Mica not showing harmonization status in harmonization protocol

[Sofia Siampani]

Hi,

Our Mica server was updated this morning to 5.2 and reading the documentation I see that the Opal dependency as the main data provider has been removed. Since then, we are unable to see the harmonization status of the variables in each study that is part of the harmonization protocol. Unfortunately, I didn't capture a screenshot cause in an attempt to rectify the issue, I deleted the studies in the Study-Specific Tables.. However, I see that the same issue applies in the mica demo server https://mica-demo.obiba.org/dataset/chpt-generic-ds. Now, when I try to input a new study in the harmonization protocol I get an error. (see attachment). 

Your help on the matter is greatly appreciated!

Thanks,

Sofa

[Ramin H.A.]

Hi Sofia,

The problem may be related to taxonomies in Mica. We will take a look and get back to you.

Best,

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[Ramin H.A.]

Hi Sofia,

There is a new release Mica 5.2.1 that fixes the issue.

Here are few things to check after installation:

• Go to Administration / Taxonomies section
• Make sure you see a list of taxonomies and the ones you need are visible (eye icon crossed)

Best,

[Sofia Siampani]

Hi Ramin, 

Thank you for the quick action. The issue in our mica (https://mica.mdc-berlin.de/) seems partly resolved. I can now add the studies back with no error but the harmonization status is not shown in the harmonization protocol level. I can, however, see it in the variable level. I have checked the Taxonomies section and can se the Harmonization tab with an eye icon crossed. Also, I can no longer see the Variables Classification tab. See attachments. 

[Ramin H.A.]

Hi Sofia,

The problem is resolved, you need to install the latest version of mica-search-es version 1.4.1. Either you or the administrator must follow the following steps:

• Stop Mica
• Go to Mica home folder on the server

  If Mica is installed via a package the home folder is under /var/lib/mica2
  If mica is installed via Docker, the home folder is under MICA-DOCKER-VOLUME

• Go to plugins folder
• Delete the current mica-search-es-* folder

  You can also move this folder somewhere else in case you have custom settings in the site.properties file… to copy them onto the new version later

• Start Mica to automatically download the latest version
• Once Mica is up and running, go to Administration / Indexing Section
• Click on All to index all Mica documents
• Index once more Individual Studies / Harmonization Initiatives to update the inferred study annotations (new in 5.2.0)

The problem should be resolved.

Best,

To view this discussion on the web visit https://groups.google.com/d/msgid/obiba-users/73e69368-a7a1-491f-8f87-260d70c4812cn%40googlegroups.com.

[Ramin H.A.]

Hi Sofia,

Just a little note, here is another way to update your plugin via the Python Plugin command. 

Ramin