[dna-issues] [JBoss JIRA] Updated: (DNA-105) Sequence content from delimited text files

[Brian Carothers (JIRA)]

     [ https://jira.jboss.org/jira/browse/DNA-105?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Brian Carothers updated DNA-105:
--------------------------------

    Attachment: DNA-105_preview.patch


Attached patch that adds a new project with two new sequencers, one for parsing sequencing files and one for sequencing fixed width files.  Both sequencers are row-based and assume that the file is allocated at one row per line with the EOL character being recognizable by BufferedReader.readLine().  Both sequencers support basic functionality like being able to specify a comment character and custom factory for creating the record associated with each row.

The DelimitedTextSequencer allows users to specify a particular regular expression that is used to split each line into columns.  This value defaults to ",", presumably allowing this solution to address DNA-229 as well.  Since any valid regular expression can be used, this also allows for the use of multiple delimiters.

The FixedWidthTextSequencer allows users to specify the column index at which each column starts either as an array of ints or as a single, comma-delimited string.  As an example, a user could specify { 3, 6 } as this index to sequence this line: 

 onetwothree

into this array of columns: 

one, two, three

The attached patch is about as undocumented as possible, but it's exceedingly straightforward.  In fact, there's only about 100 lines of actual code.  The rest is just test cases and test data.  I'm going to leave this out for a day or two in case anyone has comments.  If no major concerns are expressed, I'm going to add documentation, commit this, and then treat any future bugs or feature requests as separate issues.





> Sequence content from delimited text files
> ------------------------------------------
>
>                 Key: DNA-105
>                 URL: https://jira.jboss.org/jira/browse/DNA-105
>             Project: DNA
>          Issue Type: Feature Request
>          Components: Sequencers
>            Reporter: Greg Haber
>            Priority: Minor
>             Fix For: Future Releases
>
>         Attachments: DNA-105_preview.patch
>
>
> It is a somewhat common practice for delimited text files such as comma-separated (CSV) or tab delimited files to contain a list of column names in the first line of the file.  A sequencer to capture this metadata could be useful,and should be straightforward to implement.

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