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LabKey Client APIs
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Overview
The client-side library for Java developers is a separate JAR from the LabKey Server code base. It can be used by any Java program, including another Java web application.
Resources:
LabKey Java Client API Reference
Search the LabKey Java Client API Reference
Download LabKey Java Client API Library
Download LabKey Java Client API Source Code
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Release Notes 14.3
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12.3 Video Demonstrations
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12.2 Video Demonstrations
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11.2 Release Notes
11.2 Video Demonstrations
Learn What's New in 11.1
11.1 Release Notes
11.1 Release Webinar
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10.3 Release Notes
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What's New 17.2
Release Notes 17.2
Data Basics
Build User Interface
Add Web Parts
Manage Web Parts
Web Part Inventory
Use Tabs
Add Custom Menus
Web Parts: Permissions Required to View
Data Grids
Data Grids: Basics
Import Data
Sort Data
Filter Data
Filtering Expressions
Column Summary Statistics
Select Rows
Customize Grid Views
Saved Filters and Sorts
Join Columns from Multiple Tables
Lookup Columns
Export Data
Participant Details View
Query Scope: Filter by Folder
Field Properties Reference
URL Field Property
String Expression Format Functions
Conditional Formats
Date & Number Display Formats
Date and Number Formats Reference
Reports and Visualizations
Report Web Part: Display a Report or Chart
Data Views Browser
Bar Charts
Box Plots
Pie Charts
Scatter Plots
Time Charts
Column Visualizations
Quick Charts
Query Snapshot
R Reports
RStudio and LabKey Server
R Report Builder
Saved R Reports
Datasets in R
Multi-Panel R Plots
Lattice Plots
Participant Charts in R
R Reports with knitr
Input/Output Substitutions Reference
FAQs for LabKey R Reports
R Tutorial Video
JavaScript Reports
Attachment Reports
Link Reports
Participant Reports
Query Report
Manage Reports and Charts
Manage Categories
Manage Thumbnail Images
Measure and Dimension Columns
Legacy Reports
Advanced Reports / External Reports
Chart Views
Crosstab Reports
SQL Queries
LabKey SQL Tutorial
SQL Query Browser
LabKey SQL Reference
Lookups: SQL Syntax
Create a SQL Query
Edit SQL Query Source
Query Metadata
Query Metadata: Examples
Edit Query Properties
Query Web Part: Display a Query
Add a Calculated Column to a Query
Create a Pivot Query
Parameterized SQL Queries
SQL Examples: JOIN, Calculated Columns, GROUP BY
Cross-Folder Queries
SQL Synonyms
External Schemas and Data Sources
External MySQL Data Sources
External Oracle Data Sources
External Microsoft SQL Server Data Sources
External PostgreSQL Data Sources
External SAS Data Sources
Linked Schemas and Tables
Manage Remote Connections
LabKey Data Structures
Preparing Data for Import
Data Quality Control
Lists
List Tutorial
List Tutorial: Setup
Create a Joined Grid
Add a URL Property
Create and Populate Lists
Create a List by Defining Fields
Populate a List
Import a List Archive
Manage Lists
Connect Lists
Edit a List Design
Choose a Primary Key
Search
Search Administration
Laboratory Data
Tutorial: Design a General Purpose Assay Type (GPAT)
Step 1: Assay Tutorial Setup
Step 2: Infer an Assay Design from Spreadsheet Data
Step 3: Import Assay Data
Step 4: Work with Assay Data
Step 5: Data Validation
Step 6: Integrate Assay Data into a Study
ELISA Assay Tutorial
ELISpot Assay
ELISpot Assay Tutorial
Import ELISpot Data
Review ELISpot Data
ELISpot Properties
Flow Cytometry
LabKey Flow Module
Supported FlowJo Versions
Flow Cytometry Overview
Tutorial: Import a Flow Workspace
Step 1: Set Up a Flow Folder
Step 2: Upload Files to Server
Step 3: Import a Flow Workspace and Analysis
FCS File Resolution
Step 4: Customize Your Grid View
Step 5: Examine Graphs
Step 6: Examine Well Details
Step 7: Export Flow Data
Tutorial: Perform a LabKey Flow Analysis
Step 1: Define a Compensation Calculation
Step 2: Define an Analysis
Step 3: Apply a Script
Step 4: View Results
Add Sample Descriptions
Custom Flow Queries
Add Statistics to FCS Queries
Calculate Suites of Statistics for Every Well
Flow Module Schema
Analysis Archive Format
FCS Express
Tutorial: Import Flow Data from FCS Express
FCS keyword utility
Flow Team Members
FluoroSpot Assay
Genomics Workflows
Set Up a Genotyping Dashboard
Example Workflow: LabKey and Galaxy
Example Workflow: LabKey and Illumina
Example Workflow: LabKey and PacBio
Example Workflow: O'Connor Module
Import Haplotype Assignment Data
Work with Haplotype Assay Data
HPLC - High-Performance Liquid Chromatography
Luminex
Luminex Assay Tutorial Level I
Setup Luminex Tutorial Project
Step 1: Create a New Luminex Assay Design
Step 2: Import Luminex Run Data
Step 3: Exclude Analytes for QC
Step 4: Import Multi-File Runs
Step 5: Copy Luminex Data to Study
Luminex Assay Tutorial Level II
Step 1: Import Lists and Assay Archives
Step 2: Configure R, Packages and Script
Step 3: Import Luminex Runs
Step 4: View 4pl and 5pl Curve Fits
Step 5: Track Analyte Quality Over Time
Step 7: Use Guide Sets for QC
Step 8: Compare Standard Curves Across Runs
Track Single-Point Controls in Levey-Jennings Plots
Import Luminex Runs
Luminex Calculations
Luminex QC Reports and Flags
Luminex Reference
Review Luminex Assay Design
Luminex Properties
Luminex File Formats
Review Well Roles
Luminex Conversions
Customize Luminex Assay for Script
Review Fields for Script
Troubleshoot Luminex Transform Scripts and Curve Fit Results
Microarray
Microarray Assay Tutorial
Expression Matrix Assay Tutorial
Microarray Properties
NAb (Neutralizing Antibody) Assays
NAb Assay Tutorial
Step 1: Create a NAb Assay Design
Step 2: Import NAb Assay Data
Step 3: View High-Throughput NAb Data
Step 4: Explore NAb Graph Options
Work with Low-Throughput NAb Data
Use NAb Data Identifiers
NAb Assay QC
Work with Multiple Viruses per Plate
NAb Plate File Formats
Customize NAb Plate Template
NAb Properties
Proteomics
Proteomics Tutorial
Step 1: Set Up for Proteomics Analysis
Step 2: Search mzXML Files
Step 3: View PeptideProphet Results
Step 4: View ProteinProphet Results
Step 5: Compare Runs
Step 6: Search for a Specific Protein
Proteomics Video
Work with MS2 Data
Search MS2 Data Via the Pipeline
Set Up MS2 Search Engines
Set Up Mascot
Set Up Sequest
Set Up Comet
Working with mzML files
Search and Process MS2 Data
Configure Common Parameters
Configure X! Tandem Parameters
Configure Mascot Parameters
Configure Sequest Parameters
Sequest Parameters
MzXML2Search Parameters
Examples of Commonly Modified Parameters
Configure Comet Parameters
Import Existing Analysis Results
Trigger MS2 Processing Automatically
Set Proteomics Search Tools Version
Explore the MS2 Dashboard
View an MS2 Run
Customize Display Columns
Peptide Columns
Protein Columns
View Peptide Spectra
View Protein Details
View Gene Ontology Information
Experimental Annotations for MS2 Runs
Protein Search
Peptide Search
Compare MS2 Runs
Compare ProteinProphet
Export MS2 Runs
Working with Small Molecule Targets
Export Spectra Libraries
View, Filter and Export All MS2 Runs
Work with Mascot Runs
Loading Public Protein Annotation Files
Using Custom Protein Annotations
Using ProteinProphet
Using Quantitation Tools
Protein Expression Matrix Assay
Link Protein Expression Data with Annotations
Spectra Counts
Label-Free Quantitation
Combine XTandem Results
MS1
MS1 Pipelines
Panorama - Targeted Proteomics
Configure Panorama Folder
Panorama QC Dashboard
Panorama QC Plots
Panorama Plot Types
Panorama QC Annotations
Panorama QC Guide Sets
Pareto Plots
Panorama: Clustergrammer Heat Maps
Panorama Document Revision Tracking
Proteomics Team
Signal Data Assay
Assay Administrator Guide
Assay Feature Matrix
Set Up Folder For Assays
Assay Designs and Types
Import Assay Design
Design a New Assay
General Properties
Design a Plate-Based Assay
Edit Plate Templates
Participant/Visit Resolver
Manage an Assay Design
Improve Data Entry Consistency & Accuracy
Set up a Data Transformation Script
Copy Assay Data into a Study
Copy-To-Study History
Experiment Descriptions & Archives (XARs)
Experiment Terminology
XAR Files
Uses of XAR.xml Files
Import a XAR.xml
Troubleshoot XAR Import
Import XAR Files Using the Data Pipeline
Example 1: Review a Basic XAR.xml
Examples 2 & 3: Describe Protocols
Examples 4, 5 & 6: Describe LCMS2 Experiments
Design Goals and Directions
Life Science Identifiers (LSIDs)
LSID Substitution Templates
Assay User Guide
Import Assay Runs
Reimport Assay Runs
Sample Sets
Import Sample Sets
Samples: Unique IDs
View SampleSets and Samples
Link Assay Data to Sample Sets
Parent Samples: Derivation and Lineage
Sample Sets: Examples
'Active' Sample Set
Run Groups
DataClasses
Electronic Laboratory Notebooks (ELN)
Tutorial: Electronic Lab Notebook
Step 1: Create the User Interface
Step 2: Import Lab Data
Step 3: Link Assays to Samples
Step 4: Using and Extending the ELN
Assay Request Tracker
Assay Request Tracker: User Documentation
Assay Request Tracker: Administrator Documentation
Reagent Inventory
Research Studies
Study Tour
Tutorial: Cohort Studies
Step 1: Install the Sample Study
Step 2: Study Data Dashboards
Step 3: Integrate Data from Different Sources
Step 4: Compare Participant Performance
Tutorial: Set Up a New Study
Step 1: Define Study Properties
Step 2: Import Datasets
Step 3: Assign Cohorts
Step 4: Import Specimens
Step 5: Visualizations and Reports
Study User Guide
Study Navigation
The Study Navigator
Study Data Browser
Cohorts
Participant Groups
Comments
Dataset Quality Control States
Study Administrator Guide
Create a Study
Create and Populate Datasets
Create a Dataset from a File
Create a Dataset by Defining Fields
Create Multiple Dataset Definitions from a TSV File
Import Data to a Dataset
Import via Copy/Paste
Import From a Dataset Archive
Create Pipeline Configuration File
Import Study Data From REDCap Projects
Dataset Properties
Edit Dataset Properties
Dataset System Fields
Use Visits or Timepoints/Dates
Create Visits
Edit Visits or Timepoints
Import Visit Map
Import Visit Names / Aliases
Manage a Study
Custom Study Properties
Manage Datasets
Manage Visits or Timepoints
Study Schedule
Manage Locations
Manage Cohorts
Manage Participant IDs
Alternate Participant IDs
Alias Participant IDs
Manage Comments
Manage Study Security (Dataset-Level Security)
Configure Permissions for Reports & Views
Matrix of Permissions
Securing Portions of a Dataset (Row and Column Level Security)
Manage Dataset QC States
Manage Study Products
Manage Treatments
Manage Assay Schedule
Demonstration Mode
Create a Vaccine Study Design
Continuous Studies
Import, Export, and Reload a Study
Export Study Objects
Study Import/Export Files and Formats
Serialized Elements and Attributes of Lists and Datasets
Publish a Study
Publish a Study: Protected Health Information
Publish a Study: Refresh Snapshots
Ancillary Studies
Shared Datasets and Timepoints
Data Aliasing
Study Data Model
Linking Data Records with External Files
Specimen Tracking
Specimen Request Tutorial
Step 1: Repository Setup (Admin)
Step 2: Request System (Specimen Coordinator)
Step 3: Request Specimens (User)
Step 4: Track Requests (Specimen Coordinator)
Specimens: Administrator Guide
Import Specimen Spreadsheet Data
Import a Specimen Archive
Specimen Archive File Reference
Specimen Archive Data Destinations
Troubleshoot Specimen Import
Import FreezerPro Data
Delete Specimens
Specimen Properties and Rollup Rules
Customize Specimens Web Part
Flag Specimens for Quality Control
Edit Specimen Data
Customize the Specimen Request Email Template
Export a Specimen Archive
Specimen Coordinator Guide
Email Specimen Lists
View Specimen Data
Generate Specimen Reports
Laboratory Information Management System (LIMS)
Electronic Health Records (EHR)
EHR: Animal History
EHR: Animal Search
EHR: Data Entry
EHR: Administration
EHR Team
Collaboration
Collaboration Tutorial
Step 1: Use the Message Board
Step 2: Collaborate Using a Wiki
Step 3: Track Issues
File Repository Tutorial
Step 1: Set Up a File Repository
Step 2: File Repository Administration
Step 3: Search the Repository
Step 4: Import Data from the Repository
Files
Using the Files Repository
Share and View Files
File Sharing and URLs
Import Data from Files
File Administrator Guide
Files Web Part Administration
Upload Files: WebDAV
Set File Roots
Troubleshoot File Roots and Pipeline Overrides
File Terminology
Integrating S3 Cloud Data Storage
Data Processing Pipeline
Set a Pipeline Override
Pipeline Protocols
Enterprise Pipeline
Install Prerequisites for the Enterprise Pipeline
JMS Queue
RAW to mzXML Converters
Configure LabKey Server to use the Enterprise Pipeline
Configure the Conversion Service
Configure Remote Pipeline Server
Configure Pipeline Path Mapping
Use the Enterprise Pipeline
Troubleshoot the Enterprise Pipeline
Messages
Use Message Boards
Administer Message Boards
Object-Level Discussions
Wikis
Wiki Admin Guide
Copy Wiki Pages
Wiki User Guide
Wiki Syntax
Wiki Syntax: Macros
Special Wiki Pages
Embed Live Content in HTML Pages or Messages
Examples: Embedded Web Parts
Web Part Configuration Properties
Add Screenshots to a Wiki
Manage Wiki Attachment List
Issue/Bug Tracking
Using the Issue Tracker
Administering the Issue Tracker
Workflow Module
Workflow Tutorial
Step 1: Set Up Workflow Tutorial
Step 2: Run Sample Workflow Process
Step 3: Workflow Process Definition
Step 4: Customize Workflow Process Definition
Workflow Process Definition
Electronic Data Capture (EDC)
Survey Designer: Basics
Survey Designer: Customization
Survey Designer: Reference
Survey Designer: Example Questions
REDCap Survey Data Integration
Adjudication Module
Set Up an Adjudication Folder
Initiate an Adjudication Case
Make an Adjudication Determination
Monitor Adjudication
Infection Monitor
Role Guide: Adjudicator
Role Guide: Adjudication Lab Personnel
Tours for New Users
Contacts
Development
LabKey Client APIs
JavaScript API
Tutorial: Create Applications with the JavaScript API
Step 1: Create Request Form
Step 2: Confirmation Page
Step 3: R Histogram (Optional)
Step 4: Summary Report For Managers
Repackaging the App as a Module
Tutorial: Use URLs to Pass Data and Filter Grids
Choose Parameters
Show Filtered Grid
Tutorial Video: Building Reports and Custom User Interfaces
JavaScript API - Samples
Adding Report to a Data Grid with JavaScript
Export Data Grid as a Script
Export Chart as JavaScript
Custom HTML/JavaScript Participant Details View
Custom Button Bars
Insert into Audit Table via API
Declare Dependencies
Loading ExtJS On Each Page
Licensing for the ExtJS API
Search API Documentation
Naming & Documenting JavaScript APIs
Naming Conventions for JavaScript APIs
How to Generate JSDoc
JsDoc Annotation Guidelines
Java API
Prototype LabKey JDBC Driver
Remote Login API
Security Bulk Update via API
Perl API
Python API
Rlabkey Package
Troubleshooting Rlabkey Connections
SAS Macros
SAS Setup
SAS Macros
SAS Security
SAS Demos
HTTP Interface
Examples: Controller Actions
Example: Access APIs from Perl
Compliant Access via Session Key
Set up a Development Machine
Enlisting in the Version Control Project
Enlisting Proteomics Binaries
Customizing the Build
Machine Security
Notes on Setting up a Mac for LabKey Development
Creating Production Builds
Encoding in Tomcat 7
Gradle Build
Develop Modules
Tutorial: Hello World Module
Map of Module Files
Example Modules
Modules: Queries, Views and Reports
Module Directories Setup
Module Query Views
Module SQL Queries
Module R Reports
Module HTML and Web Parts
Modules: JavaScript Libraries
Modules: Assay Types
Tutorial: Define an Assay Type in a Module
Assay Custom Domains
Assay Custom Views
Example Assay JavaScript Objects
Assay Query Metadata
Customize Batch Save Behavior
SQL Scripts for Module-Based Assays
Transformation Scripts
Example Workflow: Develop a Transformation Script (perl)
Example Transformation Scripts (perl)
Transformation Scripts in R
Transformation Scripts in Java
Transformation Scripts for Module-based Assays
Run Properties Reference
Transformation Script Substitution Syntax
Warnings in Tranformation Scripts
Modules: ETLs
Tutorial: Extract-Transform-Load (ETL)
ETL Tutorial: Set Up
ETL Tutorial: Run an ETL Process
ETL Tutorial: Create a New ETL Process
ETL: User Interface
ETL: Configuration and Schedules
ETL: Column Mapping
ETL: Queuing ETL Processes
ETL: Stored Procedures
ETL: Stored Procedures in MS SQL Server
ETL: Functions in PostgreSQL
ETL: Check For Work From a Stored Procedure
ETL: SQL Scripts
ETL: Remote Connections
ETL: Logs and Error Handling
ETL: All Jobs History
ETL: Examples
ETL: Reference
Modules: Java
Module Architecture
Getting Started with the Demo Module
Creating a New Java Module
The LabKey Server Container
Implementing Actions and Views
Implementing API Actions
Integrating with the Pipeline Module
Integrating with the Experiment Module
Using SQL in Java Modules
GWT Integration
GWT Remote Services
Java Testing Tips
HotSwapping Java classes
Deprecated Components
Modules: Folder Types
Modules: Query Metadata
Modules: Report Metadata
Modules: Custom Footer
Modules: SQL Scripts
Modules: Database Transition Scripts
Modules: Domain Templates
Deploy Modules to a Production Server
Upgrade Modules
Main Credits Page
Module Properties Reference
Common Development Tasks
Trigger Scripts
Availability of Server-side Trigger Scripts
Script Pipeline: Running R and Other Scripts in Sequence
LabKey URLs
URL Actions
How To Find schemaName, queryName & viewName
LabKey/Rserve Setup Guide
Web Application Security
HTML Encoding
Cross-Site Request Forgery (CSRF) Protection
MiniProfiler
LabKey Open Source Project
Source Code
Release Schedule
Issue Tracker
LabKey Scrum FAQ
Developer Email List
Branch Policy
Test Procedures
Running Automated Tests
Hotfix Policy
Previous Releases
Previous Releases -- Details
Submit Contributions
Confidential Data
CSS Design Guidelines
UI Design Patterns
Design Guidelines Supplemental
Documentation Style Guide
Check in to the Source Project
Renaming files in Subversion
Developer Reference
Administration
Tutorial: Security
Step 1: Configure Permissions
Step 2: Test Security with Impersonation
Step 3: Audit User Activity
Step 4: Handle Protected Health Information (PHI)
Projects and Folders
Navigate Site
Project and Folder Basics
Site Structure: Best Practices
Manage Projects and Folders
Create a Project or Folder
Move, Delete, Rename Projects and Folders
Enable a Module in a Folder
Export / Import a Folder
Export and Import Permission Settings
Manage Email Notifications
Define Hidden Folders
Folder Types
Community Modules
Workbooks
Establish Terms of Use
Security
Configure Permissions
Security Groups
Global Groups
Site Groups
Project Groups
Guests / Anonymous Users
Security Roles Reference
Site Administrator
Matrix of Report, Chart, and Grid Permissions
Role / Permissions Table
User Accounts
Add Users
Manage Users
My Account
Manage Project Users
Authentication
Configure LDAP
Configure Database Authentication
Passwords
Password Reset & Security
Configure SAML Authentication
Configure CAS Single Sign On Authentication
Configure Duo Two-Factor Authentication
Create a .netrc or _netrc file
HTTP Basic Authentication
Test Security Settings by Impersonation
Compliance
Compliance: Protected Health Information
Compliance Settings
Compliance Terms of Use
Compliance Module Logging
Admin Console
Site Settings
Usage/Exception Reporting - Details
Look and Feel Settings
Branding
Web Site Theme
Email Template Customization
Experimental Features
Manage Missing Value Indicators / Out of Range Values
Short URLs
Configure System Maintenance
Configure Scripting Engines
Audit Site Activity
SQL Query Logging
Actions Diagnostics
Cache Statistics
Dump Heap
Memory Usage
Running Threads
Query Performance
Site/Container Validation
Install LabKey
Installation Basics
Install LabKey Server (Windows Graphical Installer)
Install LabKey Manually
Install Required Components
Configure the LabKey Web Application
labkey.xml Configuration File
Third-Party Components and Licenses
Install a Remote Pipeline Server via the Windows Installer
PremiumStats Install
Supported Technologies
Troubleshoot Installation
Installation Error Messages
Dump Memory and Thread Usage Debugging Information
Common Install Tasks
Install Microsoft SQL Server
Install PostgreSQL (Windows)
Install PostgreSQL (Linux, Unix or Macintosh)
Install LabKey Server on Solaris
Notes on Installing PostgreSQL on All Platforms
Install and Set Up R
Determine Available Graphing Functions
Install SAS/SHARE for Integration with LabKey Server
Configure Webapp Memory
Set Up Robots.txt and Sitemaps
GROUP_CONCAT Install
Example Setups and Configurations
Example Hardware/Software Configuration
Set up a JMS-Controlled Remote Pipeline Server
Example Installation of Flow Cytometry on Mac OSX
Configure R on Linux
Configure the Virtual Frame Buffer on Linux
Example Linux Installation
Upgrade LabKey
Manual Upgrade Checklist
Manual Upgrade Script for Linux, MacOSX, and Solaris
Upgrade Support Policy
Backup and Maintenance
Backup Checklist
A Sample Backup Plan
Sample Scripts for Backup Scenarios
PostgreSQL Maintenance
Administer the Site Down Servlet
Staging, Test and Production Servers
Example of a Large-Scale Installation
Tips for Configuring a Staging Server
Products and Services
LabKey Server Editions
Training
Custom Community Modules
LabKey Argos
Argos Tour
LabKey Natural Language Pipeline (NLP)
Configure LabKey NLP
Process Files Using Natural Language Pipeline (NLP)
Document Abstraction Workflow
Automatic Assignment for Abstraction
Manual Assignment for Abstraction
Document Abstraction
Review Document Abstraction
LabKey Biologics
LabKey Biologics: Preview
Panorama Partners Program
LabKey User Conference Resources
LabKey User Conference 2016
LabKey User Conference 2015
LabKey User Conference 2014
LabKey User Conference 2013
LabKey User Conference 2012
LabKey User Conference 2011
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