Tripal eutils.module.fix

NAL-i5K / tripal_eutils

ncbi loader via the eutils interface

GNU General Public License v3.0

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Tripal eutils.module.fix #229

Closed dsenalik closed 3 years ago

dsenalik commented 3 years ago

Pull request for Issue #228

The missing parameter (an empty array) is added to the call to tripal_report_error()

dsenalik commented 3 years ago

Sorry for the mess of commits, there is only one small change actually made

dsenalik commented 3 years ago

I added a second change to define a default assembly method is none was specified, needed because there is a NOT NULL constraint on the program and programversion columns in the chado.analysis table. This problem showed up on NCBI assembly GCA_902728035.1 which is what triggered my discovery of the first error.

mpoelchau commented 3 years ago

Thanks @dsenalik, I think the placeholder text that you added is good. The next question would be how to work with NCBI and the submitters to add a method, but that's out of scope of this module...

Thanks for submitting the PR!

dsenalik commented 3 years ago

Check has failed on a request to NCBI. I am occasionally getting timeouts locally on requests to NCBI. Maybe we can rerun the checks again later?

1) Tests\EUtilsTest::testConvertingAccession with data set #5 ('biosample', 'SAMN02981385', '2981385') Exception: ERROR Could not make request: Status: 400