diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index a79843d046a..8e3fee4eae1 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -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
+ #
+ #
+ #
+ 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")
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index a3e07c5985d..5c7d068f861 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -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 )
diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py
index f0630198355..d14b6bfe04d 100644
--- a/lib/galaxy/webapps/reports/controllers/jobs.py
+++ b/lib/galaxy/webapps/reports/controllers/jobs.py
@@ -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' ) ] )
diff --git a/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako b/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
index c4818677f5a..92b8158330e 100644
--- a/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
+++ b/lib/galaxy/webapps/reports/templates/jobs_per_month_in_error.mako
@@ -2,7 +2,7 @@
<%def name="main_body()">
-
Jobs In Error Per Month ( includes jobs deleted before finishing )
+
Jobs In Error Per Month
Click Month to view the number of jobs in error for each day of that month
%if msg:
@@ -11,7 +11,7 @@
%endif
%if len( jobs ) == 0:
- | There are no jobs in the deleted or error state |
+ | There are no jobs in the error state |
%else: