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PecanProject / pecan

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.
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Resolving db.exists in Utils.R #206

Closed apourmok closed 9 years ago

apourmok commented 10 years ago

We need a new way to check the existence of a database since right now we comment it out in Utils.R in order to make the fia2ED.R working.

zhangwenx commented 9 years ago

created a pull request https://github.com/PecanProject/pecan/pull/360

dlebauer commented 9 years ago

360 looks okay, but it is hard to assess the problem it is addressing.

@apourmok It's not clear what the problem is - though it seems that there is perhaps some functionality to be added to db.exists. What is the functionality?

More importantly, it seems that there is an issue with fia2ed.r. What is the issue?

Please see https://github.com/PecanProject/pecan/wiki/ Github-issues for how to write a good bug report.

apourmok commented 9 years ago

That problem is resolved. There is no issue with fia2ed.r The part that I working on now is speeding up the query since it takes 7-8 minutes for single extraction. I am using "explain analyze" to find out the bottleneck and as soon as I resolve it, I will push it to main line.

dlebauer commented 9 years ago

how was the problem resolved? Can this issue be closed?

How is this related to #360? I don't see the connection with changes to db.exists?

On Thursday, February 5, 2015, Afshin Pourmokhtarian < notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

That problem is resolved. There is no issue with fia2ed.r The part that I working on now is speeding up the query since it takes 7-8 minutes for single extraction. I am using "explain analyze" to find out the bottleneck and as soon as I resolve it, I will push it to main line.

— Reply to this email directly or view it on GitHub https://github.com/PecanProject/pecan/issues/206#issuecomment-73178838.

robkooper commented 9 years ago

This solves the problem where the code in db.exists was commented out (using a if (FALSE)) statement that would check to see if the user has read or write permission to the database.

Initially the code would check to see if the user table could be written with a dummy record, this would only work for the bety database, but not for the FIA database, which is the problem @apourmok had. He solved it by disabling the write check. @zhangwenx has implemented a nice way to see if the database user has write permission on the database without actually needing to write.

dlebauer commented 9 years ago

Thanks Rob - sounds like these can be merged / closed On Thu, Feb 5, 2015 at 10:27 PM Rob Kooper notifications@github.com wrote:

This solves the problem where the code in db.exists was commented out (using a if (FALSE)) statement that would check to see if the user has read or write permission to the database.

Initially the code would check to see if the user table could be written with a dummy record, this would only work for the bety database, but not for the FIA database, which is the problem @apourmok https://github.com/apourmok had. He solved it by disabling the write check. @zhangwenx https://github.com/zhangwenx has implemented a nice way to see if the database user has write permission on the database without actually needing to write.

— Reply to this email directly or view it on GitHub https://github.com/PecanProject/pecan/issues/206#issuecomment-73181268.