| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2025-06-02 | Parametrize the "DataId" column for different tables. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Explicitly query for newly entered data. | Frederick Muriuki Muriithi | |
| The `cursor.executemany()` call only returned the last row that was inserted, rather than ALL the rows. This is not the correct thing to do, therefore, this commit fixes that by explicitly querying for all the newly entered data. | |||
| 2025-06-02 | Convert N/A values to NoneType objects. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Pass the phenotypes name-to-id map to functions. | Frederick Muriuki Muriithi | |
| 2025-06-02 | Compute the map from a phenotype's name to its ID. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Refactor: Extract common pattern into separate function | Frederick Muriuki Muriithi | |
| Extract the common pattern into a separate, more generalized function and pass the new function the data it requires to perform its tasks for the different file types. | |||
| 2025-05-30 | Add typing to load_data function and invoke it. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Save standard errors and counts. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Get the species, population and dataset. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Add more tables to lock list. | Frederick Muriuki Muriithi | |
| 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 | Add new file type. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Add dataset_id and bundle path to job metadata. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix typo: Fix table name. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Bug: Loop until the data is exhausted. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix typo, and bug. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Fix indentation. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Refactor out common `__row_to_dataitems__` function. | Frederick Muriuki Muriithi | |
| 2025-05-30 | Use full table names rather than aliases | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-05-28 | Add missing import. | Frederick Muriuki Muriithi | |
| 2025-05-28 | Pass path to bundle extraction dir, and make paths relative to it. | Frederick Muriuki Muriithi | |
| 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. | |||
| 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. | Frederick Muriuki Muriithi | |
| 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. | |||
| 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. | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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