Age | Commit message (Collapse) | Author |
|
|
|
ProbeSet_DataMatrix files
|
|
|
|
500 correlations for sample correlations of non-probeset traits (which it was previously doing and caused many wrong results
|
|
* wqflask/wqflask/views.py (show_trait_page): Use a dataset's name -
from the query parameters - to fetch metadata.
|
|
|
|
* 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
|
|
* 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
|
|
* wqflask/wqflask/correlation/show_corr_results.py: Check for `None`
and display "--" in its place.
|
|
* wqflask/wqflask/correlation/rust_correlation.py: Add
`Probe_Target_Description` to the description field for "ProbeSet"
traits.
|
|
* wqflask/wqflask/correlation/show_corr_results.py: Use scientific
notation with 2 decimal places
|
|
* 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.
|
|
|
|
* wqflask/base/data_set/dataset.py: Delete itertools, DictCursor.
(DataSet.get_accession_id): Handle a case where query_sql returns a
None value.
|
|
* wqflask/tests/unit/base/test_data_set.py (TestDatasetAccessionId):
New test cases.
|
|
* wqflask/tests/unit/base/test_data_set.py (TestDataSetTypes)
[test_set_dataset_key_mrna, test_set_dataset_key_pheno,
test_set_dataset_geno]: Delete.
|
|
|
|
- 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
|
|
currently the case if you use Github or ORCID to log-in)
|
|
|
|
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
causing them to not work as dict keys
|
|
* this stage is already handled by the rust code hence doing positional comparison lead to different results than expected
|
|
|
|
* wqflask/wqflask/templates/search_result_page.html: Replace
metadata.accession_id with dataset.accession_id.
* wqflask/wqflask/templates/show_trait.html: Ditto.
|
|
* 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.
|
|
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
|
|
* 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.
|
|
|
|
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-bugfix/metadata-fetching
|
|
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-chores/code-refactoring
|
|
github.com:Alexanderlacuna/genenetwork2 into Alexanderlacuna-bugfix/use-f1-parents
|
|
|
|
|
|
* 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.
|
|
|
|
|
|
* 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.
|
|
|
|
|
|
* 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.
|
|
* wqflask/wqflask/correlation/show_corr_results.py
(set_template_vars): Convert monadict_dict to a normal dictionary.
(correlation_json_for_table): Ditto.
|
|
* 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.
|
|
* 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.
|