…r-auth

Feature: Add multi provider authentication

…ndpoint

Feature: Add agent crud endpoints

* update get_term_search_query to support multilanguages search

* rename var

* fix search lang suffix to use underscore not @

* add multilangual search test

---------

Co-authored-by: Syphax Bouazzouni <gs_bouazzouni@esi.dz>

…s-endpoint

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* update Goo version and add submissions filters test

* add detach a view from an ontology test

* fix populate_from_params help to reset object value to empty

* reset to master branch the api dependecies

* add class tree test with scheme and collection filters

* make the class tree endpoit load isInActiveScheme and isInActiveCollection for the select class

…fixes (#52)

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

…(#57)

* add agent usage attribute tests

* optimize fetching all agents usages query by batch loading them

* add docker build CI

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

…#61)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* update ontoportal script to handle local gems bindq

* update ontoportal script to handle binding to local gem for development

* fixing the test runner after the new changes in the ontoportal script

…r-auth (#44)

Feature: Add multi provider authentication

* Merge pull request #34 from ontoportal-lirmm/feature/paginate-and-filter-ontologies-endpoint

Feature: Implement pagination and filters to submissions endpoint

* Merge pull request #36 from ontoportal-lirmm/feature/paginate-and-filter-ontologies-endpoint

Feature: Add oder by and filters for ontologies endpoint

* Merge pull request #32 from ontoportal-lirmm/feature/support-multilingual-read-one-language-from-request-parameter

Feature: Support multilingual - Add request_lang middleware

* Feature: Add support of multilingual search (#40)

* update get_term_search_query to support multilanguages search

* rename var

* fix search lang suffix to use underscore not @

* add multilangual search test

---------

Co-authored-by: Syphax Bouazzouni <gs_bouazzouni@esi.dz>

---------

Co-authored-by: HADDAD Zineddine <hz_haddad@esi.dz>

* Merge pull request #33 from feature/update-submission-mdetamodel-2023

* Merge pull request #39 from ontoportal-lirmm/feature/add-agent-crud-endpoint

Feature: Add agent crud endpoints

* add request_lang middleware

* pin redis gem version to 4.8.1

* update Gemfile.lock

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* update Gemfile to use ontologies_linked_data new metadata branch

* update TestOntologySubmissionsController to be adapted to the new model

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* [ontoportal-bot] Gemfile.lock update

* in submission_metadata rename display with category

* add to submission_metadata description and example fields

* add the option to do pagination for the submission endpoint

* extract retrieve_latest_submissions method to submission helper

* implement apply_filters to submissions endpoint using SPARQL FILTERs

* add test for submissions endpoint pagination

* [ontoportal-bot] Gemfile.lock update

* fix private only submission filter

* add hasFormalityLevel filter for submissions endpoint

* add  for ontology: reviews, notes, projects on the submissions endpoints

* bring submission metrics for submissions  endpoints

* bring all contact attributes if asked in the submissions endpoints

* refactor submissions endpoint filters by extracting some methods

* add ontology acronym or name filters for submissions endpoints

* add submissions endpoint order_by option

* [ontoportal-bot] Gemfile.lock update

* fix including ontology and contacts in the submissions endpoints

* fix list admin filter_access control (e.g for submissions  endpoints)

* [ontoportal-bot] Gemfile.lock update

* check access of ontologies in /ontologies/:acronym/submissions endpoint

* include ontology viewOf attribute in the submission endpoints

* make apply_filters helper generic for any of model attributes

* add Agents controller

* add pagination to agents index endpoint if asked

* make agents routes work for /Agent and /agent

* handle agent indentifiers and affiliations attributes  save and update

* make agent controller work for affiliations attribute

* add agent controller tests

* don't update affiliations if only 'id' sent in params

* bring identifier attributes when we update an agent

* update agent test to work with the new Agent validators

* bring the agent attributes on display all of the submissions endpoints

* handle exception for  class attribute but aren't in populate_from_params

* update Gemfile to use development branch of OLD

* refactor user controller to extract reset password helpers

* remove the send notification on user creation, now handled by user.save

* add access token authentication

* fix test after enforcing the uniqueness of user emails

* fix search test

* add oauth_authentication test

* bring the correct attributes when the oauth_authenticate is used

* Feature: Add support of multilingual search (#40)

* update get_term_search_query to support multilanguages search

* rename var

* fix search lang suffix to use underscore not @

* add multilangual search test

---------

Co-authored-by: Syphax Bouazzouni <gs_bouazzouni@esi.dz>

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* update Goo version and add submissions filters test

* Fix: display contact for get submissions  (#45)

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* Fix: Submissions filters with order_by  for the same attribute  (#46)

* add get submission all including all properties test

* extract and use submission_include_params where we use submission.bring

* use retrieve_submissions helper in the :acronym/submissions endpoint

* update Goo version and add submissions filters test

* make the ontology submissions endpoint include views

* include all metrics attribues in the submissions endpoints (#53)

* add ontology submissions filter by status (#56)

* add agent usage attribute tests (#55)

* Fix: optimize fetching all agents usages query by batch loading them (#57)

* add agent usage attribute tests

* optimize fetching all agents usages query by batch loading them

* Feature: Add ontologies_api docker image build CI  (#58)

* add docker build CI

* Feature: add ontoportal bash script (#59)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* Feature: add ontoportal bash script (#59)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* fix date list properties population helper

* Feature: update ontoportal bash script to handle local gems binding   (#61)

* add ontoportal bash script to run test and development servers

* update README.md

* update docker CI to work in production releases

* update ontoportal script to handle local gems bindq

* update ontoportal script to handle binding to local gem for development

* fixing the test runner after the new changes in the ontoportal script

* add description filter to the submissions endpoint (#62)

---------

Co-authored-by: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Co-authored-by: HADDAD Zineddine <hz_haddad@esi.dz>

…es (#63)

Merge to master: Release v2.3.1

…RI content negotiation and Ontology metadata and data indexation (#73)

* Feature: Migrate to virtuoso (#67)

* set up multiple triple store test environment

* optimize api tests

* Fix: update ncbo_annotator gem version (#71)

* update ncbo_annotator gem version

* update alegrograph to version 8.1.0

* Feature: use the new  SOLR Schema API instead of SOLR config files  (#68)

* update docker compose to use standard SOLR not the ontoportal configured

* update term search to use the new Schema API and remove config files

* update properties search to use the new Schema API & remove config files

* update class and properties schema to use the existent dynamic names

* Feature: resolving resources within specific ontologies, supporting various output formats(#69)

* remove useless line preventing sending the reset password email (#65)

* [ontoportal-bot] Gemfile.lock update

* Feature: api endpoint returns json-ld  for the element with that URI

* implement GET, POST requests, and GET /parse to submit INRATHES ontology

* Enhance tests using real data submission

* Enhance bin/ontoportal to make it able to run localy with UI

* Small fixes

- change controller name and test controller name
- remove /parse endpoint
- rackup to shotgun in bin/ontoportal

* Fix test dereference resource controller

- in json test, before we test the result we sort the hashes with the function (sort_nested_hash)
- in xml, ntriples and turtle, we split the result and the expected result, sort them and compare them

* update gemfile: add json-ld (3.0.2)

* change derefrencement namespacing and clean code

* Fix dereference resource tests expected resultsto handle parse triples

* fix xml serialization test for AG and Gb by cleaning the xml string

---------

Co-authored-by: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Co-authored-by: imadbourouche <ji_bourouche@esi.dz>

* Feature: URI drerfrencement content negotiation (#72)

* remove useless line preventing sending the reset password email (#65)

* [ontoportal-bot] Gemfile.lock update

* Feature: api endpoint returns json-ld  for the element with that URI

* implement GET, POST requests, and GET /parse to submit INRATHES ontology

* Enhance tests using real data submission

* Enhance bin/ontoportal to make it able to run localy with UI

* Small fixes

- change controller name and test controller name
- remove /parse endpoint
- rackup to shotgun in bin/ontoportal

* Fix test dereference resource controller

- in json test, before we test the result we sort the hashes with the function (sort_nested_hash)
- in xml, ntriples and turtle, we split the result and the expected result, sort them and compare them

* update gemfile: add json-ld (3.0.2)

* change derefrencement namespacing and clean code

* Fix dereference resource tests expected resultsto handle parse triples

* Feature: add content negotiation middleware

* Add headers to tests instead of output_format

* Apply middleware to only /ontologies/:acronym/resolve/:uri

* Add test cases for AllegroGraph and fix xml test

* move the content_negotiation middleware into rack folder and  module

* re-implement again the usage of  the output_format param if no format is given in the request header

* clean the tests for no more necessary checks

* clean and simplify the content negotiation middleware

* add the accepted format in the error response of resolvability endpoint

* refactor the content negotiation middleware code to be more clear

---------

Co-authored-by: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Co-authored-by: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>

* Fix: user creation security  (#60)

* extract slice tests helper to the parent class for reusability

* add a test for the creation of an admin user

* enforce the security of admin user creation

* update slices controller to enforce admin security

* Fix: the content negotiation by removing a no needed require

* Feature: Indexation administration & Ontologies and Agents search  (#70)

* index submission and agents metadata

* add search administration endpoints to init schema and index batch

* add ontology and agent search endpoints

* add agent and ontology search tests

* add admin search in collections

* make the search admin use directly the solr connector

* implement search ontologies content search endpoint

* enforce solr models indexing one by one to prevent batch fails

* add detType tov search ontologies  content search endpoint

* fix content ontology search pagination

* add ontology search content types filter

* Feature: Add accessibility security to ontology metadata & content search results  (#74)

* add ontology accessibility restriction  to ontology metadata search

* add ontology accessibility restriction  to ontology content search

* add search results accessibility security test

* fix: enable user creation notification (#76)

* Fix: Invalidating cache on insert & fix Redis warning (#77)

* Merge pull request https://github.com/ncbo/ontologies_api/pull/120from ncbo/remove_redis-activesupport

Remove redis activesupport

* use the branch development of sparql client

* Feature: mappings statistics slices support (#78)

* restrict mapping statistics ontologies to the ontologies of the current slice

* add a test for the mappings slices support

* add test for mappings statistics slices support

---------

Co-authored-by: OntoPortal Bot <ontoportal.bot.lirmm@gmail.com>
Co-authored-by: imadbourouche <ji_bourouche@esi.dz>
Co-authored-by: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com>

…by URI length (#79)

…rtal-reset