wrong
information. Rather than auto-update, explicitly indicate the error,
and let the user manually edit the record to avoid data inconsistency.
| Frederick Muriuki Muriithi |
| 2025-04-28 | Implement creating publications. | Frederick Muriuki Muriithi |
| 2025-04-28 | Add logging.•••Without this logging statement, the chunk merging fails with an error
that it cannot find one of the chunks when attempting to delete
it. That error disappears as soon as I attempt to log out the error
and debug.
| Frederick Muriuki Muriithi |
| 2025-04-28 | Enable autofill of information from PubMed. | Frederick Muriuki Muriithi |
| 2025-04-28 | Move functions to fetch pubmed data out into a separate js file. | Frederick Muriuki Muriithi |
| 2025-04-28 | Move generic utility functions to the utils.js file. | Frederick Muriuki Muriithi |
| 2025-04-28 | Provide UI for publication creation. | Frederick Muriuki Muriithi |
| 2025-04-28 | Mark unimplemented features. | Frederick Muriuki Muriithi |
| 2025-04-28 | Provide tooltip text. | Frederick Muriuki Muriithi |
