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You are here: Home Community Minutes Mini Group meetings OMERO/HIC Meetings 2011.05.27


Attending: Andy, Jason, Josh, Simon


  • Action points from last time
    • CVs to Andy
    • Status from Andy on joins, aliasing, specific typing, string lengths
  • Josh: description of service (See listing 1)


HIC: Jason, Simon, Andy, Josh

  • Admin

    • Getting Andy access
    • Jason: emails for interviews, etc?
      • Andy is ok with all times (Monday)
      • Jason will forward to Josh
  • Data info

    • Andy: haven't had time
  • FS/service (josh)

    • Architecting a "Haven" as a subclass of Repository
    • Andy: shouldn't use the word Haven
    • Other good words:
      • Semantic Type
      • Agents
    • Andy: could certainly seem new data coming in.
      • GoDARTs just added aliasing
      • Could envision one master copy come in (with anonymisation)
      • and then splitting it for the individual projects
  • Querying

    • Not very done.
  • Mid-July is deadline to show something

    • Tyson (?Kison?) should be someone we can work with. (and Colin...)
    • SNP imputing against version XYZ
    • Tools are command-line based.
    • Not HDF5.
    • Scenario:
      • Load full CSV
      • Research goes to command-line
      • Runs a query with joins
        • Biochemistry: give me the patients who have type 2 with BMI in this range
          • All columns? Probably
        • Select the rows with a BMI over this.
        • Longitudinal all rows / subset
      • PLink computer or whatever
        • Andy needs to understand more
        • Takes one file of phenotypical data in a particular file format
        • Need to sit down.
      • See results as txt file
    • Installing / Testing new files
      • Andy: One set of data. Load it into DB
      • Josh: But we're developing the DB (and SQL ...)
      • Jason: how useful is it there is file system
      • Andy: simon come to visit to see the work.
        • Up to 100 student projects a year
        • for GoDARTs its reasonably stable
        • but could understand the "Your data is ready"
  • Plan

    • For next week, @@having scaffolding of the CLI in place
      • then Simon has a visit with Andy to compare the workflows
    • Andy: @@data flow diagram (from Simon)
      • Where does the stats package sit?
      • Then get auditing working
      • Then a website with simple queries
    • No meeting currently planned
      • Jason: Next 2 months ain't good
      • Andy: keen to get the workflow (been asking the same questions)
      • @@Andy will setup visit, inviting Simon

Listing 1

   class TestHavens(lib.ITest):

def testSimple(self):

    if False: ##### Possible service styles ####

        grid = self.client.sf.sharedResources()

        # Pure repo solution. Need to under
        repoMap = grid.repositories() # Returns "Repository" mimetype
        repoMap = grid.repositoriesOfType("Haven") # Mimetype
        hic = "..." # Get the appropriate on somehow
        hic.attachAgent("/Patients", "HavenType", {"schema":original_file_id})
        client.upload("/Patients", "test.csv")

        # Shared resource solution
        haven_prx = grid.getRepositoryForHaven(haven_obj)

        # Share solution
        haven_obj = iSharePrx.creatShare("...", haven = True)

        # Object solution
        haven_prx = grid.findHaven("test")
        haven_prx = grid.openHaven(HavenI(1, False))

        # Or is the repo a group, i.e. a shared pot?!?!?!

        # Negative tests
        assertRaises(createHaven, "no.periods")
        assertRaises(createHaven, "no spaces")
        assertRaises(createHaven, "no_punctunation")
        assertRaises(createHaven, "no-punctunation")

    # Result of the above should be a single haven prx
    haven_prx = Haven()

    # Admin
    original_file = client.upload("test.xml")
    haven_prx.addType("test", original_file)

    original_file = client.upload("test.csv")
    haven_prx.addData("test", original_file)

    # Audit settings

    # Audit information
    logs = haven_prx.getEventLogs() # Return own ITime
    for log in logs:
        print log.action,
        print log.entityType, # "<TYPE>.<columnname>
        print log.entityId,   # row, -1 for no record row access

    # User
    names = haven_prx.getTypes()
    for name in names:
        print name

        cols = haven_prx.getColumns(name)
        for col in cols:
            print col.description,
            print col.originalName,
            print col.originalPosition
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