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
- Overview
- Supported Projects
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Sample Manager Guide
- Accessing the Accept or Reject Samples page
- Guidelines for Searching Profiles and Samples on the Accept or Reject Page
- Guidelines for Sample Managers Assigned to Multiple Manifest Groups
- 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
Profiles
Data Submissions
- Uploading Data Files
- Submitting Samples
- Submitting Reads
- Submitting Assemblies
- Submitting Single-cell Data
- Submitting Sequence Annotations
- Submitting Barcoding Data
- Submitting Images
- Submitting Permits
- Downloading Submitted Data
- Publishing Data
Data Updates
Data Discovery & Retrieval
- Data Templates and Instructions
- Spreadsheet Wizard for Easy Data Submission
- Finding Data Submission IDs
- Tree of Life Dashboard
- Submission Statistics
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Using COPO Programmatically
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API End-points
- API key Endpoint
- Audit Endpoints
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Manifest Endpoints
- Fetch Manifests
- Fetch Manifests Filtered by Sequencing Centre
- Fetch Current Manifest Versions
- Fetch Sample in Manifest by Manifest ID
- Fetch Manifests between Dates
- Fetch Manifests between Dates for a Project
- Fetch Sample 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 Profile Titles & Associated Tube or Well IDs
- Fetch Sample Records between Dates
- Fetch Updatable Fields by Project
- Fetch Sample Records by COPO ID
- Fetch Sample Records by Biosample Accession
- Fetch Sample Records by Field and Values
- Fetch Sample Records by Sequencing Centre
- Fetch Sample Records by Taxon ID
- Fetch Sample Records that have Image Submissions
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Profile Endpoints
- Create Profile Record
- Fetch Profile Records
- Fetch Profile Record by ID
- Update Profile Record by ID
- Fetch Data File Names by Profile ID
- Fetch Data File Upload URL by Profile ID
- Fetch Single-cell Checklists
- Fetch Studies in a profile
- Update Studies
- Export Study Data by Study ID (Spreadsheet or JSON-LD)
- Submit Study to Public Repository
- Fetch Study Submission Status
- Fetch Study Submission Accession Number
- Publish Study
- Statistics Endpoints
- Mapping Endpoints
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API End-points
Advanced
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Local Setup Instructions
- Project Setup With Docker
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Project Setup Without Docker
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Set Up 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 Project on Windows
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Set Up Project on Linux
- Understanding COPO’s Project Structure
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Managing COPO Using Admin Tools
- Getting Started with COPO Admin Tools
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Setting Up Profiles with Python/Django
- 1. Defining the Profile Structure
- 2. Defining Django Model
- 3. Registering Django Model with Django Admin Site
- 4. Make Migrations and Migrate the Django Model
- 5. Automating Profile Creation with manage.py
- Visual Representation of Profile Subparts
- Related Topics
- Using Django Admin for Profiles
Policies
Help
Research Outputs & Presentations