On Wed, Jul 31, 2013 at 3:44 PM, Mark Fortner <phidia...@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 > -- E-Mail: garydgreg...@gmail.com | ggreg...@apache.org Java Persistence with Hibernate, Second Edition<http://www.manning.com/bauer3/> JUnit in Action, Second Edition <http://www.manning.com/tahchiev/> Spring Batch in Action <http://www.manning.com/templier/> Blog: http://garygregory.wordpress.com Home: http://garygregory.com/ Tweet! http://twitter.com/GaryGregory
