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Module 2: ENA flat file validator

Introduction

You can use the ENA flat file validator to validate your sequence flat files before submitting them through Webin.

The validator is changed frequently. Please check every few weeks if a new version is available.

Download the program

The latest version of the validator can be downloaded from:

https://github.com/enasequence/sequencetools/releases

The program is a self executing Java jar file: embl-api-validator-<version>.jar (for example: embl-api-validator-1.0.0.jar).

It requires Java 1.8 or newer which can be downloaded from:

https://java.com/en/download

The latest version of the validator is also available from Maven together with the following additional jar files:

  • embl-api-core: flat file reader, data model and writer
  • embl-api-ff: flat file validator and fixer

Using the program

You need to run the validator with the -r option to show that you are running it remotely. This will exclude checks that require EBI's internal infrastructure.

You will provide file name(s) to the validator which may include wildcards (*).

For example, two files file1.txt and file2.txt:

java -jar embl-api-validator-1.0.0.jar -r file1.txt file2.txt

Or all files ending with *.txt in the current working directory:

java -jar embl-api-validator-1.0.0..jar -r *.txt

You can set the output level by using the -l argument:

  • 0 is silent
  • 1 is summary only
  • 2 is full report

For example:

java -jar embl-api-validator-1.0.0..jar -r -l 2 *.txt

Validation reports

A summary output is shown on the console at the end of execution. This summary allows you to quickly see if there were any errors in your files. Full error reports are written to text files.

Validation messages have three severities:

  • info: no problem with the flat file, just a comment
  • warning: the flat file can be submitted but you may be able to improve the quality of the information
  • error: the flat file is invalid and must be corrected

If a message occurs multiple times then the message will be shown once in the "compressed messages" section.

The "file summary" section shows you the results for each file while the "summary" shows an overall number of validated and possibly failed flat file entries. Please ignore the fixed and unchanged entry counts. These are for when running the validator in the "fix" mode, which you will not be using.

The validator produces the following reports:

  • VAL_SUMMARY.txt: the summary output is also saved into this file
  • VAL_ERROR.txt: error messages
  • VAL_REPORTS.txt: some validation messages include extended information written into this file. For example, CDS translation errors include a detailed translation report.
  • VAL_INFO.txt: info and warning messages
  • VAL_FIXES.txt: fixes applied in the "fix" mode (you will not be using this)

Proxy servers

If your organisation uses a https proxy you can set the following Java properties to instruct the validator to use them:

  • https.proxyHost
  • https.proxyPort

For example:

java -Dhttps.proxyHost=proxy.com -Dhttps.proxyPort=8080 -jar embl-api-validator-1.0.0..jar -r *.txt