| Age | Commit message (Expand) | Author |
|---|
| 2022-10-11 | Fix block_by_index ID referenced in show_trait.js | zsloan |
| 2022-10-11 | Change Interval Analyst table to use new GeneList table...The query changes in GeneUtil.pyi (to insert column names using string formatting) are definitely some sort of SQL injection issue, but I'm not sure how else to do it
Also, the table name will be changed later, once the new table has been tested for a while.
| zsloan |
| 2022-10-11 | Remove logging from validation.js | zsloan |
| 2022-10-10 | Replace GeneList table name with new table...Once this is confirmed to be working as expected, it will be changed back to GeneList (and the old table's name will be changed)
| zsloan |
| 2022-10-08 | Added Shelby to credits | Pjotr Prins |
| 2022-10-08 | Update link to public datasets | Pjotr Prins |
| 2022-10-06 | DEBUG: More info | Frederick Muriuki Muriithi |
| 2022-10-06 | DEBUG: More debug of CI/CD. | Frederick Muriuki Muriithi |
| 2022-10-06 | DEBUG: Collect more info to debug CI/CD | Frederick Muriuki Muriithi |
| 2022-10-06 | Check for incompatible datasets for various correlation types. | Frederick Muriuki Muriithi |
| 2022-10-05 | fix bug use target dataset for top n correlation | Alexander_Kabui |
| 2022-10-05 | remove data preprocessing for top n samples | Alexander_Kabui |
| 2022-10-05 | Handle correlation error...* Handle the correlation error such that it gives the user a better
message for the cause of the error, instead of displaying the
exception.
| Frederick Muriuki Muriithi |
| 2022-10-05 | Bug: Check for compatible datasets for a correlation type | Frederick Muriuki Muriithi |
| 2022-10-05 | bug: Use target dataset when computing tissue correlations | Frederick Muriuki Muriithi |
| 2022-10-04 | Fix bug where dataset_name was being passed into get_samplelist query instead... | zsloan |
| 2022-10-04 | Pass redis_conn to get_samplelist | zsloan |
| 2022-10-04 | Initialize result_list for /traits endpoint JSON output | zsloan |
| 2022-10-04 | Remove unnecessary variable...Just assign the value of the function call directly to the dictionary
key rather than using an intermediate variable.
| Frederick Muriuki Muriithi |
| 2022-10-04 | Add more information to exception to help in debugging | Frederick Muriuki Muriithi |
| 2022-10-03 | Bug: Don't process data for output early...* The ",".join(...) call was processing the data for output to file,
way too early, which would lead to errors down the line, very far
removed from the actual cause of the error.
| Frederick Muriuki Muriithi |
| 2022-09-30 | Reformat statement | Frederick Muriuki Muriithi |
| 2022-09-30 | Remove unused table and simplify query | Frederick Muriuki Muriithi |
| 2022-09-30 | Raise hard-limit on search results to 10k....* wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): Set to 10k.
| Arun Isaac |
| 2022-09-30 | Disregard permissions when displaying search results....* wqflask/wqflask/gsearch.py: Do not import types.
(is_permitted_for_listing): Delete function.
(GSearch.__init__): Do not call is_permitted_for_listing.
| Arun Isaac |
| 2022-09-29 | Fix identation issues in attribute query code | zsloan |
| 2022-09-29 | Curry function passed to Maybe.apply....* wqflask/wqflask/gsearch.py (GSearch.__init__): Curry function passed
to Maybe.apply to construct the display name.
| Arun Isaac |
| 2022-09-29 | Hard-limit the number of search results....* wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): New constant.
(GSearch.__init__): Hard-limit the number of search results to
MAX_SEARCH_RESULTS.
| Arun Isaac |
| 2022-09-29 | Support prefix search and range queries....* wqflask/wqflask/gsearch.py (GSearch.__init__): Support prefix search
and range queries.
| Arun Isaac |
| 2022-09-29 | Retrieve year as integer....* wqflask/scripts/index.py (main): Retrieve year as an integer from
the SQL database.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Convert year from
integer to string.
| Arun Isaac |
| 2022-09-29 | Index prefixed fields and add values....* wqflask/scripts/index.py (main): Index fields with prefixes, and add
values for range queries.
| Arun Isaac |
| 2022-09-29 | Replace MonadicDictCursor with generator function....* wqflask/utility/monads.py (MonadicDictCursor): Delete class.
(sql_query_mdict): New function.
* wqflask/scripts/index.py: Import sql_query_mdict instead of
MonadicDictCursor.
(main): Use sql_query_mdict.
| Arun Isaac |
| 2022-09-29 | Open xapian database once, but SQL database once for each query....We reopen the SQL database once for each query because it times out if
kept waiting.
* wqflask/scripts/index.py (main): Open xapian database once, but SQL
database once for each query.
| Arun Isaac |
| 2022-09-29 | Remove empty first line in docstrings....* wqflask/utility/monads.py (MonadicDict, MonadicDictCursor): Remove
empty first line in docstrings.
| Arun Isaac |
| 2022-09-29 | Ignore None values early when initializing MonadicDict....* wqflask/utility/monads.py (MonadicDict.__init__): Ignore None values
early instead of converting them to Nothing and then ignoring them.
| Arun Isaac |
| 2022-09-29 | Return monadic value from MonadicDictCursor.fetchone....* wqflask/utility/monads.py (MonadicDictCursor.fetchone): Return
monadic value.
| Arun Isaac |
| 2022-09-29 | Abstract out writing documents into a xapian database....* wqflask/scripts/index.py (write_document): New function.
(main): Use write_document.
| Arun Isaac |
| 2022-09-29 | Close xapian database even if error occurs....* wqflask/wqflask/database.py (xapian_database,
xapian_writable_database): Close xapian database even if error occurs.
| Arun Isaac |
| 2022-09-29 | Remove empty rows, and conversion for output...Remove any rows that do not have values since they are not useful to
the computations and only lead to errors.
Remove the conversion to output format here: only convert the values
for output at the point of output, and not earlier.
| Frederick Muriuki Muriithi |
| 2022-09-28 | Do not assume transactions in database connections....Not all database queries need transactions. If transactions are
required, they should be made a separate context manager and called
only when required.
* wqflask/wqflask/database.py (database_connection): Do not rollback
or commit.
| Arun Isaac |
| 2022-09-27 | Fix indentation in get_species_list for-loop | zsloan |
| 2022-09-27 | Unit Test: Fix unit test for Chromosome functions. | Frederick Muriuki Muriithi |
| 2022-09-26 | Add REST API endpoint for viewing a group's genotype file metadata | zsloan |
| 2022-09-26 | Get heatmap and mapping working again with changing to species.py | zsloan |
| 2022-09-26 | Remove unused database_connection import from species.py | zsloan |
| 2022-09-26 | Implement global search using xapian....* wqflask/wqflask/gsearch.py: Import Just and Maybe from
pymonad.maybe; curry from pymonad.tools; xapian; MonadicDict from
utility.monads; xapian_database from wqflask.database. Do not import
datetime; database_connection from wqflask.database; base.data_set;
base.trait; db; utility.type_checking; utility.
(is_permitted_for_listing): New function.
(GSearch.__init__): Reimplement using xapian.
* wqflask/wqflask/templates/gsearch_gene.html (block js): Accept
dictionaries with missing keys, replacing them with "N/A".
| Arun Isaac |
| 2022-09-26 | Add indexing script for global search....* wqflask/scripts/index.py: New file.
| Arun Isaac |
| 2022-09-26 | Add xapian database connection utilities....* etc/default_settings.py (XAPIAN_DB_PATH): New variable.
* wqflask/wqflask/database.py: Import xapian.
(xapian_database, xapian_writable_database): New functions.
| Arun Isaac |
| 2022-09-26 | Generalize sql_uri function to get any setting....* wqflask/wqflask/database.py (sql_uri): Generalize to get_setting.
(database_connection): Call get_setting instead of sql_uri.
| Arun Isaac |
| 2022-09-25 | Fix issue where the display name was used in the hmac for phenotype traits | zsloan |
