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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 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
2022-10-05Bug: 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 instead...zsloan
2022-10-04Pass redis_conn to get_samplelistzsloan
2022-10-04Initialize result_list for /traits endpoint JSON outputzsloan
2022-10-04Remove unnecessary variable...Just assign the value of the function call directly to the dictionary key rather than using an intermediate variable. Frederick Muriuki Muriithi
2022-10-04Add more information to exception to help in debuggingFrederick Muriuki Muriithi
2022-10-03Bug: 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
2022-09-30Reformat statementFrederick Muriuki Muriithi
2022-09-30Remove unused table and simplify queryFrederick Muriuki Muriithi
2022-09-30Raise hard-limit on search results to 10k....* wqflask/wqflask/gsearch.py (MAX_SEARCH_RESULTS): Set to 10k. Arun Isaac
2022-09-30Disregard 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
2022-09-29Fix identation issues in attribute query codezsloan
2022-09-29Curry function passed to Maybe.apply....* wqflask/wqflask/gsearch.py (GSearch.__init__): Curry function passed to Maybe.apply to construct the display name. Arun Isaac
2022-09-29Hard-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
2022-09-29Support prefix search and range queries....* wqflask/wqflask/gsearch.py (GSearch.__init__): Support prefix search and range queries. Arun Isaac
2022-09-29Retrieve 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
2022-09-29Index prefixed fields and add values....* wqflask/scripts/index.py (main): Index fields with prefixes, and add values for range queries. Arun Isaac
2022-09-29Replace 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
2022-09-29Open 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
2022-09-29Remove empty first line in docstrings....* wqflask/utility/monads.py (MonadicDict, MonadicDictCursor): Remove empty first line in docstrings. Arun Isaac
2022-09-29Ignore 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
2022-09-29Return monadic value from MonadicDictCursor.fetchone....* wqflask/utility/monads.py (MonadicDictCursor.fetchone): Return monadic value. Arun Isaac
2022-09-29Abstract out writing documents into a xapian database....* wqflask/scripts/index.py (write_document): New function. (main): Use write_document. Arun Isaac
2022-09-29Close xapian database even if error occurs....* wqflask/wqflask/database.py (xapian_database, xapian_writable_database): Close xapian database even if error occurs. Arun Isaac
2022-09-29Remove 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
2022-09-28Do 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
2022-09-27Fix 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....* 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
2022-09-26Add indexing script for global search....* wqflask/scripts/index.py: New file. Arun Isaac
2022-09-26Add 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
2022-09-26Generalize 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
2022-09-25Fix issue where the display name was used in the hmac for phenotype traitszsloan
2022-09-23Remove click handler on global search....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. Arun Isaac
2022-09-22Fix bug in GeneUtil.py query where extra quotes caused an errorzsloan
2022-09-22Use passed in cursor instead of initialising a new cursor.Frederick Muriuki Muriithi
2022-09-22Provide database cursor as argument for TheSpecies and Chromosomes...Provide the database cursor as an argument to the methods of the two classes: * wqflask.base.species.TheSpecies * wqflask.base.species.Chromosomes Also update dependent code to initialise and pass the cursor where these classes are used. Frederick Muriuki Muriithi
2022-09-22Update tests: pass in missing arguments.Frederick Muriuki Muriithi
2022-09-21Added Markers/HumanMarkers import to datasetgroup.py and removed it from...__init__.py Previously it threw an error when it tried to use Markers/HumanMarkers in datasetgroup.py; since Markers/HumanMarkers doesn't seem to be used anywhere else, I think it's okay for the import to only be in datasetgroup.py zsloan
2022-09-21Refactor: pass redis and db connections as argument...Pass the redis and database connection/cursors as arguments to the class methods, and do not retain a copy of the connections/cursors. This allows us to do the connection management in the context managers elsewhere - ideally, at the top-level. For now the context manager is within the `create_dataset` function, but this should be moved out to a higher level once the lower levels are verified to be working as expected. Frederick Muriuki Muriithi
2022-09-20Make -logP columns uniformzsloan