| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2022-11-08 | Remove string check for 'None' in HTML template...In Jinja, you can use dot notation to check for values. If a value
does not exist, you get None by default.
* wqflask/base/data_set/dataset.py (Dataset.get_accession_id): Remove
returning a string version of None.
* wqflask/wqflask/templates/correlation_page.html: Delete `!= 'None'`.
| Munyoki Kilyungi |
| 2022-11-08 | Remove unused imports...* wqflask/wqflask/correlation/show_corr_results.py: Delete os, Path,
TMPDIR, fetch_all_cached_metadata and cache_new_traits_metadata.
* wqflask/wqflask/db_info.py: Remove http.client.
| Munyoki Kilyungi |
| 2022-11-08 | Use DictCursor to fetch results into a dictionary...* wqflask/wqflask/db_info.py: Import DictCursor.
(InfoPage.get_info): Add aliases in SQL that will be used as keys
later by DictCursor..
(process_query_results): Delete it.
| Munyoki Kilyungi |
| 2022-11-08 | De-duplicate fetching results after a query...* wqflask/wqflask/db_info.py (InfoPage.get_info): run
cursor.fetchone() only once.
| Munyoki Kilyungi |
| 2022-11-08 | Delete unused JavaScript files...* wqflask/wqflask/static/new/javascript/dataset_select_menu.js: Delete.
* wqflask/wqflask/static/new/javascript/dataset_select_menu_edit_trait.js:
Ditto.
| Munyoki Kilyungi |
| 2022-11-07 | Change sample correlations to use full samplelist, including f1s/parents | zsloan |
| 2022-11-07 | include f1 parents for correlation | AlexanderKabui |
| 2022-11-02 | Update Phenogen URL to rn7 | zsloan |
| 2022-11-02 | Enable Verify button for Genotype traits | zsloan |
| 2022-10-31 | Fix error when there's no human data in GeneList | zsloan |
| 2022-10-31 | Only show Tissue in trait page for ProbeSet traits | zsloan |
| 2022-10-31 | Add md5 js file (needed for adding to collections) | zsloan |
| 2022-10-31 | Update Rat links to rn7 | zsloan |
| 2022-10-30 | Address situations where Additive Effect is an empty string for view...collection page
I think the Monad stuff Bonface/Arun are doing might address situations
like this better.
| zsloan |
| 2022-10-28 | Add `sample_data` argument to function call.run-corrs-in-external-process | Frederick Muriuki Muriithi |
| 2022-10-28 | Fix imports...* Fix imports I broke when rebasing.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Refactor: run correlation computation externally...* wqflask/scripts/corr_compute.py: move correlation computation to
external script.
* wqflask/wqflask/templates/loading_corrs.html: Provide UI to display
while computation is still not complete.
* wqflask/wqflask/views.py: Dispatch correlation computation to
external script and display appropriate UI for each valid state of
the computation.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Settings: Add the `REDIS_URL` setting. | Frederick Muriuki Muriithi |
| 2022-10-28 | Declutter stdout...* wqflask/utility/tools.py: Output extraneous messages to stderr
rather than stdout to avoid cluttering the output.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Refactor: Pass user id to `check_resource_availability`...* Pass the user_id for the current user to the
`check_resource_availability` function as an argument, rather than
using the global `g.user_session.user_id` value.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Add external process manager...* wqflask/jobs/__init__.py: New jobs module
* wqflask/jobs/jobs.py: New jobs module
* wqflask/scripts/run_external.py: new external process manager.
| Frederick Muriuki Muriithi |
| 2022-10-28 | Query genenetwork3 API for search....genenetwork2 should be a thin wrapper web UI around the genenetwork3
API. Hence, this move.
* etc/default_settings.py (XAPIAN_DB_PATH): Delete variable.
* wqflask/wqflask/database.py: Remove xapian import.
(xapian_database, xapian_writable_database): Delete functions.
* wqflask/wqflask/gsearch.py: Do not import json, xapian, Nothing from
pymonad.maybe, base, utility.authentication_tools and
wqflask.database. Import MonadicDict from gn3.monads instead of
utility.monads and GN3_LOCAL_URL from utility.tools.
(GSearch.__init__): Query genenetwork3 search API instead of directly
reading a Xapian index.
| Arun Isaac |
| 2022-10-28 | Remove xapian indexing script....The xapian indexing script has been moved to genenetwork3. All further
development will happen there.
* wqflask/scripts/index.py: Delete file.
| Arun Isaac |
| 2022-10-27 | init fix for querying for datasets | Alexander_Kabui |
| 2022-10-26 | Remove Owner from phenotype editing, since it only applies to the GN1 Owner f... | zsloan |
