sanger-pathogens / annot-web Goto Github PK

The current Captcha on the site is provided by ReCAPTCHA, a service run by Google. Google is not guaranteed to be accessible in all locations and/or networks. To allow users from everywhere to access Companion, a self-hosted solution should be implemented.

Multiple users have problem running Companion with Leishmania mexicana. I have found the issue has been first reported in the repo for standalone version, so I wanted to also bring it to attention here.

I see the same error as the user who reported the original issue, I include the error below for completeness:

/www/companion/annot-web/app/workers/hard_worker.rb:34:in `add_result_file': required file not present: /www/companion/annot-web/public/jobs/9dbbee2d4a721d45b3ef72bd/pseudochr.fasta.gz (RuntimeError)
	/www/companion/annot-web/app/workers/hard_worker.rb:142:in `perform'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:150:in `execute_job'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:132:in `block (2 levels) in process'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:127:in `block in invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-status-0.6.0/lib/sidekiq-status/server_middleware.rb:37:in `call'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/active_record.rb:6:in `call'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/retry_jobs.rb:74:in `call'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/logging.rb:11:in `block in call'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/logging.rb:30:in `with_context'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/server/logging.rb:7:in `call'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:129:in `block in invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/middleware/chain.rb:132:in `invoke'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:127:in `block in process'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:166:in `stats'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:126:in `process'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:79:in `process_one'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/processor.rb:67:in `run'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/util.rb:16:in `watchdog'
	/www/companion/annot-web/vendor/ruby/2.3.0/gems/sidekiq-4.0.2/lib/sidekiq/util.rb:24:in `block in safe_thread'

Since non-coding genes are not handled by our OrthoMCL clustering, they always end up as singletons in the list. They should not be included here as they may give a wrong impression about the numbers, and are not contributing useful information.

Feedback from a workshop suggests that the links to the output format specifications are best placed directly within each row of the output file table.

It should be possible to download a zipped file with all results generated by Companion, similar to what would end up in the standalone pipeline's output directory, plus extra parameterization info. This could be implemented in a way similar to the bulk Circos plot download function.
Let jc17 know when this is ready.

It should be possible for an admin to cancel jobs from the management interface, regardless of whether they have started or not. Jobs might be hung in the Nextflow stage indefinitely or using too much run time and need be run somewhere else to make room for other jobs.
This means that the Sidekiq worker needs to be able to start the Nextflow process separately and still react to cancel messages, killing Nextflow if necessary. Currently this is not possible as the Sidekiq worker blocks until Nextflow returns, making it necessary to stop Sidekiq as a whole (and this is not possible via the web interface).

The collapsed history pane in the tree view of the results browser is not useful and does not serve a purpose. It should be removed from the view altogether.

The result download table should contain links to the specifications for each output format to make it clearer to the users how to interpret each of the result files (e.g. AGP, GFF3, ...)

It should be possible to download the content of all browseable tables in the Companion results in CSV/XLS/... format. This chould probably be easy with a DataTables plugin.

The result page does currently not list pseudogenes, but they are still counted when determining number of genes with assigned functions. This might lead to confusing results in which the number of functional genes is larger than the number of total genes, like this:

Genes and pseudogenes need to be broken down separately into hypothetical and non-hypothetical ones.