Updates from May, 2011 Toggle Comment Threads | Keyboard Shortcuts

  • Eamonn Maguire 3:09 pm on May 31, 2011 Permalink | Reply  

    As we loaded the new InnoMed data into… 

    As we loaded the new InnoMed data into the BII (16 studies with approximately 1000 samples per study), we found some places were the BII web application just didn’t work as we expected: performance and display wise. So, the following enhancements have been added:

    • Caching at the application server level to improve performance for all users – we have reduced response times on average by 800%!
    • New display of the sample attributes and characteristics. You can see the new view here: http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1
    • Proper display of sample attribute and factor values along with their units
    • Better data locations support. Those of you who have deployed the BII before may have noticed that when you have assays of the same time distributed in a mix of public and private repositories that the data-locations.xml didn’t allow you to specify multiple possible locations for data files to go…so now, if you have ArrayExpress accessions in your ISAtab submission, and you have the ArrayExpress repository information added into your data locations file, the web application will automatically link out to ArrayExpress. If you don’t, the link will be to your local file system. Or, if you have an GEO accession instead, the link will be made out to GEO. The default data locations file we will server out in the new release of the BII data manager will have all these options specified for you in advance, so you only need to have the accessions in your ISAtab file.
     
  • Eamonn Maguire 10:24 am on May 13, 2011 Permalink | Reply
    Tags: configurable, , , , JList   

    Configurable form views & reorderable JList 

    Form views are now configurable. In itself, this was quite a bit of work to automatically generate an interface from an XML description. So now, the view like that shown in figure 1 below can be customised like the rest of the ISAcreator views (spreadsheets).

    Figure 1 - ISAcreator form view for entry of Investigation information

    However, after working on this new feature, I realised that due to there being clearly defined sections for Investigation Contacts, Publications etc (see figure 2), it’d be useful if users could move these sections around without having to click forever on a move up button in the ISAconfigurator.

    Figure 2 - configure the form view in the ISAconfigurator

    So, after looking at the Swing Hacks book, which demonstrates how to move single items in a JList, I modified this code and made it possible to move entire blocks up/down in a JList as shown in figure 3 below.

    Figure 3 - Moving an entire section around in the JList

    From what I know, this is the first (at least public) implementation of such a JList. The code can be found on the ISAconfigurator GitHub repository. I will probably move this to its own repository in the next few days when I get a little time.

    Thanks to Joshua Marinacci for allowing me to reuse his code. Check out his new project called Amino, it’s very cool for developing Swing applications. You can even skin UI components using CSS.

     
  • Eamonn Maguire 5:49 pm on May 12, 2011 Permalink | Reply  

    ISAcreator 1.4 beta 2 released 

    Hi all,

    We’ve solved the problem being experienced on Windows (we hope!), so please test this latest version of ISAcreator. The final release of 1.4 with many more new features will be released on June 3rd!

    Get it here!

    The anatomy of ISAcreator

     
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