[OTDev] how to get compound URIs for the compounds I add to a dataset?

Nina Jeliazkova jeliazkova.nina at gmail.com
Fri Oct 29 17:40:19 CEST 2010


On 29 October 2010 18:30, Egon Willighagen <egon.willighagen at gmail.com>wrote:

> On Fri, Oct 29, 2010 at 5:23 PM, Nina Jeliazkova
> <jeliazkova.nina at gmail.com> wrote:
> > Yet another option.
>
> OK, something related... I'm now creating a data set and then
> requesting it's features with:
>
> http://apps.ideaconsult.net:8080/ambit2/dataset/11955/features
>
> (data sets I remove afterwards, so this link will not work...)
>




>
> I'm using this code (fullURI is the one above):
>
> HttpMethod method = new GetMethod(fullURI);
>                method.setRequestHeader("Accept", "text/uri-list");
>                client.executeMethod(method);
>                System.out.println(method.getResponseBodyAsString());
>                method.releaseConnection();
>                List<String> features = new ArrayList<String>();
>                BufferedReader reader = new BufferedReader(
>                        new StringReader(method.getResponseBodyAsString())
>                );
>                String line;
>                while ((line = reader.readLine()) != null) {
>                        line = line.trim();
>                        if (line.length() > 0) features.add(line);
>                }
>                return features;
>
> But I get an HTML page instead of the URIs of the features instead...
>
> What Accept should I be using? Can't find this in the 1.1 specs...
>

This should work (but the link above is nonexistent)

curl -H "Accept:text/uri-list"
http://apps.ideaconsult.net:8080/ambit2/dataset/1/feature
http://apps.ideaconsult.net:8080/ambit2/feature/1
http://apps.ideaconsult.net:8080/ambit2/feature/2
http://apps.ideaconsult.net:8080/ambit2/feature/3
http://apps.ideaconsult.net:8080/ambit2/feature/4
http://apps.ideaconsult.net:8080/ambit2/feature/5
http://apps.ideaconsult.net:8080/ambit2/feature/6
http://apps.ideaconsult.net:8080/ambit2/feature/7
http://apps.ideaconsult.net:8080/ambit2/feature/8
http://apps.ideaconsult.net:8080/ambit2/feature/9
http://apps.ideaconsult.net:8080/ambit2/feature/10
http://apps.ideaconsult.net:8080/ambit2/feature/11
http://apps.ideaconsult.net:8080/ambit2/feature/12
http://apps.ideaconsult.net:8080/ambit2/feature/13
http://apps.ideaconsult.net:8080/ambit2/feature/14
http://apps.ideaconsult.net:8080/ambit2/feature/15
http://apps.ideaconsult.net:8080/ambit2/feature/16
http://apps.ideaconsult.net:8080/ambit2/feature/17

You could get features with "Accept:application/rdf+xml" as well.

Nina

>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Research Associate
> University of Cambridge
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
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