|
FS
OMERO.fsOMERO.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 DropBoxThe 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 DropBoxIn its default configuration the monitored area of the file system is a
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 filesThe log files Advanced useOMERO.dropbox can be configured in several ways through 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. One example alternative configuration would be to watch specific directories for specific users. In the example below two directories are monitored, one for user
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,
Here only the image types listed in For a full description of the properties see below. PropertiesEach 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
The absolute directory path of interest for each user. The default is empty.
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
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
A list of file extensions of interest. An empty list implies all file extensions are monitored. The default is an empty list.
A list of subdirectories to ignore. Not currently supported.
This timeout in seconds is used by one-shot monitors. This property is not used by DropBox.
The number of events that should be propagated to DropBox in one go. Zero implies all events possible. The default is zero.
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
If this is True then the creation and modification of subdirectories is not reported to DropBox. The default is 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.
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.
A string of extra arguments supplied to the importer. This could include, for example, an email address to report failed imports to:
ExampleHere's a full example of a configuration for two users:
Document Actions |