extralit-server 0.2.1__tar.gz → 0.6.0__tar.gz

extralit_server-0.6.0/LICENSE

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extralit_server-0.6.0/LICENSE_HEADER

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+Copyright 2024-present, Extralit Labs, Inc.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
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+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

extralit_server-0.6.0/PKG-INFO

@@ -0,0 +1,197 @@
+Metadata-Version: 2.1
+Name: extralit-server
+Version: 0.6.0
+Summary: Open-source tool for accurate & fast scientific literature data extraction with LLM and human-in-the-loop.
+Keywords: literature-review,data-annotation,artificial-intelligence,machine-learning,human-in-the-loop,mlops
+Author-Email: Extralit Labs <extralit.contact@gmail.com>
+Maintainer-Email: Extralit Labs <extralit.contact@gmail.com>
+License: Apache-2.0
+Project-URL: homepage, https://extralit.ai
+Project-URL: documentation, https://docs.extralit.ai
+Project-URL: repository, https://github.com/extralit/extralit
+Requires-Python: >=3.9
+Requires-Dist: fastapi~=0.115.0
+Requires-Dist: pydantic~=2.9.0
+Requires-Dist: pydantic-settings~=2.6.0
+Requires-Dist: uvicorn[standard]~=0.32.0
+Requires-Dist: opensearch-py~=2.0.0
+Requires-Dist: elasticsearch8[async]~=8.7.0
+Requires-Dist: brotli-asgi~=1.4.0
+Requires-Dist: backoff~=2.2.0
+Requires-Dist: alembic~=1.13.0
+Requires-Dist: SQLAlchemy~=2.0.0
+Requires-Dist: greenlet~=3.1.0
+Requires-Dist: aiosqlite==0.20.0
+Requires-Dist: aiofiles~=24.1.0
+Requires-Dist: PyYAML<6.1.0,>=5.4.1
+Requires-Dist: python-jose[cryptography]~=3.3.0
+Requires-Dist: bcrypt~=4.2.0
+Requires-Dist: python-multipart~=0.0.16
+Requires-Dist: httpx~=0.27.0
+Requires-Dist: oauthlib~=3.2.0
+Requires-Dist: social-auth-core~=4.5.0
+Requires-Dist: rq~=1.16.2
+Requires-Dist: psutil<5.10,~=5.8
+Requires-Dist: rich!=13.1.0
+Requires-Dist: typer<0.10.0,>=0.6.0
+Requires-Dist: packaging>=23.2
+Requires-Dist: standardwebhooks>=1.0.0
+Requires-Dist: datasets>=3.0.1
+Requires-Dist: pillow>=10.4.0
+Requires-Dist: huggingface-hub>=0.26.2
+Requires-Dist: Jinja2>=3.1.4
+Requires-Dist: minio>=7.2.7
+Provides-Extra: postgresql
+Requires-Dist: psycopg2~=2.9.0; extra == "postgresql"
+Requires-Dist: asyncpg~=0.30.0; extra == "postgresql"
+Description-Content-Type: text/markdown
+
+<h1 align="center">
+  <a href=""><img src="https://github.com/extralit/extralit/raw/develop/extralit/docs/assets/logo.svg" alt="Extralit" width="150"></a>
+  <br>
+  Extralit Server
+  <br>
+</h1>
+<h3 align="center">Extract structured data from scientific literature with human validation</h2>
+
+<p align="center">
+<a href="https://pypi.org/project/extralit/">
+<img alt="CI" src="https://img.shields.io/pypi/v/extralit.svg?style=flat-round&logo=pypi&logoColor=white">
+</a>
+<img alt="Codecov" src="https://codecov.io/gh/extralit/extralit/branch/main/graph/badge.svg"/>
+<a href="https://pepy.tech/project/extralit">
+<img alt="Downloads" src="https://static.pepy.tech/personalized-badge/extralit?period=month&units=international_system&left_color=grey&right_color=blue&left_text=pypi%20downloads/month">
+</a>
+</p>
+
+<p align="center">
+<a href="https://www.linkedin.com/company/extralit-ai">
+<img src="https://img.shields.io/badge/linkedin-blue?logo=linkedin"/>
+</a>
+</p>
+
+This repository contains developer information about the backend server components. For general usage, please refer to our [main repository](https://github.com/extralit/extralit) or our [documentation](https://docs.extralit.ai/latest/).
+
+## Source Code Structure
+
+The server components are split into two main services:
+
+```
+/extralit_server
+  /api # Core extraction API endpoints
+    /handlers # FastAPI request handlers
+    /schemas # Data models and validation
+    /services # Business logic services
+    /utils # Helper utilities
+  /ml # Machine learning components
+    /extractors # Document extraction models
+    /ocr # OCR processing
+    /pipeline # Extraction pipeline orchestration
+  /storage # Data persistence layer
+    /models # Database models
+    /search # Search engine integration
+    /vector # Vector store
+```
+
+```
+/extralit_server
+  /api # Annotation UI API endpoints
+    /handlers
+    /schemas
+  /models # Database models
+  /auth # Authentication
+  /tasks # Background jobs
+```
+
+## Development Environment
+
+The development environment uses Docker Compose to run all required services. Key commands:
+
+```sh
+# Start all services
+docker-compose up -d
+
+# Run server in dev mode
+pdm run dev
+
+# Run tests
+pdm test
+
+# Format and lint
+pdm format
+pdm lint
+
+# Run all checks
+pdm all
+```
+
+## Key Components
+
+### FastAPI Servers
+
+- **Extraction Server**: Handles document processing, extraction pipeline, and ML model serving
+- **Annotation Server**: Manages UI, data validation workflow, and user collaboration
+
+### Databases
+
+- **PostgreSQL**: Main database for user data, annotations, and metadata
+- **Elasticsearch**: Vector store for semantic search and document indexing
+- **Weaviate**: Vector database for table and section embeddings
+
+### Background Processing
+
+Uses Celery for asynchronous tasks like:
+
+- Document OCR and preprocessing
+- ML model inference
+- Batch extraction jobs
+- Data export
+
+## CLI Commands
+
+Key management commands:
+
+```sh
+# Database management
+python -m extralit_server db migrate
+python -m extralit_server db create-user
+
+# Start servers
+python -m extralit_server start
+python -m extralit_server start
+
+# Run workers
+python -m extralit_server worker
+```
+
+See full CLI documentation in our [developer docs](https://docs.extralit.ai/latest/developer).
+
+## Running Tests
+
+The pytest suite is primarily designed to run in the CI environment using GitHub Actions as defined in `.github/workflows/extralit-server.yml`. This workflow sets up the necessary dependencies including Elasticsearch, PostgreSQL, Redis, and Minio.
+
+Note that some tests are specifically skipped when running locally due to differences between the CI environment and local development environments. These tests may involve:
+
+- Search engine dynamics (Elasticsearch/OpenSearch compatibility)
+- File storage operations with Minio
+- Authentication and permission checks
+
+To run tests in CI, create a pull request to trigger the test workflow.
+
+If you need to run a specific test locally for debugging purposes, you can use:
+
+```bash
+cd extralit-server
+python -m pytest [test_path] -v
+```
+
+However, expect some tests to fail or be skipped when running locally.
+
+
+## Contributing
+
+Check our [contribution guide](https://docs.extralit.ai/latest/community/contributor) and join our [Slack community](https://join.slack.com/t/extralit/shared_invite/zt-2kt8t12r7-uFj0bZ5SPAOhRFkxP7ZQaQ).
+
+## Roadmap
+
+See our [development roadmap](https://github.com/orgs/extralit/projects/2/views/1) and share your ideas!

extralit_server-0.6.0/README.md

@@ -0,0 +1,149 @@
+<h1 align="center">
+  <a href=""><img src="https://github.com/extralit/extralit/raw/develop/extralit/docs/assets/logo.svg" alt="Extralit" width="150"></a>
+  <br>
+  Extralit Server
+  <br>
+</h1>
+<h3 align="center">Extract structured data from scientific literature with human validation</h2>
+
+<p align="center">
+<a href="https://pypi.org/project/extralit/">
+<img alt="CI" src="https://img.shields.io/pypi/v/extralit.svg?style=flat-round&logo=pypi&logoColor=white">
+</a>
+<img alt="Codecov" src="https://codecov.io/gh/extralit/extralit/branch/main/graph/badge.svg"/>
+<a href="https://pepy.tech/project/extralit">
+<img alt="Downloads" src="https://static.pepy.tech/personalized-badge/extralit?period=month&units=international_system&left_color=grey&right_color=blue&left_text=pypi%20downloads/month">
+</a>
+</p>
+
+<p align="center">
+<a href="https://www.linkedin.com/company/extralit-ai">
+<img src="https://img.shields.io/badge/linkedin-blue?logo=linkedin"/>
+</a>
+</p>
+
+This repository contains developer information about the backend server components. For general usage, please refer to our [main repository](https://github.com/extralit/extralit) or our [documentation](https://docs.extralit.ai/latest/).
+
+## Source Code Structure
+
+The server components are split into two main services:
+
+```
+/extralit_server
+  /api # Core extraction API endpoints
+    /handlers # FastAPI request handlers
+    /schemas # Data models and validation
+    /services # Business logic services
+    /utils # Helper utilities
+  /ml # Machine learning components
+    /extractors # Document extraction models
+    /ocr # OCR processing
+    /pipeline # Extraction pipeline orchestration
+  /storage # Data persistence layer
+    /models # Database models
+    /search # Search engine integration
+    /vector # Vector store
+```
+
+```
+/extralit_server
+  /api # Annotation UI API endpoints
+    /handlers
+    /schemas
+  /models # Database models
+  /auth # Authentication
+  /tasks # Background jobs
+```
+
+## Development Environment
+
+The development environment uses Docker Compose to run all required services. Key commands:
+
+```sh
+# Start all services
+docker-compose up -d
+
+# Run server in dev mode
+pdm run dev
+
+# Run tests
+pdm test
+
+# Format and lint
+pdm format
+pdm lint
+
+# Run all checks
+pdm all
+```
+
+## Key Components
+
+### FastAPI Servers
+
+- **Extraction Server**: Handles document processing, extraction pipeline, and ML model serving
+- **Annotation Server**: Manages UI, data validation workflow, and user collaboration
+
+### Databases
+
+- **PostgreSQL**: Main database for user data, annotations, and metadata
+- **Elasticsearch**: Vector store for semantic search and document indexing
+- **Weaviate**: Vector database for table and section embeddings
+
+### Background Processing
+
+Uses Celery for asynchronous tasks like:
+
+- Document OCR and preprocessing
+- ML model inference
+- Batch extraction jobs
+- Data export
+
+## CLI Commands
+
+Key management commands:
+
+```sh
+# Database management
+python -m extralit_server db migrate
+python -m extralit_server db create-user
+
+# Start servers
+python -m extralit_server start
+python -m extralit_server start
+
+# Run workers
+python -m extralit_server worker
+```
+
+See full CLI documentation in our [developer docs](https://docs.extralit.ai/latest/developer).
+
+## Running Tests
+
+The pytest suite is primarily designed to run in the CI environment using GitHub Actions as defined in `.github/workflows/extralit-server.yml`. This workflow sets up the necessary dependencies including Elasticsearch, PostgreSQL, Redis, and Minio.
+
+Note that some tests are specifically skipped when running locally due to differences between the CI environment and local development environments. These tests may involve:
+
+- Search engine dynamics (Elasticsearch/OpenSearch compatibility)
+- File storage operations with Minio
+- Authentication and permission checks
+
+To run tests in CI, create a pull request to trigger the test workflow.
+
+If you need to run a specific test locally for debugging purposes, you can use:
+
+```bash
+cd extralit-server
+python -m pytest [test_path] -v
+```
+
+However, expect some tests to fail or be skipped when running locally.
+
+
+## Contributing
+
+Check our [contribution guide](https://docs.extralit.ai/latest/community/contributor) and join our [Slack community](https://join.slack.com/t/extralit/shared_invite/zt-2kt8t12r7-uFj0bZ5SPAOhRFkxP7ZQaQ).
+
+## Roadmap
+
+See our [development roadmap](https://github.com/orgs/extralit/projects/2/views/1) and share your ideas!