Merge pull request #42 from GMOD/automate_namefixes

Automate namefixes

wiki/2009_GMOD_Summer_School_-_Americas.md

@@ -143,9 +143,7 @@ course overview</td>
 </tr>
 <tr class="even">
 <td style="background-color: #ccffff">10:25am</td>
-<td style="text-align: center; background-color: #ddffff;"><strong><a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> and <a
+<td style="text-align: center; background-color: #ddffff;"><strong>VMware and <a
 href="BioPerl" title="BioPerl">BioPerl</a> Setup</strong><br />
 <strong>Everyone</strong><br />
 Get the GMOD Summer School <a href="#System_Requirements">VMware</a>
@@ -429,9 +427,7 @@ as homework to be done prior to the course's start.**
 |----|----|
 | <a href="http://www.vmware.com" rel="nofollow" title="VMware"><img
 src="https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/e/ec/VmwareLogoSmall.jpg" width="100"
-height="26" alt="VMware" /></a> | *Participants are required to bring their own laptops, already capable of running a <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> system image.* |
+height="26" alt="VMware" /></a> | *Participants are required to bring their own laptops, already capable of running a VMware system image.* |
 
 The course started with getting a <a
 href="ftp://ftp.gmod.org/pub/gmod/Courses/2009/SummerSchoolAmericas/GmodSumSch2009Amer1.zip"

wiki/2010_GMOD_Summer_School_-_Americas.md

@@ -145,9 +145,7 @@ course overview</td>
 </tr>
 <tr class="even">
 <td style="background-color: #ccffff">10:25am</td>
-<td style="text-align: center; background-color: #ddffff;"><strong><a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> and <a
+<td style="text-align: center; background-color: #ddffff;"><strong>VMware and <a
 href="BioPerl" title="BioPerl">BioPerl</a> Setup</strong><br />
 <strong>Everyone</strong><br />
 Get the GMOD Summer School <a href="#System_Requirements">VMware</a>
@@ -401,9 +399,7 @@ height="26" alt="VMware" /></a>
 
 
 <span style="font-size: 110%">**Participants are required to bring their
-own laptops, already capable of running a <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> system
+own laptops, already capable of running a VMware system
 image.**</span>
 
 The course starts with getting a VMware image (built specifically for

wiki/2011_GMOD_Spring_Training.md

@@ -117,11 +117,8 @@ title="Tripal Tutorial">Tripal Tutorial</a></li>
 <td>   </td>
 <td data-valign="top"><p>And these tutorials will be added:</p>
 <ul>
-<li><a
-href="http://gmod.org/mediawiki/index.php?title=InterMine_2011_Tutorial&amp;action=edit&amp;redlink=1"
-class="new"
-title="InterMine 2011 Tutorial (page does not exist)">InterMine
-Tutorial</a></li>
+<li>InterMine
+Tutorial</li>
 <li><a href="SOBA_2011_Tutorial" title="SOBA 2011 Tutorial">SOBA
 Tutorial</a></li>
 </ul></td>
@@ -278,17 +275,13 @@ height="26" alt="VMware" /></a>
 
 
 <span style="font-size: 110%">**Participants are required to bring their
-own laptops, already capable of running a virtual system (e.g. <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a>)
+own laptops, already capable of running a virtual system (e.g. VMware)
 image.**</span>
 
 The course starts with getting a virtual system image (built
 specifically for the course) up and running on your machine. We then
 build upon that image in each succeeding session. We will probably use
-<a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> for the
+VMware for the
 course:
 
 ### <span id="VMware_on_Windows_and_Linux" class="mw-headline">VMware on Windows and Linux</span>

wiki/AGS2011.md

@@ -141,15 +141,11 @@ title="AGS2011">GMOD.org/wiki/AGS2011</a>
 
 # <span id="VMware_Image" class="mw-headline">VMware Image</span>
 
-A <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> image was
+A VMware image was
 used during this workshop. That image can be <a
 href="ftp://ftp.gmod.org/pub/gmod/Meetings/2011/AGS/GMODAGS2011.tar.gz"
 class="external text" rel="nofollow">downloaded</a>, installed, and run
-locally on your system. See <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> for details.
+locally on your system. See VMware for details.
 
 # <span id="Worked_Examples" class="mw-headline">Worked Examples</span>
 
@@ -312,9 +308,7 @@ workshop).
 
 # <span id="VMware_Image_2" class="mw-headline">VMware Image</span>
 
-A <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> image will
+A VMware image will
 be made available to participants of the workshop. We will use this
 image during the workshop
 

wiki/Apollo_Tutorial.md

@@ -185,9 +185,7 @@ We'll just install everything with the default options.
 
 ### <span id="Checking_Out_the_Code_From_SVN" class="mw-headline">Checking Out the Code From SVN</span>
 
-You can also checkout the code from SourceForge <a
-href="http://gmod.org/mediawiki/index.php?title=GMOD:SVN&amp;action=edit&amp;redlink=1"
-class="new" title="GMOD:SVN (page does not exist)">SVN</a>. You'll need
+You can also checkout the code from SourceForge SVN. You'll need
 a SVN client to do so. This will guarantee that you'll get the latest
 Apollo code. Note that you'll be getting the development version and as
 such might not be fully stable. The following commands apply to Unix

wiki/Apollo_Tutorial_2010.md

@@ -95,13 +95,9 @@ title="Apollo Tutorial">Apollo Tutorial</a> page.
 
 ## <span id="VMware" class="mw-headline">VMware</span>
 
-This tutorial was taught using a <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> system image
+This tutorial was taught using a VMware system image
 as a starting point. If you want to start with the same system, download
-and install the start image (below). See <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> for what
+and install the start image (below). See VMware for what
 software you need to use a VMware system image and for directions on how
 to get the image up and running on your machine.
 
@@ -228,9 +224,7 @@ We'll just install everything with the default options.
 
 ### <span id="Checking_Out_the_Code_From_SVN" class="mw-headline">Checking Out the Code From SVN</span>
 
-You can also checkout the code from SourceForge <a
-href="http://gmod.org/mediawiki/index.php?title=GMOD:SVN&amp;action=edit&amp;redlink=1"
-class="new" title="GMOD:SVN (page does not exist)">SVN</a>. You'll need
+You can also checkout the code from SourceForge SVN. You'll need
 a SVN client to do so. This will guarantee that you'll get the latest
 Apollo code. Note that you'll be getting the development version and as
 such might not be fully stable. The following commands apply to Unix

wiki/Apollo_Tutorial_2011.md

@@ -182,9 +182,7 @@ We'll just install everything with the default options.
 
 ### <span id="Checking_Out_the_Code_From_SVN" class="mw-headline">Checking Out the Code From SVN</span>
 
-You can also checkout the code from SourceForge <a
-href="http://gmod.org/mediawiki/index.php?title=GMOD:SVN&amp;action=edit&amp;redlink=1"
-class="new" title="GMOD:SVN (page does not exist)">SVN</a>. You'll need
+You can also checkout the code from SourceForge SVN. You'll need
 a SVN client to do so. This will guarantee that you'll get the latest
 Apollo code. Note that you'll be getting the development version and as
 such might not be fully stable. The following commands apply to Unix

wiki/April_2012_GMOD_Meeting.md

@@ -202,10 +202,8 @@ site</a></td>
 <tr class="even">
 <td>9:45</td>
 <td><a href="Tripal.1" title="Tripal">Tripal</a></td>
-<td><a
-href="http://gmod.org/mediawiki/index.php?title=User%253ALaceyanne_sanderson&amp;action=edit&amp;redlink=1"
-class="new" title="User%253ALaceyanne sanderson (page does not exist)">Lacey
-Sanderson</a></td>
+<td>Lacey
+Sanderson</td>
 <td><a
 href="https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/0/09/LaceySanderson_Tripal_GMOD2012.ppt"
 class="internal" title="LaceySanderson Tripal GMOD2012.ppt">PPT</a></td>

wiki/Arthropod_Genomics_2011.1.md

@@ -104,7 +104,7 @@ please add it here.
 ## <span id="Brochure" class="mw-headline">Brochure</span>
 
 Download
-<a hrefhttps://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/f/fd/AGS2011Brochure.pdf" class="internal"
+<a href="https://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/f/fd/AGS2011Brochure.pdf" class="internal"
 title="AGS2011Brochure.pdf">conference brochure</a>.
 
 [Category](/wiki/Special%253ACategories "Special%253ACategories"):

wiki/Arthropod_Genomics_2011/Genome_Project_101_Workshop.md

@@ -139,15 +139,11 @@ title="AGS2011">GMOD.org/wiki/AGS2011</a>
 
 # <span id="VMware_Image" class="mw-headline">VMware Image</span>
 
-A <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> image was
+A VMware image was
 used during this workshop. That image can be <a
 href="ftp://ftp.gmod.org/pub/gmod/Meetings/2011/AGS/GMODAGS2011.tar.gz"
 class="external text" rel="nofollow">downloaded</a>, installed, and run
-locally on your system. See <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> for details.
+locally on your system. See VMware for details.
 
 # <span id="Worked_Examples" class="mw-headline">Worked Examples</span>
 
@@ -310,9 +306,7 @@ workshop).
 
 # <span id="VMware_Image_2" class="mw-headline">VMware Image</span>
 
-A <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> image will
+A VMware image will
 be made available to participants of the workshop. We will use this
 image during the workshop
 

wiki/BA2009.md

@@ -93,9 +93,7 @@ The worked example demonstrating how to display
 title="Next generation sequencing">next generation sequencing</a> (NGS)
 data in [GBrowse](GBrowse.1 "GBrowse") is now available as a GMOD
 [tutorial](Category%253ATutorials "Category%253ATutorials"), complete with a
-starting <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> image.
+starting VMware image.
 
 ## <span id="Agenda" class="mw-headline">Agenda</span>
 

wiki/Bio%3A%3AChado%3A%3ASchema.md

@@ -128,12 +128,8 @@ feed</span></span>
 
 |  |  |
 |----|----|
-| <a
-href="http://gmod.org/mediawiki/index.php?title=Property:Chado&amp;action=edit&amp;redlink=1"
-class="new" title="Property:Chado (page does not exist)">Chado</a> | Schema <span class="smwsearch">[+](Special%253ASearchByProperty/Chado/Schema "Special%253ASearchByProperty/Chado/Schema")</span> |
-| <a
-href="http://gmod.org/mediawiki/index.php?title=Property:Talk:Bio&amp;action=edit&amp;redlink=1"
-class="new" title="Property:Talk:Bio (page does not exist)">Talk:Bio</a> | Schema <span class="smwsearch">[+](Special%253ASearchByProperty/Talk%253ABio/Schema "Special%253ASearchByProperty/Talk%253ABio/Schema")</span> |
+| Chado | Schema <span class="smwsearch">[+](Special%253ASearchByProperty/Chado/Schema "Special%253ASearchByProperty/Chado/Schema")</span> |
+| Talk:Bio | Schema <span class="smwsearch">[+](Special%253ASearchByProperty/Talk%253ABio/Schema "Special%253ASearchByProperty/Talk%253ABio/Schema")</span> |
 
 
 

wiki/BioMart.md

@@ -63,10 +63,7 @@ rel="nofollow">LGPL</a> <span class="smwsearch">[+](Special%253ASearchByProperty
 | [Has title](Property%253AHas_title "Property:Has title") | BioMart user community <span class="smwsearch">[+](Special%253ASearchByProperty/Has-20title/BioMart-20user-20community "Special%253ASearchByProperty/Has-20title/BioMart-20user-20community")</span> |
 | [Has topic](Property%253AHas_topic "Property:Has topic") | **BioMart** <span class="smwsearch">[+](Special%253ASearchByProperty/Has-20topic/BioMart "Special%253ASearchByProperty/Has-20topic/BioMart")</span> |
 | [Interaction type](Property%253AInteraction_type "Property:Interaction type") | provides data for <span class="smwsearch">[+](Special%253ASearchByProperty/Interaction-20type/provides-20data-20for "Special%253ASearchByProperty/Interaction-20type/provides-20data-20for")</span> |
-| <a
-href="http://gmod.org/mediawiki/index.php?title=Property:Interactor&amp;action=edit&amp;redlink=1"
-class="new"
-title="Property:Interactor (page does not exist)">Interactor</a> | BioMart <span class="smwsearch">[+](Special%253ASearchByProperty/Interactor/BioMart "Special%253ASearchByProperty/Interactor/BioMart")</span> |
+| Interactor | BioMart <span class="smwsearch">[+](Special%253ASearchByProperty/Interactor/BioMart "Special%253ASearchByProperty/Interactor/BioMart")</span> |
 | [Interacts with](Property%253AInteracts_with "Property:Interacts with") | [GBrowse](GBrowse.1 "GBrowse") <span class="smwsearch">[+](Special%253ASearchByProperty/Interacts-20with/GBrowse "Special%253ASearchByProperty/Interacts-20with/GBrowse")</span> |
 | [Is open source](Property%253AIs_open_source "Property:Is open source") | Yes <span class="smwsearch">[+](Special%253ASearchByProperty/Is-20open-20source/Yes "Special%253ASearchByProperty/Is-20open-20source/Yes")</span> |
 | [Link type](Property%253ALink_type "Property:Link type") | download <span class="smwsearch">[+](Special%253ASearchByProperty/Link-20type/download "Special%253ASearchByProperty/Link-20type/download")</span>, website <span class="smwsearch">[+](Special%253ASearchByProperty/Link-20type/website "Special%253ASearchByProperty/Link-20type/website")</span> and wild URL <span class="smwsearch">[+](Special%253ASearchByProperty/Link-20type/wild-20URL "Special%253ASearchByProperty/Link-20type/wild-20URL")</span> |

wiki/Biopackages_HOWTO.md

@@ -186,10 +186,8 @@ operating system will be maintained as a clean, RPM-only environment.
 
 # <span id="Authors" class="mw-headline">Authors</span>
 
-<a
-href="http://gmod.org/mediawiki/index.php?title=User%253ABoconnor&amp;action=edit&amp;redlink=1"
-class="new" title="User%253ABoconnor (page does not exist)">Brian
-O'Connor</a>
+Brian
+O'Connor
 
 
 

wiki/Category%3AWebapollo-minutes.md

@@ -22,10 +22,7 @@
 2010-11-17
 [agenda](Web-apollo-meeting-agenda-2010-11-18 "Web-apollo-meeting-agenda-2010-11-18")
 [minutes](Web-apollo-meeting-minutes-2010-11-18 "Web-apollo-meeting-minutes-2010-11-18")  
-2010-12-02 <a
-href="http://gmod.org/mediawiki/index.php?title=Web-apollo-meeting-agenda-2010-12-02&amp;action=edit&amp;redlink=1"
-class="new"
-title="Web-apollo-meeting-agenda-2010-12-02 (page does not exist)">agenda</a>
+2010-12-02 agenda
 [minutes](Web-apollo-meeting-minutes-2010-12-02 "Web-apollo-meeting-minutes-2010-12-02")  
 
 

wiki/Chado_Django_HOWTO.md

@@ -17,9 +17,7 @@
 
 
 
---<a
-href="http://gmod.org/mediawiki/index.php?title=User%253AVdejager&amp;action=edit&amp;redlink=1"
-class="new" title="User%253AVdejager (page does not exist)">Vdejager</a>
+--Vdejager
 11:07, 1 September 2008 (UTC)
 
 

wiki/Chado_Natural_Diversity_Module/natdiv_schema_changes_call.md

@@ -77,9 +77,7 @@ module](../Chado_Natural_Diversity_Module.1 "Chado Natural Diversity Module").
     - implement after paper publishing
     - do not implement
 2.  Bio%253A%253AChado%253A%253ASchema update
-    - can someone do one after the changes have been made? <a
-      href="http://gmod.org/mediawiki/index.php?title=User%253AMaccallr&amp;action=edit&amp;redlink=1"
-      class="new" title="User%253AMaccallr (page does not exist)">Maccallr</a>
+    - can someone do one after the changes have been made? Maccallr
       14:37, 26 May 2011 (UTC)
 
 ## <span id="Proposed_changes" class="mw-headline">Proposed changes</span>
@@ -185,9 +183,7 @@ module](../Chado_Natural_Diversity_Module.1 "Chado Natural Diversity Module").
   - +1, could definitely use this for same reasons (e,g, same
     insecticide resistance assay protocol, but with different
     insecticides, exposure times, and/or concentrations; currently using
-    nd_experimentprop) <a
-    href="http://gmod.org/mediawiki/index.php?title=User%253AMaccallr&amp;action=edit&amp;redlink=1"
-    class="new" title="User%253AMaccallr (page does not exist)">Maccallr</a>
+    nd_experimentprop) Maccallr
     13:24, 30 May 2011 (UTC)
     - Can we make multiple protocols, such as NaCl 100mM, NaCl 10mM,
       etc, (or insecticide resistance assay 1, 2, etc) and link to
@@ -257,9 +253,7 @@ module](../Chado_Natural_Diversity_Module.1 "Chado Natural Diversity Module").
   - Chado has some way to
     <a href="../Chado_CV_Module#Post-coordinating_Terms"
     class="external text" rel="nofollow">post-compose cvterms</a> which
-    <a
-    href="http://gmod.org/mediawiki/index.php?title=User%253AMaccallr&amp;action=edit&amp;redlink=1"
-    class="new" title="User%253AMaccallr (page does not exist)">Maccallr</a>
+    Maccallr
     11:56, 17 May 2011 (UTC) doesn't understand.
     - It looks rather complex.
       --[Yuri](../User%253AYbendana "User%253AYbendana")

wiki/Chado_Tutorial_2010.md

@@ -236,13 +236,9 @@ about how to use a Chado database.
 
 # <span id="VMware" class="mw-headline">VMware</span>
 
-This tutorial was taught using a <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> system image
+This tutorial was taught using a VMware system image
 as a starting point. If you want to start with the same system, download
-and install the start image (below). See <a
-href="http://gmod.org/mediawiki/index.php?title=VMware&amp;action=edit&amp;redlink=1"
-class="new" title="VMware (page does not exist)">VMware</a> for what
+and install the start image (below). See VMware for what
 software you need to use a VMware system image and for directions on how
 to get the image up and running on your machine.
 

wiki/Drupal2wiki.md

@@ -17,9 +17,7 @@
 
 
 
-Perl script written by <a
-href="http://gmod.org/mediawiki/index.php?title=Eric_Just&amp;action=edit&amp;redlink=1"
-class="new" title="Eric Just (page does not exist)">Eric Just</a> to
+Perl script written by Eric Just to
 copy Drupal nodes to a MediaWiki:
 
 

wiki/GBrowse_2.0_Configuration_HOWTO.md

@@ -779,10 +779,8 @@ the user. It is a space-delimited list of plugin names. Plugins are Perl
 .pm modules that can be found in the plugins subdirectory of the
 GBrowse2 configuration directory. Select the ones you wish to activate,
 and put their in this configuration directive, minus the ".pm"
-extension. See <a
-href="http://gmod.org/mediawiki/index.php?title=GBrowse2_Plugins&amp;action=edit&amp;redlink=1"
-class="new" title="GBrowse2 Plugins (page does not exist)">GBrowse2
-Plugins</a> for a description of what each plugin does.
+extension. See GBrowse2
+Plugins for a description of what each plugin does.
 
 <!-- -->
 

wiki/GBrowse_2.0_HOWTO.md

@@ -776,10 +776,8 @@ the user. It is a space-delimited list of plugin names. Plugins are Perl
 .pm modules that can be found in the plugins subdirectory of the
 GBrowse2 configuration directory. Select the ones you wish to activate,
 and put their in this configuration directive, minus the ".pm"
-extension. See <a
-href="http://gmod.org/mediawiki/index.php?title=GBrowse2_Plugins&amp;action=edit&amp;redlink=1"
-class="new" title="GBrowse2 Plugins (page does not exist)">GBrowse2
-Plugins</a> for a description of what each plugin does.
+extension. See GBrowse2
+Plugins for a description of what each plugin does.
 
 <!-- -->
 

wiki/GBrowse_2.0_Install_HOWTO.1.md

@@ -121,9 +121,7 @@ Then proceed to install Bio::Graphics::Browser2 as described above.
 ## <span id="Installing_Manually" class="mw-headline">Installing Manually</span>
 
 Alternatively, you can download and install the bleeding edge version
-via <a
-href="http://gmod.org/mediawiki/index.php?title=GIT&amp;action=edit&amp;redlink=1"
-class="new" title="GIT (page does not exist)">GIT</a>. For a smooth
+via GIT. For a smooth
 experience, please install all [GBrowse 2.0
 Prerequisites](GBrowse_2.0_Prerequisites "GBrowse 2.0 Prerequisites")
 before proceeding.