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860 lines
40 KiB
HTML
860 lines
40 KiB
HTML
<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="January, 2018" />
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<meta property="og:description" content="2018-01-02
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Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
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I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
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The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
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In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
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And just before that I see this:
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Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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Ah hah! So the pool was actually empty!
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I need to increase that, let’s try to bump it up from 50 to 75
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After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw
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I notice this error quite a few times in dspace.log:
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2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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And there are many of these errors every day for the past month:
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$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains
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" />
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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/2018-01/" />
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<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
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<meta property="article:modified_time" content="2018-01-11T08:36:59+02:00"/>
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<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="January, 2018"/>
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<meta name="twitter:description" content="2018-01-02
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Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
|
|
I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
|
|
The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
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In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
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And just before that I see this:
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Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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Ah hah! So the pool was actually empty!
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I need to increase that, let’s try to bump it up from 50 to 75
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|
After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw
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|
I notice this error quite a few times in dspace.log:
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2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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And there are many of these errors every day for the past month:
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$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains
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"/>
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<meta name="generator" content="Hugo 0.32.3" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "January, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-01/",
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"wordCount": "2324",
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"datePublished": "2018-01-02T08:35:54-08:00",
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"dateModified": "2018-01-11T08:36:59+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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},
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-01/">
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<title>January, 2018 | CGSpace Notes</title>
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<!-- combined, minified CSS -->
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<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-O8wjsnz02XiyrPxnhfF6AVOv6YLBaEGRCnVF+DL3gCPBy9cieyHcpixIrVyD2JS5" crossorigin="anonymous">
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</head>
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-01-02">2018-01-02</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
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<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
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<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li>And just before that I see this:</li>
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</ul>
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<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
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</code></pre>
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<ul>
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<li>Ah hah! So the pool was actually empty!</li>
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<li>I need to increase that, let’s try to bump it up from 50 to 75</li>
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<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li>
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<li>I notice this error quite a few times in dspace.log:</li>
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</ul>
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<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre>
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<ul>
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<li>And there are many of these errors every day for the past month:</li>
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</ul>
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<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre>
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<ul>
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<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</li>
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</ul>
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<p></p>
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<h2 id="2018-01-03">2018-01-03</h2>
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<ul>
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<li>I woke up to more up and down of CGSpace, this time UptimeRobot noticed a few rounds of up and down of a few minutes each and Linode also notified of high CPU load from 12 to 2 PM</li>
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<li>Looks like I need to increase the database pool size again:</li>
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</ul>
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<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
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dspace.log.2018-01-01:0
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dspace.log.2018-01-02:1972
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dspace.log.2018-01-03:1909
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</code></pre>
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<ul>
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<li>For some reason there were a lot of “active” connections last night:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/01/postgres_connections-day.png" alt="CGSpace PostgreSQL connections" /></p>
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<ul>
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<li>The active IPs in XMLUI are:</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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607 40.77.167.141
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611 2a00:23c3:8c94:7800:392c:a491:e796:9c50
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663 188.226.169.37
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759 157.55.39.245
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887 68.180.229.254
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1037 157.55.39.175
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1068 216.244.66.245
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1495 66.249.64.91
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1934 104.196.152.243
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2219 134.155.96.78
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</code></pre>
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<ul>
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<li>134.155.96.78 appears to be at the University of Mannheim in Germany</li>
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<li>They identify as: Mozilla/5.0 (compatible; heritrix/3.2.0 +<a href="http://ifm.uni-mannheim.de">http://ifm.uni-mannheim.de</a>)</li>
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<li>This appears to be the <a href="https://github.com/internetarchive/heritrix3">Internet Archive’s open source bot</a></li>
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<li>They seem to be re-using their Tomcat session so I don’t need to do anything to them just yet:</li>
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</ul>
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<pre><code>$ grep 134.155.96.78 dspace.log.2018-01-03 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
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2
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</code></pre>
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<ul>
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<li>The API logs show the normal users:</li>
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</ul>
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<pre><code># cat /var/log/nginx/rest.log /var/log/nginx/rest.log.1 /var/log/nginx/oai.log /var/log/nginx/oai.log.1 | grep -E "3/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
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32 207.46.13.182
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38 40.77.167.132
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38 68.180.229.254
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43 66.249.64.91
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46 40.77.167.141
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49 157.55.39.245
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79 157.55.39.175
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1533 50.116.102.77
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4069 70.32.83.92
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9355 45.5.184.196
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</code></pre>
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<ul>
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<li>In other related news I see a sizeable amount of requests coming from python-requests</li>
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<li>For example, just in the last day there were 1700!</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -c python-requests
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1773
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</code></pre>
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<ul>
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<li>But they come from hundreds of IPs, many of which are 54.x.x.x:</li>
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</ul>
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<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep python-requests | awk '{print $1}' | sort -n | uniq -c | sort -h | tail -n 30
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9 54.144.87.92
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9 54.146.222.143
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9 54.146.249.249
|
|
9 54.158.139.206
|
|
9 54.161.235.224
|
|
9 54.163.41.19
|
|
9 54.163.4.51
|
|
9 54.196.195.107
|
|
9 54.198.89.134
|
|
9 54.80.158.113
|
|
10 54.198.171.98
|
|
10 54.224.53.185
|
|
10 54.226.55.207
|
|
10 54.227.8.195
|
|
10 54.242.234.189
|
|
10 54.242.238.209
|
|
10 54.80.100.66
|
|
11 54.161.243.121
|
|
11 54.205.154.178
|
|
11 54.234.225.84
|
|
11 54.87.23.173
|
|
11 54.90.206.30
|
|
12 54.196.127.62
|
|
12 54.224.242.208
|
|
12 54.226.199.163
|
|
13 54.162.149.249
|
|
13 54.211.182.255
|
|
19 50.17.61.150
|
|
21 54.211.119.107
|
|
139 164.39.7.62
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I have no idea what these are but they seem to be coming from Amazon…</li>
|
|
<li>I guess for now I just have to increase the database connection pool’s max active</li>
|
|
<li>It’s currently 75 and normally I’d just bump it by 25 but let me be a bit daring and push it by 50 to 125, because I used to see at least 121 connections in pg_stat_activity before when we were using the shitty default pooling</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-04">2018-01-04</h2>
|
|
|
|
<ul>
|
|
<li>CGSpace went down and up a bunch of times last night and ILRI staff were complaining a lot last night</li>
|
|
<li>The XMLUI logs show this activity:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep -E "4/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
|
|
968 197.211.63.81
|
|
981 213.55.99.121
|
|
1039 66.249.64.93
|
|
1258 157.55.39.175
|
|
1273 207.46.13.182
|
|
1311 157.55.39.191
|
|
1319 157.55.39.197
|
|
1775 66.249.64.78
|
|
2216 104.196.152.243
|
|
3366 66.249.64.91
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Again we ran out of PostgreSQL database connections, even after bumping the pool max active limit from 50 to 75 to 125 yesterday!</li>
|
|
</ul>
|
|
|
|
<pre><code>2018-01-04 07:36:08,089 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
|
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-256] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:125; busy:125; idle:0; lastwait:5000].
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>So for this week that is the number one problem!</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
|
|
dspace.log.2018-01-01:0
|
|
dspace.log.2018-01-02:1972
|
|
dspace.log.2018-01-03:1909
|
|
dspace.log.2018-01-04:1559
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I will just bump the connection limit to 300 because I’m fucking fed up with this shit</li>
|
|
<li>Once I get back to Amman I will have to try to create different database pools for different web applications, like recently discussed on the dspace-tech mailing list</li>
|
|
<li>Create accounts on CGSpace for two CTA staff km4ard@cta.int and bheenick@cta.int</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-05">2018-01-05</h2>
|
|
|
|
<ul>
|
|
<li>Peter said that CGSpac was down last night and Tsega restarted Tomcat</li>
|
|
<li>I don’t see any alerts from Linode or UptimeRobot, and there are no PostgreSQL connection errors in the dspace logs for today:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-*
|
|
dspace.log.2018-01-01:0
|
|
dspace.log.2018-01-02:1972
|
|
dspace.log.2018-01-03:1909
|
|
dspace.log.2018-01-04:1559
|
|
dspace.log.2018-01-05:0
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Daniel asked for help with their DAGRIS server (linode2328112) that has no disk space</li>
|
|
<li>I had a look and there is one Apache 2 log file that is 73GB, with lots of this:</li>
|
|
</ul>
|
|
|
|
<pre><code>[Fri Jan 05 09:31:22.965398 2018] [:error] [pid 9340] [client 213.55.99.121:64476] WARNING: Unable to find a match for "9-16-1-RV.doc" in "/home/files/journals/6//articles/9/". Skipping this file., referer: http://dagris.info/reviewtool/index.php/index/install/upgrade
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I will delete the log file for now and tell Danny</li>
|
|
<li>Also, I’m still seeing a hundred or so of the “ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer” errors in dspace logs, I need to search the dspace-tech mailing list to see what the cause is</li>
|
|
<li>I will run a full Discovery reindex in the mean time to see if it’s something wrong with the Discovery Solr core</li>
|
|
</ul>
|
|
|
|
<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
|
|
$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
|
|
|
|
real 110m43.985s
|
|
user 15m24.960s
|
|
sys 3m14.890s
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Reboot CGSpace and DSpace Test for new kernels (4.14.12-x86_64-linode92) that partially mitigate the <a href="https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/">Spectre and Meltdown CPU vulnerabilities</a></li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-06">2018-01-06</h2>
|
|
|
|
<ul>
|
|
<li>I’m still seeing Solr errors in the DSpace logs even after the full reindex yesterday:</li>
|
|
</ul>
|
|
|
|
<pre><code>org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1983+TO+1989]': Encountered " "]" "] "" at line 1, column 32.
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I posted a message to the dspace-tech mailing list to see if anyone can help</li>
|
|
</ul>
|
|
|
|
<h2 id="2018-01-09">2018-01-09</h2>
|
|
|
|
<ul>
|
|
<li>Advise Sisay about blank lines in some IITA records</li>
|
|
<li>Generate a list of author affiliations for Peter to clean up:</li>
|
|
</ul>
|
|
|
|
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv;
|
|
COPY 4515
|
|
</code></pre>
|
|
|
|
<h2 id="2018-01-10">2018-01-10</h2>
|
|
|
|
<ul>
|
|
<li>I looked to see what happened to this year’s Solr statistics sharding task that should have run on 2018-01-01 and of course it failed:</li>
|
|
</ul>
|
|
|
|
<pre><code>Moving: 81742 into core statistics-2010
|
|
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
|
|
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2010
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
|
|
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
|
|
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
|
|
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.apache.http.client.ClientProtocolException
|
|
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
|
|
... 10 more
|
|
Caused by: org.apache.http.client.NonRepeatableRequestException: Cannot retry request with a non-repeatable request entity. The cause lists the reason the original request failed.
|
|
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:659)
|
|
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:487)
|
|
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:863)
|
|
... 14 more
|
|
Caused by: java.net.SocketException: Connection reset
|
|
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:115)
|
|
at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
|
|
at org.apache.http.impl.io.AbstractSessionOutputBuffer.flushBuffer(AbstractSessionOutputBuffer.java:159)
|
|
at org.apache.http.impl.io.AbstractSessionOutputBuffer.write(AbstractSessionOutputBuffer.java:179)
|
|
at org.apache.http.impl.io.ChunkedOutputStream.flushCacheWithAppend(ChunkedOutputStream.java:124)
|
|
at org.apache.http.impl.io.ChunkedOutputStream.write(ChunkedOutputStream.java:181)
|
|
at org.apache.http.entity.InputStreamEntity.writeTo(InputStreamEntity.java:132)
|
|
at org.apache.http.entity.HttpEntityWrapper.writeTo(HttpEntityWrapper.java:89)
|
|
at org.apache.http.impl.client.EntityEnclosingRequestWrapper$EntityWrapper.writeTo(EntityEnclosingRequestWrapper.java:108)
|
|
at org.apache.http.impl.entity.EntitySerializer.serialize(EntitySerializer.java:117)
|
|
at org.apache.http.impl.AbstractHttpClientConnection.sendRequestEntity(AbstractHttpClientConnection.java:265)
|
|
at org.apache.http.impl.conn.ManagedClientConnectionImpl.sendRequestEntity(ManagedClientConnectionImpl.java:203)
|
|
at org.apache.http.protocol.HttpRequestExecutor.doSendRequest(HttpRequestExecutor.java:236)
|
|
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:121)
|
|
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:685)
|
|
... 16 more
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>DSpace Test has the same error but with creating the 2017 core:</li>
|
|
</ul>
|
|
|
|
<pre><code>Moving: 2243021 into core statistics-2017
|
|
Exception: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
|
|
org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr//statistics-2017
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:566)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
|
|
at org.dspace.statistics.SolrLogger.shardSolrIndex(SourceFile:2243)
|
|
at org.dspace.statistics.util.StatisticsClient.main(StatisticsClient.java:106)
|
|
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.apache.http.client.ClientProtocolException
|
|
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:867)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:106)
|
|
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:57)
|
|
at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:448)
|
|
... 10 more
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>There is interesting documentation about this on the DSpace Wiki: <a href="https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-SolrShardingByYear">https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-SolrShardingByYear</a></li>
|
|
<li>I’m looking to see maybe if we’re hitting the issues mentioned in <a href="https://jira.duraspace.org/browse/DS-2212">DS-2212</a> that were apparently fixed in DSpace 5.2</li>
|
|
<li>I can apparently search for records in the Solr stats core that have an empty <code>owningColl</code> field using this in the Solr admin query: <code>-owningColl:*</code></li>
|
|
<li>On CGSpace I see 48,000,000 records that have an <code>owningColl</code> field and 34,000,000 that don’t:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ http 'http://localhost:3000/solr/statistics/select?q=owningColl%3A*&wt=json&indent=true' | grep numFound
|
|
"response":{"numFound":48476327,"start":0,"docs":[
|
|
$ http 'http://localhost:3000/solr/statistics/select?q=-owningColl%3A*&wt=json&indent=true' | grep numFound
|
|
"response":{"numFound":34879872,"start":0,"docs":[
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I tested the <code>dspace stats-util -s</code> process on my local machine and it failed the same way</li>
|
|
<li>It doesn’t seem to be helpful, but the dspace log shows this:</li>
|
|
</ul>
|
|
|
|
<pre><code>2018-01-10 10:51:19,301 INFO org.dspace.statistics.SolrLogger @ Created core with name: statistics-2016
|
|
2018-01-10 10:51:19,301 INFO org.dspace.statistics.SolrLogger @ Moving: 3821 records into core statistics-2016
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Terry Brady has written some notes on the DSpace Wiki about Solr sharing issues: <a href="https://wiki.duraspace.org/display/%7Eterrywbrady/Statistics+Import+Export+Issues">https://wiki.duraspace.org/display/%7Eterrywbrady/Statistics+Import+Export+Issues</a></li>
|
|
<li>Uptime Robot said that CGSpace went down at around 9:43 AM</li>
|
|
<li>I looked at PostgreSQL’s <code>pg_stat_activity</code> table and saw 161 active connections, but no pool errors in the DSpace logs:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -c "Timeout: Pool empty." dspace.log.2018-01-10
|
|
0
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>The XMLUI logs show quite a bit of activity today:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep "10/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
|
|
951 207.46.13.159
|
|
954 157.55.39.123
|
|
1217 95.108.181.88
|
|
1503 104.196.152.243
|
|
6455 70.36.107.50
|
|
11412 70.36.107.190
|
|
16730 70.36.107.49
|
|
17386 2607:fa98:40:9:26b6:fdff:feff:1c96
|
|
21566 2607:fa98:40:9:26b6:fdff:feff:195d
|
|
45384 2607:fa98:40:9:26b6:fdff:feff:1888
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>The user agent for the top six or so IPs are all the same:</li>
|
|
</ul>
|
|
|
|
<pre><code>"Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari/537.36"
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li><code>whois</code> says they come from <a href="http://www.perfectip.net/">Perfect IP</a></li>
|
|
<li>I’ve never seen those top IPs before, but they have created 50,000 Tomcat sessions today:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ grep -E '(2607:fa98:40:9:26b6:fdff:feff:1888|2607:fa98:40:9:26b6:fdff:feff:195d|2607:fa98:40:9:26b6:fdff:feff:1c96|70.36.107.49|70.36.107.190|70.36.107.50)' /home/cgspace.cgiar.org/log/dspace.log.2018-01-10 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | uniq | wc -l
|
|
49096
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Rather than blocking their IPs, I think I might just add their user agent to the “badbots” zone with Baidu, because they seem to be the only ones using that user agent:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep "Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari
|
|
/537.36" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
|
|
6796 70.36.107.50
|
|
11870 70.36.107.190
|
|
17323 70.36.107.49
|
|
19204 2607:fa98:40:9:26b6:fdff:feff:1c96
|
|
23401 2607:fa98:40:9:26b6:fdff:feff:195d
|
|
47875 2607:fa98:40:9:26b6:fdff:feff:1888
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I added the user agent to nginx’s badbots limit req zone but upon testing the config I got an error:</li>
|
|
</ul>
|
|
|
|
<pre><code># nginx -t
|
|
nginx: [emerg] could not build map_hash, you should increase map_hash_bucket_size: 64
|
|
nginx: configuration file /etc/nginx/nginx.conf test failed
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>According to nginx docs the <a href="https://nginx.org/en/docs/hash.html">bucket size should be a multiple of the CPU’s cache alignment</a>, which is 64 for us:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /proc/cpuinfo | grep cache_alignment | head -n1
|
|
cache_alignment : 64
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>On our servers that is 64, so I increased this parameter to 128 and deployed the changes to nginx</li>
|
|
<li>Almost immediately the PostgreSQL connections dropped back down to 40 or so, and UptimeRobot said the site was back up</li>
|
|
<li>So that’s interesting that we’re not out of PostgreSQL connections (current pool maxActive is 300!) but the system is “down” to UptimeRobot and very slow to use</li>
|
|
<li>Linode continues to test mitigations for Meltdown and Spectre: <a href="https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/">https://blog.linode.com/2018/01/03/cpu-vulnerabilities-meltdown-spectre/</a></li>
|
|
<li>I rebooted DSpace Test to see if the kernel will be updated (currently Linux 4.14.12-x86_64-linode92)… nope.</li>
|
|
<li>It looks like Linode will reboot the KVM hosts later this week, though</li>
|
|
<li>Udana from WLE asked if we could give him permission to upload CSVs to CGSpace (which would require super admin access)</li>
|
|
<li>Citing concerns with metadata quality, I suggested adding him on DSpace Test first</li>
|
|
<li>I opened a ticket with Atmire to ask them about DSpace 5.8 compatibility: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560</a></li>
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</ul>
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<h2 id="2018-01-11">2018-01-11</h2>
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<ul>
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<li>The PostgreSQL and firewall graphs from this week show clearly the load from the new bot from PerfectIP.net yesterday:</li>
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</ul>
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<p><img src="/cgspace-notes/2018/01/postgres_connections-day-perfectip.png" alt="PostgreSQL load" />
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<img src="/cgspace-notes/2018/01/firewall-perfectip.png" alt="Firewall load" /></p>
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<ul>
|
|
<li>Linode rebooted DSpace Test and CGSpace for their host hypervisor kernel updates</li>
|
|
<li>Following up with the Solr sharding issue on the dspace-tech mailing list, I noticed this interesting snippet in the Tomcat <code>localhost_access_log</code> at the time of my sharding attempt on my test machine:</li>
|
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</ul>
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<pre><code>127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?q=type%3A2+AND+id%3A1&wt=javabin&version=2 HTTP/1.1" 200 107
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|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?q=*%3A*&rows=0&facet=true&facet.range=time&facet.range.start=NOW%2FYEAR-18YEARS&facet.range.end=NOW%2FYEAR%2B0YEARS&facet.range.gap=%2B1YEAR&facet.mincount=1&wt=javabin&version=2 HTTP/1.1" 200 447
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|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/admin/cores?action=STATUS&core=statistics-2016&indexInfo=true&wt=javabin&version=2 HTTP/1.1" 200 76
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|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/admin/cores?action=CREATE&name=statistics-2016&instanceDir=statistics&dataDir=%2FUsers%2Faorth%2Fdspace%2Fsolr%2Fstatistics-2016%2Fdata&wt=javabin&version=2 HTTP/1.1" 200 63
|
|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/select?csv.mv.separator=%7C&q=*%3A*&fq=time%3A%28%5B2016%5C-01%5C-01T00%5C%3A00%5C%3A00Z+TO+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%5D+NOT+2017%5C-01%5C-01T00%5C%3A00%5C%3A00Z%29&rows=10000&wt=csv HTTP/1.1" 200 2137630
|
|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "GET /solr/statistics/admin/luke?show=schema&wt=javabin&version=2 HTTP/1.1" 200 16253
|
|
127.0.0.1 - - [10/Jan/2018:10:51:19 +0200] "POST /solr//statistics-2016/update/csv?commit=true&softCommit=false&waitSearcher=true&f.previousWorkflowStep.split=true&f.previousWorkflowStep.separator=%7C&f.previousWorkflowStep.encapsulator=%22&f.actingGroupId.split=true&f.actingGroupId.separator=%7C&f.actingGroupId.encapsulator=%22&f.containerCommunity.split=true&f.containerCommunity.separator=%7C&f.containerCommunity.encapsulator=%22&f.range.split=true&f.range.separator=%7C&f.range.encapsulator=%22&f.containerItem.split=true&f.containerItem.separator=%7C&f.containerItem.encapsulator=%22&f.p_communities_map.split=true&f.p_communities_map.separator=%7C&f.p_communities_map.encapsulator=%22&f.ngram_query_search.split=true&f.ngram_query_search.separator=%7C&f.ngram_query_search.encapsulator=%22&f.containerBitstream.split=true&f.containerBitstream.separator=%7C&f.containerBitstream.encapsulator=%22&f.owningItem.split=true&f.owningItem.separator=%7C&f.owningItem.encapsulator=%22&f.actingGroupParentId.split=true&f.actingGroupParentId.separator=%7C&f.actingGroupParentId.encapsulator=%22&f.text.split=true&f.text.separator=%7C&f.text.encapsulator=%22&f.simple_query_search.split=true&f.simple_query_search.separator=%7C&f.simple_query_search.encapsulator=%22&f.owningComm.split=true&f.owningComm.separator=%7C&f.owningComm.encapsulator=%22&f.owner.split=true&f.owner.separator=%7C&f.owner.encapsulator=%22&f.filterquery.split=true&f.filterquery.separator=%7C&f.filterquery.encapsulator=%22&f.p_group_map.split=true&f.p_group_map.separator=%7C&f.p_group_map.encapsulator=%22&f.actorMemberGroupId.split=true&f.actorMemberGroupId.separator=%7C&f.actorMemberGroupId.encapsulator=%22&f.bitstreamId.split=true&f.bitstreamId.separator=%7C&f.bitstreamId.encapsulator=%22&f.group_name.split=true&f.group_name.separator=%7C&f.group_name.encapsulator=%22&f.p_communities_name.split=true&f.p_communities_name.separator=%7C&f.p_communities_name.encapsulator=%22&f.query.split=true&f.query.separator=%7C&f.query.encapsulator=%22&f.workflowStep.split=true&f.workflowStep.separator=%7C&f.workflowStep.encapsulator=%22&f.containerCollection.split=true&f.containerCollection.separator=%7C&f.containerCollection.encapsulator=%22&f.complete_query_search.split=true&f.complete_query_search.separator=%7C&f.complete_query_search.encapsulator=%22&f.p_communities_id.split=true&f.p_communities_id.separator=%7C&f.p_communities_id.encapsulator=%22&f.rangeDescription.split=true&f.rangeDescription.separator=%7C&f.rangeDescription.encapsulator=%22&f.group_id.split=true&f.group_id.separator=%7C&f.group_id.encapsulator=%22&f.bundleName.split=true&f.bundleName.separator=%7C&f.bundleName.encapsulator=%22&f.ngram_simplequery_search.split=true&f.ngram_simplequery_search.separator=%7C&f.ngram_simplequery_search.encapsulator=%22&f.group_map.split=true&f.group_map.separator=%7C&f.group_map.encapsulator=%22&f.owningColl.split=true&f.owningColl.separator=%7C&f.owningColl.encapsulator=%22&f.p_group_id.split=true&f.p_group_id.separator=%7C&f.p_group_id.encapsulator=%22&f.p_group_name.split=true&f.p_group_name.separator=%7C&f.p_group_name.encapsulator=%22&wt=javabin&version=2 HTTP/1.1" 409 156
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>The new core is created but when DSpace attempts to POST to it there is an HTTP 409 error</li>
|
|
<li>This is apparently a common Solr error code that means “version conflict”: <a href="http://yonik.com/solr/optimistic-concurrency/">http://yonik.com/solr/optimistic-concurrency/</a></li>
|
|
<li>Looks like that bot from the PerfectIP.net host ended up making about 450,000 requests to XMLUI alone yesterday:</li>
|
|
</ul>
|
|
|
|
<pre><code># cat /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/library-access.log /var/log/nginx/library-access.log.1 | grep "Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/38.0.2125.111 Safari/537.36" | grep "10/Jan/2018" | awk '{print $1}' | sort -n | uniq -c | sort -h | tail
|
|
21572 70.36.107.50
|
|
30722 70.36.107.190
|
|
34566 70.36.107.49
|
|
101829 2607:fa98:40:9:26b6:fdff:feff:195d
|
|
111535 2607:fa98:40:9:26b6:fdff:feff:1c96
|
|
161797 2607:fa98:40:9:26b6:fdff:feff:1888
|
|
</code></pre>
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</article>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2018-01/">January, 2018</a></li>
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<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
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<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
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<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
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<h4>Links</h4>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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