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Allow `remove_value` filter on data tables

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The `RemoveValueFilter.filter_options()` method was expecting `options` to
be a list of lists, where each inner list contains exactly 3-elements
(name, value, selected), which is the format returned by the `data_meta`
filter. In fact, the only known use of the `remove_falue` filter is in the
tool `tools/maf/maf_to_interval.xml`, to filter dataset metadata.

This commit generalises the filter to look for a column of the dynamic
options named `value`, and use it during the filtering.

Fix https://github.com/galaxyproject/tools-iuc/issues/2151
This commit is contained in:
Nicola Soranzo
2018-10-24 01:41:35 +01:00
parent 096fe9b7b9
commit 5dfb743ae1
1 changed files with 10 additions and 5 deletions
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lib/galaxy/tools/parameters/dynamic_options.py
+10 -5
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@@ -388,7 +388,7 @@ class RemoveValueFilter(Filter):
self.ref_name = elem.get("ref", None)
self.meta_ref = elem.get("meta_ref", None)
self.metadata_key = elem.get("key", None)
assert self.value is not None or ((self.ref_name is not None or self.meta_ref is not None)and self.metadata_key is not None), ValueError("Required 'value' or 'ref' and 'key' attributes missing from filter")
assert self.value is not None or ((self.ref_name is not None or self.meta_ref is not None) and self.metadata_key is not None), ValueError("Required 'value' or 'ref' and 'key' attributes missing from filter")
self.multiple = string_as_bool(elem.get("multiple", "False"))
self.separator = elem.get("separator", ",")
@@ -401,13 +401,14 @@ class RemoveValueFilter(Filter):
if self.multiple:
option_value = option_value.split(self.separator)
for value in filter_value:
if value not in filter_value:
if value not in option_value:
return False
return True
return option_value in filter_value
if self.multiple:
return filter_value in option_value.split(self.separator)
return option_value == filter_value
value = self.value
if value is None:
if self.ref_name is not None:
@@ -419,7 +420,9 @@ class RemoveValueFilter(Filter):
if not isinstance(data_ref, HistoryDatasetAssociation) and not isinstance(data_ref, galaxy.tools.wrappers.DatasetFilenameWrapper):
return options # cannot modify options
value = data_ref.metadata.get(self.metadata_key, None)
return [(disp_name, optval, selected) for disp_name, optval, selected in options if not compare_value(optval, value)]
# Default to the second column (i.e. 1) since this used to work only on options produced by the data_meta filter
value_col = self.dynamic_option.columns.get('value', 1)
return [option for option in options if not compare_value(option[value_col], value)]
class SortByColumnFilter(Filter):
@@ -615,11 +618,13 @@ class DynamicOptions(object):
# Ensure parsing dynamic options does not consume more than a megabyte worth memory.
path = dataset.file_name
if os.path.getsize(path) < 1048576:
options = self.parse_file_fields(open(path))
with open(path) as fh:
options = self.parse_file_fields(fh)
else:
# Pass just the first megabyte to parse_file_fields.
log.warning("Attempting to load options from large file, reading just first megabyte")
contents = open(path, 'r').read(1048576)
with open(path, 'r') as fh:
contents = fh.read(1048576)
options = self.parse_file_fields(StringIO(contents))
elif self.tool_data_table:
options = self.tool_data_table.get_fields()