Appendix 1 - OMERO.importer
2 Overview
The OMERO.importer is a user friendly client created to facilitate the import of data into the OMERO system. There are currently two ways to import your data into OMERO through the standalone client or from within OMERO insight. The instructions for the standalone importer are documented below and the instructions for the Insight Importer are available at insight-importer tutorial.
Launching OMERO.importer
- Locate the OMERO.Importer icon
on your
desktop. - Launch OMERO.importer by double clicking on the icon.
Upon launching the OMERO.importer you will be presented with the OMERO login screen.
2.2 The OMERO Login Screen
The OMERO login screen is common to all OMERO clients.
There are four main components to the screen.
The Server
List: This is where you can configure the list of servers the client can connect
to.
Secure Data
Transfer: Enabling this icon forces the client to transmit all data with
encryption.- Username: The username used to connect to the server.
- Password: The password to authenticate the account.
The Server List
The first step is to add a valid OMERO server to the server list. To do so click on the
icon. This
will bring up the following screen:
Now enter the following address as the OMERO server: omero.nbi.bbsrc.ac.uk and click APPLY.
Exercise 1:
- Try adding, removing and editing servers to the list.
Logging in
In your delegate pack you will have been given your OMERO login details. Fill in the username and password details in the appropriate sections. Once you have filled in you account details and selected the omero.nbi.bbsrc.ac.uk server from the server list, proceed to click on the LOGIN button.
The File Chooser Screen
The OMERO.importer file chooser screen is made up of two sections: (1) and (2).
* Section (1) is the local file system. * Section (2) is the current import queue.
Importing an Image
We will start by selecting a sample image to import to the OMERO server. Locate an image
file by using the local file browser, (1), and
navigate to the folder called Sample Data found on your Desktop. In this
folder select an image file. Then press the 
icon to add the
file to the import queue (2). This will bring up the
following screen:
To import an image it is necessary to specify ''how and where'' the image gets imported.
To specify ''where'' the image is uploaded you are asked to specify a Project and
Dataset to associate the image with. You can either select existing Projects/Datasets by
using the drop down menus, 
, or create new ones by clicking on the 
icons. The OMERO.importer
also allows you to choose ''how'' to handle file names.
- short version e.g. myImage.tiff
- full version e.g. C:importantWork/stuff/myImage.tiff
- customised version i.e. the short version plus a number of leading directories e.g. stuff/myImage.tiff
Exercise 2:
- Try adding more image files to the queue.
- Try removing images from the queue.
Once you have finished selecting images, press the Import button. You can view the progress in the ''Status'' column of the ''Import Queue''.
Exercise 3:
- Import all the data found in the Sample Data directory.
- Try creating new Projects and Datasets to import the new images to.
The Import History Screen
OMERO.importer includes a feature to record your import history, saving this information on the OMERO.server you are connected to. This feature allows you to import files, and then later upon review, re-import those same files if necessary. This is especially helpful if you are queuing and running an import at one location (for example, at work) and want to later review the status of your running import from somewhere else (for example, at home). You can also use this feature as a record of what files you have imported, to discover which files have failed to import so you can retry them later.
Using the History Feature
The importer History tab is divided into two general areas:
- The left hand 'side' panel allows you to search for your imports by date.
- The right hand 'main' panel displays the results of your search.
The Date Filter allows you to search for imports between a given date range, which you can either enter manually using the YY/MM/DD format, or by using the calender pop-up available by pressing the down arrow button. After you have selected a date range, hitting the 'Search' button will display all imports between those dates.
The Quick Date area allows you to quickly find imports for some of the more common date ranges such as 'Today', 'Yesterday', 'Last Week', etc. The list of imports under these tables will also show you the general status of that import with an icon: a green check mark indicates a fully successful import, whereas a yellow alert icon indicates one or more failed files in your imported file set. Selecting any of these import sets will automatically populate the right hand search results table with the files from that import session.
Re-Importing Your Images
Once you have filtered your import set by date and populated the right hand search results table, you can re-import any of the files displayed by clicking on that file and clicking the 'Reimport' button at the bottom of the window. Multi-selecting files on this list can be done using the standard method for your operating system (most typically the 'Shift' and 'Control' keys).
Exercise 4- Try reimporting one of your images.
Handling Import Errors
Although the OMERO.importer supports a large number of file formats, sometimes errors will occur in the import process. When this happens, OMERO.importer will generally present you with an error dialog and to alert you of the problem.
Examining Your Errors
When an error does occur, you can usually get a technical overview of the problem by examining the Debug Text tab. This may give you hints as to why your import failed, which can often be attributed to misplaced or renamed files, corrupted images, unsupported formats, or other easily fixed problems. For even more technical information you can also examine the importer's log file by choosing the Show log file location option under the Help menu. Opening this log file in a text editor will show you all the technical information collected during your import.
The Import Errors Tab
In cases where a file has failed to import, the error message generated is also added to the Error Message Queue, which can be found by clicking on the Import Errors Tab. From this tab, you can review all the import errors collected during the import session, as well as select which image files you wish to send us by using the check-box beside each error.
Submitting Errors
You can submit your errors to us using the Send Feedback button at the bottom of the Import Errors tab, which will display a feedback dialogue so you can include an optional message and email address. The bottom of this dialogue also gives you a chance to opt out of sending us your images and log file should you so desire, however providing us with this information will allow us to more accurately duplicate and fix your problem, thereby improving the reliability of our software as a whole.
[[Image:ImportErrorsFeedback.png|512px]]
