| Age | Commit message (Expand) | Author |
|---|
| 2025-05-30 | Use full table names rather than aliases•••Using aliases leads to errors when you have to use table locking to
prevent data corruption. This commit updates queries to use the full
table names rather than aliases, in order to prevent such troubles.
| Frederick Muriuki Muriithi |
| 2025-05-28 | Bug: Fix actual data value, not result set. | Frederick Muriuki Muriithi |
| 2025-05-28 | Bug: Add missing commas. | Frederick Muriuki Muriithi |
| 2025-05-28 | Maintain single list of tables — build logs and query from list•••Maintain a list of tables to lock when running the script and build
the logging messages, and lock query from the list for easier
maintenance.
| Frederick Muriuki Muriithi |
| 2025-05-28 | Add missing import. | Frederick Muriuki Muriithi |
| 2025-05-28 | Pass path to bundle extraction dir, and make paths relative to it.•••Pass the path where the bundle was extracted to the function doing the
work. Make the paths for the files being used be relative to the
extraction directory thus passed.
| Frederick Muriuki Muriithi |
| 2025-05-28 | Add javascript debugging function. | Frederick Muriuki Muriithi |
| 2025-05-19 | Extract the bundle first. | Frederick Muriuki Muriithi |
| 2025-05-19 | Add "Publication" table to locked tables. | Frederick Muriuki Muriithi |
| 2025-05-19 | Bug: Connection objects do not have execute() function. | Frederick Muriuki Muriithi |
| 2025-05-19 | Handle case where the given publication_id does not exist. | Frederick Muriuki Muriithi |
| 2025-05-19 | Fix generic bugs | Frederick Muriuki Muriithi |
| 2025-05-19 | Import missing symbols. | Frederick Muriuki Muriithi |
| 2025-05-19 | Provide extra metadata to the job. | Frederick Muriuki Muriithi |
| 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 |
