OMERO.dropbox
=============
DropBox was originally designed as the first stage of the file
system changes referred to as :doc:`/developers/Server/FS`. It utilizes a file
system monitor to find newly uploaded files and run a fully automatic
import on those files if possible. This release of OMERO.dropbox runs on
the same machine as the OMERO.server and watches designated areas of the
local filesystem for new or modified files. If those files are
importable, then an automatic import is initiated. OMERO.dropbox is
started automatically when the OMERO.server starts and it will run if
the prerequisites below are met.
Prerequisites
-------------
In addition to the general :doc:`system-requirements` OMERO.dropbox has
the following more specific requirements:
- OMERO.dropbox is built on underlying OS file-notification system, and so
is only available for specific versions of certain operating systems.
OMERO.dropbox will currently function on the following systems:
- Linux with kernel 2.6.13 and higher.
- Mac OS 10.6 and later.
- Windows XP and Windows Server 2003.
- In addition some platforms require further Python packages to be
available:
- Mac OS systems that use a macports install of Python will need to
have FSEvents available in the PYTHONPATH. This will require a
path of the form
``/System/Library/Frameworks/Python.framework/Versions/2.X/Extras/lib/python/PyObjC/``
to be added, according to the version of Python used.
- The filesystem which OMERO.dropbox watches must be local to the given
operating system. Watching a network-attached share (NAS) is strictly
***not*** supported.
Using DropBox
-------------
In its default configuration the monitored area of the file system is a
``DropBox`` subdirectory of the OmeroBinaryRepository directory. The
system administrator should create ``DropBox`` and then under that a
directory for each user, using their omero username. The ownership and
permissions should be set so that a user can copy files into their
DropBox directory:
::
/OMERO/DropBox/amy
/emily
/edgar
/root
/zak
Experimenters can add subdirectories under their named directory for
convenience. Copying or moving a file of an importable file type into a
named directory or nested subdirectory will initiate an automatic import
of that file for that user. Multi-file formats will be imported after
the last required file of a set is copied into the directory.
Acquisition systems can then be configured to drop a user's images into
a given DropBox.
.. note::
The DropBox system is designed for images filesets to be copied in at
normal acquisition rates. Copying numbers of files en masse may result in
files failing to import.
Log files
---------
The log files :file:`var/log/FileServer.log`, :file:`var/log/MonitorServer.log`
and :file:`var/log/DropBox.log` will indicate success or otherwise of start-up
of the two components.
Once running, :file:`var/log/MonitorServer.log` will log file events seen within
designated file areas and :file:`var/log/DropBox.log` will log the progress
of any file imports.
Advanced use
------------
OMERO.dropbox can be configured in several ways through
:file:`etc/grid/templates.xml`. In its default configuration, as detailed
above, it monitors the subdirectory ``DropBox`` of the OMERO data
directory for all users.
A number of the properties in :file:`templates.xml` accept a semi-colon
separated list of values. This extended configuration allows a site to
watch multiple directories, and configure each for a different user, a
different type of file, etc. Any value missing from the configuration
(e.g. ``value="1;;2"``) will be replaced by the default value.
One example alternative configuration would be to watch specific
directories for specific users. In the example below two directories are
monitored, one for user ``amy`` and one for ``zak``:
::
<property name="omero.fs.importUsers" value="amy;zak"/>
<property name="omero.fs.watchDir" value="/home/amy/myData;/home/zak/work/data"/>
The remaining properties have been left at their default values for both
users.
To limit DropBox to import only files belonging to specific image types
the following property can be set,
::
<property name="omero.fs.readers" value="/home/amy/my_readers.txt;"/>
Here only the image types listed in :file:`my_readers.txt` will be imported
for the user ``amy`` while the system-wide :file:`readers.txt` will be used
for ``zak``.
For a full description of the properties see below.
Properties
^^^^^^^^^^
Each property takes the form of a single item or a semi-colon separated
list of items. Where the item is a list, values within that list should
be comma separated.
- importUsers
The importUsers is either ``default`` for the standard DropBox
configuration or a list of OMERO user names. The default is default.
::
<property name="omero.fs.importUsers" value="default"/>
- watchDir
The absolute directory path of interest for each user. The default is
empty.
::
<property name="omero.fs.watchDir" value=""/>
- eventTypes
For automatic import Creation and Modification events are monitored. It
is also possible to monitor Deletion events though these are not used by
DropBox. The default is Creation,Modification.
::
<property name="omero.fs.eventTypes" value="Creation,Modification"/>
- pathMode
By default existing and newly created subdirectories are monitored. It
is possible to restrict monitoring to a single directory ("Flat"), only
existing subdirectories ("Recurse"), or all subdirectories ("Follow").
For DropBox to function correctly the mode should be Follow. The default
is Follow.
::
<property name="omero.fs.pathMode" value="Follow"/>
- whitelist
A list of file extensions of interest. An empty list implies all file
extensions are monitored. The default is an empty list.
::
<property name="omero.fs.whitelist" value=""/>
- blacklist
A list of subdirectories to ignore. Not currently supported.
::
<property name="omero.fs.blacklist" value=""/>
- timeout
This timeout in seconds is used by one-shot monitors. This property is
not used by DropBox.
::
property name="omero.fs.timeout" value="0.0"/>
- blockSize
The number of events that should be propagated to DropBox in one go.
Zero implies all events possible. The default is zero.
::
<property name="omero.fs.blockSize" value="0"/>
- ignoreSysFiles
If this is True events concerning system files, such as filenames
beginning with a dot or default new folder names, are ignored. The exact
events ignored will be OS-dependent. The default is True.
::
<property name="omero.fs.ignoreSysFiles" value="True"/>
- ignoreDirEvents
If this is True then the creation and modification of subdirectories is
not reported to DropBox. The default is True.
::
<property name="omero.fs.ignoreDirEvents" value="True"/>
- dirImportWait
The time in seconds that DropBox should wait after being notified of a
file before starting an import on that file. This allows for companion
files or filesets to be copied. If a new file is added to a fileset
during this wait period DropBox begins waiting again. The default is 60
seconds.
::
<property name="omero.fs.dirImportWait" value="60"/>
- fileBatch
The number of files that can be copied in before processing the batch.
In cases where there are large numbers of files in a typical file set it
may be more efficient to set this value higher. The default is 10.
::
<property name="omero.fs.fileBatch" value="10"/>
- throttleImport
The time in seconds that DropBox should wait after initiating an import
before initiating a second import. If imports are started too close
together connection issues can arise. The default is 10 seconds.
::
<property name="omero.fs.throttleImport" value="10"/>
- readers
A file of readers. If this is a valid file then it is used to filter
those events that are of interest. Only files corresponding to a reader
in the file will be imported. The default is empty.
::
<property name="omero.fs.readers" value=""/>
- importArgs
A string of extra arguments supplied to the importer. This could
include, for example, an email address to report failed imports to:
``--report --email test@example.com``. The default is empty. For
details on available extra arguments see :doc:`/users/command-line-import`.
::
<property name="omero.fs.importArgs" value=""/>
Example
^^^^^^^
Here's a full example of a configuration for two users:
::
<property name="omero.fs.importUsers" value="amy;zak"/>
<property name="omero.fs.watchDir" value="/home/amy/myData;/home/zak/work/data"/>
<property name="omero.fs.eventTypes" value="Creation,Modification;Creation,Modification"/>
<property name="omero.fs.pathMode" value="Follow;Follow"/>
<property name="omero.fs.whitelist" value=";"/>
<property name="omero.fs.blacklist" value=";"/>
<property name="omero.fs.timeout" value="0.0;0.0"/>
<property name="omero.fs.blockSize" value="0;0"/>
<property name="omero.fs.ignoreSysFiles" value="True;True"/>
<property name="omero.fs.ignoreDirEvents" value="True;True"/>
<property name="omero.fs.dirImportWait" value="60;60"/>
<property name="omero.fs.fileBatch" value="10;10"/>
<property name="omero.fs.throttleImport" value="10;10"/>
<property name="omero.fs.readers" value="/home/amy/my_readers.txt;"/>
<property name="omero.fs.importArgs" value="--report;--report --email zak@example.com"/>