Refactor CRISPR functionality and fix DNA ID retrieval in ElitismUtil…

src/Creature.ts

@@ -1,7 +1,7 @@
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
-import { yellow } from "https://deno.land/std@0.223.0/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.223.0/fmt/duration.ts";
-import { emptyDirSync } from "https://deno.land/std@0.223.0/fs/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
+import { yellow } from "https://deno.land/std@0.224.0/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.224.0/fmt/duration.ts";
+import { emptyDirSync } from "https://deno.land/std@0.224.0/fs/mod.ts";
 import {
   addTag,
   getTag,

src/architecture/CreatureUtils.ts

@@ -1,4 +1,4 @@
-import { generate as generateV5 } from "https://deno.land/std@0.223.0/uuid/v5.ts";
+import { generate as generateV5 } from "https://deno.land/std@0.224.0/uuid/v5.ts";
 import { Creature } from "../Creature.ts";
 
 export class CreatureUtil {

src/architecture/ElitismUtils.ts

@@ -5,7 +5,7 @@ import {
   red,
   white,
   yellow,
-} from "https://deno.land/std@0.223.0/fmt/colors.ts";
+} from "https://deno.land/std@0.224.0/fmt/colors.ts";
 import { addTag, getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../Creature.ts";
 

src/architecture/FineTune.ts

@@ -1,4 +1,4 @@
-import { blue, bold, cyan } from "https://deno.land/std@0.223.0/fmt/colors.ts";
+import { blue, bold, cyan } from "https://deno.land/std@0.224.0/fmt/colors.ts";
 import { addTag, getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../Creature.ts";
 import { CreatureUtil } from "./CreatureUtils.ts";

src/architecture/Neat.ts

@@ -1,6 +1,6 @@
-import { blue } from "https://deno.land/std@0.223.0/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.223.0/fmt/duration.ts";
-import { ensureDirSync } from "https://deno.land/std@0.223.0/fs/mod.ts";
+import { blue } from "https://deno.land/std@0.224.0/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.224.0/fmt/duration.ts";
+import { ensureDirSync } from "https://deno.land/std@0.224.0/fs/mod.ts";
 import {
   addTag,
   getTag,
@@ -21,7 +21,7 @@ import { makeElitists } from "./ElitismUtils.ts";
 import { fineTuneImprovement } from "./FineTune.ts";
 import { Fitness } from "./Fitness.ts";
 import { Offspring } from "./Offspring.ts";
-import { assert } from "https://deno.land/std@0.223.0/assert/assert.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/assert.ts";
 import { creatureValidate } from "./CreatureValidate.ts";
 import { DeDuplicator } from "./DeDuplicator.ts";
 

src/architecture/Offspring.ts

@@ -3,7 +3,7 @@ import { Creature } from "../Creature.ts";
 import { SynapseExport, SynapseInternal } from "./SynapseInterfaces.ts";
 import { Neuron } from "./Neuron.ts";
 import { creatureValidate } from "./CreatureValidate.ts";
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
 
 class OffspringError extends Error {
   constructor(message: string) {

src/architecture/Training.ts

@@ -1,6 +1,6 @@
-import { blue, yellow } from "https://deno.land/std@0.223.0/fmt/colors.ts";
-import { format } from "https://deno.land/std@0.223.0/fmt/duration.ts";
-import { ensureDirSync } from "https://deno.land/std@0.223.0/fs/mod.ts";
+import { blue, yellow } from "https://deno.land/std@0.224.0/fmt/colors.ts";
+import { format } from "https://deno.land/std@0.224.0/fmt/duration.ts";
+import { ensureDirSync } from "https://deno.land/std@0.224.0/fs/mod.ts";
 import { Costs } from "../Costs.ts";
 import { Creature } from "../Creature.ts";
 import { TrainOptions } from "../config/TrainOptions.ts";

src/multithreading/workers/WorkerHandler.ts

@@ -1,4 +1,4 @@
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { addTag, getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../../Creature.ts";
 import { TrainOptions } from "../../config/TrainOptions.ts";

src/multithreading/workers/WorkerProcessor.ts

@@ -3,7 +3,7 @@ import { RequestData, ResponseData } from "./WorkerHandler.ts";
 import { CostInterface, Costs } from "../../Costs.ts";
 import { Creature } from "../../Creature.ts";
 import { trainDir } from "../../architecture/Training.ts";
-import { assert } from "https://deno.land/std@0.223.0/assert/assert.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/assert.ts";
 import { creatureValidate } from "../../architecture/CreatureValidate.ts";
 
 export class WorkerProcessor {

src/reconstruct/CRISPR.ts

@@ -1,4 +1,4 @@
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
 import {
   addTag,
   getTag,
@@ -80,6 +80,7 @@ export class CRISPR {
       UUIDs.set(node.uuid, node.index);
     });
 
+    let adjustIndx = 0;
     if (dna.neurons) {
       let firstDnaOutputIndex: number = -1;
       dna.neurons.forEach((neuron) => {
@@ -98,12 +99,20 @@ export class CRISPR {
           }
           ((neuron as unknown) as { type: string }).type = "hidden";
           if (neuron.uuid?.startsWith("output-")) {
-            neuron.uuid = crypto.randomUUID();
+            const uuid = crypto.randomUUID();
+            dna.synapses.forEach((synapse) => {
+              if (synapse.fromUUID == neuron.uuid) {
+                synapse.fromUUID = uuid;
+              }
+            });
+
+            neuron.uuid = uuid;
+            UUIDs.set(uuid, indx);
           }
         }
       });
 
-      const adjustIndx = firstNetworkOutputIndex - firstDnaOutputIndex +
+      adjustIndx = firstNetworkOutputIndex - firstDnaOutputIndex +
         dna.neurons.length;
 
       let outputIndx: number = 0;
@@ -117,15 +126,15 @@ export class CRISPR {
             ? UUIDs.has(dnaNeuron.uuid) ? crypto.randomUUID() : dnaNeuron.uuid
             : crypto.randomUUID();
 
-          if (uuid.startsWith("output-")) {
-            uuid = crypto.randomUUID();
-          }
+          // if (uuid.startsWith("output-")) {
+          //   uuid = crypto.randomUUID();
+          // }
         }
         let indx;
         if (dnaNeuron.index !== undefined) {
           indx = dnaNeuron.index + adjustIndx;
         } else {
-          indx = tmpCreature.neurons.length;
+          indx = UUIDs.size - 1; //tmpCreature.neurons.length;
         }
 
         const neuron = new Neuron(
@@ -136,72 +145,84 @@ export class CRISPR {
           dnaNeuron.squash,
         );
         neuron.index = indx;
-
+        UUIDs.set(uuid, indx);
         addTag(neuron, "CRISPR", dna.id);
         if (dnaNeuron.comment) {
           addTag(neuron, "comment", dnaNeuron.comment);
         }
         tmpCreature.neurons.push(neuron);
-        if (dnaNeuron.type == "output") {
-          if (firstDnaOutputIndex == -1) {
-            firstDnaOutputIndex = indx;
-          }
-        }
-      });
-
-      dna.synapses.forEach((c) => {
-        const from = c.from !== undefined
-          ? c.from
-          : ((c.fromRelative ? c.fromRelative : 0) + adjustIndx);
-        assert(
-          from !== undefined,
-          "Invalid connection (from): " + JSON.stringify(c),
-        );
-
-        const to = c.to !== undefined
-          ? c.to
-          : ((c.toRelative ? c.toRelative : 0) + adjustIndx);
-
-        assert(
-          to !== undefined,
-          "Invalid connection (to): " + JSON.stringify(c),
-        );
-
-        tmpCreature.connect(from, to, c.weight, c.type);
+        // if (dnaNeuron.type == "output") {
+        //   if (firstDnaOutputIndex == -1) {
+        //     firstDnaOutputIndex = indx;
+        //   }
+        // }
       });
     }
-
-    dna.synapses.forEach((c) => {
-      let toIndx: number = -1;
-      if (c.toUUID) {
-        const indx = UUIDs.get(c.toUUID);
-        assert(indx !== undefined, "missing toUUID " + c.toUUID);
-        toIndx = indx;
+    tmpCreature.clearCache();
+    dna.synapses.forEach((s) => {
+      let from;
+      if (s.fromUUID) {
+        from = UUIDs.get(s.fromUUID);
       }
-
-      let fromIndx: number = -1;
-      if (c.fromUUID) {
-        const indx = UUIDs.get(c.fromUUID);
-        assert(indx !== undefined, "missing fromUUID " + c.fromUUID);
-        fromIndx = indx;
+      if (from == undefined) {
+        if (s.from !== undefined) {
+          from = s.from;
+        } else if (s.fromRelative !== undefined) {
+          from = s.fromRelative + adjustIndx;
+        } else {
+          throw new Error("Invalid connection (from): " + JSON.stringify(s));
+        }
       }
 
-      if (fromIndx !== -1 && toIndx !== -1) {
-        if (!tmpCreature.getSynapse(fromIndx, toIndx)) {
-          const synapse = tmpCreature.connect(
-            fromIndx,
-            toIndx,
-            c.weight,
-            c.type,
-          );
-          addTag(synapse, "CRISPR", dna.id);
-          if (c.comment) {
-            addTag(synapse, "comment", c.comment);
-          }
+      let to;
+      if (s.toUUID) {
+        to = UUIDs.get(s.toUUID);
+      }
+      if (to == undefined) {
+        if (s.to !== undefined) {
+          to = s.to;
+        } else if (s.toRelative !== undefined) {
+          to = s.toRelative + adjustIndx;
+        } else {
+          throw new Error("Invalid connection (to): " + JSON.stringify(s));
         }
       }
+
+      const synapse = tmpCreature.connect(from, to, s.weight, s.type);
+      addTag(synapse, "CRISPR", dna.id);
     });
 
+    // dna.synapses.forEach((c) => {
+    //   let toIndx: number = -1;
+    //   if (c.toUUID) {
+    //     const indx = UUIDs.get(c.toUUID);
+    //     assert(indx !== undefined, "missing toUUID " + c.toUUID);
+    //     toIndx = indx;
+    //   }
+
+    //   let fromIndx: number = -1;
+    //   if (c.fromUUID) {
+    //     const indx = UUIDs.get(c.fromUUID);
+    //     assert(indx !== undefined, "missing fromUUID " + c.fromUUID);
+    //     fromIndx = indx;
+    //   }
+
+    //   if (fromIndx !== -1 && toIndx !== -1) {
+    //     if (!tmpCreature.getSynapse(fromIndx, toIndx)) {
+    //       const synapse = tmpCreature.connect(
+    //         fromIndx,
+    //         toIndx,
+    //         c.weight,
+    //         c.type,
+    //       );
+    //       addTag(synapse, "CRISPR", dna.id);
+    //       if (c.comment) {
+    //         addTag(synapse, "comment", c.comment);
+    //       }
+    //     }
+    //   }
+    // });
+
     return tmpCreature;
   }
 
@@ -396,6 +417,11 @@ export class CRISPR {
     }
 
     delete modifiedCreature.uuid;
+    modifiedCreature.DEBUG = false;
+    Deno.writeTextFileSync(
+      ".crispr.json",
+      JSON.stringify(modifiedCreature.exportJSON(), null, 2),
+    );
     modifiedCreature.validate();
     const modifiedUUID = await CreatureUtil.makeUUID(modifiedCreature);
     if (uuid !== modifiedUUID) {

src/reconstruct/Upgrade.ts

@@ -1,4 +1,4 @@
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { CreatureExport } from "../architecture/CreatureInterfaces.ts";
 import { Creature } from "../Creature.ts";
 import { creatureValidate } from "../architecture/CreatureValidate.ts";

test/ActivationNames.ts

@@ -1,7 +1,7 @@
 import {
   assert,
   assertNotEquals,
-} from "https://deno.land/std@0.223.0/assert/mod.ts";
+} from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { Activations } from "../src/methods/activations/Activations.ts";
 
 Deno.test("ActivationNames", () => {

test/CRISPR/Aliases.ts

@@ -1,7 +1,7 @@
 import {
   assert,
   assertEquals,
-} from "https://deno.land/std@0.223.0/assert/mod.ts";
+} from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { CRISPR, CrisprInterface } from "../../src/reconstruct/CRISPR.ts";
 
 Deno.test("editAliases", () => {

test/CRISPR/Append.ts

@@ -0,0 +1,57 @@
+import { assertEquals } from "https://deno.land/[email protected]/assert/mod.ts";
+import { Creature } from "../../src/Creature.ts";
+import { CRISPR } from "../../src/reconstruct/CRISPR.ts";
+import { CreatureInternal } from "../../src/architecture/CreatureInterfaces.ts";
+
+((globalThis as unknown) as { DEBUG: boolean }).DEBUG = true;
+
+Deno.test("CRISPR/Append", async () => {
+  const networkTXT = Deno.readTextFileSync("test/data/CRISPR/network.json");
+  const network = Creature.fromJSON(JSON.parse(networkTXT));
+  network.validate();
+
+  const crispr = new CRISPR(network);
+  const dnaTXT = Deno.readTextFileSync("test/data/CRISPR/DNA-RANGE.json");
+
+  const networkIF = await crispr.cleaveDNA(JSON.parse(dnaTXT));
+  (networkIF as Creature).validate();
+  const expectedJSON = JSON.parse(
+    Deno.readTextFileSync("test/data/CRISPR/expected-range.json"),
+  );
+
+  const expectedTXT = JSON.stringify(
+    clean(Creature.fromJSON(expectedJSON).internalJSON()),
+    null,
+    2,
+  );
+  Deno.writeTextFileSync("test/data/CRISPR/.expected-range.txt", expectedTXT);
+
+  const actualJSON = clean((networkIF as Creature).internalJSON());
+
+  const actualTXT = JSON.stringify(
+    actualJSON,
+    null,
+    2,
+  );
+
+  Deno.writeTextFileSync(
+    "test/data/CRISPR/.actual-range.json",
+    JSON.stringify((networkIF as Creature).exportJSON(), null, 2),
+  );
+  Deno.writeTextFileSync("test/data/CRISPR/.actual-range.txt", actualTXT);
+  assertEquals(actualTXT, expectedTXT, "should have converted");
+});
+
+function clean(creature: CreatureInternal): { uuid: string | undefined } {
+  const cleanCreature = JSON.parse(JSON.stringify(creature));
+  delete cleanCreature.tags;
+  delete cleanCreature.uuid;
+  cleanCreature.neurons.forEach((neuron: { uuid: string | undefined }) => {
+    delete neuron.uuid;
+  });
+
+  cleanCreature.synapses.forEach((synapse: { tags: string | undefined }) => {
+    delete synapse.tags;
+  });
+  return cleanCreature;
+}

test/CRISPR/CRISPR.ts

@@ -1,7 +1,7 @@
 import {
   assert,
   assertEquals,
-} from "https://deno.land/std@0.223.0/assert/mod.ts";
+} from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../../src/Creature.ts";
 import { CreatureInternal } from "../../src/architecture/CreatureInterfaces.ts";

test/CRISPR/From.ts

@@ -1,7 +1,7 @@
 import {
   assert,
   assertAlmostEquals,
-} from "https://deno.land/std@0.223.0/assert/mod.ts";
+} from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { getTag } from "https://deno.land/x/[email protected]/mod.ts";
 import { Creature } from "../../src/Creature.ts";
 import { CRISPR } from "../../src/reconstruct/CRISPR.ts";

test/Clipped.ts

@@ -1,4 +1,4 @@
-import { assert } from "https://deno.land/std@0.223.0/assert/mod.ts";
+import { assert } from "https://deno.land/std@0.224.0/assert/mod.ts";
 import { Creature } from "../src/Creature.ts";
 
 import { CreatureInternal } from "../src/architecture/CreatureInterfaces.ts";