[ensembl-dev] Homology Member - schema change

[PATERSON Trevor]

Hi

One problem is that the 'declaration of intentions' doesn't seem to be archived

And it is overwritten at http://admin.ensembl.org/Changelog/Summary

Login as webadmin seems necessary to look at previous changelogs/intentions...

I checked the mailgroup archives - but the 'intentions' email only has a link to the http://admin.ensembl.org/Changelog/Summary

( I think the content of the log used to be copied in the body of the mailout
... and ensemblgenomes still do this...
as well as keeping them available as
http://ensemblgenomes.org/info/release14
http://ensemblgenomes.org/info/release13
Etc)

Would putting the intentions/changelog on the blog be a reasonable way of making these retrievable?

ta


Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
Royal (Dick) School of Veterinary Studies
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-----Original Message-----
From: Andy Yates [mailto:ayates at ebi.ac.uk] 
Sent: 18 May 2012 15:42
To: Ensembl developers list
Cc: PATERSON Trevor
Subject: Re: [ensembl-dev] Homology Member - schema change

Hi,

I should make a point that those core changes did occur but the declaration was not updated as handed over. Apologies.

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 18 May 2012, at 14:30, Matthieu Muffato wrote:

> Dear Trevor
> 
> The full list of changes is available online at 
> http://www.ensembl.org/info/website/news.html
> 
> Unfortunately, the first change you are mentioning hasn't been reported to the declaration of intentions and is therefore not on that page.
> Here is the list of the additional schema changes that you can find in Compara:
> - cigar_start and cigar_end columns dropped from gene_tree_member, 
> protein_tree_member_score, homology_member
> - peptide_align_feature_id dropped from homology_member
> - stable_id dropped from homology
> - analysis_id dropped from the peptide_align_feature_* tables
> 
> About the changes in the core meta tables, this is a "declared" intention that was half-pushed in release 67 and will be completed in release 68. Here is the original intention:
> 
> "
> The following meta keys are retired
>    species.short_name
>    species.ensembl_common_name
>    species.ensembl_alias_name
> The following meta keys will be added
>    species.url
>    species.display_name
> "
> 
> In the future, we will make sure that the Compara schema changes are all reported.
> 
> Best regards,
> Matthieu
> 
> On 17/05/12 18:09, PATERSON Trevor wrote:
>> There doesn't seem to be the usual clear documentation of schema 
>> changes with release 67.
>> Maybe I am looking in the wrong place??
>> so far i have found that a few fields ( that always seem to be null
>> anyway) have been dropped from the compara.homology_member table i.e 
>> cigar_start, cigar_end, peptide_align_feature_id also in core.meta 
>> the names of the keys used to store various names for display and 
>> aliases etc have changed...
>> Can anyone point me at a place where schema changes are documented 
>> for release67?
>> ta
>> trevor
>> 
>> **Trevor Paterson PhD ***
> 
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