executionsBio4j.xml , batchInserter.properties and uniprotData.xml files missing

[Siddarth Ravishankar]

Hi,

executionsBio4j.xml , batchInserter.properties  and uniprotData.xml files are still missing. Can you please tell when the reorganization will be complete?

Thanks and Regards,

Siddarth

[Eduardo Pareja Tobes]

Hi Siddarth

You can start working with what we have in https://github.com/bio4j/neo4jdb. No docs still there, and we just tested it with small imports. But there shouldn't be any big changes with respect to how it is now

[roald...@student.uclouvain.be]

Hi Pablo

Since i've the same problem as Siddarth i tried your solution but the DownloadAndPrepareBio4jSources.sh still missing. So i was wondering if it was normal?

Thanks and regards
Roald

[Eduardo Pareja-Tobes]

looks like the link is broken; the file is at https://github.com/bio4j/bio4j/blob/master/docs/resources/scripts/DownloadAndPrepareBio4jSources.sh

Eduardo Pareja-Tobes

Math & CS freak

oh no sequences!

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[roald...@student.uclouvain.be]

Hi Eduardo (sorry for calling you Pablo previously )

I download the DownloadAndPrepareBio4jSources.sh file from your link and it works but I execute the scrip he cannot find the host:

roald@ubuntu:~$ sudo sh DownloadAndPrepareBio4jSources.sh [sudo] password for roald:
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:04:15 --:--:--     0
curl: (7) couldn't connect to host
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:04:15 --:--:--     0
curl: (7) couldn't connect to host
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 3929k  100 3929k    0     0   563k      0  0:00:06  0:00:06 --:--:--  872k

Can you help me again on this?

Thanks and regards,

Roald

[roald...@student.uclouvain.be]

For example, on the first line of the srcipt:

roald@ubuntu:~$ sudo curl 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz' -o uniprot_sprot.xml.gz

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:04:15 --:--:--     0
curl: (7) couldn't connect to host

[Eduardo Pareja-Tobes]

works for me, maybe some issues with your local network (firewalls, ports, who knows)?

Eduardo Pareja-Tobes

Math & CS freak

oh no sequences!

[roald...@student.uclouvain.be]

Ok thanks, i'll look at this !