lexer is super picky and doesn't highlight code with bad syntax so I …

…just set all of them to guess
intermine · Jul 31, 2019 · ee7bb02 · ee7bb02
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diff --git a/docs/data-model/data-labels.rst b/docs/data-model/data-labels.rst
@@ -86,7 +86,7 @@ Using these labels in your webapp
 A new tag library is available to help with labelling. Add the following to the top
 of any jsp you write that you want to use labels in:
 
-.. code-block:: html
+.. code-block:: guess
 
   <%@ taglib uri="/WEB-INF/functions.tld" prefix="imf" %>
 

diff --git a/docs/database/data-integrity-checks/acceptance-tests.rst b/docs/database/data-integrity-checks/acceptance-tests.rst
@@ -18,7 +18,7 @@ Types of tests
 
 You can assert that a query returns true:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	assert {
    		sql: select count(*) >= 400000 from goannotation
@@ -27,7 +27,7 @@ You can assert that a query returns true:
 
 Or doesn't have any results:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	no-results {
    		sql: select * from datasource where url is null or name is null or description is null
@@ -36,7 +36,7 @@ Or doesn't have any results:
 
 Or has at least some results:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	some-results {
    		sql: select * from organism where name = 'Anopheles gambiae'

diff --git a/docs/database/data-sources/library/proteins/uniprot.rst b/docs/database/data-sources/library/proteins/uniprot.rst
@@ -14,7 +14,7 @@ This source loads data from the UniProt website here: ftp://ftp.uniprot.org/pub/
 
 The UniProt source expects the data files to be in a special format:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	TAXONID_uniprot_sprot.xml
 	TAXONID_uniprot_trembl.xml

diff --git a/docs/database/database-building/model-merging.rst b/docs/database/database-building/model-merging.rst
@@ -12,7 +12,7 @@ An InterMine datamine is built from sources. Each source can contribute to the d
 
 Other additions files (ie. not from sources) can be explicitly merged by setting the `extra.model.paths.start` and `extra.model.paths.end` properties in the `project.properties` of your `dbmodel` directory.  An example from FlyMine's `build.gradle` is:
 
-.. code-block:: properties
+.. code-block:: groovy
 
   mineDBModelConfig {
     modelName = "genomic"

diff --git a/docs/database/performance/data-loading.rst b/docs/database/performance/data-loading.rst
@@ -110,7 +110,7 @@ In objectstore/test run ‘ant test-performance’  (requires unittest database,
 
 Build server with SATA drives:
 
-.. code-block:: properties
+::
 
 	test-performance:
 	[run-performance-test] Starting performance test...
@@ -129,7 +129,7 @@ Build server with SATA drives:
 
 Workstation with SSDs:
 
-.. code-block:: properties
+::
 
 		[run-performance-test] Starting performance test...
 	[run-performance-test] Stored 10000 employee objects, took: 8303ms

diff --git a/docs/embedding/apps-c/publication-search.rst b/docs/embedding/apps-c/publication-search.rst
@@ -363,7 +363,7 @@ Layout
 
 Let us take a look at the layout template then; in `/src/templates/layout.mustache`:
 
-.. code-block:: mustache
+.. code-block:: guess
 
     <div class="row collapse">
         <div class="small-2 columns">
@@ -439,7 +439,7 @@ Search template
 
 The search template just outputs the current value of the query:
 
-.. code-block:: mustache
+.. code-block:: guess
 
     <input type="text" placeholder="e.g. brca, gamma" value="{{ query.value }}" autofocus>
 
@@ -649,7 +649,7 @@ Alert template
 
 Each component needs a template. the alert one will look like this:
 
-.. code-block:: mustache
+.. code-block:: guess
 
     <div class="alert-box {{ type }}">
         {{{ text }}}.
@@ -682,7 +682,7 @@ Results table template
 
 As for the template that displays the results; in `/src/templates/table.mustache`:
 
-.. code-block:: mustache
+.. code-block:: guess
 
     {{ #if pubs.length }}
     <table>
@@ -729,7 +729,7 @@ Style
 
 We are going to wrap up by writing a stylesheet. For this we are going to use Stylus_; in `/src/styles/app.styl`:
 
-.. code-block:: stylus
+.. code-block:: guess
 
     @import 'nib'
 

diff --git a/docs/intermine/intermine.rst b/docs/intermine/intermine.rst
@@ -8,7 +8,7 @@ To put these on your classpath, add the correct dependencies, e.g.
 Maven
 ------
 
-.. code-block:: maven
+.. code-block:: guess
 
     <dependency>
         <groupId>org.intermine</groupId>
@@ -20,7 +20,7 @@ Maven
 Gradle
 -------
 
-.. code-block:: gradle
+.. code-block:: guess
 
     compile 'org.intermine:intermine-api:4.0.1'
 

diff --git a/docs/intermine/upgrade.rst b/docs/intermine/upgrade.rst
@@ -97,7 +97,7 @@ To Upgrade
 
 1. Change your mine's `gradle.properties` file to `3.0.+`. If you have data sources, change the version they use too.
 
- .. code-block:: javascript
+ .. code-block:: properties
 
 	# example -- flymine's gradle.properties
 	systemProp.imVersion=3.0.+

diff --git a/docs/support/troubleshooting-tips.rst b/docs/support/troubleshooting-tips.rst
@@ -71,7 +71,7 @@ This means that your version of Java is too old, you need at least Java 8 to run
 can't open datasource
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. code-block:: java
+.. code-block:: guess
 
 	java.lang.RuntimeException: can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.flatmodeunittest, ...
 

diff --git a/docs/system-requirements/software/maven.rst b/docs/system-requirements/software/maven.rst
@@ -3,7 +3,7 @@ Maven
 
 InterMine uses `Maven <https://maven.apache.org/>`_ to manage local dependencies, including your mine-specific data sources.
 
-.. code-block:: base
+.. code-block:: bash
   
   # for Ubuntu
   sudo apt-get install maven

diff --git a/docs/system-requirements/software/postgres/postgres.rst b/docs/system-requirements/software/postgres/postgres.rst
@@ -145,7 +145,7 @@ Client Authentication
 
 You should also add a line to the pg_hba.conf file to allow logging in via password:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	host    all         all         0.0.0.0/0             password
 
@@ -180,7 +180,7 @@ You should also add a line to the pg_hba.conf file to allow logging in via passw
 
 
 .. [#screenshot]
-.. code-block:: sql
+.. code-block:: guess
 
    postgres=# update pg_database set datallowconn = TRUE where datname = 'template0';
    UPDATE 1

diff --git a/docs/system-requirements/software/tomcat.rst b/docs/system-requirements/software/tomcat.rst
@@ -59,7 +59,7 @@ Server XML
 
 You also need to check in your `server.xml` file that the correct `UTF-8` encoding has been applied to all connectors in use (see  `CharacterEncoding <http://wiki.apache.org/tomcat/FAQ/CharacterEncoding>`_). Make sure that every connector element in use reads as follows:
 
-.. code-block:: xml
+.. code-block:: guess
 
    <Connector ... URIEncoding="UTF-8"/>
          ...
@@ -119,7 +119,7 @@ Out of Memory Errors
 
 To avoid `java.lang.OutOfMemory` errors, specify the JVM heap size in `$TOMCAT_HOME/bin/tomcat.sh`. You can specify the size as part of `TOMCAT_OPTS`:
 
-.. code-block:: properties
+.. code-block:: guess
 
    '-Xmx256m -Xms128m'
 

diff --git a/docs/webapp/help/index.rst b/docs/webapp/help/index.rst
@@ -35,7 +35,7 @@ Take a tour link
 
 The tour link is set in `headMenu.jsp` as:
 
-.. code-block:: properties
+.. code-block:: guess
 
 	<project.helpLocation>/tour/start
 

diff --git a/docs/webapp/properties/web-properties.rst b/docs/webapp/properties/web-properties.rst
@@ -109,7 +109,7 @@ You can add links to other websites by adding entries to the `web.properties` fi
 
 The format for this property is:
 
-.. code-block:: properties
+.. code-block:: guess
 
     # on the report page - a single identifier
     'attributelink' + unique_name + class + taxonId + attributeName + (url|imageName|text)
@@ -171,7 +171,7 @@ You can configure the URLs for querying CrossReference from external sources by
 
 The format for this property is:
 
-.. code-block:: properties
+.. code-block:: guess
 
     # on the report page
     'xreflink' + dataSource_name + (url|imageName)
@@ -270,7 +270,7 @@ define the client-id and client-secret you registered your application with, eg:
 
 .. code-block:: properties
 
-     ~/.intermine/MINE.properties
+    # ~/.intermine/MINE.properties
     oauth2.GITHUB.client-id = $GH-CLIENT-ID
     oauth2.GITHUB.client-secret = $GH-CLIENT-SECRET
 

diff --git a/docs/webapp/properties/webconfig-model.rst b/docs/webapp/properties/webconfig-model.rst
@@ -28,7 +28,7 @@ openByDefault           if sectionOnRight="true", whether or not this section sh
 
 For example:
 
-.. code-block:: xml
+.. code-block:: guess
 
 	  <class className="org.flymine.model.genomic.Protein">
  	    <fields>

diff --git a/docs/webapp/report-page/webapp-tables.rst b/docs/webapp/report-page/webapp-tables.rst
@@ -158,7 +158,7 @@ Collection Table (Vertical Column Border)
 
 .. image:: img/column-border.png
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-table column-border">
         <-- ... -->
@@ -182,7 +182,7 @@ Collection Table (Vertical Column Border by 2)
 
 .. image:: img/column-border-by-2.png
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-table column-border-by-2">
         <-- ... -->
@@ -238,7 +238,7 @@ CSS                                           Description
 Collection Table (Persistent Table Headers)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-table persistent">
         <-- ... -->
@@ -278,7 +278,7 @@ Collection of Collection Tables
 
 .. image:: img/collection-of-collections.png
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-of-collections">
         <div class="header">
@@ -309,7 +309,7 @@ Table Togglers (Less, More, Expand, Collapse, Show in table)
 
 .. image:: img/togglers.png
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-table">
         <-- ... -->
@@ -385,7 +385,7 @@ Table Warning
 
 .. image:: img/table-warning.png
 
-.. code-block:: html
+.. code-block:: guess
 
     <div class="collection-table warning">
         <-- ... -->

diff --git a/docs/webapp/third-party-tools/jbrowse.rst b/docs/webapp/third-party-tools/jbrowse.rst
@@ -61,7 +61,7 @@ Point JBrowse at your InterMine
 
 Add your new mine-based dataset to your configuration file. For example to add *D. melanogaster* data from FlyMine_ as a JBrowse dataset, the following configuration in `jbrowse_conf.json` would suffice:
 
-.. code-block:: json
+.. code-block:: guess
    
   { 
     "datasets": {