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2023-10-24Add script for creating list of ProbeSet datasets with NAs for Max QTLzsloan
2023-06-22Update calls to `database_connection` functionFrederick Muriuki Muriithi
Pass in the database URI at call time.
2023-03-08Add DataAnalyzer.py script to maintenance scriptszsloan
2023-02-03Add perf scripts that compare fetching a trait using GN API vs LMDBMunyoki Kilyungi
* scripts/performance/(README,org, timeit_gn2.py, timeit_lmdb.py): New files. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-01-26Dump metadata in addition to sample data.Munyoki Kilyungi
* scripts/sampledata: Dump metadata in addition to data.
2023-01-20Make dump script faster by using concurrency moduleMunyoki Kilyungi
2023-01-20Dump all sample data into a given directoryMunyoki Kilyungi
* scripts/sampledata.py: Import gen_dropdown_json. (main): Dump all the sample data from all the datasets into a given directory.
2023-01-20Return a trait's display name if the name is non-existentMunyoki 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.
2023-01-20Update demo to dump entire dataset for BXDPublishMunyoki Kilyungi
* scripts/sampledata.py: Import os and sys. <__name__>: Add demo to dump "BXDPublish" dataset.
2023-01-20Remove hard-coded valuesMunyoki Kilyungi
* scripts/sampledata.py (dump_sample_data): Remove hard-coded values for trait_id and dataset_name.
2023-01-20Fix typoMunyoki Kilyungi
2023-01-20Add example that demos dumping data from an entire datasetMunyoki Kilyungi
2023-01-20Add a function that fetches all the traits given the right paramsMunyoki Kilyungi
* scripts/sampledata.py (fetch_all_traits): New function.
2023-01-20Create script to dumple sample data given the dataset and trait idMunyoki Kilyungi
* scripts/sampledata.py: New file.
2022-06-03Give speciesid single quotes like the other config_dic keys, just for ↵zsloan
consistency
2022-06-03Allow GenoFreezeId to be passed in configurations to load_genotypes.pyzsloan
2022-03-11Add updated version of script for adding new expression sample datazsloan
2022-03-10Use context manager with database connectionFrederick 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.
2021-12-17Some updates to the DOL genotypes conversion scriptzsloan
2021-11-05Add created_timestamp when creating a new groupBonfaceKilz
2021-11-05Add created_timestamp when creating a new groupBonfaceKilz
2021-11-05Use members uuidBonfaceKilz
2021-11-05Add script for manually adding "editors" to each resourceBonfaceKilz
2021-10-25scripts: resource: Add value for "admin" when updating resourcesBonfaceKilz
2021-10-25scripts: resource.py: Add shebangBonfaceKilz
2021-10-25scripts: group.py: Add extra optional arg to specify uidBonfaceKilz
2021-10-25scripts: group.py: Add shebangBonfaceKilz
2021-10-22Include the admin privilege for the 'editors' group, since it wasn't being ↵zsloan
set before (which caused some problems)
2021-10-08Fixed 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
2021-10-08Adding 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
2021-10-06scripts: resource: Add option for specifying a groups uuidBonfaceKilz
2021-10-06scripts: group: Replace args.group_name with data["field"]BonfaceKilz
2021-10-06scripts: group: Update docstrings for "create_group_data"BonfaceKilz
2021-10-06scripts: group: Break up long lineBonfaceKilz
2021-10-06scripts: group: Fix indentationBonfaceKilz
2021-10-06scripts: group: Remove empty `""` value for data.getBonfaceKilz
data.get("field") will default to None if there is no value; and None is falsy.
2021-10-06scripts: group: Remove unused importBonfaceKilz
2021-10-06scripts: group: Use a unique key to identify a groupBonfaceKilz
2021-10-04Moved 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
2021-10-04Changed 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
2021-10-04scripts: group.py: Modify exit message when displaying updated dataBonfaceKilz
2021-10-04scripts: group.py: Remove "glom" dependencyBonfaceKilz
2021-10-04Decode redis response by defaultBonfaceKilz
2021-10-04Modify resource editing script to enable data backups & restorationBonfaceKilz
2021-10-04Add script that adds "editors" group to all resources in RedisBonfaceKilz
2021-10-04Add script for creating/ updating groups during authorisationBonfaceKilz
2021-08-16Add "Description" column to CaseAttributeBonfaceKilz
See: eecaad2d
2021-05-13Fix load_phenotypes to run with GN2 latestArthur Centeno
2020-10-29Replace map on strip with a list comprehension that calls strip()BonfaceKilz
* scripts/maintenance/readProbeSetSE_v7.py: In Python3 you can't map string.strip on a list of strings. Instead use a list comprehension and apply strip() on each element of the list. * wqflask/wqflask/marker_regression/plink_mapping.py: Ditto. * wqflask/wqflask/snp_browser/snp_browser.py: Ditto.
2020-08-27Replace "string.split" & "string.join" with python's inbuilt methodsBonfaceKilz
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