22. General Release

Purpose of the test is to make sure the particular application on the release day is built correctly, starts, connects and opens an image as expected (when applicable).

Click onto the application you are assigned to test in the Contents above

22.1. OMERO.clients

  1. Download and open the application and login as any user

    • (all platforms) Check other Ice versions of OMERO.insight*.zip files on artifacts page.

    • (all platforms) Check one of the OMERO.importer*.zip files on artifacts page

    • (Windows only) Check that there is no “exe4j” popup prior to Insight splashscreen.

    • (all platforms) Check that the application starts and you can log in.

    • (all platforms, Insight only) Check that you can expand a dataset and open an image with multi-z (Choose one of the .dv images in datasets named like archived dv or non-archived dv - present in almost every user/group.)

    • (all platforms, Insight only) Check that you can click onto the Projection tab in the opened image.

    • (all platforms) Check that you can execute any script.

    • (all platforms) Check that you can delete the image.

22.2. IJ/Fiji Plugin

  1. Follow Insight as Plugin ImageJ/Fiji

22.3. OMERO.server

  1. Download the appropriate OMERO.server*.zip and unzip the downloaded file.

  2. Configure the server.

  3. Start the server and the web server.

    • Check that the server starts as expected.

  4. Download and open OMERO.insight and go to the appropriate port address in your web browser to login to OMERO.web.

  5. Login in OMERO.insight and OMERO.web connecting to the server you just started.

    • Check that the clients connect to the server and login is successful.

    • Check that DropBox imports a file successfully

    • Check that you can execute (any) script using (any) client

22.4. OMERO.matlab toolbox

  1. Install Matlab (development).

  2. In order to be able to execute the testing commands in Matlab, perform the necessary steps in the workflow described in Matlab docs using the build indicated in the Standup Notes. Then, execute in Matlab (hostname, username, password and imageID needs to be substituted by valid values):

    client = loadOmero(hostname);
    % to use a different port than the default one.
    % client = loadOmero(hostname, port);
    session = client.createSession(username, password);
    image = getImages(session, imageID);
    plane = getPlane(session, image, 0, 0, 0);
    datasets  = getDatasets(session);
    figure; imshow(plane, []);
    client.closeSession();
    
  3. After you have executed the above commands,

    • Check that all 7 commands executed without errors.

    • Check that after figure; imshow(plane, []); the image is displayed in Matlab.

  4. Go to Matlab docs and find the paragraph Create a Dataset... under Writing section. Follow the commands to create a Dataset and link it to a Project.

    • Check that a Dataset was created.

  5. Go to Matlab docs and find the paragraph Creating ROI under ROIs section. Follow the commands to create a ROI and link it to an Image.

    • Check that a ROI was created.

  6. Go to Matlab docs and find the section Deleting data. Follow the commands to Delete an Image, a Dataset and a Project.

    • Check that the I/D/P was deleted.

22.5. OMERO Virtual Appliance

  1. This section is only valid for testing versions prior to 5.2.2.

  2. Follow the Virtual Appliance docs to get the Virtual Appliance started - skip the steps as appropriate in case you have already installed Virtual Box.

  3. Start OMERO.insight and OMERO.web as described in the docs and try to login.

    • Check that Insight and Web start okay and you can login successfully.

    • Check that you can import and then open a small image (any small image will do).

22.6. Bio-Formats MATLAB/Octave

Warning

Milestone or SNAPSHOT versions cannot be tested using the version of GNU Octave installed by the Ubuntu 16.04 package manager (4.0.x) as only versions of the format x.y.z are accepted by the implementation (https://wiki.octave.org/OEP:pkg#version_definition).

System installation

  1. Install MATLAB or GNU Octave on your operating system using the appropriate downloads or package manager.

  2. Install the Bio-Formats MATLAB toolbox or the Bio-Formats Octave package.

  3. Download one of our sample images. Alternatively, use any small image on your local disk or on squig.

  4. Follow the instructions here up to and including the section Displaying images.

    • Check that the image opens as expected.

  5. Set the root logger to DEBUG level:

    loci.common.DebugTools.setRootLevel('DEBUG');
    
  6. Reopen the image using the same commands as previously.

    • Check that the amount of logging increases in the MATLAB command prompt.

Docker (GNU Octave only)

  1. Clone https://github.com/openmicroscopy/bio-formats-octave-docker, update the VERSION argument and build the Docker image:

    $ docker build -t bio-formats-octave  .
    
  2. Download one of our sample images. Alternatively, use any small image on your local disk or on squig.

  3. Run the travis_test.m on the image e.g.:

    $ docker run -ti -v /data/:/data/ bio-formats-octave travis_test.m /data/tubhiswt-2D/tubhiswt_C0.ome.tif
    
    • Check that the image opens as expected.

    • Check that the amount of logging increases in the second execution.

22.7. Bio-Formats: ImageJ/Fiji testing

ImageJ

  1. Use ImageJ for this section, not Fiji.

  2. Remove any previous bioformats_package.jar or loci_tools.jar files from your ImageJ Plugins folder. Put the freshly downloaded bioformats_package.jar into the Plugins folder of ImageJ and start ImageJ.

    • Check that there is a LOCI menu item under the Plugins menu and when you select it, the submenu asks you to use Bio-Formats menu.

    • Check that there is a Bio-Formats menu item under the Plugins menu.

  3. Select Plugins > Bio-Formats > Bio-Formats Importer and import a small image (any small image will do).

    • Check that the image imports successfully.

  4. Leave the imported image open in ImageJ and Select Plugins > Bio-Formats > Bio-Formats Exporter and export this image.

    • Check that the image exports successfully.

  5. Select Plugins > Bio-Formats > Bio-Formats Remote Importer and paste the URL https://downloads.openmicroscopy.org/images/DV/U2OS/U2OS_Eg5_PH3_001_R3D.dv into the first dialog that pops up.

    • Check that the image imports successfully.

  6. Select Help > About Plugins > Bio-Formats Plugins...

    • Check that the URLs shown in the popup link to existing and sensible pages.

    • Check that the release version and date are correct.

Fiji

This testing assumes the release artifacts have been deployed to the Bio-Formats update site.

  1. Use Fiji for this section, not ImageJ.

  2. Activate the Bio-Formats update site Help -> Update… -> Manage update sites in addition to the Java-8 update site.

  3. In the ImageJ Updater Window ensure that the plugins/bio-formats_plugins.jar file and jars in the jars/bio-formats folder are listed for update.

    • Check check that the Update Site for each is listed as the Bio-Formats update site.

    • Check the Status/Action field for each should be set to Install it or Update it.

    • Check click on Advanced Mode, then select each file and ensure the date and version in the Details panel is correct.

  4. Select Help > About Plugins > Bio-Formats Plugins...

    • Check that the URLs shown in the popup link to existing and sensible pages.

    • Check that the release version and date are correct.

  5. In the ImageJ Updater Window select Apply Changes to run the update and restart FIJI

  6. Select Plugins > Bio-Formats > Bio-Formats Importer and import a small image (any small image will do).

    • Check that the image imports successfully.

  7. Leave the imported image open in ImageJ and select Plugins > Bio-Formats > Bio-Formats Exporter and export this image.

    • Check that the image exports successfully.

  8. Select Plugins > Bio-Formats > Bio-Formats Remote Importer and paste the URL https://downloads.openmicroscopy.org/images/DV/U2OS/U2OS_Eg5_PH3_001_R3D.dv into the first dialog that pops up

    • Check that the image imports successfully.

22.8. Bio-Formats command-line tools

  1. Download and unzip the bftools.zip.

  2. Move into this folder.

  3. Execute the bfconvert command on the cmd line, for example:

    $ touch test.fake
    $ ./bfconvert test.fake test.ome.tiff
    
    • Check that a new image with the name you chose and the chosen extension (for example .ome.tiff) was created.

  4. Execute the showinf command on the cmd line, using the .ome.tiff image created in previous step

    $ ./showinf -version
    
    • Check that the correct version, revision and build date are returned after the first command.

    $ ./showinf <image_path>
    
    • Check that the image in the <image_path> in the second command opens.

    $ ./showinf -omexml <image_path>
    
    • Check that the image in the <image_path> in the second command opens, the OME-XML is validated and displayed

22.9. Downloads page

  1. Go to the downloads page and

    • Check the general layout (no gross misformattings or similar)

    • Check that clicking on all links in the text everywhere (e.g. like to the docs in the first paragraph, in the explanatory texts under the download blocks) will bring you to the advertised place.

    • NO NEED to download the clients or servers

    • Check that you can download the Source code, OMERO API documentation, OMERO Java Downloads, OMERO Python Downloads

    • Check Source code links