| Age | Commit message (Expand) | Author |
|---|
| 2025-05-30 | Fix query: Add missing field and parameter. | Frederick Muriuki Muriithi |
| 2025-05-30 | Fix function names. | Frederick Muriuki Muriithi |
| 2025-05-30 | Fix processing of numerical data to save to the database. | Frederick Muriuki Muriithi |
| 2025-05-30 | Fix file paths: append the path to the extraction directory. | Frederick Muriuki Muriithi |
| 2025-05-30 | Refactor out common `__row_to_dataitems__` function. | 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 |
| 2025-05-19 | 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 | Fix generic bugs | Frederick Muriuki Muriithi |
| 2025-05-19 | Import missing symbols. | 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 | 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 | 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 |
| 2025-05-12 | Wireframe saving the data into the database. | Frederick Muriuki Muriithi |
| 2025-05-12 | Print out progress to STDOUT. | Frederick Muriuki Muriithi |
| 2025-05-12 | 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 | Allow lowercase versions of the log-level choices. | Frederick Muriuki Muriithi |
| 2025-05-05 | Init setup and script for async job to load phenotypes into database | Frederick Muriuki Muriithi |
| 2025-04-25 | Handle exceptions explicitly•••Handle any thrown exceptions explicitly to prevent the `with`
statement from swallowing them, leading to silent failure of the
script.
| Frederick Muriuki Muriithi |
| 2025-04-14 | Setup module-level loggers. | Frederick Muriuki Muriithi |
| 2025-04-14 | Compute data differences in the script. | Frederick Muriuki Muriithi |
| 2025-04-14 | Convert values to float where present. | Frederick Muriuki Muriithi |
| 2025-04-14 | Move difference computation to `run()` function. | Frederick Muriuki Muriithi |
| 2025-04-14 | Update existing linked publication(s) rather than creating new. | Frederick Muriuki Muriithi |
| 2025-04-14 | Compute new PubMed IDs. | Frederick Muriuki Muriithi |
| 2025-04-14 | Update imports. | Frederick Muriuki Muriithi |
| 2025-04-14 | Compute differences with tested function. | Frederick Muriuki Muriithi |
| 2025-04-14 | Move code to save new publications to database. | Frederick Muriuki Muriithi |
| 2025-04-11 | Move code to fetch phenotype publications from DB to publications package. | Frederick Muriuki Muriithi |
| 2025-04-11 | Move code to fetch publications from pubmed to publications module. | Frederick Muriuki Muriithi |
| 2025-04-09 | Convert PubMed_ID value from file to int | Frederick Muriuki Muriithi |
| 2025-04-09 | Compute publications differences. | Frederick Muriuki Muriithi |
| 2025-04-09 | Save new publications retrieved from NCBI's PubMed database. | Frederick Muriuki Muriithi |
