Feature Request: Add API call to trigger ontology pull from remote location #127
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This can be planned as one of the utils for the 'admin' tab for a given ontology that we plan to do with @syphax-bouazzouni |
yes, if we have that functionality in the API then we can enable ontology owners to trigger pull from the UI. |
mdorf
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mdorf
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…y pull from remote location
syphax-bouazzouni
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in ontoportal/ontologies_api
Jan 16, 2024
…onward (#4) * fix get a submission metrics * Auto stash before merge of "upstream" and "upstream/master" * add the slice get endpoint * add the slices create endpoint * add the slices delete endpoint * add the slices update endpoint * Add caching for analytics for 24 hours. * Fix for #97. Check for ontology existence before brining attributes * Handle edge case for submission downloads which do not have UploadFilePath set Fixes #98 * Gemfile.lock update * Add GH workflow for capistrano deployments * Update Gemfile.lock * fix ability to run deployment manually * Fix for deprecation notice of Rack::Attack.throttled_response Update configuration to closely match rack attack documentation in order to address deprecation notice: [DEPRECATION] Rack::Attack.throttled_response is deprecated. Please use Rack::Attack.throttled_responder instead * Update version of actions/checkout to address deprecation notices * Fix: Documentation rendering (#107) * Auto stash before merge of "upstream" and "upstream/master" * fix haml gem version * Update Gemfile * Restore branch specifier to master * Update capistrano sample config to include setting which branch to deploy from * Gemfile.lock update * Gemfile.lock update * Gemfile.lock update * Gemfile.lock update * Make sure ontology is present when accessing submissions. Fixes an internal server error when accessing submission for non-existent/deleted ontology * Remove owlapi_wrapper.jar file. It is included elsewhere * Add health checks for docker services and add more config file options * Remove wait-for-it * Add health check to AG service * Add GH workflow for publishing docker images * Add missing redis port number * Restore branch specifier to develop * Set mgrep port to 55556 * add arm64 platform * bump up version of solr-ut * Fix ncbo#116 - pinned redis-store to 1.9.1 until #358 gets resolved - fixed deprecation notices "warning: calling URI.open via Kernel#open is deprecated, call URI.open directly or use URI#open" * Restore branch specifier to master * fix for wrongly replaced string * Delete fix_purls.rb fix_purls.rb moved to a rake task under ncbo_cron project * Remove google analytics depenencies since those needed only in ncbo_cron * bump up major version of oj and faraday * remove search_index.rb script * lock gem rack-cache to 1.13.0 see ncbo#118 * remove depenency on redis-activesupport rack-attack can work with redis directly so there is no need to use redis-activesupport which is no longer being actively developed * unpin redis-store solves: ncbo#105 ncbo#106 * use redis-store from forked repo containing redis 5 compat fixes this should be reverted back to original after redis 5 copatibilty issues are resolved * use patched version of agraph v7.3.1 * unpin faraday gem * Gemfile.lock update * fixed an issue with the GA4 Analytics migration * fixed an issue with the GA4 Analytics migration * reduce request limit for resource intensive api calls (#121) * Announce deployments in NewRelic (#124) * Record deployments to NewRelic https://docs.newrelic.com/docs/apm/agents/ruby-agent/features/record-deployments-ruby-agent/ * add newrelic to deployment group github actions deployment doesn't install default group so capistrano fails to find newrelic recepies unless we add it to the deployment group * add rubocop * Gemfile update, goo version including goo#138 and goo#139 * Gemfile.lock update * Gemfile.lock update * Gemfile.lock update * update slice write operation to check if user is admin * Gemfile.lock update * fixed an accidental commit of docker compose file * fixed Gemfile after merging from master * Gemfile.lock update * update Gemfile.lock * Gemfile.lock update * redis-store gem with redis 5 compatibility fix * Gemfile.lock update * make the check_access helper use filter_access if the object is a list * add test for submissions access check with two ontologies private and pubic * check access of ontologies in /ontologies/:acronym/submissions endpoint * Set gem branch specifier to develop * reset branch specifier to master * add the slice get endpoint * add the slices create endpoint * add the slices delete endpoint * add the slices update endpoint * update slice write operation to check if user is admin * add slices creation & deletion unit tests * Gemfile.lock update * Gemfile.lock update * Merged #87 from master * fixed Gemfile after merge * Gemfile.lock update * update Gemfile.lock * Add configurable option for github org where code is deployed from * Gemfile update * Gemfile update * check existance of acroym before fetching details fixes #129 * 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 * enforce user deletion security to be admin only * Gemfile.lock update * update Gemfile.lock * Gemfile update * implemented the first pass at bmir-radx/radx-project#37 * set bundler version to be comptatible with ruby 2.7 * Gemfile.lock update * implemented #127 - Add API call to trigger ontology pull from remote location * Gemfile.lock * implemented a test for #127 - Add API call to trigger ontology pull from remote location * Gemfile.lock update * implemented a test for #127 - Add API call to trigger ontology pull from remote location * implemented a test for #127 - Add API call to trigger ontology pull from remote location * Gemfile.lock update * use agraph v8.0.0 * Gemfile.lock update * Gemfile.lock update --------- Co-authored-by: Alex Skrenchuk <alexskr@stanford.edu> Co-authored-by: mdorf <mdorf@stanford.edu> Co-authored-by: Jennifer Vendetti <vendetti@stanford.edu>
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Sample GitHub action script for triggering pull of an ontology https://github.com/ncbo/ncbo_rest_sample_code/blob/master/github_actions/publish_to_bioportal.yml |
Thanks I better understand the goal of the GitHub Action now. Might be useful indeed, especially when GitHub users have a process to produce their file directly on GitHub. |
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I would recommend to create the issue in the UI repo to think/discuss/design the corresponding UI for triggering this. A simple button or additional action in the Ontology Administration tab might be sufficient. |
syphax-bouazzouni
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…y pull from remote location
This was referenced Oct 26, 2024
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BioPortal has a mechanism for downloading ontology files from remote URLs and triggering a new submission when change is detected. This process runs on a daily schedule which currently set to once-a-day. The delay can causes a significant friction for users who need the new version of ontology/vocabulary to show up quicker in BioPortal.
ncbo_cron has a script that can be run from the command line to kick off ontology pull so we would need to add ability to trigger ontology pull from the api side so that it can be used in the ontology development pipelines.
For example, ontology development hosted in github could add a GitHub webhook or GitHub action to trigger BioPortal/OntoPortal pull mechanism when a new version of ontology is published.
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