| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-10-11 | Only compute Lit/Tissue corr when main trait's dataset is of type ProbeSet | zsloan | |
| 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 | zsloan | |
| 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. | |||
| 2022-10-11 | Remove logging from validation.js | zsloan | |
| 2022-10-10 | Replace GeneList table name with new table | zsloan | |
| 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) | |||
| 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 | mechanical-rob: Fix tests that were checking for the wrong thing | Frederick Muriuki Muriithi | |
| 2022-10-05 | Handle correlation error | Frederick Muriuki Muriithi | |
| * Handle the correlation error such that it gives the user a better message for the cause of the error, instead of displaying the exception. | |||
| 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 ↵ | zsloan | |
| instead of group_id | |||
| 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 | Frederick Muriuki Muriithi | |
| Just assign the value of the function call directly to the dictionary key rather than using an intermediate variable. | |||
| 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 | Frederick Muriuki Muriithi | |
| * 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. | |||
| 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. | Arun Isaac | |
| * wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): Set to 10k. | |||
| 2022-09-30 | Disregard permissions when displaying search results. | Arun Isaac | |
| * wqflask/wqflask/gsearch.py: Do not import types. (is_permitted_for_listing): Delete function. (GSearch.__init__): Do not call is_permitted_for_listing. | |||
| 2022-09-29 | Fix identation issues in attribute query code | zsloan | |
| 2022-09-29 | Curry function passed to Maybe.apply. | Arun Isaac | |
| * wqflask/wqflask/gsearch.py (GSearch.__init__): Curry function passed to Maybe.apply to construct the display name. | |||
| 2022-09-29 | Hard-limit the number of search results. | Arun Isaac | |
| * wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): New constant. (GSearch.__init__): Hard-limit the number of search results to MAX_SEARCH_RESULTS. | |||
| 2022-09-29 | Support prefix search and range queries. | Arun Isaac | |
| * wqflask/wqflask/gsearch.py (GSearch.__init__): Support prefix search and range queries. | |||
| 2022-09-29 | Retrieve year as integer. | Arun Isaac | |
| * 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. | |||
| 2022-09-29 | Index prefixed fields and add values. | Arun Isaac | |
| * wqflask/scripts/index.py (main): Index fields with prefixes, and add values for range queries. | |||
| 2022-09-29 | Replace MonadicDictCursor with generator function. | Arun Isaac | |
| * 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. | |||
| 2022-09-29 | Open xapian database once, but SQL database once for each query. | Arun Isaac | |
| 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. | |||
| 2022-09-29 | Remove empty first line in docstrings. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDict, MonadicDictCursor): Remove empty first line in docstrings. | |||
| 2022-09-29 | Ignore None values early when initializing MonadicDict. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDict.__init__): Ignore None values early instead of converting them to Nothing and then ignoring them. | |||
| 2022-09-29 | Return monadic value from MonadicDictCursor.fetchone. | Arun Isaac | |
| * wqflask/utility/monads.py (MonadicDictCursor.fetchone): Return monadic value. | |||
| 2022-09-29 | Abstract out writing documents into a xapian database. | Arun Isaac | |
| * wqflask/scripts/index.py (write_document): New function. (main): Use write_document. | |||
| 2022-09-29 | Close xapian database even if error occurs. | Arun Isaac | |
| * wqflask/wqflask/database.py (xapian_database, xapian_writable_database): Close xapian database even if error occurs. | |||
| 2022-09-29 | Remove empty rows, and conversion for output | Frederick Muriuki Muriithi | |
| 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. | |||
| 2022-09-29 | Add test for regression | Frederick Muriuki Muriithi | |
| 2022-09-28 | Do not assume transactions in database connections. | Arun Isaac | |
| 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. | |||
| 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. | Arun Isaac | |
| * 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". | |||
| 2022-09-26 | Add indexing script for global search. | Arun Isaac | |
| * wqflask/scripts/index.py: New file. | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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