From d2c33771c974d3b68b4514e0206a50baaba659f0 Mon Sep 17 00:00:00 2001
From: Evgeny Metelkin <metelkin@insysbio.com>
Date: Fri, 24 Nov 2023 14:07:47 +0200
Subject: [PATCH] fix dot export for abstract namespaces

---
 TODO.md                   |  3 ---
 bin/heta-build.js         |  4 ++--
 src/dot-export/index.js   | 25 ++++++++++++-------------
 src/templates/dot.dot.njk |  2 +-
 4 files changed, 15 insertions(+), 19 deletions(-)

diff --git a/TODO.md b/TODO.md
index 6f9def8d..e2b59b8c 100644
--- a/TODO.md
+++ b/TODO.md
@@ -30,9 +30,6 @@
 
 ## bugs
 
-- wrong figures for abstract namespaces in DOT: no references to compartment
-- nothing is dislayed if you use wrong cli command: `heta builds`
-
 ## features
 
 - write reusable `Build` class
diff --git a/bin/heta-build.js b/bin/heta-build.js
index a7dc18ac..7207e0bc 100644
--- a/bin/heta-build.js
+++ b/bin/heta-build.js
@@ -5,7 +5,7 @@ const fs = require('fs');
 const path = require('path');
 const { Builder } = require('../src/builder');
 const { load } = require('js-yaml'); // https://www.npmjs.com/package/js-yaml
-const _ = require('lodash');
+const _merge = require('lodash/merge');
 const semver = require('semver');
 const { version, bugs } = require('../package');
 const colors = require('colors');
@@ -100,7 +100,7 @@ program
   };
 
   // === update declaration ===
-  _.merge(declaration, CLIDeclaration);
+  _merge(declaration, CLIDeclaration);
 
   // === wrong version throws, if no version stated than skip ===
   let satisfiesVersion = declaration.builderVersion
diff --git a/src/dot-export/index.js b/src/dot-export/index.js
index 53082cf8..aceb2f92 100644
--- a/src/dot-export/index.js
+++ b/src/dot-export/index.js
@@ -51,20 +51,19 @@ class DotExport extends AbstractExport{
       .forEach((comp) => clustersDict[comp.id] = []);
     ns.selectByInstanceOf('Process')
       .forEach((proc) => {
-        let substrates = proc.actors
-          .filter((x) => x.stoichiometry < 0);
-        let hasFirstSubstrate = substrates.length > 0 
-          && substrates[0].targetObj !== undefined
-          && substrates[0].targetObj.compartment !== undefined;
-        if (hasFirstSubstrate) {
-          let mainComp = substrates[0].targetObj.compartment;
-          clustersDict[mainComp].push(proc);
-        } else {
-          clustersDict['_'].push(proc);
-        }
+        let substrates = proc.actors.filter((x) => x.stoichiometry < 0);
+        // push records
+        proc.actors.forEach((actor) => {
+          let record = ns.get(actor.target) || { id: actor.target }; // use fake record
+          let compartmentId = record.compartment || '_';
+          clustersDict[compartmentId]?.push(record) || (clustersDict[compartmentId] = [record]);
+        });
+        // push process
+        let compartmentOfFirstSubstrate = ns.get(substrates[0]?.target)?.compartment || '_';
+        clustersDict[compartmentOfFirstSubstrate]?.push(proc);
       });
+    /* display all records
     ns.selectByInstanceOf('Record')
-      .filter((rec) => rec.isDynamic)
       .forEach((rec) => {
         if (rec.compartment !== undefined) {
           clustersDict[rec.compartment].push(rec);
@@ -72,7 +71,7 @@ class DotExport extends AbstractExport{
           clustersDict['_'].push(rec);
         }
       });
-
+    */
     return {
       ns,
       clustersDict
diff --git a/src/templates/dot.dot.njk b/src/templates/dot.dot.njk
index c9a974a3..55f70b9b 100644
--- a/src/templates/dot.dot.njk
+++ b/src/templates/dot.dot.njk
@@ -20,7 +20,7 @@ digraph {{ ns.spaceName }} {
         tooltip="{{ key }}"
         //
         {%- for component in val %}
-        {%- if component.instanceOf('Process') %}
+        {%- if component.instanceOf and component.instanceOf('Process') %}
         {{ component.id }} [shape=circle,width=.1,height=.1,label=""] // xlabel="{{ component.id }}"
         {%- else %}
         {{ component.id }} [shape=box]