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CHANGELOG.md

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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

  • 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

  • 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

  • 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

Removed

  • Removed "Remote endpoint" field for non-ttl file
  • Removed "Custom_uri" field for ttl file

Security

  • Bump axios from 0.21.1 to 0.21.2
  • Bump tar from 6.1.0 to 6.1.11
  • Bump @npmcli/git from 2.0.6 to 2.1.0
  • Bump path-parse from 1.0.6 to 1.0.7
  • Bump prismjs from 1.23.0 to 1.27.0
  • Bump simple-get from 2.8.1 to 2.8.2
  • Bump ssri from 6.0.1 to 6.0.2
  • Bump follow-redirects from 1.14.4 to 1.14.8
  • Bump mkdocs from 1.0.4 to 1.2.3 in /docs
  • Bump python-ldap from 3.3.1 to 3.4.0
  • Bump minimist from 1.2.5 to 1.2.6

[4.3.1] - 2021-06-16

Fixed

  • Fixed an issue with categories
  • Fixed an issue with GFF import

[4.3.0] - 2021-06-10

Added

  • 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.

Changed

  • 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

  • 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.

Security

  • Bump hosted-git-info from 2.8.8 to 2.8.9

[4.2.2] - 2021-06-09

Fixed

  • Fixed startup issue: race condition on config file creation

[4.2.1] - 2021-03-29

Fixed

  • Fixed issues with lock files

[4.2.0] - 2021-03-15

Added

  • 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)

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)

Fixed

  • Fixed encoding issue (#160)
  • Fixed filename issue (#155)
  • Fixed retrocompatibility issue (#148)

Security

  • Bumped ini from 1.3.5 to 1.3.7
  • Bumped axios from 0.20.0 to 0.21.1
  • Bumped prismjs from 1.21.0 to 1.23.0
  • Bumped elliptic from 6.5.3 to 6.5.4
  • Bumped react-addons-update from 15.6.2 to 15.6.3
  • Bumped react-force-graph from 1.36.10 to 1.39.2
  • Bumped react-syntax-highlighter from 13.5.3 to 15.4.3