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Updating security from central

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This commit is contained in:
Guruprasad Anada
2009-01-15 13:11:47 -05:00
parent ee8779987e 19c0b7e30b
commit d4eef49e01
134 changed files with 10061 additions and 1490 deletions
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tools/data_destination/epigraph.xml
+1
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@@ -38,3 +38,4 @@ The EpiGRAPH_ web service enables biologists to uncover hidden associations in v
</help>
</tool>
tools/data_source/access_libraries.xml
+7
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@@ -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="default_action" type="hidden" value="add" />
</inputs>
</tool>
tools/data_source/encode_import_code.py
+3 -1
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@@ -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
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@@ -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:
tools/maf/maf_to_bed_code.py
+1 -1
View File
@@ -27,13 +27,13 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
fields = line.split("\t")
dbkey = fields[1]
filepath = fields[2]
newdata = app.model.HistoryDatasetAssociation( create_dataset = True )
newdata.set_size()
newdata.extension = "bed"
newdata.name = basic_name + " (" + dbkey + ")"
newdata.flush()
history.add_dataset( newdata )
app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset )
newdata.flush()
history.flush()
app.model.flush()