python-v0.11

 
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  • Introduction
    • Data Pipelines
      • What is a data pipeline?
      • What is DataJoint?
      • How DataJoint works
      • Real-life example
      • Summary of DataJoint features
    • Teamwork
      • Data management in a science project
      • Data-centric project organization
      • Team roles
    • Input and Output
      • Where are my data?
      • Do I have to manually enter all my data into the database?
      • Won’t the database get too big if all my data are there?
      • Why not just process the data and save them back to a file?
      • How do I get my data out?
      • Interfaces
    • Community
      • Multi-lab collaboratives
      • Invidiual Labs
    • Publications
    • Publishing Data
      • Provide access to a DataJoint server
      • Containerizing as a DataJoint pipeline
      • Exporting into a collection of files
    • Progress
    • License
    • Issues
    • Contribute
    • FAQs
      • How do I use GUIs with DataJoint?
      • Does DataJoint support other programming languages?
      • Is DataJoint another ORM?
      • How can I use DataJoint with a LIMS?
      • What is the difference between DataJoint and Alyx?
    • Release Notes
      • 0.11.1 – Nov 15, 2018
      • 0.11.0 – Oct 25, 2018
      • 0.10.1 – Aug 28, 2018
      • 0.10.0 – Jan 10, 2018
      • 0.9.0 – Nov 17, 2017
      • 0.8.0 – Jul 26, 2017
      • 0.5.0 (#298) – Mar 8, 2017
      • 0.4.10 (#286) – Feb 6, 2017
      • 0.4.9 (#285) – Feb 2, 2017
      • 0.4.7 (#281) – Jan 24, 2017
      • 0.4.6 (#277) – Dec 22, 2016
      • 0.4.5 (#274) – Dec 20, 2016
      • 0.4.3 (#271) – Dec 6, 2016
      • 0.4.2 (#267) – Dec 6, 2016
      • 0.4.1 (#266) – Oct 28, 2016
      • 0.3.9 – Sep 27, 2016
      • 0.3.8 – Aug 2, 2016
      • 0.3.7 – Jul 31, 2016
      • 0.3.6 – Jul 30, 2016
      • 0.3.5
      • 0.3.4
      • 0.3.3
      • 0.3.2
  • Server Administration
    • Database Server Hosting
      • Cloud hosting
      • Self hosting
      • General server / hardware support requirements
    • Relational Database Server
      • Hardware considerations
        • CPU
        • RAM
        • Disk
        • Networking
        • General recommendations
      • Large-scale installations
        • Master-slave replication
        • Multi-master replication
      • Recommendations
      • Docker
    • User Management
      • Grouping with Wildcards
    • Bulk Storage Systems
      • Why External Bulk Storage?
        • Cost
        • Flexibility
        • Performance
        • Data Sharing
      • Bulk Storage Scenarios
      • Bulk Storage Considerations
        • Performance Characteristics
        • Network Traffic
        • Data Coherency
    • External Store
      • Principles of operation
      • Configuration
      • Cleanup
    • Backups and Recovery
      • Cloud hosted backups
      • Disk-based backup
      • MySQLDump
      • Percona XTraBackup
      • Locking and DDL issues
      • Replication and snapshots for backup
  • Client Setup
    • Install and Connect
    • DataJoint Python Windows Install Guide
      • Quick steps
      • Step 1: install Python
      • Step 2: verify installation
      • Step 3: install DataJoint
      • (Optional) step 4: install packages for ERD support
        • Install Graphviz
        • Install PyDotPlus
        • Install Matplotlib
      • (Optional) step 5: install Jupyter Notebook
      • Git for Windows
      • MySQL for Windows
  • Concepts
    • Data Model
      • What is a data model?
      • Relational data model
        • Core principles of the relational data model
      • DataJoint is a refinement of the relational data model
    • Terminology
      • DataJoint: databases, schemas, packages, and modules
      • Base tables
      • Relvars and relation values
      • Metadata
    • Entity Normalization
      • Criteria of a well-formed entity set
      • Entity normalization in schema design
      • Entity normalization in data queries
      • Examples of poor normalization
        • Indirect attributes
        • Repeated attributes
        • Attributes that do not apply to all entities
        • Transient attributes
    • Data Integrity
      • Entity integrity
      • Referential integrity
      • Group integrity
      • Relationships
  • Data Definition
    • Creating Schemas
      • Schemas
      • Working with existing data
    • Creating Tables
      • Classes represent tables
        • Data tiers
      • Defining a table
        • DataJoint classes in Python
      • Valid class names
    • Table Definition
      • Table creation on the database server
      • Changing the definition of an existing table
      • Reverse-engineering the table definition
        • Examples
    • Definition Syntax
      • Attribute names
      • Default values
    • Data Tiers
      • Internal conventions for naming tables
      • Part tables
    • Datatypes
      • Most common datatypes
      • Less common (but supported) datatypes
      • Datatypes not (yet) supported
    • Primary Key
      • Primary keys in DataJoint
      • Defining a primary key
      • Entity integrity
      • Datatypes in primary keys
      • Choosing primary key attributes
        • Using hashes as primary keys
        • auto_increment
    • Dependencies
      • Understanding dependencies
      • Defining a dependency
      • How dependencies work
      • Referential integrity
      • Dependencies with renamed attributes
      • Foreign key options
    • ERD
      • Diagram notation
      • Diagramming an entire schema
        • Initializing with a single table
        • Adding ERDs together
        • Expanding ERDs upstream and downstream
    • Manual Tables
    • Lookup Tables
    • Drop
      • Dropping part tables
  • Work with Existing Pipelines
    • Virtual Modules
  • Data Manipulation
    • Manipulation
    • Insert
      • Batched inserts
      • Server-side inserts
    • Delete
      • Examples
      • Deleting from part tables
    • Cautious Update
    • Transactions
  • Queries
    • Query Objects
      • Checking for returned entities
      • Normalization in queries
    • Example Schema
      • Example schema ERD
    • Fetch
      • Entire table
      • As separate variables
      • Primary key values
      • Usage with Pandas
    • Iteration
    • Operators
      • Principles of relational algebra
      • Matching entities
        • Examples
      • Join compatibility
    • Restriction
      • Restriction operators & and -
      • Restriction by a table
        • Restriction by a table with no common attributes
        • Restriction by an empty table
      • Restriction by a mapping
      • Restriction by a string
      • Restriction by a collection
      • Restriction by a Boolean expression
      • Restriction by an AndList
      • Restriction by a Not object
      • Restriction by a query
    • Join
      • Join operator *
        • Principles of joins
        • Examples of joins
        • Properties of join
    • Proj
      • Simple projection
      • Renaming
      • Calculations
    • Aggr
      • Examples
    • Union
      • Union operator +
        • Principles of union
        • Examples of union
        • Properties of union
    • Universal Sets
  • Computation
    • Auto-populate
      • Make
      • Populate
      • Populate options
      • Progress
    • Key Source
      • Default key source
      • Custom key source
    • Master-Part Relationship
      • Populating
      • Deleting
      • Multiple parts
    • Transactions in Make
    • Distributed Computing
      • Job reservations
      • Managing connections
DataJoint Documentation
  • Docs »
  • Welcome to DataJoint Documentation

Welcome to DataJoint Documentation¶

This is a detailed manual for active users of DataJoint in Python.

This documentation can be read sequentially from start to end or used as reference for specific topics.

For a guided introduction to DataJoint, please explore our tutorials at http://tutorials.datajoint.io

  • Introduction
    • Data Pipelines
    • Teamwork
    • Input and Output
    • Community
    • Publications
    • Publishing Data
    • Progress
    • License
    • Issues
    • Contribute
    • FAQs
    • Release Notes
  • Server Administration
    • Database Server Hosting
    • Relational Database Server
    • User Management
    • Bulk Storage Systems
    • External Store
    • Backups and Recovery
  • Client Setup
    • Install and Connect
    • DataJoint Python Windows Install Guide
  • Concepts
    • Data Model
    • Terminology
    • Entity Normalization
    • Data Integrity
  • Data Definition
    • Creating Schemas
    • Creating Tables
    • Table Definition
    • Definition Syntax
    • Data Tiers
    • Datatypes
    • Primary Key
    • Dependencies
    • ERD
    • Manual Tables
    • Lookup Tables
    • Drop
  • Work with Existing Pipelines
    • Virtual Modules
  • Data Manipulation
    • Manipulation
    • Insert
    • Delete
    • Cautious Update
    • Transactions
  • Queries
    • Query Objects
    • Example Schema
    • Fetch
    • Iteration
    • Operators
    • Restriction
    • Join
    • Proj
    • Aggr
    • Union
    • Universal Sets
  • Computation
    • Auto-populate
    • Key Source
    • Master-Part Relationship
    • Transactions in Make
    • Distributed Computing
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