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Merge pull request #13039 from bernt-matthias/topic/filter-param-value-multiple

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Allow param_value filter to refer to parameters with multiple values
This commit is contained in:
Marius van den Beek
2022-01-14 15:25:44 +01:00
committed by GitHub
parent 617ea2dfa9 2e33be78ac
commit 6fdf4da441
5 changed files with 199 additions and 8 deletions
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lib/galaxy/tools/parameters/dynamic_options.py
+26 -8
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@@ -157,6 +157,7 @@ class DataMetaFilter(Filter):
self.column = d_option.column_spec_to_index(self.column)
self.multiple = string_as_bool(elem.get("multiple", "False"))
self.separator = elem.get("separator", ",")
log.error(f"data_meta.init: ref_name {self.ref_name} key {self.key} column {self.column} multiple {self.multiple} separator {self.separator}")
def get_dependency_name(self):
return self.ref_name
@@ -271,14 +272,31 @@ class ParamValueFilter(Filter):
if trans is not None and trans.workflow_building_mode:
return []
ref = other_values.get(self.ref_name, None)
for ref_attribute in self.ref_attribute:
if not hasattr(ref, ref_attribute):
return [] # ref does not have attribute, so we cannot filter, return empty list
ref = getattr(ref, ref_attribute)
ref = str(ref)
if ref is None:
ref = []
# - for HDCAs the list of contained HDAs is extracted
# - single values are transformed in a single eleent list
# - remaining cases are already lists (select and data parameters with multiple=true)
if isinstance(ref, HistoryDatasetCollectionAssociation):
ref = ref.to_hda_representative(multiple=True)
elif not isinstance(ref, list):
ref = [ref]
ref_values = []
for r in ref:
for ref_attribute in self.ref_attribute:
# ref does not have attribute, so we cannot filter,
# but other refs might have it
if not hasattr(r, ref_attribute):
break
r = getattr(r, ref_attribute)
ref_values.append(r)
ref_values = [str(_) for _ in ref_values]
rval = []
for fields in options:
if self.keep == (fields[self.column] == ref):
if self.keep == (fields[self.column] in ref_values):
rval.append(fields)
return rval
@@ -666,10 +684,10 @@ class DynamicOptions:
try:
datasets = _get_ref_data(other_values, self.dataset_ref_name)
except KeyError: # no such dataset
log.warning(f"could not create dynamic options from_dataset: {self.dataset_ref_name} unknown")
log.warning(f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} unknown")
return []
except ValueError: # not a valid dataset
log.warning(f"could not create dynamic options from_dataset: {self.dataset_ref_name} not a data or collection parameter")
log.warning(f"Parameter {self.tool_param.name}: could not create dynamic options from_dataset: {self.dataset_ref_name} not a data or collection parameter")
return []
options = []
test/functional/tool-data/fasta_indexes.loc
+2
View File
@@ -1,2 +1,4 @@
hg19_value hg19 hg19_name hg19_path
hg18_value hg18 hg18_name hg18_path
mm10_value mm10 mm10_name mm10_path
test/functional/tools/filter_param_value.xml
+53
View File
@@ -0,0 +1,53 @@
<tool id="filter_param_value" name="filter_param_value" version="0.1.0">
<description>Filter input with the param_value</description>
<command><![CDATA[
echo $select1 > '$output' &&
echo $select2 >> '$output'
]]></command>
<inputs>
<!-- define 2 selects that are initialised with entries from a data table
and use param_value filters to ensure that disjoint elements are
selected (one of them is multiple="true" to ensure that also list of
elements can be used in the filter) -->
<param name="select1" type="select" multiple="true">
<options from_data_table="test_fasta_indexes">
<column name="value" index="0"/>
<column name="name" index="1"/>
<!-- unfortunatelly this does not work (bug?): at the moment ane can
not refer to other inputs that are defined below)
<filter type="param_value" column="0" ref="select2" keep="false"/> -->
</options>
</param>
<param name="select2" type="select">
<options from_data_table="test_fasta_indexes">
<column name="value" index="0"/>
<column name="name" index="1"/>
<filter type="param_value" column="0" ref="select1" keep="false"/>
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
</outputs>
<tests>
<test expect_failure="false">
<param name="select1" value="hg18_value,hg19_value"/>
<param name="select2" value="mm10_value" />
<output name="output">
<assert_contents>
<has_line line="hg18_value,hg19_value" />
<has_line line="mm10_value" />
</assert_contents>
</output>
</test>
<test expect_failure="true">
<param name="select1" value="hg18_value,hg19_value"/>
<param name="select2" value="hg18_value" />
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/filter_param_value_ref_attribute.xml
+116
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@@ -0,0 +1,116 @@
<tool id="filter_param_value_ref_attribute" name="filter_param_value_ref_attribute" version="0.1.0">
<description>Filter input with the param_value</description>
<command><![CDATA[
#if $select_single
echo $select_single >> '$output' &&
#end if
#if $select_mult
echo $select_mult >> '$output' &&
#end if
#if $select_coll
echo $select_coll >> '$output' &&
#end if
true
]]></command>
<inputs>
<!-- this tests the param_value filter with the ref_attribute attribute
(so ref is dataset(s) or a dataset collection), the following pairs
test param_value filter refering:
- dataset
- multiple datasets
- a collection
in each case the data and the select input are optional to allow
to test them separately -->
<!-- 1. dataset (here with non-default keep) -->
<param name="data_single" type="data" format="bed" optional="true"/>
<param name="select_single" type="select" multiple="true" optional="true">
<options from_data_table="test_fasta_indexes">
<column name="value" index="0"/>
<column name="name" index="1"/>
<filter type="param_value" column="1" ref="data_single" ref_attribute="metadata.dbkey" keep="false"/>
</options>
</param>
<!-- 2. same, but with a data input accepting multiple datasets
(which may have different dbkeys .. but we can not specify them in a test) -->
<param name="data_mult" format="bed" type="data" multiple="true" optional="true"/>
<param name="select_mult" type="select" multiple="true" optional="true">
<options from_data_table="test_fasta_indexes">
<column name="value" index="0"/>
<column name="name" index="1"/>
<filter type="param_value" column="1" ref="data_mult" ref_attribute="metadata.dbkey"/>
</options>
</param>
<!-- 3. same, but with a collection input (elements may have different dbkeys) -->
<param name="data_coll" format="bed" type="data_collection" collection_type="list" optional="true"/>
<param name="select_coll" type="select" multiple="true" optional="true">
<options from_data_table="test_fasta_indexes">
<column name="value" index="0"/>
<column name="name" index="1"/>
<filter type="param_value" column="1" ref="data_coll" ref_attribute="metadata.dbkey"/>
</options>
</param>
</inputs>
<outputs>
<data format="txt" name="output" />
</outputs>
<tests>
<test expect_failure="false">
<param name="data_single" value="1.bed" ftype="bed" dbkey="hg19"/>
<param name="select_single" value="hg18_value,mm10_value"/>
<output name="output">
<assert_contents>
<has_line line="hg18_value,mm10_value"/>
</assert_contents>
</output>
</test>
<test expect_failure="true">
<param name="data_single" value="1.bed" ftype="bed" dbkey="hg19"/>
<param name="select_single" value="hg19_value"/>
</test>
<test expect_failure="false">
<param name="data_mult" value="1.bed,2.bed" dbkey="hg19"/>
<param name="select_mult" value="hg19_value"/>
<output name="output">
<assert_contents>
<has_line line="hg19_value"/>
</assert_contents>
</output>
</test>
<test expect_failure="true">
<param name="data_mult" value="1.bed,2.bed" dbkey="hg19"/>
<param name="select_mult" value="hg18_value"/>
</test>
<test expect_failure="false">
<param name="data_coll">
<collection type="list">
<element name="element1" ftype="bed" value="1.bed" dbkey="hg18"/>
<element name="element2" ftype="bed" value="2.bed" dbkey="hg19"/>
</collection>
</param>
<param name="select_coll" value="hg18_value,hg19_value"/>
<output name="output">
<assert_contents>
<has_line line="hg18_value,hg19_value"/>
</assert_contents>
</output>
</test>
<test expect_failure="true">
<param name="data_coll">
<collection type="list">
<element name="element1" ftype="bed" value="1.bed" dbkey="hg18"/>
<element name="element2" ftype="bed" value="2.bed" dbkey="hg19"/>
</collection>
</param>
<param name="select_coll" value="mm10_value"/>
</test>
</tests>
<help>
</help>
</tool>
test/functional/tools/samples_tool_conf.xml
+2
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@@ -47,6 +47,8 @@
<tool file="inputs_as_json_with_paths.xml" />
<tool file="inputs_as_json_with_staging_path_and_source_path.xml" />
<tool file="filter_multiple_splitter.xml" />
<tool file="filter_param_value.xml" />
<tool file="filter_param_value_ref_attribute.xml" />
<tool file="filter_static_regexp.xml" />
<tool file="select_from_dataset.xml" />
<tool file="select_from_dataset_optional.xml" />