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Martijn van Iersel  
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 More options Oct 10 2012, 4:47 pm
From: Martijn van Iersel <mvanier...@gmail.com>
Date: Wed, 10 Oct 2012 21:47:42 +0100
Local: Wed, Oct 10 2012 4:47 pm
Subject: call for volunteers: wikipathways testing
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Hey all,

Thanks to the help of Thomas I got the test site more or less working
again, see: http://test.wikipathways.org.

It's not completely finished, we should make a list of what's working
and what isn't.

It might be good idea to print out our manual test protocol:
http://www.pathvisio.org/wiki/WikiPathwaysTestProtocol , and mark off
what works and what doesn't. Any volunteers? Especially for our
newcomers Nuno and Sravanthi, this should be a useful exercise, because
it helps get an overview of the site.

--
Martijn


 
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Martina Kutmon  
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 More options Oct 11 2012, 2:33 am
From: Martina Kutmon <mkut...@gmail.com>
Date: Thu, 11 Oct 2012 08:33:07 +0200
Local: Thurs, Oct 11 2012 2:33 am
Subject: Re: [wp-dev] call for volunteers: wikipathways testing
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Hi Martijn,

I will go through the protocol today.

Best, Tina
On Oct 10, 2012 10:47 PM, "Martijn van Iersel" <mvanier...@gmail.com> wrote:


 
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riannefijten  
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 More options Oct 11 2012, 11:16 am
From: riannefijten <riannefij...@gmail.com>
Date: Thu, 11 Oct 2012 08:16:21 -0700 (PDT)
Local: Thurs, Oct 11 2012 11:16 am
Subject: Re: call for volunteers: wikipathways testing
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Hi Martijn,

I started testing using the test protocol you mentioned, and I found the
first problem for me. I tried searching for pathways using the phrases
"glucose" and "glucose metabolism" and received the following error:

*Error: unable to process search.*

Internal Error

Unable to locate lucene index service. Please specify the base url for the index service as $indexServiceUrl in pass.php

I will continue with the rest and let you know what happens.

Best,
Rianne


 
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riannefijten  
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 More options Oct 11 2012, 11:36 am
From: riannefijten <riannefij...@gmail.com>
Date: Thu, 11 Oct 2012 08:36:50 -0700 (PDT)
Local: Thurs, Oct 11 2012 11:36 am
Subject: Re: call for volunteers: wikipathways testing
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Also, in the curation tags, there are a lot of brackets and words that are
not supposed to be there (at least I assume). For example:

{{ #if: |

|}}

*Reactome Approved*{{ #if: |

Comment: '**
*| }}*

{{#ifeq: 42101 | 42101 | The current version | Revision *42101<http://test.wikipathways.org/index.php?title=Pathway:WP1885&oldid=42101>
* }} of this pathway was tagged by {{#if:Maintenance bot|Maintenance
bot|MaintBot }} <http://test.wikipathways.org/index.php/User:MaintBot> and
will be included in theReactome <http://www.reactome.org/> pathway archive.

{{#ifexpr: 42101 < 42101 | *This tag applies to an older revision of the
pathway!* }}
I also found an internal error when trying to create an account (since I
can't log into my own account, because it's not recognized):  

Internal error

Detected bug in an extension! Hook abortOnBadDomain failed to return a
value; should return true to continue hook processing or false to abort.

Backtrace:

#0 /var/www/wikipathways-test/includes/specials/SpecialUserlogin.php(300):
wfRunHooks('AbortNewAccount', Array)

#1 /var/www/wikipathways-test/includes/specials/SpecialUserlogin.php(153):
LoginForm->addNewAccountInternal()

#2 /var/www/wikipathways-test/includes/specials/SpecialUserlogin.php(96):
LoginForm->addNewAccount()

#3 /var/www/wikipathways-test/includes/specials/SpecialUserlogin.php(17):
LoginForm->execute()

#4 [internal function]: wfSpecialUserlogin(NULL, Object(SpecialPage))

#5 /var/www/wikipathways-test/includes/SpecialPage.php(751):
call_user_func('wfSpecialUserlo...', NULL, Object(SpecialPage))

#6 /var/www/wikipathways-test/includes/SpecialPage.php(537):
SpecialPage->execute(NULL)

#7 /var/www/wikipathways-test/includes/Wiki.php(224):
SpecialPage::executePath(Object(Title))

#8 /var/www/wikipathways-test/includes/Wiki.php(55):
MediaWiki->initializeSpecialCases(Object(Title), Object(OutputPage),
Object(WebRequest))

#9 /var/www/wikipathways-test/index.php(93):
MediaWiki->initialize(Object(Title), NULL, Object(OutputPage),
Object(User), Object(WebRequest))

#10 {main}

 This also poses a problem as I can't test the description editing, because
I can't login or create a new account.

Hope this helps :) If I can login I'll test the rest of the protocol.

Rianne


 
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Martina Kutmon  
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 More options Oct 11 2012, 12:56 pm
From: Martina Kutmon <mkut...@gmail.com>
Date: Thu, 11 Oct 2012 18:56:26 +0200
Local: Thurs, Oct 11 2012 12:56 pm
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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Hi Rianne,

For testing on the test page you need to use the test account - see at the
top of the testing protocol.
Can you actually open the editor? For me the "Edit Pathway" button doesn't
work.

Best, Tina

On Thu, Oct 11, 2012 at 5:36 PM, riannefijten <riannefij...@gmail.com>wrote:

--
*-----------------------------------------------
Martina Kutmon, MSc
email: mkut...@gmail.com
skype: mkutmon*

 
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Martina Kutmon  
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 More options Oct 11 2012, 1:03 pm
From: Martina Kutmon <mkut...@gmail.com>
Date: Thu, 11 Oct 2012 19:03:25 +0200
Local: Thurs, Oct 11 2012 1:03 pm
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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Hi Martijn,

As mentioned below, I wasn't able to check the editor yet, but attached a
simple summary of the tests I did.

Best, Tina

--
*-----------------------------------------------
Martina Kutmon, MSc
email: mkut...@gmail.com
skype: mkutmon*

  2012-10-11-wp-testing.txt
2K Download

 
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Martijn van Iersel  
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 More options Oct 11 2012, 3:15 pm
From: Martijn van Iersel <mvanier...@gmail.com>
Date: Thu, 11 Oct 2012 20:15:54 +0100
Local: Thurs, Oct 11 2012 3:15 pm
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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Allright, thanks for your help, it looks like there are a couple of
major issues to resolve still.

* Lucene indexer
* Curation tags formatting
* Edit button not working.

I think further testing is not necessary until these issues are fixed.
Unfortunately I'm on the road the coming two weeks, so I can't do
much.Alex, Thomas, Nuno, maybe you can take a look at some of these issues?

--
Martijn

On 11/10/12 18:03, Martina Kutmon wrote:


 
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Thomas Kelder  
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 More options Oct 11 2012, 3:22 pm
From: Thomas Kelder <thomaskel...@gmail.com>
Date: Thu, 11 Oct 2012 21:22:05 +0200
Local: Thurs, Oct 11 2012 3:22 pm
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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I'll take a look at the lucene indexer tomorrow. I believe an instance
is ready to run on one of the bigcat servers.

Best wishes,
Thomas

On Thu, Oct 11, 2012 at 9:15 PM, Martijn van Iersel


 
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riannefijten  
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 More options Oct 12 2012, 10:42 am
From: riannefijten <riannefij...@gmail.com>
Date: Fri, 12 Oct 2012 07:42:12 -0700 (PDT)
Local: Fri, Oct 12 2012 10:42 am
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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Oh, I thought that was just optional. I'll try out the rest when I've got
some time:)

Op donderdag 11 oktober 2012 19:03:26 UTC+2 schreef Martina Kutmon het
volgende:


 
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Egon Willighagen  
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 More options Oct 15 2012, 4:55 am
From: Egon Willighagen <egon.willigha...@gmail.com>
Date: Mon, 15 Oct 2012 10:55:13 +0200
Local: Mon, Oct 15 2012 4:55 am
Subject: Re: [wp-dev] Re: call for volunteers: wikipathways testing
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On Thu, Oct 11, 2012 at 9:15 PM, Martijn van Iersel

<mvanier...@gmail.com> wrote:
> Allright, thanks for your help, it looks like there are a couple of major
> issues to resolve still.

> * Lucene indexer
> * Curation tags formatting
> * Edit button not working.

It seems that the metabolite db for BridgeDB is not loaded either...
e.g. clicking 5-hydroxytegafur in
http://test.wikipathways.org/index.php/Pathway:WP1601 gives in the
backpage a "Invalid annotation, missing datasource!" error.

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


 
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