Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

This changelog was started for release 4.2.0.

Unreleased

Fixed an issue with forms (missing field and entity name for label & uri fields) (Issue #255)
Fixed an issue with the data endpoint for FALDO entities (Issue #279)
Fixed an issue where integration would fail when setting a category type on a empty column (#334)

Added 'scaff' for autodetection of 'reference' columns
Added a 'Label' column type: only for second column in CSV files. Will use this value if present, else default to old behavior
Added button to hide FALDO relations (included_in)
Added 'target=_blank' in query results
Remote upload is now sent in a Celery task
Added 'Status' for files (for celery upload, and later for better file management)
Added tooltips to buttons in the query form (and other forms)
Added owl integration
Add better error management for RDF files
Added 'single tenant' mode: Send queries to all graphs to speed up
Added ontologies management

Changed "Query builder" to "Form editor" in form editing interface
Changed abstraction building method for relations. (Please refer to #248 and #268)
Changed abstraction building method for attributes. (Please refer to #321 and #324)
Changed abstraction building method for 'strand': only add the required strand type, and not all three types (#277)
Updated documentation
Changed the sparql endpoint: now use the authenticated SPARQL endpoint instead of public endpoint. Write permissions are not required anymore
Reverted base docker image to alpine-13 to solve a docker issue

Added 'Date' entity type, with associated Date picker in UI
Added API-key authentication for most endpoints. The api key should be passed with the header "X-API-KEY".
Added CLI (using token-auth) (https://github.com/askomics/askoclics). Still a WIP, with the python package 'askoclics'.
"Not" filter for categories
URI management in first column (and link column). Manage both full URI and CURIE. Check #223 for details.
'Forms' : Minimal templates (users only access a basic form for modifying parameters, and not the graph) Restricted to admins. Form creators can customized entities and attributes display names to improve usability.

Faldo entity "Strand" now default to "faldo:BothStrandPosition" when the value is empty. The label will be "unknown/both" for CSV. For GFF and BED, "." will be "faldo:BothStrandPosition" instead of being ignored.
If one of the column name of a CSV file is empty, raise an Exception.
Now return the created result id (instead of celery task id) in the sparql query endpoint
Now return the created file id (instead of celery task id) in the create file endpoint
Fixed Flask version to < 2.0.0 due to compatibility issues

Fixed the console restriction to admin/users (was not fully functional)
Fixed an issue with spaces (and other characters) in URIs
Fixed an issue with "Optional" button when using categories (and faldo entities) (either wrong values or nothing showing up) (Cf Changed category)
Fixed table ordering in results for numerical values (they were managed as strings)
Fixed UNION and MINUS blocks
Fixed an issue with Faldo "same strand" (clicking on the link between Faldo nodes)
Fixed Node/Link filter issue when using values with caps.

Added File view in admin interface. Administrators can delete the files.
Added Dataset view in admin interface. Administrators can delete the datasets, and make them public/private.
Added Public queries view in admin interface. Administrators can make them private.
Added /data/ route, which list parameters (predicates and objects) for a specific URI. Results are filtered based on the user's visibility.
Added CLI script for changing Askomics namespace if some files have already been integrated.
Added documentation related to the previous CLI script.
Added enable_sparql_console related to the console change (in changed)

Restricted SPARQL query api endpoint to administrators. It can be re-enabled for logged user with the enable_sparql_console configuration value. WARNING: Check (#169) .
Set the SPARQL console read-only for non-administrators. It can be re-enabled for logged user with the enable_sparql_console configuration value. WARNING: Check (#169)