cgspace-notes/2018-12.md at 31880725539178edab70702a442fb80d54546c12

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Alan Orth a38d3c1543

Use "Notes" category instead of tag for old posts

2019-10-28 13:40:12 +02:00

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2018-12-01

Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK
I manually installed OpenJDK, then removed Oracle JDK, then re-ran the Ansible playbook to update all configuration files, etc
Then I ran all system updates and restarted the server

2018-12-02

I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week

The error when I try to manually run the media filter for one item from the command line:

org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-12989PcFN0DnJOej7%d" "-f/tmp/magick-129895Bmp44lvUfxo" "-f/tmp/magick-12989C0QFG51fktLF"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-12989PcFN0DnJOej7%d" "-f/tmp/magick-129895Bmp44lvUfxo" "-f/tmp/magick-12989C0QFG51fktLF"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
        at org.im4java.core.Info.getBaseInfo(Info.java:360)
        at org.im4java.core.Info.<init>(Info.java:151)
        at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:142)
        at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:24)
        at org.dspace.app.mediafilter.FormatFilter.processBitstream(FormatFilter.java:170)
        at org.dspace.app.mediafilter.MediaFilterManager.filterBitstream(MediaFilterManager.java:475)
        at org.dspace.app.mediafilter.MediaFilterManager.filterItem(MediaFilterManager.java:429)
        at org.dspace.app.mediafilter.MediaFilterManager.applyFiltersItem(MediaFilterManager.java:401)
        at org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:237)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)

A comment on StackOverflow question from yesterday suggests it might be a bug with the pngalpha device in Ghostscript and links to an upstream bug
I think we need to wait for a fix from Ubuntu
For what it's worth, I get the same error on my local Arch Linux environment with Ghostscript 9.26:

$ gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 -sDEVICE=pngalpha -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r72x72 -dFirstPage=1 -dLastPage=1 -sOutputFile=/tmp/out%d -f/home/aorth/Desktop/Food\ safety\ Kenya\ fruits.pdf
DEBUG: FC_WEIGHT didn't match
zsh: segmentation fault (core dumped)  gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000

When I replace the pngalpha device with png16m as suggested in the StackOverflow comments it works:

$ gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 -sDEVICE=png16m -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r72x72 -dFirstPage=1 -dLastPage=1 -sOutputFile=/tmp/out%d -f/home/aorth/Desktop/Food\ safety\ Kenya\ fruits.pdf
DEBUG: FC_WEIGHT didn't match

Start proofing the latest round of 226 IITA archive records that Bosede sent last week and Sisay uploaded to DSpace Test this weekend (IITA_Dec_1_1997 aka Daniel1807)
- One item missing the authorship type
- Some invalid countries (smart quotes, mispellings)
- Added countries to some items that mentioned research in particular countries in their abstracts
- One item had "MADAGASCAR" for ISI Journal
- Minor corrections in IITA subject (LIVELIHOOD→LIVELIHOODS)
- Trim whitespace in abstract field
- Fix some sponsors (though some with "Governments of Canada" etc I'm not sure why those are plural)
- Eighteen items had en||fr for the language, but the content was only in French so changed them to just fr
- Six items had encoding errors in French text so I will ask Bosede to re-do them carefully
- Correct and normalize a few AGROVOC subjects
Expand my "encoding error" detection GREL to include ~ as I saw a lot of that in some copy pasted French text recently:

or(
  isNotNull(value.match(/.*\uFFFD.*/)),
  isNotNull(value.match(/.*\u00A0.*/)),
  isNotNull(value.match(/.*\u200A.*/)),
  isNotNull(value.match(/.*\u2019.*/)),
  isNotNull(value.match(/.*\u00b4.*/)),
  isNotNull(value.match(/.*\u007e.*/))
)

2018-12-03

I looked at the DSpace Ghostscript issue more and it seems to only affect certain PDFs...
I can successfully generate a thumbnail for another recent item (10568/98394), but not for 10568/98930
Even manually on my Arch Linux desktop with ghostscript 9.26-1 and the pngalpha device, I can generate a thumbnail for the first one (10568/98394):

$ gs -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 -sDEVICE=pngalpha -dTextAlphaBits=4 -dGraphicsAlphaBits=4 -r72x72 -dFirstPage=1 -dLastPage=1 -sOutputFile=/tmp/out%d -f/home/aorth/Desktop/Info\ Note\ Mainstreaming\ gender\ and\ social\ differentiation\ into\ CCAFS\ research\ activities\ in\ West\ Africa-converted.pdf

So it seems to be something about the PDFs themselves, perhaps related to alpha support?
The first item (10568/98394) has the following information:

$ identify Info\ Note\ Mainstreaming\ gender\ and\ social\ differentiation\ into\ CCAFS\ research\ activities\ in\ West\ Africa-converted.pdf\[0\]
Info Note Mainstreaming gender and social differentiation into CCAFS research activities in West Africa-converted.pdf[0]=>Info Note Mainstreaming gender and social differentiation into CCAFS research activities in West Africa-converted.pdf PDF 595x841 595x841+0+0 16-bit sRGB 107443B 0.000u 0:00.000
identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/1746.

And wow, I can't even run ImageMagick's identify on the first page of the second item (10568/98930):

$ identify Food\ safety\ Kenya\ fruits.pdf\[0\]
zsh: abort (core dumped)  identify Food\ safety\ Kenya\ fruits.pdf\[0\]

But with GraphicsMagick's identify it works:

$ gm identify Food\ safety\ Kenya\ fruits.pdf\[0\]
DEBUG: FC_WEIGHT didn't match
Food safety Kenya fruits.pdf PDF 612x792+0+0 DirectClass 8-bit 1.4Mi 0.000u 0m:0.000002s

Interesting that ImageMagick's identify does work if you do not specify a page, perhaps as alluded to in the recent Ghostscript bug report:

$ identify Food\ safety\ Kenya\ fruits.pdf
Food safety Kenya fruits.pdf[0] PDF 612x792 612x792+0+0 16-bit sRGB 64626B 0.010u 0:00.009
Food safety Kenya fruits.pdf[1] PDF 612x792 612x792+0+0 16-bit sRGB 64626B 0.010u 0:00.009
Food safety Kenya fruits.pdf[2] PDF 612x792 612x792+0+0 16-bit sRGB 64626B 0.010u 0:00.009
Food safety Kenya fruits.pdf[3] PDF 612x792 612x792+0+0 16-bit sRGB 64626B 0.010u 0:00.009
Food safety Kenya fruits.pdf[4] PDF 612x792 612x792+0+0 16-bit sRGB 64626B 0.010u 0:00.009
identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/1746.

As I expected, ImageMagick cannot generate a thumbnail, but GraphicsMagick can (though it looks like crap):

$ convert Food\ safety\ Kenya\ fruits.pdf\[0\] -thumbnail 600x600 -flatten Food\ safety\ Kenya\ fruits.pdf.jpg
zsh: abort (core dumped)  convert Food\ safety\ Kenya\ fruits.pdf\[0\] -thumbnail 600x600 -flatten
$ gm convert Food\ safety\ Kenya\ fruits.pdf\[0\] -thumbnail 600x600 -flatten Food\ safety\ Kenya\ fruits.pdf.jpg
DEBUG: FC_WEIGHT didn't match

I inspected the troublesome PDF using jhove and noticed that it is using ISO PDF/A-1, Level B and the other one doesn't list a profile, though I don't think this is relevant
I found another item that fails when generating a thumbnail (10568/98391, DSpace complains:

org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-142966vQs5Di64ntH%d" "-f/tmp/magick-14296Q0rJjfCeIj3w" "-f/tmp/magick-14296k_K6MWqwvpDm"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
org.im4java.core.InfoException: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-142966vQs5Di64ntH%d" "-f/tmp/magick-14296Q0rJjfCeIj3w" "-f/tmp/magick-14296k_K6MWqwvpDm"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
        at org.im4java.core.Info.getBaseInfo(Info.java:360)
        at org.im4java.core.Info.<init>(Info.java:151)
        at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:142)
        at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:24)
        at org.dspace.app.mediafilter.FormatFilter.processBitstream(FormatFilter.java:170)
        at org.dspace.app.mediafilter.MediaFilterManager.filterBitstream(MediaFilterManager.java:475)
        at org.dspace.app.mediafilter.MediaFilterManager.filterItem(MediaFilterManager.java:429)
        at org.dspace.app.mediafilter.MediaFilterManager.applyFiltersItem(MediaFilterManager.java:401)
        at org.dspace.app.mediafilter.MediaFilterManager.main(MediaFilterManager.java:237)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
Caused by: org.im4java.core.CommandException: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-142966vQs5Di64ntH%d" "-f/tmp/magick-14296Q0rJjfCeIj3w" "-f/tmp/magick-14296k_K6MWqwvpDm"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
        at org.im4java.core.ImageCommand.run(ImageCommand.java:219)
        at org.im4java.core.Info.getBaseInfo(Info.java:342)
        ... 14 more
Caused by: org.im4java.core.CommandException: identify: FailedToExecuteCommand `"gs" -q -dQUIET -dSAFER -dBATCH -dNOPAUSE -dNOPROMPT -dMaxBitmap=500000000 -dAlignToPixels=0 -dGridFitTT=2 "-sDEVICE=pngalpha" -dTextAlphaBits=4 -dGraphicsAlphaBits=4 "-r72x72" -dFirstPage=1 -dLastPage=1 "-sOutputFile=/tmp/magick-142966vQs5Di64ntH%d" "-f/tmp/magick-14296Q0rJjfCeIj3w" "-f/tmp/magick-14296k_K6MWqwvpDm"' (-1) @ error/delegate.c/ExternalDelegateCommand/461.
        at org.im4java.core.ImageCommand.finished(ImageCommand.java:253)
        at org.im4java.process.ProcessStarter.run(ProcessStarter.java:314)
        at org.im4java.core.ImageCommand.run(ImageCommand.java:215)
        ... 15 more

And on my Arch Linux environment ImageMagick's convert also segfaults:

$ convert bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf\[0\] -thumbnail x600 -flatten bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf.jpg
zsh: abort (core dumped)  convert bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf\[0\]  x60

But GraphicsMagick's convert works:

$ gm convert bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf\[0\] -thumbnail x600 -flatten bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf.jpg

So far the only thing that stands out is that the two files that don't work were created with Microsoft Office 2016:

$ pdfinfo bnfb_biofortification\ Module_Participants\ Guide\ 2018.pdf | grep -E '^(Creator|Producer)'
Creator:        Microsoft® Word 2016
Producer:       Microsoft® Word 2016
$ pdfinfo Food\ safety\ Kenya\ fruits.pdf | grep -E '^(Creator|Producer)'
Creator:        Microsoft® Word 2016
Producer:       Microsoft® Word 2016

And the one that works was created with Office 365:

$ pdfinfo Info\ Note\ Mainstreaming\ gender\ and\ social\ differentiation\ into\ CCAFS\ research\ activities\ in\ West\ Africa-converted.pdf | grep -E '^(Creator|Producer)'
Creator:        Microsoft® Word for Office 365
Producer:       Microsoft® Word for Office 365

I remembered an old technique I was using to generate thumbnails in 2015 using Inkscape followed by ImageMagick or GraphicsMagick:

$ inkscape Food\ safety\ Kenya\ fruits.pdf -z --export-dpi=72 --export-area-drawing --export-png='cover.png'
$ gm convert -resize x600 -flatten -quality 85 cover.png cover.jpg

I've tried a few times this week to register for the Ethiopian eVisa website, but it is never successful
In the end I tried one last time to just apply without registering and it was apparently successful
Testing DSpace 5.8 (5_x-prod branch) in an Ubuntu 18.04 VM with Tomcat 8.5 and had some issues:
- JSPUI shows an internal error (log shows something about tag cloud, though, so might be unrelated)
- Atmire Listings and Reports, which use JSPUI, asks you to log in again and then doesn't work
- Content and Usage Analysis doesn't show up in the sidebar after logging in
- I can navigate to /atmire/reporting-suite/usage-graph-editor, but it's only the Atmire theme and a "page not found" message
- Related messages from dspace.log:

2018-12-03 15:44:00,030 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found
2018-12-03 15:44:03,390 ERROR com.atmire.app.webui.servlet.ExportServlet @ Error converter plugin not found: interface org.infoCon.ConverterPlugin
...
2018-12-03 15:45:01,667 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-listing-and-reports not found

I tested it on my local environment with Tomcat 8.5.34 and the JSPUI application still has an error (again, the logs show something about tag cloud, so be unrelated), and the Listings and Reports still asks you to log in again, despite already being logged in in XMLUI, but does appear to work (I generated a report and exported a PDF)
I think the errors about missing Atmire components must be important, here on my local machine as well (though not the one about atmire-listings-and-reports):

2018-12-03 16:44:00,009 WARN  org.dspace.core.ConfigurationManager @ Requested configuration module: atmire-datatables not found

This has got to be part Ubuntu Tomcat packaging, and part DSpace 5.x Tomcat 8.5 readiness...?

2018-12-04

Last night Linode sent a message that the load on CGSpace (linode18) was too high, here's a list of the top users at the time and throughout the day:

# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Dec/2018:1(5|6|7|8)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
    225 40.77.167.142
    226 66.249.64.63
    232 46.101.86.248
    285 45.5.186.2
    333 54.70.40.11
    411 193.29.13.85
    476 34.218.226.147
    962 66.249.70.27
   1193 35.237.175.180
   1450 2a01:4f8:140:3192::2
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
   1141 207.46.13.57
   1299 197.210.168.174
   1341 54.70.40.11
   1429 40.77.167.142
   1528 34.218.226.147
   1973 66.249.70.27
   2079 50.116.102.77
   2494 78.46.79.71
   3210 2a01:4f8:140:3192::2
   4190 35.237.175.180

35.237.175.180 is known to us (CCAFS?), and I've already added it to the list of bot IPs in nginx, which appears to be working:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=35.237.175.180' dspace.log.2018-12-03
4772
$ grep -o -E 'session_id=[A-Z0-9]{32}:ip_addr=35.237.175.180' dspace.log.2018-12-03 | sort | uniq | wc -l
630

I haven't seen 2a01:4f8:140:3192::2 before. Its user agent is some new bot:

Mozilla/5.0 (compatible; BLEXBot/1.0; +http://webmeup-crawler.com/)

At least it seems the Tomcat Crawler Session Manager Valve is working to re-use the common bot XMLUI sessions:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a01:4f8:140:3192::2' dspace.log.2018-12-03
5111
$ grep -o -E 'session_id=[A-Z0-9]{32}:ip_addr=2a01:4f8:140:3192::2' dspace.log.2018-12-03 | sort | uniq | wc -l
419

78.46.79.71 is another host on Hetzner with the following user agent:

Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0

This is not the first time a host on Hetzner has used a "normal" user agent to make thousands of requests
At least it is re-using its Tomcat sessions somehow:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.79.71' dspace.log.2018-12-03
2044
$ grep -o -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.79.71' dspace.log.2018-12-03 | sort | uniq | wc -l
1

In other news, it's good to see my re-work of the database connectivity in the dspace-statistics-api actually caused a reduction of persistent database connections (from 1 to 0, but still!):

2018-12-05

Discuss RSS issues with IWMI and WLE people

2018-12-06

Linode sent a message that the CPU usage of CGSpace (linode18) is too high last night
I looked in the logs and there's nothing particular going on:

# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "05/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
   1225 157.55.39.177
   1240 207.46.13.12
   1261 207.46.13.101
   1411 207.46.13.157
   1529 34.218.226.147
   2085 50.116.102.77
   3334 2a01:7e00::f03c:91ff:fe0a:d645
   3733 66.249.70.27
   3815 35.237.175.180
   7669 54.70.40.11

54.70.40.11 is some new bot with the following user agent:

Mozilla/5.0 (compatible) SemanticScholarBot (+https://www.semanticscholar.org/crawler)

But Tomcat is forcing them to re-use their Tomcat sessions with the Crawler Session Manager valve:

$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=54.70.40.11' dspace.log.2018-12-05
6980
$ grep -o -E 'session_id=[A-Z0-9]{32}:ip_addr=54.70.40.11' dspace.log.2018-12-05 | sort | uniq | wc -l
1156

2a01:7e00::f03c:91ff:fe0a:d645 appears to be the CKM dev server where Danny is testing harvesting via Drupal
It seems they are hitting the XMLUI's OpenSearch a bit, but mostly on the REST API so no issues here yet
Drupal is already in the Tomcat Crawler Session Manager Valve's regex so that's good!

2018-12-10

I ran into Mia Signs in Addis and we discussed Altmetric as well as RSS feeds again
- We came up with an OpenSearch query for all items tagged with the WLE CRP subject (where the sort_by=3 parameter is the accession date, as configured in dspace.cfg)
- About Altmetric she was wondering why some low-ranking items of theirs do not have the Handle/DOI relationship, but high-ranking ones do
- It sounds kinda crazy, but she said when she talked to Altmetric about their Twitter harvesting they said their coverage is not perfect, so it might be some kinda prioritization thing where they only do it for popular items?
- I am testing this by tweeting one WLE item from CGSpace that currently has no Altmetric score
- Interestingly, after about an hour I see it has already been picked up by Altmetric and has my tweet as well as some other tweet from over a month ago...
- I tweeted a link to the item's DOI to see if Altmetric will notice it, hopefully associated with the Handle I tweeted earlier

2018-12-11

I checked the latest tweet of the IWMI item with a DOI and it was picked up by Altmetric
- There is one curious other tweet from another user where they used the NCBI link, and that is also associated with our Handle on Altmetric
- So that means Altmetric is picking up the DOI from the NCBI metadata and making the association properly

2018-12-13

Oh this is very interesting: WorldFish's repository is live now
It's running DSpace 5.9-SNAPSHOT running on KnowledgeArc and the OAI and REST interfaces are active at least
Also, I notice they ended up registering a Handle (they had been considering taking KnowledgeArc's advice to not use Handles!)
Did some coordination work on the hotel bookings for the January AReS workshop in Amman

2018-12-17

Linode alerted me twice today that the load on CGSpace (linode18) was very high
Looking at the nginx logs I see a few new IPs in the top 10:

# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "17/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
    927 157.55.39.81
    975 54.70.40.11
   2090 50.116.102.77
   2121 66.249.66.219
   3811 35.237.175.180
   4590 205.186.128.185
   4590 70.32.83.92
   5436 2a01:4f8:173:1e85::2
   5438 143.233.227.216
   6706 94.71.244.172

94.71.244.172 and 143.233.227.216 are both in Greece and use the following user agent:

Mozilla/3.0 (compatible; Indy Library)

I see that I added this bot to the Tomcat Crawler Session Manager valve in 2017-12 so its XMLUI sessions are getting re-used
2a01:4f8:173:1e85::2 is some new bot called BLEXBot/1.0 which should be matching the existing "bot" pattern in the Tomcat Crawler Session Manager regex

2018-12-18

Open a ticket with Atmire to ask them to prepare the Metadata Quality Module for our DSpace 5.8 code

2018-12-19

Update Atmire Listings and Reports to add the journal title (dc.source) to bibliography and update example bibliography values (#405)

2018-12-20

Testing compression of PostgreSQL backups with xz and gzip:

$ time xz -c cgspace_2018-12-19.backup > cgspace_2018-12-19.backup.xz
xz -c cgspace_2018-12-19.backup > cgspace_2018-12-19.backup.xz  48.29s user 0.19s system 99% cpu 48.579 total
$ time gzip -c cgspace_2018-12-19.backup > cgspace_2018-12-19.backup.gz
gzip -c cgspace_2018-12-19.backup > cgspace_2018-12-19.backup.gz  2.78s user 0.09s system 99% cpu 2.899 total
$ ls -lh cgspace_2018-12-19.backup*
-rw-r--r-- 1 aorth aorth 96M Dec 19 02:15 cgspace_2018-12-19.backup
-rw-r--r-- 1 aorth aorth 94M Dec 20 11:36 cgspace_2018-12-19.backup.gz
-rw-r--r-- 1 aorth aorth 93M Dec 20 11:35 cgspace_2018-12-19.backup.xz

Looks like it's really not worth it...
Peter pointed out that Discovery filters for CTA subjects on item pages were not working
It looks like there were some mismatches in the Discovery index names and the XMLUI configuration, so I fixed them (#406)
Peter asked if we could create a controlled vocabulary for publishers (dc.publisher)
I see we have about 3500 distinct publishers:

# SELECT COUNT(DISTINCT(text_value)) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=39;
 count
-------
  3522
(1 row)

I reverted the metadata changes related to "Unrestricted Access" and "Restricted Access" on DSpace Test because we're not pushing forward with the new status terms for now
Purge remaining Oracle Java 8 stuff from CGSpace (linode18) since we migrated to OpenJDK a few months ago:

# dpkg -P oracle-java8-installer oracle-java8-set-default

Update usage rights on CGSpace as we agreed with Maria Garruccio and Peter last month:

$ ./fix-metadata-values.py -i /tmp/2018-11-27-update-rights.csv -f dc.rights -t correct -m 53 -db dspace -u dspace -p 'fuu' -d
Connected to database.
Fixed 466 occurences of: Copyrighted; Any re-use allowed

Upgrade PostgreSQL on CGSpace (linode18) from 9.5 to 9.6:

# apt install postgresql-9.6 postgresql-client-9.6 postgresql-contrib-9.6 postgresql-server-dev-9.6
# pg_ctlcluster 9.5 main stop
# tar -cvzpf var-lib-postgresql-9.5.tar.gz /var/lib/postgresql/9.5
# tar -cvzpf etc-postgresql-9.5.tar.gz /etc/postgresql/9.5
# pg_ctlcluster 9.6 main stop
# pg_dropcluster 9.6 main
# pg_upgradecluster 9.5 main
# pg_dropcluster 9.5 main
# dpkg -l | grep postgresql | grep 9.5 | awk '{print $2}' | xargs dpkg -r

I've been running PostgreSQL 9.6 for months on my local development and public DSpace Test (linode19) environments
Run all system updates on CGSpace (linode18) and restart the server
Try to run the DSpace cleanup script on CGSpace (linode18), but I get some errors about foreign key constraints:

$ dspace cleanup -v
 - Deleting bitstream information (ID: 158227)
 - Deleting bitstream record from database (ID: 158227)
Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
  Detail: Key (bitstream_id)=(158227) is still referenced from table "bundle".
...

As always, the solution is to delete those IDs manually in PostgreSQL:

$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (158227, 158251);'
UPDATE 1

After all that I started a full Discovery reindex to get the index name changes and rights updates

2018-12-29

CGSpace went down today for a few minutes while I was at dinner and I quickly restarted Tomcat
The top IP addresses as of this evening are:

# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "29/Dec/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
    963 40.77.167.152
    987 35.237.175.180
   1062 40.77.167.55
   1464 66.249.66.223
   1660 34.218.226.147
   1801 70.32.83.92
   2005 50.116.102.77
   3218 66.249.66.219
   4608 205.186.128.185
   5585 54.70.40.11

And just around the time of the alert:

# zcat --force /var/log/nginx/*.log.1 /var/log/nginx/*.log.2.gz | grep -E "29/Dec/2018:1(6|7|8)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
    115 66.249.66.223
    118 207.46.13.14
    123 34.218.226.147
    133 95.108.181.88
    137 35.237.175.180
    164 66.249.66.219
    260 157.55.39.59
    291 40.77.167.55
    312 207.46.13.129
   1253 54.70.40.11

All these look ok (54.70.40.11 is known to us from earlier this month and should be reusing its Tomcat sessions)
So I'm not sure what was going on last night...

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