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PecanProject / pecan

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.
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Pull data from DataOne to Inputs #302

Open mdietze opened 9 years ago

mdietze commented 9 years ago

support for DataOne is in the PEcAn 2 proposal and, as noted in the email from Ankur (below) from June, there's lots of useful data there and an R client

DataOne is a distributed network of servers for sharing biogeochem data. Their online tool allows for geographic and keyword based searching and includes data relevant to Pecan (for example a quick search of Wisconsin brought up a whole dataset of carbon and nitrogen content of leaves that I hadn't seen before or a subset of Ben Bond-Lamberty's soil respiration database). Anyway, say in the NEON newsletter that they now have an R client for data query and access: http://releases.dataone.org/online/dataone_r/

Add to the pile of interesting types and places of data useful for pecan. -ankur

This task will probably need to be broken down into a number of sub-tasks, and eventually we'll want to work with data dynamically rather than storing a copy of everything in the INPUTS table.

Probably the first step is to support downloading a dataset with known name / identifier

cli <- D1Client() packageOfInterest <- getPackage(cli,"interestingStuff") members <- getIdentifiers(packageOfInterest) member1 <- getMember(packageOfInterest,members[1]) getData(member1)

or

cli <- D1Client() item <- getD1Object(cli,"interestingObject")

From there we can move to searching (by variable, time, and location), and eventually to the capacity to upload PEcAn projects to repositories

dlebauer commented 9 years ago

data dynamically rather than storing a copy of everything in the INPUTS table.

I don't think we need to store the data locally, but would be good if we can use the inputs table as pointers to the client, package / object, date of acquisition.

Also, once we come up with a proposal, we should ask for feedback from the DataOne and Ropensci groups for feedback.

ashiklom commented 6 years ago

This has been tackled in the following PRs (and possibly a few others around the same time): #1554, #1578, #1647, #1648, #1666.

@mdietze Not sure about the status of completeness, so you should check if this can be closed?

mdietze commented 6 years ago

Far from complete. Should be a high-priority GSOC option.

github-actions[bot] commented 4 years ago

This issue is stale because it has been open 365 days with no activity.