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Add the ability to define datatypes in the configuration file.

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Datatypes are defined like:
[galaxy:datatypes]
bed = galaxy.datatypes.interval:Bed
png = galaxy.datatypes.images:Image,image/png

where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
This commit is contained in:
Daniel Blankenberg
2007-06-01 19:25:19 +00:00
parent 437399fc66
commit 4cbfce361b
17 changed files with 204 additions and 108 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/data_source/biomart_filter.py
+1 -1
View File
@@ -11,7 +11,7 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
data_type = param_dict.get( 'type', 'text' )
if data_type == 'text': data_type='interval' #All data from biomart is TSV, assume interval
name, data = out_data.items()[0]
data = datatypes.change_datatype(data, data_type)
data = app.datatypes_registry.change_datatype(data, data_type)
data.name = data_name
out_data[name] = data
tools/data_source/encode_import_code.py
+1 -1
View File
@@ -117,7 +117,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
data.name = data.name + " (" + description + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype( data, file_type )
data = app.datatypes_registry.change_datatype( data, file_type )
data.init_meta()
data.set_peek()
app.model.flush()
tools/data_source/hbvar_filter.py
+2 -2
View File
@@ -10,7 +10,7 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
data_type = param_dict.get( 'type', 'text' )
if data_type == 'text': data_type='interval' #All data is TSV, assume interval
name, data = out_data.items()[0]
data = datatypes.change_datatype(data, data_type)
data = app.datatypes_registry.change_datatype(data, data_type)
data.name = data_name
out_data[name] = data
@@ -70,6 +70,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
shutil.move(temp_filename,data.file_name)
else:
data = datatypes.change_datatype(data, 'tabular')
data = app.datatypes_registry.change_datatype(data, 'tabular')
data.set_peek()
data.flush()
tools/data_source/microbial_import_code.py
+1 -1
View File
@@ -225,7 +225,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
data.dbkey = dbkey
data.info = data.name
datatypes.change_datatype( data, file_type )
data = app.datatypes_registry.change_datatype( data, file_type )
data.init_meta()
data.set_peek()
app.model.flush()
tools/data_source/ucsc_tablebrowser_code.py
+3 -4
View File
@@ -21,9 +21,8 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
ext = outputType
try: ext = outputType_to_ext[outputType]
except: pass
if ext not in datatypes.datatypes_by_extension: ext = 'interval'
data = datatypes.change_datatype(data, ext)
if ext not in app.datatypes_registry.datatypes_by_extension: ext = 'interval'
data = app.datatypes_registry.change_datatype(data, ext)
#store ucsc parameters temporarily in output file
out = open(data.file_name,'w')
@@ -40,6 +39,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval):
data.set_meta()
if data.missing_meta(): data = datatypes.change_datatype(data, 'tabular')
if data.missing_meta(): data = app.datatypes_registry.change_datatype(data, 'tabular')
data.set_peek()
data.flush()