Sync: BioPortal v6.1.0 release - #4
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Develop to master merge, release v6.0.0
update path of the appliance version manifest
…aths, simplify pid default
* config.rb
• move log_path derivation **after** user block;
• default log_dir → File.expand_path("logs", Dir.pwd) (never gem‑relative);
• default pid_path → File.join(Dir.pwd, "ncbo_cron.pid") – drops /var/run heuristic.
* bin/ncbo_cron
• mkdir_p the chosen log directory **before** Dante::Runner is built;
abort with clear message if creation fails (no stdout fallback for now).
• keep existing daemon behaviour; systemd units can still override
--log and --pid.
* addreses unwanted behavior where ontologies_api writes to $GEM_HOME/gems/ncbo_cron/logs
fix(logging+pid): respect custom log_dir
- Renamed default log directory from 'logs' to 'log' - Aligns with common Ruby/Rails conventions (e.g., log/scheduler.log) - Helps reduce confusion across components like ontologies_api which already use 'log' - Does not affect behavior if log_dir is explicitly set in config
Rename logs directory to log for consistency with standard layout
Raise MissingPullLocationException when an ontology has no pullLocation set, and catch it in the ontology pull loop to avoid logging a full stack trace. Log a concise warning instead.
Develop -> Master merge, release v6.2.0
…new submission attribute definitions
… records and homepage not being fixed
…t just those with errors
Setting $0 = "ncbo_cron" before `require` calls causes Ruby to misreport errors as "cannot load such file -- ncbo_cron"
…ion-handling Handle ontologies with missing pullLocation gracefully in pull job
Develop to Master merge, release v6.3.0
scripts in bin directory are not inteded to be executables when this gem is included as a dependency
remove executable directives and add development dependencies
Add email notifications to CloudflareAnalytics job; support multiple hostnames
Develop to Master merge, release v6.4.1
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https://github.com/ncbo/ncbo_cron/releases/tag/v6.1.0
https://github.com/ncbo/ncbo_cron/releases/tag/v6.0.0