[ensembl-dev] Species meta data on rapid [EXT]
Michael Paulini
mh6 at sanger.ac.uk
Mon Jul 22 16:57:34 BST 2024
Thanks :-)
M
On 22 Jul 2024, at 16:44, John Tate <jgt at ebi.ac.uk> wrote:
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 [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=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=sx0TT7fjiXj6R8peN2WvXGaxQQnBeAH1cQ-OAEvm6u8&e=>
--2024-07-22 11:07:30-- 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=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=sx0TT7fjiXj6R8peN2WvXGaxQQnBeAH1cQ-OAEvm6u8&e=>
Resolving ftp.ensembl.org [ftp.ensembl.org]<https://urldefense.proofpoint.com/v2/url?u=http-3A__ftp.ensembl.org_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=dlKDUfCS4BkNAxVmG7MDyU6N7Vlg2I7v-PtmkCotvMo&m=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=JiNxzSKdeeyryx_IlhOhho7wJbJQBiwlYVt_ksbRgqU&e=> (ftp.ensembl.org [ftp.ensembl.org]<https://urldefense.proofpoint.com/v2/url?u=http-3A__ftp.ensembl.org_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=dlKDUfCS4BkNAxVmG7MDyU6N7Vlg2I7v-PtmkCotvMo&m=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=JiNxzSKdeeyryx_IlhOhho7wJbJQBiwlYVt_ksbRgqU&e=>)... 193.62.193.169
Connecting to ftp.ensembl.org [ftp.ensembl.org]<https://urldefense.proofpoint.com/v2/url?u=http-3A__ftp.ensembl.org_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=dlKDUfCS4BkNAxVmG7MDyU6N7Vlg2I7v-PtmkCotvMo&m=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=JiNxzSKdeeyryx_IlhOhho7wJbJQBiwlYVt_ksbRgqU&e=> (ftp.ensembl.org [ftp.ensembl.org]<https://urldefense.proofpoint.com/v2/url?u=http-3A__ftp.ensembl.org_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=dlKDUfCS4BkNAxVmG7MDyU6N7Vlg2I7v-PtmkCotvMo&m=REuB3adgnkSZakONYo5GZPuYFeiElreb-WxoOlUctodc3RGEE85eIbHaR08A-Sjt&s=JiNxzSKdeeyryx_IlhOhho7wJbJQBiwlYVt_ksbRgqU&e=>)|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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