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).

  • 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).

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 out

    • Export 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

  1. 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.

      ../_images/0017.png

      DownloadED001:





























      ../_images/0026.png

      DownloadED002:





























      ../_images/0035.png

      DownloadED003





























      ../_images/0045.png

      DownloadED004





























      ../_images/0054.png

      DownloadED005













































      ../_images/0072.png

      DownloadED007:






























      ../_images/007b.png

      DownloadED007b:




























      ../_images/0092.png

      DownloadED009:





























      ../_images/0103.png

      DownloadED010:






























      ../_images/010a.png

      DownloadED010a:





























      ../_images/010b.png

      DownloadED010b:




























      ../_images/0112.png

      DownloadED011


































      ../_images/FS011.png

      FSDownloadED011




























      ../_images/0122.png

      DownloadED012





























      ../_images/0132.png

      DownloadED013






























      ../_images/013b.png

      DownloadED013b






























      ../_images/013c.png

      the screenshot shows the expected situation after 1st image of the 56 images of the 050118.lei set was selected & downloaded






























      ../_images/013d.png

      DownloadED013d






























      ../_images/013e.png

      DownloadED013e






























      ../_images/013f.png

      DownloadED013f































      ../_images/013p.png

      example of test_images_good/lei/leica-original/050118.lei when 1st image only was selected.






















      ../_images/0142.png

      DownloadED014:





























      ../_images/0152.png

      DownloadED015:





























      ../_images/0162.png

      DownloadED016





























      ../_images/0171.png

      DownloadED017:






























      ../_images/017b.png

      DownloadED017b:






























      ../_images/017c.png

      DownloadED017c:





























      ../_images/0181.png

      DownloadED018:





























      ../_images/0191.png

      DownloadED019





























      ../_images/0201.png

      DownloadED020





























      ../_images/0211.png

      DownloadED021