Changeset 1630:311ee61dc989

Timestamp:

11/13/08 14:56:33 (2 months ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

Message:

Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports.

Files:

• lib/galaxy/tools/__init__.py (modified) (1 diff)
• lib/galaxy/util/__init__.py (modified) (1 diff)
• lib/galaxy/webapps/reports/controllers/jobs.py (modified) (3 diffs)
• lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako (modified) (2 diffs)
• lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako (modified) (2 diffs)
• lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako (modified) (2 diffs)
• tools/data_source/ucsc_tablebrowser.xml (modified) (1 diff)
• tools/data_source/ucsc_tablebrowser_archaea.xml (modified) (1 diff)
• tools/data_source/ucsc_tablebrowser_test.xml (modified) (1 diff)

lib/galaxy/tools/__init__.py

@@ -243 +243 @@
-                    trans_list.append( req_param.get( "galaxy_name" ) )
-                    trans_list.append( req_param.get( "missing" ) )
+                    if req_param.get( "galaxy_name" ) == "data_type":
+                        # The req_param tag for data_type is special in that it can contain another tag set like
+                        # <data_type_translation>
+                        #    <format galaxy_format="tabular" remote_format="selectedFields" />
+                        # </data_type_translation>
+                        format_trans = req_param.find( "data_type_translation" )
+                        if format_trans is not None:
+                            format_trans_dict = {}
+                            for format in format_trans.findall( "format" ):
+                                remote_format = format.get( "remote_format" )
+                                galaxy_format = format.get( "galaxy_format" )                        
+                                format_trans_dict[ remote_format ] = galaxy_format
+                            trans_list.append( format_trans_dict )
-                    self.param_trans_dict[ remote_name ] = trans_list
-        # Command line (template). Optional for tools that do not invoke a local program  

lib/galaxy/util/__init__.py

@@ -156 +156 @@
-                    if key in tool.param_trans_dict:
-                        new_key = tool.param_trans_dict[ key ][0]
-
+
+
+
+
+
+
+
+
+
+
+
-                            new_value = tool.param_trans_dict[ key ][1]
-                if key not in self.NEVER_SANITIZE and sanitize:

lib/galaxy/webapps/reports/controllers/jobs.py

@@ -92 +92 @@
-        q = sa.select( ( sa.func.date( galaxy.model.Job.table.c.create_time ).label( 'date' ),
-                         sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ),
-
-
+
-                                              galaxy.model.Job.table.c.create_time >= start_date, 
-                                              galaxy.model.Job.table.c.create_time < end_date ),
@@ -135 +134 @@
-                         ( galaxy.model.User.table.c.email ).label( 'user_email' ),
-                         galaxy.model.GalaxySession.table.c.remote_addr ),
-
-
+
-                                              galaxy.model.Job.table.c.create_time >= start_date, 
-                                              galaxy.model.Job.table.c.create_time < end_date ),
@@ -306 +304 @@
-        q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ).label( 'date' ),
-                         sa.func.count( galaxy.model.Job.table.c.id ).label( 'total_jobs' ) ),
-
-
+
-                       from_obj = [ galaxy.model.Job.table ],
-                       group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ) ],

lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako

@@ -3 +3 @@
-<%def name="main_body()">
-  <div class="reportBody">
- ( includes jobs deleted before finishing )
+
-    <h4 align="center">Click Month to view the number of jobs in error for each day of that month</h4>
-    %if msg:
@@ -12 +12 @@
-    <table align="center" width="60%" class="colored">
-      %if len( jobs ) == 0:
-deleted or 
+
-      %else:
-        <tr class="header">

lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako

@@ -11 +11 @@
-    <table align="center" width="60%" class="colored">
-      %if len( jobs ) == 0:
-deleted or 
+
-      %else:
-        %for job in jobs:
@@ -18 +18 @@
-            if state == 'error':
-              rowdef = '<tr class="headererror">'
-            elif state == 'deleted':
-              rowdef = '<tr class="headerdeleted">'
-            else:
-              rowdef = '<tr class="headerunknown">'

lib/galaxy/webapps/reports/templates/jobs_specified_month_in_error.mako

@@ -3 +3 @@
-<%def name="main_body()">
-  <div class="reportBody">
- ( includes jobs deleted before finishing )
+
-    <h4 align="center">Click Jobs in Error to view jobs in error for that day</h4>
-    %if msg:
@@ -12 +12 @@
-    <table align="center" width="60%" class="colored">
-      %if len( jobs ) == 0:
-error
+the error state
-      %else:
-        <tr class="header">

tools/data_source/ucsc_tablebrowser.xml

@@ -22 +22 @@
-            <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" />
-            <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
-
+
+
+
+
+
-        </request_param_translation>
-        <uihints minwidth="800"/>

tools/data_source/ucsc_tablebrowser_archaea.xml

@@ -22 +22 @@
-        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
-        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-
+
+
+
+
+
-    </request_param_translation>
-        <uihints minwidth="800"/>

tools/data_source/ucsc_tablebrowser_test.xml

@@ -22 +22 @@
-        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
-        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-
+
+
+
+
+
-    </request_param_translation>
-        <uihints minwidth="800"/>