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Merge to master: Release 2.8.0 - Search everywhere anything, Visualiz…
…e mappings cloud and OntoPortal URIs (#564) * Fix: Annotator fast context special chars issues & statistics page syntax 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 * Feature: Add json button to search page (#562) * 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]> * Feature: Adding Content Finder Page (#511) * 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]> * Feature: Add ontology concepts exporters to diffrent formats (xml, ntriples, 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]> * Feature: update admin page UI to use vertical tabs (#566) * 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 * Feature: Add indexation admin page (#567) * 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 * Feature: Update search input in homepage and topnav to use the indexed 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 * Feature: Improve Browse page performance (#572) * 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 * Feature: Add OntoPortal tools age (#559) * 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 * Feature: Add concepts mappings button in search page results (#569) * 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 * Feature: Add search bars for the instances, properties, collections and 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 * Feature: Update concept mappings table style (#574) * 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: submission date and summary not ready (#576) * 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 * Feature: Improve browse page search ranking and performance (#575) * 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 * Feature: Add terms and conditions to signup and footer links (#579) * 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]> * Fix: new instance search feature to filter strictly only NamedIndividual (#581) * fix the paginated list selected value ti not select on each new page * fix instance search type filter to not include everything * Feature: Dynamic routes for ontologies content dereferencement (#568) * 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]> * Feature: Update mappings page (#538) * 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) * fix search page results broken links (#583) * Fix: admin delete submission route (#585) * add back admin routes to fix delete submission * remove admin duplicated routes * Fix: Restore the new sample text of the annotator and recommender (#593) * restore the new sample text of the annotator and recommender * add french translation for annotator and recommender sample text * Fix: search results selected language (#595) * 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 * Fix: new instance details page, properties selected property display 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 * Feature: add a script to import or export CSV of the i18n locals (#597) * Fix: Remove duplicated ontology scheme rows (#584) * 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: summary page for ontologies with no submissions * Fix: Note thread show action (#606) * 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 (#605) * fix user reset password internationalisation issue * get user info in reset password * fix card message component image * fix: trim the copied text in the clipboard stimulus controller (#611) * Feature: Add recommender system tests (#599) * 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 * Feature: add htaccess URIs redirection modal help (#580) * 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 --------- Co-authored-by: Syphax bouazzouni <[email protected]> * Fix: Release 2.8.0 grouped issues - Summary, Concept, Notes, Mappings pages (#613) * fix hidden multiple synonyms in concept details * remove unecessary search icon from concepts, instances and schemes trees search inputs * fix the style of add comment and add proposal buttons * include page url auto in the errors page feedback form * add the selected bubble to the mappings legend tooltip * update the fix of hidden synonyms to prevent possible breaks * fix concept details raw data values alignement to use divs breaking line * fix recommender result ontology link to redirect to UI not API * fix summary ofaire tooltip breaking to a new line the card header * fix opening the concept tree view link in a new tab showing only html * fix french dates internationalization * fix edit submission up front help message in english version * handle the case of ontologies returning an error when roots are called * add no properties alert message to the ontology viewer * prevent ontology show redirection if summaryOnly show summary directly * localize the mappings vizualization legend text --------- Co-authored-by: Syphax Bouazzouni <[email protected]> * fix data tables warning issue (#624) --------- Co-authored-by: Bilel Kihal <[email protected]> Co-authored-by: Imad Bourouche <[email protected]> Co-authored-by: Jennifer Vendetti <[email protected]>
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