Contents
19. Download/Export/Downgrade
To test in: Web, Insight
Purpose of the test is to check the Download, Export and Downgrade features and the downloaded files - depending on whether archived image was created at import and whether this was an OMERO 5 import or OMERO 4 import.
Note: if several images have to be downloaded a zip will be created (Web and Insight) - this might take couple of seconds with no warning.
19.1. Download non-image files (both in OMERO 5 and OMERO 4)
To test in: Web, Insight
Import an image with a companion file e.g.
data_repo/test_images_good/dv/CFPNEAT01_R3D.dv
(or see column “Extra information” in [here
])Select the image, go to the right-hand panel, Acquisition tab, Companion files, and (Insight only) left-click on icon to the right of the filename to see a menu.
Check that you can see Info [DownloadED001:][DownloadED002:]and View the file
Download the Companion file [DownloadED003][DownloadED004] - open downloaded file in text editor,
Check that the size is not zero.[DownloadED005]
Download the metadata file created by OMERO i.e.
original_metadata.txt
[original_metadata.txt
] (Web only - Acquisition tab) [DownloadED007:].Download the original metadata file using the menu item under the icon above right-hand pane (Insight only) [DownloadED007b:].
Check the downloaded file [
008
].Download the companion files as well as original metadata both into your home directory as well as to your Desktop.
19.2. OMERO 4 Download/Export images
To test in: Web, Insight
Import an image - tick the “Archive” option after putting it into the Queue [DownloadED009:] (Insight only)
When the import is finished, select the image
Go to the right-hand panel General tab,
Check that you see the image is shown as
Archived
in Insight [DownloadED010a:].in Insight, press the Saving icon (2nd from right) and choose Download.[DownloadED010b:].
in Web click on the arrow in General tab [DownloadED011].
Download both into your home directory as well as to your Desktop.
Check that the image has correctly been downloaded [DownloadED012].
Re-import the image: import in Insight, but check in Web as well.
Check Compare the image originally imported and the re-imported image (check also the metadata) [DownloadED013].
Import an image composed of several files, e.g. test_images_good/lei/leica-original/050118.lei - tick the “Archive” option after putting it into the Queue [DownloadED009:] (Insight only).
Select the download option on the right-hand side.
Download the image - a zip will be created [DownloadED013b].
Download both into your home directory as well as to your Desktop.
Check that the image has been downloaded correctly [the screenshot shows the expected situation after 1st image of the 56 images of the 050118.lei set was selected & downloaded].
Re-import the image: import in Insight, but check in Web as well.
Compare the image originally imported and the re-imported image (check also the metadata).
- Now Select an image which had the “Archive” option off at import. If not sure, re-import an image with the “Archive” option off.
Check that you see the image is not shown as
Archived
in Insight [DownloadED013d].Check that the Download option is not available neither in Insight (greyed out) [DownloadED013e] nor Web (menu item missing) [DownloadED013f].
19.3. OMERO 5 Download/Export images (perform on OMERO 5 server with OMERO 5 imported data only database)
To test in: Web, Insight
OMERO 5-Single image
Import an image
Select the download option on the right-hand side [DownloadED010b:, FSDownloadED011]
Download the image both into your home directory as well as to your Desktop.
Check that the image has been correctly downloaded [DownloadED012]
Re-import the image.(import in Insight, but check in Web as well)
Compare the image originally imported and the re-imported image (check also the metadata) [DownloadED013].
OMERO 5-multi-image - repeat the “OMERO 5-Single image” step importing a multi-image file (e.g. test_images_good/lei/leica-original/050118.lei).
Check that the whole multi-image fileset (MIF) has been downloaded. See [example of test_images_good/lei/leica-original/050118.lei when 1st image only was selected.].
19.4. Mixed OMERO 5 imported & OMERO 4 imported images Download/Export (this is to be performed on OMERO 5 server with a database consisting of OMERO 5 as well as OMERO 4 imported images)
To test in: Web, Insight
Choosing images imported using OMERO 4 and skipping importing, go through the “18.2 OMERO 4 Download/Export images:” step. The images have to have been Archived during OMERO 4 import, look for example for Datasets like
archivedv
.Go through the “18.3 OMERO 5 Download/Export images” step.
19.5. Downgrade
To test in: Web, Insight
When performing the following steps, export both into your home directory as well as to your Desktop.
Select an image and go to the right-hand panel.
Export the image as JPEG (Web & Insight) [DownloadED016, DownloadED017:], PNG (Insight only), TIFF (Insight only)
Check the result
Export the image as OME-TIFF [DownloadED017b:, DownloadED017c:]
for Web, just export and check the file - for Insight, see below
(Insight only) Check that when you select a single big image or select couple of images which consist of big and small images, the
Export as OME-TIFF
option is greyed outExport using the current schema:[DownloadED018:] (Insight only)
Check the exported file,
Check Open the file
Check the XML section the schema version should indicate the latest version e.g. 2012..[DownloadED019].-Do it from command line [tiffinfo command from libtiff library - download tiffinfo using Homebrew][DownloadED020]
Export using an older schema:(Insight only)
Check the exported file
Check Open the file
Check the XML section, the schema version should match the selected schema.[DownloadED021] - Check from command line using tiffinfo
Re-Import the exported files
(OME-TIFF only) Check that the re-import does not take longer than the import of the original file from which the ome-tiff was generated.
19.6. Command line download
Go to the command line,
cd
to your downloaded server and connect to the testing server (e.g. gretzky). and try to download files using following commands.bin/omero download file_id target
bin/omero download OriginalFile:file_id target
bin/omero download FileAnnotation:fa_id target
bin/omero download Image:image_id target
Using these commands, download
Multi-image filesets (MIFs), for example
lei
Archived pre-OMERO 5 images (look for example for Datasets like
archivedv
).OMERO 5 imported images
Original files/Companion files (of for example
.dv
files)File annotations
Check that the files are downloaded in the
target
file after each command.