[ensembl-dev] Homology Member - schema change

[Andy Yates]

Hi Trevor,

The declaration of intentions become our release notes and are available with every release e.g.

http://www.ensembl.org/info/website/news.html - 67 release notes

http://www.ensembl.org/info/website/news.html?id=66&submit=Go - 66 release notes

Andy

On 18 May 2012, at 16:22, PATERSON Trevor wrote:

> 
> 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
> University of Edinburgh
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> 
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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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>