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Merge to master: Release 2.8.1 (#631)
* fix: home annotator block redirection to annotator page with empty text (#629) * Fix: Download button in summary export metadata (#628) * fix xml download button in summary page, export metadata * adjust the position of the export metadata download button and make the hover cursor pointer for it * Fix: the contexual json icon for to the concept adapt to the select tab (#539) * refactor concepts json code and put it in a stimulus controller * adjust the position of the concepts json link * remove non related code to concepts json PR * remove non related code to contextual json pull request * pass base class URL directly to concepts json stimulus controller * clean concepts json stimulus code * remove undesired code from concepts json button PR * fix typo in agent_search_input_component.html.haml * rename concepts json button stimulus controller * clean concepts json button controller code * clean concepts json button related code --------- Co-authored-by: Syphax bouazzouni <gs_bouazzouni@esi.dz> Co-authored-by: Bilel KIHAL <kb_kihal@esi.dz> Co-authored-by: @SirineMhedhbi * feature: make view of clickable in summary page header (#643) * feature: use the ontologies selector by name and acronym in edit groups and categories (#641) * Fix: Reject the current ontology from appearing in the ontologies selector in editing the submission's relations (#640) * reject current ontology from the ontologies selector in relations section - edit submission * pass reject ontology as a param in generate ontology seect input method * Feature: Make text area resisable in upload ontology and edit submission forms (#644) * make text areas resisable in upload ontology and edit submission forms * make forms list input text areas resisable * Fix: The issue when the agent has no acronym (#645) * fix the issue when the agent has no acronym * clean agent affiliations combination * fix: the concepts chips links redirecting to the wrong destination (#638) * Feature: Scroll to the selected term in the tree view component (#646) * scroll to the selected term in the tree view * prevent the whole page scrolling when centring the scroll to the selected tree view element * fix: change local test "URL" to "URI" in check resolvability components (#651) * Feature: Add content negotiation redirection tests (#622) * Add uri redirection for /ontologies/:acronym/:id to the appropriate page * small fixes: remove binding.pry and return resource_id in find_type_by_search * Add copy agroportal link functionality - this functionality is using the ClipboardComponent because it works the same but differ only in the content and icon - the clipboard component has been changed to accept title and icon * redirect to content finder page when no type is valid * Updated route to use redirect action instead of show_redirection * Use default icon and title arguments in the Clipboard Component * rename and internationalize clipboard component titles * small fix: remove % from svg icon * Add the copy title to the components section in en.yml and fr.yml * Show the generated uri when user hover over the copy link icon * Make the dynamic route content negotiable - based on the accept header we will - if "text/html" we will redirect to the agroportal page - else we will call the api and get the content serialized in the format specified and return it * update serialize content to return accept_header * translate copy_original_uri and copy_portal_uri to french * reuse search content concern in uri redirection concern * remove duplicate link_last_part method * Add htaccess functionality * Add apache and nginx instruction for htaccess redirection * Clean te code in the view file * Add OntologiesRedirectionController - remove redirect and generate_htaccess from ontologies_controller - clean code the generate_htaccess method - add "ontology_portal_uri" in @Identifiers * Regroupe routes * Make ontologies_redirection controller and refactor generate_htaccess code * Internationalization of redirection rewrite rules modal * Add note for url that has # * link contact support button to the feedback page * Change regex to redirect only url of type: /path/resource_id - for urls that has the # it will redirect to the ontology page * Add ontology redirection based on the accept header format * move the ontology redirection route to the bottom to have less priority * Change rewrite rules note using alert component * Add /ontologies/ACRONYM/download?format=FORMAT route * ontology redirection based on the accept header using /ontologies/acronym/download route * Add redirect assertion in ontologies controller test * Fix content serialization when calling /ontologies/:acronym/:id * create private function for accept header and remove ontology redirection * remove generate_rewrite_rules function * remove redirect assertion in ontologies controller test * change htaccess route to /ontologies/:acronym/htaccess * fix copy internal links in LinkFieldComponent * add raw to copy internal links in identifiers card * return all response and add text/n3 format in content serializer * escape id when redirecting to content_finder * choose the right result from the results of search content * add algorithm to choose the right accept header, not_acceptable if no format valid * add an additional security to the uri redirection to have an exact match * make the check resolvability icon clickable & redirect to the tool page * make the check resolvability extend to accept equivalent formats * move the redirection function from ontologies_controller to uri concern * fix check_resolvability_tool to redirect to the full url not only the path - the problem was because everytime it is redirecting to the uri.path and uri.path does not include the ?format parameter - add the octet-stream accept header in the accepted format for xml * add reference to the url of the original file when format not acceptable * put again the resolvability timeout to 5 secondes * setup content negotiation and redirection tests * remove redirection when request ontology with format - the redirection is removed when request ontology in any format, by making request to the api and forward the result * add ids to the resource format icons and modal * assert the content type for html and json - the xml and csv is returning 500 internal server error from the api, but it's working locally * refactor content_redirection tests - still not completed * add multiple response status for ontology xml and csv format * add test for the content format of the resource * add turtle format based on hasOntologySyntax field * assert success and not_acceptable in turtle format it depends on hasOntologySyntax * add NTriples format for ontologies based on hasOntologySyntax field * test content negotiation for ontology resources * fix redirection url for resource html format * fix ontologies controller test indentation * assert redirection location in resource html format * update the admin user creation in tests possible only by an admin now --------- Co-authored-by: Syphax bouazzouni <gs_bouazzouni@esi.dz> * Feature: add Annotator UI tests (#627) * setup annotator page UI tests * check if all the inputs and filters are present in annotator page test * add annotator http requests to test fixtures * test annotator results and count them * test annotator empty illustration * add comments in annotator page tests * use dynamic api in recommender tests * test that we have the exact correct annotations in the annotator test * undo adding ids for elements to run annotator tests * add a default ANNOTATOR_URL value for test config --------- Co-authored-by: Syphax bouazzouni <gs_bouazzouni@esi.dz> * Fix: multiple highlighted terms in concepts date view (#657) * Fix multiple highlighted terms in the date view * refactor concepts by date method code * Fix: concept details table layout max-with when long strings (#649) * fix concepts table layout when we put very long strings * fix concepts json button position * use a css class intead of an id for the concepts_json_button * move concepts_json_button css class from concept details file to concepts file * remvoe #concepts_json_link unsued style --------- Co-authored-by: Syphax Bouazzouni <gs_bouazzouni@esi.dz> * Feature: Clean no more used gems and code (#658) * remove cube ruby * remove not used gems and add documentation to the Gemfile * remove miniprofiler * remove bpdi resolver and redirect_to_new_api * remove ajax proxy and no more used helpers * remove no more used helpers * handle the case reset_agents in edit submissions error state are already Agents (#663) * Feature: Add issues and requests link to the footer and feedback form (#665) * add issues and requests link to the footer and feedback form * add $GITHUB_ISSUES to sample config file * Fix a typo in bioportal_config_env.rb.sample * fix: upload ontology on errors non returned values and no default values (#625) * move pry gem outside development block in gemfile (#671) * Feature: Add back slices (#598) * Add slices section to home page * Update the design of the slice top notice bar * fix home slice name styles * fix slices error on home page, when there are no slices available * make the annotator support slices * make browse page compatible with slices * update home slices section to include the number of ontologies per slice and the description * make mappings page supports slices * rearrange home page sections to be in this order: slices, ontoportal instances then collaborations * remove unnecessary code in submission filter file * Adjust the slice link to comply with the production URL * update home page slices section style * add a description to the home page slice section * update home page slices section style * update ontoportal instances and support home sections styles * change the button of add new slice to suggest a new group/slice in the home page * update slices descriptive texti in the home page * add a description for ontoportal instances in the home page * move home_ontoportal_tooltip to home helper * add ontoportal links in config file * remove http from slice link to make it work with https * add slice notice to lang local files * remove mappings statistics slices support in the UI cause it's already done in the back * update ontoportal website links to be upper case * fix slices https issue --------- Co-authored-by: Syphax bouazzouni <gs_bouazzouni@esi.dz> * fix docker compose to make local env dev work in port 3000 * Fix: submissions properties selector labels and include ontologies properties (#669) * add ontologies properties to the submission properties selector * show submission attributes label instead of the keys in the selector * make slices open in the same tab not in a new tab * put the ontoportal instances directly before the logos instead of a tooltip * Fix: Redirect to the login page when accessing private ontology while being not authenticated (#673) * Feature: Distinguish reused terms in tree view (#650) * distinguish reused properties in the tree view * use preferredNamespaceUri to distinguish reused terms in the tree view if uriRegexPattern is not present * use preferredNamespaceUri to distinguish reused properties in the tree view * distinguish reuses for instances tree * clean terms reuses code * extract is_reused to a separate function in components helper * add concepts reuses to the date view * pass submission directly instead of ontology_uri_pattern * pass direcly the submission instead of passing by a function in terms reuses * Clean terms reuses concern code * add reuses to schemes tree * add reuses to schemes tree when we perform a search * add reuses for collections tree * add reuses to properties tree when we perform a search * add reuses for concepts list view * Clean terms reuses code * extract submission variable form the concept date render helper * remove binding.pry comments left in the code --------- Co-authored-by: Syphax Bouazzouni <gs_bouazzouni@esi.dz> --------- Co-authored-by: Bilel Kihal <61744974+Bilelkihal@users.noreply.github.com> Co-authored-by: SirineMhedhbi <31127782+SirineMhedhbi@users.noreply.github.com> Co-authored-by: Bilel KIHAL <kb_kihal@esi.dz> Co-authored-by: Imad Bourouche <ji_bourouche@esi.dz>
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