From 1d017ffd1c71937ff3fd7978407e83119da9a68f Mon Sep 17 00:00:00 2001
From: Dave Bouvier <dave@bx.psu.edu>
Date: Wed, 8 Aug 2012 10:37:27 -0400
Subject: [PATCH] Improved generation and display of local genome/indexes
 table. Handle missing tool data table entries.

---
 lib/galaxy/web/controllers/data_admin.py      | 42 ++++++++++---------
 .../{betajob.mako => generic_error.mako}      |  2 +-
 templates/admin/data_admin/local_data.mako    | 33 +++++++++------
 3 files changed, 45 insertions(+), 32 deletions(-)
 rename templates/admin/data_admin/{betajob.mako => generic_error.mako} (87%)

diff --git a/lib/galaxy/web/controllers/data_admin.py b/lib/galaxy/web/controllers/data_admin.py
index 5e37efd5736..83f29e01ff2 100644
--- a/lib/galaxy/web/controllers/data_admin.py
+++ b/lib/galaxy/web/controllers/data_admin.py
@@ -30,25 +30,28 @@ class DataAdmin( BaseUIController ):
     @web.expose
     @web.require_admin
     def manage_data( self, trans, **kwd ):
-        genomes = dict()
         if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False:
-            return trans.fill_template( '/admin/data_admin/betajob.mako' )
-        for line in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data:
-            defstate = dict( state='Generate', style=self.jobstyles[ 'new' ] )
-            indexers = dict( bowtie_indexes=defstate, bowtie2_indexes=defstate, bwa_indexes=defstate, perm_base_indexes=defstate, srma_indexes=defstate, sam_fa_indexes=defstate )
-            dbkey = line[0]
-            name = line[2]
-            indexers[ 'name' ] = name
-            indexers[ 'fapath' ] = line[3]
-            genomes[ dbkey ] = indexers
-        for table in [ 'bowtie_indexes', 'bowtie2_indexes', 'bwa_indexes', 'srma_indexes' ]:
-            for line in trans.app.tool_data_tables.data_tables[ table ].data:
-                dbkey = line[0]
-                genomes[ dbkey ][ table ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
-        for line in trans.app.tool_data_tables.data_tables[ 'sam_fa_indexes' ].data:
-            genomes[ line[1] ][ 'sam_fa_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
-        for line in trans.app.tool_data_tables.data_tables[ 'perm_base_indexes' ].data:
-            genomes[ line[1].split(':')[0] ][ 'perm_base_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] )
+            return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' )
+        if 'all_fasta' not in trans.app.tool_data_tables.data_tables:
+            return trans.fill_template( '/admin/data_admin/generic_error.mako', message='The local data manager requires that an all_fasta entry exists in your tool_data_table_conf.xml.' )
+        indextable = {}
+        dbkeys = []
+        labels = { 'bowtie_indexes': 'Bowtie', 'bowtie2_indexes': 'Bowtie 2', 'bwa_indexes': 'BWA', 'srma_indexes': 'Picard', 'sam_fa_indexes': 'SAM', 'perm_base_indexes': 'PerM' }
+        tablenames = { 'Bowtie': 'bowtie_indexes', 'Bowtie 2': 'bowtie2_indexes', 'BWA': 'bwa_indexes', 'Picard': 'srma_indexes', 'SAM': 'sam_fa_indexes', 'PerM': 'perm_base_indexes' }
+        indexfuncs = dict( bowtie_indexes='bowtie', bowtie2_indexes='bowtie2', bwa_indexes='bwa', srma_indexes='picard', sam_fa_indexes='sam', perm_base_indexes='perm' )
+        for genome in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data:
+            dbkey = genome[0]
+            dbkeys.append( dbkey )
+            indextable[ dbkey ] = dict( indexes=dict(), name=genome[2], path=genome[3] )
+        for genome in indextable:
+            for label in labels:
+                indextable[ genome ][ 'indexes' ][ label ] = 'Generate'
+                if label not in trans.app.tool_data_tables.data_tables:
+                    indextable[ genome ][ 'indexes' ][ label ] = 'Disabled'
+                else:
+                    for row in trans.app.tool_data_tables.data_tables[ label ].data:
+                        if genome in row or row[0].startswith( genome ):
+                            indextable[ genome ][ 'indexes' ][ label ] = 'Generated'
         jobgrid = []
         sa_session = trans.app.model.context.current
         jobs = sa_session.query( model.GenomeIndexToolData ).order_by( model.GenomeIndexToolData.created_time.desc() ).filter_by( user_id=trans.get_user().id ).group_by( model.GenomeIndexToolData.deferred ).limit( 20 ).all()
@@ -65,7 +68,8 @@ class DataAdmin( BaseUIController ):
                 jobtype = 'index'
             indexers = ', '.join( params['indexes'] )
             jobgrid.append( dict( jobtype=jobtype, indexers=indexers, rowclass=state, deferred=job.deferred.id, state=state, intname=job.deferred.params[ 'intname' ], dbkey=job.deferred.params[ 'dbkey' ] ) )
-        return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, genomes=genomes )
+        styles = dict( Generate=self.jobstyles['new'], Generated=self.jobstyles['ok'], Disabled=self.jobstyles['error'] )
+        return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, indextable=indextable, labels=labels, dbkeys=dbkeys, styles=styles, indexfuncs=indexfuncs )
     
     @web.expose
     @web.require_admin
diff --git a/templates/admin/data_admin/betajob.mako b/templates/admin/data_admin/generic_error.mako
similarity index 87%
rename from templates/admin/data_admin/betajob.mako
rename to templates/admin/data_admin/generic_error.mako
index 04524d8e965..2c70ed051df 100644
--- a/templates/admin/data_admin/betajob.mako
+++ b/templates/admin/data_admin/generic_error.mako
@@ -32,4 +32,4 @@
 ##
 ## Override methods from base.mako and base_panels.mako
 ##
-<p class="panel-error-message">This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.</p>
\ No newline at end of file
+<p class="panel-error-message">${message}</p>
\ No newline at end of file
diff --git a/templates/admin/data_admin/local_data.mako b/templates/admin/data_admin/local_data.mako
index e46483fc874..84f0f9e650c 100644
--- a/templates/admin/data_admin/local_data.mako
+++ b/templates/admin/data_admin/local_data.mako
@@ -44,6 +44,7 @@
     td, th { padding-left: 10px; padding-right: 10px; }
     td.state-color-new { text-decoration: underline; }
     td.panel-done-message { background-image: none; padding: 0px 10px 0px 10px; }
+    td.panel-error-message { background-image: none; padding: 0px 10px 0px 10px; }
 </style>
 <div class="toolForm">
     %if message:
@@ -52,19 +53,23 @@
     <div class="toolFormTitle">Currently tracked builds <a class="action-button" href="${h.url_for( controller='data_admin', action='add_genome' )}">Add new</a></div>
     <div class="toolFormBody">
         <h2>Locally cached data:</h2>
-        <h3>NOTE: Indexers queued here will not be reflected in the table until Galaxy is restarted.</h3>
+        <h3>NOTE: Indexes generated here will not be reflected in the table until Galaxy is restarted.</h3>
         <table id="locfiles">
-            <tr><th>Database ID</th><th>Name</th><th>Bowtie</th><th>Bowtie 2</th><th>BWA</th><th>Sam</th><th>Picard</th><th>PerM</th></tr>
-            %for dbkey in sorted(genomes.keys()):
+            <tr>
+                <th>DB Key</th>
+                <th>Name</th>
+                %for label in labels:
+                    <th>${labels[label]}</th>
+                %endfor
+            </tr>
+            %for dbkey in sorted(dbkeys):
                 <tr>
                     <td>${dbkey}</td>
-                    <td>${genomes[dbkey]['name']}</td>
-                    <td id="${dbkey}-bowtie" class="indexcell ${genomes[dbkey]['bowtie_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie_indexes']['state']}</td>
-                    <td id="${dbkey}-bowtie2" class="indexcell ${genomes[dbkey]['bowtie2_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie2" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie2_indexes']['state']}</td>
-                    <td id="${dbkey}-bwa" class="indexcell ${genomes[dbkey]['bwa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bwa" data-dbkey="${dbkey}">${genomes[dbkey]['bwa_indexes']['state']}</td>
-                    <td id="${dbkey}-sam" class="indexcell ${genomes[dbkey]['sam_fa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="sam" data-dbkey="${dbkey}">${genomes[dbkey]['sam_fa_indexes']['state']}</td>
-                    <td id="${dbkey}-picard" class="indexcell ${genomes[dbkey]['srma_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="picard" data-dbkey="${dbkey}">${genomes[dbkey]['srma_indexes']['state']}</td>
-                    <td id="${dbkey}-perm" class="indexcell ${genomes[dbkey]['perm_base_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="perm" data-dbkey="${dbkey}">${genomes[dbkey]['perm_base_indexes']['state']}</td>
+                    <td>${indextable[dbkey]['name']}</td>
+                    %for label in labels:
+                        <td id="${dbkey}-${indexfuncs[label]}" class="indexcell ${styles[indextable[dbkey]['indexes'][label]]}" data-fapath="${indextable[dbkey]['path']}" data-longname="${indextable[dbkey]['name']}" data-index="${indexfuncs[label]}" data-dbkey="${dbkey}">${indextable[dbkey]['indexes'][label]}</td>
+                    %endfor
+
                 </tr>
             %endfor
         </table>
@@ -124,6 +129,7 @@
             jsondata["name"] = $('#job-' + jobid).attr('data-name');
             jsondata["dbkey"] = $('#job-' + jobid).attr('data-dbkey');
             jsondata["indexes"] = $('#job-' + jobid).attr('data-indexes');
+            tdid = jq(jsondata["dbkey"] + '-' + jsondata["indexes"]);
             newhtml = makeNewHTML(jsondata);
             $('#job-' + jobid).replaceWith(newhtml);
             if ($.inArray(jsondata["status"], finalstates) == -1) {
@@ -133,7 +139,7 @@
                 });
             }
             if (jsondata["status"] == 'done' || jsondata["status"] == 'ok') {
-                elem = $('#' + jsondata["dbkey"] + '-' + jsondata["indexes"]);
+                elem = $(tdid);
                 elem.html('Generated');
                 elem.attr('class', 'indexcell panel-done-message');
             }
@@ -156,5 +162,8 @@
             }
         });
     });
-
+    
+    function jq(id) { 
+        return '#' + id.replace(/(:|\.)/g,'\\$1');
+    }
 </script>
\ No newline at end of file