commit 22f8a3144a8d354982b1d3ac85df9927f765dfd0
Author: Ján Malinovský <jan.malinovsky@student.tuke.sk>
Date:   Sat May 16 06:22:02 2026 +0000

    Nahrát soubory do „/“

diff --git a/graph_builder.py b/graph_builder.py
new file mode 100644
index 0000000..a74231c
--- /dev/null
+++ b/graph_builder.py
@@ -0,0 +1,411 @@
+import json
+import os
+import networkx as nx
+import re
+import hashlib
+
+from ingest import load_documents
+from llm import llm_call
+
+# Cleans response to avoid errors
+def clean_llm_response(text: str) -> str:
+    """
+    Removes markdown, extra text, and extracts JSON safely.
+    """
+
+    if not text:
+        raise ValueError("LLM returned empty response")
+
+    text = text.strip()
+
+    # Remove ```json or ``` wrappers
+    text = re.sub(r"^```json", "", text)
+    text = re.sub(r"^```", "", text)
+    text = re.sub(r"```$", "", text)
+
+    text = text.strip()
+
+    # Try to extract JSON object if model adds extra text
+    match = re.search(r"\{.*\}", text, re.DOTALL)
+    if match:
+        return match.group(0)
+
+    return text
+
+# Gets cached extraction for a chunk, or extracts and caches it
+def get_cached_extraction(chunk, cache_dir="cache"):
+
+    os.makedirs(cache_dir, exist_ok=True)
+
+    # Create unique hash for chunk
+    chunk_hash = hashlib.md5(
+        chunk.encode("utf-8")
+    ).hexdigest()
+
+    cache_path = os.path.join(
+        cache_dir,
+        f"{chunk_hash}.json"
+    )
+
+    
+    # Cache Load (if exists) 
+    if os.path.exists(cache_path):
+
+        print(f"[CACHE HIT] {chunk_hash}")
+
+        with open(cache_path, "r", encoding="utf-8") as f:
+            return json.load(f)
+
+   
+    # Extract json and store in cache
+    print(f"[CACHE MISS] {chunk_hash}")
+
+    extraction = extract_entities_and_relations(chunk)
+
+    
+    # Save cache
+    with open(cache_path, "w", encoding="utf-8") as f:
+        json.dump(
+            extraction,
+            f,
+            indent=2,
+            ensure_ascii=False
+        )
+
+    return extraction
+
+# Calls LLM to get entities and realtions (.json) and saves them to cache
+def extract_entities_and_relations(text):
+
+    text = text[:8000]  # prevent context overflow
+
+    prompt = f"""
+You are an educational knowledge graph extraction system.
+
+Your task:
+
+Extract educational entities and relations.
+
+Rules:
+- Return ONLY EXACT JSON
+- Use ONLY meaningful educational concepts
+- NO markdown
+- NO explanations
+- NO extra text
+- Use these relations ONLY:
+[  "is_a",
+  "part_of",
+  "uses",
+  "teaches",
+  "requires",
+  "depends_on",
+  "implements",
+  "applies_to",
+  "subfield_of",
+  "contains",
+  "defined_by"]
+- Entity names must be normalized:
+    GOOD:
+    - "Machine Learning"
+    - "Artificial Intelligence"
+    BAD:
+    - "machine learning"
+    - "ML"
+    - "AI systems"
+- Prefer fewer HIGH QUALITY relations over many weak relations
+- Every entity should participate in at least one relation
+
+OUTPUT FORMAT EXACTLY:
+{{
+  "entities": [
+    {{"name": "...", "type": "..."}}
+  ],
+  "relations": [
+    {{
+      "source": "...",
+      "target": "...",
+      "relation": "..."
+    }}
+  ]
+}}
+
+TEXT:
+{text}
+"""
+
+    response = llm_call([
+        {"role": "user", "content": prompt}
+    ])
+
+    cleaned = clean_llm_response(response)
+
+    try:
+        data = json.loads(cleaned)
+
+    except json.JSONDecodeError:
+        print("\nINVALID JSON")
+        print(cleaned)
+        raise
+
+    # Checks if llm output is valid
+    entities = data.get("entities", [])
+    relations = data.get("relations", [])
+
+    # Normalize entity names
+    normalized_entities = {}
+
+    for ent in entities:
+
+        name = ent["name"].strip()
+
+        # title case normalization
+        name = " ".join(word.capitalize() for word in name.split())
+
+        normalized_entities[name] = {
+            "name": name,
+            "type": ent.get("type", "concept")
+        }
+
+    entity_names = set(normalized_entities.keys())
+
+    valid_relations = []
+
+    for rel in relations:
+
+        source = rel["source"].strip()
+        target = rel["target"].strip()
+        relation = rel["relation"].strip()
+
+        source = " ".join(word.capitalize() for word in source.split())
+        target = " ".join(word.capitalize() for word in target.split())
+
+        # Skip self-loops
+        if source == target:
+            continue
+
+        # Ensure both entities exist
+        if source not in entity_names:
+            continue
+
+        if target not in entity_names:
+            continue
+
+        valid_relations.append({
+            "source": source,
+            "target": target,
+            "relation": relation
+        })
+
+    # Remove isolated entities
+    connected = set()
+
+    for rel in valid_relations:
+        connected.add(rel["source"])
+        connected.add(rel["target"])
+
+    final_entities = [
+        ent for ent in normalized_entities.values()
+        if ent["name"] in connected
+    ]
+
+    return {
+        "entities": final_entities,
+        "relations": valid_relations
+    }
+
+# Chunks document into chunks (with overlap)
+def chunk_text(text, chunk_size=8000, overlap=300):
+
+    text = text.replace("\r", " ")
+
+    paragraphs = text.split("\n")
+
+    chunks = []
+    current = ""
+
+    for para in paragraphs:
+
+        para = para.strip()
+
+        # Skip useless tiny paragraphs
+        if len(para) < 40:
+            continue
+
+        if len(current) + len(para) < chunk_size:
+
+            current += para + "\n"
+
+        else:
+
+            chunks.append(current)
+
+            # overlap keeps context continuity
+            current = current[-overlap:] + "\n" + para + "\n"
+
+    if current:
+        chunks.append(current)
+
+    return chunks
+
+# Builds graph from documents (must be in documents folder [.pdf, .txt, .docx])
+def build_graph_from_documents(folder="documents"):
+
+    G = nx.DiGraph()
+
+    docs = load_documents(folder)
+
+    for doc in docs:
+
+        print(f"\n[INFO] Processing document: {doc['filename']}")
+
+        # Document is split into chunks
+        chunks = chunk_text(doc["content"])
+
+        print(f"[INFO] Total chunks: {len(chunks)}")
+
+        # Process chunk by chunk
+        for idx, chunk in enumerate(chunks):
+
+            print(f"[INFO] Processing chunk {idx + 1}/{len(chunks)}")
+
+            try:
+                extraction = get_cached_extraction(chunk)
+
+            except Exception as e:
+
+                print(f"[WARN] Extraction failed on chunk {idx + 1}")
+                print(e)
+
+                continue
+
+            # Add entities (nodes) to graph
+            for ent in extraction["entities"]:
+
+                G.add_node(
+                    ent["name"],
+                    type=ent["type"],
+                    source_doc=doc["filename"]
+                )
+
+            # Adds entity realtions (links nodes)
+            for rel in extraction["relations"]:
+
+                G.add_edge(
+                    rel["source"],
+                    rel["target"],
+                    relation=rel["relation"],
+                    source_doc=doc["filename"]
+                )
+
+    return G
+
+# Saves graph to file 
+def save_graph(G, path="graph/kg.graphml"):
+    os.makedirs(os.path.dirname(path), exist_ok=True)
+    nx.write_graphml(G, path)
+    print(f"Graph saved to {path}")
+
+# Loads graph from file
+def load_graph(path="graph/kg.graphml"):
+    return nx.read_graphml(path)
+
+# Adds document to graph
+def add_document(filepath, G):
+
+    docs = load_documents(folder=filepath)
+
+    if not docs:
+        print(f"[WARN] No documents found in: {filepath}")
+        return
+
+    doc = docs[0]
+
+    print(f"\n[INFO] Adding document: {doc['filename']}")
+
+    # Document is split into chunks 
+    chunks = chunk_text(doc["content"])
+
+    print(f"[INFO] Total chunks: {len(chunks)}")
+
+    # Process chunk by chunk
+    for idx, chunk in enumerate(chunks):
+
+        print(f"[INFO] Processing chunk {idx + 1}/{len(chunks)}")
+
+        try:
+
+            extraction = get_cached_extraction(chunk)
+
+        except Exception as e:
+
+            print(f"[WARN] Extraction failed on chunk {idx + 1}")
+            print(e)
+
+            continue
+
+        # Add entities (nodes) to graph
+        for ent in extraction["entities"]:
+
+            G.add_node(
+                ent["name"],
+                type=ent["type"],
+                source_doc=doc["filename"]
+            )
+
+        # Adds entity realtions (links nodes)
+        for rel in extraction["relations"]:
+
+            G.add_edge(
+                rel["source"],
+                rel["target"],
+                relation=rel["relation"],
+                source_doc=doc["filename"]
+            )
+
+    print(f"[INFO] Finished adding {doc['filename']}")
+
+# Removes document from graph
+def remove_document(filename, G):
+
+    edges_to_remove = []
+
+    for u, v, data in G.edges(data=True):
+
+        if data.get("source_doc") == filename:
+            edges_to_remove.append((u, v))
+
+    G.remove_edges_from(edges_to_remove)
+
+    # Remove orphan nodes
+    isolated_nodes = list(nx.isolates(G))
+
+    G.remove_nodes_from(isolated_nodes)
+
+    print(f"[INFO] Removed document: {filename}")
+
+'''
+#test
+if __name__ == "__main__":
+
+    docs = load_documents()
+
+    extraction = extract_entities_and_relations(
+        docs[0]["content"]
+    )
+
+    print(extraction)
+'''
+
+#test
+if __name__ == "__main__":
+
+    #G2 = load_graph()
+
+    #print(G2.nodes(data=True))
+    G = build_graph_from_documents()
+
+    save_graph(G)
+    #print(G.nodes(data=True))
+
+    #print(G.edges(data=True))
+
diff --git a/ingest.py b/ingest.py
new file mode 100644
index 0000000..407975d
--- /dev/null
+++ b/ingest.py
@@ -0,0 +1,43 @@
+from pathlib import Path
+from pypdf import PdfReader
+from docx import Document
+
+def load_documents(folder="documents"):
+    docs = []
+
+    for file in Path(folder).glob("*"):
+        if file.suffix == ".txt":
+            text = file.read_text(encoding="utf-8")
+
+            docs.append({
+                "filename": file.name,
+                "content": text
+            })
+            
+        elif file.suffix == ".pdf":
+            reader = PdfReader(file)
+            text = ""
+            for page in reader.pages:
+                text += page.extract_text()
+
+            docs.append({
+                "filename": file.name,
+                "content": text
+            })
+
+        elif file.suffix == ".docx":
+            doc = Document(file)
+            text = "\n".join([paragraph.text for paragraph in doc.paragraphs])
+
+            docs.append({
+                "filename": file.name,
+                "content": text
+            })
+
+    return docs
+
+#test
+if __name__ == "__main__":
+    docs = load_documents()
+
+    print(docs)
\ No newline at end of file
diff --git a/llm.py b/llm.py
new file mode 100644
index 0000000..d801831
--- /dev/null
+++ b/llm.py
@@ -0,0 +1,35 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Dict, List
+import requests
+
+# TUKE LLM Connection
+UNIVERSITY_BASE_URL = "https://ui.tukekemt.xyz/api/v1/chat/completions"
+UNIVERSITY_API_KEY  = "sk-06098ff9afb946c2b9d197cb400cd752"
+UNIVERSITY_MODEL    = "model2"
+
+# LLM call
+def llm_call(messages: List[Dict[str, str]]) -> str:
+    """Send a list of {role, content} dicts to the university LLM and return the reply text."""
+    resp = requests.post(
+        UNIVERSITY_BASE_URL,
+        json={"model": UNIVERSITY_MODEL, "messages": messages, "stream": False},
+        headers={
+            "Authorization": f"Bearer {UNIVERSITY_API_KEY}",
+            "Content-Type": "application/json",
+        },
+        timeout=600,
+    )
+    resp.raise_for_status()
+    return resp.json()["choices"][0]["message"]["content"]
+
+#test
+if __name__ == "__main__":
+    response = llm_call([
+        {
+            "role": "user",
+            "content": "Say hello"
+        }
+    ])
+
+    print(response)
\ No newline at end of file
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..97ec983
--- /dev/null
+++ b/main.py
@@ -0,0 +1,88 @@
+from graph_builder import (
+    build_graph_from_documents,
+    save_graph,
+    load_graph
+)
+from react_agent import react_agent  
+from visualization import visualize_graph
+
+GRAPH_PATH = "graph/kg.graphml"
+
+# Create graph or load existing one
+def get_or_build_graph(force_rebuild=False):
+
+    if not force_rebuild:
+        try:
+            print("\n[INFO] Loading existing graph...")
+            G = load_graph(GRAPH_PATH)
+
+            print(f"[INFO] Loaded graph: {len(G.nodes())} nodes, {len(G.edges())} edges")
+            return G
+
+        except Exception as e:
+            print(f"[WARN] Could not load graph: {e}")
+            print("[INFO] Rebuilding graph...")
+
+    print("\n[INFO] Building graph from documents...")
+    G = build_graph_from_documents()
+
+    print(f"[INFO] Built graph: {len(G.nodes())} nodes, {len(G.edges())} edges")
+
+    print("\n[INFO] Saving graph...")
+    save_graph(G, GRAPH_PATH)
+    return G
+
+# Testing questions (query)
+def ask_question(G, question):
+
+    print("\n" + "=" * 60)
+    print(f"QUESTION: {question}")
+    print("=" * 60)
+
+    history = []
+
+    result = react_agent(
+        user_message=question,
+        history=history,
+        G=G
+    )
+
+    print("\n--- FINAL ANSWER ---")
+    print(result.answer)
+
+    print("\n--- EVIDENCE (GRAPH) ---")
+    print(result.evidence)
+
+    return result
+
+
+# Visualisation
+def show_graph(G):
+
+    print("\n[INFO] Generating visualization...")
+
+    visualize_graph(G)
+
+    print("[INFO] Graph saved as kg.html")
+
+# Run main
+if __name__ == "__main__":
+
+    # Create graph or load existing one
+    G = get_or_build_graph(force_rebuild=False)
+
+    # Run visualisation.py (optional and for testing)
+    #show_graph(G)
+
+    # Testing questions (query)
+    test_questions = [
+        #"What is taught in Informatics?",
+        #"What is used in machine learning?",
+        #"What Literary Texts are taught in Slovak Language And Slovak Literature?",
+        "Čo sa učí na predmete Slovenský jazyk a literatúra?"
+    ]
+
+    for q in test_questions:
+        ask_question(G, q)
+
+    print("\n[INFO] PIPELINE COMPLETED")
\ No newline at end of file
diff --git a/models.py b/models.py
new file mode 100644
index 0000000..b4b0ddd
--- /dev/null
+++ b/models.py
@@ -0,0 +1,30 @@
+from dataclasses import dataclass
+from typing import Optional, List
+
+@dataclass
+class GraphRAGResponse:
+
+    question: str
+
+    answer: str
+
+    evidence: Optional[str] = None
+
+    entities_used: Optional[List[str]] = None
+
+    relations_used: Optional[List[str]] = None
+
+    source_documents: Optional[List[str]] = None
+
+    def __str__(self):
+
+        return (
+            "\nGraphRAGResponse(\n"
+            f"  question          = {self.question!r}\n"
+            f"  answer            = {self.answer!r}\n"
+            f"  evidence          = {self.evidence!r}\n"
+            f"  entities_used     = {self.entities_used!r}\n"
+            f"  relations_used    = {self.relations_used!r}\n"
+            f"  source_documents  = {self.source_documents!r}\n"
+            ")"
+        )
\ No newline at end of file
diff --git a/react_agent.py b/react_agent.py
new file mode 100644
index 0000000..c2cf4c7
--- /dev/null
+++ b/react_agent.py
@@ -0,0 +1,82 @@
+from tools import TOOL_MAP
+from llm import llm_call
+import re
+from typing import List, Dict
+from models import GraphRAGResponse
+
+SYSTEM_PROMPT = """
+You are an educational GraphRAG assistant for schools.
+
+You MUST use tools when answering knowledge questions.
+
+Available tool:
+- query_knowledge_graph
+
+Format:
+Action: query_knowledge_graph
+Action Input: <question>
+
+OR:
+
+Final Answer: <answer>
+"""
+
+def parse_action(text: str):
+    action = re.search(r"Action:\s*(\w+)", text)
+    input_ = re.search(r"Action Input:\s*(.+)", text)
+
+    if action and input_:
+        return action.group(1), input_.group(1)
+
+    return None
+
+def parse_final(text: str):
+    m = re.search(r"Final Answer:\s*(.+)", text, re.DOTALL)
+    return m.group(1).strip() if m else None
+
+def react_agent(user_message: str, history: List[Dict], G=None, max_steps: int = 5):
+
+    messages = (
+        [{"role": "system", "content": SYSTEM_PROMPT}]
+        + history
+        + [{"role": "user", "content": user_message}]
+    )
+
+    last = ""
+
+    for _ in range(max_steps):
+
+        reply = llm_call(messages)
+        last = reply
+
+        final = parse_final(reply)
+        if final:
+            return GraphRAGResponse(
+                question=user_message,
+                answer=final,
+                evidence=""
+            )
+
+        action = parse_action(reply)
+
+        if action:
+
+            tool_name, tool_input = action
+
+            if tool_name == "query_knowledge_graph":
+                result = TOOL_MAP[tool_name](tool_input, G)
+
+                messages.append({"role": "assistant", "content": reply})
+                messages.append({"role": "user", "content": f"Observation: {result}"})
+
+                return GraphRAGResponse(
+                    question=user_message,
+                    answer=result["answer"],
+                    evidence=result["evidence"]
+                )
+
+    return GraphRAGResponse(
+        question=user_message,
+        answer=last,
+        evidence=""
+)
\ No newline at end of file
diff --git a/retrieval.py b/retrieval.py
new file mode 100644
index 0000000..645b459
--- /dev/null
+++ b/retrieval.py
@@ -0,0 +1,37 @@
+def retrieve_subgraph(G, query):
+    query = query.lower()
+
+    context = []
+
+    for node in G.nodes(data=True):
+
+        node_name = node[0].lower()
+
+        if (
+            query in node_name
+            or node_name in query
+        ):
+
+            for neighbor in G.neighbors(node[0]):
+
+                edge = G[node[0]][neighbor]
+
+                context.append(
+                    f"{node[0]} --{edge.get('relation','related_to')}--> {neighbor}"
+                )
+
+    return "\n".join(context)
+
+#test
+from graph_builder import load_graph
+
+if __name__ == "__main__":
+
+    G = load_graph()
+
+    result = retrieve_subgraph(
+        G,
+        "Python"
+    )
+
+    print(result)
\ No newline at end of file
diff --git a/tools.py b/tools.py
new file mode 100644
index 0000000..c4f5e45
--- /dev/null
+++ b/tools.py
@@ -0,0 +1,50 @@
+from retrieval import retrieve_subgraph
+from llm import llm_call
+
+def query_knowledge_graph(question: str, G):
+
+    graph_context = retrieve_subgraph(G, question)
+
+    prompt = f"""
+You are an educational assistant.
+
+Use ONLY the graph knowledge below to answer.
+
+Graph Knowledge:
+{graph_context}
+
+Question:
+{question}
+
+Rules:
+- If graph is empty, say "No information in knowledge graph"
+- Be concise and educational
+"""
+
+    response = llm_call([
+        {"role": "user", "content": prompt}
+    ])
+
+    return {
+        "answer": response,
+        "evidence": graph_context
+    }
+
+
+TOOL_MAP = {
+    "query_knowledge_graph": query_knowledge_graph,
+}
+
+#test
+from graph_builder import load_graph
+
+if __name__ == "__main__":
+
+    G = load_graph()
+
+    result = query_knowledge_graph(
+        "What is used in machine learning?",
+        G
+    )
+
+    print(result)
\ No newline at end of file
diff --git a/visualization.py b/visualization.py
new file mode 100644
index 0000000..e935878
--- /dev/null
+++ b/visualization.py
@@ -0,0 +1,31 @@
+from pyvis.network import Network
+from graph_builder import load_graph
+
+def visualize_graph(G):
+    net = Network(
+        directed=True,
+        notebook=False   
+    )
+
+    for node in G.nodes():
+        net.add_node(node)
+
+    for u, v, data in G.edges(data=True):
+        net.add_edge(
+            u,
+            v,
+            label=data.get("relation", "")
+        )
+
+    output_path = "kg.html"
+
+    net.write_html(output_path)
+
+    print(f"Graph saved to {output_path}")
+    
+#test
+if __name__ == "__main__":
+
+    G = load_graph()
+
+    visualize_graph(G)
\ No newline at end of file