omnibiofex 4.2.0 → 4.3.0

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Files changed (2) hide show
  1. package/package.json +1 -1
  2. package/src/commands/diagram.js +123 -93
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "omnibiofex",
3
- "version": "4.2.0",
3
+ "version": "4.3.0",
4
4
  "description": "OmniBioFex X - The Autonomous Research Operating System",
5
5
  "main": "bin/obx",
6
6
  "bin": {
package/src/commands/diagram.js CHANGED
@@ -21,136 +21,162 @@ const STYLES = {
21
21
  network: { name: 'Network', cost: 70, description: 'Interconnected nodes' }
22
22
  };
23
23
 
24
- // Generate ASCII banner
24
+ // Generate ASCII banner (single line)
25
25
  function banner(title, width = 80) {
26
- const top = `╔${'═'.repeat(width)}╗`;
27
- const bottom = `╚${'═'.repeat(width)}╝`;
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- const padding = Math.max(0, width - title.length - 2);
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+ const safeTitle = (title || 'DIAGRAM').substring(0, width - 4);
27
+ const padding = width - safeTitle.length - 4;
29
28
  const leftPad = Math.floor(padding / 2);
30
29
  const rightPad = padding - leftPad;
31
- const content = `║ ${' '.repeat(leftPad)}${title}${' '.repeat(rightPad)} ║`;
32
- return `${top}\n${content}\n${bottom}`;
30
+ return `╔${'═'.repeat(width)}╗\n║ ${' '.repeat(leftPad)}${safeTitle}${' '.repeat(rightPad)} ║\n╚${'═'.repeat(width)}╝`;
33
31
  }
34
32
 
35
- // Generate node box
36
- function node(text, width = 20) {
37
- const safeText = text.substring(0, width - 2);
38
- const padding = Math.max(0, width - safeText.length - 2);
33
+ // Generate single-line node
34
+ function nodeLine(text, width = 40) {
35
+ const safeText = (text || '').substring(0, width - 4);
36
+ const padding = width - safeText.length - 4;
39
37
  const leftPad = Math.floor(padding / 2);
40
38
  const rightPad = padding - leftPad;
41
- const top = `┌${'─'.repeat(width)}┐`;
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- const bottom = `└${'─'.repeat(width)}┘`;
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- const content = `│ ${' '.repeat(leftPad)}${safeText}${' '.repeat(rightPad)} │`;
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- return `${top}\n${content}\n${bottom}`;
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+ return `┌${'─'.repeat(width)}┐\n│ ${' '.repeat(leftPad)}${safeText}${' '.repeat(rightPad)} │\n└${'─'.repeat(width)}┘`;
45
40
  }
46
41
 
47
42
  // Generate arrow
48
- function arrow(direction = 'down') {
49
- switch (direction) {
50
- case 'down': return '│\n▼';
51
- case 'right': return '───▶';
52
- case 'left': return '◀───';
53
- case 'up': return '▲\n│';
54
- default: return '│\n▼';
55
- }
43
+ function arrow() {
44
+ return '│\n▼';
56
45
  }
57
46
 
58
- // Generate detailed diagram
47
+ // Generate detailed diagram (vertical layout)
59
48
  function generateDetailedDiagram(topic, data) {
60
- const width = 80;
61
- let diagram = banner(`${topic.toUpperCase()} RESEARCH ECOSYSTEM`, width) + '\n\n';
49
+ const width = 60;
50
+ let lines = [];
51
+
52
+ lines.push(banner(`${topic.toUpperCase()} RESEARCH ECOSYSTEM`, width));
53
+ lines.push('');
54
+
55
+ // Problem
56
+ lines.push(nodeLine('Research Problem', width));
57
+ lines.push(arrow());
58
+
59
+ // Input sources (vertical list)
60
+ const sources = (data.components && data.components.length > 0)
61
+ ? data.components.slice(0, 3)
62
+ : ['Literature Review', 'Data Collection', 'Theory Analysis'];
62
63
 
63
- // Problem identification
64
- diagram += `${' '.repeat(25)}${node('Research Problem', 25)}\n`;
65
- diagram += `${' '.repeat(37)}${arrow('down')}\n\n`;
64
+ lines.push(nodeLine('Input Sources', width));
65
+ lines.push(arrow());
66
+ sources.forEach(source => {
67
+ lines.push(` • ${source}`);
68
+ });
69
+ lines.push(arrow());
66
70
 
67
- // Three input sources
68
- const sources = data.components?.slice(0, 3) || ['Literature', 'Data', 'Theory'];
69
- diagram += `${' '.repeat(5)}${node(sources[0] || 'Literature', 18)} ${node(sources[1] || 'Data', 18)} ${node(sources[2] || 'Theory', 18)}\n`;
70
- diagram += `${' '.repeat(14)}\\ | /\n`;
71
- diagram += `${' '.repeat(15)}\\ | /\n`;
72
- diagram += `${' '.repeat(16)}\\ | /\n`;
73
- diagram += `${' '.repeat(17)}▼ ▼ ▼\n`;
74
- diagram += `${' '.repeat(15)}${node('Integration Layer', 30)}\n`;
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- diagram += `${' '.repeat(29)}${arrow('down')}\n`;
71
+ // Integration
72
+ lines.push(nodeLine('Integration Layer', width));
73
+ lines.push(arrow());
76
74
 
77
75
  // Analysis phase
78
- diagram += `${' '.repeat(20)}${node('Analysis Phase', 25)}\n`;
79
- diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
76
+ lines.push(nodeLine('Analysis Phase', width));
77
+ lines.push(arrow());
78
+
79
+ const methods = (data.methods && data.methods.length > 0)
80
+ ? data.methods.slice(0, 4)
81
+ : ['Statistical Analysis', 'Qualitative Review', 'Comparative Study', 'Predictive Modeling'];
80
82
 
81
- // Four analysis types
82
- const methods = data.methods?.slice(0, 4) || ['Statistical', 'Qualitative', 'Comparative', 'Predictive'];
83
- diagram += `${node(methods[0], 14)} ${node(methods[1], 14)} ${node(methods[2], 14)} ${node(methods[3], 14)}\n`;
84
- diagram += `${' '.repeat(7)}\\ | | /\n`;
85
- diagram += `${' '.repeat(8)}\\ | | /\n`;
86
- diagram += `${' '.repeat(9)}\\ | | /\n`;
87
- diagram += `${' '.repeat(10)}▼ ▼ ▼ ▼\n`;
88
- diagram += `${' '.repeat(15)}${node('Synthesis & Insights', 35)}\n`;
89
- diagram += `${' '.repeat(32)}${arrow('down')}\n`;
83
+ lines.push(nodeLine('Methods', width));
84
+ lines.push(arrow());
85
+ methods.forEach(method => {
86
+ lines.push(` • ${method}`);
87
+ });
88
+ lines.push(arrow());
89
+
90
+ // Synthesis
91
+ lines.push(nodeLine('Synthesis & Insights', width));
92
+ lines.push(arrow());
90
93
 
91
94
  // Output phase
92
- diagram += `${' '.repeat(20)}${node('Output Phase', 25)}\n`;
93
- diagram += `${' '.repeat(32)}${arrow('down')}\n\n`;
95
+ lines.push(nodeLine('Output Phase', width));
96
+ lines.push(arrow());
94
97
 
95
- // Three outputs
96
- const outputs = data.outputs?.slice(0, 3) || ['Publication', 'Implementation', 'Future Work'];
97
- diagram += `${node(outputs[0], 18)} ${node(outputs[1], 18)} ${node(outputs[2], 18)}\n`;
98
+ const outputs = (data.outputs && data.outputs.length > 0)
99
+ ? data.outputs.slice(0, 3)
100
+ : ['Publication', 'Implementation', 'Future Work'];
98
101
 
99
- return diagram;
102
+ lines.push(nodeLine('Outputs', width));
103
+ lines.push(arrow());
104
+ outputs.forEach(output => {
105
+ lines.push(` • ${output}`);
106
+ });
107
+
108
+ return lines.join('\n');
100
109
  }
101
110
 
102
111
  // Generate minimal diagram
103
112
  function generateMinimalDiagram(topic, data) {
104
- const width = 60;
105
- let diagram = banner(topic.toUpperCase(), width) + '\n\n';
113
+ const width = 50;
114
+ let lines = [];
106
115
 
107
- diagram += `${' '.repeat(20)}${node('Problem', 20)}\n`;
108
- diagram += `${' '.repeat(29)}${arrow('down')}\n`;
109
- diagram += `${' '.repeat(10)}${node('Research', 20)}\n`;
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- diagram += `${' '.repeat(19)}${arrow('down')}\n`;
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- diagram += `${' '.repeat(10)}${node('Analysis', 20)}\n`;
112
- diagram += `${' '.repeat(19)}${arrow('down')}\n`;
113
- diagram += `${' '.repeat(10)}${node('Solution', 20)}\n`;
116
+ lines.push(banner(topic.toUpperCase(), width));
117
+ lines.push('');
118
+ lines.push(nodeLine('Problem', width));
119
+ lines.push(arrow());
120
+ lines.push(nodeLine('Research', width));
121
+ lines.push(arrow());
122
+ lines.push(nodeLine('Analysis', width));
123
+ lines.push(arrow());
124
+ lines.push(nodeLine('Solution', width));
114
125
 
115
- return diagram;
126
+ return lines.join('\n');
116
127
  }
117
128
 
118
129
  // Generate flowchart diagram
119
130
  function generateFlowchartDiagram(topic, data) {
120
- const width = 60;
121
- const steps = data.steps?.length > 0 ? data.steps : ['Research', 'Analysis', 'Implementation'];
122
- let diagram = banner(`${topic.toUpperCase()} WORKFLOW`, width) + '\n\n';
131
+ const width = 55;
132
+ const steps = (data.steps && data.steps.length > 0)
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+ ? data.steps
134
+ : ['Research', 'Analysis', 'Implementation', 'Testing', 'Deployment'];
135
+
136
+ let lines = [];
137
+ lines.push(banner(`${topic.toUpperCase()} WORKFLOW`, width));
138
+ lines.push('');
123
139
 
124
140
  steps.forEach((step, i) => {
125
- const stepText = `Step ${i + 1}: ${step}`;
126
- diagram += `${' '.repeat(15)}${node(stepText, 45)}\n`;
141
+ lines.push(nodeLine(`Step ${i + 1}: ${step}`, width));
127
142
  if (i < steps.length - 1) {
128
- diagram += `${' '.repeat(37)}${arrow('down')}\n`;
143
+ lines.push(arrow());
129
144
  }
130
145
  });
131
146
 
132
- diagram += `\n${' '.repeat(25)}${node('✓ Complete', 20)}\n`;
133
- return diagram;
147
+ lines.push('');
148
+ lines.push(nodeLine('✓ Complete', width));
149
+
150
+ return lines.join('\n');
134
151
  }
135
152
 
136
153
  // Generate network diagram
137
154
  function generateNetworkDiagram(topic, data) {
138
- const width = 70;
139
- const nodes = data.nodes?.slice(0, 3) || ['Component A', 'Component B', 'Component C'];
140
- let diagram = banner(`${topic.toUpperCase()} NETWORK`, width) + '\n\n';
155
+ const width = 50;
156
+ const nodes = (data.nodes && data.nodes.length > 0)
157
+ ? data.nodes.slice(0, 5)
158
+ : ['Component A', 'Component B', 'Component C', 'Component D', 'Component E'];
159
+
160
+ let lines = [];
161
+ lines.push(banner(`${topic.toUpperCase()} NETWORK`, width));
162
+ lines.push('');
163
+
164
+ // Central node
165
+ lines.push(nodeLine(topic, width));
166
+ lines.push(arrow());
167
+
168
+ // Connected nodes
169
+ lines.push(nodeLine('Connected Components', width));
170
+ lines.push(arrow());
171
+ nodes.forEach(node => {
172
+ lines.push(` ├─ ${node}`);
173
+ });
174
+ lines.push(arrow());
141
175
 
142
- diagram += `${' '.repeat(25)}${node(topic, 25)}\n`;
143
- diagram += `${' '.repeat(37)}|\n`;
144
- diagram += `${' '.repeat(20)}┌────────┼────────┐\n`;
145
- diagram += `${' '.repeat(20)}│ │ │\n`;
146
- diagram += `${' '.repeat(20)}▼ ▼ ▼\n`;
147
- diagram += `${node(nodes[0], 18)} ${node(nodes[1], 18)} ${node(nodes[2], 18)}\n`;
148
- diagram += `${' '.repeat(9)}│ │ │\n`;
149
- diagram += `${' '.repeat(9)}└────────┼────────┘\n`;
150
- diagram += `${' '.repeat(18)}▼\n`;
151
- diagram += `${' '.repeat(15)}${node('Integration', 25)}\n`;
176
+ // Integration
177
+ lines.push(nodeLine('Integration & Synthesis', width));
152
178
 
153
- return diagram;
179
+ return lines.join('\n');
154
180
  }
155
181
 
156
182
  // Main diagram command
@@ -189,7 +215,7 @@ async function diagram(topic, options = {}) {
189
215
  spinner.update('Analyzing topic with AI');
190
216
  await sleep(500);
191
217
 
192
- // ✅ FIX: Use DEEP_RESEARCH task type (already supported by backend)
218
+ // Use DEEP_RESEARCH task type (already supported by backend)
193
219
  const response = await fetch(BACKEND_URL, {
194
220
  method: 'POST',
195
221
  headers: {
@@ -197,15 +223,15 @@ async function diagram(topic, options = {}) {
197
223
  'Authorization': `Bearer ${token}`
198
224
  },
199
225
  body: JSON.stringify({
200
- taskType: 'DEEP_RESEARCH', // ← Use existing task type
226
+ taskType: 'DEEP_RESEARCH',
201
227
  message: `Generate a structured breakdown of "${topic}" for an ASCII diagram.
202
228
 
203
229
  Return ONLY a valid JSON object with this exact structure (no other text):
204
230
  {
205
- "components": ["component1", "component2", "component3", "component4"],
231
+ "components": ["component1", "component2", "component3"],
206
232
  "methods": ["method1", "method2", "method3", "method4"],
207
233
  "steps": ["step1", "step2", "step3", "step4", "step5"],
208
- "nodes": ["node1", "node2", "node3"],
234
+ "nodes": ["node1", "node2", "node3", "node4", "node5"],
209
235
  "outputs": ["output1", "output2", "output3"]
210
236
  }
211
237
 
@@ -225,7 +251,7 @@ Return ONLY the JSON object, nothing else.`,
225
251
 
226
252
  const data = await response.json();
227
253
 
228
- // Parse AI response - extract JSON from the response
254
+ // Parse AI response with safe defaults
229
255
  let aiData = {
230
256
  components: [],
231
257
  methods: [],
@@ -235,12 +261,16 @@ Return ONLY the JSON object, nothing else.`,
235
261
  };
236
262
 
237
263
  try {
238
- // Try to find JSON in the response
239
264
  const responseText = data.response || '';
240
265
  const jsonMatch = responseText.match(/\{[\s\S]*\}/);
241
266
 
242
267
  if (jsonMatch) {
243
- aiData = JSON.parse(jsonMatch[0]);
268
+ const parsed = JSON.parse(jsonMatch[0]);
269
+ aiData.components = Array.isArray(parsed.components) ? parsed.components : [];
270
+ aiData.methods = Array.isArray(parsed.methods) ? parsed.methods : [];
271
+ aiData.steps = Array.isArray(parsed.steps) ? parsed.steps : [];
272
+ aiData.nodes = Array.isArray(parsed.nodes) ? parsed.nodes : [];
273
+ aiData.outputs = Array.isArray(parsed.outputs) ? parsed.outputs : [];
244
274
  }
245
275
  } catch (e) {
246
276
  console.log(chalk.yellow(' ⚠ Using default structure'));