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We have two status options for annotations, and these have to be manually updated for each new organism. The only way I can sort out how to do it is through the admin interface, which is clunky, and I can't seem to get the web service calls set right to add in the new organism to these statuses. The reason I'm looking into using the web service calls directly is that it is that the web interface is less manageable as we get up to a hundred organisms, and it would also be nice to script this as part of our onboarding process.
When I try the web service endpoint, it gives limited information only for the FeatureTypes (e.g. gene, mRNA, etc). It does not return any information on what organisms have this status available.
One option would be to add in options for "all", so the status can be globally available. This would be nice to have on both the FeatureType and the Organism fields.
Alternatively, is there something I am just missing when making these calls? What does the command need to look like to get the list of organisms?
Ideally, I'd just like to add my new organism to a status, but I could also handle two calls, one to get a list of all organisms, then a second call to update the status with the full list.
For reference, here is the JSON returned when I use showStatus for "Approved". curl -i -X POST -H "Content-Type: application/json" -d '{ "username": "<user>", "password": "<pass>", name: "Approved"}' https://<server>/apollo/availableStatus/showStatus
Global statuses are possible, if you don't select an organism or a feature when creating the status, they should be available everywhere.
I have noticed that there seems to be a bug, though, in the admin interface so that once you select a feature type, you aren't able to un-select it and make the status global, so it's something you can probably only currently test with a new status and not an existing one.
Let me know if making a new global status works for you, and if you're able to delete and re-create your existing statuses as global.
We have two status options for annotations, and these have to be manually updated for each new organism. The only way I can sort out how to do it is through the admin interface, which is clunky, and I can't seem to get the web service calls set right to add in the new organism to these statuses. The reason I'm looking into using the web service calls directly is that it is that the web interface is less manageable as we get up to a hundred organisms, and it would also be nice to script this as part of our onboarding process.
When I try the web service endpoint, it gives limited information only for the FeatureTypes (e.g. gene, mRNA, etc). It does not return any information on what organisms have this status available.
One option would be to add in options for "all", so the status can be globally available. This would be nice to have on both the FeatureType and the Organism fields.
Alternatively, is there something I am just missing when making these calls? What does the command need to look like to get the list of organisms?
Ideally, I'd just like to add my new organism to a status, but I could also handle two calls, one to get a list of all organisms, then a second call to update the status with the full list.
For reference, here is the JSON returned when I use showStatus for "Approved".
curl -i -X POST -H "Content-Type: application/json" -d '{ "username": "<user>", "password": "<pass>", name: "Approved"}' https://<server>/apollo/availableStatus/showStatus
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