| Age | Commit message (Expand) | Author |
|---|
| 2022-03-26 | Make creation of database connections more flexible...* Pass the URI string to parse into `gn3.db_utils.parse_db_url` rather than
relying on a global variable.
* Pass the URI string to use to generate the database connection to the
`gn3.db_utils.database_connector` function rather than depending on a global
variable. Use the global `SQL_URI` variable as a default value if one is not
provided when calling the function.
The changes above make the creation of the database connection more flexible,
since the database URI passed into the function can be changed at the site
where the call is made.
The port is also parsed, and used where present, to allow for either a socket
connection or one based on a port.
| Frederick Muriuki Muriithi |
| 2022-03-23 | Run python-black on file and fix other pylint issues....See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126>
* gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also,
manually fix other pylint issues.
| BonfaceKilz |
| 2022-03-22 | Fixes pylint errors | zsloan |
| 2022-03-22 | Fixed mypy typing errors | zsloan |
| 2022-03-22 | Tried to make the docstrings more consistent | zsloan |
| 2022-03-22 | Add typing to some functions | zsloan |
| 2022-03-22 | Add functions for getting proximal/distal markers for each pseudomarker posit... | zsloan |
| 2022-03-22 | Fix issue that causes R/qtl to always run pair-scan even if pair-scan isn't s... | zsloan |
| 2022-03-22 | Added genofile name to inputs for processing R/qtl pair-scan results, since i... | zsloan |
| 2022-03-22 | Removed quotes from beginning and end of chromosome string | zsloan |
| 2022-03-22 | Fixed a cople function calls to use the updated function names | zsloan |
| 2022-03-22 | Create pairscan_for_figure and pairscan_for_table functions that return the D... | zsloan |
| 2022-03-22 | Fix imports to import both process_rqtl_mapping and process_rqtl_pairscan in ... | zsloan |
| 2022-03-22 | Added pairscan boolean kwarg and process_rqtl_pairscan function for reading i... | zsloan |
| 2022-03-18 | Clean all csv fields before diffing...There was a subtle bug where "csvdiff" generated an error related to
"different column headings" caused something akin to diffing: "a, b \n, ..."
with "a, b\n, ...".
* gn3/csvcmp.py (csv_diff): Clean csv texts before any diffing.
* tests/unit/test_csvcmp.py (test_csv_diff_same_columns): Modify test case to
capture aforementioned bug.
| BonfaceKilz |
| 2022-03-18 | Create new function for cleaning individual fields in csv text...* gn3/csvcmp.py (clean_csv_text): New function.
* tests/unit/test_csvcmp.py: Import "csv_text".
(test_clean_csv_text): Test case for the above.
| BonfaceKilz |
| 2022-03-15 | Feature/refactored pca (#79)...* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca | Alexander Kabui |
| 2022-03-14 | Dummy White Space commit to fix laminar | BonfaceKilz |
| 2022-03-14 | Only loop through the diff's modifications if it exists | BonfaceKilz |
| 2022-03-14 | Given a csv text and permissible headers, extract invalid headers...* gn3/csvcmp.py (extract_invalid_csv_headers): New function.
* tests/unit/test_csvcmp.py: Import "extract_invalid_csv_headers".
(test_extract_invalid_csv_headers_with_some_wrong_headers): Test case for the
above.
| BonfaceKilz |
| 2022-03-14 | Get all permissible column data...* gn3/csvcmp.py: Import "Any" and "List".
(get_allowable_sampledata_headers): New function.
* tests/unit/test_csvcmp: Import "get_allowable_sampledata_headers".
(test_get_allowable_csv_headers): Test case for the above.
| BonfaceKilz |
| 2022-03-12 | Remove unused imports | BonfaceKilz |
| 2022-03-12 | Fix mypy issues | BonfaceKilz |
| 2022-03-12 | Fix pylint issues | BonfaceKilz |
| 2022-03-12 | Compose csv-diff command within single quotes...* gn3/csvcmp.py (csv_diff): Use single quotes. There was a change in 6d39c92
that broke this.
| BonfaceKilz |
| 2022-03-12 | Delete noisy "print" statement | BonfaceKilz |
| 2022-03-12 | Store the first element as strain_id | BonfaceKilz |
| 2022-03-12 | Append the strain name when extracting "actions"...* gn3/db/sample_data.py (__extract_actions): During updates, make sure that
the strain name is part of the returned string when extracting "actions".
* tests/unit/db/test_sample_data.py: Add test cases for the above.
| BonfaceKilz |
| 2022-03-12 | Apply auto-pep8 to sample_data.py and it's test file | BonfaceKilz |
| 2022-03-12 | Add missing return type-annotations...* tests/unit/db/test_sample_data.py (delete_sample_data): Add missing return
type for type annotations.
(insert_sample_data): Ditto.
| BonfaceKilz |
| 2022-03-12 | Update how data is updated by re-using existing functions...* gn3/db/sample_data.py (get_sample_data_ids): Re-use "delete_sample_data" and
"insert_sample_data" when updating data; and also add logic for updating
modified data.
* tests/unit/db/test_sample_data.py: Add tests for the above.
| BonfaceKilz |
| 2022-03-12 | Create action dict that's created when updating data...* gn3/db/sample_data.py (__extract_actions): An update on a vector of data can
contain: inserts, deletes and updates. This functions extracts these actions
during an update.
* tests/unit/db/test_sample_data.py (test_extract_actions): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Remove check for inserted data when inserting individual data...* gn3/db/sample_data.py (insert_sample_data)[__insert_data]: Move check to the
main body. With this check here, you have 3 redundant checks. For a successful
insert, it will insert the first value to the `PublishData` table and ignore the
rest of the inserts.
| BonfaceKilz |
| 2022-03-12 | Make `_map` a constant...* gn3/db/sample_data.py: Now constant, `_MAP`.
(delete_sample_data)[__delete_data]: Replace `_map` with `_MAP`.
(insert_sample_data)[__insert_data]: Ditto.
| BonfaceKilz |
| 2022-03-12 | Fix faulty SQL query string when deleting case-attributes | BonfaceKilz |
| 2022-03-12 | Explicitly get CaseAttributeId and fix broken sql query...* gn3/db/sample_data.py (insert_sample_data): Use correct query string. Also,
use CaseAttributeId to determine whether case-attributes were inserted. If so,
do not attempt an insert.
| BonfaceKilz |
| 2022-03-12 | Remove duplicate params...* gn3/db/sample_data.py (insert_sample_data)[__insert_case_attribute]: Remove
extra parameters.
| BonfaceKilz |
| 2022-03-12 | Remove dead code | BonfaceKilz |
| 2022-03-12 | Check whether publish data already exists before inserting...* gn3/db/sample_data.py (insert_sample_data): If data already exists in the
table, do not attempt an insert; otherwise, an error will be generated.
| BonfaceKilz |
| 2022-03-12 | Fill in empty values in csv text with: "x"...* gn3/csvcmp.py (fill_csv): Update this function to allow empty lists to be
filled with the default value(set in the args).
* tests/unit/test_csvcmp.py (test_fill_csv): Update test to capture above.
| BonfaceKilz |
| 2022-03-12 | Fetch id's separately for the insertion edge-case...* gn3/db/sample_data (get_sample_data_ids): Add an extra condition that caters
for inserts: during inserts, joins won't work when fetching the strain_id,
publishdata_id, and strain_name. In this case, just create 2 separate queries
to do that work.
| BonfaceKilz |
| 2022-03-12 | Extract a strain name given a csv string and it's header...* gn3/csvcmp.py (extract_strain_name): New function.
* gn3/db/sample_data (delete_sample_data): Use the aforementioned function.
(insert_sample_data): Ditto.
* tests/unit/test_csvcmp: Test cases for above.
| BonfaceKilz |
| 2022-03-12 | Allow deleting case-attribute data during deletion...* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow
deleting case-attribute values.
| BonfaceKilz |
| 2022-03-12 | Allow inserting case-attribute data during inserts...* gn3/db/sample_data.py (insert_sample_data): Modify this function to allow
inserting case-attribute values.
| BonfaceKilz |
| 2022-03-12 | Fetch InbredSetId...* gn3/db/sample_data.py (get_sample_data_ids): Extend to also fetch
InbredSetId.
(update_sample_data): Discard the returned value of InbredSetId.
(delete_sample_data): Ditto.
| BonfaceKilz |
| 2022-03-12 | Create a new function for retrieving strain_id and publishdata_id...* gn3/db/sample_data.py: Import Any, Tuple.
(get_sample_data_ids): New function that fetches the strain_id and
publishdata_id of a given data point.
(update_sample_data): Use `get_sample_data_ids`.
(delete_sample_data): Ditto.
(insert_sample_data): Ditto.
| BonfaceKilz |
| 2022-03-12 | Move operations on sample_data to it's own module | BonfaceKilz |
| 2022-03-12 | Don't add extra key "Column" to dict if there are no changes...gn3/csvcmp.py (csv_diff): If the diff is empty, don't add an extra key
"Column" to the dictionary.
tests/unit/test_csvcmp (test_csv_diff_only_column_change): Add test-case for
the above.
| BonfaceKilz |
| 2022-03-12 | Fill CSV text if there are non-even rows...Should you try to run `csvdiff` against 2 csv files with either file having a
non-even columns, there will be an error. As such, the csv files need to be
"filled" before running `csvdiff`.
* gn3/csvcmp (csv_diff): For non-even rows in the csv files, fill the csv
rows.
| BonfaceKilz |
| 2022-03-12 | Create new method for filling csv with a default value...* gn3/csvcmp.py (fill_csv): Given a csv text with uneven or incomplete fields
whole length are less than width, fill them with a value which defaults to
"x".
* tests/unit/test_csvcmp.py (test_fill_csv): Test cases for the above.
| BonfaceKilz |
