merge

lib/galaxy/web/controllers/genetrack.py

@@ -167,7 +167,10 @@ class WebRoot(BaseController):
         param = atlas.Param( word=word )
         
         # search for a given 
-        session = sql.get_session( conf.SQL_URI )
+        try:
+            session = sql.get_session( conf.SQL_URI )
+        except:
+            return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
 
         if param.word:
             def search_query( word, text ):
@@ -208,7 +211,11 @@ class WebRoot(BaseController):
             FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
             PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
             )
-        session = sql.get_session( conf.SQL_URI )
+
+        try:
+            session = sql.get_session( conf.SQL_URI )
+        except:
+            return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
 
         if os.path.exists( conf.HDF_DATABASE ):
             db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )

tools/visualization/genetrack.xml

@@ -3,8 +3,8 @@
     <description>Track creator/viewer</description>
 	
 	<code file="genetrack_code.py">
-      <hook exec_after_process="exec_after_process" />
-	</code>
+         <hook exec_after_process="exec_after_process" />
+       </code>
   	
     <command interpreter="python">
         genetrack.py -l $data_label
@@ -24,14 +24,14 @@
     
     <inputs>
     	  <param name="data_label" type="text" label="Track Label" size="50">
-	        <validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
+	        <validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
     	  </param>
-		  <param name="fit_data" type="data" format="coverage" label="Coverage Dataset" optional="true" />
+          <param name="fit_data" type="data" format="coverage" label="Coverage Dataset (optional)" optional="true" />
     	  <repeat name="feature_data" title="Features">
     	  	<param name="input" type="data" format="interval" label="Dataset" />
     	  	<param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25">
-	        	<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
-			</param>
+	        	<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator>
+		</param>
     	  </repeat>
    </inputs>
 
@@ -47,16 +47,27 @@
      <requirement type="python-module">numpy</requirement>
    </requirements>
  <help>
-This tool takes the input Fit Data and creates a peak and curve plot showing 
-the reads and fitness on each basepair.  Features can be plotted below as tracks.
+This tool takes the input Fit Data and creates a peak and curve plot
+showing the reads and fitness on each basepair.  Features can be
+plotted below as tracks.  Fit data is coverage output from tools like
+the Lastz tool.  Features are simply interval datasets that may be
+plotted as tracks below the optional fit data.  Both the fit data and
+feature datasets are optional, but at least one of either is required
+to generate a track.
 
 -----
 
 **Syntax**
 
 - **Track Label** is the name of the generated track.
-- **Fit Data** are the datasets to calculate coverage/reads across basepairs and generate a curve.
-- **Features** are additional datasets (interval format) to be plotted below as tracks.
+
+- **Fit Data** is the dataset to calculate coverage/reads across
+    basepairs and generate a curve.  This is optional, and tracks may
+    be created simply showing features.
+
+- **Features** are datasets (interval format) to be plotted as tracks.
+    These are also optional, but at least 1 feature track or 1 fit
+    data is required to generate a track.
 
 </help>
 </tool>

tools/visualization/genetrack_code.py

@@ -10,4 +10,3 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
     out_data['genetrack'].metadata.label = param_dict['data_label']
     out_data['genetrack'].info = "Use the link below to view the custom track."
     out_data['bed_out'].info = ""
-