Protein Feature patch

Created by: epaule

this time on the master

Created by: epaule

there is a typo in the apache license header of patch_87_88_c.sql

Created by: nerdstrike

Broadly ok, but are you/should you try to absorb all possible SQL errors e.g. server gone away. I presume the state of RaiseError is true at this point, so you might have to do: local $dbh->{RaiseError} for your print statements to fire. What states have you tried?

Created by: epaule

I had a quick look at the mysql driver and RaiseError is set to 1, so it should die in error cases and my print statement for the error case never happen.

as far as the documentation goes, the states for $sth->err should be

undef for no messages '' for info messages 0 for warnings

0 for errors

On 27 January 2017 at 17:03, Kieron Taylor notifications@github.com wrote:

Broadly ok, but are you/should you try to absorb all possible SQL errors e.g. server gone away. I presume the state of RaiseError is true at this point, so you might have to do: local $dbh->{RaiseError} for your print statements to fire. What states have you tried?

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Created by: magaliruffier

you will need to patch the test databases to include the change, documentation on this can be found here: https://www.ebi.ac.uk/seqdb/confluence/display/ENSCORE/Patching+test+databases

Created by: epaule

you think that is the reason for:

Failed test 'patch_87_88_c.sql|protein_featue_uniqueness in original database' at modules/t/schemaPatches.t line 176.

Created by: epaule

still barfs at comparing the meta tables ... is there any other obscure file that needs to be changed and isn't covered by the patch_test_databases ?

Created by: magaliruffier

the table.sql file does not contain the update to the meta table, so creating a database using table.sql will not yield the same result as running the patch file on an existing database

Created by: epaule

no table.sql in modules/t has any content for the meta table. Isn't that loaded from meta.txt ?

Created by: magaliruffier

the original table.sql in the sql directory if you look at previous patches, we add a patch file that modified meta and the actual patch, and we update table.sql to include the same changes

Created by: coveralls

Coverage decreased (-0.002%) to 81.579% when pulling bd37edb6 on epaule:master into 39fbd676 on Ensembl:master.

Created by: magaliruffier

It's looking fine for merge now