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Warning: This section is documentation for an OLD release of our software!
 

FS

OMERO.fs

OMERO.fs is planned as a system of services for accessing image data on server filesystems from the OMERO.server without the need to import the pixel data into the server. The underlying OMERO.fs servers are file system monitors which notify interested OMERO.fs clients of newly created, modified or deleted files in a particular part of a file system.

As of 4.2, the FS services do not prevent the data duplication issue which has often been discussed, but instead provides a background client, "DropBox", which can automatically import data into OMERO.

Prerequisites

  • OMERO.fs has the following general requirements:

    • Ice 3.3
    • Python 2.4 or above

  • OMERO.fs is built on underlying OS file-notification system, and so is only available for specific versions of certain operating systems. OMERO.fs will currently function on the following systems:

    • Linux with kernel 2.6.13 and higher.
    • Mac OS 10.5 and above.
    • Windows XP and Windows Server 2003.

  • In addition some platforms require further Python packages to be available:

    • Linux servers 4.2.x or earlier require Pyinotify 0.7.x or Pyinotify 0.8.x. Some Linux distributions have one or other of these packages pre-installed. Some distributions of Pyinotify versions 0.8.6 and 0.8.7 are not compatible with Python 2.4. If your system runs Python 2.4 Pyinotify 0.8.5 or lower is recommended.
    • Linux systems running Python 2.4 also requires ctypes (bundled with Python 2.5+) which is available from http://python.net/crew/theller/ctypes/
    • 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.fs watches must be local to the given operating system. Watching a network-attached share (NAS) is strictly not supported.

OMERO DropBox

The first application of OMERO.fs is OMERO.dropbox which utilises 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 above prerequisites are met.

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.

Important 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 var/logs/FSServer.log and var/logs/DropBox.log will indicate success or otherwise of start-up of the two components. Once running, var/logs/FSServer.log will log file events seen within designated file areas and var/logs/DropBox.log will log the progress of any file imports.

Advanced use

OMERO.dropbox can be configured in several ways through 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 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 my_readers.txt will be imported for the user amy while the system-wide 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.

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"/>

The absolute directory path of interest for each user. The default is empty. 

    <property name="omero.fs.watchDir"  value=""/>

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"/>

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"/>

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=""/>

A list of subdirectories to ignore. Not currently supported. 

    <property name="omero.fs.blacklist"  value=""/>

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"/>

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"/>

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"/>

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"/>

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"/>

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=""/>

A string of extra arguments supplied to the importer. This could include, for example, an email address to report failed imports to: --report --send -email=test@example.com The default is empty. 

    <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.readers"         value="/home/amy/my_readers.txt;"/>
    <property name="omero.fs.importArgs"      value="-report;-report -send -email=zak@example.com"/>
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