Clarification about commercial licenses

[InesdeSantiago]

Clarification about commercial licenses

[deeenes]

Hi,

This is a good point, I'll try to implement it.

The license parameter currently only makes sure that each record is supported by at least one evidence that fits the chosen licensing requirements. All other columns (sources, references) remain unchanged. Recently we introduced a feature that is able to reconstruct the data frames based on any subset of resources. Currently it doesn't care about the license, but it would be easy to fix that.

[InesdeSantiago]

Thank you!

[corinabioinformatic]

Hello @deeenes and @InesdeSantiago do you have any update related to this ticket?
I am using the following queries:

options(omnipath.license = 'commercial')
omnipath_show_db()
as.data.frame(get_annotation_resources())
as.data.frame(get_resources(query_type, datasets = NULL, generic_categories = NULL))

but the result is the same as if I run this:

options(omnipath.license = 'academic')
omnipath_show_db()
as.data.frame(get_annotation_resources())
as.data.frame(get_resources(query_type, datasets = NULL, generic_categories = NULL))

Ideally what I would expect is that the sources that cannot be used, wont appear right?

Later looking in your nicely and very well commented code I found this function resource_info() that list in kind of a json :

library(tidyverse)
resource_info_json <- resource_info()
#if you want the json:
jsonlite::toJSON(resource_info_json, auto_unbox = TRUE) %>% jsonlite::prettify()

My suggestions:

1. would it be possible maybe to include the link to the original URL?(this may help to ping the page and keep an eye in changes in the licensing)
2. and also include in the documentation that when we see something like this:
   

(I mean a resource associated with another resource with underscore) this means that the first_resource_name is used by the second_resource_name, and that's the only one to be used for the "Queries" described by the resource_info() object?

I understand it is a huge project and not sure if I am big enough to push some changes into it. But I could try, at least with the documentation atm if that helps.
Many thanks for this great effort!