| Age | Commit message (Expand) | Author |
|---|
| 2022-12-06 | Use a dataset's name to fetch it's metadata...* wqflask/wqflask/views.py (show_trait_page): Use a dataset's name -
from the query parameters - to fetch metadata.
| Munyoki Kilyungi |
| 2022-12-05 | Put metadata fetching for show_trait_page in try/except to get it working again | zsloan |
| 2022-12-05 | scripts: add GN2 results parsing to parser script...* wqflask/scripts/parse_corr_gn1_results_to_csv.py: Rename script
* wqflask/scripts/parse_corr_html_results_to_csv.py:
* Use argparse to parse CLI arguments
* Add parsing for GN2 results
| Frederick Muriuki Muriithi |
| 2022-12-03 | jobs: Add debug UI...* wqflask/scripts/run_external.py: Save the actual return code
* wqflask/wqflask/__init__.py: Use new jobs blueprint
* wqflask/wqflask/api/jobs.py: Add new jobs debug route
* wqflask/wqflask/templates/jobs/debug.html: new template for when job
is found
* wqflask/wqflask/templates/jobs/no-such-job.html: new template for
when the job is not found
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlations: display "--" whenever "lit_corr" is None...* wqflask/wqflask/correlation/show_corr_results.py: Check for `None`
and display "--" in its place.
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlations: Fix description...* wqflask/wqflask/correlation/rust_correlation.py: Add
`Probe_Target_Description` to the description field for "ProbeSet"
traits.
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlations: Format `sample_r` value correctly....* wqflask/wqflask/correlation/show_corr_results.py: Use scientific
notation with 2 decimal places
| Frederick Muriuki Muriithi |
| 2022-12-02 | correlation: Remove unused argument...* wqflask/wqflask/correlation/rust_correlation.py: The
`get_sample_corr_data` function no longer has the `all_samples`
parameter, thus passing the argument leads to a failure. This commit
removes the argument from the call.
| Frederick Muriuki Muriithi |
| 2022-12-01 | Return Chr and Mb separately for phenotype /traits API request | zsloan |
| 2022-12-01 | Fix Exception that's raised when query_sql returns None...* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor.
(DataSet.get_accession_id): Handle a case where query_sql returns a
None value.
| Munyoki Kilyungi |
| 2022-12-01 | Reproduce ValueError when query_sql returns None...* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId):
New test cases.
| Munyoki Kilyungi |
| 2022-12-01 | Delete complicated unmaintainable test-cases marked for skipping...* wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes)
[test_set_dataset_key_mrna, test_set_dataset_key_pheno,
test_set_dataset_geno]: Delete.
| Munyoki Kilyungi |
| 2022-12-01 | Change API Phenotype query to get other fields, including Locus position | zsloan |
| 2022-12-01 | Variety of changes to basic stats figures...- Left-aligned bar-chart title
- Changed y-axis label for Violin Plot to 'Density'
- Always display modebar options
- Increase font size for y axis label for Violin Plot
| zsloan |
| 2022-12-01 | Prevent error when user account doesn't have an email address (which is curre... | zsloan |
| 2022-12-01 | Fix group-management URL | zsloan |
| 2022-12-01 | Remove min-width for trait page main div | zsloan |
| 2022-12-01 | Increase width of email/password inputs on login page + change some text | zsloan |
| 2022-12-01 | Add line-break below probability plot | zsloan |
| 2022-11-30 | Remove box plot (violin plot is enough) | zsloan |
| 2022-11-30 | Remove check for shortnames/fullnames in probeset metadata query...Some rows in InfoFiles have NULL values thereby causing an exception
to be raised. All InfoFiles.DB_Name are unique.
* wqflask/base/data_set/dataset.py (DataSet.get_accession_id): Remove
shortname/fullname check in query.
| Munyoki Kilyungi |
| 2022-11-29 | remove unnecessary function argument (#754) | Alexander Kabui |
| 2022-11-28 | Fix bugs in show_corr_results.py | zsloan |
| 2022-11-28 | Convert trait name to str, since phenotype trait names being numerical was ca... | zsloan |
| 2022-11-28 | this commit remove the stage for parsing rows to remove nan values...* this stage is already handled by the rust code hence doing positional comparison lead to different results than expected
| AlexanderKabui |
| 2022-11-28 | Fix bug where single chromosome mapping view wouldn't work for the X chromosome | zsloan |
| 2022-11-28 | Fetch the accession_id from the dataset object...* wqflask/wqflask/templates/search_result_page.html: Replace
metadata.accession_id with dataset.accession_id.
* wqflask/wqflask/templates/show_trait.html: Ditto.
| Munyoki Kilyungi |
| 2022-11-25 | mechanical-rob: Parser for GN1 results and some sample results...* test/requests/correlation_results_text_files/*results.csv: csv files
with sample results from GN1 for the trait `1435464_at` in dataset
`HC_M2_0606_P`.
* wqflask/scripts/parse_corr_gn1_results_to_csv.py: parser for results
from GN1 when saved to a html file.
| Frederick Muriuki Muriithi |
| 2022-11-23 | Make some changes to prevent show_corr_results.py bugs (details below)...At one point the MonadicDict of the dataset ob was being passed to create_trait, which does not work. I changed it back to passing the object
Another place calls "as_dict" on the dataset ob, which doesn't work; I had to call as_monadic_dict().data for that
Some traits are also None for some reason, which caused an error in the filter. For now I just used an if/else, but someone can deal with this differently later
| zsloan |
| 2022-11-23 | Replace GN3 library rdf queries with a call to a gn3 endpoint...* wqflask/wqflask/database.py: Delete SPARQLWrapper, JSON imports
(sparql_connection): Delete.
* wqflask/wqflask/views.py: Import requests and urljoin. Delete
get_dataset_metadata and sparql_connection import.
(show_trait_page): Fetch metadata by calling a GN enpoint.
| Munyoki Kilyungi |
| 2022-11-23 | bug: Fix syntax error: missing comma | Frederick Muriuki Muriithi |
| 2022-11-22 | Merge branch 'bugfix/metadata-fetching' of github.com:Alexanderlacuna/genenet... | Frederick Muriuki Muriithi |
| 2022-11-22 | Merge branch 'chores/code-refactoring' of github.com:Alexanderlacuna/genenetw... | Frederick Muriuki Muriithi |
| 2022-11-22 | Merge branch 'bugfix/use-f1-parents' of github.com:Alexanderlacuna/genenetwor... | Frederick Muriuki Muriithi |
| 2022-11-21 | fix merge conflicts | AlexanderKabui |
| 2022-11-21 | minor refactoring | AlexanderKabui |
| 2022-11-16 | Pass a sparql connection object to get_dataset_metadata...* wqflask/wqflask/database.py (database_connection): New function.
* wqflask/wqflask/views.py: Import sparql_connection
(show_trait_page): Pass sparql_connection object to
get_dataset_metadata.
| Munyoki Kilyungi |
| 2022-11-13 | add check when parsing floats | AlexanderKabui |
| 2022-11-13 | add check for dataset type | AlexanderKabui |
| 2022-11-11 | Notify user when they modify probeset data...* wqflask/wqflask/metadata_edits.py (update_probeset): Flash a success
messages when user updates something. Otherwise flash a warning message
* wqflask/wqflask/templates/edit_probeset.html: Display flash
messages.
| Munyoki Kilyungi |
| 2022-11-11 | Parse metadata.about_data_processing correctly | Munyoki Kilyungi |
| 2022-11-10 | Fix typo in probeset editing form | Munyoki Kilyungi |
| 2022-11-10 | Display a dataset's metadata in the "Trait Data and Analysis" page...* wqflask/wqflask/static/new/css/show_trait.css: Show a pointer when a
user hovers over summary data. Add extra styling for the metadata
table.
* wqflask/wqflask/templates/search_result_page.html: Replace
dataset.accession_id with metadata.accession_id.
* wqflask/wqflask/templates/show_metadata_details.html: New template.
file that displays a dataset's metadata in tabular form.
* wqflask/wqflask/templates/show_trait.html: Sub-template
'show_metadata_details' conditionally.
* wqflask/wqflask/views.py (show_trait_page): Explicitly pass metadata
as a dictionary to the template.
| Munyoki Kilyungi |
| 2022-11-10 | Convert monadic_dict to normal dictionaries...* wqflask/wqflask/correlation/show_corr_results.py
(set_template_vars): Convert monadict_dict to a normal dictionary.
(correlation_json_for_table): Ditto.
| Munyoki Kilyungi |
| 2022-11-10 | Rename dataset.as_dict to dataset.as_monadic_dict...* wqflask/base/data_set/dataset.py (DataSet.as_dict): Rename this to ...
(as_monadic_dict): ... this.
* wqflask/wqflask/correlation/show_corr_results.py
(set_template_vars): Rename as_dict to as_monadic_dict.
(correlation_json_for_table): Ditto.
| Munyoki Kilyungi |
| 2022-11-10 | Use the Maybe Monad when fetching the accession_id of a dataset...* wqflask/base/data_set/dataset.py: Import itertools, DictCursor, MonadicDict,
Maybe, Nothing and query_sql.
(DataSet.__init__): Initialize accession_id to Nothing.
(DataSet.as_dict): Rename this to ...
(Dataset.as_monadic_dict): ... this which returns a monadic
dictionary.
(DataSet.get_accession_id): Query for the accession_id and return it
as a maybe monad.
| Munyoki Kilyungi |
| 2022-11-09 | delete unecessary code | AlexanderKabui |
| 2022-11-09 | add filter checkers | AlexanderKabui |
| 2022-11-09 | refactor:apply use filters | AlexanderKabui |
| 2022-11-09 | init code refactoring | AlexanderKabui |
