41. OMERO.searcher

To test in: Web

Purpose of the test is to check that the OMERO.searcher as an OMERO.Web application is functioning correctly.

NB: Because the image features are being stored in two different places, which may occasionally get out of sync, it is important to run the Omero searcher Rebuild Content DB script in following cases:
  • after you deleted features

  • after you got an error when calculating features normally (= as described in step 2 below)

  • after you disabled content DB update (by ticking a box in the feature calculation script, see step 4 below)

  1. Login to the server mentioned in PR or testing setup.

  2. Run the Feature Calculation script “normally”

    • Select an image and go Scripts > searcher > Omero searcher feature calculation [OMERO.searcher001a:]

    • In the script dialog, make sure you tick Advanced Features and Recalculate Existing Features [OMERO.searcher001b:]

    • Do not tick Disable ContentDB Update [OMERO.searcher001b:]

    • Check that an attachment was created with the calculated features (cannot be viewed atm)

  3. Run 2 Feature Calculation scripts in parallel with an error

    • make sure you have 2 projects or datasets ready with many images in each of them

    • start the Feature Calculation script as in step 2 above on one of the 2 P/Ds

    • immediately (when the previous calculation is still in progress) start a second Feature Calculation script running on the other P/D

    • Check that you get an error in the script run saying something like WARNING:omero.gateway:OptimisticLockException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'>

  4. Run 2 Feature Calculation scripts in parallel without any error

    • repeat step 3, this time checking the box Advanced Features, Recalculate Existing Features AND Disable ContentDB Update in both script runs [OMERO.searcher002]

    • Check that this time both scripts ended successfully and the attachments on images inside the datasets (not on the datasets themselves) were created

  5. Run Rebuild Content DB script

    • Go Scripts > searcher > Rebuild Content DB

    • Check that the script ended up successfully [002b].

  6. Search for images

    • Select an image which you have calculated the features for.

    • Go to the searcher tab (right-hand pane).

    • Select the Featureset for which you Rebuilt Content DB [OMERO.searcher003]

    • Click Do Search

    • Check that a list of images was found in the middle panel

  7. Refine search

    • In the list of images found in previous step, select the positive and negative examples to refine your search (click the radio button)

    • Click the Refine Search button in the left-hand pane

    • Check that the search results match now better the original image

    • Change the Retrieved images number from 100 to 20

    • Click Refine Serach

    • Check that the results are now identical with the top 20 results of the previous search

    • Change the Retrieved images number back to 100

    • Check that after click on “Refine Search” you get the same results as before

    • Check that there are no duplicates in the search results

    • Check that the images you deemed to be negative do not appear in the search results or appear near the end of the search results if there are not many images in the database.

  8. Additional search filters

    • Click Enable additional search filters (may slow down queries).

    • Deselect some of the Projects / Datasets

    • Click Refine Search

    • Check that the search results are filtered as intended

  9. Change group in OMERO.web (from a default group to non-default group or the other way round) and start a new search

    • Check that the search results are taken only from the group you have on display, not the other group.

      ../_images/001a1.png

      OMERO.searcher001a:





























      ../_images/001b1.png

      OMERO.searcher001b:





























      ../_images/00221.png

      OMERO.searcher002





























      ../_images/00317.png

      OMERO.searcher003