Feature: Distinguish reused terms in tree view #650
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…ntax error (#561) * fix statistics page syntax error * update ontoportal instances home section title * fix fast context option in annotator page * remove special chars from annotator's input on submit to avoid errors
* add json button ui to search page * extract json_link method from annotator controller to application controller * build the search page json link using json_link method * move the search json button down besides the advanced options button * remove this usage of api_params instead of direct params in search controller --------- Co-authored-by: Syphax Bouazzouni <[email protected]>
* Adding Content Finder Page * use ontologies selector instead of the url input * Change the controller to add use the accept headers - use the Net::HTTP instead of Linked::Client::HTTP to use the accept header * use ontologies selector in the content finder page * use the rest_url helper instead of the global variable REST_URI * remove content finder link from the topnav * close the array items in navitems method that causes an error * use Faraday instead of Net::HTTP * Remove result in content_finder_controller and use this.element.textContent * use this.contentTarget.textContent instead element in the content finder * Add html view using the concept details component * use tool layout for the content finder page --------- Co-authored-by: Syphax Bouazzouni <[email protected]>
…riples, turtle) (#547) * add feature to display resouce content in different formats * Add download and copy buttons to the raw data section * Add css to highlight the content of turtle and ntriples * Add the copy functionality to the resource raw data for formts: json, xml, ntriples and turtle * Remove the clipboard component and change the HTML title to Raw Data * Add clipboard component to the resource-content * Use Net::HTTP instead of Linked::Client::HTTP to include accept header * Add the content formats for instances and Properties * Remove copy_concept_content method in clipboard component * Use the highlight-js in the metadata controller and remove content_finder_controller * Remove code duplication for content formats - add content_formats method in application helper and use it for concepts, properties and instances * Remove content finder controller from index.js * Small fix: remove a condition in metadata_downloader * Add content_formats method to ontologies_helper and remove it from application_helper * Use Faraday instead of Net::HTTP * Add helpers for content finder controller * change content finder route to /ontologies/:acronym/:id/serialize/:output_format * Add concept details component to schemes and collections and fix code * rename the metadata downloader controller and remove the result value * update the concept formats tab UI to use icons and open in modal * update the content finder page code to re-use concept format code * update the content formats icons to use the primary color of the portal * extract commun code in content finder and concept formats in a concern * extract rdf highlighter component from concept format and content finder * rename the concept formats file and action to content_serlizer * in content finder don't call the backend serializer if format is html * fix the content finder container width * clean unused css code for the content finder * extract link_to_format_modal function in the concept details component * abstract the usage of a highlighter from the dependency highlight.js * update instance details page to use the concept details component --------- Co-authored-by: Syphax bouazzouni <[email protected]>
* create vertical_tabs component * use the vertical tabs component in the admin page * enable sort in the users admin table * fix the padding and marging of the metadata administration page * fix analytics admin page locals * fix an error in table component after rebasing the branch * remove an unused file * remove the paths escaping in the actions of user admin table * add again the link to API for the users admin page * implement for the vertical tabs the option to save the selected tab
* create vertical_tabs component * use the vertical tabs component in the admin page * add search admin page * translate the admin search tab to french * create number_input helper for Input::NumberComponent * make the regular button hide the loading state after request processed * remove an unused file * translate the search admin page to french and english
…d content (#505) * fix styling warning of flex "end" deperection * fix search input text overflowing out of the container * add search content by rdfs label in additoon of skos prefLabel * implement search redirection to the good page * use ontologies_content_autocomplete helper in homepage and topnav * add the search ontology content route * clean unused agent search code from this branch * move the code in search helper to a concern * re-integrate search input loader code to show a loader while searching
* optimize fetched attributes in the browse page in API mode * update ontologies browse to use API or Index * add cache for the fair_score and submission endpoint * internationalize a sentence in the browse and ontologies selector views * fix browse hasFormality and isOfType filters * prfioritize API filtring over the index in the browse page * fix a bug with edit submission returning nil error on submission
* add tools page * extract search input in the search page to re-use in url checker tool * internationlize the tools page * add tools link to the footer * fix the tools page block widths * add top padding to tools cards
* add mappings to concepts search results * fix mapping count in concept page * add new more from this ontology icon * move concept_mappings_loader function to mappings helper * remove indesired comment from _concept_mappings.html.haml file * put url escape functions in a separate helper
…nd schemes pages (#550) * remove forgotten binding.pry's from the code * add the option to the tree link component to open in modals * add type value to properties show view * create paginated search list helpers * update instances UI and add search bar * add a search bar to the properties show page * add a search bar for the collections show page * implement a search bar for the schemes show page * add search icon to the concepts search box * fix a typo in the search content concerns * move _instace_details file to _details * remove top padding from the search bar in properties and instances tree * implement selected in the paginated_list_component * use link_last_part in the tree link component to get the label from id * prioritize the label from the id in the ontology search content * remvoe top padding from search bar in the schemes and collection tree * translate missing word in the properties details view * clean the ontologies routes by defining a scope a removing duplicates * remove agent code not relevant in this branch * fix left padding of collections, schemes and properties views * fix tree autoclicking for collections, instances and schemes * move the html rendering from the search concern to helper * fix tests after changing the routes * translate missing words in the new ontologies section search bars * remove no more used instances js code
* fix search page search button style * fix search page json button style * update concepts mappings table style * add back chip button overflow wraping in concepts mappings table
* fix the copy of creation date on new submission * fix ontology viewer to hidde the data sections if any submission ready * prevent infinite redirection in the ontology controller show action
* enhance the ontology search input to include ontology names * fix new instances of page rendering * add browse page search ranking if API mode * include views by default to be cached and filter them by request after * remove no more used instances of controller and helpers code
* put terms and conditions check box in register page in french and english * add terms and conditions link to the config file * make the acceptation of the terms and conditions required for user registration * update the style of the register form errors * add terms and conditions links to the footer * add terms_and_conditions to login_flows_test * fix login flow integration test after adding terms and conditions * clean the config sample file --------- Co-authored-by: Syphax bouazzouni <[email protected]>
…ual (#581) * fix the paginated list selected value ti not select on each new page * fix instance search type filter to not include everything
* 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 * update the ontology redirection action to use ontology URI if resource_id nil * update the content serializer to translate ntriples to an html table if asked for html format * in the ontology redirection by default redirect to content finder with in html format * remove the ":" from the copy the portal URI tooltip text * change the order of the icons in the link_with_action component --------- Co-authored-by: Syphax bouazzouni <[email protected]>
* install D3 js and display a sample of ontology mappings bubbles * add zoom feature for mappings bubble view * fix bubble view style in mappings page * fix a scss selector in the annotator css that affects all a tags * mappings page layout * add ontologies select in mappings page * add upload new mappings in mappings page * add mappings table turbo frame * display the table view for ontology mappings * fix turbo frame issue in mappings page * Make the modal work in mappings table * improve mappings table view style * make mappings bubbles grow in a log way instead of a linear way * Highlighting mappings for the selected bubble * enable bubble deselection in mappings page * disable non highlighted bubbles in mappings page * show mappings page bubbles mappings in modal * make mappings page bubbles modal show correct values * customize mappings page bubbles tooltip * Link the table and the bubble view in mappings page * show highlighted bubbles with a gradient color related to the number of mappings * upload mappings in a separate tab * add concepts mappings to search page results * fix upload mappings tab style * display ontologies in ontologies selector * finalize ontologies selector design * put ontologies selector in the modal component * fix ontologies result display in ontologies selector * Make ontologies selector search bar work * show ontologies results count in ontologies selector * make groups filter work in ontologies selector * make filter by categories work in ontologies selector * add ontologies selector loading animation * make submission related filters work for ontologies selector * make select all work in ontologies selector * make retired ontologies and views filters work in ontologies selector * show tab selected checks count in ontologies selector * Add loading animation to ontologies selector * make ontology selection work in ontologies selector * make ontologies selector component * remove duplicated cross icon in ontologies selector * replace use cases of the old ontologies selector * convert ontologies selector ui component into a helper * replace 'selector' by 'ontologies_selector' in ontologies controller * enhance mapping page ontologies filtring style * add search page mappings count * add mappings bubble view to the ontology details page * make upload mappings work in mapping page * change seach results more ontologies button icon * fix concepts table mappings count * add a loading animation to the mappings bubble view * extract mappings page tab sections into partials * add internationalization to mappings page * clean mappings bubble view code * give more significant name for mappings ontologies table route * Clean mappings controller code * remove mappings search page part from main mappings PR * update new mapping form style * fix mappings section style and add search to its table in summary page * fix create new mapping for concept issue * fix upload mappings example style issue * update mappings ontologies table style * update the style the search filter of mappings table in mappings tab section * fix mappings bubble view modal link value * replace var by let in mappings visu stimulus controller * make hard coded mappings-bubble-view id by a dynamic * remove undesired #getLastPartOfUrl function from mappings vizu stimulus controller * extract #init_mappings_section_bubble_view() to a separate function in mappings visu stimulus controller * Add a default value for zoomRatio stimulus value in mappings visu controller * Add a default value for type stimulus value in mappings visu controller * refactor submit function in mappings visu stimulus controller * refactor select bubble method in mappings visu stimulus controller * put center_scroll method inside draw bubble method to not repeat code in mappings visu stimulus controller * refactor normalization ration function in mappings visu stimulus controller * use a better comprehensive helper for the empty modal in mappings page * add a legend for mappings bubble view * add back external mappings to mappings table view, and clean visu stimulus controller * move rest_url function to application_helper to be used by views * set table container box-sizing to not overflow if padding set * remove the new created to mappings actions and use the count action * remove the no more used loader action * move some mappings helpers and remove unused ones * use component helpers instead calling render & use reveal component * remove no more used partials in mappings * refactor and clean the mappings stimulus controller * extract from mappings stimulus the drawBubble logic in a file * fix mappings bubble view legend (bubble size)
* add back admin routes to fix delete submission * remove admin duplicated routes
* restore the new sample text of the annotator and recommender * add french translation for annotator and recommender sample text
* add language param to search results links * use helpers.request_lang instead of passing lang variable in search aggregator * make the selection of the closest preflabel to the query case unsensitive
…and browse page ontology type filter (#596) * fix the auto selection of isOfType filter on browse page * fix search properties redirection to use propertyid not instanceid * fix admin ontologies visits sorting * fix ontologies browse page to show ontologies with no submissions * fix the sort by dates order in browse page * add apikey to the fairness cache key * show in the search box result "ontology view" for views
* remove duplicated ontology scheme rows * move the concept details row duplication logic to filter_properties function * clean concept details component code * reject bottom set keys from leftover in concepts details component * fix skos-xl not been displayed in the raw data section
* Fix undefined method error Resolves #308 * escape username when creating an ontology subscribtion * fix missing roots message for nil classes --------- Co-authored-by: Jennifer Vendetti <[email protected]>
* fix user reset password internationalisation issue * get user info in reset password * fix card message component image
* install Webmock gem * setup recommender page test * mock recommender api results in recommender system test * add test edit text area and submit in recommender test * disable webmock after the test ends in recommender test * make add comment/proposal buttons smaller * remove non related code to recommender tests PR * put the a correct recommendations fixture * check the number of results in recommender test * check the number of the highlighted annotations in recommender test * Disable webmock before each test to insure the non mocking of the different requests * use dynamic host and apikey in recommender webmocking
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* 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 <[email protected]> Co-authored-by: Bilel KIHAL <[email protected]> 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> --------- Co-authored-by: Bilel Kihal <[email protected]> Co-authored-by: SirineMhedhbi <[email protected]> Co-authored-by: Bilel KIHAL <[email protected]> Co-authored-by: Imad Bourouche <[email protected]>
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* 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 <[email protected]> Co-authored-by: Bilel KIHAL <[email protected]> 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * Fix: run production mode (#679) * remove duplicate from gemfile * add port 3000 for production to use it with ontoportal_docker * add commands to run production correctly * Fix: json file extention in export metadata summary page (#683) * hide analytics features if not enabled (#691) * add search placeholder to data table component (#688) * fix browse page contact titleizing (#689) * fix mappings concept link not opening empty pages (#690) * Fix docker compose to make tests work (#695) * Fix: check resolvability tool redirection (#694) * Feature: add rewrite condition in URI redirection rules (#684) * add rewrite condition in the rewrite rules * refactor and clean code of htaccess and nginx redirection rules * Fix: User ontologies custom set updating (#685) * Fix ontologies custom set feature * enhance custom set feature style * remove duplicated action in home controller account, which is the same as show in users controller * clean application helper ontologies selector code * remove unecessary server calls in account page * Remove JQuery code in accounts page * remove repeated server call in custom ontologies features * fix the login flow test after deleting the repeated action related to `/acount` * Feauture: add acronym column in the agents table in the admin page (#704) * Fix: subscribe button issues (#681) * fix clicking on subscribe button while being not logged in * remove non related code to fix subscribe button issues PR * fix subscribe button displays wrong values when using french * replace UnWatch by unwatch * clean subscriptions method code in ontologies controller * Fix the color of the loader component spinning loader * remove duplicated code in subscription button fix * disable cache for subscription button calls * remove invalidate cache for the user calls * Feature: add response time calculation in check resolvability tool (#717) * add response time calculation in check resolvability tool * add other format equivalents to handle most cases of request accept header * move the AVG time to check_resolvability_message instead of appending it * remove the usage of inexistent variable in that block scope * remove comment as the variable name is already clear --------- Co-authored-by: Syphax Bouazzouni <[email protected]> * Feature: add ontology viewOf to the summary page relation network (#716) * Feature: Remove subject values from the project and usage block in summary page (#719) * Feature: Add cookie banner (#702) * add cookies action to show and save cookie state in a session * add link button component helper * add cookie modal view * enhance the style of the cookies banner --------- Co-authored-by: Bilel KIHAL <[email protected]> * Fix: update summary page categories display to show acronym with tooltip (#713) * update summary page categories display to show acronym with tooltip * fix submission flow system tests after changing their display * make show_category return the full domain if not a category * update the show category name to use clickable state if not a category and is a link * fix remove agent usages (#697) * Feature: Enhance agents search input component (#703) * make agents search field component results unlimited to only 4 * make agents cherchable by acronym, affiliations, email and home page * Update the agent search input to display the result in this format Orga name (ACRONYM) – ROR:003vg9w96 and for persons Person Name – ORCID:0000-1524-5487-5487 * chagne display mode value type from string to boolean in search input component * remove agents search logic from UI side and limit it to only name, acronym and identifiers * use the endpoint '/search/agents' for the agents search input component * Fix: saving and cancel button locals text capitalization (#724) * Feature: add qf param in agents search (#727) * Fix: Hide affiliations when agent is organization in agent form (#696) * Hide affiliations when the agent is an organization in the agents form * Change the name of the function affliations? to is_organization? to make it more clear * fix submission flows test after the fix of the PR #713 * fix agent tests after changing the behavior of displaying affiliations --------- Co-authored-by: Syphax <[email protected]> * Feature: Make agent indentifiers field set by default based on agent type (#721) * remove the restriction for certain submission fields to create only organization type or person type agents * make orcid or ror default input based on agent type in agent form * fix disappeared signup form icons * fix nested agents creation * fix agent form not filling saved identifier values * create an agent identifier input helper * disable cookie banner in development and test mode * fix agent tests after enforcing ROR for organizations --------- Co-authored-by: Syphax <[email protected]> * Fix: propertyid param auto added to summary page URL (#723) * Fix propertyId param auto added to summary page URL * remove added PropertyId param to the URL when opening summary page * Fix auto added propertyId to the summary page URL * Fix auto added instanceid to the summary page URL * Fix auto added propertyId to the summary page URL * add back the constraint of making frames loading lazy while env.development * make by default properties section displays the first property * make by default instances section displays the first instance * change the name of the function instances_tree_first_id by search_first_instance_id * add a clarification comment in search_first_instance_id method * move get_property function to properties controller --------- Co-authored-by: Syphax <[email protected]> * fix losing context when changing language in concepts page * fix concept not added to browser URL param issue * refrech the whole page when we change concepts language * fix not saving the current url context when changing the language * Revert "Merge remote-tracking branch 'origin/fix/change-language-lost-context' into fix/change-language-lost-context" This reverts commit c7b6d08, reversing changes made to cb3b7ba. * update turbo frame controller to handle ontology viewer special case --------- Co-authored-by: SirineMhedhbi <[email protected]> Co-authored-by: Syphax bouazzouni <[email protected]> Co-authored-by: Imad Bourouche <[email protected]>
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