| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-10-29 | Read connection detail from file. Use contextmanager. | Frederick Muriuki Muriithi | |
| Read connection details from file to make it easier to change host(s) in use. Use contextmanager to manage the connections. | |||
| 2024-10-29 | Use argparse.ArgumentParser to collect CLI args from user | Frederick Muriuki Muriithi | |
| Collect arguments from the CLI using argparse rather than sys.argv directly. | |||
| 2024-10-29 | Change indentation, wrap code in function and create entry-point. | Frederick Muriuki Muriithi | |
| 2024-03-22 | Update ProbeSetSE table schema. | Frederick Muriuki Muriithi | |
| 2024-01-02 | Move default settings into gn2 module. | Arun Isaac | |
| 2023-10-24 | Add script for converting the HXBBXH genotype file provided by Hao. | zsloan | |
| Paths and sample/chromosome lists are hard-coded just because this was probably a one-time thing, but still commiting it since it's good to have it around in case we need to use it again | |||
| 2023-10-24 | Add script for creating list of ProbeSet datasets with NAs for Max QTL | zsloan | |
| 2023-06-22 | Update calls to `database_connection` function | Frederick Muriuki Muriithi | |
| Pass in the database URI at call time. | |||
| 2023-03-08 | Add DataAnalyzer.py script to maintenance scripts | zsloan | |
| 2023-02-03 | Add perf scripts that compare fetching a trait using GN API vs LMDB | Munyoki Kilyungi | |
| * scripts/performance/(README,org, timeit_gn2.py, timeit_lmdb.py): New files. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2023-01-26 | Dump metadata in addition to sample data. | Munyoki Kilyungi | |
| * scripts/sampledata: Dump metadata in addition to data. | |||
| 2023-01-20 | Make dump script faster by using concurrency module | Munyoki Kilyungi | |
| 2023-01-20 | Dump all sample data into a given directory | Munyoki Kilyungi | |
| * scripts/sampledata.py: Import gen_dropdown_json. (main): Dump all the sample data from all the datasets into a given directory. | |||
| 2023-01-20 | Return a trait's display name if the name is non-existent | Munyoki Kilyungi | |
| * scripts/sampledata.py (fetch_all_traits): Should the name of a trait not exists, e.g. in probeset data, return it's display name. | |||
| 2023-01-20 | Update demo to dump entire dataset for BXDPublish | Munyoki Kilyungi | |
| * scripts/sampledata.py: Import os and sys. <__name__>: Add demo to dump "BXDPublish" dataset. | |||
| 2023-01-20 | Remove hard-coded values | Munyoki Kilyungi | |
| * scripts/sampledata.py (dump_sample_data): Remove hard-coded values for trait_id and dataset_name. | |||
| 2023-01-20 | Fix typo | Munyoki Kilyungi | |
| 2023-01-20 | Add example that demos dumping data from an entire dataset | Munyoki Kilyungi | |
| 2023-01-20 | Add a function that fetches all the traits given the right params | Munyoki Kilyungi | |
| * scripts/sampledata.py (fetch_all_traits): New function. | |||
| 2023-01-20 | Create script to dumple sample data given the dataset and trait id | Munyoki Kilyungi | |
| * scripts/sampledata.py: New file. | |||
| 2022-06-03 | Give speciesid single quotes like the other config_dic keys, just for ↵ | zsloan | |
| consistency | |||
| 2022-06-03 | Allow GenoFreezeId to be passed in configurations to load_genotypes.py | zsloan | |
| 2022-03-11 | Add updated version of script for adding new expression sample data | zsloan | |
| 2022-03-10 | Use context manager with database connection | Frederick Muriuki Muriithi | |
| Use the `with` context manager with database connections and cursors to ensure that they are closed once they are no longer needed. Where it was not feasible to use the `with` context manager without a huge refactor/rewrite, the cursors and connections are closed manually. | |||
| 2021-12-17 | Some updates to the DOL genotypes conversion script | zsloan | |
| 2021-11-05 | Add created_timestamp when creating a new group | BonfaceKilz | |
| 2021-11-05 | Add created_timestamp when creating a new group | BonfaceKilz | |
| 2021-11-05 | Use members uuid | BonfaceKilz | |
| 2021-11-05 | Add script for manually adding "editors" to each resource | BonfaceKilz | |
| 2021-10-25 | scripts: resource: Add value for "admin" when updating resources | BonfaceKilz | |
| 2021-10-25 | scripts: resource.py: Add shebang | BonfaceKilz | |
| 2021-10-25 | scripts: group.py: Add extra optional arg to specify uid | BonfaceKilz | |
| 2021-10-25 | scripts: group.py: Add shebang | BonfaceKilz | |
| 2021-10-22 | Include the admin privilege for the 'editors' group, since it wasn't being ↵ | zsloan | |
| set before (which caused some problems) | |||
| 2021-10-08 | Fixed the sort to account for both chr and pos in a kind of hack-y way + ↵ | zsloan | |
| added some comments + changed EOL to LF because the file suddenly started including EOL characters | |||
| 2021-10-08 | Adding convert_dol_genotypes.py to scripts; everything is hard-coded in it ↵ | zsloan | |
| since I was only writing it to generate a specific file and it probably won't be re-used | |||
| 2021-10-06 | scripts: resource: Add option for specifying a groups uuid | BonfaceKilz | |
| 2021-10-06 | scripts: group: Replace args.group_name with data["field"] | BonfaceKilz | |
| 2021-10-06 | scripts: group: Update docstrings for "create_group_data" | BonfaceKilz | |
| 2021-10-06 | scripts: group: Break up long line | BonfaceKilz | |
| 2021-10-06 | scripts: group: Fix indentation | BonfaceKilz | |
| 2021-10-06 | scripts: group: Remove empty `""` value for data.get | BonfaceKilz | |
| data.get("field") will default to None if there is no value; and None is falsy. | |||
| 2021-10-06 | scripts: group: Remove unused import | BonfaceKilz | |
| 2021-10-06 | scripts: group: Use a unique key to identify a group | BonfaceKilz | |
| 2021-10-04 | Moved REDIS_CONN back into if __name__ == '__main__' since it doesn't need ↵ | zsloan | |
| to be globally accessed anymore (I think I intiially moved it because I was calling it in create_group_data, but that ended up being unnecessary | |||
| 2021-10-04 | Changed the group.py script to replace user e-mails with IDs and to include ↵ | zsloan | |
| id, name, changed_timestamp, and created_timestamp in group details | |||
| 2021-10-04 | scripts: group.py: Modify exit message when displaying updated data | BonfaceKilz | |
| 2021-10-04 | scripts: group.py: Remove "glom" dependency | BonfaceKilz | |
| 2021-10-04 | Decode redis response by default | BonfaceKilz | |
| 2021-10-04 | Modify resource editing script to enable data backups & restoration | BonfaceKilz | |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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