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Interwiki link to BLAST at wikiomics: wikiomics:BLAST


Contents

Template examples

Created Template:PM to simplify Module linking.

By typing {{PM|Bio::SeqIO}} you automatically get a link that looks like this:

Bio::SeqIO

It's a one parameter macro to save duplicate typing of the module name.

--Tseemann 19:19, 27 December 2005 (EST)

Testing new CPAN macro: Digest::MD5

Underscore issues...

Problem with underscores?

Or is it the Doclink macro?

Bio::Graph::IO::psi_xml
PDoc Bio::Graph::IO::psi_xml
CPAN Bio::Graph::IO::psi_xml
metaCPAN Bio::Graph::IO::psi_xml


Here's my version:

{{#default|1|"Bio::Graph::IO::psi xml"}} {{#setvar | mod | {{#preg_replace | / / | _ | Bio::Graph::IO::psi xml }} }} {{#setvar | dir | {{#preg_replace | /.*Tools::Run::StandAloneBlast/ | bioperl-live | {{#var|mod}} }} }} {{#setvar | dir | {{#preg_replace | /.*Tools::Run::RemoteBlast/ | bioperl-live | {{#var|dir}} }} }} {{#setvar | dir | {{#preg_replace | /.*Tools::Run.*/ | bioperl-run | {{#var|dir}} }} }} {{#setvar | dir | {{#preg_replace | /^Bio::.+/ | bioperl-live | {{#var|dir}} }} }} {{#setvar | url | {{#preg_replace | /::/ | / | {{#var|mod}} }}.html }} BEFORE

  • _1_ = Bio::Graph::IO::psi xml
  • mod = {{#var|mod}}
  • dir = {{#var|dir}}
  • url = {{#var|url}}



AFTER

  • _1_ = Bio::Graph::IO::psi xml
  • mod = {{#var|mod}}
  • dir = {{#var|dir}}
  • url = {{#var|url}}


The problem still occurs on this page Bio::Graph::IO::psi_xml - I guess the underscore means space in Wiki article names, but not in a macro paramter?

--Tseemann 18:56, 31 December 2005 (EST)

So this looks to be resolved now. In the future {{PAGENAMEE}} apparently gives you back the pagename with underscores. See PAGENAME and PAGENAMEE and Spaces vs underscores

--jason stajich 12:38, 3 January 2006 (EST)

HOWTO

Testing new HOWTO macro: SearchIO HOWTO (should link to HOWTO:SearchIO ...)

--Tseemann 16:06, 29 December 2005 (EST)

Bio::Tools::Run::PiseApplication


RSS Feed testing

Short on:

full is not working

Call for Organization Admins for OBF?s 2014 Google Summer of Code participation

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14. OBF participated on behalf of … Continue reading

BioPerl release 1.6.923
BioPerl v.1.6.910 released
Travis-CI for Testing

BioRuby, Biopython and BioPerl are now using Travis-CI.org, a hosted continuous integration service for the open source community, to run their unit tests automatically whenever their GitHub repositories are updated. Continue reading
BioPerl-DB, BioPerl-Run, BioPerl-Network 1.6.9 released

The latest BioPerl-DB, BioPerl-Run, and BioPerl-Network code has been released to CPAN: BioPerl-Run BioPerl-DB BioPerl-Network Please report any bugs to our Redmine server. Enjoy! chris
BioPerl 1.6.9 released
OBF and Google Summer of Code 2011

Google announced today the Open Bioinformatics Foundation (OBF) has been accepted as a mentoring organization for the 2011 Google Summer of Code! Continue reading
Introduction of OpenID logins for OBF wikis

Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new user account creation and adding OpenID logins for the OBF wikis (BioPerl example). User account creation via the old login … Continue reading

OBF Redmine server now available
BioPerl has moved to GitHub

--jason stajich 19:59, 23 April 2006 (EDT)


Dumb test

References

I like the wikipedia linking to articles within an article, but the Biblio plugin is so much cooler for not having to type in a whole reference .

  1. Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006 Oct 26;443(7114):931-49. PubMed ID:17073008 | HubMed [honeybee2006]

Transcribing/editing template tests

Your emanuensis trying out some typing-savers...

{{#if|Fred||^.||{{#error|Need a name in parm1}} }} {{#if|{{{2}}}||[[User:{{{2}}}|Fred]]||Fred }} {{#if|Banjovi||^.||{{#error|Need a name in parm1}} }} {{#if|Majensen||Banjovi||Banjovi }}

{{#parm1 @= Wittgenstein }} {{#parm2 @= Sartre }}

Parm1 is {{#var parm1}}. On the other hand, Parm2 is, in fact, {{#var parm2}}. Funny how these things work out.


How's your mom, {{#function|present||{{#not|{{#strpos|{{#1}}|{{#2}}}}}}}}{{#var|Tname|@=|}}{{#if|{{#present|{{#var|Tname}}|2}}||--[[User:Majensen|]]||--Ed.}} ?

Marxism: "Time flies like an arrow, but fruitflies like a banana." {{#function|present||{{#not|{{#strpos|{{#1}}|{{#2}}}}}}}}{{#var|Tname|@=|Groucho}}{{#if|{{#present|{{#var|Tname}}|2}}||--Groucho||--Ed.}}

{{#comment| test whether user set the "named" parameter }} {{#function|present||{{#not|{{#strpos|{{#1}}|{{#2}}}}}}}} {{#var|See|@=|{{{2}}}}} {{#var|sp|@=| }} {{#if|{{#present|{{#var|See}}|2}}||{{#var|See|@=|{{{2}}}{{#var|sp}}}}||{{#var|See|@=|^.}}}} ({{#if|{{#present|{{#var|See}}|2}}||{{#var|See}}||see{{#var|sp}} }}thread)

{{#comment| test whether user set the "named" parameter }} {{#function|present||{{#not|{{#strpos|{{#1}}|{{#2}}}}}}}} {{#var|See|@=|}} {{#var|sp|@=| }} {{#if|{{#present|{{#var|See}}|2}}||{{#var|See|@=|{{#var|sp}}}}||{{#var|See|@=|^.}}}} ({{#if|{{#present|{{#var|See}}|2}}||{{#var|See}}||see{{#var|sp}} }}thread)

{{#comment| test whether user set the "named" parameter }} {{#function|present||{{#not|{{#strpos|{{#1}}|{{#2}}}}}}}} {{#var|See|@=|for a good time, click}} {{#var|sp|@=| }} {{#if|{{#present|{{#var|See}}|2}}||{{#var|See|@=|for a good time, click{{#var|sp}}}}||{{#var|See|@=|^.}}}} ({{#if|{{#present|{{#var|See}}|2}}||{{#var|See}}||see{{#var|sp}} }}thread)


TreeAndMenu

Let's test the TreeAndMenu

  • Root1
    • Sub-item
    • Another sub-item
  • Root2
    • Sub-item
    • Another sub-item


Widgets

Create a Winter add-in that works like the gravatar add-in:

<winterPreWiki> {{#ohloh|maj|Tiny}} </winterPreWiki>

No biscuit:

{{#ohloh|maj?ruin=true|Tiny}}

No biscuit either:

{{#ohloh|maj|Furshlugginer}}



{{#comment|Don't really need a widget to make the widget, do I?}} {{#comment|arg1 is the user name, arg2 is the widget type}} account_Tiny.gif

{{#function|isit||{{#if|{{#op|{{#str_replace|{{#1}}|zzyxx|{{#2}}}}|==|zzyxx}}||1||0}}}} {{#if|{{#op|{{#op|{{#isit|Tiny|Happy}}|or|{{#isit|Detailed|Happy}}}}|or|{{#isit|Rank|Happy}}}}||Yes||NO}}

{{#function|isit||{{#if|{{#op|{{#str_replace|{{#1}}|zzyxx|{{#2}}}}|==|zzyxx}}||1||0}}}} {{#if|{{#op|{{#op|{{#isit|Tiny|Tiny}}|or|{{#isit|Detailed|Tiny}}}}|or|{{#isit|Rank|Tiny}}}}||Yes||NO}}

{{#function|isit||{{#if|{{#op|{{#str_replace|{{#1}}|zzyxx|{{#2}}}}|==|zzyxx}}||1||0}}}} {{#if|{{#op|{{#op|{{#isit|Tiny|Detailed}}|or|{{#isit|Detailed|Detailed}}}}|or|{{#isit|Rank|Detailed}}}}||Yes||NO}}

{{#function|isit||{{#if|{{#op|{{#str_replace|{{#1}}|zzyxx|{{#2}}}}|==|zzyxx}}||1||0}}}} {{#if|{{#op|{{#op|{{#isit|Tiny|Rank}}|or|{{#isit|Detailed|Rank}}}}|or|{{#isit|Rank|Rank}}}}||Yes||NO}}

{{#function|isit||{{#if|{{#op|{{#str_replace|{{#1}}|zzyxx|{{#2}}}}|==|zzyxx}}||1||0}}}} {{#if|{{#op|{{#op|{{#isit|Tiny|Glorf}}|or|{{#isit|Detailed|Glorf}}}}|or|{{#isit|Rank|Glorf}}}}||Yes||NO}}


can we render the external stuff as-is?? sometimes... set

$wgAllowExternalImagesFrom = array( 'http://www.ohloh.net/' );

then this should work

https://www.ohloh.net/accounts/40601?ref=Tiny

but it doesn't, because this does point directly to a file with an img extension, probably.

or maybe

[1]

No. Hmm.

Firebug to the rescue!! Try....

account_detailed.gif

https://www.ohloh.net/accounts/maj/widgets/account_detailed.gif

YES! Now to create the php widget, so that Ohloh is duly linked back to.


try the custom ohloh gadget

UNIQ30c149a85e483f8d-widget-00000005-QINU

Ok, a wiki render timing issue. The placement of the widget-generated text comes after point at which figure urls are parsed and rendered. What happens if we template it?

{{Cruft:Ohloh|maj|Tiny}}

Forget about the WikiWidget; just template it:

{{Cruft:OhlohWidget|maj|Tiny}}

OOOOH! That works!


bad widget, no biscuit:

UNIQ30c149a85e483f8d-widget-00000008-QINU

bad widget, down boy!:

UNIQ30c149a85e483f8d-widget-00000009-QINU



try:

UNIQ30c149a85e483f8d-widget-0000000A-QINU

... Yes we can -- but how safe??? try the ohloh gadget:

UNIQ30c149a85e483f8d-widget-0000000B-QINU

works but Google cruft everywhere.

Gravatars

should see one here:

a95faf027ae8ac4d34e3e94847b374fa.jpg

Sweet. Now...what about the new Winter function?...

{{#gravatar|maj@fortinbras.us}}

Again, a timing problem.

<winterPreWiki> {{#gravatar|maj -at- fortinbras -dot- us}} </winterPreWiki>

{{#gravatar|maj-at-fortinbras-dot-us}} {{#gravatar|maj at fortinbras dot us}}

<winterPreWiki> {{#gravatar|maj -at- fortinbras -dot- us}} </winterPreWiki>

Templating just won't get the url to the page on time. Have to resort to Winter itself.

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