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Improve diagnostic messages in SBGN AF Schematron validation rules #74

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37 changes: 20 additions & 17 deletions validation/rules/sbgn_af.sch
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Original file line number Diff line number Diff line change
Expand Up @@ -44,20 +44,24 @@ Schematron validation for SBGN AF
<iso:rule context="//*[@id]">
<iso:let name="id" value="@id"/>
<iso:assert
id="00001"
role="error"
test="count(//@id[. = current()/@id]) = 1" diagnostics="id">ID needs to be unique.</iso:assert>
id="00001"
role="error"
test="count(//@id[. = current()/@id]) = 1" diagnostics="id">
Error: Each SBGN element must have a unique ID. Duplicate ID detected in the diagram.
</iso:assert>
</iso:rule>
</iso:pattern>

<iso:pattern id="00002">
<iso:rule context="sbgn:arc">
<iso:let name="target" value="@target"/>
<iso:assert
id="00002"
role="error"
test="//*/@id[. = $target]" diagnostics="target">An arc target should be a glyph defined in the diagram.</iso:assert>
</iso:rule>
id="00002"
role="error"
test="//*/@id[. = $target]" diagnostics="target">
Error: The target attribute of this arc references an ID that does not exist as a glyph in the diagram.
Ensure that all arc targets reference valid glyph IDs.
</iso:assert>
</iso:pattern>

<iso:pattern id="af10101">
Expand Down Expand Up @@ -98,7 +102,7 @@ Schematron validation for SBGN AF
test="
$target-class='biological activity' or
$target-class='phenotype'"
diagnostics="id target target-class port-class">Incorrect target reference for influence arc
diagnostics="id target target-class port-class">IError: Influence arcs must target a valid node such as 'biological activity' or 'phenotype'.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -121,7 +125,7 @@ Schematron validation for SBGN AF
$class='necessary stimulation' or
$class='unknown influence'
"
diagnostics="id class">This arc class is not allowed in Activity Flow
diagnostics="id class">Error: This arc class is not valid for SBGN Activity Flow diagrams.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand Down Expand Up @@ -149,7 +153,7 @@ Schematron validation for SBGN AF
$class='perturbation' or
$class='phenotype'
"
diagnostics="id class">This glyph class is not allowed in Activity Flow
diagnostics="id class">Error: This glyph class is not allowed in SBGN Activity Flow diagrams.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -166,7 +170,7 @@ Schematron validation for SBGN AF
see="sbgn-af-L1V1.0-3.3.1"
test="
$source-class='biological activity'"
diagnostics="id source source-class">Incorrect source reference for arc with class "logic arc"
diagnostics="id source source-class">Error: Logic arcs must originate from a 'biological activity' glyph.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -187,7 +191,7 @@ Schematron validation for SBGN AF
$port-class='or' or
$port-class='not' or
$port-class='delay'"
diagnostics="id target target-class port-class">Incorrect target reference for arc with class "logic arc"
diagnostics="id target target-class port-class">Error: Logic arcs must target a logic operator glyph such as 'and', 'or', 'not', or 'delay'.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -204,8 +208,7 @@ Schematron validation for SBGN AF
role="error"
see="sbgn-pd-L1V1.3-3.4.1"
test="$count = 1"
diagnostics="id port-id count">'not' glyph can only be connected to one logic arc glyph.
</iso:assert>
diagnostics="id port-id count">Error: A 'not' logic glyph must have exactly one incoming logic arc connection.
</iso:rule>
</iso:pattern>

Expand All @@ -222,7 +225,7 @@ Schematron validation for SBGN AF
test="
$source-class='biological activity' or
$source-class='compartment'"
diagnostics="id source source-class">Incorrect source reference for arc with class "equivalence arc"
diagnostics="id source source-class">Error: Equivalence arcs must originate from a 'biological activity' or 'compartment' glyph.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -240,7 +243,7 @@ Schematron validation for SBGN AF
$target-class='tag' or
$target-class='submap' or
$target-class='terminal'"
diagnostics="id target target-class">Incorrect target reference for arc with class "equivalence arc"
diagnostics="id target target-class">Error: Equivalence arcs must target a 'tag', 'submap', or 'terminal' glyph.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand All @@ -255,7 +258,7 @@ Schematron validation for SBGN AF
role="error"
test="
(($compartment-count = 0) and not (@compartmentRef)) or (($compartment-count &gt; 0) and @compartmentRef)"
diagnostics="id">If there are compartments defined, top-level glyphs must have a compartmentRef"
diagnostics="id">Error: If compartments exist in the diagram, each top-level biological activity glyph must define a valid compartmentRef.
</iso:assert>
</iso:rule>
</iso:pattern>
Expand Down