[ensembl-dev] Species meta data on rapid [EXT]

[John Tate]

Hi Michael,

> It looks ike all new ones haven’t been included in the file (as it is from the 8th).

Apologies. We’ve regenerated the file and uploaded it to FTP. It now contains the example that you’re looking for:

[~/Downloads] 8271% curl -LO https://ftp.ensembl.org/pub/rapid-release/species_metadata.json
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  875k  100  875k    0     0   787k      0  0:00:01  0:00:01 --:--:—  788k
[~/Downloads] 8271% grep GCA_963555685.1 species_metadata.json
      "assembly_accession" : "GCA_963555685.1",
[~/Downloads] 8273% grep Acrobasis_consociella_GCA_963555685.1 species_metadata.json
[~/Downloads] 8273% grep Acrobasis species_metadata.json
      "species" : "Acrobasis consociella",
      "species" : "Acrobasis repandana",
      "species" : "Acrobasis suavella",
      "species" : "Acrobasis suavella",

Thanks for your help with this.

Cheers,

John.


> 
> I appended a bit to show what I mean.
> 
> Greetings,
> 
> Michael
> 
> As example:
> 
> mib118490s:tmp mh6$ wget https://ftp.ensembl.org/pub/rapid-release/species_metadata.json
> --2024-07-22 11:07:30--  https://ftp.ensembl.org/pub/rapid-release/species_metadata.json
> Resolving ftp.ensembl.org <http://ftp.ensembl.org/> (ftp.ensembl.org <http://ftp.ensembl.org/>)... 193.62.193.169
> Connecting to ftp.ensembl.org <http://ftp.ensembl.org/> (ftp.ensembl.org <http://ftp.ensembl.org/>)|193.62.193.169|:443... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 861592 (841K) [application/json]
> Saving to: ‘species_metadata.json’
> 
> species_metadata.json                                           100%[=======================================================================================================================================================>] 841.40K  --.-KB/s    in 0.1s    
> 
> 2024-07-22 11:07:30 (6.91 MB/s) - ‘species_metadata.json’ saved [861592/861592]
> 
> mib118490s:tmp mh6$ grep GCA_963555685.1 species_metadata.json 
> mib118490s:tmp mh6$ grep Acrobasis_consociella_GCA_963555685.1 species_metadata.json 
> mib118490s:tmp mh6$ grep Acrobasis species_metadata.json 
>       "species" : "Acrobasis repandana",
>       "species" : "Acrobasis suavella",
>       "species" : "Acrobasis suavella",
> 
> 
>> On 22 Jul 2024, at 10:54, John Tate <jgt at ebi.ac.uk <mailto:jgt at ebi.ac.uk>> wrote:
>> 
>> Hi Michael,
>> 
>>> Could it be that the https://ftp.ensembl.org/pub/rapid-release/species_metadata.json [ftp.ensembl.org] <https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ensembl.org_pub_rapid-2Drelease_species-5Fmetadata.json&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=dlKDUfCS4BkNAxVmG7MDyU6N7Vlg2I7v-PtmkCotvMo&m=DjwEFZ_egaksW12-K0-TqsFUfdSqVHKiQ48anEk9Zt-wmGA2JHxuEpJr3HM7VDwM&s=N1YKX5zLbudJhTcSpRfHHL0MDXoaefVvTK4gC5PXJeY&e=> hasn’t been updated in the last rapid release from the 17th ?
>> 
>> 
>> The release files like the species metadata JSON dump were generated on 7 July and copied to the FTP area on 8 July, but updating the website itself took a little longer this time, hence the lag between the dates. The JSON file should be up to date with the website, but please do let us know if you find any discrepancy.
>> 
>> Cheers,
>> 
>> John.
>> 
>> -- 
>> John Tate
>> e: jgt at ebi.ac.uk
>> a: European Bioinformatics Institute (EMBL-EBI), CB10 1SD, UK
>> 
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-- 
John Tate
e: jgt at ebi.ac.uk
a: European Bioinformatics Institute (EMBL-EBI), CB10 1SD, UK

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