diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 000000000..1a90cc65a --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,7 @@ + + +## Description + + +## DCO Affirmation +I affirm that all code in every commit of this pull request conforms to the terms of the Topoteretes Developer Certificate of Origin diff --git a/.github/workflows/approve_dco.yaml b/.github/workflows/approve_dco.yaml new file mode 100644 index 000000000..467e5cc0d --- /dev/null +++ b/.github/workflows/approve_dco.yaml @@ -0,0 +1,53 @@ +name: DCO Check + +on: + pull_request: + types: [opened, edited, reopened, synchronize, ready_for_review] + +jobs: + check-dco: + runs-on: ubuntu-latest + steps: + - name: Validate Developer Certificate of Origin statement + uses: actions/github-script@v6 + with: + # If using the built-in GITHUB_TOKEN, ensure it has 'read:org' permission. + # In GitHub Enterprise or private orgs, you might need a PAT (personal access token) with read:org scope. + github-token: ${{ secrets.GITHUB_TOKEN }} + script: | + const orgName = 'YOUR_ORGANIZATION_NAME'; // Replace with your org + const prUser = context.payload.pull_request.user.login; + const prBody = context.payload.pull_request.body || ''; + + // Exact text you require in the PR body + const requiredStatement = "I affirm that all code in every commit of this pull request conforms to the terms of the Topoteretes Developer Certificate of Origin"; + + // 1. Check if user is in the org + let isOrgMember = false; + try { + // Attempt to get membership info + const membership = await github.rest.orgs.getMembershipForUser({ + org: orgName, + username: prUser, + }); + // If we get here without an error, user is in the org + isOrgMember = true; + console.log(`${prUser} is a member of ${orgName}. Skipping DCO check.`); + } catch (error) { + // If we get a 404, user is NOT an org member + if (error.status === 404) { + console.log(`${prUser} is NOT a member of ${orgName}. Enforcing DCO check.`); + } else { + // Some other error—fail the workflow or handle accordingly + core.setFailed(`Error checking organization membership: ${error.message}`); + } + } + + // 2. If user is not in the org, enforce the DCO statement + if (!isOrgMember) { + if (!prBody.includes(requiredStatement)) { + core.setFailed( + `DCO check failed. The PR body must include the following statement:\n\n${requiredStatement}` + ); + } + } diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml index b48dde2cc..1f5a6ca59 100644 --- a/.github/workflows/dockerhub.yml +++ b/.github/workflows/dockerhub.yml @@ -1,8 +1,9 @@ -name: build | Build and Push Docker Image to DockerHub +name: build | Build and Push Docker Image to dockerhub on: push: branches: + - dev - main jobs: @@ -10,42 +11,38 @@ jobs: runs-on: ubuntu-latest steps: - - name: Checkout repository - uses: actions/checkout@v4 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 - - - name: Log in to Docker Hub - uses: docker/login-action@v3 - with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} - - - name: Extract Git information - id: git-info - run: | - echo "BRANCH_NAME=${GITHUB_REF_NAME}" >> "$GITHUB_ENV" - echo "COMMIT_SHA=${GITHUB_SHA::7}" >> "$GITHUB_ENV" - - - name: Build and Push Docker Image - run: | - IMAGE_NAME=cognee/cognee - TAG_VERSION="${BRANCH_NAME}-${COMMIT_SHA}" - - echo "Building image: ${IMAGE_NAME}:${TAG_VERSION}" - docker buildx build \ - --platform linux/amd64,linux/arm64 \ - --push \ - --tag "${IMAGE_NAME}:${TAG_VERSION}" \ - --tag "${IMAGE_NAME}:latest" \ - . - - - name: Verify pushed Docker images - run: | - # Verify both platform variants - for PLATFORM in "linux/amd64" "linux/arm64"; do - echo "Verifying image for $PLATFORM..." - docker buildx imagetools inspect "${IMAGE_NAME}:${TAG_VERSION}" --format "{{.Manifest.$PLATFORM.Digest}}" - done - echo "Successfully verified images in Docker Hub" + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + + - name: Log in to Docker Hub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKER_USERNAME }} + password: ${{ secrets.DOCKER_PASSWORD }} + + - name: Extract metadata + id: meta + uses: docker/metadata-action@v5 + with: + images: cognee/cognee + tags: | + type=ref,event=branch + type=sha,prefix={{branch}}- + type=raw,value=latest,enable={{is_default_branch}} + + - name: Build and push + uses: docker/build-push-action@v5 + with: + context: . + platforms: linux/amd64,linux/arm64 + push: true + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} + cache-from: type=registry,ref=cognee/cognee:buildcache + cache-to: type=registry,ref=cognee/cognee:buildcache,mode=max + + - name: Image digest + run: echo ${{ steps.build.outputs.digest }} \ No newline at end of file diff --git a/.github/workflows/test_python_3_10.yml b/.github/workflows/test_python_3_10.yml index 2cf620a17..90c437eb8 100644 --- a/.github/workflows/test_python_3_10.yml +++ b/.github/workflows/test_python_3_10.yml @@ -42,6 +42,10 @@ jobs: - name: Install dependencies run: poetry install --no-interaction -E docs + - name: Download NLTK tokenizer data + run: | + poetry run python -m nltk.downloader punkt_tab averaged_perceptron_tagger_eng + - name: Run unit tests run: poetry run pytest cognee/tests/unit/ diff --git a/.github/workflows/test_python_3_11.yml b/.github/workflows/test_python_3_11.yml index b119dbcb2..83f98c6ed 100644 --- a/.github/workflows/test_python_3_11.yml +++ b/.github/workflows/test_python_3_11.yml @@ -44,6 +44,11 @@ jobs: - name: Install dependencies run: poetry install --no-interaction -E docs + - name: Download NLTK tokenizer data + run: | + poetry run python -m nltk.downloader punkt_tab averaged_perceptron_tagger_eng + + - name: Run unit tests run: poetry run pytest cognee/tests/unit/ diff --git a/.github/workflows/test_python_3_12.yml b/.github/workflows/test_python_3_12.yml index 5a032144a..14e33551a 100644 --- a/.github/workflows/test_python_3_12.yml +++ b/.github/workflows/test_python_3_12.yml @@ -43,6 +43,9 @@ jobs: - name: Install dependencies run: poetry install --no-interaction -E docs + - name: Download NLTK tokenizer data + run: | + poetry run python -m nltk.downloader punkt_tab averaged_perceptron_tagger_eng - name: Run unit tests run: poetry run pytest cognee/tests/unit/ diff --git a/cognee-mcp/README.md b/cognee-mcp/README.md index 4ffa41e8f..54b607ce5 100644 --- a/cognee-mcp/README.md +++ b/cognee-mcp/README.md @@ -37,7 +37,15 @@ source .venv/bin/activate 4. Add the new server to your Claude config: The file should be located here: ~/Library/Application\ Support/Claude/ +``` +cd ~/Library/Application\ Support/Claude/ +``` You need to create claude_desktop_config.json in this folder if it doesn't exist +Make sure to add your paths and LLM API key to the file bellow +Use your editor of choice, for example Nano: +``` +nano claude_desktop_config.json +``` ``` @@ -83,3 +91,17 @@ npx -y @smithery/cli install cognee --client claude Define cognify tool in server.py Restart your Claude desktop. + + +To use debugger, run: +```bash +npx @modelcontextprotocol/inspector uv --directory /Users/name/folder run cognee +``` + +To apply new changes while development you do: + +1. Poetry lock in cognee folder +2. uv sync --dev --all-extras --reinstall +3. npx @modelcontextprotocol/inspector uv --directory /Users/vasilije/cognee/cognee-mcp run cognee + + diff --git a/cognee-mcp/cognee_mcp/server.py b/cognee-mcp/cognee_mcp/server.py index 19dc999d7..6ae93934e 100644 --- a/cognee-mcp/cognee_mcp/server.py +++ b/cognee-mcp/cognee_mcp/server.py @@ -3,6 +3,8 @@ import asyncio from contextlib import redirect_stderr, redirect_stdout +from sqlalchemy.testing.plugin.plugin_base import logging + import cognee import mcp.server.stdio import mcp.types as types @@ -10,6 +12,8 @@ from cognee.shared.data_models import KnowledgeGraph from mcp.server import NotificationOptions, Server from mcp.server.models import InitializationOptions +from PIL import Image + server = Server("cognee-mcp") @@ -87,9 +91,46 @@ async def handle_list_tools() -> list[types.Tool]: }, }, ), + types.Tool( + name="visualize", + description="Visualize the knowledge graph.", + inputSchema={ + "type": "object", + "properties": { + "query": {"type": "string"}, + }, + }, + ), ] +def get_freshest_png(directory: str) -> Image.Image: + if not os.path.exists(directory): + raise FileNotFoundError(f"Directory {directory} does not exist") + + # List all files in 'directory' that end with .png + files = [f for f in os.listdir(directory) if f.endswith(".png")] + if not files: + raise FileNotFoundError("No PNG files found in the given directory.") + + # Sort by integer value of the filename (minus the '.png') + # Example filename: 1673185134.png -> integer 1673185134 + try: + files_sorted = sorted(files, key=lambda x: int(x.replace(".png", ""))) + except ValueError as e: + raise ValueError("Invalid PNG filename format. Expected timestamp format.") from e + + # The "freshest" file has the largest timestamp + freshest_filename = files_sorted[-1] + freshest_path = os.path.join(directory, freshest_filename) + + # Open the image with PIL and return the PIL Image object + try: + return Image.open(freshest_path) + except (IOError, OSError) as e: + raise IOError(f"Failed to open PNG file {freshest_path}") from e + + @server.call_tool() async def handle_call_tool( name: str, arguments: dict | None @@ -154,6 +195,20 @@ async def handle_call_tool( text="Pruned", ) ] + + elif name == "visualize": + with open(os.devnull, "w") as fnull: + with redirect_stdout(fnull), redirect_stderr(fnull): + try: + results = await cognee.visualize_graph() + return [ + types.TextContent( + type="text", + text=results, + ) + ] + except (FileNotFoundError, IOError, ValueError) as e: + raise ValueError(f"Failed to create visualization: {str(e)}") else: raise ValueError(f"Unknown tool: {name}") diff --git a/cognee-mcp/pyproject.toml b/cognee-mcp/pyproject.toml index aaef31c41..5da82f935 100644 --- a/cognee-mcp/pyproject.toml +++ b/cognee-mcp/pyproject.toml @@ -4,6 +4,7 @@ version = "0.1.0" description = "A MCP server project" readme = "README.md" requires-python = ">=3.10" + dependencies = [ "mcp>=1.1.1", "openai==1.59.4", @@ -51,7 +52,7 @@ dependencies = [ "pydantic-settings>=2.2.1,<3.0.0", "anthropic>=0.26.1,<1.0.0", "sentry-sdk[fastapi]>=2.9.0,<3.0.0", - "fastapi-users[sqlalchemy]", # Optional + "fastapi-users[sqlalchemy]>=14.0.0", # Optional "alembic>=1.13.3,<2.0.0", "asyncpg==0.30.0", # Optional "pgvector>=0.3.5,<0.4.0", # Optional @@ -91,4 +92,4 @@ dev = [ ] [project.scripts] -cognee = "cognee_mcp:main" +cognee = "cognee_mcp:main" \ No newline at end of file diff --git a/cognee-mcp/uv.lock b/cognee-mcp/uv.lock index 46f6c198b..503a1ba82 100644 --- a/cognee-mcp/uv.lock +++ b/cognee-mcp/uv.lock @@ -561,7 +561,7 @@ name = "click" version = "8.1.7" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "colorama", marker = "platform_system == 'Windows'" }, + { name = "colorama", marker = "sys_platform == 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/96/d3/f04c7bfcf5c1862a2a5b845c6b2b360488cf47af55dfa79c98f6a6bf98b5/click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de", size = 336121 } wheels = [ @@ -570,7 +570,7 @@ wheels = [ [[package]] name = "cognee" -version = "0.1.21" +version = "0.1.22" source = { directory = "../" } dependencies = [ { name = "aiofiles" }, @@ -633,7 +633,7 @@ requires-dist = [ { name = "dlt", extras = ["sqlalchemy"], specifier = ">=1.4.1,<2.0.0" }, { name = "falkordb", marker = "extra == 'falkordb'", specifier = "==1.0.9" }, { name = "fastapi", specifier = ">=0.109.2,<0.116.0" }, - { name = "fastapi-users", extras = ["sqlalchemy"] }, + { name = "fastapi-users", extras = ["sqlalchemy"], specifier = "==14.0.0" }, { name = "filetype", specifier = ">=1.2.0,<2.0.0" }, { name = "graphistry", specifier = ">=0.33.5,<0.34.0" }, { name = "groq", marker = "extra == 'groq'", specifier = "==0.8.0" }, @@ -647,12 +647,12 @@ requires-dist = [ { name = "langfuse", specifier = ">=2.32.0,<3.0.0" }, { name = "langsmith", marker = "extra == 'langchain'", specifier = "==0.2.3" }, { name = "litellm", specifier = "==1.57.2" }, - { name = "llama-index-core", marker = "extra == 'llama-index'", specifier = ">=0.12.10.post1,<0.13.0" }, + { name = "llama-index-core", marker = "extra == 'llama-index'", specifier = ">=0.12.11,<0.13.0" }, { name = "matplotlib", specifier = ">=3.8.3,<4.0.0" }, { name = "neo4j", marker = "extra == 'neo4j'", specifier = ">=5.20.0,<6.0.0" }, { name = "nest-asyncio", specifier = "==1.6.0" }, { name = "networkx", specifier = ">=3.2.1,<4.0.0" }, - { name = "nltk", specifier = ">=3.8.1,<4.0.0" }, + { name = "nltk", specifier = "==3.9.1" }, { name = "numpy", specifier = "==1.26.4" }, { name = "openai", specifier = "==1.59.4" }, { name = "pandas", specifier = "==2.2.3" }, @@ -674,7 +674,7 @@ requires-dist = [ { name = "tiktoken", specifier = "==0.7.0" }, { name = "transformers", specifier = ">=4.46.3,<5.0.0" }, { name = "typing-extensions", specifier = "==4.12.2" }, - { name = "unstructured", extras = ["csv", "doc", "docx", "epub", "md", "odt", "org", "ppt", "pptx", "rst", "rtf", "tsv", "xlsx"], marker = "extra == 'docs'", specifier = ">=0.16.10,<0.17.0" }, + { name = "unstructured", extras = ["csv", "doc", "docx", "epub", "md", "odt", "org", "ppt", "pptx", "rst", "rtf", "tsv", "xlsx"], marker = "extra == 'docs'", specifier = ">=0.16.13,<0.17.0" }, { name = "uvicorn", specifier = "==0.22.0" }, { name = "weaviate-client", marker = "extra == 'weaviate'", specifier = "==4.9.6" }, ] @@ -777,7 +777,7 @@ requires-dist = [ { name = "dlt", extras = ["sqlalchemy"], specifier = ">=1.4.1,<2.0.0" }, { name = "falkordb", specifier = "==1.0.9" }, { name = "fastapi", specifier = ">=0.109.2,<0.110.0" }, - { name = "fastapi-users", extras = ["sqlalchemy"] }, + { name = "fastapi-users", extras = ["sqlalchemy"], specifier = ">=14.0.0" }, { name = "filetype", specifier = ">=1.2.0,<2.0.0" }, { name = "gitpython", specifier = ">=3.1.43,<4.0.0" }, { name = "graphistry", specifier = ">=0.33.5,<0.34.0" }, @@ -3359,7 +3359,7 @@ name = "portalocker" version = "2.10.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "pywin32", marker = "platform_system == 'Windows'" }, + { name = "pywin32", marker = "sys_platform == 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/ed/d3/c6c64067759e87af98cc668c1cc75171347d0f1577fab7ca3749134e3cd4/portalocker-2.10.1.tar.gz", hash = "sha256:ef1bf844e878ab08aee7e40184156e1151f228f103aa5c6bd0724cc330960f8f", size = 40891 } wheels = [ @@ -4954,7 +4954,7 @@ name = "tqdm" version = "4.67.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "colorama", marker = "platform_system == 'Windows'" }, + { name = "colorama", marker = "sys_platform == 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/a8/4b/29b4ef32e036bb34e4ab51796dd745cdba7ed47ad142a9f4a1eb8e0c744d/tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2", size = 169737 } wheels = [ diff --git a/cognee/__init__.py b/cognee/__init__.py index 4ffd39577..241dd1ad6 100644 --- a/cognee/__init__.py +++ b/cognee/__init__.py @@ -4,7 +4,7 @@ from .api.v1.datasets.datasets import datasets from .api.v1.prune import prune from .api.v1.search import SearchType, get_search_history, search -from .api.v1.visualize import visualize +from .api.v1.visualize import visualize_graph from .shared.utils import create_cognee_style_network_with_logo # Pipelines diff --git a/cognee/api/v1/visualize/visualize.py b/cognee/api/v1/visualize/visualize.py index 3267f9d3d..4c4c613c8 100644 --- a/cognee/api/v1/visualize/visualize.py +++ b/cognee/api/v1/visualize/visualize.py @@ -10,5 +10,6 @@ async def visualize_graph(label: str = "name"): logging.info(graph_data) graph = await create_cognee_style_network_with_logo(graph_data, label=label) + logging.info("The HTML file has been stored on your home directory! Navigate there with cd ~") return graph diff --git a/cognee/infrastructure/databases/graph/neo4j_driver/adapter.py b/cognee/infrastructure/databases/graph/neo4j_driver/adapter.py index 3543418fc..2f9d42b06 100644 --- a/cognee/infrastructure/databases/graph/neo4j_driver/adapter.py +++ b/cognee/infrastructure/databases/graph/neo4j_driver/adapter.py @@ -62,10 +62,12 @@ async def has_node(self, node_id: str) -> bool: async def add_node(self, node: DataPoint): serialized_properties = self.serialize_properties(node.model_dump()) - query = dedent("""MERGE (node {id: $node_id}) + query = dedent( + """MERGE (node {id: $node_id}) ON CREATE SET node += $properties, node.updated_at = timestamp() ON MATCH SET node += $properties, node.updated_at = timestamp() - RETURN ID(node) AS internal_id, node.id AS nodeId""") + RETURN ID(node) AS internal_id, node.id AS nodeId""" + ) params = { "node_id": str(node.id), @@ -182,13 +184,15 @@ async def add_edge( ): serialized_properties = self.serialize_properties(edge_properties) - query = dedent("""MATCH (from_node {id: $from_node}), + query = dedent( + """MATCH (from_node {id: $from_node}), (to_node {id: $to_node}) MERGE (from_node)-[r]->(to_node) ON CREATE SET r += $properties, r.updated_at = timestamp(), r.type = $relationship_name ON MATCH SET r += $properties, r.updated_at = timestamp() RETURN r - """) + """ + ) params = { "from_node": str(from_node), diff --git a/cognee/infrastructure/databases/hybrid/falkordb/FalkorDBAdapter.py b/cognee/infrastructure/databases/hybrid/falkordb/FalkorDBAdapter.py index 77bfd74e6..dd8934c34 100644 --- a/cognee/infrastructure/databases/hybrid/falkordb/FalkorDBAdapter.py +++ b/cognee/infrastructure/databases/hybrid/falkordb/FalkorDBAdapter.py @@ -88,23 +88,27 @@ async def create_data_point_query(self, data_point: DataPoint, vectorized_values } ) - return dedent(f""" + return dedent( + f""" MERGE (node:{node_label} {{id: '{str(data_point.id)}'}}) ON CREATE SET node += ({{{node_properties}}}), node.updated_at = timestamp() ON MATCH SET node += ({{{node_properties}}}), node.updated_at = timestamp() - """).strip() + """ + ).strip() async def create_edge_query(self, edge: tuple[str, str, str, dict]) -> str: properties = await self.stringify_properties(edge[3]) properties = f"{{{properties}}}" - return dedent(f""" + return dedent( + f""" MERGE (source {{id:'{edge[0]}'}}) MERGE (target {{id: '{edge[1]}'}}) MERGE (source)-[edge:{edge[2]} {properties}]->(target) ON MATCH SET edge.updated_at = timestamp() ON CREATE SET edge.updated_at = timestamp() - """).strip() + """ + ).strip() async def create_collection(self, collection_name: str): pass @@ -195,12 +199,14 @@ async def add_edges(self, edges: list[tuple[str, str, str, dict]]): self.query(query) async def has_edges(self, edges): - query = dedent(""" + query = dedent( + """ UNWIND $edges AS edge MATCH (a)-[r]->(b) WHERE id(a) = edge.from_node AND id(b) = edge.to_node AND type(r) = edge.relationship_name RETURN edge.from_node AS from_node, edge.to_node AS to_node, edge.relationship_name AS relationship_name, count(r) > 0 AS edge_exists - """).strip() + """ + ).strip() params = { "edges": [ @@ -279,14 +285,16 @@ async def search( [label, attribute_name] = collection_name.split(".") - query = dedent(f""" + query = dedent( + f""" CALL db.idx.vector.queryNodes( '{label}', '{attribute_name}', {limit}, vecf32({query_vector}) ) YIELD node, score - """).strip() + """ + ).strip() result = self.query(query) diff --git a/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py b/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py index 6c3c5029d..68561979d 100644 --- a/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py +++ b/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py @@ -93,10 +93,12 @@ async def get_schema_list(self) -> List[str]: if self.engine.dialect.name == "postgresql": async with self.engine.begin() as connection: result = await connection.execute( - text(""" + text( + """ SELECT schema_name FROM information_schema.schemata WHERE schema_name NOT IN ('pg_catalog', 'pg_toast', 'information_schema'); - """) + """ + ) ) return [schema[0] for schema in result.fetchall()] return [] diff --git a/cognee/shared/utils.py b/cognee/shared/utils.py index affd92c87..6b1ca7f8f 100644 --- a/cognee/shared/utils.py +++ b/cognee/shared/utils.py @@ -11,9 +11,7 @@ import pandas as pd import matplotlib.pyplot as plt import tiktoken -import nltk -import base64 - +import time import logging import sys @@ -23,13 +21,40 @@ from uuid import uuid4 import pathlib - +import nltk from cognee.shared.exceptions import IngestionError # Analytics Proxy Url, currently hosted by Vercel proxy_url = "https://test.prometh.ai" +def get_entities(tagged_tokens): + nltk.download("maxent_ne_chunker", quiet=True) + from nltk.chunk import ne_chunk + + return ne_chunk(tagged_tokens) + + +def extract_pos_tags(sentence): + """Extract Part-of-Speech (POS) tags for words in a sentence.""" + + # Ensure that the necessary NLTK resources are downloaded + nltk.download("words", quiet=True) + nltk.download("punkt", quiet=True) + nltk.download("averaged_perceptron_tagger", quiet=True) + + from nltk.tag import pos_tag + from nltk.tokenize import word_tokenize + + # Tokenize the sentence into words + tokens = word_tokenize(sentence) + + # Tag each word with its corresponding POS tag + pos_tags = pos_tag(tokens) + + return pos_tags + + def get_anonymous_id(): """Creates or reads a anonymous user id""" home_dir = str(pathlib.Path(pathlib.Path(__file__).parent.parent.parent.resolve())) @@ -243,33 +268,6 @@ async def render_graph( # return df.replace([np.inf, -np.inf, np.nan], None) -def get_entities(tagged_tokens): - nltk.download("maxent_ne_chunker", quiet=True) - from nltk.chunk import ne_chunk - - return ne_chunk(tagged_tokens) - - -def extract_pos_tags(sentence): - """Extract Part-of-Speech (POS) tags for words in a sentence.""" - - # Ensure that the necessary NLTK resources are downloaded - nltk.download("words", quiet=True) - nltk.download("punkt", quiet=True) - nltk.download("averaged_perceptron_tagger", quiet=True) - - from nltk.tag import pos_tag - from nltk.tokenize import word_tokenize - - # Tokenize the sentence into words - tokens = word_tokenize(sentence) - - # Tag each word with its corresponding POS tag - pos_tags = pos_tag(tokens) - - return pos_tags - - logging.basicConfig(level=logging.INFO) @@ -396,6 +394,7 @@ async def create_cognee_style_network_with_logo( from bokeh.embed import file_html from bokeh.resources import CDN + from bokeh.io import export_png logging.info("Converting graph to serializable format...") G = await convert_to_serializable_graph(G) @@ -445,13 +444,14 @@ async def create_cognee_style_network_with_logo( logging.info(f"Saving visualization to {output_filename}...") html_content = file_html(p, CDN, title) - with open(output_filename, "w") as f: - f.write(html_content) - logging.info("Visualization complete.") + home_dir = os.path.expanduser("~") + + # Construct the final output file path + output_filepath = os.path.join(home_dir, output_filename) + with open(output_filepath, "w") as f: + f.write(html_content) - if bokeh_object: - return p return html_content @@ -512,7 +512,7 @@ def setup_logging(log_level=logging.INFO): G, output_filename="example_network.html", title="Example Cognee Network", - node_attribute="group", # Attribute to use for coloring nodes + label="group", # Attribute to use for coloring nodes layout_func=nx.spring_layout, # Layout function layout_scale=3.0, # Scale for the layout logo_alpha=0.2, diff --git a/cognee/tests/integration/documents/AudioDocument_test.py b/cognee/tests/integration/documents/AudioDocument_test.py index e07a2431b..dbd43ddda 100644 --- a/cognee/tests/integration/documents/AudioDocument_test.py +++ b/cognee/tests/integration/documents/AudioDocument_test.py @@ -36,12 +36,12 @@ def test_AudioDocument(): for ground_truth, paragraph_data in zip( GROUND_TRUTH, document.read(chunk_size=64, chunker="text_chunker") ): - assert ground_truth["word_count"] == paragraph_data.word_count, ( - f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' - ) - assert ground_truth["len_text"] == len(paragraph_data.text), ( - f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' - ) - assert ground_truth["cut_type"] == paragraph_data.cut_type, ( - f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' - ) + assert ( + ground_truth["word_count"] == paragraph_data.word_count + ), f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' + assert ground_truth["len_text"] == len( + paragraph_data.text + ), f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' + assert ( + ground_truth["cut_type"] == paragraph_data.cut_type + ), f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' diff --git a/cognee/tests/integration/documents/ImageDocument_test.py b/cognee/tests/integration/documents/ImageDocument_test.py index b8d585419..c0877ae99 100644 --- a/cognee/tests/integration/documents/ImageDocument_test.py +++ b/cognee/tests/integration/documents/ImageDocument_test.py @@ -25,12 +25,12 @@ def test_ImageDocument(): for ground_truth, paragraph_data in zip( GROUND_TRUTH, document.read(chunk_size=64, chunker="text_chunker") ): - assert ground_truth["word_count"] == paragraph_data.word_count, ( - f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' - ) - assert ground_truth["len_text"] == len(paragraph_data.text), ( - f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' - ) - assert ground_truth["cut_type"] == paragraph_data.cut_type, ( - f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' - ) + assert ( + ground_truth["word_count"] == paragraph_data.word_count + ), f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' + assert ground_truth["len_text"] == len( + paragraph_data.text + ), f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' + assert ( + ground_truth["cut_type"] == paragraph_data.cut_type + ), f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' diff --git a/cognee/tests/integration/documents/PdfDocument_test.py b/cognee/tests/integration/documents/PdfDocument_test.py index fc4307846..8f28815d3 100644 --- a/cognee/tests/integration/documents/PdfDocument_test.py +++ b/cognee/tests/integration/documents/PdfDocument_test.py @@ -27,12 +27,12 @@ def test_PdfDocument(): for ground_truth, paragraph_data in zip( GROUND_TRUTH, document.read(chunk_size=1024, chunker="text_chunker") ): - assert ground_truth["word_count"] == paragraph_data.word_count, ( - f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' - ) - assert ground_truth["len_text"] == len(paragraph_data.text), ( - f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' - ) - assert ground_truth["cut_type"] == paragraph_data.cut_type, ( - f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' - ) + assert ( + ground_truth["word_count"] == paragraph_data.word_count + ), f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' + assert ground_truth["len_text"] == len( + paragraph_data.text + ), f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' + assert ( + ground_truth["cut_type"] == paragraph_data.cut_type + ), f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' diff --git a/cognee/tests/integration/documents/TextDocument_test.py b/cognee/tests/integration/documents/TextDocument_test.py index 6daec62b7..1e143d563 100644 --- a/cognee/tests/integration/documents/TextDocument_test.py +++ b/cognee/tests/integration/documents/TextDocument_test.py @@ -39,12 +39,12 @@ def test_TextDocument(input_file, chunk_size): for ground_truth, paragraph_data in zip( GROUND_TRUTH[input_file], document.read(chunk_size=chunk_size, chunker="text_chunker") ): - assert ground_truth["word_count"] == paragraph_data.word_count, ( - f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' - ) - assert ground_truth["len_text"] == len(paragraph_data.text), ( - f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' - ) - assert ground_truth["cut_type"] == paragraph_data.cut_type, ( - f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' - ) + assert ( + ground_truth["word_count"] == paragraph_data.word_count + ), f'{ground_truth["word_count"] = } != {paragraph_data.word_count = }' + assert ground_truth["len_text"] == len( + paragraph_data.text + ), f'{ground_truth["len_text"] = } != {len(paragraph_data.text) = }' + assert ( + ground_truth["cut_type"] == paragraph_data.cut_type + ), f'{ground_truth["cut_type"] = } != {paragraph_data.cut_type = }' diff --git a/cognee/tests/integration/documents/UnstructuredDocument_test.py b/cognee/tests/integration/documents/UnstructuredDocument_test.py index 773dc2293..e0278de81 100644 --- a/cognee/tests/integration/documents/UnstructuredDocument_test.py +++ b/cognee/tests/integration/documents/UnstructuredDocument_test.py @@ -71,32 +71,32 @@ def test_UnstructuredDocument(): for paragraph_data in pptx_document.read(chunk_size=1024, chunker="text_chunker"): assert 19 == paragraph_data.word_count, f" 19 != {paragraph_data.word_count = }" assert 104 == len(paragraph_data.text), f" 104 != {len(paragraph_data.text) = }" - assert "sentence_cut" == paragraph_data.cut_type, ( - f" sentence_cut != {paragraph_data.cut_type = }" - ) + assert ( + "sentence_cut" == paragraph_data.cut_type + ), f" sentence_cut != {paragraph_data.cut_type = }" # Test DOCX for paragraph_data in docx_document.read(chunk_size=1024, chunker="text_chunker"): assert 16 == paragraph_data.word_count, f" 16 != {paragraph_data.word_count = }" assert 145 == len(paragraph_data.text), f" 145 != {len(paragraph_data.text) = }" - assert "sentence_end" == paragraph_data.cut_type, ( - f" sentence_end != {paragraph_data.cut_type = }" - ) + assert ( + "sentence_end" == paragraph_data.cut_type + ), f" sentence_end != {paragraph_data.cut_type = }" # TEST CSV for paragraph_data in csv_document.read(chunk_size=1024, chunker="text_chunker"): assert 15 == paragraph_data.word_count, f" 15 != {paragraph_data.word_count = }" - assert "A A A A A A A A A,A A A A A A,A A" == paragraph_data.text, ( - f"Read text doesn't match expected text: {paragraph_data.text}" - ) - assert "sentence_cut" == paragraph_data.cut_type, ( - f" sentence_cut != {paragraph_data.cut_type = }" - ) + assert ( + "A A A A A A A A A,A A A A A A,A A" == paragraph_data.text + ), f"Read text doesn't match expected text: {paragraph_data.text}" + assert ( + "sentence_cut" == paragraph_data.cut_type + ), f" sentence_cut != {paragraph_data.cut_type = }" # Test XLSX for paragraph_data in xlsx_document.read(chunk_size=1024, chunker="text_chunker"): assert 36 == paragraph_data.word_count, f" 36 != {paragraph_data.word_count = }" assert 171 == len(paragraph_data.text), f" 171 != {len(paragraph_data.text) = }" - assert "sentence_cut" == paragraph_data.cut_type, ( - f" sentence_cut != {paragraph_data.cut_type = }" - ) + assert ( + "sentence_cut" == paragraph_data.cut_type + ), f" sentence_cut != {paragraph_data.cut_type = }" diff --git a/cognee/tests/test_deduplication.py b/cognee/tests/test_deduplication.py index 89c866f12..9c2df032d 100644 --- a/cognee/tests/test_deduplication.py +++ b/cognee/tests/test_deduplication.py @@ -30,9 +30,9 @@ async def test_deduplication(): result = await relational_engine.get_all_data_from_table("data") assert len(result) == 1, "More than one data entity was found." - assert result[0]["name"] == "Natural_language_processing_copy", ( - "Result name does not match expected value." - ) + assert ( + result[0]["name"] == "Natural_language_processing_copy" + ), "Result name does not match expected value." result = await relational_engine.get_all_data_from_table("datasets") assert len(result) == 2, "Unexpected number of datasets found." @@ -61,9 +61,9 @@ async def test_deduplication(): result = await relational_engine.get_all_data_from_table("data") assert len(result) == 1, "More than one data entity was found." - assert hashlib.md5(text.encode("utf-8")).hexdigest() in result[0]["name"], ( - "Content hash is not a part of file name." - ) + assert ( + hashlib.md5(text.encode("utf-8")).hexdigest() in result[0]["name"] + ), "Content hash is not a part of file name." await cognee.prune.prune_data() await cognee.prune.prune_system(metadata=True) diff --git a/cognee/tests/test_falkordb.py b/cognee/tests/test_falkordb.py index af0e87916..07ece9eb2 100755 --- a/cognee/tests/test_falkordb.py +++ b/cognee/tests/test_falkordb.py @@ -85,9 +85,9 @@ async def main(): from cognee.infrastructure.databases.relational import get_relational_engine - assert not os.path.exists(get_relational_engine().db_path), ( - "SQLite relational database is not empty" - ) + assert not os.path.exists( + get_relational_engine().db_path + ), "SQLite relational database is not empty" from cognee.infrastructure.databases.graph import get_graph_config diff --git a/cognee/tests/test_library.py b/cognee/tests/test_library.py index 192b67506..8352b4161 100755 --- a/cognee/tests/test_library.py +++ b/cognee/tests/test_library.py @@ -82,9 +82,9 @@ async def main(): from cognee.infrastructure.databases.relational import get_relational_engine - assert not os.path.exists(get_relational_engine().db_path), ( - "SQLite relational database is not empty" - ) + assert not os.path.exists( + get_relational_engine().db_path + ), "SQLite relational database is not empty" from cognee.infrastructure.databases.graph import get_graph_config diff --git a/cognee/tests/test_pgvector.py b/cognee/tests/test_pgvector.py index 73b6be974..c241177f0 100644 --- a/cognee/tests/test_pgvector.py +++ b/cognee/tests/test_pgvector.py @@ -24,28 +24,28 @@ async def test_local_file_deletion(data_text, file_location): data_hash = hashlib.md5(encoded_text).hexdigest() # Get data entry from database based on hash contents data = (await session.scalars(select(Data).where(Data.content_hash == data_hash))).one() - assert os.path.isfile(data.raw_data_location), ( - f"Data location doesn't exist: {data.raw_data_location}" - ) + assert os.path.isfile( + data.raw_data_location + ), f"Data location doesn't exist: {data.raw_data_location}" # Test deletion of data along with local files created by cognee await engine.delete_data_entity(data.id) - assert not os.path.exists(data.raw_data_location), ( - f"Data location still exists after deletion: {data.raw_data_location}" - ) + assert not os.path.exists( + data.raw_data_location + ), f"Data location still exists after deletion: {data.raw_data_location}" async with engine.get_async_session() as session: # Get data entry from database based on file path data = ( await session.scalars(select(Data).where(Data.raw_data_location == file_location)) ).one() - assert os.path.isfile(data.raw_data_location), ( - f"Data location doesn't exist: {data.raw_data_location}" - ) + assert os.path.isfile( + data.raw_data_location + ), f"Data location doesn't exist: {data.raw_data_location}" # Test local files not created by cognee won't get deleted await engine.delete_data_entity(data.id) - assert os.path.exists(data.raw_data_location), ( - f"Data location doesn't exists: {data.raw_data_location}" - ) + assert os.path.exists( + data.raw_data_location + ), f"Data location doesn't exists: {data.raw_data_location}" async def test_getting_of_documents(dataset_name_1): @@ -54,16 +54,16 @@ async def test_getting_of_documents(dataset_name_1): user = await get_default_user() document_ids = await get_document_ids_for_user(user.id, [dataset_name_1]) - assert len(document_ids) == 1, ( - f"Number of expected documents doesn't match {len(document_ids)} != 1" - ) + assert ( + len(document_ids) == 1 + ), f"Number of expected documents doesn't match {len(document_ids)} != 1" # Test getting of documents for search when no dataset is provided user = await get_default_user() document_ids = await get_document_ids_for_user(user.id) - assert len(document_ids) == 2, ( - f"Number of expected documents doesn't match {len(document_ids)} != 2" - ) + assert ( + len(document_ids) == 2 + ), f"Number of expected documents doesn't match {len(document_ids)} != 2" async def main(): diff --git a/cognee/tests/unit/processing/chunks/chunk_by_paragraph_2_test.py b/cognee/tests/unit/processing/chunks/chunk_by_paragraph_2_test.py index d8680a604..53098fc67 100644 --- a/cognee/tests/unit/processing/chunks/chunk_by_paragraph_2_test.py +++ b/cognee/tests/unit/processing/chunks/chunk_by_paragraph_2_test.py @@ -17,9 +17,9 @@ def test_chunk_by_paragraph_isomorphism(input_text, paragraph_length, batch_paragraphs): chunks = chunk_by_paragraph(input_text, paragraph_length, batch_paragraphs) reconstructed_text = "".join([chunk["text"] for chunk in chunks]) - assert reconstructed_text == input_text, ( - f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" - ) + assert ( + reconstructed_text == input_text + ), f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" @pytest.mark.parametrize( @@ -36,9 +36,9 @@ def test_paragraph_chunk_length(input_text, paragraph_length, batch_paragraphs): chunk_lengths = np.array([len(list(chunk_by_word(chunk["text"]))) for chunk in chunks]) larger_chunks = chunk_lengths[chunk_lengths > paragraph_length] - assert np.all(chunk_lengths <= paragraph_length), ( - f"{paragraph_length = }: {larger_chunks} are too large" - ) + assert np.all( + chunk_lengths <= paragraph_length + ), f"{paragraph_length = }: {larger_chunks} are too large" @pytest.mark.parametrize( @@ -50,6 +50,6 @@ def test_chunk_by_paragraph_chunk_numbering(input_text, paragraph_length, batch_ data=input_text, paragraph_length=paragraph_length, batch_paragraphs=batch_paragraphs ) chunk_indices = np.array([chunk["chunk_index"] for chunk in chunks]) - assert np.all(chunk_indices == np.arange(len(chunk_indices))), ( - f"{chunk_indices = } are not monotonically increasing" - ) + assert np.all( + chunk_indices == np.arange(len(chunk_indices)) + ), f"{chunk_indices = } are not monotonically increasing" diff --git a/cognee/tests/unit/processing/chunks/chunk_by_paragraph_test.py b/cognee/tests/unit/processing/chunks/chunk_by_paragraph_test.py index e420b2e9f..e7d9a54ba 100644 --- a/cognee/tests/unit/processing/chunks/chunk_by_paragraph_test.py +++ b/cognee/tests/unit/processing/chunks/chunk_by_paragraph_test.py @@ -58,9 +58,9 @@ def run_chunking_test(test_text, expected_chunks): for expected_chunks_item, chunk in zip(expected_chunks, chunks): for key in ["text", "word_count", "cut_type"]: - assert chunk[key] == expected_chunks_item[key], ( - f"{key = }: {chunk[key] = } != {expected_chunks_item[key] = }" - ) + assert ( + chunk[key] == expected_chunks_item[key] + ), f"{key = }: {chunk[key] = } != {expected_chunks_item[key] = }" def test_chunking_whole_text(): diff --git a/cognee/tests/unit/processing/chunks/chunk_by_sentence_test.py b/cognee/tests/unit/processing/chunks/chunk_by_sentence_test.py index efa053077..d1c75d7ed 100644 --- a/cognee/tests/unit/processing/chunks/chunk_by_sentence_test.py +++ b/cognee/tests/unit/processing/chunks/chunk_by_sentence_test.py @@ -16,9 +16,9 @@ def test_chunk_by_sentence_isomorphism(input_text, maximum_length): chunks = chunk_by_sentence(input_text, maximum_length) reconstructed_text = "".join([chunk[1] for chunk in chunks]) - assert reconstructed_text == input_text, ( - f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" - ) + assert ( + reconstructed_text == input_text + ), f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" @pytest.mark.parametrize( @@ -36,6 +36,6 @@ def test_paragraph_chunk_length(input_text, maximum_length): chunk_lengths = np.array([len(list(chunk_by_word(chunk[1]))) for chunk in chunks]) larger_chunks = chunk_lengths[chunk_lengths > maximum_length] - assert np.all(chunk_lengths <= maximum_length), ( - f"{maximum_length = }: {larger_chunks} are too large" - ) + assert np.all( + chunk_lengths <= maximum_length + ), f"{maximum_length = }: {larger_chunks} are too large" diff --git a/cognee/tests/unit/processing/chunks/chunk_by_word_test.py b/cognee/tests/unit/processing/chunks/chunk_by_word_test.py index d79fcdbc8..fb26638cb 100644 --- a/cognee/tests/unit/processing/chunks/chunk_by_word_test.py +++ b/cognee/tests/unit/processing/chunks/chunk_by_word_test.py @@ -17,9 +17,9 @@ def test_chunk_by_word_isomorphism(input_text): chunks = chunk_by_word(input_text) reconstructed_text = "".join([chunk[0] for chunk in chunks]) - assert reconstructed_text == input_text, ( - f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" - ) + assert ( + reconstructed_text == input_text + ), f"texts are not identical: {len(input_text) = }, {len(reconstructed_text) = }" @pytest.mark.parametrize( diff --git a/poetry.lock b/poetry.lock index ddcaf6618..51cd2474e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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