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.

2026-09-21 13:50:20 +08:00 · 2008-11-13 14:56:33 -05:00
parent 511510797a
commit c454370ff7
9 changed files with 47 additions and 17 deletions
@@ -242,6 +242,19 @@ class Tool:
                    remote_name = req_param.get( "remote_name" )
                    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  
        command = root.find("command")
@@ -155,7 +155,17 @@ class Params:
                if tool and tool.tool_type == 'data_source':
                    if key in tool.param_trans_dict:
                        new_key = tool.param_trans_dict[ key ][0]
-                        if not value:
+                        if new_key == 'data_type':
+                            try:
+                                # The Galaxy "data_type entry is special in that it can include the ability
+                                # to translate the format to a Galaxy supported format.  In the dict, this entry
+                                # looks something like:  {'hgta_outputType': ['data_type', 'bed', {'selectedFields': 'tabular'}] }
+                                format_trans_dict = tool.param_trans_dict[ key ][2]
+                                if value in format_trans_dict:
+                                    new_value = format_trans_dict[ value ]
+                            except:
+                                pass
+                        if not value and not new_value:
                            new_value = tool.param_trans_dict[ key ][1]
                if key not in self.NEVER_SANITIZE and sanitize:
                    self.__dict__[ new_key ] = sanitize_param( new_value )
@@ -91,8 +91,7 @@ class Jobs( BaseController ):
        year_label = start_date.strftime( "%Y" )
        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' ) ),
-                       whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', 
-                                                      galaxy.model.Job.table.c.state == 'deleted' ),
+                       whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error',
                                              galaxy.model.Job.table.c.create_time >= start_date, 
                                              galaxy.model.Job.table.c.create_time < end_date ),
                       from_obj = [ sa.outerjoin( galaxy.model.Job.table, 
@@ -134,8 +133,7 @@ class Jobs( BaseController ):
                         galaxy.model.Job.table.c.info,
                         ( galaxy.model.User.table.c.email ).label( 'user_email' ),
                         galaxy.model.GalaxySession.table.c.remote_addr ),
-                       whereclause = sa.and_( sa.or_( galaxy.model.Job.table.c.state == 'error', 
-                                                      galaxy.model.Job.table.c.state == 'deleted' ),
+                       whereclause = sa.and_( galaxy.model.Job.table.c.state == 'error',
                                              galaxy.model.Job.table.c.create_time >= start_date, 
                                              galaxy.model.Job.table.c.create_time < end_date ),
                       from_obj = [ sa.outerjoin( galaxy.model.Job.table, 
@@ -305,8 +303,7 @@ class Jobs( BaseController ):
        msg = ''
        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' ) ),
-                       whereclause = sa.or_( galaxy.model.Job.table.c.state == 'error', 
-                                             galaxy.model.Job.table.c.state == 'deleted' ),
+                       whereclause = galaxy.model.Job.table.c.state == 'error',
                       from_obj = [ galaxy.model.Job.table ],
                       group_by = [ sa.func.date_trunc( 'month', sa.func.date( galaxy.model.Job.table.c.create_time ) ) ],
                       order_by = [ sa.desc( 'date' ) ] )
@@ -2,7 +2,7 @@

 <%def name="main_body()">
  <div class="reportBody">
-    <h3 align="center">Jobs In Error Per Month ( includes jobs deleted before finishing )</h3>
+    <h3 align="center">Jobs In Error Per Month</h3>
    <h4 align="center">Click Month to view the number of jobs in error for each day of that month</h4>
    %if msg:
      <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5">
@@ -11,7 +11,7 @@
    %endif
    <table align="center" width="60%" class="colored">
      %if len( jobs ) == 0:
-        <tr><td colspan="2">There are no jobs in the deleted or error state</td></tr>
+        <tr><td colspan="2">There are no jobs in the error state</td></tr>
      %else:
        <tr class="header">
          <td>Month</td>
@@ -10,15 +10,13 @@
    %endif
    <table align="center" width="60%" class="colored">
      %if len( jobs ) == 0:
-        <tr><td colspan="5">There are no jobs in the deleted or error state for ${day_label},&nbsp;${month_label}&nbsp;${day_of_month},&nbsp;${year_label}</td></tr>
+        <tr><td colspan="5">There are no jobs in the error state for ${day_label},&nbsp;${month_label}&nbsp;${day_of_month},&nbsp;${year_label}</td></tr>
      %else:
        %for job in jobs:
          <% 
            state = job[0]
            if state == 'error':
              rowdef = '<tr class="headererror">'
-            elif state == 'deleted':
-              rowdef = '<tr class="headerdeleted">'
            else:
              rowdef = '<tr class="headerunknown">'
          %>
@@ -2,7 +2,7 @@

 <%def name="main_body()">
  <div class="reportBody">
-    <h3 align="center">Jobs in Error for ${month_label}&nbsp;${year_label} ( includes jobs deleted before finishing )</h3>
+    <h3 align="center">Jobs in Error for ${month_label}&nbsp;${year_label}</h3>
    <h4 align="center">Click Jobs in Error to view jobs in error for that day</h4>
    %if msg:
      <table align="center" width="70%" class="border" cellpadding="5" cellspacing="5">
@@ -11,7 +11,7 @@
    %endif
    <table align="center" width="60%" class="colored">
      %if len( jobs ) == 0:
-        <tr><td colspan="3">There are no jobs in error for ${month_label}&nbsp;${year_label}</td></tr>
+        <tr><td colspan="3">There are no jobs in the error state for ${month_label}&nbsp;${year_label}</td></tr>
      %else:
        <tr class="header">
          <td>Day</td>
@@ -21,7 +21,11 @@
        <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
 	    <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 galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+	    <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+            <data_type_translation>
+                <format galaxy_format="tabular" remote_format="selectedFields" />
+            </data_type_translation>
+        </request_param>
 	</request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
@@ -21,7 +21,11 @@
        <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+            <data_type_translation>
+                <format galaxy_format="tabular" remote_format="selectedFields" />
+            </data_type_translation>
+        </request_param>
    </request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>
@@ -21,7 +21,11 @@
        <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
        <request_param galaxy_name="table" remote_name="hgta_track" missing="" />
        <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
-        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
+        <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" >
+            <data_type_translation>
+                <format galaxy_format="tabular" remote_format="selectedFields" />
+            </data_type_translation>
+        </request_param>
    </request_param_translation>
 	<uihints minwidth="800"/>
 	<outputs>