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make param_value filter work with multi data inputs
ie data with multiple=true and collections
This commit is contained in:
Matthias Bernt
@@ -272,19 +272,31 @@ class ParamValueFilter(Filter):
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if trans is not None and trans.workflow_building_mode:
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return []
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ref = other_values.get(self.ref_name, None)
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for ref_attribute in self.ref_attribute:
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if not hasattr(ref, ref_attribute):
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return [] # ref does not have attribute, so we cannot filter, return empty list
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ref = getattr(ref, ref_attribute)
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if ref is None:
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ref = []
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elif isinstance(ref, list):
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ref = [str(_) for _ in ref]
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else:
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ref = [str(ref)]
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# - for HDCAs the list of contained HDAs is extracted
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# - single values are transformed in a single eleent list
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# - remaining cases are already lists (select and data parameters with multiple=true)
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if isinstance(ref, HistoryDatasetCollectionAssociation):
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ref = ref.to_hda_representative(multiple=True)
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elif not isinstance(ref, list):
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ref = [ref]
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ref_values = []
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for r in ref:
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for ref_attribute in self.ref_attribute:
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# ref does not have attribute, so we cannot filter,
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# but other refs might have it
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if not hasattr(r, ref_attribute):
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break
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r = getattr(r, ref_attribute)
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ref_values.append(r)
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ref_values = [str(_) for _ in ref_values]
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rval = []
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for fields in options:
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if self.keep == (fields[self.column] in ref):
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if self.keep == (fields[self.column] in ref_values):
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rval.append(fields)
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return rval
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@@ -13,11 +13,13 @@
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<options from_data_table="test_fasta_indexes">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<!-- <filter type="param_value" column="0" ref="select2" keep="false"/> -->
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<!-- unfortunatelly this does not work (bug?): at the moment ane can
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not refer to other inputs that are defined below)
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<filter type="param_value" column="0" ref="select2" keep="false"/> -->
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</options>
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</param>
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<param name="select2" type="select">
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<options from_data_table="test_fasta_indexes">
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<options from_data_table="test_fasta_indexes">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<filter type="param_value" column="0" ref="select1" keep="false"/>
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@@ -0,0 +1,116 @@
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<tool id="filter_param_value_ref_attribute" name="filter_param_value_ref_attribute" version="0.1.0">
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<description>Filter input with the param_value</description>
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<command><![CDATA[
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#if $select_single
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echo $select_single >> '$output' &&
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#end if
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#if $select_mult
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echo $select_mult >> '$output' &&
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#end if
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#if $select_coll
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echo $select_coll >> '$output' &&
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#end if
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true
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]]></command>
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<inputs>
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<!-- this tests the param_value filter with the ref_attribute attribute
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(so ref is dataset(s) or a dataset collection), the following pairs
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test param_value filter refering:
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- dataset
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- multiple datasets
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- a collection
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in each case the data and the select input are optional to allow
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to test them separately -->
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<!-- 1. dataset (here with non-default keep) -->
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<param name="data_single" type="data" format="bed" optional="true"/>
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<param name="select_single" type="select" multiple="true" optional="true">
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<options from_data_table="test_fasta_indexes">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<filter type="param_value" column="1" ref="data_single" ref_attribute="metadata.dbkey" keep="false"/>
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</options>
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</param>
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<!-- 2. same, but with a data input accepting multiple datasets
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(which may have different dbkeys .. but we can not specify them in a test) -->
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<param name="data_mult" format="bed" type="data" multiple="true" optional="true"/>
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<param name="select_mult" type="select" multiple="true" optional="true">
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<options from_data_table="test_fasta_indexes">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<filter type="param_value" column="1" ref="data_mult" ref_attribute="metadata.dbkey"/>
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</options>
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</param>
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<!-- 3. same, but with a collection input (elements may have different dbkeys) -->
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<param name="data_coll" format="bed" type="data_collection" collection_type="list" optional="true"/>
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<param name="select_coll" type="select" multiple="true" optional="true">
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<options from_data_table="test_fasta_indexes">
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<column name="value" index="0"/>
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<column name="name" index="1"/>
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<filter type="param_value" column="1" ref="data_coll" ref_attribute="metadata.dbkey"/>
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</options>
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</param>
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</inputs>
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<outputs>
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<data format="txt" name="output" />
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</outputs>
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<tests>
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<test expect_failure="false">
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<param name="data_single" value="1.bed" ftype="bed" dbkey="hg19"/>
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<param name="select_single" value="hg18_value,mm10_value"/>
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<output name="output">
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<assert_contents>
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<has_line line="hg18_value,mm10_value"/>
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</assert_contents>
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</output>
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</test>
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<test expect_failure="true">
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<param name="data_single" value="1.bed" ftype="bed" dbkey="hg19"/>
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<param name="select_single" value="hg19_value"/>
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</test>
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<test expect_failure="false">
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<param name="data_mult" value="1.bed,2.bed" dbkey="hg19"/>
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<param name="select_mult" value="hg19_value"/>
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<output name="output">
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<assert_contents>
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<has_line line="hg19_value"/>
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</assert_contents>
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</output>
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</test>
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<test expect_failure="true">
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<param name="data_mult" value="1.bed,2.bed" dbkey="hg19"/>
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<param name="select_mult" value="hg18_value"/>
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</test>
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<test expect_failure="false">
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<param name="data_coll">
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<collection type="list">
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<element name="element1" ftype="bed" value="1.bed" dbkey="hg18"/>
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<element name="element2" ftype="bed" value="2.bed" dbkey="hg19"/>
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</collection>
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</param>
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<param name="select_coll" value="hg18_value,hg19_value"/>
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<output name="output">
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<assert_contents>
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<has_line line="hg18_value,hg19_value"/>
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</assert_contents>
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</output>
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</test>
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<test expect_failure="true">
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<param name="data_coll">
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<collection type="list">
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<element name="element1" ftype="bed" value="1.bed" dbkey="hg18"/>
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<element name="element2" ftype="bed" value="2.bed" dbkey="hg19"/>
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</collection>
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</param>
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<param name="select_coll" value="mm10_value"/>
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</test>
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</tests>
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<help>
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</help>
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</tool>
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@@ -48,6 +48,7 @@
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<tool file="inputs_as_json_with_staging_path_and_source_path.xml" />
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<tool file="filter_multiple_splitter.xml" />
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<tool file="filter_param_value.xml" />
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<tool file="filter_param_value_ref_attribute.xml" />
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<tool file="filter_static_regexp.xml" />
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<tool file="select_from_dataset.xml" />
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<tool file="select_from_dataset_optional.xml" />
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