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From Gary Gregory <garydgreg...@gmail.com>
Subject Re: [CSV] Headers and the first record
Date Wed, 31 Jul 2013 19:56:41 GMT
On Wed, Jul 31, 2013 at 3:44 PM, Mark Fortner <phidias51@gmail.com> wrote:

> Hi Gary,
> One other complication I forgot to mention.  Compounds are usually run
> multiple times.  So the same compound will appear with the same set of
> concentrations.  In practice you would end up with column headers that have
> the same text in them, so this issue with using a Set vs String[] for the
> column names would complicate things.
>
>
> > CSVFormat implements Serializable, so you can use plain old Java
> > serialization, it's not human readable, but it's something.
> >
>
> A human readable configuration would probably be a high priority.
>
>
> >
> > If we moved to Java 6, we could annotate CSVFormat with JAXB so you can
> > have XML IO. Personally, I do not think we should do our own XML IO, so
> > JAXB is the best path IMO since it is built-in Java 6.
> >
>
> It would be best if there were a CSVFormat serializer so that the CSVFormat
> could be injected.  Using JAXB would be fine as a default implementation,
> but I imagine that the configuration format would change.  Or that a user
> might decide to store individual configuration items in a database.
>
>
> >
> > What do you currently use to parse your CSV files?
> >
>
> Most biotech companies have their own home grown tools for parsing
> instrument files.  There isn't a standard library.
>
>
> >
> > Would Commons-CSV work for you as well? If not, how so?
> >
>
> As I understand it, the code doesn't support "experiment condition"-type
> parameters, like this:
>
> Date: 12/10/13
> Protocol: Selectivity Profile 1        Instrument Name: Gandalf
> Scientist: John Smith
>

This does not look like a classic CSV file.

It sounds like your files contain different sections in different formats.

In its current state, commons-csv might not be right for you. What does the
rest of the file look like?

Gary


>
>
> > Would you be willing to experiment with the current code?
> >
> >
> Sure. If the previous issues were addressed.
>
> I'm curious if other industries have similar issues?  I assume that anyone
> that deals with instrument data might have similar needs.
>
> Mark
>



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