Guideline for Web Services

This document is a guideline to design of web services toward integration.

• REST
  • For a database service, REST services to get entries and search by a keyword should be provided.
  • To unify a format of a query, a query language should conform to Common Query Language.
  • A method to get the number of hits for a keyword should be provided.
  • A method to get the list of hit entries for a keyword should be provided.
  • A method to get the entry from an ID should be provided.
    • If the entry does not exist, the method should return code 404 and an empty entry.
  • Path parameters (/foo/bar/baz) should be used for a REST URL and query parameters (param1=value1&param2=value2) should not used.
    • Lower-case letters should be used for path parameters in principle.
    • If a URL ends "/", a list of possible strings after the URL should be returned in principle.
  • When a method return a list, each line should correspond to an entry and each field should be divided by tab.

• SOAP
  • A manual for each method should be prepared.
    • The manual should include an example of parameters such that the method works well by them.
  • Each method should be verified to use Java, Perl, Ruby and Python.
    • Providing sample codes for such languages is better.
  • For asynchronous services, a job ID should be provided.
  • When any error occurs during processing at a server, a method should return "SOAP Fault".

• The following types should be used:
  • INSDC for sequences,
  • MIAMI for expression data,
  • GLYDE-II for glycans,
  • tab format for key-value.

• REST or SOAP
  • For a method to get an entry or search entries by keyword, REST is recommended. For a method of analysis service, SOAP is recommonded.

TogoWS TogoWS Guidelines

REST

TogoWS stated the rulers as below:

•  http://togows.dbcls.jp/site/services.html
•  http://togows.dbcls.jp/site/rest.html

How to call the entries

http://togows.dbcls.jp/entry/database/entry_id[,entry_id2,...]/field[.format]

If the name space of the databases are in URL：

•  http://frnadb.example.org/entry/id instead of  http://frnadb.example.org/entry/frnadb/id

How to add the name spaces for the institution, release_numer of the database:

•  http://togows.dbcls.jp/entry/birc-hinv-5.0/HIT0012345

NOTE: The default fotmat for the entries is “.txt”, and can be in the specified format by adding the suffix, such as “.xml”.

エントリの部分要素取得について：

エントリの一部を field 名で取得できる機能は BioRuby/BioPerl を利用した TogoWS の拡張ですが、 バックエンドが XML データベースの場合など、field の代わりに XPath を利用することも検討可能。

How to search the entries

http://togows.dbcls.jp/search/database/query+string[.format][/offset,limit[.format]] 
http://togows.dbcls.jp/search/database/query+string/count

The format of "query string" to be based on “Common Query Language"  Common Query Language

The conversion of data format and ID

http://togows.dbcls.jp/convert/data_source.format

Metadata

• The list of the databases

http://togows.dbcls.jp/entry/
http://togows.dbcls.jp/search/

• The list of the fields

http://togows.dbcls.jp/entry/DBname/

• The list of the formats

http://togows.dbcls.jp/entry/DBname/formats

SOAP

• Required test environment
  • Perl: Soap::Lite 0.69
  • Ruby: SOAP4R 1.5.5 (Ruby 1.8.6 bundle)
  • Python: SOAPpy 0.12.0
  • Java: Axis 1.4
• SOAP version 1.2, at least
• Calling a method with asynchronous
  • The name for the method with asynchronous end with “Async” and return job ID
  • Rerurn job ID to “CheckAsyncStatus??” method and give either RUNNING, COMPLETED, or ERROR
  • Method name for the method with asynchronous mst be” BeginInvoke? methods＋Result” and stae job ID as a parameter

History

• version Manifest2.0_e? (2009/03/20)