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Modify metadata update script to update metadata of all tabular based files. Special case for interval files (interval,

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bed) to not override interval specific assignments.
This commit is contained in:
Daniel Blankenberg
2007-10-17 15:23:09 +00:00
parent 42c130c85b
commit 74a9f2ecbf
1 changed files with 21 additions and 21 deletions
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scripts/update_metadata.py
+21 -21
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@@ -43,29 +43,29 @@ def main():
# data.flush()
#Search out tabular datatypes and make sure that number of columns is set.
#print "Seeking out tabular based files and setting number of columns."
#for row in app.model.Dataset.table.select().execute():
# data = app.model.Dataset.get(row.id)
# if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
# print row.id
# #The set_meta() function for tabular subclasses are responsible for determining
# #the number of 'problem' lines to skip in the file. Problem lines are comment lines
# #that do not begin with a '#' character, etc. When the number of lines to skip is determined,
# #Tabular().set_meta is called, passing the number of lines to skip. Nothing besides this is
# #currently done in set_meta() functions of subclasses of Tabular.
# data.set_meta()
# data.flush()
#Search out tabular datatypes (and subclasses) and initialize metadata
print "Seeking out tabular based files and initializing metadata"
for row in app.model.Dataset.table.select().execute():
data = app.model.Dataset.get(row.id)
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('tabular'))):
print row.id, data.extension
#Call meta_data for all tabular files
#special case interval type where we do not want to overwrite chr, start, end, etc assignments
if issubclass(type(data.datatype), type(app.datatypes_registry.get_datatype_by_extension('interval'))):
galaxy.datatypes.tabular.Tabular().set_meta(data)
else:
data.set_meta()
data.flush()
#Search out maf datatypes and make sure that available species is set.
print "Seeking out maf files and setting available species."
for row in app.model.Dataset.table.select(app.model.Dataset.table.c.extension == 'maf').execute():
print row.id
sys.stdout.flush()
data = app.model.Dataset.get(row.id)
if data.missing_meta:
data.set_meta() #Call maf set metadata method, setting available species
data.flush()
#print "Seeking out maf files and setting available species."
#for row in app.model.Dataset.table.select(app.model.Dataset.table.c.extension == 'maf').execute():
# print row.id
# sys.stdout.flush()
# data = app.model.Dataset.get(row.id)
# if data.missing_meta:
# data.set_meta() #Call maf set metadata method, setting available species
# data.flush()
app.shutdown()
sys.exit(0)