put the volvox bigwig test track configuration snippet in a separate …

…file and integrate it with the selenium tests and setup.sh example data using add-track-json.pl
GMOD · Aug 3, 2012 · 47d5b21 · 47d5b21
1 parent 10e2140
commit 47d5b21
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Showing 3 changed files with 10 additions and 13 deletions.
diff --git a/docs/tutorial/data_files/volvox_microarray.bw.conf b/docs/tutorial/data_files/volvox_microarray.bw.conf
@@ -0,0 +1,8 @@
+#configuration snippet for the volvox bigwig test track
+{
+    "label": "volvox_microarray.bw",
+    "key": "volvox_microarray.bw",
+    "urlTemplate": "../../raw/volvox/volvox_microarray.bw",
+    "type":       "JBrowse/View/Track/Wiggle",
+    "storeClass": "JBrowse/Store/BigWig"
+}
diff --git a/setup.sh b/setup.sh
@@ -30,9 +30,9 @@ echo -n "Formatting Volvox example data ...";
     rm -rf sample_data/json/volvox;
     bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox;
     bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox;
+    bin/add-track-json.pl sample_data/raw/volvox/volvox_microarray.bw.conf sample_data/json/volvox/trackList.json
     bin/generate-names.pl -v --out sample_data/json/volvox;
 
-
     # also recreate some symlinks used by tests and such
     if [ -d sample_data/json/modencode ]; then
         mkdir -p sample_data/json/modencode/tracks;

diff --git a/tests/selenium_tests/volvox_biodb_test.py b/tests/selenium_tests/volvox_biodb_test.py
@@ -14,18 +14,7 @@ def setUp( self ):
         call( "bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox/", shell=True )
         call( "bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox/", shell=True )
         call( "bin/wig-to-json.pl --out sample_data/json/volvox/ --wig docs/tutorial/data_files/volvox_microarray.wig", shell=True )
-
-        # add a definition for the volvox bigwig test track
-        addtrack = subprocess.Popen( ["bin/add-track-json.pl","sample_data/json/volvox/trackList.json"], stdin=PIPE );
-        addtrack.stdin.write("""{
-         "label": "volvox_microarray.bw",
-         "key": "volvox_microarray.bw",
-         "urlTemplate": "../../raw/volvox/volvox_microarray.bw",
-         "type":       "JBrowse/View/Track/Wiggle",
-         "storeClass": "JBrowse/Store/BigWig"
-      }""")
-        addtrack.stdin.close()
-
+        call( "bin/add-track-json.pl sample_data/raw/volvox/volvox_microarray.bw.conf sample_data/json/volvox/trackList.json", shell=True )
         call( "bin/generate-names.pl --dir sample_data/json/volvox/", shell=True )
         super( AbstractVolvoxBiodbTest, self ).setUp()