emanuil-tolev
commented
8 years ago A bit of an idea. It'll crystallise soon enough. cc @richard-jones @Steven-Eardley did we not have to deal with a similar error on article pages before?
If not we'll investigate more thoroughly (though I think we have enough info to replicate). Below is the error log, and below that, the article's JSON record in Elasticsearch so we can replicate locally.
Looks like we might need to escalate that job which will refresh article metadata based on the journal info - this article has issns so it's reachable via a journal ToC and the discovery API, but has no "journal" section in the JSON. This is I believe planned as part of the Harvester project since it deals with refreshing article metadata automatically too. Nonetheless, to fix this we could create a separate script from the current portality/scripts/journalinfo.py which looks for articles without a "journal" section or which have a "journal" but no "journal.bibjson" (just in case) - and updates them. Let me know if you have any thoughts about doing it differently or if I'm wrong about the cause of this.
2015-12-09 13:52:28,556 - portality.core - ERROR - Exception on /article/000c38480c3d4d1383444cf8b24bc85d [GET]
Traceback (most recent call last):
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/app.py", line 1687, in wsgi_app
response = self.full_dispatch_request()
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/app.py", line 1360, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/app.py", line 1358, in full_dispatch_request
rv = self.dispatch_request()
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/app.py", line 1344, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/home/cloo/repl/production/doaj/src/doaj/portality/view/doaj.py", line 278, in article_page
return render_template('doaj/article.html', article=article, journal=journal)
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/templating.py", line 125, in render_template
context, ctx.app)
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/flask/templating.py", line 107, in _render
rv = template.render(context)
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/jinja2/environment.py", line 989, in render
return self.environment.handle_exception(exc_info, True)
File "/home/cloo/repl/production/doaj/local/lib/python2.7/site-packages/jinja2/environment.py", line 754, in handle_exception
reraise(exc_type, exc_value, tb)
File "/home/cloo/repl/production/doaj/src/doaj/portality/templates/doaj/article.html", line 1, in top-level template code
{% extends "base.html" %}
File "/home/cloo/repl/production/doaj/src/doaj/portality/templates/base.html", line 21, in top-level template code
{% block extra_meta_tags %}{% endblock %}
File "/home/cloo/repl/production/doaj/src/doaj/portality/templates/doaj/article.html", line 18, in block "extra_meta_tags"
{% set jbib = journal.bibjson() %}
UndefinedError: 'None' has no attribute 'bibjson'{
"_index":"doaj",
"_type":"article",
"_id":"000c38480c3d4d1383444cf8b24bc85d",
"_version":2,
"found":true,
"_source":{
"index":{
"publisher":[
"Centro de Estudos de Venenos e Animais Pe\u00e7onhentos - CEVAP, Universidade Estadual Paulista - UNESP"
],
"schema_subject":[
"LCC:Medicine",
"LCC:Zoology",
"DOAJ:Health Sciences",
"LCC:Internal medicine",
"DOAJ:Biology and Life Sciences",
"LCC:Arctic medicine. Tropical medicine",
"DOAJ:Medicine (General)",
"DOAJ:Internal medicine",
"DOAJ:Biology",
"DOAJ:Zoology",
"LCC:Special situations and conditions",
"LCC:Science"
],
"license":[
"CC by-nc"
],
"classification":[
"Internal medicine",
"Biology and Life Sciences",
"Biology",
"Health Sciences",
"Special situations and conditions",
"Science",
"Medicine (General)",
"Arctic medicine. Tropical medicine",
"Zoology",
"Medicine"
],
"classification_paths":[
"Medicine: Internal medicine: Special situations and conditions: Arctic medicine. Tropical medicine",
"Science: Zoology"
],
"country":"Brazil",
"issn":[
"1678-4936",
"0104-7930"
],
"unpunctitle":"PRELIMINARY INVESTIGATION ABOUT THE ANTICOMPLEMENT PROPERTIES OF PARTIALLY SEPARATED Vipera ammodytes VENOM",
"language":[
"English"
],
"date":"1997-01-01T00:00:00Z",
"schema_code":[
"LCC:RC955-962",
"LCC:RC952-1245",
"LCC:RC31-1245",
"LCC:R",
"LCC:Q",
"LCC:QL1-991"
],
"asciiunpunctitle":"PRELIMINARY INVESTIGATION ABOUT THE ANTICOMPLEMENT PROPERTIES OF PARTIALLY SEPARATED Vipera ammodytes VENOM",
"subject":[
"Internal medicine",
"Biology and Life Sciences",
"Biology",
"Health Sciences",
"Special situations and conditions",
"Science",
"Medicine (General)",
"Arctic medicine. Tropical medicine",
"Zoology",
"Medicine"
]
},
"last_updated":"2015-04-22T01:21:44Z",
"created_date":"2013-08-31T05:26:16Z",
"admin":{
"in_doaj":true
},
"id":"000c38480c3d4d1383444cf8b24bc85d",
"bibjson":{
"start_page":"37",
"title":"PRELIMINARY INVESTIGATION ABOUT THE ANTI-COMPLEMENT PROPERTIES OF PARTIALLY SEPARATED Vipera ammodytes VENOM",
"journal":{
"publisher":"Centro de Estudos de Venenos e Animais Pe\u00e7onhentos - CEVAP, Universidade Estadual Paulista - UNESP",
"license":[
{
"type":"CC by-nc",
"title":"CC by-nc"
}
],
"language":[
"English"
],
"title":"Journal of Venomous Animals and Toxins including Tropical Diseases",
"country":"BR",
"number":"1",
"volume":"3"
},
"author":[
{
"name":"S. STANILOVA"
},
{
"name":"Z. ZHELEV"
},
{
"name":"I. MATEV"
}
],
"link":[
{
"url":"http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0104-79301997000100005",
"type":"fulltext"
}
],
"year":"1997",
"keywords":[
"Anti-complement",
"venom",
"Vipera ammodytes"
],
"identifier":[
{
"type":"doi",
"id":"10.1590/S0104-79301997000100005"
},
{
"type":"pissn",
"id":"0104-7930"
},
{
"type":"eissn",
"id":"1678-4936"
}
],
"abstract":"The present study demonstrates that Vipera ammodytes venom is a potent inhibitor of human complement activation. Crude venom was fractionated by ion-exchange chromatography and each fraction was then tested for proteolytic, hemolytic and anti-complement activities. Three peaks decreased the hemolytic activity of human serum when measured using assays for the classical and alternative pathways of activation. One of the anti-complement peaks contains a protease capable of cleaving the C3 component of complement.",
"subject":[
{
"code":"RC955-962",
"term":"Arctic medicine. Tropical medicine",
"scheme":"LCC"
},
{
"code":"RC952-1245",
"term":"Special situations and conditions",
"scheme":"LCC"
},
{
"code":"RC31-1245",
"term":"Internal medicine",
"scheme":"LCC"
},
{
"code":"R",
"term":"Medicine",
"scheme":"LCC"
},
{
"term":"Internal medicine",
"scheme":"DOAJ"
},
{
"term":"Medicine (General)",
"scheme":"DOAJ"
},
{
"term":"Health Sciences",
"scheme":"DOAJ"
},
{
"code":"QL1-991",
"term":"Zoology",
"scheme":"LCC"
},
{
"code":"Q",
"term":"Science",
"scheme":"LCC"
},
{
"term":"Zoology",
"scheme":"DOAJ"
},
{
"term":"Biology",
"scheme":"DOAJ"
},
{
"term":"Biology and Life Sciences",
"scheme":"DOAJ"
},
{
"scheme":"LCC",
"term":"Arctic medicine. Tropical medicine",
"code":"RC955-962"
},
{
"scheme":"LCC",
"term":"Special situations and conditions",
"code":"RC952-1245"
},
{
"scheme":"LCC",
"term":"Internal medicine",
"code":"RC31-1245"
},
{
"scheme":"LCC",
"term":"Medicine",
"code":"R"
},
{
"term":"Internal medicine",
"scheme":"DOAJ"
},
{
"term":"Medicine (General)",
"scheme":"DOAJ"
},
{
"term":"Health Sciences",
"scheme":"DOAJ"
},
{
"scheme":"LCC",
"term":"Zoology",
"code":"QL1-991"
},
{
"scheme":"LCC",
"term":"Science",
"code":"Q"
},
{
"term":"Zoology",
"scheme":"DOAJ"
},
{
"term":"Biology",
"scheme":"DOAJ"
},
{
"term":"Biology and Life Sciences",
"scheme":"DOAJ"
},
{
"code":"RC955-962",
"term":"Arctic medicine. Tropical medicine",
"scheme":"LCC"
},
{
"code":"RC952-1245",
"term":"Special situations and conditions",
"scheme":"LCC"
},
{
"code":"RC31-1245",
"term":"Internal medicine",
"scheme":"LCC"
},
{
"code":"R",
"term":"Medicine",
"scheme":"LCC"
},
{
"term":"Internal medicine",
"scheme":"DOAJ"
},
{
"term":"Medicine (General)",
"scheme":"DOAJ"
},
{
"term":"Health Sciences",
"scheme":"DOAJ"
},
{
"code":"QL1-991",
"term":"Zoology",
"scheme":"LCC"
},
{
"code":"Q",
"term":"Science",
"scheme":"LCC"
},
{
"term":"Zoology",
"scheme":"DOAJ"
},
{
"term":"Biology",
"scheme":"DOAJ"
},
{
"term":"Biology and Life Sciences",
"scheme":"DOAJ"
},
{
"scheme":"LCC",
"term":"Arctic medicine. Tropical medicine",
"code":"RC955-962"
},
{
"scheme":"LCC",
"term":"Special situations and conditions",
"code":"RC952-1245"
},
{
"scheme":"LCC",
"term":"Internal medicine",
"code":"RC31-1245"
},
{
"scheme":"LCC",
"term":"Medicine",
"code":"R"
},
{
"term":"Internal medicine",
"scheme":"DOAJ"
},
{
"term":"Medicine (General)",
"scheme":"DOAJ"
},
{
"term":"Health Sciences",
"scheme":"DOAJ"
},
{
"scheme":"LCC",
"term":"Zoology",
"code":"QL1-991"
},
{
"scheme":"LCC",
"term":"Science",
"code":"Q"
},
{
"term":"Zoology",
"scheme":"DOAJ"
},
{
"term":"Biology",
"scheme":"DOAJ"
},
{
"term":"Biology and Life Sciences",
"scheme":"DOAJ"
},
{
"code":"RC955-962",
"term":"Arctic medicine. Tropical medicine",
"scheme":"LCC"
},
{
"code":"RC952-1245",
"term":"Special situations and conditions",
"scheme":"LCC"
},
{
"code":"RC31-1245",
"term":"Internal medicine",
"scheme":"LCC"
},
{
"code":"R",
"term":"Medicine",
"scheme":"LCC"
},
{
"code":"QL1-991",
"term":"Zoology",
"scheme":"LCC"
},
{
"code":"Q",
"term":"Science",
"scheme":"LCC"
},
{
"scheme":"LCC",
"term":"Arctic medicine. Tropical medicine",
"code":"RC955-962"
},
{
"scheme":"LCC",
"term":"Special situations and conditions",
"code":"RC952-1245"
},
{
"scheme":"LCC",
"term":"Internal medicine",
"code":"RC31-1245"
},
{
"scheme":"LCC",
"term":"Medicine",
"code":"R"
},
{
"scheme":"LCC",
"term":"Zoology",
"code":"QL1-991"
},
{
"scheme":"LCC",
"term":"Science",
"code":"Q"
}
]
}
}
}
dommitchell
richard-jones
Steven-Eardley
http://bit.ly/1OT479U
These are all article of the license type 'CC by-nc' which is an old license type and shouldn't be on the site. Note that there are 2 CC BY-NC listing under license now:
CC BY-NC (350137) CC by-nc (2619)
Any idea what is going on?