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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
2020-08-26Replace tabs with spacesBonfaceKilz
* scripts/maintenance/readProbeSetMean_v7.py: Run python-autopep8 on this file.
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-08-19Make Python more idiomaticBonfaceKilz
Run `2to3-3.8 -f idioms -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
2020-08-19Convert `raw_input` to `input`BonfaceKilz
Run `2to3-3.8 -f raw_input -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raw_input>
2020-08-19Convert the use of iterator’s next() methods to the next() functionBonfaceKilz
Run `2to3-3.8 -f next -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-next>
2020-08-19Change `dict.has_key(key)` to `key in dict`BonfaceKilz
Run `2to3-3.8 -f has_key -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-has_key>
2020-08-19Fix dictionary iteration methodsBonfaceKilz
Run `2to3-3.8 -f dict -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and <https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
2020-08-19Wrap `map()` in a `list` callBonfaceKilz
Run `2to3-3.8 -f map -w .` See: <https://docs.python.org/2/library/2to3.html#2to3fixer-map>
2020-08-18Replace "raw_input" with "input"BonfaceKilz
* scripts/maintenance/readProbeSetMean_v7.py: Use "input". See https://docs.python.org/3/whatsnew/3.0.html#builtins
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 08:42:06 +0000