Skip to content

Add 2 missing validation rules #71

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
abhinaverma97 wants to merge 1 commit into
base: master
Choose a base branch
from
+44 −2
Open

Add 2 missing validation rules #71

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 44 additions & 2 deletions validation/rules/sbgn_pd.sch
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,9 @@ Schematron validation for SBGN PD
<iso:active pattern="pd10134"/>
<iso:active pattern="pd10140"/>
<iso:active pattern="pd10141"/>
<iso:active pattern="pd10142"/>
<iso:active pattern="pd10142"/>
<iso:active pattern="pd10143"/>
<iso:active pattern="pd10144"/>
</iso:phase>

<iso:pattern id="00000">
Expand Down Expand Up @@ -618,6 +620,43 @@ Schematron validation for SBGN PD
</iso:assert>
</iso:rule>
</iso:pattern>

<!-- NEW RULE pd10143: State variables must be unique within a stateful EPN -->
<!-- SBGN PD Spec Section 3.5.1, Rule 1 -->
<iso:pattern id="pd10143">
<iso:rule context="sbgn:glyph[@class='macromolecule' or @class='nucleic acid feature' or @class='complex' or @class='macromolecule multimer' or @class='nucleic acid feature multimer' or @class='complex multimer']">
<iso:let name="id" value="@id"/>
<iso:let name="state-vars" value="sbgn:glyph[@class='state variable']/sbgn:state/@variable"/>
<iso:let name="state-count" value="count($state-vars)"/>
<iso:let name="unique-count" value="count(distinct-values($state-vars))"/>
<iso:assert
id="pd10143"
name="unique-state-variables"
role="error"
see="sbgn-pd-L1V2.0-3.5.1"
test="$state-count = $unique-count"
diagnostics="id state-count unique-count">All state variables within a stateful EPN must be unique. Duplicate state variable found.
</iso:assert>
</iso:rule>
</iso:pattern>

<!-- NEW RULE pd10144: At most one catalysis arc per process -->
<!-- SBGN PD Spec Section 3.5.2.4, Rule 8 -->
<iso:pattern id="pd10144">
<iso:rule context="sbgn:glyph[@class='process' or @class='omitted process' or @class='uncertain process' or @class='association' or @class='dissociation']">
<iso:let name="id" value="@id"/>
<iso:let name="port-ids" value="sbgn:port/@id"/>
<iso:let name="catalysis-count" value="count(//sbgn:arc[@class='catalysis' and (@target=current()/@id or @target=current()/sbgn:port/@id)])"/>
<iso:assert
id="pd10144"
name="single-catalysis-per-process"
role="error"
see="sbgn-pd-L1V2.0-3.5.2.4"
test="$catalysis-count &lt;= 1"
diagnostics="id catalysis-count">At most one catalysis arc can be assigned to a process node. Found multiple catalysis arcs targeting this process.
</iso:assert>
</iso:rule>
</iso:pattern>

<iso:diagnostics>
<iso:diagnostic id="id"><iso:value-of select="$id"/></iso:diagnostic>
Expand All @@ -628,6 +667,9 @@ Schematron validation for SBGN PD
<iso:diagnostic id="class"><iso:value-of select="$class"/></iso:diagnostic>
<iso:diagnostic id="port-class"><iso:value-of select="$port-class"/></iso:diagnostic>
<iso:diagnostic id="count"><iso:value-of select="$count"/></iso:diagnostic>
<iso:diagnostic id="arc-count"><iso:value-of select="$arc-count"/></iso:diagnostic>
<iso:diagnostic id="arc-count"><iso:value-of select="$arc-count"/></iso:diagnostic>
<iso:diagnostic id="state-count"><iso:value-of select="$state-count"/></iso:diagnostic>
<iso:diagnostic id="unique-count"><iso:value-of select="$unique-count"/></iso:diagnostic>
<iso:diagnostic id="catalysis-count"><iso:value-of select="$catalysis-count"/></iso:diagnostic>
</iso:diagnostics>
</iso:schema>