Dtool-irods

--------------------

Added
^^^^^

- Writing of ``.dtool/structure.json`` file to the IrodsStorageBroker; a file
for describing the structure of the dtool dataset in a computer readable format
- Writing of ``.dtool/README.txt`` file to the IrodsStorageBroker; a file
for describing the structure of the dtool dataset in a human readable format


Changed
^^^^^^^

- Make use of version 3 of the dtoolcore API. Specifically making use of the
new ``base_uri`` argument that replaces ``prefix`` in the ``list_dataset_uri``
and ``generate_uri`` class methods.

--------------------

Fixed
^^^^^

- Fixed ``IrodsStorageBroker.generate_uri`` class method
- Made ``.dtool/manifest.json`` content created by IrodsStorageBroker human
readable by adding new lines and indentation to the JSON formatting.
- Added rule to catch ``CAT_INVALID_USER`` string for giving a more informative
error message when iRODS authentication times out

--------------------

Changed
^^^^^^^

- Improved speed of freezing a dataset in iRODS by making use of
caches to reduce the number of calls made to iRODS during this
process


Fixed
^^^^^

- More informative error message when iRODS has not been configured
- More informative error message when iRODS authentication times out
- Stopped client hanging when iRODS authentication has timed out
- storagebroker's ``put_item`` method now returns relpath
- Made the ``IrodsStorageBroker.create_structure`` method more
robust by checking if the parent collection exists

--------------------

Fixed
^^^^^

- Fixed defect in iRODS storage broker where files with white space resulted in
broken identifiers

--------------------

Fixed
^^^^^

- Fix defect where ``IrodsStorageBroker.put_item`` raised SystemError when
trying to overwrite an existing file

--------------------

Added
^^^^^

- Ensure ``dtool verify`` will work as expected by forcing iRODS to
re-calculate the file hash when asking for it, which ensures that a cached
copy is not used.