chore: release version 0.2.4

feat(ontology): Implement OntologyIngestor and update exports

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        exclude: 'neptune-setup\.yaml$'
       - id: check-json
       - id: check-toml
       - id: check-added-large-files
@@ -49,9 +50,15 @@ repos:
     hooks:
       - id: yamllint
         args: ['-d', '{extends: default, rules: {line-length: {max: 120}}}']
+        exclude: 'neptune-setup\.yaml$'
+
+  - repo: https://github.com/aws-cloudformation/cfn-lint
+    rev: v1.43.3
+    hooks:
+      - id: cfn-lint
+        files: 'neptune-setup\.yaml$'
 
   # Removed slow hooks for faster development:
   # - mypy: Type checking (can be run manually or in CI)
   # - bandit: Security scanning (can be run separately)
   # - pytest: Testing (should be run manually, not on every commit)
-

CHANGELOG.md

@@ -7,6 +7,67 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.2.4] - 2026-01-22
+
+### Added
+- **Ontology Ingestion Module**:
+    - Implemented `OntologyIngestor` in `semantica.ingest` for parsing RDF/OWL files (Turtle, RDF/XML, JSON-LD, N3) into standardized `OntologyData` objects.
+    - Added `ingest_ontology` convenience function and integrated it into the unified `ingest(source_type="ontology")` interface.
+    - Added recursive directory scanning support for batch ontology ingestion.
+    - Exposed ingestion tools in `semantica.ontology` for better discoverability.
+    - Added `OntologyData` dataclass for consistent metadata handling (source path, format, timestamps).
+- **Documentation**:
+    - **Ontology Usage Guide**: Updated `ontology_usage.md` with comprehensive examples for single-file and directory ingestion.
+    - **API Reference**: Updated `ontology.md` with `OntologyIngestor` class documentation and method details.
+- **Tests**:
+    - **Comprehensive Test Suite**: Added `tests/ingest/test_ontology_ingestor.py` covering all supported formats, error handling, and unified interface integration.
+    - **Demo Script**: Added `examples/demo_ontology_ingest.py` for end-to-end usage demonstration.
+
+## [0.2.3] - 2026-01-20
+
+### Fixed
+- **LLM Relation Extraction Parsing**:
+    - Fixed relation extraction returning zero relations despite successful API calls to Groq and other providers
+    - Normalized typed responses from instructor/OpenAI/Groq to consistent dict format before parsing
+    - Added structured JSON fallback when typed generation yields zero relations to avoid silent empty outputs
+    - Removed acceptance of extra kwargs (`max_tokens`, `max_entities_prompt`) from relation extraction internals
+    - Filtered kwargs passed to provider LLM calls to only `temperature` and `verbose`
+- **API Parameter Handling**:
+    - Limited kwargs forwarded in chunked extraction helper to prevent parameter leakage
+    - Ensured minimal, safe parameters are passed to provider calls
+- **Pipeline Circular Import (Issues #192, #193)**:
+    - Fixed circular import between `pipeline_builder` and `pipeline_validator` triggered during `semantica.pipeline` import
+    - Lazy-loaded `PipelineValidator` inside `PipelineBuilder.__init__` and guarded type hints with `TYPE_CHECKING`
+    - Ensured `from semantica.deduplication import DuplicateDetector` no longer fails even when pipeline module is imported
+- **JupyterLab Progress Output (Issue #181)**:
+    - Added `SEMANTICA_DISABLE_JUPYTER_PROGRESS` environment variable to disable rich Jupyter/Colab progress tables
+    - When enabled, progress falls back to console-style output, preventing infinite scrolling and JupyterLab out-of-memory errors
+
+### Added
+- **Comprehensive Test Suite**:
+-    - Added unit tests (`tests/test_relations_llm.py`) with mocked LLM provider covering both typed and structured response paths
+-    - Added integration tests (`tests/integration/test_relations_groq.py`) for real Groq API calls with environment variable API key
+-    - Tests validate relation extraction completion and result parsing across different response formats
+- **Amazon Neptune Dev Environment**:
+-    - Added CloudFormation template (`cookbook/introduction/neptune-setup.yaml`) to provision a dev Neptune cluster with public endpoint and IAM auth enabled
+-    - Documented deployment, cost estimates, and IAM User vs IAM Role best practices in `cookbook/introduction/21_Amazon_Neptune_Store.ipynb`
+-    - Added `cfn-lint` to `.pre-commit-config.yaml` for validating CloudFormation templates while excluding `neptune-setup.yaml` from generic YAML linters
+- **Vector Store High-Performance Ingestion**:
+-    - Added `VectorStore.add_documents` for high-throughput ingestion with automatic embedding generation, batching, and parallel processing
+-    - Added `VectorStore.embed_batch` helper for generating embeddings for lists of texts without immediately storing them
+-    - Enabled default parallel ingestion in `VectorStore` with `max_workers=6` for common workloads
+-    - Added dedicated documentation page `docs/vector_store_usage.md` describing high-performance vector store usage and configuration
+-    - Added `tests/vector_store/test_vector_store_parallel.py` covering parallel vs sequential performance, error handling, and edge cases for `add_documents` and `embed_batch`
+
+### Changed
+- **Relation Extraction API**:
+-    - Simplified parameter interface by removing unused kwargs that were previously ignored
+-    - Improved error handling and verbose logging for debugging relation extraction issues
+-    - Enhanced robustness of post-response parsing across different LLM providers
+- **Vector Store Defaults and Examples**:
+-    - Standardized `VectorStore` default concurrency to `max_workers=6` for parallel ingestion
+-    - Updated vector store reference documentation and usage guides to rely on implicit defaults instead of requiring manual `max_workers` configuration in examples
+
 
 ## [0.2.2] - 2026-01-15
 

README.md

@@ -28,7 +28,7 @@
 
 *The missing fabric between raw data and AI engineering. A comprehensive open-source framework for building semantic layers and knowledge engineering systems that transform unstructured data into AI-ready knowledge — powering Knowledge Graph-Powered RAG (GraphRAG), AI Agents, Multi-Agent Systems, and AI applications with structured semantic knowledge.*
 
-**100% Open Source** • **MIT Licensed** • **Latest Version: 0.2.2** • **Production Ready** • **Community Driven**
+**100% Open Source** • **MIT Licensed** • **Latest Version: 0.2.4** • **Production Ready** • **Community Driven**
 
 [**Discord**](https://discord.gg/pMHguUzG)
 

RELEASE.md

@@ -26,10 +26,10 @@ Before releasing, ensure:
 
 The project uses GitHub Actions for automated releases to PyPI.
 
-1. **Tag the commit**: Create a new git tag for the version (e.g., `v0.2.2`).
+1.29. **Tag the commit**: Create a new git tag for the version (e.g., `v0.2.3`).
    ```bash
-   git tag -a v0.2.2 -m "Release v0.2.2"
-   git push origin v0.2.2
+   git tag -a v0.2.3 -m "Release v0.2.3"
+   git push origin v0.2.3
    ```
 2. **GitHub Action**: The `Release` workflow will automatically trigger, build the package, create a GitHub Release, and publish to PyPI using Trusted Publishing.
 

SECURITY.md

@@ -6,6 +6,7 @@ We actively support the following versions of Semantica with security updates:
 
 | Version | Supported          |
 | ------- | ------------------ |
+| 0.2.3   | :white_check_mark: |
 | 0.2.2   | :white_check_mark: |
 | 0.2.1   | :white_check_mark: |
 | 0.2.0   | :white_check_mark: |

cookbook/introduction/21_Amazon_Neptune_Store.ipynb

@@ -25,6 +25,57 @@
     "- AWS credentials configured (boto3, environment variables, or IAM role)\n",
     "- Network access to your Neptune cluster (VPC, security groups)\n",
     "\n",
+    "#### Quick Setup with CloudFormation\n",
+    "\n",
+    "If you don't have a Neptune cluster, use the provided CloudFormation template to create one with a public endpoint and IAM authentication:\n",
+    "\n",
+    "```bash\n",
+    "# Deploy the Neptune stack (takes ~15-20 minutes)\n",
+    "aws cloudformation create-stack \\\n",
+    "  --stack-name semantica-neptune \\\n",
+    "  --template-body file://neptune-setup.yaml \\\n",
+    "  --capabilities CAPABILITY_NAMED_IAM\n",
+    "\n",
+    "# Wait for stack creation to complete\n",
+    "aws cloudformation wait stack-create-complete --stack-name semantica-neptune\n",
+    "\n",
+    "# Get the outputs (endpoint, port, credentials)\n",
+    "aws cloudformation describe-stacks --stack-name semantica-neptune \\\n",
+    "  --query 'Stacks[0].Outputs' --output table\n",
+    "```\n",
+    "\n",
+    "The template creates:\n",
+    "- VPC with public subnets and Internet Gateway\n",
+    "- Neptune cluster (`db.t3.medium`) with IAM authentication enabled\n",
+    "- IAM user with least-privilege access for OpenCypher queries\n",
+    "- Security group allowing Bolt protocol (port 8182) access\n",
+    "\n",
+    "> ⚠️ **Security Note**: This template creates an IAM User with static access keys for simplicity in demo/test environments. For production use, we recommend IAM Roles (EC2 instance roles, ECS task roles, Lambda execution roles) which provide temporary credentials that are automatically rotated. The secret access key in the Cloudformation outputs is provided in plaintext to simplify initial setup - in production, use AWS Secrets Manager.\n",
+    "\n",
+    "**Outputs:**\n",
+    "- `NeptuneEndpoint` - Cluster hostname (use as `NEPTUNE_ENDPOINT`)\n",
+    "- `NeptunePort` - 8182 (use as `NEPTUNE_PORT`)\n",
+    "- `AwsAccessKeyId` - IAM user access key (use as `AWS_ACCESS_KEY_ID`)\n",
+    "- `AwsSecretAccessKey` - IAM user secret key in **plaintext** (use as `AWS_SECRET_ACCESS_KEY`)\n",
+    "- `AwsRegion` - Deployment region (use as `AWS_REGION`)\n",
+    "\n",
+    "**Cleanup:**\n",
+    "```bash\n",
+    "aws cloudformation delete-stack --stack-name semantica-neptune\n",
+    "```\n",
+    "\n",
+    "**Estimated Monthly Cost (approximately 100-105 USD/month at 100% utilization):**\n",
+    "\n",
+    "| Resource | Cost (USD) |\n",
+    "| --- | --- |\n",
+    "| Neptune db.t3.medium instance | ~96/month (0.132/hr) |\n",
+    "| Storage (10 GB) | ~1/month |\n",
+    "| I/O requests | ~1-5/month |\n",
+    "| Public IPv4 address | ~3.60/month (0.005/hr) |\n",
+    "| VPC, subnets, route tables, Internet Gateway, IAM | No Additional Charge |\n",
+    "\n",
+    "> **Free Tier**: New Neptune users get 30 days free (750 hours of db.t3.medium, 10M I/Os, 1 GB storage). Delete the stack when not in use to avoid charges.\n",
+    "\n",
     "---"
    ]
   },
@@ -70,14 +121,21 @@
     "import os\n",
     "\n",
     "# Neptune cluster configuration - REPLACE WITH YOUR VALUES\n",
+    "# (Get these from CloudFormation stack outputs)\n",
     "os.environ[\"NEPTUNE_ENDPOINT\"] = \"your-cluster.us-east-1.neptune.amazonaws.com\"\n",
     "os.environ[\"NEPTUNE_PORT\"] = \"8182\"\n",
     "os.environ[\"AWS_REGION\"] = \"us-east-1\"\n",
     "\n",
-    "# AWS credentials (if using IAM Auth and not relying on IAM role or ~/.aws/credentials)\n",
-    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"your-access-key-id\"\n",
-    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"your-secret-access-key\"\n",
-    "# os.environ[\"AWS_SESSION_TOKEN\"] = \"your-session-token\"\n",
+    "# AWS credentials for IAM Authentication\n",
+    "# Option 1: IAM User (static credentials from CloudFormation template)\n",
+    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"AKIA...\"  # From AwsAccessKeyId output\n",
+    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"...\"  # From AwsSecretAccessKey output\n",
+    "# Note: No AWS_SESSION_TOKEN needed for IAM users\n",
+    "\n",
+    "# Option 2: IAM Role / Temporary credentials (e.g., STS AssumeRole, EC2 instance role)\n",
+    "# os.environ[\"AWS_ACCESS_KEY_ID\"] = \"ASIA...\"  # Temporary access key\n",
+    "# os.environ[\"AWS_SECRET_ACCESS_KEY\"] = \"...\"  # Temporary secret key\n",
+    "# os.environ[\"AWS_SESSION_TOKEN\"] = \"...\"      # REQUIRED for temporary credentials\n",
     "\n",
     "print(f\"Neptune Endpoint: {os.environ.get('NEPTUNE_ENDPOINT')}\")\n",
     "print(f\"AWS Region: {os.environ.get('AWS_REGION')}\")"

cookbook/introduction/neptune-setup.yaml

@@ -0,0 +1,228 @@
+AWSTemplateFormatVersion: '2010-09-09'
+Description: >
+  Amazon Neptune cluster with public endpoint, IAM authentication, and least-privilege
+  IAM user for Semantica cookbook. Uses db.t3.medium (most cost-effective Neptune instance type).
+
+Parameters:
+  EnvironmentName:
+    Type: String
+    Default: semantica-neptune
+    Description: Environment name prefix for resource naming
+
+Resources:
+  # =============================================================================
+  # VPC & NETWORKING
+  # =============================================================================
+
+  VPC:
+    Type: AWS::EC2::VPC
+    Properties:
+      CidrBlock: 10.0.0.0/16
+      EnableDnsHostnames: true
+      EnableDnsSupport: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-vpc
+
+  InternetGateway:
+    Type: AWS::EC2::InternetGateway
+    Properties:
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-igw
+
+  InternetGatewayAttachment:
+    Type: AWS::EC2::VPCGatewayAttachment
+    Properties:
+      InternetGatewayId: !Ref InternetGateway
+      VpcId: !Ref VPC
+
+  PublicSubnet1:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [0, !GetAZs '']
+      CidrBlock: 10.0.1.0/24
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-subnet-1
+
+  PublicSubnet2:
+    Type: AWS::EC2::Subnet
+    Properties:
+      VpcId: !Ref VPC
+      AvailabilityZone: !Select [1, !GetAZs '']
+      CidrBlock: 10.0.2.0/24
+      MapPublicIpOnLaunch: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-subnet-2
+
+  PublicRouteTable:
+    Type: AWS::EC2::RouteTable
+    Properties:
+      VpcId: !Ref VPC
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-public-rt
+
+  DefaultPublicRoute:
+    Type: AWS::EC2::Route
+    DependsOn: InternetGatewayAttachment
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      DestinationCidrBlock: 0.0.0.0/0
+      GatewayId: !Ref InternetGateway
+
+  PublicSubnet1RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      SubnetId: !Ref PublicSubnet1
+
+  PublicSubnet2RouteTableAssociation:
+    Type: AWS::EC2::SubnetRouteTableAssociation
+    Properties:
+      RouteTableId: !Ref PublicRouteTable
+      SubnetId: !Ref PublicSubnet2
+
+  # =============================================================================
+  # SECURITY GROUP
+  # =============================================================================
+
+  NeptuneSecurityGroup:
+    Type: AWS::EC2::SecurityGroup
+    Properties:
+      GroupName: !Sub ${EnvironmentName}-neptune-sg
+      GroupDescription: Security group for Neptune cluster - allows Bolt protocol access
+      VpcId: !Ref VPC
+      SecurityGroupIngress:
+        - IpProtocol: tcp
+          FromPort: 8182
+          ToPort: 8182
+          CidrIp: 0.0.0.0/0
+          Description: Allow Bolt protocol access from anywhere
+      SecurityGroupEgress:
+        - IpProtocol: -1
+          CidrIp: 0.0.0.0/0
+          Description: Allow all outbound traffic
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-neptune-sg
+
+  # =============================================================================
+  # NEPTUNE CLUSTER
+  # =============================================================================
+
+  NeptuneSubnetGroup:
+    Type: AWS::Neptune::DBSubnetGroup
+    Properties:
+      DBSubnetGroupDescription: Subnet group for Neptune cluster
+      DBSubnetGroupName: !Sub ${EnvironmentName}-subnet-group
+      SubnetIds:
+        - !Ref PublicSubnet1
+        - !Ref PublicSubnet2
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-subnet-group
+
+  NeptuneCluster:
+    Type: AWS::Neptune::DBCluster
+    Properties:
+      DBClusterIdentifier: !Sub ${EnvironmentName}-cluster
+      DBSubnetGroupName: !Ref NeptuneSubnetGroup
+      VpcSecurityGroupIds:
+        - !Ref NeptuneSecurityGroup
+      EngineVersion: '1.4.6.3'
+      IamAuthEnabled: true
+      StorageEncrypted: true
+      DeletionProtection: false
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-cluster
+
+  NeptuneInstance:
+    Type: AWS::Neptune::DBInstance
+    Properties:
+      DBInstanceIdentifier: !Sub ${EnvironmentName}-instance
+      DBInstanceClass: db.t3.medium
+      DBClusterIdentifier: !Ref NeptuneCluster
+      PubliclyAccessible: true
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-instance
+
+  # =============================================================================
+  # IAM USER WITH LEAST PRIVILEGES
+  # =============================================================================
+
+  NeptuneUser:
+    Type: AWS::IAM::User
+    Properties:
+      UserName: !Sub ${EnvironmentName}-user
+      Tags:
+        - Key: Name
+          Value: !Sub ${EnvironmentName}-user
+
+  NeptuneUserPolicy:
+    Type: AWS::IAM::Policy
+    Properties:
+      PolicyName: !Sub ${EnvironmentName}-neptune-access
+      Users:
+        - !Ref NeptuneUser
+      PolicyDocument:
+        Version: '2012-10-17'
+        Statement:
+          - Sid: NeptuneDataAccess
+            Effect: Allow
+            Action:
+              - neptune-db:connect
+              - neptune-db:ReadDataViaQuery
+              - neptune-db:WriteDataViaQuery
+              - neptune-db:DeleteDataViaQuery
+            Resource: !Sub
+              - arn:aws:neptune-db:${AWS::Region}:${AWS::AccountId}:${ClusterResourceId}/*
+              - ClusterResourceId: !GetAtt NeptuneCluster.ClusterResourceId
+
+  NeptuneUserAccessKey:
+    Type: AWS::IAM::AccessKey
+    Properties:
+      UserName: !Ref NeptuneUser
+
+# =============================================================================
+# OUTPUTS
+# =============================================================================
+
+Outputs:
+  NeptuneEndpoint:
+    Description: Neptune cluster endpoint (hostname only) - use as NEPTUNE_ENDPOINT
+    Value: !GetAtt NeptuneCluster.Endpoint
+
+  NeptunePort:
+    Description: Neptune cluster port - use as NEPTUNE_PORT
+    Value: !GetAtt NeptuneCluster.Port
+
+  AwsAccessKeyId:
+    Description: Access key ID for the Neptune IAM user - use as AWS_ACCESS_KEY_ID
+    Value: !Ref NeptuneUserAccessKey
+
+  AwsSecretAccessKey:
+    Description: Secret access key for the Neptune IAM user - use as AWS_SECRET_ACCESS_KEY
+    Value: !GetAtt NeptuneUserAccessKey.SecretAccessKey
+
+  AwsRegion:
+    Description: AWS region where Neptune is deployed - use as AWS_REGION
+    Value: !Ref AWS::Region
+
+  NeptuneClusterResourceId:
+    Description: Neptune cluster resource ID (for IAM policy reference)
+    Value: !GetAtt NeptuneCluster.ClusterResourceId
+
+  VpcId:
+    Description: VPC ID
+    Value: !Ref VPC
+
+  SecurityGroupId:
+    Description: Neptune security group ID
+    Value: !Ref NeptuneSecurityGroup

cookbook/use_cases/finance/03_Earnings_Call_Analysis.ipynb

@@ -371,8 +371,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from concurrent.futures import ThreadPoolExecutor, TimeoutError\n",
     "from semantica.semantic_extract import RelationExtractor\n",
     "\n",
+    "MAX_ENTITIES = 30\n",
+    "CHUNK_TIMEOUT = 60\n",
+    "\n",
     "relation_extractor = RelationExtractor(\n",
     "    method=\"llm\",\n",
     "    confidence_threshold=0.6,\n",
@@ -385,22 +389,79 @@
     "        \"FOR_PERIOD\",\n",
     "        \"RELATED_TO\",\n",
     "    ],\n",
+    "    provider=\"groq\",\n",
+    "    llm_model=\"llama-3.1-8b-instant\",\n",
     "    api_key=GROQ_API_KEY,\n",
+    "    temperature=0.0,\n",
+    "    verbose=False,\n",
     ")\n",
     "\n",
-    "relationships = [\n",
-    "    r\n",
-    "    for c in chunks\n",
-    "    for r in relation_extractor.extract_relations(\n",
-    "        text=get_chunk_text(c),\n",
-    "        entities=all_entities,\n",
-    "        provider=\"groq\",\n",
-    "        llm_model=\"llama-3.1-8b-instant\",\n",
-    "        temperature=0.0,\n",
+    "\n",
+    "def filter_entities(text, entities):\n",
+    "    t = text.lower()\n",
+    "    return [e for e in entities if e.text.lower() in t]\n",
+    "\n",
+    "\n",
+    "def process_chunk(idx, chunk, total):\n",
+    "    text = get_chunk_text(chunk).strip()\n",
+    "\n",
+    "    remaining = total - (idx + 1)\n",
+    "\n",
+    "    if not text:\n",
+    "        print(f\"Chunk {idx+1}/{total} | remaining {remaining} | skipped (empty)\")\n",
+    "        return []\n",
+    "\n",
+    "    chunk_entities = filter_entities(text, all_entities)[:MAX_ENTITIES]\n",
+    "\n",
+    "    if len(chunk_entities) < 2:\n",
+    "        print(\n",
+    "            f\"Chunk {idx+1}/{total} | remaining {remaining} | \"\n",
+    "            f\"skipped (entities={len(chunk_entities)})\"\n",
+    "        )\n",
+    "        return []\n",
+    "\n",
+    "    print(\n",
+    "        f\"Chunk {idx+1}/{total} | remaining {remaining} | \"\n",
+    "        f\"entities={len(chunk_entities)}\"\n",
     "    )\n",
-    "    if get_chunk_text(c).strip()\n",
-    "]\n",
-    "print(\"Relationships:\", len(relationships))\n"
+    "\n",
+    "    return relation_extractor.extract_relations(\n",
+    "        text=text,\n",
+    "        entities=chunk_entities,\n",
+    "        verbose=False,\n",
+    "    )\n",
+    "\n",
+    "\n",
+    "relationships = []\n",
+    "total_chunks = len(chunks)\n",
+    "\n",
+    "with ThreadPoolExecutor(max_workers=1) as executor:\n",
+    "    for i, c in enumerate(chunks):\n",
+    "        future = executor.submit(process_chunk, i, c, total_chunks)\n",
+    "\n",
+    "        try:\n",
+    "            rels = future.result(timeout=CHUNK_TIMEOUT)\n",
+    "            relationships.extend(rels)\n",
+    "            print(f\"  relations={len(rels)}\")\n",
+    "\n",
+    "        except TimeoutError:\n",
+    "            remaining = total_chunks - (i + 1)\n",
+    "            print(\n",
+    "                f\"Chunk {i+1}/{total_chunks} | remaining {remaining} | timed out\"\n",
+    "            )\n",
+    "\n",
+    "        except Exception as e:\n",
+    "            remaining = total_chunks - (i + 1)\n",
+    "            print(\n",
+    "                f\"Chunk {i+1}/{total_chunks} | remaining {remaining} | failed: {e}\"\n",
+    "            )\n",
+    "\n",
+    "print(f\"Done {total_chunks}/{total_chunks}\")\n",
+    "print(f\"Total relationships: {len(relationships)}\")\n",
+    "\n",
+    "if relationships:\n",
+    "    for r in relationships[:10]:\n",
+    "        print(f\"{r.subject.text} → {r.predicate} → {r.object.text}\")\n"
    ]
   },
   {
@@ -421,39 +482,69 @@
     "from semantica.conflicts import SourceTracker, SourceReference, ConflictDetector\n",
     "\n",
     "source_tracker = SourceTracker()\n",
+    "\n",
     "conflict_detector = ConflictDetector(\n",
     "    source_tracker=source_tracker,\n",
     "    similarity_threshold=0.8,\n",
     "    confidence_threshold=0.7,\n",
     ")\n",
     "\n",
-    "for entity in all_entities:\n",
-    "    entity_id = getattr(entity, \"id\", None) or getattr(entity, \"text\", \"\")\n",
-    "    entity_text = getattr(entity, \"text\", \"\")\n",
-    "    entity_label = getattr(entity, \"label\", \"UNKNOWN\")\n",
+    "entities = all_entities\n",
+    "extracted_relationships = relationships\n",
     "\n",
+    "for e in entities:\n",
+    "    entity_id = getattr(e, \"id\", None) or e.text\n",
     "    source_tracker.track_property_source(\n",
-    "        entity_id,\n",
-    "        \"name\",\n",
-    "        entity_text,\n",
-    "        # FIXED: Changed 'source' to 'document' to match SourceReference signature\n",
+    "        entity_id=entity_id,\n",
+    "        property_name=\"name\",\n",
+    "        value=e.text,\n",
     "        source=SourceReference(\n",
-    "            document=\"earnings_call\",  # Was incorrect: source=\"earnings_call\"\n",
+    "            document=\"earnings_call\",\n",
     "            timestamp=\"2024-Q1\",\n",
-    "            metadata={\"entity_type\": entity_label},\n",
+    "            metadata={\"entity_type\": getattr(e, \"label\", \"UNKNOWN\")},\n",
     "        ),\n",
     "    )\n",
     "\n",
-    "value_conflicts = conflict_detector.detect_value_conflicts(\n",
-    "    [{\"id\": getattr(e, \"id\", \"\"), \"name\": getattr(e, \"text\", \"\")} for e in all_entities],\n",
+    "entity_records = [\n",
+    "    {\n",
+    "        \"id\": getattr(e, \"id\", None) or e.text,\n",
+    "        \"name\": e.text,\n",
+    "    }\n",
+    "    for e in entities\n",
+    "]\n",
+    "\n",
+    "entity_value_conflicts = conflict_detector.detect_value_conflicts(\n",
+    "    entity_records,\n",
     "    property_name=\"name\",\n",
     ")\n",
     "\n",
-    "relationship_conflicts = conflict_detector.detect_relationship_conflicts(relationships)\n",
+    "normalized_relationships = [\n",
+    "    {\n",
+    "        \"id\": getattr(r, \"id\", None),\n",
+    "        \"source_id\": getattr(r.subject, \"id\", None) or r.subject.text,\n",
+    "        \"target_id\": getattr(r.object, \"id\", None) or r.object.text,\n",
+    "        \"type\": r.predicate,\n",
+    "        \"confidence\": getattr(r, \"confidence\", 1.0),\n",
+    "        \"metadata\": {},\n",
+    "    }\n",
+    "    for r in extracted_relationships\n",
+    "]\n",
+    "\n",
+    "relationship_conflicts = conflict_detector.detect_relationship_conflicts(\n",
+    "    normalized_relationships\n",
+    ")\n",
     "\n",
     "print(\"Conflict detection completed\")\n",
-    "print(\"Value conflicts:\", len(value_conflicts))\n",
-    "print(\"Relationship conflicts:\", len(relationship_conflicts))"
+    "print(\"Entity value conflicts:\", len(entity_value_conflicts))\n",
+    "print(\"Relationship conflicts:\", len(relationship_conflicts))\n",
+    "\n",
+    "if entity_value_conflicts:\n",
+    "    print(\"\\nSample entity conflict:\")\n",
+    "    print(entity_value_conflicts[0])\n",
+    "\n",
+    "if relationship_conflicts:\n",
+    "    print(\"\\nSample relationship conflict:\")\n",
+    "    print(relationship_conflicts[0])"
    ]
   },
   {
@@ -478,20 +569,36 @@
     "    source_tracker=source_tracker,\n",
     ")\n",
     "\n",
-    "resolved_conflicts = []\n",
+    "resolved_entity_value_conflicts = []\n",
+    "resolved_relationship_conflicts = []\n",
     "\n",
-    "for conflict in value_conflicts:\n",
-    "    resolved_conflicts.append(\n",
-    "        conflict_resolver.resolve_conflict(conflict, strategy=\"voting\")\n",
+    "for conflict in entity_value_conflicts:\n",
+    "    resolved_entity_value_conflicts.append(\n",
+    "        conflict_resolver.resolve_conflict(\n",
+    "            conflict,\n",
+    "            strategy=\"voting\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "for conflict in relationship_conflicts:\n",
-    "    resolved_conflicts.append(\n",
-    "        conflict_resolver.resolve_conflict(conflict, strategy=\"voting\")\n",
+    "    resolved_relationship_conflicts.append(\n",
+    "        conflict_resolver.resolve_conflict(\n",
+    "            conflict,\n",
+    "            strategy=\"voting\",\n",
+    "        )\n",
     "    )\n",
     "\n",
     "print(\"Conflict resolution completed\")\n",
-    "print(\"Total conflicts resolved:\", len(resolved_conflicts))\n"
+    "print(\"Entity value conflicts resolved:\", len(resolved_entity_value_conflicts))\n",
+    "print(\"Relationship conflicts resolved:\", len(resolved_relationship_conflicts))\n",
+    "\n",
+    "if resolved_entity_value_conflicts:\n",
+    "    print(\"\\nSample resolved entity conflict:\")\n",
+    "    print(resolved_entity_value_conflicts[0])\n",
+    "\n",
+    "if resolved_relationship_conflicts:\n",
+    "    print(\"\\nSample resolved relationship conflict:\")\n",
+    "    print(resolved_relationship_conflicts[0])"
    ]
   },
   {
@@ -510,38 +617,80 @@
    "outputs": [],
    "source": [
     "from semantica.deduplication import DuplicateDetector, EntityMerger\n",
+    "import time\n",
     "\n",
-    "duplicate_detector = DuplicateDetector(\n",
-    "    similarity_threshold=0.8,\n",
-    "    confidence_threshold=0.7,\n",
+    "start_time = time.time()\n",
+    "\n",
+    "raw = []\n",
+    "for i, e in enumerate(entities):\n",
+    "    raw.append({\n",
+    "        \"id\": getattr(e, \"id\", None) or f\"entity_{i}_{getattr(e, 'text', str(e))}\",\n",
+    "        \"name\": (getattr(e, \"text\", getattr(e, \"name\", \"\")) or \"\").strip(),\n",
+    "        \"type\": getattr(e, \"label\", \"UNKNOWN\"),\n",
+    "        \"confidence\": float(getattr(e, \"confidence\", 1.0) or 1.0),\n",
+    "        \"metadata\": getattr(e, \"metadata\", {}),\n",
+    "    })\n",
+    "\n",
+    "filtered = [r for r in raw if r[\"name\"] and len(r[\"name\"]) >= 3]\n",
+    "\n",
+    "collapsed = {}\n",
+    "for ent in filtered:\n",
+    "    key = (ent[\"type\"], ent[\"name\"].lower())\n",
+    "    best = collapsed.get(key)\n",
+    "    if best is None or ent[\"confidence\"] > best[\"confidence\"]:\n",
+    "        collapsed[key] = ent\n",
+    "\n",
+    "entity_dicts = list(collapsed.values())\n",
+    "\n",
+    "detector = DuplicateDetector(\n",
+    "    similarity_threshold=0.96,\n",
+    "    confidence_threshold=0.92,\n",
+    "    use_clustering=True,\n",
     ")\n",
     "\n",
-    "entity_dicts = [\n",
-    "    {\n",
-    "        \"id\": getattr(e, \"id\", \"\"),\n",
-    "        \"name\": getattr(e, \"text\", \"\"),\n",
-    "        \"type\": getattr(e, \"label\", \"UNKNOWN\"),\n",
-    "        \"confidence\": getattr(e, \"confidence\", 1.0),\n",
-    "        \"metadata\": getattr(e, \"metadata\", {}),\n",
-    "    }\n",
-    "    for e in resolved_entities\n",
-    "]\n",
+    "detector.detect_duplicate_groups(entity_dicts)\n",
     "\n",
-    "duplicates = duplicate_detector.detect_duplicates(entity_dicts)\n",
+    "merger = EntityMerger(\n",
+    "    preserve_provenance=True,\n",
+    "    detector={\n",
+    "        \"similarity_threshold\": 0.96,\n",
+    "        \"confidence_threshold\": 0.92,\n",
+    "        \"use_clustering\": True,\n",
+    "    },\n",
+    "    strategy={\"default_strategy\": \"keep_most_complete\"},\n",
+    ")\n",
     "\n",
-    "entity_merger = EntityMerger(preserve_provenance=True)\n",
-    "\n",
-    "merge_operations = entity_merger.merge_duplicates(\n",
-    "    entity_dicts,\n",
+    "merge_operations = merger.merge_duplicates(\n",
+    "    entities=entity_dicts,\n",
     "    strategy=\"keep_most_complete\",\n",
     ")\n",
     "\n",
-    "merged_entities = [op.merged_entity for op in merge_operations]\n",
+    "deduplicated_entities = [op.merged_entity for op in merge_operations] or entity_dicts\n",
     "\n",
-    "print(\"Entity deduplication completed\")\n",
-    "print(\"Original entities:\", len(entity_dicts))\n",
-    "print(\"Merged entities:\", len(merged_entities))\n",
-    "print(\"Duplicates removed:\", len(entity_dicts) - len(merged_entities))\n"
+    "entity_id_mapping = {}\n",
+    "for op in merge_operations:\n",
+    "    mid = op.merged_entity[\"id\"]\n",
+    "    for sid in op.source_ids:\n",
+    "        entity_id_mapping[sid] = mid\n",
+    "\n",
+    "deduplicated_relationships = []\n",
+    "for rel in normalized_relationships:\n",
+    "    s = entity_id_mapping.get(rel[\"source_id\"], rel[\"source_id\"])\n",
+    "    t = entity_id_mapping.get(rel[\"target_id\"], rel[\"target_id\"])\n",
+    "    if s != t:\n",
+    "        r = rel.copy()\n",
+    "        r[\"source_id\"], r[\"target_id\"] = s, t\n",
+    "        deduplicated_relationships.append(r)\n",
+    "\n",
+    "print({\n",
+    "    \"time_seconds\": round(time.time() - start_time, 2),\n",
+    "    \"entities_in\": len(raw),\n",
+    "    \"entities_after_filter\": len(filtered),\n",
+    "    \"entities_after_exact\": len(entity_dicts),\n",
+    "    \"entities_out\": len(deduplicated_entities),\n",
+    "    \"duplicates_removed\": len(entity_dicts) - len(deduplicated_entities),\n",
+    "    \"relationships_updated\": len(deduplicated_relationships),\n",
+    "})"
    ]
   },
   {
@@ -561,28 +710,17 @@
    "source": [
     "from semantica.kg import GraphBuilder\n",
     "\n",
+    "# Deduplication is already done; avoid additional entity resolution/merging\n",
     "graph_builder = GraphBuilder(\n",
-    "    merge_entities=True,\n",
-    "    entity_resolution_strategy=\"fuzzy\",\n",
+    "    merge_entities=False,\n",
+    "    entity_resolution_strategy=\"none\",\n",
     ")\n",
     "\n",
-    "triplet_relationships = [\n",
-    "    {\n",
-    "        \"source\": t.subject,\n",
-    "        \"predicate\": t.predicate,\n",
-    "        \"target\": t.object,\n",
-    "        \"confidence\": t.confidence,\n",
-    "        \"metadata\": t.metadata,\n",
-    "    }\n",
-    "    for t in validated_triplets\n",
-    "]\n",
-    "\n",
-    "final_relationships = resolved_relationships + triplet_relationships\n",
+    "final_relationships = deduplicated_relationships\n",
     "\n",
     "kg_data = {\n",
-    "    \"entities\": merged_entities,\n",
+    "    \"entities\": deduplicated_entities,\n",
     "    \"relationships\": final_relationships,\n",
-    "    \"triplets\": validated_triplets,\n",
     "    \"metadata\": {\n",
     "        \"source\": \"earnings_call_transcript\",\n",
     "        \"extraction_method\": \"Groq LLM\",\n",
@@ -591,12 +729,12 @@
     "\n",
     "knowledge_graph = graph_builder.build(\n",
     "    sources=[kg_data],\n",
-    "    merge_entities=True,\n",
+    "    merge_entities=False,\n",
     ")\n",
     "\n",
-    "print(\"Knowledge graph build completed\")\n",
+    "print(\"Knowledge graph build completed (no additional merging)\")\n",
     "print(\"Final entities:\", len(knowledge_graph.get(\"entities\", [])))\n",
-    "print(\"Final relationships:\", len(knowledge_graph.get(\"relationships\", [])))\n"
+    "print(\"Final relationships:\", len(knowledge_graph.get(\"relationships\", [])))"
    ]
   },
   {
@@ -641,12 +779,10 @@
     "connectivity = graph_analyzer.analyze_connectivity(knowledge_graph)\n",
     "metrics = graph_analyzer.compute_metrics(knowledge_graph)\n",
     "\n",
-    "top_entities = centrality.get(\"rankings\", [])[:5]\n",
     "num_communities = len(communities.get(\"communities\", []))\n",
     "\n",
     "print(\"Graph analysis completed\")\n",
-    "print(\"Communities:\", num_communities)\n",
-    "print(\"Top entities:\", len(top_entities))\n"
+    "print(\"Communities:\", num_communities)"
    ]
   },
   {
@@ -779,31 +915,62 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import time\n",
     "from semantica.vector_store import VectorStore\n",
     "from semantica.context import ContextRetriever\n",
     "\n",
-    "vector_store = VectorStore(backend=\"faiss\")\n",
+    "if 'chunks' not in locals() or not chunks:\n",
+    "    raise ValueError(\"Chunks not found. Please run Step 3 first.\")\n",
     "\n",
-    "vector_store.add(\n",
-    "    texts=[parsed_doc[\"full_text\"]],\n",
-    "    metadata=[{\"source\": \"earnings_call\", \"type\": \"transcript\"}],\n",
+    "# Extract text content safely\n",
+    "chunk_texts = [getattr(c, \"content\", getattr(c, \"text\", \"\")) for c in chunks]\n",
+    "chunk_metadatas = [\n",
+    "    {\n",
+    "        \"source\": \"earnings_call\", \n",
+    "        \"type\": \"transcript\", \n",
+    "        \"chunk_index\": i,\n",
+    "        **(getattr(c, \"metadata\", {}) or {})\n",
+    "    }\n",
+    "    for i, c in enumerate(chunks)\n",
+    "]\n",
+    "\n",
+    "# Initialize Vector Store (Optimized for Speed)\n",
+    "# dimension=384 matches the default fast model (BAAI/bge-small-en-v1.5)\n",
+    "vector_store = VectorStore(\n",
+    "    backend=\"faiss\", \n",
+    "    dimension=384,  \n",
+    "    max_workers=16\n",
     ")\n",
     "\n",
+    "print(f\"Storing {len(chunks)} chunks with high-performance settings...\")\n",
+    "start_time = time.time()\n",
+    "\n",
+    "# Store in large batches with parallel processing\n",
+    "vector_ids = vector_store.add_documents(\n",
+    "    documents=chunk_texts,\n",
+    "    metadata=chunk_metadatas,\n",
+    "    batch_size=128,\n",
+    "    parallel=True\n",
+    ")\n",
+    "\n",
+    "print(f\"✅ Stored in {time.time() - start_time:.2f}s\")\n",
+    "\n",
+    "# Initialize Hybrid Retriever\n",
     "context_retriever = ContextRetriever(\n",
-    "    knowledge_graph=knowledge_graph,\n",
+    "    knowledge_graph=knowledge_graph, # Assumes knowledge_graph exists\n",
     "    vector_store=vector_store,\n",
     "    hybrid_alpha=0.6,\n",
     "    use_graph_expansion=True,\n",
     "    max_expansion_hops=2,\n",
     ")\n",
     "\n",
+    "# Test Retrieval\n",
     "queries = [\n",
     "    \"What was the company's revenue guidance?\",\n",
     "    \"What were the key financial metrics discussed?\",\n",
     "]\n",
     "\n",
     "retrieved_contexts = []\n",
-    "\n",
     "for query in queries:\n",
     "    results = context_retriever.retrieve(\n",
     "        query=query,\n",
@@ -813,8 +980,7 @@
     "    retrieved_contexts.append(results)\n",
     "\n",
     "print(\"Hybrid GraphRAG configured\")\n",
-    "print(\"Queries processed:\", len(queries))\n",
-    "print(\"Sample results:\", len(retrieved_contexts[0]) if retrieved_contexts else 0)\n"
+    "print(\"Sample results:\", len(retrieved_contexts[0]) if retrieved_contexts else 0)"
    ]
   },
   {
@@ -857,10 +1023,13 @@
     "    retention_days=30,\n",
     ")\n",
     "\n",
+    "entity_count = len(knowledge_graph.get(\"entities\", []))\n",
+    "relationship_count = len(knowledge_graph.get(\"relationships\", []))\n",
+    "\n",
     "memory_contents = [\n",
     "    f\"Earnings call transcript: {parsed_doc['metadata'].get('title', 'Earnings Call')}\",\n",
-    "    f\"Financial metrics extracted: {sum(len(v) for v in financial_metrics.values())}\",\n",
-    "    f\"Key entities identified: {len(merged_entities)}\",\n",
+    "    f\"Graph entities: {entity_count}\",\n",
+    "    f\"Graph relationships: {relationship_count}\",\n",
     "]\n",
     "\n",
     "memory_ids = []\n",
@@ -885,7 +1054,7 @@
     "print(\"Agent memory configured\")\n",
     "print(\"Memories stored:\", len(memory_ids))\n",
     "print(\"Total memories:\", memory_stats.get(\"total_memories\", 0))\n",
-    "print(\"Retrieved memories:\", len(financial_memories))\n"
+    "print(\"Retrieved memories:\", len(financial_memories))"
    ]
   },
   {
@@ -936,7 +1105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -964,7 +1133,7 @@
     ")\n",
     "\n",
     "memory_id = agent_context.store(\n",
-    "    content=parsed_doc[\"full_text\"][:1000],\n",
+    "    content=chunks,\n",
     "    metadata={\"source\": \"earnings_call\", \"date\": \"2024-Q1\"},\n",
     "    extract_entities=True,\n",
     "    extract_relationships=True,\n",
@@ -1008,32 +1177,71 @@
     "\n",
     "generated_answers = []\n",
     "\n",
+    "print(\"--- Generating Enhanced Answers ---\\n\")\n",
+    "\n",
+    "def format_context(retrieved_contexts):\n",
+    "    \"\"\"Formats retrieved context with graph information.\"\"\"\n",
+    "    formatted_parts = []\n",
+    "    \n",
+    "    for i, ctx in enumerate(retrieved_contexts):\n",
+    "        content = getattr(ctx, \"content\", \"\")\n",
+    "        source = getattr(ctx, \"source\", \"unknown\")\n",
+    "        \n",
+    "        # Format related entities from the graph\n",
+    "        related_entities = getattr(ctx, \"related_entities\", [])\n",
+    "        entities_str = \", \".join([\n",
+    "            f\"{e.get('name', 'Unknown')} ({e.get('type', 'Entity')})\" \n",
+    "            for e in related_entities[:5]  # Limit to top 5 per chunk\n",
+    "        ])\n",
+    "        \n",
+    "        # Format related relationships\n",
+    "        related_rels = getattr(ctx, \"related_relationships\", [])\n",
+    "        rels_str = \"; \".join([\n",
+    "            f\"{r.get('source', '')} -> {r.get('type', '')} -> {r.get('target', '')}\"\n",
+    "            for r in related_rels[:3]  # Limit to top 3 per chunk\n",
+    "        ])\n",
+    "        \n",
+    "        part = f\"Source {i+1} ({source}):\\n{content}\\n\"\n",
+    "        if entities_str:\n",
+    "            part += f\"Related Entities: {entities_str}\\n\"\n",
+    "        if rels_str:\n",
+    "            part += f\"Graph Connections: {rels_str}\\n\"\n",
+    "            \n",
+    "        formatted_parts.append(part)\n",
+    "        \n",
+    "    return \"\\n---\\n\".join(formatted_parts)\n",
+    "\n",
     "for question in financial_questions:\n",
+    "    print(f\"Question: {question}\")\n",
+    "    \n",
+    "    # Retrieve with graph expansion enabled and higher limits\n",
     "    retrieved_contexts = context_retriever.retrieve(\n",
     "        query=question,\n",
-    "        max_results=3,\n",
+    "        max_results=10,          # Increased from 3\n",
     "        min_relevance_score=0.2,\n",
+    "        use_graph_expansion=True, # Explicitly enable graph expansion\n",
+    "        max_hops=2               # Traverse up to 2 hops in the graph\n",
     "    )\n",
     "\n",
-    "    context_text = \"\\n\\n\".join(\n",
-    "        ctx.get(\"content\", ctx.get(\"text\", \"\"))\n",
-    "        for ctx in retrieved_contexts\n",
-    "    )[:1000]\n",
+    "    # Use the rich formatter\n",
+    "    context_text = format_context(retrieved_contexts)\n",
     "\n",
-    "    entity_names = [\n",
-    "        entity.get(\"name\", \"\")\n",
-    "        for entity in knowledge_graph.get(\"entities\", [])[:5]\n",
+    "    # Get global key entities (optional, but good for high-level context)\n",
+    "    global_entities = [\n",
+    "        f\"{e.get('name', '')} ({e.get('type', '')})\"\n",
+    "        for e in knowledge_graph.get(\"entities\", [])[:10]\n",
     "    ]\n",
-    "    entities_text = \", \".join(entity_names) or \"N/A\"\n",
+    "    global_entities_text = \", \".join(global_entities)\n",
     "\n",
     "    prompt = f\"\"\"\n",
-    "Answer the question using only the context below.\n",
+    "Answer the question comprehensively using the provided context.\n",
+    "The context includes text chunks and knowledge graph connections (entities and relationships).\n",
     "If the answer is not present, say so.\n",
     "\n",
     "Context:\n",
     "{context_text}\n",
     "\n",
-    "Key entities: {entities_text}\n",
+    "Global Key Entities: {global_entities_text}\n",
     "\n",
     "Question:\n",
     "{question}\n",
@@ -1044,16 +1252,18 @@
     "    try:\n",
     "        answer = groq_llm.generate(\n",
     "            prompt,\n",
-    "            temperature=0.7,\n",
-    "            max_tokens=400,\n",
+    "            temperature=0.3, # Lower temperature for more factual answers\n",
+    "            max_tokens=1000, # Allow longer answers\n",
     "        )\n",
     "    except Exception as error:\n",
     "        answer = f\"Answer generation failed: {error}\"\n",
     "\n",
     "    generated_answers.append(answer)\n",
+    "    print(f\"Answer: {answer}\\n\")\n",
+    "    print(\"-\" * 50 + \"\\n\")\n",
     "\n",
     "print(\"Answer generation completed\")\n",
-    "print(\"Questions answered:\", len(generated_answers))\n"
+    "print(\"Questions answered:\", len(generated_answers))"
    ]
   },
   {
@@ -1072,28 +1282,44 @@
    "outputs": [],
    "source": [
     "from semantica.export import JSONExporter, RDFExporter\n",
+    "import json\n",
     "\n",
+    "# Initialize exporters\n",
     "json_exporter = JSONExporter()\n",
     "rdf_exporter = RDFExporter()\n",
     "\n",
-    "kg_json = json_exporter.export(knowledge_graph, format=\"json\")\n",
-    "kg_rdf = rdf_exporter.export_to_rdf(knowledge_graph, format=\"turtle\")\n",
+    "# Define output file paths\n",
+    "json_output_path = \"knowledge_graph.json\"\n",
+    "rdf_output_path = \"knowledge_graph.ttl\"\n",
     "\n",
+    "# Export to files (required by the API)\n",
+    "json_exporter.export(knowledge_graph, file_path=json_output_path, format=\"json\")\n",
+    "\n",
+    "# FIXED: Use .export() instead of .export_to_rdf() to write to disk\n",
+    "rdf_exporter.export(knowledge_graph, file_path=rdf_output_path, format=\"turtle\")\n",
+    "\n",
+    "# Load the RDF file content to check its size\n",
+    "with open(rdf_output_path, \"r\", encoding=\"utf-8\") as f:\n",
+    "    kg_rdf_content = f.read()\n",
+    "\n",
+    "# Create analysis summary\n",
     "analysis_summary = {\n",
     "    \"entities\": len(knowledge_graph.get(\"entities\", [])),\n",
     "    \"relationships\": len(knowledge_graph.get(\"relationships\", [])),\n",
-    "    \"conflicts_resolved\": len(resolved_conflicts),\n",
-    "    \"merged_entities\": len(merged_entities),\n",
-    "    \"communities\": num_communities,\n",
+    "    \"entity_conflicts_resolved\": len(locals().get(\"resolved_entity_value_conflicts\", [])),\n",
+    "    \"relationship_conflicts_resolved\": len(locals().get(\"resolved_relationship_conflicts\", [])),\n",
+    "    \"deduplicated_entities\": len(locals().get(\"deduplicated_entities\", [])),\n",
+    "    \"communities\": locals().get(\"num_communities\", 0),\n",
     "    \"questions_answered\": len(generated_answers),\n",
-    "    \"llm_model\": groq_llm.model,\n",
+    "    \"llm_model\": getattr(groq_llm, \"model\", \"unknown\"),\n",
     "}\n",
     "\n",
     "print(\"Export completed\")\n",
     "print(\"KG JSON entities:\", analysis_summary[\"entities\"])\n",
-    "print(\"KG RDF size (chars):\", len(kg_rdf))\n",
+    "print(\"KG RDF size (chars):\", len(kg_rdf_content))\n",
     "print(\"Questions answered:\", analysis_summary[\"questions_answered\"])\n",
-    "print(\"LLM model:\", analysis_summary[\"llm_model\"])\n"
+    "print(\"LLM model:\", analysis_summary[\"llm_model\"])\n",
+    "print(\"Conflicts resolved:\", analysis_summary[\"entity_conflicts_resolved\"] + analysis_summary[\"relationship_conflicts_resolved\"])"
    ]
   }
  ],

docs/citation.md

@@ -12,22 +12,22 @@ How to cite Semantica in academic papers and research.
   author = {Hawksight AI},
   year = {2026},
   url = {https://github.com/Hawksight-AI/semantica},
-  version = {0.2.2},
+  version = {0.2.3},
   doi = {10.5281/zenodo.XXXXXXX}
 }
 ```
 
 ### APA
-Hawksight AI. (2026). *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering* (Version 0.2.2) [Computer software]. https://github.com/Hawksight-AI/semantica
+Hawksight AI. (2026). *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering* (Version 0.2.3) [Computer software]. https://github.com/Hawksight-AI/semantica
 
 ### MLA
-Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.2, GitHub, 2026, https://github.com/Hawksight-AI/semantica.
+Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.3, GitHub, 2026, https://github.com/Hawksight-AI/semantica.
 
 ### Chicago
-Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.2. GitHub, 2026. https://github.com/Hawksight-AI/semantica.
+Hawksight AI. *Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering*. Version 0.2.3. GitHub, 2026. https://github.com/Hawksight-AI/semantica.
 
 ### IEEE
-Hawksight AI, "Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering," Version 0.2.2, GitHub, 2026. [Online]. Available: https://github.com/Hawksight-AI/semantica
+Hawksight AI, "Semantica: An Open Source Framework for Semantic Layers and Knowledge Engineering," Version 0.2.3, GitHub, 2026. [Online]. Available: https://github.com/Hawksight-AI/semantica
 
 ---
 

docs/index.md

@@ -17,7 +17,7 @@
   
   <p><em>The missing fabric between raw data and AI engineering. A comprehensive open-source framework for building semantic layers and knowledge engineering systems that transform unstructured data into AI-ready knowledge — powering Knowledge Graph-Powered RAG (GraphRAG), AI Agents, Multi-Agent Systems, and AI applications with structured semantic knowledge.</em></p>
   
-  <p>🆓 <strong>100% Open Source</strong> • 📜 <strong>MIT Licensed</strong> • 🚀 <strong>Latest Version: 0.1.1</strong> • 🚀 <strong>Production Ready</strong> • 🌍 <strong>Community Driven</strong></p>
+  <p>🆓 <strong>100% Open Source</strong> • 📜 <strong>MIT Licensed</strong> • 🚀 <strong>Latest Version: 0.2.3</strong> • 🚀 <strong>Production Ready</strong> • 🌍 <strong>Community Driven</strong></p>
   
   <p>
     <a href="getting-started/" class="md-button md-button--primary">Get Started</a>

docs/js/version-selector.js

@@ -9,7 +9,12 @@ document.addEventListener("DOMContentLoaded", function () {
 
         // Define versions
         var versions = [
-            { name: "0.1.1", url: "#", current: true },
+            { name: "0.2.4", url: "#", current: true },
+            { name: "0.2.3", url: "#", current: false },
+            { name: "0.2.2", url: "#", current: false },
+            { name: "0.2.1", url: "#", current: false },
+            { name: "0.2.0", url: "#", current: false },
+            { name: "0.1.1", url: "#", current: false },
             { name: "0.1.0", url: "#", current: false }
         ];
 

docs/reference/ontology.md

@@ -63,6 +63,29 @@ The module uses several inference algorithms:
 
 ---
 
+## Ontology Ingestion
+
+Ingest existing ontology files directly into usable data structures using `OntologyIngestor`.
+
+**Function:** `ingest_ontology(source, method="file")`
+
+| Argument | Description |
+|----------|-------------|
+| `source` | File path, directory path, or list of paths |
+| `method` | Ingestion method (default: "file") |
+
+**Example:**
+
+```python
+from semantica.ontology import ingest_ontology
+
+# Ingest file
+data = ingest_ontology("ontology.ttl")
+
+# Ingest directory
+dataset = ingest_ontology("ontologies/")
+```
+
 ## Main Classes
 
 ### OntologyEngine
@@ -170,6 +193,17 @@ Manages external dependencies.
 | `import_external_ontology(uri, ontology)` | Load and merge external ontology |
 | `evaluate_alignment(uri, ontology)` | Assess alignment and compatibility |
 
+### OntologyIngestor
+
+Handles ingestion of existing ontologies from files and directories.
+
+**Methods:**
+
+| Method | Description |
+|--------|-------------|
+| `ingest_ontology(file_path)` | Ingest a single ontology file |
+| `ingest_directory(directory_path)` | Recursively ingest ontology files from a directory |
+
 ---
 
 ## Unified Engine Examples

docs/reference/vector_store.md

@@ -112,6 +112,8 @@ The main facade for all vector operations.
 | Method | Description |
 |--------|-------------|
 | `store_vectors(vectors, metadata)` | Store embeddings |
+| `add_documents(documents, metadata, batch_size, parallel)` | **(New)** Store documents with automatic embedding generation and parallelization |
+| `embed_batch(texts)` | **(New)** Generate embeddings for a batch of texts |
 | `search(query, k)` | Semantic search |
 | `delete(ids)` | Remove vectors |
 
@@ -120,15 +122,24 @@ The main facade for all vector operations.
 ```python
 from semantica.vector_store import VectorStore
 
-# Initialize (defaults to FAISS)
+# Initialize (defaults to FAISS, parallel enabled by default with 6 workers)
 store = VectorStore(backend="faiss", dimension=1536)
 
-# Store
+# 1. Store pre-computed vectors
 ids = store.store_vectors(
     vectors=[[0.1, 0.2, ...], ...],
     metadata=[{"text": "Hello"}, ...]
 )
 
+# 2. Store raw documents (High Performance)
+# Automatically handles embedding generation in parallel batches (uses default 6 workers)
+ids = store.add_documents(
+    documents=["Doc 1", "Doc 2", ...],
+    metadata=[{"id": 1}, {"id": 2}, ...],
+    batch_size=32,
+    parallel=True
+)
+
 # Search
 results = store.search(query_vector=[0.1, 0.2, ...], k=5)
 ```
@@ -771,6 +782,7 @@ print(f"Context: {context}")
 ---
 
 ## See Also
+- [High-Performance Usage Guide](../vector_store_usage.md) - **(New)** Parallel ingestion and batching guide
 - [Embeddings Module](embeddings.md) - Generates the vectors
 - [Context Module](context.md) - Uses vector store for memory
 - [Ingest Module](ingest.md) - Source of data

docs/vector_store_usage.md

@@ -0,0 +1,101 @@
+# High-Performance Vector Store Usage
+
+This guide demonstrates how to leverage the new high-performance features of the Semantica Vector Store, specifically designed for efficient batch processing and parallel ingestion of large document sets.
+
+## 🚀 Key Features
+
+- **Parallel Ingestion**: Utilize multi-threading to embed and store documents concurrently.
+- **Batch Processing**: Automatically group documents into batches to minimize overhead.
+- **Unified API**: A single `add_documents` method handles embedding generation and storage.
+
+---
+
+## ⚡ Quick Start: Parallel Ingestion
+
+The fastest way to ingest documents is using the `add_documents` method. Parallelization is enabled by default with optimized settings (6 workers).
+
+```python
+from semantica.vector_store import VectorStore
+import time
+
+store = VectorStore(
+    backend="faiss",
+    dimension=768,
+)
+
+documents = [f"This is document number {i} with some content." for i in range(1000)]
+metadata = [{"source": "generated", "id": i} for i in range(1000)]
+
+start_time = time.time()
+ids = store.add_documents(
+    documents=documents,
+    metadata=metadata,
+    batch_size=64,
+    parallel=True,
+)
+print(f"Ingested {len(ids)} documents in {time.time() - start_time:.2f}s")
+```
+
+---
+
+## 📊 Performance Comparison
+
+### Old Method (Sequential Loop)
+*Slower due to sequential processing and overhead per single item.*
+
+```python
+for doc in documents:
+    emb = embedder.generate(doc)
+    store.store_vectors([emb], [{"text": doc}])
+```
+
+### New Method (Parallel Batching)
+*Significantly faster (3x-10x) by utilizing thread pools and batch operations.*
+
+```python
+store.add_documents(documents, parallel=True)
+```
+
+---
+
+## 🛠 Configuration & Tuning
+
+### `max_workers`
+Controls the number of concurrent threads used for embedding generation.
+- **Default**: 6 (Optimized for most systems)
+- **Recommendation**: You generally don't need to change this. If you have very high core counts or specific throughput needs, you can override it.
+
+```python
+store = VectorStore(max_workers=16)
+```
+
+### `batch_size`
+Controls how many documents are processed in a single chunk.
+- **Default**: 32
+- **Recommendation**: 
+    - **Local Models**: 32-64 usually works well.
+    - **API Models (OpenAI, etc.)**: Larger batches (e.g., 100-200) can reduce network latency overhead.
+
+```python
+store.add_documents(documents, batch_size=100)
+```
+
+---
+
+## 🧩 Advanced: Manual Batch Embedding
+
+If you need the embeddings without storing them immediately, use `embed_batch`.
+
+```python
+vectors = store.embed_batch(
+    texts=documents[:100],
+)
+
+print(f"Generated {len(vectors)} vectors")
+```
+
+## ⚠️ Best Practices
+
+1.  **Metadata Consistency**: Ensure your `metadata` list has the same length as your `documents` list.
+2.  **Error Handling**: The `add_documents` method will propagate exceptions if embedding fails. Ensure your data is clean.
+3.  **Memory Usage**: Very large `batch_size` combined with high `max_workers` can increase memory usage. Monitor your system resources.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "semantica"
-version = "0.2.2"
+version = "0.2.4"
 description = "🧠 Semantica - An Open Source Framework for building Semantic Layers and Knowledge Engineering"
 readme = "README.md"
 license = { text = "MIT" }

semantica/__init__.py

@@ -10,7 +10,7 @@ Main exports:
     - Config: Configuration management
 """
 
-__version__ = "0.2.2"
+__version__ = "0.2.4"
 __author__ = "Semantica Contributors"
 __license__ = "MIT"
 

semantica/ingest/__init__.py

@@ -86,6 +86,7 @@ Main Classes:
     - RepoIngestor: Git repository processing
     - EmailIngestor: Email protocol handling
     - DBIngestor: Database export handling
+    - OntologyIngestor: Ontology file processing
     - MethodRegistry: Registry for custom ingestion methods
     - IngestConfig: Configuration manager for ingest module
 
@@ -98,6 +99,7 @@ Convenience Functions:
     - ingest_repository: Repository ingestion wrapper
     - ingest_email: Email ingestion wrapper
     - ingest_database: Database ingestion wrapper
+    - ingest_ontology: Ontology ingestion wrapper
 
 
 Example Usage:
@@ -134,6 +136,7 @@ from .methods import (
     ingest_feed,
     ingest_file,
     ingest_mcp,
+    ingest_ontology,
     ingest_repository,
     ingest_stream,
     ingest_web,
@@ -166,6 +169,8 @@ from .web_ingestor import (
     WebIngestor,
 )
 
+from .ontology_ingestor import OntologyData, OntologyIngestor
+
 __all__ = [
     # File ingestion
     "FileIngestor",
@@ -216,6 +221,9 @@ __all__ = [
     "MCPClient",
     "MCPResource",
     "MCPTool",
+    # Ontology ingestion
+    "OntologyIngestor",
+    "OntologyData",
     # Registry and Methods
     "MethodRegistry",
     "method_registry",
@@ -227,6 +235,7 @@ __all__ = [
     "ingest_repository",
     "ingest_email",
     "ingest_database",
+    "ingest_ontology",
     "ingest_mcp",
     "get_ingest_method",
     "list_available_methods",

semantica/ingest/methods.py

@@ -150,6 +150,7 @@ from .email_ingestor import EmailData, EmailIngestor
 from .feed_ingestor import FeedData, FeedIngestor
 from .file_ingestor import FileIngestor, FileObject
 from .mcp_ingestor import MCPData, MCPIngestor
+from .ontology_ingestor import OntologyData, OntologyIngestor
 from .registry import method_registry
 from .repo_ingestor import RepoIngestor
 from .stream_ingestor import StreamIngestor, StreamProcessor
@@ -537,6 +538,66 @@ def ingest_email(
         raise
 
 
+def ingest_ontology(
+    source: Union[str, Path, List[Union[str, Path]]], method: str = "file", **kwargs
+) -> Union[OntologyData, List[OntologyData]]:
+    """
+    Ingest ontology from source (convenience function).
+
+    This is a user-friendly wrapper that ingests ontologies using the specified method.
+
+    Args:
+        source: Ontology file path, directory path, or list of paths
+        method: Ingestion method (default: "file")
+            - "file": Single file ingestion
+            - "directory": Directory ingestion with recursive scanning
+        **kwargs: Additional options passed to OntologyIngestor
+
+    Returns:
+        OntologyData, List[OntologyData] with ingestion results
+
+    Examples:
+        >>> from semantica.ingest.methods import ingest_ontology
+        >>> ontology = ingest_ontology("ontology.ttl")
+        >>> ontologies = ingest_ontology("./ontologies", method="directory")
+    """
+    # Check for custom method in registry
+    custom_method = method_registry.get("ontology", method)
+    if custom_method and custom_method != ingest_ontology:
+        try:
+            return custom_method(source, **kwargs)
+        except Exception as e:
+            logger.warning(
+                f"Custom method {method} failed: {e}, falling back to default"
+            )
+
+    try:
+        # Get config
+        config = ingest_config.get_method_config("ontology")
+        config.update(kwargs)
+
+        ingestor = OntologyIngestor(**config)
+
+        source_path = str(source) if isinstance(source, (str, Path)) else None
+        
+        if method == "file" and source_path:
+            if isinstance(source, list):
+                return [ingestor.ingest_ontology(str(s), **kwargs) for s in source]
+            return ingestor.ingest_ontology(source_path, **kwargs)
+        elif method == "directory" and source_path:
+             recursive = kwargs.get("recursive", ingest_config.get("recursive", True))
+             return ingestor.ingest_directory(source_path, recursive=recursive, **kwargs)
+        else:
+             # Default: try as file
+             if isinstance(source, list):
+                return [ingestor.ingest_ontology(str(s), **kwargs) for s in source]
+             return ingestor.ingest_ontology(str(source), **kwargs)
+
+    except Exception as e:
+        logger.error(f"Failed to ingest ontology: {e}")
+        raise
+
+
 def ingest_database(
     source: Union[str, Dict[str, Any]], method: Optional[str] = None, **kwargs
 ) -> Union[TableData, List[TableData], Dict[str, Any]]:
@@ -769,6 +830,7 @@ def ingest(
             - "repo": Repository ingestion
             - "email": Email ingestion
             - "db": Database ingestion
+            - "ontology": Ontology ingestion
         method: Optional specific ingestion method
         **kwargs: Additional options passed to ingestor
 
@@ -802,6 +864,8 @@ def ingest(
                 ("git@", "https://github.com", "https://gitlab.com")
             ):
                 source_type = "repo"
+            elif source_str.endswith((".ttl", ".owl", ".rdf", ".jsonld", ".n3", ".nt")):
+                source_type = "ontology"
             else:
                 source_type = "file"
         else:
@@ -830,6 +894,8 @@ def ingest(
             raise ProcessingError("Email ingestion requires configuration dictionary")
     elif source_type == "db":
         return {"data": ingest_database(sources, method=method, **kwargs)}
+    elif source_type == "ontology":
+        return {"ontology": ingest_ontology(sources, method=method or "file", **kwargs)}
     elif source_type == "mcp":
         return {"data": ingest_mcp(sources, method=method or "resources", **kwargs)}
     else:
@@ -909,5 +975,8 @@ method_registry.register("mcp", "default", ingest_mcp)
 method_registry.register("mcp", "resources", ingest_mcp)
 method_registry.register("mcp", "tools", ingest_mcp)
 method_registry.register("mcp", "all", ingest_mcp)
+method_registry.register("ontology", "default", ingest_ontology)
+method_registry.register("ontology", "file", ingest_ontology)
+method_registry.register("ontology", "directory", ingest_ontology)
 method_registry.register("ingest", "default", ingest)
 method_registry.register("ingest", "unified", ingest)

semantica/ingest/ontology_ingestor.py

@@ -0,0 +1,392 @@
+"""
+Ontology Ingestion Module
+
+This module provides capabilities to ingest external ontologies from files (OWL, RDF, TTL, etc.)
+and convert them into Semantica's internal ontology dictionary format.
+
+Supported Formats:
+    - Turtle (.ttl): Terse RDF Triple Language. A concise, human-readable
+      format for representing RDF graphs. Commonly used for writing
+      ontologies by hand.
+    - RDF/XML (.rdf, .owl): The XML serialization of RDF. The standard
+      format for OWL (Web Ontology Language) ontologies and often used
+      for data interchange.
+    - JSON-LD (.jsonld): JSON for Linked Data. A lightweight Linked Data
+      format that is easy for humans to read and for machines to parse
+      and generate. Ideal for web-based applications.
+    - N-Triples (.nt): A line-based, plain text format for encoding an
+      RDF graph. Each line represents a single triple. Very simple to
+      parse but verbose.
+    - Notation3 (.n3): A superset of Turtle that adds features like logic
+      and rules.
+
+Key Features:
+    - Support for multiple RDF formats (Turtle, RDF/XML, JSON-LD, N3, NT)
+    - Automatic parsing using rdflib
+    - Conversion to Semantica ontology structure
+    - Batch processing of ontology files
+    - Extraction of classes, properties, and metadata
+
+Example Usage:
+    >>> from semantica.ingest import OntologyIngestor
+    >>> ingestor = OntologyIngestor()
+    >>> ontology = ingestor.ingest_ontology("my_ontology.ttl")
+"""
+
+import os
+from dataclasses import dataclass, field
+from datetime import datetime
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Union
+
+import rdflib
+from rdflib import RDF, RDFS, OWL, Graph
+
+from ..utils.exceptions import ProcessingError, ValidationError
+from ..utils.logging import get_logger
+from ..utils.progress_tracker import get_progress_tracker
+
+
+@dataclass
+class OntologyData:
+    """Ontology data representation."""
+
+    data: Dict[str, Any]
+    source_path: str
+    format: str
+    metadata: Dict[str, Any] = field(default_factory=dict)
+    ingested_at: datetime = field(default_factory=datetime.now)
+
+
+class OntologyIngestor:
+    """
+    Ontology ingestion handler.
+
+    This class parses OWL/RDF files and converts them to Semantica's ontology dictionary format.
+    """
+
+    def __init__(self, config: Optional[Dict[str, Any]] = None, **kwargs):
+        """
+        Initialize ontology ingestor.
+
+        Args:
+            config: Optional configuration dictionary
+            **kwargs: Additional configuration parameters
+        """
+        self.logger = get_logger("ontology_ingestor")
+        self.progress = get_progress_tracker()
+        self.config = config or {}
+        self.config.update(kwargs)
+
+    def ingest_ontology(self, file_path: Union[str, Path], format: Optional[str] = None, **kwargs) -> OntologyData:
+        """
+        Ingest an ontology file.
+
+        Args:
+            file_path: Path to the ontology file (string or Path object)
+            format: Optional format hint (e.g., 'turtle', 'xml'). If None, rdflib guesses.
+            **kwargs: Additional arguments for rdflib parsing
+
+        Returns:
+            OntologyData object containing the parsed ontology and metadata
+        """
+        file_path = Path(file_path)
+
+        # Track file ingestion
+        tracking_id = self.progress.start_tracking(
+            file=str(file_path),
+            module="ingest",
+            submodule="OntologyIngestor",
+            message=f"Ontology: {file_path.name}",
+        )
+
+        try:
+            # Validate file exists
+            if not file_path.exists():
+                raise ValidationError(f"File not found: {file_path}")
+
+            self.progress.update_tracking(tracking_id, message="Parsing RDF graph...")
+            g = Graph()
+            
+            # Use provided format or let rdflib guess based on extension
+            parse_kwargs = kwargs.copy()
+            if format:
+                parse_kwargs['format'] = format
+            
+            try:
+                g.parse(file_path, **parse_kwargs)
+            except Exception as e:
+                # Fallback: try to guess format from extension if not provided and initial parse failed
+                if not format:
+                    ext = os.path.splitext(file_path)[1].lower()
+                    fmt_map = {
+                        '.ttl': 'turtle',
+                        '.owl': 'xml', # OWL is often XML
+                        '.rdf': 'xml',
+                        '.jsonld': 'json-ld',
+                        '.n3': 'n3',
+                        '.nt': 'nt'
+                    }
+                    guessed_fmt = fmt_map.get(ext)
+                    if guessed_fmt:
+                        self.logger.info(f"Retrying with guessed format: {guessed_fmt}")
+                        g.parse(file_path, format=guessed_fmt, **kwargs)
+                    else:
+                        raise e
+                else:
+                    raise e
+
+            self.progress.update_tracking(tracking_id, message="Converting to internal format...")
+            
+            # Determine format for metadata
+            used_format = format
+            if not used_format:
+                ext = os.path.splitext(file_path)[1].lower()
+                fmt_map = {
+                    '.ttl': 'turtle',
+                    '.owl': 'xml',
+                    '.rdf': 'xml',
+                    '.jsonld': 'json-ld',
+                    '.n3': 'n3',
+                    '.nt': 'nt'
+                }
+                used_format = fmt_map.get(ext, 'unknown')
+
+            ontology_dict = self._convert_to_dict(g, source_path=str(file_path), format=used_format)
+
+            ontology_data = OntologyData(
+                data=ontology_dict,
+                source_path=str(file_path),
+                format=used_format,
+                metadata=ontology_dict.get("metadata", {}).copy()
+            )
+
+            self.progress.stop_tracking(
+                tracking_id,
+                status="completed",
+                message=f"Successfully ingested ontology from {file_path}",
+            )
+            
+            return ontology_data
+
+        except Exception as e:
+            self.logger.error(f"Failed to ingest ontology: {str(e)}")
+            self.progress.stop_tracking(
+                tracking_id, status="failed", message=str(e)
+            )
+            raise ProcessingError(f"Failed to ingest ontology: {str(e)}") from e
+
+    def ingest_directory(self, directory_path: Union[str, Path], recursive: bool = True, **kwargs) -> List[OntologyData]:
+        """
+        Ingest all ontology files in a directory.
+
+        Args:
+            directory_path: Path to the directory (string or Path object)
+            recursive: Whether to search recursively
+            **kwargs: Additional arguments
+
+        Returns:
+            List of OntologyData objects
+        """
+        directory_path = Path(directory_path)
+        ontologies = []
+        extensions = {'.ttl', '.owl', '.rdf', '.jsonld', '.n3', '.nt'}
+        
+        # Track directory ingestion
+        tracking_id = self.progress.start_tracking(
+            file=str(directory_path),
+            module="ingest",
+            submodule="OntologyIngestor",
+            message=f"Directory: {directory_path.name}",
+        )
+
+        try:
+            if not directory_path.exists():
+                raise ValidationError(f"Directory not found: {directory_path}")
+                
+            if not directory_path.is_dir():
+                raise ValidationError(f"Path is not a directory: {directory_path}")
+
+            files_to_process = []
+            for root, _, files in os.walk(directory_path):
+                for file in files:
+                    ext = os.path.splitext(file)[1].lower()
+                    if ext in extensions:
+                        files_to_process.append(os.path.join(root, file))
+                
+                if not recursive:
+                    break
+            
+            total_files = len(files_to_process)
+            self.progress.update_tracking(
+                tracking_id, message=f"Processing {total_files} ontology files"
+            )
+
+            for idx, file_path in enumerate(files_to_process, 1):
+                try:
+                    ont_data = self.ingest_ontology(file_path, **kwargs)
+                    ontologies.append(ont_data)
+                    
+                    self.progress.update_progress(
+                        tracking_id,
+                        processed=idx,
+                        total=total_files,
+                        message=f"Processing {idx}/{total_files}: {Path(file_path).name}"
+                    )
+                except Exception as e:
+                    self.logger.warning(f"Skipping {file_path}: {e}")
+            
+            self.progress.stop_tracking(
+                tracking_id,
+                status="completed",
+                message=f"Ingested {len(ontologies)} ontologies",
+            )
+            return ontologies
+
+        except Exception as e:
+            self.progress.stop_tracking(
+                tracking_id, status="failed", message=str(e)
+            )
+            raise
+
+    def _convert_to_dict(self, graph: Graph, source_path: str, format: str = "unknown") -> Dict[str, Any]:
+        """
+        Convert rdflib Graph to Semantica ontology dictionary.
+
+        Args:
+            graph: Parsed rdflib Graph
+            source_path: Source file path
+            format: Format of the ontology file
+
+        Returns:
+            Ontology dictionary
+        """
+        ontology = {
+            "uri": "",
+            "name": os.path.basename(source_path),
+            "version": "1.0",
+            "classes": [],
+            "properties": [],
+            "metadata": {
+                "source_path": source_path,
+                "ingested_at": datetime.now().isoformat(),
+                "format": format
+            }
+        }
+
+        # 1. Extract Ontology Metadata
+        for s, p, o in graph.triples((None, RDF.type, OWL.Ontology)):
+            ontology["uri"] = str(s)
+            
+            # Try to find label/comment/versionInfo
+            for _, _, label in graph.triples((s, RDFS.label, None)):
+                ontology["name"] = str(label)
+                
+            for _, _, comment in graph.triples((s, RDFS.comment, None)):
+                ontology["description"] = str(comment)
+                
+            for _, _, version in graph.triples((s, OWL.versionInfo, None)):
+                ontology["version"] = str(version)
+            
+            # Break after first ontology definition found (usually only one per file)
+            break
+            
+        # 2. Extract Classes
+        classes = {}
+        # Union of owl:Class and rdfs:Class
+        class_types = [OWL.Class, RDFS.Class]
+        for c_type in class_types:
+            for s, p, o in graph.triples((None, RDF.type, c_type)):
+                if isinstance(s, rdflib.BNode):
+                    continue # Skip blank nodes for now
+                    
+                uri = str(s)
+                if uri not in classes:
+                    cls_def = {
+                        "uri": uri,
+                        "name": self._get_local_name(uri),
+                        "type": "class"
+                    }
+                    
+                    # Add label/comment
+                    label = graph.value(s, RDFS.label)
+                    if label:
+                        cls_def["label"] = str(label)
+                        cls_def["name"] = str(label) # Prefer label as name if available? Or keep URI fragment? 
+                        # Keeping local name from URI is safer for internal IDs, label for display. 
+                        # But Semantica seems to use "name" for the identifier in some examples.
+                        # Let's keep name as local name or label if simple.
+                    
+                    comment = graph.value(s, RDFS.comment)
+                    if comment:
+                        cls_def["description"] = str(comment)
+                        
+                    # Superclasses
+                    parents = []
+                    for _, _, parent in graph.triples((s, RDFS.subClassOf, None)):
+                        if isinstance(parent, rdflib.URIRef):
+                            parents.append(str(parent))
+                    if parents:
+                        cls_def["parents"] = parents
+                        
+                    classes[uri] = cls_def
+        
+        ontology["classes"] = list(classes.values())
+
+        # 3. Extract Properties
+        properties = {}
+        # Object Properties
+        for s, p, o in graph.triples((None, RDF.type, OWL.ObjectProperty)):
+            self._add_property(graph, s, "object", properties)
+            
+        # Datatype Properties
+        for s, p, o in graph.triples((None, RDF.type, OWL.DatatypeProperty)):
+            self._add_property(graph, s, "data", properties)
+            
+        # RDF Properties (generic)
+        for s, p, o in graph.triples((None, RDF.type, RDF.Property)):
+            if str(s) not in properties: # Don't overwrite if already found as specific type
+                self._add_property(graph, s, "annotation", properties) # Default to annotation or generic
+        
+        ontology["properties"] = list(properties.values())
+        
+        return ontology
+
+    def _add_property(self, graph: Graph, subject: rdflib.term.Node, prop_type: str, properties_dict: Dict):
+        if isinstance(subject, rdflib.BNode):
+            return
+
+        uri = str(subject)
+        if uri in properties_dict:
+            return
+            
+        prop_def = {
+            "uri": uri,
+            "name": self._get_local_name(uri),
+            "type": prop_type
+        }
+        
+        label = graph.value(subject, RDFS.label)
+        if label:
+            prop_def["label"] = str(label)
+            
+        comment = graph.value(subject, RDFS.comment)
+        if comment:
+            prop_def["description"] = str(comment)
+            
+        # Domain and Range
+        domain = graph.value(subject, RDFS.domain)
+        if domain and isinstance(domain, rdflib.URIRef):
+            prop_def["domain"] = str(domain)
+            
+        range_val = graph.value(subject, RDFS.range)
+        if range_val and isinstance(range_val, rdflib.URIRef):
+            prop_def["range"] = str(range_val)
+            
+        properties_dict[uri] = prop_def
+
+    def _get_local_name(self, uri: str) -> str:
+        """Extract local name from URI."""
+        if '#' in uri:
+            return uri.split('#')[-1]
+        return uri.split('/')[-1]

semantica/kg/graph_builder.py

@@ -161,7 +161,14 @@ class GraphBuilder:
             }
             all_relationships.append(rel_dict)
         elif isinstance(item, dict):
-            # Detect and normalize Entity objects inside dict
+            if "source_id" in item and "source" not in item:
+                item["source"] = item["source_id"]
+            if "target_id" in item and "target" not in item:
+                item["target"] = item["target_id"]
+            if "subject" in item and "source" not in item:
+                item["source"] = item["subject"]
+            if "object" in item and "target" not in item:
+                item["target"] = item["object"]
             if "source" in item and not isinstance(item["source"], str):
                 src = item["source"]
                 item["source"] = getattr(src, "id", getattr(src, "text", str(src)))
@@ -347,6 +354,21 @@ class GraphBuilder:
         elif not isinstance(sources, list):
             sources = [sources]
 
+        # Count input relationships for warning if all are dropped
+        input_relationships_count = 0
+        if isinstance(source_dict, dict):
+            rels = source_dict.get("relationships", [])
+            if isinstance(rels, list):
+                input_relationships_count += len(rels)
+            elif rels is not None:
+                input_relationships_count += 1
+        if explicit_relationships:
+            for rel_item in explicit_relationships:
+                if isinstance(rel_item, list):
+                    input_relationships_count += len(rel_item)
+                else:
+                    input_relationships_count += 1
+
         # Track graph building
         build_start_time = time.time()
         
@@ -468,11 +490,12 @@ class GraphBuilder:
                         pipeline_id=pipeline_id,
                     )
                     
-                    # Check if relationships are already in dictionary format
                     sample_rel = relationships_list[0] if relationships_list else None
                     is_dict_format = isinstance(sample_rel, dict) and (
-                        "source" in sample_rel and "target" in sample_rel
-                    ) and not hasattr(sample_rel, "__dict__") # Ensure it's not a class instance
+                        ("source" in sample_rel and "target" in sample_rel)
+                        or ("source_id" in sample_rel and "target_id" in sample_rel)
+                        or ("subject" in sample_rel and "object" in sample_rel)
+                    ) and not hasattr(sample_rel, "__dict__")
                     
                     if is_dict_format:
                         # Fast path: directly append dictionaries after normalizing source/target
@@ -481,8 +504,15 @@ class GraphBuilder:
                             batch = relationships_list[i:i + batch_size]
                             for item in batch:
                                 if isinstance(item, dict):
-                                    # Normalize source/target if they are objects
                                     rel_dict = item.copy()
+                                    if "source_id" in rel_dict and "source" not in rel_dict:
+                                        rel_dict["source"] = rel_dict["source_id"]
+                                    if "target_id" in rel_dict and "target" not in rel_dict:
+                                        rel_dict["target"] = rel_dict["target_id"]
+                                    if "subject" in rel_dict and "source" not in rel_dict:
+                                        rel_dict["source"] = rel_dict["subject"]
+                                    if "object" in rel_dict and "target" not in rel_dict:
+                                        rel_dict["target"] = rel_dict["object"]
                                     if "source" in rel_dict and not isinstance(rel_dict["source"], str):
                                         src = rel_dict["source"]
                                         rel_dict["source"] = getattr(src, "id", getattr(src, "text", str(src)))
@@ -571,6 +601,14 @@ class GraphBuilder:
                     f"Entity resolution complete: {len(all_entities)} -> {len(resolved_entities)} unique entities"
                 )
 
+            if input_relationships_count > 0 and len(all_relationships) == 0:
+                warning_msg = (
+                    f"All relationships were dropped during graph building: "
+                    f"{input_relationships_count} input relationships, 0 in final graph"
+                )
+                self.logger.warning(warning_msg)
+                print(f"Warning: {warning_msg}")
+
             # Build graph structure
             print("Building graph structure...")
             structure_start = time.time()
@@ -682,6 +720,14 @@ class GraphBuilder:
             )
             raise
 
+    def build_single_source(
+        self,
+        kg_data: Dict[str, Any],
+        pipeline_id: Optional[str] = None,
+        **options,
+    ) -> Dict[str, Any]:
+        return self.build(kg_data, pipeline_id=pipeline_id, **options)
+
     def add_temporal_edge(
         self,
         graph,

semantica/ontology/__init__.py

@@ -109,12 +109,14 @@ Convenience Functions:
     - create_associative_class: Associative class creation wrapper
     - get_ontology_method: Get ontology method by name
     - list_available_methods: List registered methods
+    - ingest_ontology: Ingest ontology from file or directory
 
 Example Usage:
-    >>> from semantica.ontology import generate_ontology, infer_classes, OntologyGenerator
+    >>> from semantica.ontology import generate_ontology, infer_classes, OntologyGenerator, ingest_ontology
     >>> # Using convenience functions
     >>> ontology = generate_ontology({"entities": [...], "relationships": [...]}, method="default")
     >>> classes = infer_classes(entities, method="default")
+    >>> data = ingest_ontology("ontology.ttl")
     >>> # Using classes directly
     >>> from semantica.ontology import OntologyGenerator, ClassInferrer, PropertyGenerator
     >>> generator = OntologyGenerator(base_uri="https://example.org/ontology/")
@@ -155,6 +157,8 @@ from .registry import MethodRegistry, method_registry
 from .requirements_spec import RequirementsSpec, RequirementsSpecManager
 from .reuse_manager import ReuseDecision, ReuseManager
 from .version_manager import OntologyVersion, VersionManager
+from semantica.ingest import OntologyData, OntologyIngestor
+from .methods import ingest_ontology
 
 __all__ = [
     # Main generators
@@ -200,4 +204,7 @@ __all__ = [
     # Configuration
     "OntologyConfig",
     "ontology_config",
+    "ingest_ontology",
+    "OntologyData",
+    "OntologyIngestor",
 ]

semantica/ontology/methods.py

@@ -111,15 +111,19 @@ Main Functions:
     - create_associative_class: Associative class creation wrapper
     - get_ontology_method: Get ontology method by name
     - list_available_methods: List registered methods
+    - ingest_ontology: Ingest ontology from file or directory (via semantica.ingest)
 
 Example Usage:
-    >>> from semantica.ontology.methods import generate_ontology, infer_classes
+    >>> from semantica.ontology.methods import generate_ontology, infer_classes, ingest_ontology
     >>> ontology = generate_ontology({"entities": [...], "relationships": [...]}, method="default")
     >>> classes = infer_classes(entities, method="default")
+    >>> data = ingest_ontology("ontology.ttl")
 """
 
-from typing import Any, Callable, Dict, List, Optional
+from typing import Any, Callable, Dict, List, Optional, Union
+from pathlib import Path
 
+from semantica.ingest import ingest_ontology as _ingest_ontology, OntologyData
 from .registry import method_registry
 
 
@@ -172,4 +176,23 @@ def list_available_methods(task: Optional[str] = None) -> Dict[str, List[str]]:
     return method_registry.list_all(task)
 
 
-pass
+def ingest_ontology(
+    source: Union[str, Path, List[Union[str, Path]]], 
+    method: str = "file", 
+    **kwargs
+) -> Union[OntologyData, List[OntologyData]]:
+    """
+    Ingest ontology from source.
+    
+    This is a convenience wrapper around semantica.ingest.ingest_ontology.
+    
+    Args:
+        source: Ontology file path, directory path, or list of paths
+        method: Ingestion method (default: "file")
+        **kwargs: Additional options
+        
+    Returns:
+        OntologyData or List[OntologyData]
+    """
+    return _ingest_ontology(source, method=method, **kwargs)
+

semantica/ontology/ontology_usage.md

@@ -42,6 +42,18 @@ classes = inferrer.infer_classes(entities, build_hierarchy=True)
 properties = prop_gen.infer_properties(entities, relationships, classes)
 ```
 
+### Ingesting Ontologies
+
+```python
+from semantica.ingest import OntologyIngestor
+
+# Create ingestor
+ingestor = OntologyIngestor()
+
+# Ingest ontology
+ontology_data = ingestor.ingest_ontology("ontology.ttl")
+```
+
 ## Ontology Generation
 
 ### Basic Ontology Generation
@@ -115,6 +127,49 @@ ontology = engine.from_data(
 )
 ```
 
+## Ontology Ingestion
+
+### Basic Ingestion
+
+Ingest existing ontologies from files (Turtle, RDF/XML, JSON-LD, etc.) into `OntologyData` objects.
+
+```python
+from semantica.ontology import ingest_ontology
+
+# Ingest a single file
+ontology_data = ingest_ontology("path/to/ontology.ttl")
+
+print(f"Source: {ontology_data.source_path}")
+print(f"Format: {ontology_data.format}")
+print(f"Data keys: {ontology_data.data.keys()}")
+```
+
+### Ingesting Directories
+
+Ingest all ontology files in a directory recursively.
+
+```python
+from semantica.ontology import ingest_ontology
+
+# Ingest a directory
+ontologies = ingest_ontology("path/to/ontologies_dir/")
+
+for ont in ontologies:
+    print(f"Ingested: {ont.source_path} ({ont.format})")
+```
+
+### Unified Ingestion Interface
+
+You can also use the unified `semantica.ingest` interface.
+
+```python
+from semantica.ingest import ingest
+
+# Ingest as "ontology" source type
+result = ingest("path/to/ontology.ttl", source_type="ontology")
+ontology_data = result["ontology"]
+```
+
 ## Class Inference
 
 ### Basic Class Inference

semantica/ontology/reuse_manager.py

@@ -363,3 +363,90 @@ class ReuseManager:
     def list_known_ontologies(self) -> List[str]:
         """List known ontology URIs."""
         return list(self.known_ontologies.keys())
+
+    def merge_ontology_data(
+        self, target: Dict[str, Any], source: Dict[str, Any], **options
+    ) -> Dict[str, Any]:
+        """
+        Merge source ontology data into target ontology.
+
+        Merges classes, properties, and metadata from source to target.
+        Handles deduplication based on URI and name.
+
+        Args:
+            target: Target ontology dictionary (modified in-place)
+            source: Source ontology dictionary
+            **options: Merge options:
+                - overwrite: Whether to overwrite existing elements (default: False)
+                - merge_metadata: Whether to merge metadata (default: True)
+
+        Returns:
+            Merged target ontology
+        """
+        tracking_id = self.progress_tracker.start_tracking(
+            module="ontology",
+            submodule="ReuseManager",
+            message=f"Merging ontology {source.get('name', 'unknown')} into {target.get('name', 'unknown')}",
+        )
+
+        try:
+            overwrite = options.get("overwrite", False)
+            
+            # Helper to merge lists of dicts (classes/properties)
+            def merge_lists(target_list, source_list, key_field="uri"):
+                existing_keys = {item.get(key_field): i for i, item in enumerate(target_list) if item.get(key_field)}
+                
+                for item in source_list:
+                    key = item.get(key_field)
+                    if not key:
+                        # Fallback to name if URI missing
+                        key = item.get("name")
+                        
+                    if key in existing_keys:
+                        if overwrite:
+                            target_list[existing_keys[key]] = item
+                    else:
+                        target_list.append(item)
+                        if key:
+                            existing_keys[key] = len(target_list) - 1
+
+            # Merge Classes
+            if "classes" in source:
+                if "classes" not in target:
+                    target["classes"] = []
+                merge_lists(target["classes"], source["classes"])
+
+            # Merge Properties
+            if "properties" in source:
+                if "properties" not in target:
+                    target["properties"] = []
+                merge_lists(target["properties"], source["properties"])
+
+            # Merge Metadata
+            if options.get("merge_metadata", True) and "metadata" in source:
+                if "metadata" not in target:
+                    target["metadata"] = {}
+                # Update with source metadata, preserving target's specific fields if needed
+                # Here we just update
+                target["metadata"].update(source["metadata"])
+                
+            # Merge Imports
+            if "imports" in source:
+                if "imports" not in target:
+                    target["imports"] = []
+                for imp in source["imports"]:
+                    if imp not in target["imports"]:
+                        target["imports"].append(imp)
+
+            self.progress_tracker.stop_tracking(
+                tracking_id,
+                status="completed",
+                message=f"Merged ontology data successfully",
+            )
+            return target
+
+        except Exception as e:
+            self.progress_tracker.stop_tracking(
+                tracking_id, status="failed", message=str(e)
+            )
+            raise

semantica/pipeline/pipeline_builder.py

@@ -32,12 +32,14 @@ License: MIT
 
 from dataclasses import dataclass, field
 from enum import Enum
-from typing import Any, Callable, Dict, List, Optional, Union
+from typing import Any, Callable, Dict, List, Optional, Union, TYPE_CHECKING
 
 from ..utils.exceptions import ProcessingError, ValidationError
 from ..utils.logging import get_logger
 from ..utils.progress_tracker import get_progress_tracker
-from .pipeline_validator import PipelineValidator
+
+if TYPE_CHECKING:
+    from .pipeline_validator import PipelineValidator
 
 
 class StepStatus(Enum):
@@ -104,6 +106,8 @@ class PipelineBuilder:
         if not self.progress_tracker.enabled:
             self.progress_tracker.enabled = True
 
+        from .pipeline_validator import PipelineValidator
+
         self.validator = PipelineValidator(**self.config)
         self.steps: List[PipelineStep] = []
         self.step_registry: Dict[str, Callable] = {}

semantica/semantic_extract/coreference_resolver.py

@@ -240,6 +240,12 @@ class CoreferenceResolver:
             self.progress_tracker.stop_tracking(
                 tracking_id, status="failed", message=str(e)
             )
+            verbose_mode = options.get("verbose", False) or self.config.get("verbose", False)
+            if verbose_mode:
+                import sys
+                print(f"    [CoreferenceResolver] ERROR: Resolution failed: {e}", flush=True, file=sys.stderr)
+                import traceback
+                traceback.print_exc(file=sys.stderr)
             raise
 
     def resolve(

semantica/semantic_extract/llm_extraction.py

@@ -108,7 +108,12 @@ class LLMExtraction:
 
         # Initialize provider using new system
         try:
-            self.provider = create_provider(provider, **config)
+            # Sanitize config: remove api_key if it's None/empty to allow fallback
+            provider_config = config.copy()
+            if "api_key" in provider_config and not provider_config["api_key"]:
+                del provider_config["api_key"]
+                
+            self.provider = create_provider(provider, **provider_config)
         except Exception as e:
             self.logger.warning(f"Failed to initialize {provider} provider: {e}")
             self.provider = None

semantica/semantic_extract/methods.py

@@ -786,7 +786,7 @@ def extract_entities_llm(
 
     # Pass api_key if provided in kwargs (needed for all providers)
     provider_kwargs = kwargs.copy()
-    if "api_key" not in provider_kwargs:
+    if "api_key" not in provider_kwargs or not provider_kwargs["api_key"]:
         # Try to get from environment as fallback for all providers
         import os
         env_key = f"{provider.upper()}_API_KEY"
@@ -1563,18 +1563,24 @@ def extract_relations_llm(
 
     # Pass api_key if provided in kwargs
     provider_kwargs = kwargs.copy()
-    if "api_key" not in provider_kwargs:
+    
+    # Check if api_key is provided but empty, or not provided at all
+    if "api_key" not in provider_kwargs or not provider_kwargs["api_key"]:
         import os
         env_key = f"{provider.upper()}_API_KEY"
         api_key = os.getenv(env_key)
         if api_key:
             provider_kwargs["api_key"] = api_key
+            
+    # Remove None/empty API key if still present to avoid provider errors
+    if "api_key" in provider_kwargs and not provider_kwargs["api_key"]:
+        del provider_kwargs["api_key"]
 
     # 2. PROVIDER VALIDATION
     try:
         llm = create_provider(provider, model=model, **provider_kwargs)
         if not llm.is_available():
-            error_msg = f"{provider} provider not available for relation extraction."
+            error_msg = f"{provider} provider not available for relation extraction (key missing?)."
             logger.error(error_msg)
             if not silent_fail:
                 raise ProcessingError(error_msg)
@@ -1606,12 +1612,8 @@ def extract_relations_llm(
         )
 
     original_entities = entities
-    max_entities_prompt = kwargs.get("max_entities_prompt", kwargs.get("max_entities", 80))
-    try:
-        max_entities_prompt = int(max_entities_prompt)
-    except Exception:
-        max_entities_prompt = 80
-
+    # Use a fixed internal default for prompt entity cap (do not accept overrides from kwargs)
+    max_entities_prompt = 80
     prompt_entities = original_entities
     if max_entities_prompt > 0 and len(original_entities) > max_entities_prompt:
         prompt_entities = filter_entities_for_text(
@@ -1635,6 +1637,11 @@ If a relation doesn't fit any of the preferred types, use the most appropriate t
 Extract meaningful relationships between entities. Use appropriate relation types that accurately describe how entities are connected.
 Common relation types include: related_to, part_of, located_in, created_by, uses, depends_on, interacts_with, and similar variations."""
     
+    verbose_mode = kwargs.get("verbose", False)
+    if verbose_mode:
+        import sys
+        print(f"    [methods.extract_relations_llm] Constructing prompt for {len(prompt_entities)} entities...", flush=True, file=sys.stdout)
+    
     if not SCHEMAS_AVAILABLE:
         raise ImportError("Pydantic schemas not available. Install pydantic/instructor to use LLM extraction.")
 
@@ -1663,29 +1670,65 @@ Entities found in text: {entities_str}"""
     try:
         # Use typed generation with Pydantic schema
         # Pass kwargs to allow max_tokens and other parameters to be used
-        result_obj = llm.generate_typed(prompt, schema=RelationsResponse, **kwargs)
+        if verbose_mode:
+             import sys
+             print(f"    [methods.extract_relations_llm] Calling llm.generate_typed ({provider}/{model})...", flush=True, file=sys.stdout)
+        # Only forward minimal, safe parameters to provider calls
+        call_kwargs = {}
+        if "temperature" in kwargs:
+            call_kwargs["temperature"] = kwargs["temperature"]
+        if "verbose" in kwargs:
+            call_kwargs["verbose"] = kwargs["verbose"]
+
+        result_obj = llm.generate_typed(prompt, schema=RelationsResponse, **call_kwargs)
+        if verbose_mode:
+             import sys
+             print(f"    [methods.extract_relations_llm] Received response from {provider}.", flush=True, file=sys.stdout)
         
-        # Convert back to internal Relation format
-        relations = []
-        for r_out in result_obj.relations:
-            # Find matching entities using hybrid similarity
-            subject_entity = match_entity(r_out.subject, original_entities)
-            object_entity = match_entity(r_out.object, original_entities)
-            
-            if subject_entity and object_entity:
-                relations.append(Relation(
-                    subject=subject_entity,
-                    predicate=r_out.predicate,
-                    object=object_entity,
-                    confidence=r_out.confidence,
-                    context=text, # Simplified context
-                    metadata={
-                        "provider": provider, 
-                        "model": model, 
-                        "extraction_method": "llm_typed"
-                    }
-                ))
+        # Convert back to internal Relation format (robust across providers)
+        # Normalize typed result to a plain dict compatible with _parse_relation_result
+        try:
+            if hasattr(result_obj, "model_dump"):
+                parsed = result_obj.model_dump()
+            elif isinstance(result_obj, dict):
+                parsed = result_obj
+            elif hasattr(result_obj, "relations"):
+                # Instructor may return objects for each relation; convert where possible
+                rel_items = []
+                for r in getattr(result_obj, "relations", []):
+                    if hasattr(r, "model_dump"):
+                        rel_items.append(r.model_dump())
+                    elif isinstance(r, dict):
+                        rel_items.append(r)
+                    else:
+                        # Best-effort attribute access
+                        rel_items.append({
+                            "subject": getattr(r, "subject", ""),
+                            "object": getattr(r, "object", ""),
+                            "predicate": getattr(r, "predicate", "related_to"),
+                            "confidence": getattr(r, "confidence", 0.9),
+                        })
+                parsed = {"relations": rel_items}
+            else:
+                parsed = result_obj
+        except Exception:
+            parsed = result_obj
+
+        # Use common parser to build internal Relation objects
+        relations = _parse_relation_result(parsed, original_entities, text, provider, model)
         
+        # If typed path returned no relations, attempt a structured JSON fallback
+        if not relations:
+            try:
+                if verbose_mode:
+                    import sys
+                    print("    [methods.extract_relations_llm] Typed result empty, attempting structured JSON fallback...", flush=True, file=sys.stdout)
+                raw_json = llm.generate_structured(prompt, **call_kwargs)
+                relations = _parse_relation_result(raw_json, original_entities, text, provider, model)
+            except Exception as _e:
+                # Keep relations as empty if fallback fails
+                pass
+
         logger.info(f"Successfully extracted {len(relations)} relations using {provider}/{model} (typed)")
         _result_cache.set("relations", text, relations, **cache_params)
         return relations
@@ -1813,6 +1856,8 @@ def _extract_relations_chunked(
                 
             logger.debug(f"Scheduling relation extraction for chunk {i+1}/{len(chunks)} with {len(chunk_entities)} entities")
             
+            # Only pass minimal kwargs downstream
+            limited_kwargs = {k: kwargs[k] for k in ("relation_types", "temperature", "verbose") if k in kwargs}
             future = executor.submit(
                 extract_relations_llm,
                 chunk.text,
@@ -1822,7 +1867,7 @@ def _extract_relations_chunked(
                 silent_fail=False,
                 max_text_length=len(chunk.text) + 1,
                 structured_output_mode=structured_output_mode,
-                **kwargs
+                **limited_kwargs
             )
             future_to_chunk[future] = i
             
@@ -2009,12 +2054,18 @@ def extract_triplets_llm(
 
     # Pass api_key if provided in kwargs
     provider_kwargs = kwargs.copy()
-    if "api_key" not in provider_kwargs:
+    
+    # Check if api_key is provided but empty, or not provided at all
+    if "api_key" not in provider_kwargs or not provider_kwargs["api_key"]:
         import os
         env_key = f"{provider.upper()}_API_KEY"
         api_key = os.getenv(env_key)
         if api_key:
             provider_kwargs["api_key"] = api_key
+            
+    # Remove None/empty API key if still present to avoid provider errors
+    if "api_key" in provider_kwargs and not provider_kwargs["api_key"]:
+        del provider_kwargs["api_key"]
 
     # 2. PROVIDER VALIDATION
     try:

semantica/semantic_extract/ner_extractor.py

@@ -375,14 +375,13 @@ class NERExtractor:
                         method_options["model"] = all_options.get(
                             "llm_model", all_options.get("model")
                         )
-                        # Pass api_key if provided (needed for all providers)
-                        if "api_key" in all_options:
-                            method_options["api_key"] = all_options["api_key"]
-                        elif "api_key" not in method_options:
-                            # Try to get from environment as fallback
+                        # Ensure api_key is populated: check explicitly provided or fallback to env
+                        current_key = method_options.get("api_key")
+                        if not current_key:
+                            # Not found or empty/None, try environment
                             import os
-                            provider = method_options.get("provider", "openai")
-                            env_key = f"{provider.upper()}_API_KEY"
+                            provider_name = method_options.get("provider", "openai")
+                            env_key = f"{provider_name.upper()}_API_KEY"
                             api_key = os.getenv(env_key)
                             if api_key:
                                 method_options["api_key"] = api_key

semantica/semantic_extract/providers.py

@@ -243,68 +243,136 @@ class BaseProvider:
                 mode = instructor.Mode.TOOLS  # Default mode
                 
                 if provider_name == "OpenAIProvider" and self.client:
-                    client = instructor.from_openai(self.client)
-                elif provider_name == "AnthropicProvider" and self.client:
-                    client = instructor.from_anthropic(self.client)
-                elif provider_name == "GeminiProvider" and self.client:
-                    client = instructor.from_gemini(
-                        self.client, 
-                        mode=instructor.Mode.GEMINI_JSON
-                    )
-                elif provider_name == "GroqProvider" and self.client:
-                    # Try using from_groq if available (newer instructor versions)
-                    if hasattr(instructor, "from_groq"):
-                        client = instructor.from_groq(self.client, mode=instructor.Mode.JSON)
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"openai/{kwargs.get('model', self.model)}", 
+                                api_key=self.api_key
+                            )
+                        except Exception:
+                            client = instructor.from_openai(self.client)
                     else:
-                        # Fallback: Create OpenAI client pointing to Groq
-                        # This avoids the "Client should be an instance of openai.OpenAI" warning
+                        client = instructor.from_openai(self.client)
+                elif provider_name == "AnthropicProvider" and self.client:
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"anthropic/{kwargs.get('model', self.model)}", 
+                                api_key=self.api_key
+                            )
+                        except Exception:
+                            client = instructor.from_anthropic(self.client)
+                    else:
+                        client = instructor.from_anthropic(self.client)
+                elif provider_name == "GeminiProvider" and self.client:
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"gemini/{kwargs.get('model', self.model)}", 
+                                api_key=self.api_key
+                            )
+                        except Exception:
+                            client = instructor.from_gemini(
+                                self.client, 
+                                mode=instructor.Mode.GEMINI_JSON
+                            )
+                    else:
+                        client = instructor.from_gemini(
+                            self.client, 
+                            mode=instructor.Mode.GEMINI_JSON
+                        )
+                elif provider_name == "GroqProvider" and self.client:
+                    # Try using from_provider which is recommended for Groq in latest instructor
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"groq/{kwargs.get('model', self.model)}", 
+                                api_key=self.api_key
+                            )
+                        except Exception:
+                            client = None
+
+                    if not client:
+                        # Try using from_groq if available (newer instructor versions)
+                        if hasattr(instructor, "from_groq"):
+                            client = instructor.from_groq(self.client, mode=instructor.Mode.JSON)
+                        else:
+                            # Fallback: Create OpenAI client pointing to Groq
+                            # This avoids the "Client should be an instance of openai.OpenAI" warning
+                            try:
+                                from openai import OpenAI
+                                # Fix: Use self.api_key instead of self.client.api_key
+                                groq_client = OpenAI(
+                                    base_url="https://api.groq.com/openai/v1",
+                                    api_key=self.api_key,
+                                )
+                                client = instructor.from_openai(groq_client, mode=instructor.Mode.JSON)
+                            except Exception:
+                                # Last resort: try passing the groq client directly
+                                client = instructor.from_openai(self.client, mode=instructor.Mode.JSON)
+                elif provider_name == "OllamaProvider":
+                    # Try from_provider for Ollama if available
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"ollama/{kwargs.get('model', self.model)}",
+                            )
+                        except Exception:
+                            client = None
+                    
+                    if not client:
+                        # Create OpenAI-compatible client for Ollama
                         try:
                             from openai import OpenAI
-                            groq_client = OpenAI(
-                                base_url="https://api.groq.com/openai/v1",
-                                api_key=self.client.api_key,
+                            # Ollama typically runs on localhost:11434/v1
+                            base_url = getattr(self, "base_url", "http://localhost:11434")
+                            if not base_url.endswith("/v1"):
+                                base_url = f"{base_url.rstrip('/')}/v1"
+                            
+                            ollama_client = OpenAI(
+                                base_url=base_url,
+                                api_key="ollama", # required but unused
                             )
-                            client = instructor.from_openai(groq_client, mode=instructor.Mode.JSON)
-                        except Exception:
-                            # Last resort: try passing the groq client directly
-                            client = instructor.from_openai(self.client, mode=instructor.Mode.JSON)
-                elif provider_name == "OllamaProvider":
-                    # Create OpenAI-compatible client for Ollama
-                    try:
-                        from openai import OpenAI
-                        # Ollama typically runs on localhost:11434/v1
-                        base_url = getattr(self, "base_url", "http://localhost:11434")
-                        if not base_url.endswith("/v1"):
-                            base_url = f"{base_url.rstrip('/')}/v1"
-                        
-                        ollama_client = OpenAI(
-                            base_url=base_url,
-                            api_key="ollama", # required but unused
-                        )
-                        client = instructor.from_openai(ollama_client, mode=instructor.Mode.JSON)
-                    except ImportError:
-                        pass
+                            client = instructor.from_openai(ollama_client, mode=instructor.Mode.JSON)
+                        except ImportError:
+                            pass
                 elif provider_name == "DeepSeekProvider" and self.client:
-                    # DeepSeek is OpenAI compatible
-                    # We need to wrap the underlying client if it exposes the OpenAI interface
-                    # or create a new OpenAI client if self.client is a deepseek.Client (which might be just a wrapper)
-                    # Assuming deepseek.Client is compatible or we can use OpenAI client
-                    try:
-                        # DeepSeek usually works with standard OpenAI client
-                        # If self.client is deepseek.Client, check if we can wrap it
-                        # Otherwise create a new OpenAI client
-                        from openai import OpenAI
-                        if isinstance(self.client, OpenAI):
-                             client = instructor.from_openai(self.client, mode=instructor.Mode.JSON)
-                        else:
-                             # Try creating fresh client
-                             ds_client = OpenAI(
-                                 api_key=self.api_key, 
-                                 base_url="https://api.deepseek.com"
-                             )
-                             client = instructor.from_openai(ds_client, mode=instructor.Mode.JSON)
-                    except Exception:
-                        pass
+                    # Try from_provider for DeepSeek
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            client = instructor.from_provider(
+                                provider=f"deepseek/{kwargs.get('model', self.model)}",
+                                api_key=self.api_key
+                            )
+                        except Exception:
+                            client = None
+
+                    if not client:
+                        # DeepSeek is OpenAI compatible
+                        try:
+                            from openai import OpenAI
+                            if isinstance(self.client, OpenAI):
+                                 client = instructor.from_openai(self.client, mode=instructor.Mode.JSON)
+                            else:
+                                 # Try creating fresh client
+                                 ds_client = OpenAI(
+                                     api_key=self.api_key, 
+                                     base_url="https://api.deepseek.com"
+                                 )
+                                 client = instructor.from_openai(ds_client, mode=instructor.Mode.JSON)
+                        except Exception:
+                            pass
+
+                # Global LiteLLM support - if litellm is passed in kwargs or config
+                if not client and (kwargs.get("litellm") or self.config.get("litellm")):
+                    if hasattr(instructor, "from_provider"):
+                        try:
+                            # Format for litellm in instructor is litellm/model_name
+                            provider_model = kwargs.get("model", self.model)
+                            litellm_provider = f"litellm/{provider_model}"
+                            client = instructor.from_provider(litellm_provider, api_key=self.api_key)
+                        except Exception:
+                            pass
 
                 if client:
                     # Map generate arguments to client arguments
@@ -318,6 +386,11 @@ class BaseProvider:
                         "temperature": kwargs.get("temperature", 0.1), # Low temp for structured
                     }
                     
+                    verbose_mode = kwargs.get("verbose", False)
+                    if verbose_mode:
+                        import sys
+                        print(f"    [BaseProvider.generate_typed] Using instructor via {provider_name}. Client: {type(client)}", flush=True, file=sys.stdout)
+
                     # Pass through other common parameters
                     for param in ["max_tokens", "max_completion_tokens", "top_p", "frequency_penalty", "presence_penalty", "seed", "stop", "logit_bias", "user", "top_k"]:
                         if param in kwargs:
@@ -328,6 +401,9 @@ class BaseProvider:
                         create_kwargs["response_format"] = {"type": "json_object"}
                     
                     response = client.chat.completions.create(**create_kwargs)
+                    if verbose_mode:
+                        import sys
+                        print(f"    [BaseProvider.generate_typed] Typed response received via instructor ({provider_name}).", flush=True, file=sys.stdout)
                     return response
             except Exception as e:
                 self.logger.warning(f"Instructor generation failed ({e}), falling back to manual repair loop.")
@@ -706,7 +782,15 @@ class GroqProvider(BaseProvider):
             if param in kwargs:
                 create_kwargs[param] = kwargs[param]
 
+        verbose_mode = kwargs.get("verbose", False)
+        if verbose_mode:
+            import sys
+            print(f"    [GroqProvider.generate] Sending request to Groq API (model: {create_kwargs['model']})...", flush=True, file=sys.stdout)
+
         response = self.client.chat.completions.create(**create_kwargs)
+        if verbose_mode:
+            import sys
+            print(f"    [GroqProvider.generate] Response received from Groq.", flush=True, file=sys.stdout)
         return response.choices[0].message.content
 
     def generate_structured(self, prompt: str, **kwargs) -> dict:
@@ -737,7 +821,15 @@ class GroqProvider(BaseProvider):
             if param in kwargs:
                 create_kwargs[param] = kwargs[param]
 
+        verbose_mode = kwargs.get("verbose", False)
+        if verbose_mode:
+            import sys
+            print(f"    [GroqProvider.generate_structured] Sending structured request to Groq API (model: {create_kwargs['model']})...", flush=True, file=sys.stdout)
+
         response = self.client.chat.completions.create(**create_kwargs)
+        if verbose_mode:
+            import sys
+            print(f"    [GroqProvider.generate_structured] Structured response received from Groq.", flush=True, file=sys.stdout)
         try:
             return self._parse_json(response.choices[0].message.content)
         except Exception as e:

semantica/semantic_extract/relation_extractor.py

@@ -419,14 +419,13 @@ class RelationExtractor:
                         method_options["model"] = all_options.get(
                             "llm_model", all_options.get("model")
                         )
-                        # Pass api_key if provided (needed for all providers)
-                        if "api_key" in all_options:
-                            method_options["api_key"] = all_options["api_key"]
-                        elif "api_key" not in method_options:
-                            # Try to get from environment as fallback
+                        # Ensure api_key is populated: check explicitly provided or fallback to env
+                        current_key = method_options.get("api_key")
+                        if not current_key:
+                            # Not found or empty/None, try environment
                             import os
-                            provider = method_options.get("provider", "openai")
-                            env_key = f"{provider.upper()}_API_KEY"
+                            provider_name = method_options.get("provider", "openai")
+                            env_key = f"{provider_name.upper()}_API_KEY"
                             api_key = os.getenv(env_key)
                             if api_key:
                                 method_options["api_key"] = api_key
@@ -440,6 +439,12 @@ class RelationExtractor:
                     if verbose_mode and method_name == "llm":
                         import sys
                         print(f"    [RelationExtractor] Processing with {method_name}...", flush=True, file=sys.stdout)
+                        print(f"    [RelationExtractor Debug] method_options keys: {list(method_options.keys())}", flush=True, file=sys.stdout)
+                        if "api_key" in method_options:
+                            masked = method_options["api_key"][:4] + "..." if method_options["api_key"] else "None"
+                            print(f"    [RelationExtractor Debug] api_key present: {masked}", flush=True, file=sys.stdout)
+                        else:
+                            print(f"    [RelationExtractor Debug] api_key NOT present", flush=True, file=sys.stdout)
                     
                     relations = method_func(text, entities, **method_options)
                     
@@ -482,6 +487,11 @@ class RelationExtractor:
 
                 except Exception as e:
                     self.logger.warning(f"Method {method_name} failed: {e}")
+                    if verbose_mode:
+                        import sys
+                        print(f"    [RelationExtractor] ERROR: Method {method_name} failed: {e}", flush=True, file=sys.stderr)
+                        import traceback
+                        traceback.print_exc(file=sys.stderr)
                     continue
 
             # Use first successful method or combine

semantica/semantic_extract/semantic_network_extractor.py

@@ -239,6 +239,10 @@ class SemanticNetworkExtractor:
                         return idx, network
                     except Exception as e:
                         self.logger.warning(f"Failed to process item {idx}: {e}")
+                        verbose_mode = kwargs.get("verbose", False) or self.config.get("verbose", False)
+                        if verbose_mode:
+                            import sys
+                            print(f"    [SemanticNetworkExtractor] ERROR: Batch item {idx} failed: {e}", flush=True, file=sys.stderr)
                         return idx, None
 
                 if max_workers > 1:
@@ -434,6 +438,12 @@ class SemanticNetworkExtractor:
             self.progress_tracker.stop_tracking(
                 tracking_id, status="failed", message=str(e)
             )
+            verbose_mode = options.get("verbose", False) or self.config.get("verbose", False)
+            if verbose_mode:
+                import sys
+                print(f"    [SemanticNetworkExtractor] ERROR: Extraction failed: {e}", flush=True, file=sys.stderr)
+                import traceback
+                traceback.print_exc(file=sys.stderr)
             raise
 
     def _build_network(

semantica/semantic_extract/triplet_extractor.py

@@ -461,18 +461,28 @@ class TripletExtractor:
                         method_options["model"] = all_options.get(
                             "llm_model", all_options.get("model")
                         )
-                        # Pass api_key if provided (needed for all providers)
-                        if "api_key" in all_options:
-                            method_options["api_key"] = all_options["api_key"]
-                        elif "api_key" not in method_options:
-                            # Try to get from environment as fallback
+                        # Ensure api_key is populated: check explicitly provided or fallback to env
+                        current_key = method_options.get("api_key")
+                        if not current_key:
+                            # Not found or empty/None, try environment
                             import os
-                            provider = method_options.get("provider", "openai")
-                            env_key = f"{provider.upper()}_API_KEY"
+                            provider_name = method_options.get("provider", "openai")
+                            env_key = f"{provider_name.upper()}_API_KEY"
                             api_key = os.getenv(env_key)
                             if api_key:
                                 method_options["api_key"] = api_key
 
+                    # Print progress if verbose mode is enabled (only for LLM method to avoid spam)
+                    verbose_mode = options.get("verbose", False) or self.config.get("verbose", False)
+                    if verbose_mode and method_name == "llm":
+                        import sys
+                        print(f"    [TripletExtractor] Processing with {method_name}...", flush=True, file=sys.stdout)
+                        if "api_key" in method_options:
+                             masked = method_options["api_key"][:4] + "..." if method_options["api_key"] else "None"
+                             print(f"    [TripletExtractor Debug] api_key present: {masked}", flush=True, file=sys.stdout)
+                        else:
+                             print(f"    [TripletExtractor Debug] api_key NOT present", flush=True, file=sys.stdout)
+
                     triplets = method_func(
                         text,
                         entities=entities,
@@ -480,6 +490,11 @@ class TripletExtractor:
                         **method_options,
                     )
 
+                    # Print result count if verbose (only for LLM method)
+                    if verbose_mode and method_name == "llm" and len(triplets) > 0:
+                        import sys
+                        print(f"    [TripletExtractor] Extracted {len(triplets)} triplets", flush=True, file=sys.stdout)
+
                     # Apply weighted scoring if triplet_types are provided
                     if triplet_types:
                         try:
@@ -515,6 +530,12 @@ class TripletExtractor:
 
                 except Exception as e:
                     self.logger.warning(f"Method {method_name} failed: {e}")
+                    verbose_mode = options.get("verbose", False) or self.config.get("verbose", False)
+                    if verbose_mode:
+                        import sys
+                        print(f"    [TripletExtractor] ERROR: Method {method_name} failed: {e}", flush=True, file=sys.stderr)
+                        import traceback
+                        traceback.print_exc(file=sys.stderr)
                     continue
 
             # Use first successful method or fallback to relation conversion

semantica/utils/progress_tracker.py

@@ -34,6 +34,7 @@ License: MIT
 """
 
 import inspect
+import os
 import sys
 import threading
 import time
@@ -46,6 +47,13 @@ from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 from .logging import get_logger
 
+DISABLE_JUPYTER_PROGRESS = os.getenv("SEMANTICA_DISABLE_JUPYTER_PROGRESS", "").strip().lower() in (
+    "1",
+    "true",
+    "yes",
+    "on",
+)
+
 # Try to import IPython for Jupyter support
 try:
     from IPython import get_ipython
@@ -1017,6 +1025,7 @@ class ProgressTracker:
 
         # Detect environment - will be checked dynamically
         self.is_jupyter = self._detect_jupyter()
+        self.disable_jupyter_progress = DISABLE_JUPYTER_PROGRESS
 
         # Create displays
         self.displays: List[ProgressDisplay] = []
@@ -1024,7 +1033,7 @@ class ProgressTracker:
         # Always try Jupyter first if available, fallback to console
         if IPYTHON_AVAILABLE:
             # Try to detect Jupyter - if available, use it
-            if self.is_jupyter:
+            if self.is_jupyter and not self.disable_jupyter_progress:
                 self.displays.append(JupyterProgressDisplay(use_emoji=use_emoji))
             # Also add console as fallback for immediate feedback
             self.displays.append(
@@ -1213,7 +1222,11 @@ class ProgressTracker:
         if IPYTHON_AVAILABLE and not self.is_jupyter:
             self.is_jupyter = self._detect_jupyter()
             # If Jupyter is now detected and we don't have a Jupyter display, add it
-            if self.is_jupyter and not any(isinstance(d, JupyterProgressDisplay) for d in self.displays):
+            if (
+                self.is_jupyter
+                and not self.disable_jupyter_progress
+                and not any(isinstance(d, JupyterProgressDisplay) for d in self.displays)
+            ):
                 # Insert Jupyter display at the beginning for priority
                 self.displays.insert(0, JupyterProgressDisplay(use_emoji=self.use_emoji))
 
@@ -1341,7 +1354,11 @@ class ProgressTracker:
         if IPYTHON_AVAILABLE and not self.is_jupyter:
             self.is_jupyter = self._detect_jupyter()
             # If Jupyter is now detected and we don't have a Jupyter display, add it
-            if self.is_jupyter and not any(isinstance(d, JupyterProgressDisplay) for d in self.displays):
+            if (
+                self.is_jupyter
+                and not self.disable_jupyter_progress
+                and not any(isinstance(d, JupyterProgressDisplay) for d in self.displays)
+            ):
                 # Insert Jupyter display at the beginning for priority
                 self.displays.insert(0, JupyterProgressDisplay(use_emoji=self.use_emoji))
 
@@ -1526,7 +1543,11 @@ def get_progress_tracker() -> ProgressTracker:
     if IPYTHON_AVAILABLE and not _global_tracker.is_jupyter:
         _global_tracker.is_jupyter = _global_tracker._detect_jupyter()
         # If Jupyter is now detected and we don't have a Jupyter display, add it
-        if _global_tracker.is_jupyter and not any(isinstance(d, JupyterProgressDisplay) for d in _global_tracker.displays):
+        if (
+            _global_tracker.is_jupyter
+            and not _global_tracker.disable_jupyter_progress
+            and not any(isinstance(d, JupyterProgressDisplay) for d in _global_tracker.displays)
+        ):
             # Insert Jupyter display at the beginning for priority
             _global_tracker.displays.insert(0, JupyterProgressDisplay(use_emoji=_global_tracker.use_emoji))
     

semantica/vector_store/vector_store.py

@@ -38,6 +38,7 @@ License: MIT
 """
 
 from typing import Any, Dict, List, Optional, Tuple, Union
+import concurrent.futures
 
 import numpy as np
 
@@ -61,7 +62,7 @@ class VectorStore:
 
     SUPPORTED_BACKENDS = {"faiss", "weaviate", "qdrant", "milvus", "inmemory"}
 
-    def __init__(self, backend="faiss", config=None, **kwargs):
+    def __init__(self, backend="faiss", config=None, max_workers: int = 6, **kwargs):
         """Initialize vector store."""
         if backend.lower() not in self.SUPPORTED_BACKENDS:
             raise ValueError(
@@ -72,6 +73,7 @@ class VectorStore:
         self.logger = get_logger("vector_store")
         self.config = config or {}
         self.config.update(kwargs)
+        self.max_workers = max_workers
         self.progress_tracker = get_progress_tracker()
         # Ensure progress tracker is enabled
         if not self.progress_tracker.enabled:
@@ -127,6 +129,141 @@ class VectorStore:
         self.logger.warning("Using random fallback embedding")
         return np.random.rand(self.dimension).astype(np.float32)
 
+    def embed_batch(self, texts: List[str]) -> List[np.ndarray]:
+        """
+        Generate embeddings for a list of texts using the internal embedder.
+        
+        Args:
+            texts: List of texts to embed
+            
+        Returns:
+            List of numpy arrays
+        """
+        if self.embedder:
+            try:
+                # generate_embeddings handles list input
+                embeddings = self.embedder.generate_embeddings(texts)
+                # Ensure it returns a list of arrays (it returns 2D array or list)
+                if isinstance(embeddings, np.ndarray):
+                    return list(embeddings)
+                return embeddings
+            except Exception as e:
+                self.logger.warning(f"Batch embedding generation failed: {e}")
+        
+        # Fallback
+        self.logger.warning("Using random fallback embeddings for batch")
+        return [np.random.rand(self.dimension).astype(np.float32) for _ in texts]
+
+    def add_documents(
+        self,
+        documents: List[str],
+        metadata: Optional[List[Dict[str, Any]]] = None,
+        batch_size: int = 32,
+        parallel: bool = True,
+        **options,
+    ) -> List[str]:
+        """
+        Add multiple documents to the store with parallel embedding generation.
+        
+        Args:
+            documents: List of document texts
+            metadata: List of metadata dictionaries
+            batch_size: Number of documents to process in one batch
+            parallel: Whether to use parallel processing for embeddings
+            **options: Additional options
+            
+        Returns:
+            List[str]: Vector IDs
+        """
+        if not documents:
+            return []
+            
+        num_docs = len(documents)
+        metadata = metadata or [{} for _ in range(num_docs)]
+        
+        if len(metadata) != num_docs:
+            raise ValueError("Metadata list length must match documents length")
+            
+        all_vectors = [None] * num_docs
+        
+        # Helper for processing a batch
+        def process_batch(start_idx: int, end_idx: int):
+            batch_texts = documents[start_idx:end_idx]
+            batch_embeddings = self.embed_batch(batch_texts)
+            return start_idx, batch_embeddings
+
+        # Calculate batches
+        batches = []
+        for i in range(0, num_docs, batch_size):
+            batches.append((i, min(i + batch_size, num_docs)))
+            
+        tracking_id = self.progress_tracker.start_tracking(
+            module="vector_store",
+            submodule="VectorStore",
+            message=f"Processing {num_docs} documents (parallel={parallel})",
+        )
+
+        try:
+            if parallel and self.max_workers > 1:
+                self.progress_tracker.update_tracking(
+                    tracking_id, message=f"Embedding with {self.max_workers} workers..."
+                )
+                with concurrent.futures.ThreadPoolExecutor(max_workers=self.max_workers) as executor:
+                    futures = [
+                        executor.submit(process_batch, start, end)
+                        for start, end in batches
+                    ]
+                    
+                    completed = 0
+                    for future in concurrent.futures.as_completed(futures):
+                        start_idx, embeddings = future.result()
+                        # Place results in correct order
+                        for i, emb in enumerate(embeddings):
+                            all_vectors[start_idx + i] = emb
+                        
+                        completed += 1
+                        if completed % 5 == 0:  # Update progress periodically
+                            self.progress_tracker.update_tracking(
+                                tracking_id, 
+                                message=f"Embedded batch {completed}/{len(batches)}"
+                            )
+            else:
+                # Sequential processing
+                self.progress_tracker.update_tracking(
+                    tracking_id, message="Embedding sequentially..."
+                )
+                for i, (start, end) in enumerate(batches):
+                    _, embeddings = process_batch(start, end)
+                    for j, emb in enumerate(embeddings):
+                        all_vectors[start + j] = emb
+                    
+                    if i % 5 == 0:
+                        self.progress_tracker.update_tracking(
+                            tracking_id, 
+                            message=f"Embedded batch {i+1}/{len(batches)}"
+                        )
+                        
+            # Verify all embeddings generated
+            if any(v is None for v in all_vectors):
+                raise ProcessingError("Failed to generate all embeddings")
+                
+            # Store all vectors in one go
+            self.progress_tracker.update_tracking(tracking_id, message="Storing vectors...")
+            vector_ids = self.store_vectors(all_vectors, metadata=metadata, **options)
+            
+            self.progress_tracker.stop_tracking(
+                tracking_id,
+                status="completed",
+                message=f"Added {len(vector_ids)} documents",
+            )
+            return vector_ids
+            
+        except Exception as e:
+            self.progress_tracker.stop_tracking(
+                tracking_id, status="failed", message=str(e)
+            )
+            raise
+
     def store(
         self,
         vectors: List[np.ndarray],

tests/ingest/test_ontology_ingestor.py

@@ -0,0 +1,214 @@
+import os
+import shutil
+import tempfile
+import pytest
+from pathlib import Path
+from semantica.ingest import OntologyIngestor, ingest, ingest_ontology, OntologyData
+
+class TestOntologyIngestor:
+    @pytest.fixture
+    def sample_ttl_content(self):
+        return """
+        @prefix : <http://example.org/ontology/> .
+        @prefix owl: <http://www.w3.org/2002/07/owl#> .
+        @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+        @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+        @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+        <http://example.org/ontology/> rdf:type owl:Ontology ;
+            rdfs:label "Test Ontology" .
+
+        :Person rdf:type owl:Class ;
+            rdfs:label "Person" .
+
+        :hasName rdf:type owl:DatatypeProperty ;
+            rdfs:domain :Person ;
+            rdfs:range xsd:string .
+        """
+
+    def test_ingest_single_file(self, sample_ttl_content):
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".ttl", mode="w") as tmp:
+            tmp.write(sample_ttl_content)
+            tmp_path = tmp.name
+
+        try:
+            ingestor = OntologyIngestor()
+            result = ingestor.ingest_ontology(tmp_path)
+            
+            assert isinstance(result, OntologyData)
+            assert result.data["name"] == "Test Ontology" or result.data["name"] == os.path.basename(tmp_path)
+            assert any(cls["name"] == "Person" for cls in result.data["classes"])
+            assert any(prop["name"] == "hasName" for prop in result.data["properties"])
+            assert result.metadata["format"] == "ttl" or result.metadata["format"] == "turtle"
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+    def test_ingest_directory(self, sample_ttl_content):
+        with tempfile.TemporaryDirectory() as tmp_dir:
+            # Create two ontology files
+            file1 = os.path.join(tmp_dir, "ont1.ttl")
+            file2 = os.path.join(tmp_dir, "ont2.rdf")
+            
+            with open(file1, "w") as f:
+                f.write(sample_ttl_content)
+            
+            # Simple RDF/XML content for the second file
+            rdf_content = """
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+                     xmlns:owl="http://www.w3.org/2002/07/owl#">
+              <owl:Ontology rdf:about="http://example.org/ont2"/>
+              <owl:Class rdf:about="http://example.org/ont2/Animal"/>
+            </rdf:RDF>
+            """
+            with open(file2, "w") as f:
+                f.write(rdf_content)
+            
+            ingestor = OntologyIngestor()
+            results = ingestor.ingest_directory(tmp_dir)
+            
+            assert len(results) == 2
+            assert all(isinstance(r, OntologyData) for r in results)
+            
+            # Verify results contain expected classes
+            classes = [cls["name"] for res in results for cls in res.data["classes"]]
+            assert "Person" in classes
+            assert "Animal" in classes
+
+    def test_unified_ingest_function(self, sample_ttl_content):
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".ttl", mode="w") as tmp:
+            tmp.write(sample_ttl_content)
+            tmp_path = tmp.name
+            
+        try:
+            # Test auto-detection via unified ingest
+            result = ingest(tmp_path)
+            assert "ontology" in result
+            assert isinstance(result["ontology"], OntologyData)
+            assert len(result["ontology"].data["classes"]) > 0
+            
+            # Test explicit source type
+            result_explicit = ingest(tmp_path, source_type="ontology")
+            assert "ontology" in result_explicit
+            assert result_explicit["ontology"].metadata["source_path"] == tmp_path
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+    def test_convenience_function(self, sample_ttl_content):
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".n3", mode="w") as tmp:
+            tmp.write(sample_ttl_content)
+            tmp_path = tmp.name
+            
+        try:
+            result = ingest_ontology(tmp_path)
+            assert isinstance(result, OntologyData)
+            assert len(result.data["classes"]) > 0
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+    def test_ingest_formats(self):
+        """Test ingestion of all supported formats."""
+        ingestor = OntologyIngestor()
+        
+        # 1. JSON-LD
+        jsonld_content = """
+        {
+          "@context": {
+            "owl": "http://www.w3.org/2002/07/owl#",
+            "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+            "rdfs": "http://www.w3.org/2000/01/rdf-schema#"
+          },
+          "@id": "http://example.org/jsonld",
+          "@type": "owl:Ontology",
+          "rdfs:label": "JSON-LD Ontology",
+          "owl:versionInfo": "1.0"
+        }
+        """
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".jsonld", mode="w") as tmp:
+            tmp.write(jsonld_content)
+            tmp_path = tmp.name
+        try:
+            result = ingestor.ingest_ontology(tmp_path)
+            assert result.data["name"] == "JSON-LD Ontology"
+            assert result.metadata["format"] == "json-ld"
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+        # 2. N-Triples
+        nt_content = '<http://example.org/nt/Class> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> .\n'
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".nt", mode="w") as tmp:
+            tmp.write(nt_content)
+            tmp_path = tmp.name
+        try:
+            result = ingestor.ingest_ontology(tmp_path)
+            # N-Triples often doesn't have ontology metadata, so name might default to basename
+            assert result.data["name"] == os.path.basename(tmp_path)
+            assert any(cls["uri"] == "http://example.org/nt/Class" for cls in result.data["classes"])
+            assert result.metadata["format"] == "nt"
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+        # 3. Notation3
+        n3_content = """
+        @prefix : <http://example.org/n3/> .
+        @prefix owl: <http://www.w3.org/2002/07/owl#> .
+        :N3Class a owl:Class .
+        """
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".n3", mode="w") as tmp:
+            tmp.write(n3_content)
+            tmp_path = tmp.name
+        try:
+            result = ingestor.ingest_ontology(tmp_path)
+            assert any(cls["uri"] == "http://example.org/n3/N3Class" for cls in result.data["classes"])
+            # format might be 'n3' or 'turtle' depending on rdflib detection as they are similar
+            assert result.metadata["format"] in ["n3", "turtle"] 
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+        # 4. RDF/XML (.owl)
+        owl_content = """
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+                 xmlns:owl="http://www.w3.org/2002/07/owl#"
+                 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+          <owl:Ontology rdf:about="http://example.org/owl"/>
+          <owl:Class rdf:about="http://example.org/owl/OwlClass">
+            <rdfs:label>OwlClass</rdfs:label>
+          </owl:Class>
+        </rdf:RDF>
+        """
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".owl", mode="w") as tmp:
+            tmp.write(owl_content)
+            tmp_path = tmp.name
+        try:
+            result = ingestor.ingest_ontology(tmp_path)
+            assert any(cls["name"] == "OwlClass" for cls in result.data["classes"])
+            assert result.metadata["format"] in ["xml", "rdf", "owl"]
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)
+
+    def test_error_handling(self):
+        ingestor = OntologyIngestor()
+        with pytest.raises(Exception): # Specific exception type depends on implementation, likely ValidationError or FileNotFoundError
+            ingestor.ingest_ontology("non_existent_file.ttl")
+
+    def test_invalid_content(self):
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".ttl", mode="w") as tmp:
+            tmp.write("This is not valid turtle content")
+            tmp_path = tmp.name
+            
+        try:
+            ingestor = OntologyIngestor()
+            # Depending on implementation, this might raise an exception or return partial/empty result with error in metadata
+            # Given current implementation uses g.parse(), it likely raises an exception which is caught or propagated
+            # If propagated:
+            with pytest.raises(Exception):
+                ingestor.ingest_ontology(tmp_path)
+        finally:
+            if os.path.exists(tmp_path):
+                os.remove(tmp_path)

tests/integration/test_relations_groq.py

@@ -0,0 +1,98 @@
+import os
+import unittest
+import time
+
+from semantica.semantic_extract import NERExtractor, RelationExtractor
+
+# Use environment variable for API key
+_GROQ_KEY = os.getenv("GROQ_API_KEY") or os.getenv("GROQ_TEST_API_KEY")
+@unittest.skipUnless(_GROQ_KEY, "Groq key not set; skipping live integration test")
+class TestGroqRelationsIntegration(unittest.TestCase):
+    def setUp(self):
+        self.api_key = _GROQ_KEY
+        self.model = "llama-3.1-8b-instant"
+        # Short, unambiguous finance snippet
+        self.text_short = (
+            "Apple reported revenue of $4.4 billion in Q1 2024 and provided guidance for FY 2025."
+        )
+        # Longer text to exercise chunking and ensure no hang
+        self.text_long = (
+            "Apple reported revenue of $4.4 billion in Q1 2024. "
+            "The company also reported growth of 12% year-over-year and provided guidance for FY 2025. "
+            "Microsoft reported revenue of $6.1 billion in Q2 2024 and expects sequential growth. "
+            "NVIDIA reported record revenue in 2024 Q1 and guided for higher revenue in Q2 2024. "
+        ) * 20  # expand length
+
+    def _extract_entities(self, text):
+        ner = NERExtractor(
+            method="llm",
+            provider="groq",
+            llm_model=self.model,
+            api_key=self.api_key,
+            temperature=0.0,
+        )
+        entities = ner.extract_entities(text, entity_types=["ORGANIZATION", "MONEY", "DATE", "EVENT", "PERCENT"])
+        self.assertIsInstance(entities, list)
+        return entities
+
+    def test_relations_short_text(self):
+        entities = self._extract_entities(self.text_short)
+        self.assertGreater(len(entities), 0, "NER should extract entities for short text")
+
+        relation_extractor = RelationExtractor(
+            method="llm",
+            relation_types=[
+                "HAS_REVENUE",
+                "HAS_GROWTH",
+                "PROVIDES_GUIDANCE",
+                "IN_QUARTER",
+                "FOR_PERIOD",
+                "RELATED_TO",
+            ],
+            provider="groq",
+            llm_model=self.model,
+            api_key=self.api_key,
+            temperature=0.0,
+            verbose=True,
+        )
+
+        start = time.time()
+        relations = relation_extractor.extract_relations(text=self.text_short, entities=entities)
+        elapsed = time.time() - start
+
+        self.assertIsInstance(relations, list)
+        # Ensure call completes reasonably fast (network dependent; allow generous bound)
+        self.assertLess(elapsed, 60, f"Extraction took too long: {elapsed:.2f}s")
+        # Do not strictly assert >0 as model output may vary, but log for diagnostics
+        if relations:
+            sample = relations[0]
+            self.assertTrue(hasattr(sample, "subject") and hasattr(sample, "predicate") and hasattr(sample, "object"))
+
+    def test_relations_long_text_chunking(self):
+        entities = self._extract_entities(self.text_long)
+        self.assertGreater(len(entities), 0, "NER should extract entities for long text")
+
+        relation_extractor = RelationExtractor(
+            method="llm",
+            relation_types=["RELATED_TO", "HAS_REVENUE", "IN_QUARTER"],
+            provider="groq",
+            llm_model=self.model,
+            api_key=self.api_key,
+            temperature=0.0,
+            verbose=True,
+        )
+
+        start = time.time()
+        relations = relation_extractor.extract_relations(text=self.text_long, entities=entities)
+        elapsed = time.time() - start
+
+        self.assertIsInstance(relations, list)
+        # Ensure completion (chunked path) and no hang
+        self.assertLess(elapsed, 120, f"Chunked extraction took too long: {elapsed:.2f}s")
+        if relations:
+            for r in relations[:3]:
+                self.assertTrue(hasattr(r, "subject") and hasattr(r, "predicate") and hasattr(r, "object"))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/kg/test_graph_builder_external.py

@@ -0,0 +1,232 @@
+import unittest
+from unittest.mock import MagicMock, patch
+
+from semantica.kg.graph_builder import GraphBuilder
+
+
+class TestGraphBuilderExternal(unittest.TestCase):
+    def setUp(self):
+        self.mock_tracker_patcher = patch("semantica.utils.progress_tracker.get_progress_tracker")
+        self.mock_get_tracker = self.mock_tracker_patcher.start()
+        self.mock_tracker = MagicMock()
+        self.mock_get_tracker.return_value = self.mock_tracker
+
+        self.mock_resolver_patcher = patch("semantica.kg.entity_resolver.EntityResolver")
+        self.mock_resolver_cls = self.mock_resolver_patcher.start()
+
+        self.mock_conflict_patcher = patch("semantica.conflicts.conflict_detector.ConflictDetector")
+        self.mock_conflict_cls = self.mock_conflict_patcher.start()
+
+    def tearDown(self):
+        self.mock_tracker_patcher.stop()
+        self.mock_resolver_patcher.stop()
+        self.mock_conflict_patcher.stop()
+
+    def test_single_source_dict_with_source_id_target_id(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        entities = [
+            {"id": "drug:1", "name": "Aspirin", "type": "Drug"},
+            {"id": "disease:1", "name": "Myocardial infarction", "type": "Disease"},
+        ]
+        relationships = [
+            {"source_id": "drug:1", "target_id": "disease:1", "type": "TREATS"},
+        ]
+
+        source = {"entities": entities, "relationships": relationships}
+
+        kg = builder.build(source)
+
+        self.assertEqual(len(kg["entities"]), 2)
+        self.assertEqual(len(kg["relationships"]), 1)
+        rel = kg["relationships"][0]
+        self.assertEqual(rel.get("source"), "drug:1")
+        self.assertEqual(rel.get("target"), "disease:1")
+        self.assertEqual(kg["metadata"]["num_relationships"], 1)
+
+    def test_sources_list_merge_with_external_relationships(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        source1 = {
+            "entities": [{"id": "1", "name": "A"}],
+            "relationships": [{"source_id": "1", "target_id": "2", "type": "REL_1"}],
+        }
+        source2 = {
+            "entities": [{"id": "2", "name": "B"}],
+            "relationships": [{"source_id": "2", "target_id": "1", "type": "REL_2"}],
+        }
+
+        kg = builder.build([source1, source2])
+
+        self.assertEqual(len(kg["entities"]), 2)
+        self.assertEqual(len(kg["relationships"]), 2)
+        sources = {r["source"] for r in kg["relationships"]}
+        targets = {r["target"] for r in kg["relationships"]}
+        self.assertEqual(sources, {"1", "2"})
+        self.assertEqual(targets, {"1", "2"})
+
+    def test_build_with_explicit_relationships_argument_external_ids(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        entities = [
+            {"id": "1", "name": "A"},
+            {"id": "2", "name": "B"},
+        ]
+        relationships = [
+            {"source_id": "1", "target_id": "2", "type": "REL"},
+        ]
+
+        kg = builder.build(entities, relationships=relationships)
+
+        self.assertEqual(len(kg["entities"]), 2)
+        self.assertEqual(len(kg["relationships"]), 1)
+        rel = kg["relationships"][0]
+        self.assertEqual(rel.get("source"), "1")
+        self.assertEqual(rel.get("target"), "2")
+
+    def test_build_single_source_external_graph(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        source = {
+            "entities": [{"id": "1", "name": "A"}],
+            "relationships": [{"source_id": "1", "target_id": "1", "type": "SELF"}],
+        }
+
+        kg = builder.build_single_source(source)
+
+        self.assertEqual(len(kg["entities"]), 1)
+        self.assertEqual(len(kg["relationships"]), 1)
+        rel = kg["relationships"][0]
+        self.assertEqual(rel.get("source"), "1")
+        self.assertEqual(rel.get("target"), "1")
+
+    def test_relationship_key_variants_normalized(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        entities = [
+            {"id": "1", "name": "A"},
+            {"id": "2", "name": "B"},
+            {"id": "3", "name": "C"},
+            {"id": "4", "name": "D"},
+        ]
+        relationships = [
+            {"source_id": "1", "target_id": "2", "type": "R1"},
+            {"source": "2", "target": "3", "type": "R2"},
+            {"subject": "3", "object": "4", "type": "R3"},
+        ]
+
+        kg = builder.build({"entities": entities, "relationships": relationships})
+
+        self.assertEqual(len(kg["relationships"]), 3)
+        ids = {(r["source"], r["target"]) for r in kg["relationships"]}
+        self.assertIn(("1", "2"), ids)
+        self.assertIn(("2", "3"), ids)
+        self.assertIn(("3", "4"), ids)
+
+    def test_warning_when_all_relationships_dropped(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        source = {
+            "entities": [],
+            "relationships": [{"foo": "x"}, {"bar": "y"}],
+        }
+
+        with patch.object(builder.logger, "warning") as mock_warning:
+            kg = builder.build(source)
+
+        self.assertEqual(len(kg["relationships"]), 0)
+        mock_warning.assert_called()
+        args, _ = mock_warning.call_args
+        self.assertIn("All relationships were dropped", args[0])
+
+    def test_no_warning_when_some_relationships_kept(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        source = {
+            "entities": [{"id": "1"}, {"id": "2"}],
+            "relationships": [
+                {"source_id": "1", "target_id": "2", "type": "REL"},
+                {"foo": "x"},
+            ],
+        }
+
+        with patch.object(builder.logger, "warning") as mock_warning:
+            kg = builder.build(source)
+
+        self.assertEqual(len(kg["relationships"]), 2)
+        mock_warning.assert_not_called()
+
+    def test_issue_208_minimal_reproduction_shape(self):
+        builder = GraphBuilder(
+            merge_entities=False,
+            entity_resolution_strategy="none",
+            resolve_conflicts=False,
+        )
+
+        entities = [
+            {"id": "e1", "name": "Entity 1"},
+            {"id": "e2", "name": "Entity 2"},
+            {"id": "e3", "name": "Entity 3"},
+        ]
+        relationships = [
+            {"source_id": "e1", "target_id": "e2", "type": "REL_1"},
+            {"source_id": "e2", "target_id": "e3", "type": "REL_2"},
+        ]
+
+        entity_ids = {e["id"] for e in entities}
+        for r in relationships:
+            self.assertIn(r["source_id"], entity_ids)
+            self.assertIn(r["target_id"], entity_ids)
+
+        kg = builder.build(
+            sources=[{"entities": entities, "relationships": relationships}],
+            merge_entities=False,
+        )
+
+        self.assertEqual(len(kg["entities"]), 3)
+        self.assertEqual(len(kg["relationships"]), 2)
+        pairs = {(r["source"], r["target"]) for r in kg["relationships"]}
+        self.assertIn(("e1", "e2"), pairs)
+        self.assertIn(("e2", "e3"), pairs)
+
+    def test_issue_206_earnings_call_shape(self):
+        builder = GraphBuilder(
+            merge_entities=False,
+            entity_resolution_strategy="none",
+            resolve_conflicts=False,
+        )
+
+        entities = [
+            {
+                "id": "entity_446_MDA Space Ltd.",
+                "name": "MDA Space Ltd.",
+                "type": "ORGANIZATION",
+            },
+            {
+                "id": "entity_500_$409.8 million",
+                "name": "$409.8 million",
+                "type": "MONEY",
+            },
+        ]
+
+        relationships = [
+            {
+                "id": None,
+                "source_id": "MDA Space Ltd.",
+                "target_id": "$409.8 million",
+                "type": "HAS_REVENUE",
+                "confidence": 0.975,
+                "metadata": {},
+            }
+        ]
+
+        kg = builder.build(
+            sources=[{"entities": entities, "relationships": relationships}],
+            merge_entities=False,
+        )
+
+        self.assertEqual(len(kg["entities"]), 2)
+        self.assertEqual(len(kg["relationships"]), 1)
+        rel = kg["relationships"][0]
+        self.assertEqual(rel.get("source"), "MDA Space Ltd.")
+        self.assertEqual(rel.get("target"), "$409.8 million")

tests/kg/test_kg.py

@@ -91,6 +91,30 @@ class TestGraphBuilder(unittest.TestCase):
         graph2 = builder.build(source_list)
         self.assertEqual(len(graph2["entities"]), 2)
 
+    def test_build_with_external_relationship_ids(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        entities = [
+            {"id": "1", "name": "A"},
+            {"id": "2", "name": "B"},
+        ]
+        relationships = [
+            {"source_id": "1", "target_id": "2", "type": "rel"},
+        ]
+
+        source = {
+            "entities": entities,
+            "relationships": relationships,
+        }
+
+        graph = builder.build(source)
+
+        self.assertEqual(len(graph["entities"]), 2)
+        self.assertEqual(len(graph["relationships"]), 1)
+        rel = graph["relationships"][0]
+        self.assertEqual(rel.get("source"), "1")
+        self.assertEqual(rel.get("target"), "2")
+
     def test_build_with_conflict_resolution(self):
         """Test building with conflict resolution enabled"""
         builder = GraphBuilder(resolve_conflicts=True)
@@ -106,6 +130,50 @@ class TestGraphBuilder(unittest.TestCase):
         self.mock_conflict_cls.return_value.detect_conflicts.assert_called_once()
         self.mock_conflict_cls.return_value.resolve_conflicts.assert_called_once()
 
+    def test_build_single_source(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+        source = {
+            "entities": [{"id": "1", "name": "A"}],
+            "relationships": [{"source_id": "1", "target_id": "1", "type": "self"}],
+        }
+        graph = builder.build_single_source(source)
+        self.assertEqual(len(graph["entities"]), 1)
+        self.assertEqual(len(graph["relationships"]), 1)
+
+    def test_build_with_explicit_relationships_argument(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+
+        entities = [
+            {"id": "1", "name": "A"},
+            {"id": "2", "name": "B"},
+        ]
+        relationships = [
+            {"source_id": "1", "target_id": "2", "type": "rel"},
+        ]
+
+        graph = builder.build(entities, relationships=relationships)
+
+        self.assertEqual(len(graph["entities"]), 2)
+        self.assertEqual(len(graph["relationships"]), 1)
+        rel = graph["relationships"][0]
+        self.assertEqual(rel.get("source"), "1")
+        self.assertEqual(rel.get("target"), "2")
+
+    def test_build_warns_when_all_relationships_dropped(self):
+        builder = GraphBuilder(merge_entities=False, resolve_conflicts=False)
+        source = {
+            "entities": [],
+            "relationships": [{"foo": "x"}, {"bar": "y"}],
+        }
+
+        with patch.object(builder.logger, "warning") as mock_warning:
+            graph = builder.build(source)
+
+        self.assertEqual(len(graph["relationships"]), 0)
+        mock_warning.assert_called()
+        args, _ = mock_warning.call_args
+        self.assertIn("All relationships were dropped", args[0])
+
 class TestGraphAnalyzer(unittest.TestCase):
     def setUp(self):
         self.mock_tracker_patcher = patch("semantica.kg.graph_analyzer.get_progress_tracker")

tests/pipeline/test_pipeline.py

@@ -107,5 +107,25 @@ class TestPipelineModule(unittest.TestCase):
         
         self.assertEqual(execution_order, ["A", "B", "C"])
 
+    def test_imports_no_circular_dependencies(self):
+        import semantica
+
+        _ = semantica.pipeline
+
+        from semantica.pipeline import PipelineBuilder, PipelineValidator
+        from semantica.deduplication import DuplicateDetector
+
+        builder = PipelineBuilder()
+        builder.add_step("step1", "dummy")
+        pipeline = builder.build("import_test_pipeline")
+
+        validator = PipelineValidator()
+        result = validator.validate_pipeline(pipeline)
+
+        self.assertTrue(result.valid)
+
+        detector = DuplicateDetector()
+        self.assertIsNotNone(detector)
+
 if __name__ == "__main__":
     unittest.main()

tests/test_relations_llm.py

@@ -0,0 +1,118 @@
+import unittest
+
+from semantica.semantic_extract.methods import extract_relations_llm
+from semantica.semantic_extract.ner_extractor import Entity
+
+
+class FakeProvider:
+    def __init__(self, typed_payload=None, structured_payload=None):
+        self._typed_payload = typed_payload
+        self._structured_payload = structured_payload
+
+    def is_available(self):
+        return True
+
+    # Simulate typed output return: can be dict or an object with relations
+    def generate_typed(self, prompt, schema, **kwargs):
+        return self._typed_payload if self._typed_payload is not None else {"relations": []}
+
+    def generate_structured(self, prompt, **kwargs):
+        return self._structured_payload if self._structured_payload is not None else {"relations": []}
+
+
+class TestLLMRelationExtraction(unittest.TestCase):
+    def setUp(self):
+        # Minimal realistic text and entities
+        self.text = "Apple reported revenue of $4.4 billion in Q1 2024."
+        self.entities = [
+            Entity(text="Apple", label="ORGANIZATION", start_char=0, end_char=5, confidence=0.99),
+            Entity(text="$4.4 billion", label="MONEY", start_char=26, end_char=39, confidence=0.99),
+            Entity(text="Q1 2024", label="DATE", start_char=43, end_char=51, confidence=0.99),
+        ]
+
+    def _monkeypatch_provider(self, provider_instance):
+        # Monkeypatch create_provider used by extract_relations_llm
+        import semantica.semantic_extract.methods as methods
+        self._orig_create_provider = methods.create_provider
+
+        def _fake_create_provider(provider, model=None, **kwargs):
+            return provider_instance
+
+        methods.create_provider = _fake_create_provider
+
+    def tearDown(self):
+        # Restore original create_provider if patched
+        try:
+            import semantica.semantic_extract.methods as methods
+            if hasattr(self, "_orig_create_provider"):
+                methods.create_provider = self._orig_create_provider
+        except Exception:
+            pass
+
+    def test_typed_relations_parsed(self):
+        # Typed returns a dict compatible with parser
+        typed_payload = {
+            "relations": [
+                {
+                    "subject": "Apple",
+                    "predicate": "HAS_REVENUE",
+                    "object": "$4.4 billion",
+                    "confidence": 0.92,
+                },
+                {
+                    "subject": "Apple",
+                    "predicate": "IN_QUARTER",
+                    "object": "Q1 2024",
+                    "confidence": 0.9,
+                },
+            ]
+        }
+        fake = FakeProvider(typed_payload=typed_payload)
+        self._monkeypatch_provider(fake)
+
+        rels = extract_relations_llm(
+            text=self.text,
+            entities=self.entities,
+            provider="groq",
+            model="llama-3.1-8b-instant",
+            relation_types=["HAS_REVENUE", "IN_QUARTER"],
+            verbose=True,
+        )
+        self.assertGreaterEqual(len(rels), 2, "Expected at least two relations from typed payload")
+        preds = {(r.subject.text, r.predicate, r.object.text) for r in rels}
+        self.assertIn(("Apple", "HAS_REVENUE", "$4.4 billion"), preds)
+        self.assertIn(("Apple", "IN_QUARTER", "Q1 2024"), preds)
+
+    def test_structured_fallback_used(self):
+        # Typed returns zero, structured has content
+        typed_payload = {"relations": []}
+        structured_payload = {
+            "relations": [
+                {
+                    "subject": "Apple",
+                    "predicate": "HAS_REVENUE",
+                    "object": "$4.4 billion",
+                    "confidence": 0.88,
+                }
+            ]
+        }
+        fake = FakeProvider(typed_payload=typed_payload, structured_payload=structured_payload)
+        self._monkeypatch_provider(fake)
+
+        rels = extract_relations_llm(
+            text=self.text,
+            entities=self.entities,
+            provider="groq",
+            model="llama-3.1-8b-instant",
+            relation_types=["HAS_REVENUE"],
+            verbose=True,
+        )
+        self.assertEqual(len(rels), 1, "Expected fallback to structured JSON to yield one relation")
+        r = rels[0]
+        self.assertEqual(r.subject.text, "Apple")
+        self.assertEqual(r.object.text, "$4.4 billion")
+        self.assertEqual(r.predicate, "HAS_REVENUE")
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/vector_store/test_vector_store_parallel.py

@@ -0,0 +1,149 @@
+
+import unittest
+import numpy as np
+import time
+import sys
+import os
+import logging
+from unittest.mock import MagicMock, patch
+
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
+
+from semantica.vector_store import VectorStore
+from semantica.utils.exceptions import ProcessingError
+
+
+class TestVectorStoreParallel(unittest.TestCase):
+    def setUp(self):
+        logging.getLogger("vector_store").setLevel(logging.ERROR)
+
+        self.dimension = 4
+        self.store = VectorStore(
+            backend="inmemory",
+            dimension=self.dimension,
+        )
+
+        self.store.embedder = MagicMock()
+
+    def test_embed_batch_success(self):
+        texts = ["a", "b", "c"]
+        expected_embeddings = [
+            np.array([0.1] * 4, dtype=np.float32),
+            np.array([0.2] * 4, dtype=np.float32),
+            np.array([0.3] * 4, dtype=np.float32),
+        ]
+
+        self.store.embedder.generate_embeddings.return_value = expected_embeddings
+
+        results = self.store.embed_batch(texts)
+
+        self.assertEqual(len(results), 3)
+        self.assertTrue(np.allclose(results[0], expected_embeddings[0]))
+        self.store.embedder.generate_embeddings.assert_called_once_with(texts)
+
+    def test_embed_batch_fallback(self):
+        texts = ["a", "b"]
+
+        self.store.embedder.generate_embeddings.side_effect = Exception("Model error")
+
+        results = self.store.embed_batch(texts)
+
+        self.assertEqual(len(results), 2)
+        self.assertEqual(results[0].shape, (self.dimension,))
+        self.assertTrue(isinstance(results[0], np.ndarray))
+
+    def test_add_documents_empty(self):
+        ids = self.store.add_documents([])
+        self.assertEqual(ids, [])
+
+    def test_add_documents_metadata_mismatch(self):
+        with self.assertRaises(ValueError):
+            self.store.add_documents(["doc1"], metadata=[{}, {}])
+
+    def test_add_documents_parallel_success(self):
+        num_docs = 10
+        documents = [f"doc_{i}" for i in range(num_docs)]
+        metadata = [{"id": i} for i in range(num_docs)]
+
+        def mock_embed_batch(texts):
+            return [np.full(self.dimension, float(i)) for i, _ in enumerate(texts)]
+
+        with patch.object(self.store, "embed_batch", side_effect=mock_embed_batch):
+            ids = self.store.add_documents(
+                documents,
+                metadata,
+                batch_size=2,
+                parallel=True,
+            )
+
+        self.assertEqual(len(ids), num_docs)
+        self.assertEqual(len(self.store.vectors), num_docs)
+
+        for i, vec_id in enumerate(ids):
+            stored_meta = self.store.get_metadata(vec_id)
+            self.assertEqual(stored_meta["id"], i)
+
+    def test_add_documents_sequential_success(self):
+        num_docs = 5
+        documents = [f"doc_{i}" for i in range(num_docs)]
+
+        with patch.object(self.store, "embed_batch") as mock_batch:
+            mock_batch.return_value = [np.zeros(self.dimension) for _ in range(num_docs)]
+
+            ids = self.store.add_documents(documents, parallel=False)
+
+            self.assertEqual(len(ids), num_docs)
+            self.assertEqual(mock_batch.call_count, 1)
+
+    def test_add_documents_error_propagation(self):
+        documents = ["doc1", "doc2"]
+
+        with patch.object(self.store, "embed_batch", side_effect=ValueError("Embedding Error")):
+            with self.assertRaises(Exception):
+                self.store.add_documents(documents, parallel=True)
+
+    def test_performance_simulation(self):
+        num_batches = 4
+        batch_delay = 0.1
+        batch_size = 1
+        documents = [f"doc_{i}" for i in range(num_batches)]
+
+        def slow_embed(texts):
+            time.sleep(batch_delay)
+            return [np.zeros(self.dimension) for _ in texts]
+
+        with patch.object(self.store, "embed_batch", side_effect=slow_embed):
+            start_seq = time.time()
+            self.store.add_documents(documents, batch_size=batch_size, parallel=False)
+            dur_seq = time.time() - start_seq
+
+            self.store.vectors = {}
+
+            start_par = time.time()
+            self.store.add_documents(documents, batch_size=batch_size, parallel=True)
+            dur_par = time.time() - start_par
+
+            print(f"\nPerformance Test:")
+            print(f"Sequential Duration: {dur_seq:.4f}s")
+            print(f"Parallel Duration:   {dur_par:.4f}s")
+            print(f"Speedup:             {dur_seq / dur_par:.2f}x")
+
+            self.assertLess(dur_par, dur_seq * 0.7)
+
+    def test_add_documents_batch_size_edge_cases(self):
+        documents = ["a", "b", "c"]
+
+        with patch.object(self.store, "embed_batch") as mock_batch:
+            mock_batch.side_effect = lambda texts: [np.zeros(4) for _ in texts]
+
+            self.store.add_documents(documents, batch_size=100)
+            self.assertEqual(mock_batch.call_count, 1)
+
+            mock_batch.reset_mock()
+
+            self.store.add_documents(documents, batch_size=1)
+            self.assertEqual(mock_batch.call_count, 3)
+
+
+if __name__ == "__main__":
+    unittest.main()