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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.

[4.5.0] - Unreleased

Deprecation warning

  • Due to a change in the way strands are integrated for FALDO entities, you will need to re-integrate them.
  • 'Results' from older version of Askomics using 'Minus' or 'Union' blocks will use 'legacy' mode. (Meaning, they will not have recursive block support). To enable recursive block support, please recreate the query from scratch, or manually delete the blocks and re-create them.

Added

  • Added 'anonymous_query' and 'anonymous_query_cleanup' variables
    • These enable 'anonymous query' mode, allowing anonymous users to send 'full queries'. See documentation
  • Added 'overview' button in the query page. This button will show all 'selected' attributes, and allow users to quickly select the related entity.
  • Added 'Abstraction' tab on the navbar. This will print the whole abstraction as a 2d/3d graph.
  • Added 'distance' notion, using attribute link. This allows user to filter a value based on another value, with an optional modifier.
  • Added 'custom distance' option for faldo relation (instead of just 'included_in' and 'overlap_with')
  • Store 'version' value when storing results. Not used for now, but might be used in deprecation warnings later
  • Removed some lines from coverage computation
  • Added 'indirect relations': Two entities will be linked on the graph, without a direct relation between them (same as faldo relations). This is intended to be used with 'linked attributes' (ex: get all entities B where B.color is the same as A.color, without a direct relation between A and B)
  • Basic support for 'skos:broader' and 'skos:narrower' for ontologies.

Fixed

  • Fixed new linting
  • Fixed logs for production setup
  • Fixed profile update & password reset tab in user profile page
  • Fixed Gff Faldo integration (was only integrating the last selected entity)
  • Fixed an issue when using filters and an 'UNION' node
  • Fixed an issue when launching a query with a 'linked' attribute toggled but unselected
  • Fixed missing includeIn and includeInReference in bed files
  • Fixed 'overlap_with' faldo query

Changed

  • Added contact_message config option, displayed in a new 'Contact' page
  • Added front_message config option, displayed on the front page
  • Now print reset link into logs if there are no mailer configured
  • Fixed markupsafe to 2.0.1
  • Increased Galaxy timeout for tests
  • Fix documentation build
  • Force all 'user queries'(ask/sparql interfaces) to go to the unauthenticated endpoint, to increase security (no write permissions)
  • Force all queries to use 'POST' instead of 'GET' to avoid max length issues
  • Changed the way 'strands' are integrated, to quicken FALDO queries. (Require re-integrating the data)
  • 'Same strand' queries will now match 'BothStrand' with a forward or reverse strand
  • Use '+', '-' and '.' for strand values in CSV instead of raw value (for homogenization)
  • Now allows 'infinite' recursive blocks (ie, a Minus block inside a Union block, or the opposite)
  • Overhaul faldo relation: add 'direct shortcut' triples between entities and values, to avoid using slow property paths when using faldo queries

Security

  • Bump markdown-captions from 2 to 2.1.2
  • Bump http-cache-semantics from 4.1.0 to 4.1.1
  • Bump minimatch from 3.0.4 to 3.1.2
  • Bump json5 from 1.0.1 to 1.0.2
  • Bump qs from 6.10.1 to 6.10.3
  • Bump decode-uri-component from 0.2.0 to 0.2.2
  • Bump loader-utils from 1.4.0 to 1.4.2

[4.4.0] - 2022-07-01

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)
  • Fixed an issue with saved queries for non-logged users

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
  • Added prefixes management
  • Added 'external graph' management for federated request: federated requests will only target this remote graph
  • Added support for multithread in web server, with the WORKERS env variable when calling make

Changed

  • Changed "Query builder" to "Form editor" in form editing interface
  • Changed abstraction building method for relations. (Please refer to #248 and #268). Correct 'phantom' relations
  • Changed abstraction building method for attributes. (Please refer to #321 and #324). Correct 'attributes' relations
  • 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