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PecanProject / bety

Web-interface to the Biofuel Ecophysiological Traits and Yields Database (used by PEcAn and TERRA REF)
https://www.betydb.org
BSD 3-Clause "New" or "Revised" License
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Bulk Upload Not accepting File #384

Closed abstewa2 closed 8 years ago

abstewa2 commented 8 years ago

When I try to upload this file: phenotypes.txt

To the terra-test instance (http://pecandev.igb.illinois.edu/terra-test) of BETYdb, it doesn't recognize the variable names although they match the variables table. I get the following:

image

abstewa2 commented 8 years ago

It appears that the list of accepted traits is empty http://pecandev.igb.illinois.edu/terra-test/trait_covariate_associations

gsrohde commented 8 years ago

@abstewa2 Yes, that's the problem (the only problem, I hope).

The "canonical" list of trait_covariate_associations, the one we use on https://betydb.org is here: https://www.betydb.org/trait_covariate_associations You should be able to see it without having administrative privileges if you log in as a guest and then go to the URL directly.

I was about to copy the table from the betydb.org database to the terra-test database but realized the foreign-key values have to be different because the variables tables aren't identical.

Unfortunately, we don't currently have a Web interface for modifying this table. If you can let me know which columns in the CSV file correspond to the primary trait variable and which correspond to covariates, I can add the needed entries manually.

dlebauer commented 8 years ago

Only leafT is a covariate. Can we import the variables we need from betydb.org? On Fri, Feb 19, 2016 at 11:08 AM Scott Rohde notifications@github.com wrote:

@abstewa2 https://github.com/abstewa2 Yes, that's the problem (the only problem, I hope).

The "canonical" list of trait_covariate_associations, the one we use on https://betydb.org is here: https://www.betydb.org/trait_covariate_associations You should be able to see it without having administrative privileges if you log in as a guest and then go to the URL directly.

I was about to copy the table from the betydb.org database to the terra-test database but realized the foreign-key values have to be different because the variables tables aren't identical.

Unfortunately, we don't currently have a Web interface for modifying this table. If you can let me know which columns in the CSV file correspond to the primary trait variable and which correspond to covariates, I can add the needed entries manually.

— Reply to this email directly or view it on GitHub https://github.com/PecanProject/bety/issues/384#issuecomment-186307918.

gsrohde commented 8 years ago

@dlebauer leafT is the only needed variable that is not already in the terra-test database.

gsrohde commented 8 years ago

That said, we could wipe the terra-test variables table (and the two entries in the traits table, since they refer to it) and copy all or only the needed variables from betydb.org. This would ensure that all column values on terra-test match the values for the corresponding variable on betydb.org. If we use the same id column values as well, then we could just copy down the trait_covariate_associations table as is.

dlebauer commented 8 years ago

Yes, please wipe the traits and variables table and import the variables that we need. On Fri, Feb 19, 2016 at 11:55 AM Scott Rohde notifications@github.com wrote:

That said, we could wipe the terra-test variables table (and the two entries in the traits table, since they refer to it) and copy all or only the needed variables from betydb.org. This would ensure that all column values on terra-test match the values for the corresponding variable on betydb.org. If we use the same id column values as well, then we could just copy down the trait_covariate_associations table as is.

— Reply to this email directly or view it on GitHub https://github.com/PecanProject/bety/issues/384#issuecomment-186331780.

abstewa2 commented 8 years ago

Thanks Scott!

gsrohde commented 8 years ago

Yes, please wipe the traits and variables table and import the variables that we need.

Done. I imported all the variables, but if you want me to delete the ones not referred to in the CSV file, I can.

Note that I did test out the CSV file, and there are some problems, some or most of which might be resolved by adding some entries to the trait_covariate_associations table.

gsrohde commented 8 years ago

Assuming this is fixed. Closing.