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Update notes
This commit is contained in:
parent
11ce30438c
commit
3c61d0a06b
@ -168,3 +168,114 @@ UPDATE 108
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- cg.identifier.ccafsprojectpii
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- cg.subject.cifor
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- For now we will keep them in the search filters
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- I modified my `check-duplicates.py` script a bit to fix a logic error for deleted items and add similarity scores from spacy (see: https://stackoverflow.com/questions/8897593/how-to-compute-the-similarity-between-two-text-documents)
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- I want to use this with the MARLO innovation reports, to find related publications and working papers on CGSpace
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- I am curious to see how the similarity scores compare to those from trgm... perhaps we don't need them actually
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- Deploy latest changes to submission form, Discovery, and browse on CGSpace
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- Also run all system updates and reboot the host
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- Fix 152 `dcterms.relation` that are using "cgspace.cgiar.org" links instead of handles:
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```console
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UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '.*cgspace\.cgiar\.org/handle/(\d+/\d+)$', 'https://hdl.handle.net/\1') WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=180 AND text_value ~ 'cgspace\.cgiar\.org/handle/\d+/\d+$';
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```
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## 2022-07-10
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- UptimeRobot says that CGSpace is down
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- I see high load around 22, high CPU around 800%
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- Doesn't seem to be a lot of unique IPs:
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```console
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# awk '{print $1}' /var/log/nginx/{access,library-access,oai,rest}.log | sort -u | wc -l
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2243
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```
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Looking at the top twenty I see some usual IPs, but some new ones on Hetzner that are using many DSpace sessions:
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```console
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$ grep 65.109.2.97 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
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1613
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$ grep 95.216.174.97 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
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1696
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$ grep 65.109.15.213 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
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1708
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$ grep 65.108.80.78 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
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1830
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$ grep 65.108.95.23 dspace.log.2022-07-10 | grep -oE 'session_id=[A-Z0-9]{32}:ip_addr=' | sort | uniq | wc -l
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1811
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```
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![DSpace sessions week](/cgspace-notes/2022/07/jmx_dspace_sessions-week.png)
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- These IPs are using normal-looking user agents:
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- `Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:52.9) Gecko/20100101 Goanna/4.1 Firefox/52.9 PaleMoon/28.0.0.1`
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- `Mozilla/5.0 (Windows NT 10.0; WOW64; rv:40.0) Gecko/20100101 Firefox/45.0"`
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- `Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:56.0) Gecko/20100101 Firefox/56.0.1 Waterfox/56.0.1`
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- `Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/71.0.3578.85 Safari/537.36`
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- I will add networks I'm seeing now to nginx's bot-networks.conf for now (not all of Hetzner) and purge the hits later:
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- 65.108.0.0/16
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- 65.21.0.0/16
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- 95.216.0.0/16
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- 135.181.0.0/16
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- 138.201.0.0/16
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- I think I'm going to get to a point where I categorize all commercial subnets as bots by default and then whitelist those we need
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- Sheesh, there are a bunch more IPv6 addresses also on Hetzner:
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```console
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# awk '{print $1}' /var/log/nginx/{access,library-access}.log | sort | grep 2a01:4f9 | uniq -c | sort -h
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1 2a01:4f9:6a:1c2b::2
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2 2a01:4f9:2b:5a8::2
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2 2a01:4f9:4b:4495::2
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96 2a01:4f9:c010:518c::1
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137 2a01:4f9:c010:a9bc::1
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142 2a01:4f9:c010:58c9::1
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142 2a01:4f9:c010:58ea::1
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144 2a01:4f9:c010:58eb::1
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145 2a01:4f9:c010:6ff8::1
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148 2a01:4f9:c010:5190::1
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149 2a01:4f9:c010:7d6d::1
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153 2a01:4f9:c010:5226::1
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156 2a01:4f9:c010:7f74::1
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160 2a01:4f9:c010:5188::1
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161 2a01:4f9:c010:58e5::1
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168 2a01:4f9:c010:58ed::1
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170 2a01:4f9:c010:548e::1
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170 2a01:4f9:c010:8c97::1
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175 2a01:4f9:c010:58c8::1
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175 2a01:4f9:c010:aada::1
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182 2a01:4f9:c010:58ec::1
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182 2a01:4f9:c010:ae8c::1
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502 2a01:4f9:c010:ee57::1
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530 2a01:4f9:c011:567a::1
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535 2a01:4f9:c010:d04e::1
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539 2a01:4f9:c010:3d9a::1
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586 2a01:4f9:c010:93db::1
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593 2a01:4f9:c010:a04a::1
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601 2a01:4f9:c011:4166::1
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607 2a01:4f9:c010:9881::1
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640 2a01:4f9:c010:87fb::1
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648 2a01:4f9:c010:e680::1
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1141 2a01:4f9:3a:2696::2
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1146 2a01:4f9:3a:2555::2
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3207 2a01:4f9:3a:2c19::2
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```
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- Maybe it's time I ban all of Hetzner... sheesh.
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- I left for a few hours and the server was going up and down the whole time, still very high CPU and database when I got back
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![CPU day](/cgspace-notes/2022/07/cpu-day.png)
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- I am not sure what's going on
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- I extracted all the IPs and used `resolve-addresses-geoip2.py` to analyze them and extract all the Hetzner networks and block them
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- It's 181 IPs on Hetzner...
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- I rebooted the server to see if it was just some stuck locks in PostgreSQL...
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- The load is still higher than I would expect, and after a few more hours I see more Hetzner IPs coming through? Two more subnets to block
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- Start a harvest on AReS
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## 2022-07-12
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- Update an incorrect ORCID identifier for Alliance
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<!-- vim: set sw=2 ts=2: -->
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@ -19,7 +19,7 @@ Also, the trgm functions I’ve used before are case insensitive, but Levens
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-07/" />
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<meta property="article:published_time" content="2022-07-02T14:07:36+03:00" />
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<meta property="article:modified_time" content="2022-07-07T10:02:04+03:00" />
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<meta property="article:modified_time" content="2022-07-08T15:49:45+03:00" />
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@ -44,9 +44,9 @@ Also, the trgm functions I’ve used before are case insensitive, but Levens
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"@type": "BlogPosting",
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"headline": "July, 2022",
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"url": "https://alanorth.github.io/cgspace-notes/2022-07/",
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"wordCount": "1095",
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"wordCount": "1660",
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"datePublished": "2022-07-02T14:07:36+03:00",
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"dateModified": "2022-07-07T10:02:04+03:00",
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"dateModified": "2022-07-08T15:49:45+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -315,7 +315,123 @@ Also, the trgm functions I’ve used before are case insensitive, but Levens
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<li>For now we will keep them in the search filters</li>
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</ul>
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</li>
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<li>I modified my <code>check-duplicates.py</code> script a bit to fix a logic error for deleted items and add similarity scores from spacy (see: <a href="https://stackoverflow.com/questions/8897593/how-to-compute-the-similarity-between-two-text-documents">https://stackoverflow.com/questions/8897593/how-to-compute-the-similarity-between-two-text-documents</a>)
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<ul>
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<li>I want to use this with the MARLO innovation reports, to find related publications and working papers on CGSpace</li>
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<li>I am curious to see how the similarity scores compare to those from trgm… perhaps we don’t need them actually</li>
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</ul>
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</li>
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<li>Deploy latest changes to submission form, Discovery, and browse on CGSpace
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<ul>
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<li>Also run all system updates and reboot the host</li>
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</ul>
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</li>
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<li>Fix 152 <code>dcterms.relation</code> that are using “cgspace.cgiar.org” links instead of handles:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>UPDATE metadatavalue SET text_value = REGEXP_REPLACE(text_value, '.*cgspace\.cgiar\.org/handle/(\d+/\d+)$', 'https://hdl.handle.net/\1') WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=180 AND text_value ~ 'cgspace\.cgiar\.org/handle/\d+/\d+$';
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</span></span></code></pre></div><h2 id="2022-07-10">2022-07-10</h2>
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<ul>
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<li>UptimeRobot says that CGSpace is down
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<ul>
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<li>I see high load around 22, high CPU around 800%</li>
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<li>Doesn’t seem to be a lot of unique IPs:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log | sort -u | wc -l
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</span></span><span style="display:flex;"><span>2243
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</span></span></code></pre></div><p>Looking at the top twenty I see some usual IPs, but some new ones on Hetzner that are using many DSpace sessions:</p>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ grep 65.109.2.97 dspace.log.2022-07-10 | grep -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}:ip_addr='</span> | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>1613
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</span></span><span style="display:flex;"><span>$ grep 95.216.174.97 dspace.log.2022-07-10 | grep -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}:ip_addr='</span> | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>1696
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</span></span><span style="display:flex;"><span>$ grep 65.109.15.213 dspace.log.2022-07-10 | grep -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}:ip_addr='</span> | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>1708
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</span></span><span style="display:flex;"><span>$ grep 65.108.80.78 dspace.log.2022-07-10 | grep -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}:ip_addr='</span> | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>1830
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</span></span><span style="display:flex;"><span>$ grep 65.108.95.23 dspace.log.2022-07-10 | grep -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}:ip_addr='</span> | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>1811
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</span></span></code></pre></div><p><img src="/cgspace-notes/2022/07/jmx_dspace_sessions-week.png" alt="DSpace sessions week"></p>
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<ul>
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<li>
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<p>These IPs are using normal-looking user agents:</p>
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<ul>
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<li><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:52.9) Gecko/20100101 Goanna/4.1 Firefox/52.9 PaleMoon/28.0.0.1</code></li>
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<li><code>Mozilla/5.0 (Windows NT 10.0; WOW64; rv:40.0) Gecko/20100101 Firefox/45.0"</code></li>
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<li><code>Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:56.0) Gecko/20100101 Firefox/56.0.1 Waterfox/56.0.1</code></li>
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<li><code>Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/71.0.3578.85 Safari/537.36</code></li>
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</ul>
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</li>
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<li>
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<p>I will add networks I’m seeing now to nginx’s bot-networks.conf for now (not all of Hetzner) and purge the hits later:</p>
|
||||
<ul>
|
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<li>65.108.0.0/16</li>
|
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<li>65.21.0.0/16</li>
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<li>95.216.0.0/16</li>
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<li>135.181.0.0/16</li>
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<li>138.201.0.0/16</li>
|
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</ul>
|
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</li>
|
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<li>
|
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<p>I think I’m going to get to a point where I categorize all commercial subnets as bots by default and then whitelist those we need</p>
|
||||
</li>
|
||||
<li>
|
||||
<p>Sheesh, there are a bunch more IPv6 addresses also on Hetzner:</p>
|
||||
</li>
|
||||
</ul>
|
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access<span style="color:#f92672">}</span>.log | sort | grep 2a01:4f9 | uniq -c | sort -h
|
||||
</span></span><span style="display:flex;"><span> 1 2a01:4f9:6a:1c2b::2
|
||||
</span></span><span style="display:flex;"><span> 2 2a01:4f9:2b:5a8::2
|
||||
</span></span><span style="display:flex;"><span> 2 2a01:4f9:4b:4495::2
|
||||
</span></span><span style="display:flex;"><span> 96 2a01:4f9:c010:518c::1
|
||||
</span></span><span style="display:flex;"><span> 137 2a01:4f9:c010:a9bc::1
|
||||
</span></span><span style="display:flex;"><span> 142 2a01:4f9:c010:58c9::1
|
||||
</span></span><span style="display:flex;"><span> 142 2a01:4f9:c010:58ea::1
|
||||
</span></span><span style="display:flex;"><span> 144 2a01:4f9:c010:58eb::1
|
||||
</span></span><span style="display:flex;"><span> 145 2a01:4f9:c010:6ff8::1
|
||||
</span></span><span style="display:flex;"><span> 148 2a01:4f9:c010:5190::1
|
||||
</span></span><span style="display:flex;"><span> 149 2a01:4f9:c010:7d6d::1
|
||||
</span></span><span style="display:flex;"><span> 153 2a01:4f9:c010:5226::1
|
||||
</span></span><span style="display:flex;"><span> 156 2a01:4f9:c010:7f74::1
|
||||
</span></span><span style="display:flex;"><span> 160 2a01:4f9:c010:5188::1
|
||||
</span></span><span style="display:flex;"><span> 161 2a01:4f9:c010:58e5::1
|
||||
</span></span><span style="display:flex;"><span> 168 2a01:4f9:c010:58ed::1
|
||||
</span></span><span style="display:flex;"><span> 170 2a01:4f9:c010:548e::1
|
||||
</span></span><span style="display:flex;"><span> 170 2a01:4f9:c010:8c97::1
|
||||
</span></span><span style="display:flex;"><span> 175 2a01:4f9:c010:58c8::1
|
||||
</span></span><span style="display:flex;"><span> 175 2a01:4f9:c010:aada::1
|
||||
</span></span><span style="display:flex;"><span> 182 2a01:4f9:c010:58ec::1
|
||||
</span></span><span style="display:flex;"><span> 182 2a01:4f9:c010:ae8c::1
|
||||
</span></span><span style="display:flex;"><span> 502 2a01:4f9:c010:ee57::1
|
||||
</span></span><span style="display:flex;"><span> 530 2a01:4f9:c011:567a::1
|
||||
</span></span><span style="display:flex;"><span> 535 2a01:4f9:c010:d04e::1
|
||||
</span></span><span style="display:flex;"><span> 539 2a01:4f9:c010:3d9a::1
|
||||
</span></span><span style="display:flex;"><span> 586 2a01:4f9:c010:93db::1
|
||||
</span></span><span style="display:flex;"><span> 593 2a01:4f9:c010:a04a::1
|
||||
</span></span><span style="display:flex;"><span> 601 2a01:4f9:c011:4166::1
|
||||
</span></span><span style="display:flex;"><span> 607 2a01:4f9:c010:9881::1
|
||||
</span></span><span style="display:flex;"><span> 640 2a01:4f9:c010:87fb::1
|
||||
</span></span><span style="display:flex;"><span> 648 2a01:4f9:c010:e680::1
|
||||
</span></span><span style="display:flex;"><span> 1141 2a01:4f9:3a:2696::2
|
||||
</span></span><span style="display:flex;"><span> 1146 2a01:4f9:3a:2555::2
|
||||
</span></span><span style="display:flex;"><span> 3207 2a01:4f9:3a:2c19::2
|
||||
</span></span></code></pre></div><ul>
|
||||
<li>Maybe it’s time I ban all of Hetzner… sheesh.</li>
|
||||
<li>I left for a few hours and the server was going up and down the whole time, still very high CPU and database when I got back</li>
|
||||
</ul>
|
||||
<p><img src="/cgspace-notes/2022/07/cpu-day.png" alt="CPU day"></p>
|
||||
<ul>
|
||||
<li>I am not sure what’s going on
|
||||
<ul>
|
||||
<li>I extracted all the IPs and used <code>resolve-addresses-geoip2.py</code> to analyze them and extract all the Hetzner networks and block them</li>
|
||||
<li>It’s 181 IPs on Hetzner…</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>I rebooted the server to see if it was just some stuck locks in PostgreSQL…</li>
|
||||
<li>The load is still higher than I would expect, and after a few more hours I see more Hetzner IPs coming through? Two more subnets to block</li>
|
||||
<li>Start a harvest on AReS</li>
|
||||
</ul>
|
||||
<!-- raw HTML omitted -->
|
||||
|
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|
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|
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|
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Before Width: | Height: | Size: 14 KiB After Width: | Height: | Size: 15 KiB |
BIN
docs/2022/07/jmx_dspace_sessions-week.png
Normal file
BIN
docs/2022/07/jmx_dspace_sessions-week.png
Normal file
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@ -10,7 +10,7 @@
|
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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||||
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||||
|
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||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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|
||||
|
||||
|
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|
@ -10,7 +10,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2022-07-08T15:49:45+03:00" />
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|
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|
@ -10,7 +10,7 @@
|
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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|
@ -10,7 +10,7 @@
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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|
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|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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|
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|
@ -10,7 +10,7 @@
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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|
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|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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|
@ -10,7 +10,7 @@
|
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/posts/" />
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<meta property="og:updated_time" content="2022-07-07T10:02:04+03:00" />
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|
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|
||||
|
@ -3,19 +3,19 @@
|
||||
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|
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<url>
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<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
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<lastmod>2022-07-08T15:49:45+03:00</lastmod>
|
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</url><url>
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<loc>https://alanorth.github.io/cgspace-notes/</loc>
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<lastmod>2022-07-08T15:49:45+03:00</lastmod>
|
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</url><url>
|
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<loc>https://alanorth.github.io/cgspace-notes/2022-07/</loc>
|
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|
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<lastmod>2022-07-08T15:49:45+03:00</lastmod>
|
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</url><url>
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<lastmod>2022-07-08T15:49:45+03:00</lastmod>
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|
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<lastmod>2022-07-08T15:49:45+03:00</lastmod>
|
||||
</url><url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2022-06/</loc>
|
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<lastmod>2022-07-04T09:25:14+03:00</lastmod>
|
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|
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Loading…
Reference in New Issue
Block a user