From 3766616ba14b7c58a08da352f985fb2e97d72853 Mon Sep 17 00:00:00 2001
From: Carl Eberhard <carlfeberhard@gmail.com>
Date: Thu, 18 Jul 2013 16:24:18 -0400
Subject: [PATCH] Visualizations registry: move built-in vis config files to
 sample, copying them over on registry start; add vis xml files to .hgignore;
 fix test data in scatterplot.xml

---
 .hgignore                                     |  2 +-
 .../{circster.xml => circster.xml.sample}     |  0
 config/visualizations/example.xml.example     | 30 -------------------
 .../{phyloviz.xml => phyloviz.xml.sample}     |  0
 ...scatterplot.xml => scatterplot.xml.sample} |  1 -
 .../{sweepster.xml => sweepster.xml.sample}   |  0
 .../{trackster.xml => trackster.xml.sample}   |  0
 lib/galaxy/visualization/registry.py          | 15 ++++++++++
 8 files changed, 16 insertions(+), 32 deletions(-)
 rename config/visualizations/{circster.xml => circster.xml.sample} (100%)
 delete mode 100644 config/visualizations/example.xml.example
 rename config/visualizations/{phyloviz.xml => phyloviz.xml.sample} (100%)
 rename config/visualizations/{scatterplot.xml => scatterplot.xml.sample} (93%)
 rename config/visualizations/{sweepster.xml => sweepster.xml.sample} (100%)
 rename config/visualizations/{trackster.xml => trackster.xml.sample} (100%)

diff --git a/.hgignore b/.hgignore
index 51f7cbc6abb..ffb0c07f9c3 100644
--- a/.hgignore
+++ b/.hgignore
@@ -60,7 +60,7 @@ shed_tool_data_table_conf.xml
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
-visualizations_conf.xml
+config/visualizations/*.xml
 static/welcome.html.*
 static/welcome.html
 
diff --git a/config/visualizations/circster.xml b/config/visualizations/circster.xml.sample
similarity index 100%
rename from config/visualizations/circster.xml
rename to config/visualizations/circster.xml.sample
diff --git a/config/visualizations/example.xml.example b/config/visualizations/example.xml.example
deleted file mode 100644
index be6af87c81f..00000000000
--- a/config/visualizations/example.xml.example
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE visualization SYSTEM "visualization.dtd">
-<visualization name="test">
-    <data_sources>
-        <data_source>
-            <model_class>HistoryDatasetAssociation</model_class>
-            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
-            <to_param param_attr="id">dataset_id</to_param>
-            <to_param assign="bler">string</to_param>
-            <to_param assign="False">boolean</to_param>
-            <to_param assign="-5">integer</to_param>
-            <to_param assign="3.14">float</to_param>
-            <to_param assign="{}">json</to_param>
-        </data_source>
-    </data_sources>
-    <params>
-        <param>default</param>
-        <param type="str">string</param>
-        <param type="bool">boolean</param>
-        <param type="int">integer</param>
-        <param type="float">float</param>
-        <param type="json">json</param>
-        <param type="str" required="true">string</param>
-        <param type="visualization" var_name_in_template="visualization">visualization_id</param>
-        <param type="dataset" var_name_in_template="dataset">dataset_id</param>
-        <param type="hda_or_ldda">dataset_instance</param>
-        <param_modifier type="str" modifies="dataset_instance">hda_ldda</param_modifier>
-    </params>
-    <template>v_fwork_test.mako</template>
-</visualization>
diff --git a/config/visualizations/phyloviz.xml b/config/visualizations/phyloviz.xml.sample
similarity index 100%
rename from config/visualizations/phyloviz.xml
rename to config/visualizations/phyloviz.xml.sample
diff --git a/config/visualizations/scatterplot.xml b/config/visualizations/scatterplot.xml.sample
similarity index 93%
rename from config/visualizations/scatterplot.xml
rename to config/visualizations/scatterplot.xml.sample
index a4d1ef0e494..3ab023cb5bc 100644
--- a/config/visualizations/scatterplot.xml
+++ b/config/visualizations/scatterplot.xml.sample
@@ -10,7 +10,6 @@
     </data_sources>
     <params>
         <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
-        <param required="true">bler</param>
     </params>
     <template>scatterplot.mako</template>
 </visualization>
diff --git a/config/visualizations/sweepster.xml b/config/visualizations/sweepster.xml.sample
similarity index 100%
rename from config/visualizations/sweepster.xml
rename to config/visualizations/sweepster.xml.sample
diff --git a/config/visualizations/trackster.xml b/config/visualizations/trackster.xml.sample
similarity index 100%
rename from config/visualizations/trackster.xml
rename to config/visualizations/trackster.xml.sample
diff --git a/lib/galaxy/visualization/registry.py b/lib/galaxy/visualization/registry.py
index 98e26538437..5e0b8593f4d 100644
--- a/lib/galaxy/visualization/registry.py
+++ b/lib/galaxy/visualization/registry.py
@@ -67,6 +67,7 @@ class VisualizationsRegistry( object ):
         # load the registry from the xml files located in configuration_filepath using the given parser
         configuration_filepath = os.path.join( galaxy_root, configuration_filepath )
         self.configuration_filepath = self.check_conf_filepath( configuration_filepath )
+        self.move_sample_conf_files()
         self.load()
 
         # what to use to parse query strings into resources/vars for the template
@@ -82,6 +83,20 @@ class VisualizationsRegistry( object ):
             raise IOError( 'visualization configuration directory (%s) not found' %( configuration_filepath ) )
         return configuration_filepath
 
+    def move_sample_conf_files( self ):
+        """
+        Copies any `*.xml.sample` files in `configuration_filepath` to
+        `.xml` files of the same names if no file with that name already exists.
+
+        :returns: a list of the files moved
+        """
+        files_moved = []
+        for sample_file in glob.glob( os.path.join( self.configuration_filepath, '*.sample' ) ):
+            new_name = os.path.splitext( sample_file )[0]
+            if not os.path.exists( new_name ):
+                shutil.copy2( sample_file, new_name )
+                files_moved.append( new_name )
+
     def load( self ):
         """
         Builds the registry by parsing the xml in `self.configuration_filepath`