chat style prompts

.gitignore

@@ -1,6 +1,7 @@
 build.log
 dist
 node_modules
-package-lock.json
-package.json
 draft
+
+training.jsonl
+validation.jsonl

cases/0005/index0.heta

@@ -0,0 +1,6 @@
+/*
+    Create reaction in Heta notation with one substrate and one product.
+*/
+
+// reaction of s1 degradation
+r1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;

cases/0005/index1.heta

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+/*
+    Add all necessary components: species, compartments, and constants.
+*/
+// index.heta
+
+// reaction of s1 degradation
+r1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;
+
+// species 
+s1 @Species {compartment: comp1} .= 10;
+p1 @Species {compartment: comp1} .= 0;
+
+// compartment of size 1
+comp1 @Compartment .= 1;
+
+// constant of reaction
+k1 @Const = 0.01;

cases/0006/index0.heta

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+/*
+  Create reaction with no substrate and one product in Heta.
+*/
+
+// reactions
+r1 @Reaction {actors: => p1} := k1 * comp1;

cases/0006/index1.heta

@@ -0,0 +1,9 @@
+/*
+  Add necessary species
+*/
+
+// reactions
+r1 @Reaction {actors: => p1} := k1 * comp1;
+
+// species
+p1 @Species {compartment: comp1} .= 0;

cases/0007/index0.heta

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+/*
+  Create mass-action reaction in Heta notation by the stoicheometry: s1 => p1.
+*/
+
+// reactions
+r1 @Reaction {actors: s1 => p1} := k1 * s1 * comp1;
+

cases/0008/index0.heta

@@ -0,0 +1,6 @@
+/*
+  Create mass-action reaction in Heta notation by the stoicheometry: 2s1 => p1.
+*/
+
+// reactions
+r1 @Reaction {actors: 2s1 => p1} := k1 * s1^2 * comp1;

cases/0008/index1.heta

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+/*
+  Make reaction reversible
+*/
+
+// reactions
+r1 @Reaction {actors: 2s1 <=> p1} := (k1 * s1^2 - k2 * p1) * comp2;

cases/0009/index0.heta

@@ -0,0 +1,7 @@
+/*
+  Create mass-action reversible reaction in Heta notation by the stoicheometry: 2s1 => 2p1.
+*/
+// index.heta
+
+// reactions
+r1 @Reaction {actors: 2s1 => p1} := (k1 * s1^2 - k2 * p1^2) * comp1;

cases/0010/index0.heta

@@ -0,0 +1,7 @@
+/*
+  Create mass-action reversible reaction in Heta notation by the stoicheometry: s1 + 2s2 + 3s3 <=> p1 + 2p2 + 3p3.
+*/
+// index.heta
+
+// reactions
+r1 @Reaction {actors: s1 + 2s2 + 3s3 <=> p1 + 2p2 + 3p3} := (k1 * s1 * s2^2 * s3^3 - k2 * p1 * p2^2 * p3^3) * comp1;

cases/0011/index0.heta

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+/*
+    Create complete Heta model with two reactions with stoicheometry: A + 2B => C and C => D.
+*/
+// index.heta
+
+// reactions
+r1 @Reaction {actors: A + 2B => C} := k1 * A * B^2 * comp1;
+r2 @Reaction {actors: C => D} := k2 * C * comp1;
+
+// species
+A @Species {compartment: comp1} .= 1;
+B @Species {compartment: comp1} .= 10;
+C @Species {compartment: comp1} .= 0;
+D @Species {compartment: comp1} .= 0;
+
+// compartments
+comp1 @Compartment .= 1;
+
+// parameters
+k1 @Const = 0.01;
+k2 @Const = 0.001;

js/create-prompt.js

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+const path = require('path');
+const fs = require('fs');
+const { globSync } = require('glob');
+const systemPrompt = `
+    You will be provided with description of dynamic model, and your task is to create model in Heta format.
+    Try not to create supplementary text, only model and comments.
+`;
+
+const directoryPath = './cases';
+const validationPath = './validation';
+const pattern = 'index*.heta';
+
+const directories = fs.readdirSync(directoryPath, { withFileTypes: true })
+    .filter((dirent) => dirent.isDirectory())
+    .map((dirent) => dirent.name);
+
+let lines = directories.map((directory) => {
+    const files = globSync(pattern, { cwd: path.join(directoryPath, directory) }).sort();
+    let messages = [{role: 'system', content: systemPrompt}];
+
+    files.forEach((file) => {
+        const filePath = path.join(directoryPath, directory, file);
+        const content = fs.readFileSync(filePath, 'utf8');
+        let matches = content.match(/\/\*([\s\S]*)\*\/([\s\S]*)/);
+        let prompt = matches[1].replace(/\s+/g, ' ');
+        let completion = matches[2].replace(/^[\s]+/, '').replace(/\r/g, '');
+        messages.push({role: 'user', content: prompt});
+        messages.push({role: 'assistant', content: completion});
+    });
+
+    return JSON.stringify({messages});
+}).join('\n');;
+
+fs.writeFileSync('training.jsonl', lines);