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legumeinfo / tripal_phylotree

LIS project- tripal module for chado phylogeny and gene families
GNU General Public License v2.0
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Fix install error. #35

Closed almasaeed2010 closed 4 years ago

almasaeed2010 commented 4 years ago

The install script didn't specify the chado schema. This PR fixes the issue by adding the required curly parentheses around the table names.

adf-ncgr commented 4 years ago

@almasaeed2010 thanks for this, I'm finally getting around to looking and I realized that at some point we switched our development efforts to the branch lis_master. This probably had something to do with trying to keep LIS-specific code separated from something more generic for the community at large but I suspect that things have diverged considerably without master having been maintained. Certainly not an ideal situation, but in any case I wanted to give you a heads up about it and maybe you can have a look at lis_master instead and see how that works out with respect to installation. May well have similar problems, but I didn't see the specific code you had changed there (although I could have gotten confused). Sorry for the confusing situation here!

almasaeed2010 commented 4 years ago

Hello @adf-ncgr sorry for the delayed response! This PR is for the lis_master branch. Since this branch is set as default we assumed it was the one being maintained and therefore it is the one we tested. This PR simply adds curly brakcets {} to sql statements that are run using chado_query() which requires that we wrap chado tables in {} or add the chado. prefix. As it stands, it's looking for a table named feature in the public schema instead of chado. This PR aims to correct that.

This addition was tested on both the latest version of Tripal 2 and the latest version of Tripal 3. If, however, it does not work on your implementation, please feel free to close the PR.

Thanks!