COPO: Guidelines
Welcome to the guidelines for submission, updates and retrieval for the Collaborative OPen Omics project. Please use the links to find instructions specific to your needs.
- Getting Started
- Projects Brokered through COPO
- New User
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Sample Managers
- Accessing the Accept or Reject Samples web page
- Guidelines for Sample Managers Assigned to More than one Manifest Group
- Accepting or Rejecting Samples
- Download Submitted Sample Manifests
- Download Submitted Permits
- View Submitted Images
- Upload Manifest or Update Submitted Manifest on behalf of Manifest Submitters
- Downloading Manifest Templates & Standard Operating Procedures (SOPs)
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Using COPO API
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API End-points
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Audit Endpoints
- Fetch Sample Updates Between Dates
- Fetch Sample Updates by Manifest ID
- Fetch Sample Updates by COPO ID
- Fetch Sample Updates by Update Type
- Fetch Sample Updates by Field and Field Value
- Fetch Sample Updates by ASG Sample Type
- Fetch Sample Updates by DTOL Sample Type
- Fetch Sample Updates by ERGA Sample Type
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Manifest Endpoints
- Fetch Manifests
- Fetch Manifests by Sequencing Centre
- Fetch Current Manifest Versions
- Fetch Sample Records in a Manifest by Manifest ID
- Fetch Manifests between Dates
- Fetch Manifests between Dates for a Project
- Fetch Sample Record Status in a Manifest
- Validate Manifest by Profile ID
- Validate Manifest by Report ID
- Validate Manifest
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Sample Endpoints
- Fetch Sample Records by Project
- Fetch Sample Records by Associated Project Type
- Fetch Sample Project Fields by Manifest Version
- Fetch Sample Records between Dates
- Fetch Sample Records between Dates
- Fetch Updatable Fields by Project
- Fetch Sample Records by COPO ID
- Fetch Sample Records by Biosample ID
- Fetch Sample Records by Field and Values
- Fetch Sample Records by Sequencing Centre
- Fetch Study Records by Sample ID
- Fetch Sample Records by Study ID
- Profile Endpoints
- Statistics’ Endpoints
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Audit Endpoints
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API End-points
- Exploring Manifest Wizard
- Tree of Life Dashboard
- Retrieving Accessions
- COPO Statistics
- Manifest Checklist
- Setting Up COPO Project Locally with Docker
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Setting Up COPO Project Locally without Docker
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Set Up COPO Project on Linux
- Install Python
- Install Python Development Tools
- Install Required Packages
- Install Integrated Development Environment (IDE)
- Configure IDE
- Declare Environment Variables
- Set up Python virtual environment
- Set Up Mongo Database in COPO Project
- Set Up PostgreSQL Database in COPO Project
- Launch COPO Website
- Set Up COPO Project on Windows
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Set Up COPO Project on Linux