Merge BETYdb table queries into a single generic function

[dlebauer]

Create a single function to query tables in BETYdb.

waiting / depends on #77

Features to implement:

• Replace betydb_<tablename> functions with one function that takes tablename as an argument
  • call should be something like betydb_query(table = 'citations', key = '', baseurl = 'https://www.betydb.org', apiversion = 'beta', ...)
  • default key, baseurl, apiversion as above
  • (@sckott is there a preferred naming?)
  • ... will accept one or more arguments of the form <field> = 'searchstring' where field is a valid API endpoint / field in the table
  • function parameter can be any valid endpoint for the table ( (docs) )

Tests

• write tests. These do not need to be comprehensive, just make sure that the fields exist and have the correct type

The following queries should work:

betydb_query(table = 'citation', id = 1)`
betydb_query(table = 'species', genus = 'Salix')`
betydb_query(table = 'variables', name = 'Vcmax', baseurl = 'https://www.betydb.org')`
betydb_query(table = 'citation', author = 'Aasamaa')` # returns 2
betydb_query(table = 'citation', author = 'Aasamaa', year = 2010)` # returns 1

References

• API description with examples: https://pecan.gitbooks.io/betydb-data-access/content/API/beta_API.html
• API Endpoint definitions: https://www.betydb.org/api/docs
• The url that needs to be constructed is like https://www.betydb.org/api/beta/citations?id=1&key=
  The BETYdb table queries betydb_traits, betydb_yields, betydb_citations, etc were removed (PR Revisions to support BETYdb 4.0 API  #27)
• these functions were last seen / can be found in ede82fc.

feedback

@sckott @gsrhode @robkooper @max-zilla.

• does this sound like a sensible approach? vs. original implementation of separate functions for each table
• any other suggestions?
• I propose all table joins be done within R; this should make it easier for me to develop without having to fiddle with constructing urls. I don't think our current api supports joins (?)

[sckott]

@dlebauer okay, thanks

[sckott]

@dlebauer should I close this ? Looks like your #27 PR address this, right?

[dlebauer]

@sckott no, I made this issue at the same time as #27 as a place-holder for re-implementing the broken functions that I removed in that pull request.

The test file in PR #29 has the following function that doesn't work, which is where I got stuck trying to put the URL together ... I'd appreciate help on that ... (here is the API documentation)

debugonce(betydb_http)
betydb_traits(genus = "Miscanthus", author = "Arundale", trait = "yield")

[sckott]

@dlebauer can this be closed, been a while, not sure about the details

[dlebauer]

Close

…

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