kencho51
commented
7 months ago Tested on production staging:
% ssh -i output/privkeys-18.166.89.134/ken ken@18.166.89.134
Activate the web console with: systemctl enable --now cockpit.socket
Last login: Mon Feb 5 03:10:38 2024 from 223.197.187.121
[ken@ip-10-99-0-147 ~]$ sudo /home/centos/postUpload.sh 100006
* About to update files' size for 100006
nb. changes: 7
Done with updating files' size for 100006. Nb of successful changes saved in file: /home/centos/uploadLogs/updating-file-size-100006.txt
* About to check that file urls are valid for 100006
| URL | Issue |
Done with checking that file urls are valid for 100006. Invalid Urls (if any) are save in file: /home/centos/uploadLogs/invalid-urls-100006.txt
* About to update files' MD5 Checksum as file attribute for 100006
Processing https://ftp.cngb.org/pub/gigadb/pub/10.5524/104001_105000/100006/100006.md5
No file found at https://ftp.cngb.org/pub/gigadb/pub/10.5524/104001_105000/100006/100006.md5
Processing https://ftp.cngb.org/pub/gigadb/pub/10.5524/103001_104000/100006/100006.md5
No file found at https://ftp.cngb.org/pub/gigadb/pub/10.5524/103001_104000/100006/100006.md5
Processing https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/100006/100006.md5
No file found at https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/100006/100006.md5
Processing https://ftp.cngb.org/pub/gigadb/pub/10.5524/101001_102000/100006/100006.md5
No file found at https://ftp.cngb.org/pub/gigadb/pub/10.5524/101001_102000/100006/100006.md5
Processing https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100006/100006.md5
Saved md5 file attribute with id: 10674
Saved md5 file attribute with id: 10672
Saved md5 file attribute with id: 10673
Saved md5 file attribute with id: 10671
Saved md5 file attribute with id: 10670
Saved md5 file attribute with id: 10669
Saved md5 file attribute with id: 10675
Done with updating files' MD5 Checksum as file attribute for 100006. Process status is saved in file: /home/centos/uploadLogs/updating-md5checksum-100006.txt
* About to create the README file for 100006
[DOI] 10.5524/100006
[Title] Genomic data from Adelie penguin (<em>Pygoscelis adeliae</em>).
[Release Date] 2011-07-06
[Citation] Wang, J; Zhang, G; Lambert, DM (2011): Genomic data from Adelie
penguin (<em>Pygoscelis adeliae</em>). GigaScience Database.
https://dx.doi.org/10.5524/100006
[Data Type] Genomic
[Data Summary] The Adelie penguin (<em>Pygoscelis adeliae</em>) is an iconic
penguin of moderate stature and a tuxedo of black and white feathers. The
penguins are only found in the Antarctic region and surrounding islands. Being
very sensitive to climate change, and due to changes in their behavior based on
minor shifts in climate, they are often used as a barometer of the Antarctic.
<br>
With its status as one of the adorable and cuddly flightless birds of
Antarctica, they serve as an example for conservation, and as a result they are
now categorised at low risk for endangerment. The sequence of the penguin can
be of use in understanding the genetic underpinnings of its evolutionary traits
and adaptation to its extreme environment; its unique system of feathers; its
prowess as a diver; and its sensitivity to climate change. We hope that this
genome data will further our understanding of one of the most remarkable
creatures to waddle the planet Earth.<br> We sequenced the genome of an adult
male from Inexpressible Island, Ross Sea, Antartica (provided by David Lambert)
to a depth of approximately 60X with short reads from a series of libraries with
various insert sizes (200bp- 20kb).
The assembled scaffolds of high quality sequences total 1.23 Gb, with the contig
and scaffold N50 values of 19 kb and 5 mb respectively. We identified 15,270
protein-coding genes with a mean length of 21.3 kb.
[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100006/
[File name] - [File Description]
readme.txt -
Pygoscelis_adeliae.fa.gz - assembled scaffolds from sequence data
Pygoscelis_adeliae.gff.gz - coding sequence annotation of assembly
Pygoscelis_adeliae.RepeatMasker.out.gz - repeat masker results
Pygoscelis_adeliae.cds.gz - coding sequence predictions on genome assembly
Pygoscelis_adeliae.scaf.fa.gz -
Pygoscelis_adeliae.pep.gz - peptide translations of CDS predictions
[License]
All files and data are distributed under the CC0 1.0 Universal (CC0 1.0) Public
Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/), unless
specifically stated otherwise, see http://gigadb.org/site/term for more details.
[Comments]
[End]
Done with creating the README file for 100006. The README file is saved in file: /home/centos/uploadLogs/readme-100006.txt
All postUpload logs have been moved to: /home/ken/uploadDir
PostUpload jobs done!
[ken@ip-10-99-0-147 ~]$
rija
pli888
User story
Acceptance criteria
Additional Info
When I ran the post upload on dataset 102495 today (1Feb2024) it updated some of the md5sum values but not all, and the error log is unclear to me why, and it didn't give an obvious error message, with the last line of the ouput just saying "PostUpload jobs done!" see below.
None of the file sizes were added to the database.
Command line output of postUpload script
Product Backlog Item Ready Checklist
Product Backlog Item Done Checklist