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2022-10-11Change Interval Analyst table to use new GeneList tablezsloan
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.
2022-10-11Remove logging from validation.jszsloan
2022-10-10Replace GeneList table name with new tablezsloan
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)
2022-10-08Added Shelby to creditsPjotr Prins
2022-10-08Update link to public datasetsPjotr Prins
2022-10-06DEBUG: More infoFrederick Muriuki Muriithi
2022-10-06DEBUG: More debug of CI/CD.Frederick Muriuki Muriithi
2022-10-06DEBUG: Collect more info to debug CI/CDFrederick Muriuki Muriithi
2022-10-06Check for incompatible datasets for various correlation types.Frederick Muriuki Muriithi
2022-10-05fix bug use target dataset for top n correlationAlexander_Kabui
2022-10-05remove data preprocessing for top n samplesAlexander_Kabui
2022-10-05Handle correlation errorFrederick 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.
2022-10-05Bug: Check for compatible datasets for a correlation typeFrederick Muriuki Muriithi
2022-10-05bug: Use target dataset when computing tissue correlationsFrederick Muriuki Muriithi
2022-10-04Fix bug where dataset_name was being passed into get_samplelist query ↵zsloan
instead of group_id
2022-10-04Pass redis_conn to get_samplelistzsloan
2022-10-04Initialize result_list for /traits endpoint JSON outputzsloan
2022-10-04Remove unnecessary variableFrederick Muriuki Muriithi
Just assign the value of the function call directly to the dictionary key rather than using an intermediate variable.
2022-10-04Add more information to exception to help in debuggingFrederick Muriuki Muriithi
2022-10-03Bug: Don't process data for output earlyFrederick 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.
2022-09-30Reformat statementFrederick Muriuki Muriithi
2022-09-30Remove unused table and simplify queryFrederick Muriuki Muriithi
2022-09-30Raise hard-limit on search results to 10k.Arun Isaac
* wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): Set to 10k.
2022-09-30Disregard 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.
2022-09-29Fix identation issues in attribute query codezsloan
2022-09-29Curry function passed to Maybe.apply.Arun Isaac
* wqflask/wqflask/gsearch.py (GSearch.__init__): Curry function passed to Maybe.apply to construct the display name.
2022-09-29Hard-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.
2022-09-29Support prefix search and range queries.Arun Isaac
* wqflask/wqflask/gsearch.py (GSearch.__init__): Support prefix search and range queries.
2022-09-29Retrieve 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.
2022-09-29Index prefixed fields and add values.Arun Isaac
* wqflask/scripts/index.py (main): Index fields with prefixes, and add values for range queries.
2022-09-29Replace 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.
2022-09-29Open 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.
2022-09-29Remove empty first line in docstrings.Arun Isaac
* wqflask/utility/monads.py (MonadicDict, MonadicDictCursor): Remove empty first line in docstrings.
2022-09-29Ignore 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.
2022-09-29Return monadic value from MonadicDictCursor.fetchone.Arun Isaac
* wqflask/utility/monads.py (MonadicDictCursor.fetchone): Return monadic value.
2022-09-29Abstract out writing documents into a xapian database.Arun Isaac
* wqflask/scripts/index.py (write_document): New function. (main): Use write_document.
2022-09-29Close xapian database even if error occurs.Arun Isaac
* wqflask/wqflask/database.py (xapian_database, xapian_writable_database): Close xapian database even if error occurs.
2022-09-29Remove empty rows, and conversion for outputFrederick 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.
2022-09-28Do 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.
2022-09-27Fix indentation in get_species_list for-loopzsloan
2022-09-27Unit Test: Fix unit test for Chromosome functions.Frederick Muriuki Muriithi
2022-09-26Add REST API endpoint for viewing a group's genotype file metadatazsloan
2022-09-26Get heatmap and mapping working again with changing to species.pyzsloan
2022-09-26Remove unused database_connection import from species.pyzsloan
2022-09-26Implement 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".
2022-09-26Add indexing script for global search.Arun Isaac
* wqflask/scripts/index.py: New file.
2022-09-26Add xapian database connection utilities.Arun Isaac
* etc/default_settings.py (XAPIAN_DB_PATH): New variable. * wqflask/wqflask/database.py: Import xapian. (xapian_database, xapian_writable_database): New functions.
2022-09-26Generalize sql_uri function to get any setting.Arun Isaac
* wqflask/wqflask/database.py (sql_uri): Generalize to get_setting. (database_connection): Call get_setting instead of sql_uri.
2022-09-25Fix issue where the display name was used in the hmac for phenotype traitszsloan
2022-09-23Remove click handler on global search.Arun Isaac
check_search_term is not relevant to global search. It checks search terms in the unrelated #or_search and #and_search fields. * wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js: Do not call check_search_term on clicking global search button.
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