Merge to master: AgroPortal release 2.8.0 #11
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…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>
* 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
…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>
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)
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This PR syncs Ecoportal with the latest version Agroportal v2.8.0 it includes the following: