Classpath issues with Jackson in KNIME

[miguelalba]

Hi all,

I am having trouble to deserialize JSON in KNIME but the same code works outside KNIME in a unittest.

The design is fairly simple. An interface EnvironmentManager with a single getEnvironment method that prepares an environment where to run a model. This interface is implemented by,

• ExistingEnvironmentManager if the directory already exists and only this directory is kept (does nothing)
• ArchivedEnvironmentManager if the resources are contained in a zip archive and need to be extracted to a temporary folder
• FilesEnvironmentManager: if the resources are hand picked by the user and put together in a temporary folder as environment.

In my workflow, the environment of a model stored in a JSON file in the port object looks like:

{
  "@class":"de.bund.bfr.knime.fsklab.nodes.environment.ArchivedEnvironmentManager",
  "archivePath":"C:\\Users\\de\\knime_workspace\\simple\\FSKX Reader (#1)\\drop\\201912090707_PiresOutbLA2011-Salmonella.fskx",
  "entries":[
    "/proportions-period-1.csv",
    "/P-estimates.csv",
    "/proportions-period-2.csv",
    "/Salmonella-all.csv"
  ]
}

This instance can be deserialized with this snippet which fails when I include it in the load method of the serializer of my port object.

File file = new File("C:/Users/de/Desktop/workingDirectory");
EnvironmentManager deserializeManager = mapper.readValue(file, EnvironmentManager.class);
System.out.println(mapper.writeValueAsString(deserializeManager));

This snippet throws InvalidTypeIdException with message

Could not resolve type id ‘de.bund.bfr.knime.fsklab.nodes.environment.ArchivedEnvironmentManager’ into a subtype of [simple type, class de.bund.bfr.knime.fsklab.nodes.environment.EnvironmentManager]: no such class found

Thanks a lot!
Miguel

[swebb]

This sounds similar to an issue I’ve had a few years ago (so a bit hazy on the details). I think my issue was caused by OSGi classpaths and Jackson not having access to the classes provided in another plugin which are provided by a different ClassLoader(?).

Sorry it’s not more helpful but maybe a pointer in the right direction?

Cheers

Sam

[gab1one]

@swebb

Jackson not having access to the classes provided in another plugin which are provided by a different ClassLoader(?).

Yes, that seems to be the case, especially considering you wrote this:

@miguelalba

I am having trouble to deserialize JSON in KNIME but the same code works outside KNIME in a unittest.

Where is the Jackson library located? Are you loading it from a bundle?

best,
Gabriel

[miguelalba]

Thanks Gabriel and Sam,

I am loading Jackson from the KNIME target with the dependencies

com.fasterxml.jackson.core.jackson-annotations;bundle-version=“2.8.9”,
com.fasterxml.jackson.core.jackson-core;bundle-version=“2.8.9”,
com.fasterxml.jackson.core.jackson-databind;bundle-version=“2.8.9”,

For testing separatedly out of KNIME I included in this unittest the snippet above to read the JSON from a file

[swebb]

The out of KNIME test that works is still using an OSGi dependency for jackson?

That to me would indicate it’s not inherently an issue through loading in different OSGi plugins then unless this is handled different for the test code.

I’d be tempted to test out quickly deploying jackson libs manually into your plugin doing the deserialisation just to double check though.

Again sorry it’s not particularly helpful

[gab1one]

You can test the eclipse dependency resolution / classloading if your run the unit test as a Junit plug-in test. That is an option that should be available to you in the run as context menu.

best,
Gabriel

[miguelalba]

I fixed it!

I had to remove the JsonSubTypes annotation. Maybe I made an error there but Jackson still deserializes even without it.

@JsonTypeInfo(use = Id.CLASS, include = As.PROPERTY)
//@JsonSubTypes({
//  @Type(value = ExistingEnvironmentManager.class, name="ExistingEnvironmentManager"),
//  @Type(value = ArchivedEnvironmentManager.class, name="ArchivedEnvironmentManager"),
//  @Type(value = FilesEnvironmentManager.class, name="FilesEnvironmentManager")
//})
public interface EnvironmentManager {
  
  @JsonIgnore
  Optional<Path> getEnvironment();
}

Best,
Miguel