[inception-users] INCEpTION 21.1

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Richard Eckart de Castilho

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Oct 19, 2021, 11:52:42 AM10/19/21
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INCEpTION 21.1

We are pleased to announce the release of INCEpTION 21.1.

INCEpTION is an extensible web-based collaborative environment for text annotation. It integrates machine-learning-based annotation support, knowledge base management and corpus building into a single comprehensive platform.

This is a bug fix release.

Notable changes

  • 🦟 #2654 - Fix to programmatically created AnnotationLayers not being curatable by default by @reckart in #2661
  • 🦟 #2655 - Fix to curated CASes being exported to the wrong spot by @reckart in #2662
  • 🦟 #2653 - Fixed to ReferenceError: fragment is not defined by @reckart in #2663
  • 🦟 #2666 - Fix to CoNLL 2000 and CoNLL 2002 format IDs being mixed up by @reckart in #2668
  • ⭐️ #2667 - Add format IDs to format documentation by @reckart in #2669
  • ⭐️ #2650 - Multi-platform docker image by @reckart in #2651

If you discover problems with this release, please report them to us via our issue tracker [2].

Thanks to the INCEpTION 21.1 team: @reckart@jcklie@Falko1

Also thanks to all issue reporters, beta testers, feature suggesters, and users!

Download

The new version can be downloaded from our website [3].

Important upgrade notes

An in-place upgrade from INCEpTION 21.0.1 to 21.1 is possible.

Back up your data before the upgrade [4].

If you upgrade from a version older than 20.0, please check the update notes for INCEpTION 20.0 [7].

If you are using MySQL or MariaDB, please ensure that default row format is set to dynamic, otherwise, you may get an error like this during upgrade:

Error creating bean with name 'liquibase' defined in class path resource [org/springframework/boot/autoconfigure/liquibase/LiquibaseAutoConfiguration$LiquibaseConfiguration.class]: Invocation of init method failed; nested exception is liquibase.exception.LiquibaseException: liquibase.exception.MigrationFailedException: Migration failed for change set de/tudarmstadt/ukp/inception/preferences/model/db-changelog.xml::20210925-1::INCEpTION Team:
     Reason: liquibase.exception.DatabaseException: (conn=242839) Index column size too large. The maximum column size is 767 bytes. [Failed SQL: (1709) ALTER TABLE `inception-testing`.default_project_preference ADD CONSTRAINT UK_default_project_preference_name_project UNIQUE (project, name)]

To set the default row format, you can add these settings to your MySQL/MariaDB config file and then restart the database:

innodb_strict_mode=1
innodb_default_row_format='dynamic'

Publication

An overview of INCEpTION can be found in

Klie, J.-C., Bugert, M., Boullosa, B., Eckart de Castilho, R. and Gurevych, I. (2018):
The INCEpTION Platform: Machine-Assisted and Knowledge-Oriented Interactive Annotation.
In Proceedings of System Demonstrations of the 27th International Conference on Computational Linguistics (COLING 2018), Santa Fe, New Mexico, USA

PDF and BibTeX as well as more publications on specific features are
available from our website [5].

License and System requirements

INCEpTION is provided as open source software under the Apache License version 2.

Running INCEpTION requires Java version 11 or higher.

By default, INCEpTION uses an embedded database which is sufficient for testing. However, the use of a MariaDB database is recommended.

INCEpTION works best with Chrome and Safari.

-- The INCEpTION developer team

Lindeberg Leite

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Oct 23, 2021, 12:30:43 PM10/23/21
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Hello everybody,

I'm running the Inception in two containers: 1 container with Inception and persistent storage (file system) and another container running mariadb without persistent storage. I had a problem with the mariadb container and it was restarted. (I lost the data from there)

I can start Inception normally, however, I can no longer see my previous projects. I know that this problem is because I don't have the metadata that was stored in the mariadb container. 

My question is: Can I recover my projects in this scenario? I checked the persistent storage (file system) and I can see the projects and annotations.
 
Thanks in advance,
Lindeberg



Richard Eckart de Castilho

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Oct 23, 2021, 12:38:51 PM10/23/21
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On 23. Oct 2021, at 18:30, Lindeberg Leite <lindp...@gmail.com> wrote:
>
> My question is: Can I recover my projects in this scenario? I checked the persistent storage (file system) and I can see the projects and annotations.

You could probably recover the most important data - namely the essentials which are required to get access back to your annotations.

First, I'd recommend you make a backup to keep the files in a safe space.

Assuming you would manage to set up a project that contains the same layers / features / users as the original project, you should be able
to copy the "ser" files into that project and INCEpTION should be able to load them again.

That said, you might not remember which layers/features/users a project might have had. There are log files for each of the projects
that you might be able to glean such informations from.

That said, such an approach is quite a bit of manual work...

If you have a large number of projects to recover, it could be worth investigating how much of that process could be automatized.

Cheers,

-- Richard

Lindeberg Leite

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Oct 28, 2021, 1:56:16 PM10/28/21
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Thank you for your reply, Richard !

I was able to recover a small project that I've created for a test only.

However, I'm having trouble recovering the real projects. I have 4 projects that I need to recover. I'm trying to recover one by one. In the first project, I have 1000 documents.

First, I created a new project and set up the layers, features and users. After that, I copied the .ser files into the project. I also uploaded the documents.  I couldn't copy the documents to the project as I did with the .ser files, I had to import them through the Inception interface

After all, I tried to open an annotated document. However, the annotations didn't appear. 

A detail: I didn't copy all the .ser files into the project at once as there are too many of them. But I only open documents where I know the .ser files have been updated (just to test if it works, i think it's not a problem to just copy some documents or users )

Do you think I missed something?

Lindeberg


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Richard Eckart de Castilho

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Oct 28, 2021, 2:12:38 PM10/28/21
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Hi,

> On 28. Oct 2021, at 19:56, Lindeberg Leite <lindp...@gmail.com> wrote:
>
> I was able to recover a small project that I've created for a test only.
>
> However, I'm having trouble recovering the real projects. I have 4 projects that I need to recover. I'm trying to recover one by one. In the first project, I have 1000 documents.
>
> First, I created a new project and set up the layers, features and users. After that, I copied the .ser files into the project. I also uploaded the documents. I couldn't copy the documents to the project as I did with the .ser files, I had to import them through the Inception interface

Right, you need to import the documents through the UI because that is creates the necessary metadata in the database.

> After all, I tried to open an annotated document. However, the annotations didn't appear.
>
> A detail: I didn't copy all the .ser files into the project at once as there are too many of them. But I only open documents where I know the .ser files have been updated (just to test if it works, i think it's not a problem to just copy some documents or users )
>
> Do you think I missed something?

The database would normally contain a record for each document that the users have annotated. This record would include e.g. the state of the document (whether it is in-progress or finished). But I am pretty sure that record should be created automatically on-demand when you open a document. Then - if a `.ser` file is already present (because you put it there), it should be used instead of being re-created.

Could you privately (off-list) send me an export of the project that you set up containing only one document and separately a single annototator `.ser` file that belongs to the document in that project?

Cheers,

-- Richard

Lindeberg Leite

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Oct 29, 2021, 2:14:02 PM10/29/21
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Sure, Richard.

I've just sent the export of the project to you.

Thank you very much for this help.

Lindeberg


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