| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 8 days | Narrow selection if cross-reference IDs are provided. | Frederick Muriuki Muriithi | |
| 11 days | Handle big deletes: Delete in batches. | Frederick Muriuki Muriithi | |
| Do avoid locking up the database server, or leading to sluggishness when doing huge deletes, do the deletions in chunks, with a tiny delay between each delete to free up the server.a See https://mariadb.com/docs/server/ha-and-performance/optimization-and-tuning/query-optimizations/big-deletes | |||
| 2026-01-23 | Add function to delete phenotypes completely. | Frederick Muriuki Muriithi | |
| 2026-01-23 | Add function to delete numeric data for phenotypes. | Frederick Muriuki Muriithi | |
| 2026-01-23 | Use correct classes for type-hints. | Frederick Muriuki Muriithi | |
| 2025-12-19 | Delete unused function. | Frederick Muriuki Muriithi | |
| 2025-12-19 | Fix issues caught by type-checker. | Frederick Muriuki Muriithi | |
| 2025-12-17 | Fix linting problems. | Frederick Muriuki Muriithi | |
| 2025-11-19 | Add function to retrieve vector data for phenotypes from the db. | Frederick Muriuki Muriithi | |
| 2025-10-13 | Fix linting errors. | Frederick Muriuki Muriithi | |
| 2025-08-25 | Create and cross-reference phenotypes | Frederick Muriuki Muriithi | |
| Update `create_new_phenotypes` function to create the phenotypes and cross-reference them to their populations, publications, and groups in one transaction to ensure consistency. | |||
| 2025-08-25 | Preprocess phenotype data and return normalised form. | Frederick Muriuki Muriithi | |
| 2025-07-14 | Fix linting issues. | Frederick Muriuki Muriithi | |
| 2025-07-14 | Fix imports | Frederick Muriuki Muriithi | |
| Remove unused imports, update old imports to newer forms and add missing imports. | |||
| 2025-07-14 | Do not enter IDs in files in the description field. | Frederick Muriuki Muriithi | |
| 2025-07-02 | Update descriptions and abbreviations | Frederick Muriuki Muriithi | |
| - Add the description to both the Original and Post-Publication fields. - Set the abbreviation fields to the identifier in the files. | |||
| 2025-06-24 | Use positional parameters rather than named ones. | Frederick Muriuki Muriithi | |
| Named parameters were causing problems on staging, where the names would be converted into bytestrings and then used to index into the dictionaries, leading to `KeyError` exceptions. | |||
| 2025-06-10 | Bug: Fix logging. | Frederick Muriuki Muriithi | |
| 2025-06-03 | Save data with `LOAD DATA INFILE …` query | Frederick Muriuki Muriithi | |
| To help speed up the saving of the data (for really huge files) into the database, use the `LOAD DATA INFILE …` command if available, and if not fallback to the one using raw queries. | |||
| 2025-06-03 | Increase number of rows per query. | Frederick Muriuki Muriithi | |
| 2025-06-03 | Debug the query: useful to figure out what's happening. | Frederick Muriuki Muriithi | |
| 2025-06-03 | Memory saving: Don't reload saved data | Frederick Muriuki Muriithi | |
| We already have all the data in memory, so we do not need to reload it and keep yet another copy. | |||
| 2025-06-02 | Add some debugging statements. | Frederick Muriuki Muriithi | |
| 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. | |||
| 2025-05-30 | 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 | 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. | |||
| 2025-05-19 | Add function to save the numerical data for phenotypes. | Frederick Muriuki Muriithi | |
| 2025-05-05 | Save/Create new phenotypes in the database. | Frederick Muriuki Muriithi | |
| 2025-04-21 | Use module-specific logger. | Frederick Muriuki Muriithi | |
| 2025-04-21 | Add "DataId" to top-level trait details. | Frederick Muriuki Muriithi | |
| The `DataId` is unique in the `PublishXRef` table. | |||
| 2025-03-21 | Add "PubMed_ID" field | Frederick Muriuki Muriithi | |
| The "PubMed_ID" field allows the user to edit the publication that's attached to each phenotype trait. | |||
| 2025-03-18 | Enable downloading of dataset's phenotype's data. | Frederick Muriuki Muriithi | |
| 2025-03-17 | Include InbredSetId: Useful for querying data. | Frederick Muriuki Muriithi | |
| 2025-01-29 | Update field name. | Frederick Muriuki Muriithi | |
| Use "xref_id" rather than "pxr.Id" since the former is a little clearer. | |||
| 2025-01-27 | Fix bug in how the SE and N values for a phenotype are fetched. | Frederick Muriuki Muriithi | |
| 2025-01-25 | Add function to retrieve a phenotype's publication data. | Frederick Muriuki Muriithi | |
| 2025-01-25 | Add the "StrainId" field to phenotype data rows. | Frederick Muriuki Muriithi | |
| 2024-11-22 | Use gn-libs code for db connection. | Frederick Muriuki Muriithi | |
| Use the code in gn-libs to connect to the database, rather than a local module. | |||
| 2024-10-07 | Create new phenotype dataset (PublishFreeze). | Frederick Muriuki Muriithi | |
| Provide the UI and code to create a new phenotype dataset. | |||
| 2024-09-30 | BugFix: Ensure all data items show up. | Frederick Muriuki Muriithi | |
| 2024-09-30 | Initialise views for a specific phenotype | Frederick Muriuki Muriithi | |
| Each phenotype is independent, of all others, and they are only put into datasets mostly for easy coralling of phenotypes related to a specific populations. As such, the system will probably need to provide a way to view (and possibly edit) each phenotype independent of all the others. This also fits in with the auth. | |||
| 2024-09-27 | Remove unused placeholders for now. | Frederick Muriuki Muriithi | |
| 2024-09-27 | Improve query for fetching a phenotype dataset's data | Frederick Muriuki Muriithi | |
| 2024-09-27 | Show some details for a phenotype dataset. | Frederick Muriuki Muriithi | |
| 2024-09-26 | Start building up the view dataset endpoint | Frederick Muriuki Muriithi | |
| 2024-09-26 | List the phenotype datasets. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
| about summary refs log tree commit diff |