Add support for simple FS-based directory listing

[jamoore]

As an initial step for FS/bioformats-based IO, the Repository API should be made usable by clients for more than just ${omero.data.dir}.

Temporary Repository

The first step will be to make ${java.io.tmpdir} available.

TODO

• passing back all files as OriginalFile objects
• allow passing back that original file to register it.
• Making OriginalFile?.name be UNIQUE
• Making bulk methods
• Add UUID to FS server name

[jmoore]

r5965 and r5966 have an initial implementation.

Assuming that the output of:

import omero
c = omero.client("localhost")
s = c.createSession("root","ome")
sr = s.sharedResources()
rm = sr.repositories()
print [x.name.val for x in rm.descriptions]

is

['/tmp', '/OMERO/']

Then:

pr = rm.proxies[0]
pr.list("/tmp")

should print out the contents of the /tmp directory. For testing, symlink any directories which you would like to see there.

Caveats

• The proper exceptions have not been decided on.
• Creation of the other services (RawPixels, etc.) is not implemented.

[jmoore]

Brief mtg. notes

.#2 FS discussion : Jean-Marie, Josh, Colin 16:54 ([[OmeroFs#2]])

 - JM had a quick look this morning
  -- looking at /tmp
  -- existing directories? yes.
  -- where logic sits java or python
  -- repomap -> /tmp -> ...
 - @Changes
  -- passing back all files as OriginalFile objects
  -- allow passing back that original file to register it.
  -- Making OriginalFile.name be UNIQUE
  -- Colin: Making bulk methods
  -- Hold off on the multiple FSes (using /tmp)
 - Graying out one of the repo's if offline
  -- Also goes for any RawFileStore access
  -- Need good exceptions
  -- Archived files? Another exception ("Do you really want to ...") ??
 - Testing & Exceptions
  -- Need to sit together (Jean-Marie & Colin, especially)
  -- Find out what can go wrong
  -- How can we react to those things
  -- Sensible (hopefully) exception hiearchies
 - Things for the future, to keep in mind
  -- one error: moved file
  -- hashing
  -- do we do monitoring now or later

[jburel]

.#3 FS discussion : Jean-Marie, Colin (OmeroFs#3)

• JM: insight status repositories implemented in insight.

Objects returned by server already considered as OriginalFile

Actions for second phase:

• passing back all files as OriginalFile objects
• displaying thumbnail while browsing the a directory. Single file for now.
• Interaction with bio-formats or importer (if we want rendering settings).
• Colin: check if using Josh's calls are using Fs.

[cblackburn]

Closed for the same reason as #1933. See #2128 and #2595