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This commit is contained in:
Greg Von Kuster
2008-12-15 10:37:16 -05:00
parent dfd5e9827f bff56d118e
commit d3b2a27cee
124 changed files with 9427 additions and 1025 deletions
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tools/data_source/access_libraries.xml
+7
View File
@@ -0,0 +1,7 @@
<?xml version="1.0"?>
<tool name="Access Libraries" id="library_access1">
<description>stored locally</description>
<inputs action="/library/browse" method="get">
<param name="bogus_param" type="hidden" value="needed" />
</inputs>
</tool>
tools/data_source/encode_import_code.py
+3 -1
View File
@@ -5,7 +5,8 @@ from shutil import copyfile
#post processing, set build for data and add additional data to history
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
base_dataset = out_data.items()[0][1]
history = base_dataset.history
if history == None:
print "unknown history!"
return
@@ -38,6 +39,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
newdata.extension = file_type
newdata.name = basic_name + " (" + description + ")"
history.add_dataset( newdata )
app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
app.model.flush()
try:
copyfile(filepath,newdata.file_name)
tools/data_source/microbial_import_code.py
+3 -1
View File
@@ -84,7 +84,8 @@ from galaxy import datatypes, config, jobs, tools
from shutil import copyfile
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
base_dataset = out_data.items()[0][1]
history = base_dataset.history
if history == None:
print "unknown history!"
return
@@ -134,6 +135,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
newdata.extension = file_type
newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
newdata.flush()
app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset )
history.add_dataset( newdata )
app.model.flush()
try: