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fix matchms outputs to existing types #438

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merged 3 commits into from
Nov 22, 2023
Merged

fix matchms outputs to existing types #438

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2db3791
fix matchms outputs to existing types
bernt-matthias Nov 21, 2023
c5923b2
fix test output types
bernt-matthias Nov 22, 2023
c0aa50b
Merge branch 'master' into topic/matchms-filetypes
hechth Nov 22, 2023
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26 changes: 13 additions & 13 deletions tools/matchms/matchms_networking.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,12 +78,12 @@
</inputs>

<outputs>
<data label="Similarity network of ${scores.name}" name="similarity_network_file" format="graphml">
<data label="Similarity network of ${scores.name}" name="similarity_network_file" format="xml">
<change_format>
<when input="graph_format" value="graphml" format="graphml"/>
<when input="graph_format" value="cyjs" format="cyjs"/>
<when input="graph_format" value="gexf" format="gexf"/>
<when input="graph_format" value="gml" format="gml"/>
<when input="graph_format" value="graphml" format="xml"/>
<when input="graph_format" value="cyjs" format="json"/>
<when input="graph_format" value="gexf" format="xml"/>
<when input="graph_format" value="gml" format="xml"/>
<when input="graph_format" value="json" format="json"/>
</change_format>
</data>
Expand All @@ -94,7 +94,7 @@
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="graphml"/>
<param name="identifier_key" value="compound_name"/>
<output name="similarity_network_file" ftype="graphml">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<is_valid_xml />
<has_line_matching expression='.*node id="C[0-9]*"\/.' n="51"/>
Expand All @@ -107,7 +107,7 @@
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="cyjs"/>
<param name="identifier_key" value="compound_name"/>
<output name="similarity_network_file" ftype="cyjs">
<output name="similarity_network_file" ftype="json">
<assert_contents>
<has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="51"/>
<has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="4"/>
Expand All @@ -118,7 +118,7 @@
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="gexf"/>
<param name="identifier_key" value="compound_name"/>
<output name="similarity_network_file" ftype="gexf">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<is_valid_xml />
<has_line_matching expression='.*node id="C[0-9]*" label="C[0-9]*" \/.' n="51"/>
Expand All @@ -130,7 +130,7 @@
<param name="scores" value="scores.json" ftype="json"/>
<param name="graph_format" value="gml"/>
<param name="identifier_key" value="compound_name"/>
<output name="similarity_network_file" ftype="gml">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<has_line_matching expression='\s*node \[\n\s*id [0-9]*\n\s*label "C[0-9]*"\n\s*\]' n="51"/>
<has_line_matching expression='\s*edge \[\n\s*source [0-9]*\n\s*target [0-9]*\n\s*weight 0\.[0-9]*\n\s*\]' n="4"/>
Expand All @@ -153,7 +153,7 @@
<param name="graph_format" value="graphml"/>
<param name="identifier_key" value="compound_name"/>
<param name="keep_unconnected_nodes" value="false"/>
<output name="similarity_network_file" ftype="graphml">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<is_valid_xml />
<has_line_matching expression='.*node id="C[0-9]*"\/.' n="8"/>
Expand All @@ -168,7 +168,7 @@
<param name="identifier_key" value="compound_name"/>
<param name="score_cutoff" value="0.4"/>
<param name="keep_unconnected_nodes" value="false"/>
<output name="similarity_network_file" ftype="graphml">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<is_valid_xml />
<has_line_matching expression='.*node id="C[0-9]*"\/.' n="20"/>
Expand All @@ -184,7 +184,7 @@
<param name="score_cutoff" value="0.8"/>
<param name="link_method" value="mutual"/>
<param name="keep_unconnected_nodes" value="false"/>
<output name="similarity_network_file" ftype="cyjs">
<output name="similarity_network_file" ftype="json">
<assert_contents>
<has_text_matching expression='{"data": {"id": "C[0-9]*", "value": "C[0-9]*", "name": "C[0-9]*"}}' n="6"/>
<has_text_matching expression='{"data": {"weight": 0\.[0-9]*, "source": "C[0-9]*", "target": "C[0-9]*"}}' n="3"/>
Expand All @@ -197,7 +197,7 @@
<param name="identifier_key" value="compound_name"/>
<param name="score_cutoff" value="0.4"/>
<param name="keep_unconnected_nodes" value="false"/>
<output name="similarity_network_file" ftype="graphml">
<output name="similarity_network_file" ftype="xml">
<assert_contents>
<is_valid_xml />
</assert_contents>
Expand Down