call for volunteers: wikipathways testing

[Martijn van Iersel]

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

[Martina Kutmon]

Hi Martijn,

I will go through the protocol today.

Best, Tina

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[riannefijten]

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

[riannefijten]

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 }} of this pathway was tagged by {{#if:Maintenance bot|Maintenance bot|MaintBot }} and will be included in theReactome 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

On Wednesday, 10 October 2012 22:47:47 UTC+2, Martijn van Iersel wrote:

[Martina Kutmon]

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

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

[Martina Kutmon]

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

[Martijn van Iersel]

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:
> 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
>
> On Thu, Oct 11, 2012 at 6:56 PM, Martina Kutmon <mku...@gmail.com
> <mailto:mku...@gmail.com>> wrote:
>
> 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
> <rianne...@gmail.com <mailto:rianne...@gmail.com>> wrote:
>
> 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!* }}

> http://www.pathvisio.org/wiki/__WikiPathwaysTestProtocol

> <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
>
> --
> You received this message because you are subscribed to the
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> wikipathw...@googlegroups.com

> <mailto:wikipathw...@googlegroups.com>.

> To unsubscribe from this group, send email to
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> <mailto:wikipathways-devel%2Bunsu...@googlegroups.com>.

> To view this discussion on the web, visit
> https://groups.google.com/d/msg/wikipathways-devel/-/BY3pmQDzcFkJ.
>
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
>
>
>
> --

> /-----------------------------------------------
> Martina Kutmon, MSc
> email: mku...@gmail.com <mailto:mku...@gmail.com>
> skype: mkutmon/
>
>
>
>
> --
> /-----------------------------------------------
> Martina Kutmon, MSc
> email: mku...@gmail.com <mailto:mku...@gmail.com>
> skype: mkutmon/

>
> --
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[Thomas Kelder]

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

[riannefijten]

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:

Best, Tina

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

[Egon Willighagen]

On Thu, Oct 11, 2012 at 9:15 PM, Martijn van Iersel
<mvani...@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/
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