A ReSTful service for MetaMapLite

A ReSTful service for MetaMapLite which includes support for Web Browsers. This is an JAX-RS service implementated using Jersey (https://eclipse-ee4j.github.io/jersey/).

Configuring the Service

In the directory: 'src/main/webapp/config/metamaplite.properties' the property: 'metamaplite.index.directory' to points to the dataset indexes to used by MetaMapLite. If the indexes are in 'src/main/webapp' then the path must be relative to 'src/main/webapp'. If the indexes reside outside of your application server then the path must be an absolute path. This is also the case for the OpenNLP models used for part-of-speech tagging and phrase chunking (the properties: 'opennlp.en-pos.bin.path' and 'opennlp.en-chunker.bin.path'.)

Compiling

Requires Maven to compile:

mvn package

The command above will generate a war file suitable for loading into a servlet engine such as Apache Tomcat or Jetty.

Development Directory Organization

Below is a pictorial representation of a possible directory organization for a servlet containing MetaMapLite. The main properties file 'metamaplite.properties' resides in the 'config' directory. The inverted file indexes used by MetaMapLite reside in the 'ivf' directory. The opennlp models reside in data/models directory.

 sample-webapp/
     |
     +- config
     +- data
     |   |
     |   +- ivf
     |   |   |
     |   |   +- strict 
     |   |         |
     |   |         +- indices
     |   |         |   |
     |   |         |   +- cuiconcept
     |   |         |   +- cuisourceinfo
     |   |         |   +- cuist
     |   |         |
     |   |         +- tables
     |   +- models
     |
     +- lib
     +- src
     |   |
     |   +- main
     |       |
     |       +- java
     |       |   |
     |       |   +- sample
     |       |   
     |       +- webapp
     |           |
     |           +- WEB-INF
     |               |
     |               +- WebContent
     |               +- classes
     |                   |
     |                   +- sample
     |                   
     +- target
         |
         +- web
             |
             +- sample

An attempt has been made to make the directory structure somewhat comformant to Maven's recommended directory organization to allow relatively painless migration to Maven if desired.

Note: the indexes for the inverted files can be outside of the container if the servlet engine supports it. Some modifications to MetaMapLiteFactory may be needed to support it. This support will probably be added in a future release.

Specifying the MetaMapLite Version

The Maven project file (pom.xml) must be modified to specify which version of MetaMapLite you wish to use. Also, for the latest version of MetaMapLite, it will be necessary to run 'mvn install' in the public_mm_lite directory to make it available when compiling metamaplite-rest. The metamaplite version specified in the dependencies of the metamaplite-rest pom.xml should be the same as the version in the top of the public_mm_lite pom.xml.

ReSTFul MetaMapLite URLs

Suggested Requests

• List of Options
• List of Available DataSets
• List of Sources
• List of Semantic Types
• List of Supported Request Formats
• List of Supported Response Formats
• annotate input

URL Examples

  Query url                                   description

  metamaplite/rest/options                    get list of options
  metamaplite/rest/options/list               
  metamaplite/rest/options/info/segmentlines  get info on use of segmentlines
  metamaplite/rest/options/info/inputformat   get list of available input formats
  metamaplite/rest/options/info/outputformat  get list of available output formats
  metamaplite/rest/datasets
  metamaplite/rest/datasets/list              get list of available data sets
  metamaplite/rest/datasets/info/base.2016AB  get info on data set base.2016AB
  metamaplite/rest/sources                    
  metamaplite/rest/sources/list               get list of sources
  metamaplite/rest/sources/info/msh
  metamaplite/rest/semantictypes              get list of semantic types
  metamaplite/rest/requestcontenttypes        get list of available content-types for requests
  metamaplite/rest/requestcontenttypes/list
  metamaplite/rest/responsecontenttypes
  metamaplite/rest/responsecontenttypes/list  get list of available content-types for responses
  metamaplite/rest/annotate                   annotate input document (POST) or term (GET)
  metamaplite/rest/chunk                      chunk input document
  metamaplite/rest/postag                     tag input document part of speech
  metamaplite/rest/acronyms                   find acronyms/abbreviations in input document

  metamaplite/rest/annotate/plain

Form submission encodings

JSON (preferred format)

content-type: application/json

XML

content-type: application/xml

EDN

content-type: application/edn

YAML

content-type: text/x-yaml

Form URLEncoded

content-type: application/x-www-form-urlencoded

Multipart Form Data

content-type: multipart/form-data

response encodings

text/plain

outputformats supported:

• brat/standoff
• MMI like
• PubTator

application/edn

outputformats supported: To be determined

application/xml

outputformats supported:

• BioC XML
• Others?

content of requests

annotation requests (POST)

post dictionary

inputtext: input text docformat: format of input document (freetext, medline, pubmed) resultformat: format of result (mmi, brat, etc.) sourceString: semanticTypeString: