Zobrazují se příspěvky se štítkemJAX-RS. Zobrazit všechny příspěvky
Zobrazují se příspěvky se štítkemJAX-RS. Zobrazit všechny příspěvky

pátek 6. října 2017

REST Web Services with Jackson, Jersey and Payara Micro ... Level II

So ... I will continue with experiments started here and do some real work ... I continued to extend the API introduced in the recent blog, and I encountered some new problems ... for example I could not send a java.util.List in REST response with the same error as I already resolved in the request and also dates were only serialized (have you ever tried to serialize the GregorianCalendar instance?).
So i started to search on StackOverflow and found several solution - but neither one worked or at least it was not easy and nice. Then I started to think how it all works ... ;-)
Now I will stop talking, see the solution. I created new implementation of the web service to be more comprehensible what it does:

Jackson and Jersey

I am so dumb, do you know that? I mixed up these two names so long! So, what is the difference?
  • Jersey is the reference implementation of JAX-RS API. Nothing more to say. THE core. It's home is here
  • Jackson enhances the Jersey with much more stuff to be really usable. It's home is here
And this is a part of pom.xml of the web services war; versions are defined in some parent POM:
    
    <!-- to use ResourceConfig class -->
    <dependency>
      <groupid>org.glassfish.jersey.core</groupid>
      <artifactid>jersey-server</artifactid>
    </dependency>
    <!-- to use JDK8 and other features, like java.time API or automatic ISO time formatting -->
    <dependency>
      <groupid>com.fasterxml.jackson.datatype</groupid>
      <artifactid>jackson-datatype-jdk8</artifactid>
      <scope>compile</scope>
    </dependency>
    <dependency>
      <groupid>org.apache.logging.log4j</groupid>
      <artifactid>log4j-api</artifactid>
      <scope>provided</scope>
    </dependency>
    <dependency>
      <groupid>org.apache.logging.log4j</groupid>
      <artifactid>log4j-core</artifactid>
      <scope>provided</scope>
    </dependency>
    <dependency>
      <groupid>org.apache.commons</groupid>
      <artifactid>commons-lang3</artifactid>
      <scope>compile</scope>
    </dependency>

    <!-- to have better javadocs than in javaee-api -->
    <dependency>
      <groupid>javax.ws.rs</groupid>
      <artifactid>javax.ws.rs-api</artifactid>
      <scope>provided</scope>
    </dependency>    

    <!-- to have all Java EE 7 specifications in one dependency, but to have also the older javadoc -->
    <dependency>
      <groupid>javax</groupid>
      <artifactid>javaee-api</artifactid>
      <scope>provided</scope>
    </dependency>
    

ResouceConfig class

This class should be in root package of all your REST services - see calling of the method named packages in the constructor, that is the magic; it enables the annotation processing. And you know, there is more magic hidden in Maven dependencies not enabled by default. What I didn't know in first blog is that even Jackson is already in Glassfish/Payara (but not everything, see the dependencies again!).

package org.dmatej.experiment.rest;

import javax.ws.rs.ApplicationPath;
import org.glassfish.jersey.server.ResourceConfig;
 

@ApplicationPath("") // use the application root
public class RestAppConfig extends ResourceConfig {
  public RestAppConfig() {
    packages(//
        RestAppConfig.class.getPackage().getName(), // search annotations in this class's package
        "com.fasterxml.jackson"// search in jackson's package
    );
  }
}

ContextResolver interface 

We enabled Jersey and Jackson, but that was not enough! Now we have to enable also the Jackson's extension modules.

package org.dmatej.experiment.rest;

import javax.ws.rs.ext.ContextResolver;
import javax.ws.rs.ext.Provider;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
 

@Provider
public class ObjectMapperContextResolver implements ContextResolver {

  private final ObjectMapper MAPPER;

  public ObjectMapperContextResolver() {
    MAPPER = new ObjectMapper();

// This did not find the Jdk8Module
    MAPPER.findAndRegisterModules();
    // enables ISO time parsing and formatting in REST communication.
    MAPPER.registerModule(new Jdk8Module());

    MAPPER.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
  }

  @Override
  public ObjectMapper getContext(Class type) {
    return MAPPER;
  }
}

And now the web service

Now it is pretty trivial and it will do what I expected. No unexplainable errors.

I think this blog entry is big enough and the implementation of Measurement transfer object is trivial, also MeasurementSaveResponse is trivial - it contains list of invalid records and some monitoring data.

The problem was the list - Jersey accepted list as a parameter but had thrown an exception if the list was in the response. Now I don't even need ArrayList in parameters and I can declare an abstract List. It also seems that those transfer objects don't need to have a complete set of getters and setters; Jersey uses reflection.

package org.dmatej.experiment;

import java.time.LocalDateTime;
import java.time.ZoneId;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;

import javax.ejb.EJB;
import javax.ws.rs.Consumes;
import javax.ws.rs.POST;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.core.GenericEntity;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

@Path("measurement")
public class MeasurementRestService {

  private static final Logger LOG = LogManager.getLogger(MeasurementRestService.class);

  // we are stateless, you know ...
  private List refusedMeasurements = new ArrayList<>();

  @POST
  @Path("save/{id1}/{id2}")
  @Consumes(MediaType.APPLICATION_JSON)
  @Produces(MediaType.APPLICATION_JSON)
  public Response save(//
      @PathParam("id1") final String id1, //
      @PathParam("id2") final String id2, //
      final List measurements) {

    final long start = System.currentTimeMillis();
    LOG.trace("save(id1={}, id2={}, measurements={})", id1, id2, measurements);

// invalid elements of the collection are moved to the refusedMeasurements collection.
    process(id1, id2, measurements);

    final MeasurementSaveResponse response = new MeasurementSaveResponse();
    response.setTimeInMillis(System.currentTimeMillis() - start);
    response.setRefusedMeasurements(this.refusedMeasurements);
    final Response restResponse = Response.ok(new GenericEntity<>(response, response.getClass())).build();
    return restResponse;
  }

Payara Micro and Uber jar 

No changes since the first blog. But we did not try it!

Call the web service!


mvn clean install; mvn fish.payara.maven.plugins:payara-micro-maven-plugin:start -pl :experiment-uberjar

... and it will start:

[2017-10-05T22:33:11.850+0200] [] [INFO] [] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1507235591850] [levelValue: 800] experiment-ws-0.0.1-SNAPSHOT was successfully deployed in 3 118 milliseconds.

[2017-10-05T22:33:11.851+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1507235591851] [levelValue: 800] Deployed 1 archive(s)

[2017-10-05T22:33:11.852+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1507235591852] [levelValue: 800] [[
 
Instance Configuration
Host: localhost
HTTP Port(s): 8080
HTTPS Port(s):
Instance Name: payara-micro
Instance Group: no-cluster
Deployed: experiment-ws-0.0.1-SNAPSHOT ( experiment-ws-0.0.1-SNAPSHOT war /experiment-ws-0.0.1-SNAPSHOT )

]]

[2017-10-05T22:33:11.865+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1507235591865] [levelValue: 800] [[
 
Payara Micro URLs
http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT

'experiment-ws-0.0.1-SNAPSHOT' REST Endpoints
POST    /experiment-ws-0.0.1-SNAPSHOT/measurement/save/{id1}/{id2}

]]

[2017-10-05T22:33:11.865+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1507235591865] [levelValue: 800] Payara Micro  4.1.2.173 #badassmicrofish (build 25) ready in 13 959 (ms)

Then open another console and run several curls:

curl -H "Content-Type: application/json" -X OPTIONS -i http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/measurement/save/dm790321/xxx;
HTTP/1.1 200 OK
Server: Payara Micro #badassfish
Allow: POST,OPTIONS
Last-modified:  t, 05 X j 2017 11:18:02 CEST
Content-Type: application/vnd.sun.wadl+xml
Date: Thu, 05 Oct 2017 09:18:02 GMT
Content-Length: 715

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<application xmlns="http://wadl.dev.java.net/2009/02">
    <doc xmlns:jersey="http://jersey.java.net/" jersey:generatedBy="Jersey: 2.25.1 2017-01-19 16:23:50"/>
    <grammars/>
    <resources base="http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/">
        <resource path="measurement/save/dm790321/xxx">
            <method id="save" name="POST">
                <request>
                    <representation mediaType="application/json"/>
                </request>
                <response>
                    <representation mediaType="*/*"/>
                </response>
            </method>
        </resource>
    </resources>
</application>

Another example:

curl -H "Content-Type: application/json" -X GET -i http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/application.wadl?detail=true
HTTP/1.1 200 OK
Server: Payara Micro #badassfish
Last-modified:  t, 05 X j 2017 15:59:02 CEST
Content-Type: application/vnd.sun.wadl+xml
Date: Thu, 05 Oct 2017 13:59:02 GMT
Content-Length: 5491

<application xmlns="http://wadl.dev.java.net/2009/02">
    <doc jersey:generatedby="Jersey: 2.25.1 2017-01-19 16:23:50" xmlns:jersey="http://jersey.java.net/">
    <doc jersey:hint="This is full WADL including extended resources. To get simplified WADL with users resources only do not use the query parameter detail. Link: http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/application.wadl" xmlns:jersey="http://jersey.java.net/">
    <grammars>
        <include href="application.wadl/xsd0.xsd">
            <doc title="Generated" xml:lang="en">
        </doc></include>
    </grammars>
    <resources base="http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/">
        <resource path="measurement">
            <resource path="save/{id1}/{id2}">
                <param name="id1" type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema" />
                <param name="id2" type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema" />
                <method id="save" name="POST">
                    <request>
                        <representation mediatype="application/json">
                    </representation></request>
                    <response>
                        <representation mediatype="application/json">
                    </representation></response>
                </method>
                <method id="apply" name="OPTIONS">
                    <request>
                        <representation mediatype="*/*">
                    </representation></request>
                    <response>
                        <representation mediatype="application/vnd.sun.wadl+xml">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
                <method id="apply" name="OPTIONS">
                    <request>
                        <representation mediatype="*/*">
                    </representation></request>
                    <response>
                        <representation mediatype="text/plain">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
                <method id="apply" name="OPTIONS">
                    <request>
                        <representation mediatype="*/*">
                    </representation></request>
                    <response>
                        <representation mediatype="*/*">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
            </resource>
        </resource>
        <resource path="application.wadl">
            <method id="getWadl" name="GET">
                <response>
                    <representation mediatype="application/vnd.sun.wadl+xml">
                    <representation mediatype="application/xml">
                </representation></representation></response>
                <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
            </method>
            <method id="apply" name="OPTIONS">
                <request>
                    <representation mediatype="*/*">
                </representation></request>
                <response>
                    <representation mediatype="text/plain">
                </representation></response>
                <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
            </method>
            <method id="apply" name="OPTIONS">
                <request>
                    <representation mediatype="*/*">
                </representation></request>
                <response>
                    <representation mediatype="*/*">
                </representation></response>
                <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
            </method>
            <resource path="{path}">
                <param name="path" type="xs:string" xmlns:xs="http://www.w3.org/2001/XMLSchema" />
                <method id="getExternalGrammar" name="GET">
                    <response>
                        <representation mediatype="application/xml">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
                <method id="apply" name="OPTIONS">
                    <request>
                        <representation mediatype="*/*">
                    </representation></request>
                    <response>
                        <representation mediatype="text/plain">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
                <method id="apply" name="OPTIONS">
                    <request>
                        <representation mediatype="*/*">
                    </representation></request>
                    <response>
                        <representation mediatype="*/*">
                    </representation></response>
                    <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
                </method>
                <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
            </resource>
            <jersey:extended xmlns:jersey="http://jersey.java.net/">true</jersey:extended>
        </resource>
    </resources>
</doc></doc></application>

And finally, let's try timestamp and lists!:

curl -H "Content-Type: application/json" -X POST -d '[{"timestamp":"2017-03-25T15:33:11.000+02:00", "channel":"15", "variable":"XXX", "value":"18"}, {"timestamp":"2017-03-25T15:33:11.000+02:00", "channel":"15", "variable":"XXX", "value":[null]}, {"timestamp":"2017-03-25T15:33:11.000+02:00", "channel":"15", "variable":[null], "value":"18"}]' -i http://localhost:8080/experiment-ws-0.0.1-SNAPSHOT/measurement/save/dm790321/fffff;
HTTP/1.1 200 OK
Server: Payara Micro #badassfish
Content-Type: application/json
Date: Thu, 05 Oct 2017 13:47:05 GMT
Content-Length: 132

{"countOfAccepted":2,"refusedMeasurements":[{"channel":15,"timestamp":"2017-03-25T15:33:11+02:00","value":18.0}],"timeInMillis":244}

úterý 12. září 2017

Experiments with the Payara Micro, level I

New company, new project, new technologies. Okay, I'm experimenting with Payara Micro. Payara team produces more and more examples in several blogs, but they are very trivial and not always usable in production environment. At this time I'm not sure if I would be able to do the evolution to the final professional system, but it is not a problem, because the application modules are simply Java EE standard modules.
The difference is only in final organisation of the modules, deployment and container configuration, so I can create the standard EAR application in parallel to UBER jar with the Payara Micro. So this style of development is perfectly safe.

Target 

Application with the following modules:
  • DAO and bussines logic service module (JPA, JTA, EJB, CDI?), created but nearly empty in this blog 
  • Web service module (JAX-RS), only one simple service method in this blog 
  • GUI module (JSF), not resolved in this blog 
And project will have also following aggregation alternatives:
  • Uber JAR with Payara Micro - experimental, responsive development 
  • EAR for standard Payara domain 
The reason for this separation of modules is that a JSF GUI application obviously have different requirements than a Web service application. It might not be a problem for some time, but it could be a problem later. This is not any premature optimization - this will force developers to keep in mind the separation line between modules and maybe to create some clean API. That will help right now and it will be simplier to split it later.

There may be even more Maven modules:
  • superpom - common Maven plugin configurations, basic dependency management 
  • project parent - aggregator of all project modules 
  • integration tests for the web service module 
  • selenium tests for the gui module

Dead-end streets and good streets 

Well, I had hard two days with the Payara Micro. Blogs helped, but I always needed more and I was always stucked in some weird state. Yes, it was always my fault, but ... okay, now you can learn from my mistakes.

LOG4J2 

I used LOG4J with SLF4J for many years, it was pretty trivial to make it work and a bit harder to grab logs of embedded Payara in integration tests. I have found a memory leak in old LOG4J's reconfiguration and I know perhaps everything about that.
Now it is worthless with LOG4J2. But finally the configuration was also simple despite I still have not found a way to merge logs of the application and Payara. Example log4j2.properties, seems like a good street:
status = info
dest = err
name = PropertiesConfig
#log4j2.debug = true

property.path = target/logs

filter.threshold.type = ThresholdFilter
filter.threshold.level = debug

appender.console.type = Console
appender.console.name = STDOUT
appender.console.layout.type = PatternLayout
appender.console.layout.pattern = %m%n
appender.console.filter.threshold.type = ThresholdFilter
appender.console.filter.threshold.level = info

appender.rolling.type = RollingFile
appender.rolling.name = RollingFile
appender.rolling.fileName = ${path}/experiment-ws.log
appender.rolling.filePattern = ${path}/experiment-ws-%d{MM-dd-yy-HH-mm-ss}-%i.log.gz
appender.rolling.layout.type = PatternLayout
appender.rolling.layout.pattern = %d %p %C{2.} [%t] %m%n
appender.rolling.policies.type = Policies
appender.rolling.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling.policies.time.interval = 2
appender.rolling.policies.time.modulate = true
appender.rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling.policies.size.size=1024MB
appender.rolling.strategy.type = DefaultRolloverStrategy
appender.rolling.strategy.max = 1

logger.ws.name = org.dmatej
logger.ws.level = debug
logger.ws.additivity = false
logger.ws.appenderRef.file.ref = RollingFile

rootLogger.level = debug
rootLogger.appenderRef.stdout.ref = STDOUT
rootLogger.appenderRef.file.ref = RollingFile  

JAX-RS, lists ... Jackson!

Creating the first JAX-RS web service is pretty trivial ... you need two classes, first to configure the context of services in the module, second to implement the service:

import javax.ws.rs.ApplicationPath;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.glassfish.jersey.server.ResourceConfig;

@ApplicationPath("rs")
public class RestAppConfig extends ResourceConfig {

  private static final Logger LOG = LogManager.getLogger(RestAppConfig.class);

  public RestAppConfig() {
    LOG.debug("RestAppConfig()");
    try {
      packages(RestAppConfig.class.getPackage().getName());
      LOG.info("REST configured!");
    } catch (final Exception e) {
      LOG.error("Cannot configure the REST web services!", e);
    }
  }
}
And the second:

import java.util.Arrays;
import java.util.List;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

@Path("user")
public class UserRestService {

  @GET
  @Path("list")
  @Produces(MediaType.APPLICATION_JSON)
  public Response list() {
    final List<String> list = Arrays.asList("Křemílek", "Vochomůrka"); // UTFG ;-)
    return Response.ok(list).build();
  }
} 
Maven command to run the application, it will be used in all following examples:
 mvn clean install;  mvn fish.payara.maven.plugins:payara-micro-maven-plugin:start -pl :experiment-uberjar
Final part of the log:

[2017-09-12T16:31:25.369+0200] [] [INFO] [AS-WEB-GLUE-00172] [javax.enterprise.web] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505226685369] [levelValue: 800] Loading application [experiment-ws-0.0.1-SNAPSHOT] at [/experiment-ws-0.0.1-SNAPSHOT]

[2017-09-12T16:31:25.681+0200] [] [INFO] [] [javax.enterprise.system.core] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505226685681] [levelValue: 800] experiment-ws-0.0.1-SNAPSHOT was successfully deployed in 12 472 milliseconds.

[2017-09-12T16:31:25.685+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505226685685] [levelValue: 800] Deployed 1 archive(s)

[2017-09-12T16:31:25.686+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505226685686] [levelValue: 800] [[
 
Instance Configuration
Host: dmatej-lenovo
HTTP Port(s): 8080
HTTPS Port(s):
Instance Name: Frail-Barracuda
Instance Group: MicroShoal
Hazelcast Member UUID cbddb9aa-5f21-4ee1-984f-78be942124d4
Deployed: experiment-ws-0.0.1-SNAPSHOT ( experiment-ws-0.0.1-SNAPSHOT war /experiment-ws-0.0.1-SNAPSHOT )

]]

[2017-09-12T16:31:25.702+0200] [] [INFO] [] [PayaraMicro] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505226685702] [levelValue: 800] [[
 
Payara Micro URLs
http://dmatej-lenovo:8080/experiment-ws-0.0.1-SNAPSHOT

'experiment-ws-0.0.1-SNAPSHOT' REST Endpoints
GET     /experiment-ws-0.0.1-SNAPSHOT/rs/user/list

]]
Ok, that was pretty simple. But the service does not work and ends up with HTTP 500 (try it with browser):

[2017-09-12T20:19:02.013+0200] [] [SEVERE] [] [org.glassfish.jersey.message.internal.WriterInterceptorExecutor] [tid: _ThreadID=22 _ThreadName=http-thread-pool::http-listener(3)] [timeMillis: 1505240342013] [levelValue: 1000] MessageBodyWriter not found for media type=application/json, type=class java.util.Arrays$ArrayList, genericType=class java.util.Arrays$ArrayList.

Solution 

Only add the dependency on Jackson to pom.xml and the following line as the first to the RestAppConfig's constructor:
register(JacksonFeature.class);
The final pom.xml of the ws module:

 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <artifactId>experiment-ws</artifactId>
  <packaging>war</packaging>
  <name>Experiment - Web Services</name>
  <parent>
    <groupId>org.dmatej.experiment</groupId>
    <artifactId>parent-pom</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <relativePath>..</relativePath>
  </parent>
  <dependencies>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-api</artifactId>
    </dependency>
    <dependency>
      <groupId>org.apache.logging.log4j</groupId>
      <artifactId>log4j-core</artifactId>
    </dependency>
    <dependency>
      <groupId>javax.ws.rs</groupId>
      <artifactId>javax.ws.rs-api</artifactId>
    </dependency>
    <dependency>
      <groupId>javax</groupId>
      <artifactId>javaee-api</artifactId>
    </dependency>
    <!-- to use optimized JAX-RS configuration -->
    <dependency>
      <groupId>org.glassfish.jersey.core</groupId>
      <artifactId>jersey-server</artifactId>
    </dependency>
    <!-- to simply use lists in JSONs -->
    <dependency>
      <groupId>org.glassfish.jersey.media</groupId>
      <artifactId>jersey-media-json-jackson</artifactId>
    </dependency>
  </dependencies>
  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>false</filtering>
        <includes>
          <include>**/*.properties</include>
        </includes>
      </resource>
    </resources>
  </build>
</project>

JDBC Pool 

This was a real pain but solution was so simple ... do you know what I hate? NullpointerException. In fact I appreciate that it exists, because it tells "the programmer was not careful". And if the programmer was not careful, it is a bug - maybe even trivial to fix. But another exception I have seen was ClassNotFoundException ... This is the pom.xml of the UBER jar:

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.dmatej.experiment</groupId>
  <artifactId>experiment-uberjar</artifactId>
  <version>0.0.1-SNAPSHOT</version>
  <name>Experiment Uberjar</name>
  <parent>
    <groupId>org.dmatej.experiment</groupId>
    <artifactId>superpom</artifactId>
    <version>0.0.1-SNAPSHOT</version>
  </parent>
  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>false</filtering>
        <includes>
          <include>**/*.txt</include>
        </includes>
      </resource>
    </resources>
    <plugins>
      <!-- HOWTO: https://github.com/payara/maven-plugins -->
      <plugin>
        <groupId>fish.payara.maven.plugins</groupId>
        <artifactId>payara-micro-maven-plugin</artifactId>
        <version>1.0.0</version>
        <executions>
          <execution>
            <goals>
              <goal>bundle</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <payaraVersion>4.1.2.173</payaraVersion>
          <useUberJar>true</useUberJar>
          <deployArtifacts>
            <deployArtifact>
              <groupId>org.dmatej.experiment</groupId>
              <artifactId>experiment-ws</artifactId>
              <version>${project.version}</version>
              <type>war</type>
            </deployArtifact>
          </deployArtifacts>
          <customJars>
            <customJar>
              <groupId>org.apache.logging.log4j</groupId>
              <artifactId>log4j-api</artifactId>
            </customJar>
            <customJar>
              <groupId>org.apache.logging.log4j</groupId>
              <artifactId>log4j-core</artifactId>
            </customJar>
            <customJar>
              <groupId>mysql</groupId>
              <artifactId>mysql-connector-java</artifactId>
            </customJar>
          </customJars>
          <commandLineOptions>
            <commandLineOption>
              <key>--autobindhttp</key>
              <value>true</value>
            </commandLineOption>
            <commandLineOption>
              <key>--prebootcommandfile</key>
              <value>${project.build.outputDirectory}/prepare-resources.txt</value>
            </commandLineOption>
          </commandLineOptions>
        </configuration>
      </plugin>
    </plugins>
  </build>
</project>
The prepare-resources.txt was this (note that empty lines are interpreted as an error):

set configs.config.server-config.admin-service.das-config.dynamic-reload-enabled=false
set configs.config.server-config.admin-service.das-config.autodeploy-enabled=false
create-jdbc-connection-pool --datasourceclassname com.mysql.cj.jdbc.MysqlDataSource --restype javax.sql.DataSource --property user=test:password=test:DatabaseName=experiment_test:ServerName=localhost:port=3306:zeroDateTimeBehavior=convertToNull:useUnicode=true:useJDBCCompliantTimezoneShift=true:useLegacyDatetimeCode=true:serverTimezone=UTC:characterEncoding=UTF-8 experiment-mysql
set resources.jdbc-connection-pool.experiment-mysql.steady-pool-size=5
set resources.jdbc-connection-pool.experiment-mysql.max-pool-size=20
set resources.jdbc-connection-pool.experiment-mysql.connection-validation-method=auto-commit
set resources.jdbc-connection-pool.experiment-mysql.is-connection-validation-required=true
set resources.jdbc-connection-pool.experiment-mysql.fail-all-connections=true
ping-connection-pool experiment-mysql
But it did not work, server startup failed and I had no idea why ... and Payara did not help me ... there were two kind of stacktraces:

java.lang.RuntimeException: Orb initialization erorr
        at org.glassfish.enterprise.iiop.api.GlassFishORBHelper.getORB(GlassFishORBHelper.java:191)
        at com.sun.enterprise.naming.impl.SerialContext.getORB(SerialContext.java:349)
        at com.sun.enterprise.naming.impl.SerialContext.getProviderCacheKey(SerialContext.java:356)
        at com.sun.enterprise.naming.impl.SerialContext.getRemoteProvider(SerialContext.java:386)
        at com.sun.enterprise.naming.impl.SerialContext.getProvider(SerialContext.java:331)
        at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:480)
        at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:440)
        at javax.naming.InitialContext.lookup(InitialContext.java:417)
        at org.glassfish.resourcebase.resources.naming.ResourceNamingService.lookup(ResourceNamingService.java:236)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.getConnectorConnectionPool(ConnectorConnectionPoolAdminServiceImpl.java:799)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.obtainManagedConnectionFactory(ConnectorConnectionPoolAdminServiceImpl.java:938)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.getUnpooledConnection(ConnectorConnectionPoolAdminServiceImpl.java:549)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.testConnectionPool(ConnectorConnectionPoolAdminServiceImpl.java:430)
        at com.sun.enterprise.connectors.ConnectorRuntime.pingConnectionPool(ConnectorRuntime.java:1162)
        at org.glassfish.connectors.admin.cli.PingConnectionPool.execute(PingConnectionPool.java:143)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:544)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:540)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:360)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:539)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:570)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:562)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:360)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:561)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1469)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1300(CommandRunnerImpl.java:111)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1851)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1727)
        at com.sun.enterprise.admin.cli.embeddable.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:169)
        at com.sun.enterprise.admin.cli.embeddable.CommandExecutorImpl.run(CommandExecutorImpl.java:94)
        at fish.payara.micro.boot.runtime.BootCommand.execute(BootCommand.java:65)
        at fish.payara.micro.boot.runtime.BootCommands.executeCommands(BootCommands.java:105)
        at fish.payara.micro.boot.runtime.BootCommands.executeCommands(BootCommands.java:99)
        at fish.payara.micro.impl.PayaraMicroImpl.bootStrap(PayaraMicroImpl.java:987)
        at fish.payara.micro.impl.PayaraMicroImpl.main(PayaraMicroImpl.java:186)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at fish.payara.micro.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
        at fish.payara.micro.boot.loader.Launcher.launch(Launcher.java:107)
        at fish.payara.micro.boot.loader.Launcher.launch(Launcher.java:70)
        at fish.payara.micro.boot.PayaraMicroLauncher.main(PayaraMicroLauncher.java:79)
        at fish.payara.micro.PayaraMicro.main(PayaraMicro.java:361)
Caused by: java.lang.NullPointerException
        at org.glassfish.enterprise.iiop.api.GlassFishORBHelper.getORB(GlassFishORBHelper.java:163)
        ... 44 more
[2017-09-12T21:42:28.782+0200] [] [SEVERE] [] [javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505245348782] [levelValue: 1000] RAR6001 : Class Not found : com.sun.gjc.spi.ResourceAdapterImpl


com.sun.appserv.connectors.internal.api.ConnectorRuntimeException: Error in creating active RAR
        at com.sun.enterprise.connectors.ActiveRAFactory.createActiveResourceAdapter(ActiveRAFactory.java:111)
        at com.sun.enterprise.connectors.service.ResourceAdapterAdminServiceImpl.createActiveResourceAdapter(ResourceAdapterAdminServiceImpl.java:212)
        at com.sun.enterprise.connectors.service.ResourceAdapterAdminServiceImpl.createActiveResourceAdapter(ResourceAdapterAdminServiceImpl.java:348)
        at com.sun.enterprise.connectors.ConnectorRuntime.createActiveResourceAdapter(ConnectorRuntime.java:405)
        at com.sun.enterprise.connectors.service.ConnectorService.loadDeferredResourceAdapter(ConnectorService.java:184)
        at com.sun.enterprise.connectors.service.ConnectorService.loadResourcesAndItsRar(ConnectorService.java:148)
        at com.sun.enterprise.connectors.service.ConnectorService.checkAndLoadPool(ConnectorService.java:325)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.getUnpooledConnection(ConnectorConnectionPoolAdminServiceImpl.java:553)
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.testConnectionPool(ConnectorConnectionPoolAdminServiceImpl.java:430)
        at com.sun.enterprise.connectors.ConnectorRuntime.pingConnectionPool(ConnectorRuntime.java:1162)
        at org.glassfish.connectors.admin.cli.PingConnectionPool.execute(PingConnectionPool.java:143)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:544)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:540)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:360)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:539)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:570)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:562)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:360)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:561)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1469)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1300(CommandRunnerImpl.java:111)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1851)
        at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1727)
        at com.sun.enterprise.admin.cli.embeddable.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:169)
        at com.sun.enterprise.admin.cli.embeddable.CommandExecutorImpl.run(CommandExecutorImpl.java:94)
        at fish.payara.micro.boot.runtime.BootCommand.execute(BootCommand.java:65)
        at fish.payara.micro.boot.runtime.BootCommands.executeCommands(BootCommands.java:105)
        at fish.payara.micro.boot.runtime.BootCommands.executeCommands(BootCommands.java:99)
        at fish.payara.micro.impl.PayaraMicroImpl.bootStrap(PayaraMicroImpl.java:987)
        at fish.payara.micro.impl.PayaraMicroImpl.main(PayaraMicroImpl.java:186)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at fish.payara.micro.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
        at fish.payara.micro.boot.loader.Launcher.launch(Launcher.java:107)
        at fish.payara.micro.boot.loader.Launcher.launch(Launcher.java:70)
        at fish.payara.micro.boot.PayaraMicroLauncher.main(PayaraMicroLauncher.java:79)
        at fish.payara.micro.PayaraMicro.main(PayaraMicro.java:361)
Caused by: java.lang.ClassNotFoundException: com.sun.gjc.spi.ResourceAdapterImpl
        at com.sun.enterprise.v3.server.APIClassLoaderServiceImpl$APIClassLoader.loadClass(APIClassLoaderServiceImpl.java:245)
        at com.sun.enterprise.v3.server.APIClassLoaderServiceImpl$APIClassLoader.loadClass(APIClassLoaderServiceImpl.java:237)
        at com.sun.enterprise.connectors.ActiveRAFactory.createActiveResourceAdapter(ActiveRAFactory.java:103)
        ... 40 more
]]

Dead-end street: comment out ping 

Okay, stacktraces are gone. But I don't know if the pool has been created and if it works.

Dead-end street: add dependencies 

Idea: add missing dependencies. The Payara versions are not in Maven Central, so I tried to add glassfish versions of org.glassfish.main.jdbc.jdbc-ra.jdbc-core:jdbc-core:4.1.2 and org.glassfish.main.jdbc.jdbc-ra.jdbc40:jdbc40:4.1.2 ... Result? Several warnings like this and finally exception. Dumb idea? Something similar helped us with old versions of the Embedded Payara started by JUnit integration tests but here it was only a cargo antipattern.

[2017-09-12T21:36:37.619+0200] [] [WARNING] [] [javax.enterprise.resource.resourceadapter.com.sun.enterprise.connectors.util] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505244997619] [levelValue: 900] RAR8000 : The method setLogJdbcCalls is not present in the class : com.sun.gjc.spi.DSManagedConnectionFactory

com.sun.appserv.connectors.internal.api.ConnectorRuntimeException: Failed to create MCF for experiment-mysql
        at com.sun.enterprise.connectors.service.ConnectorConnectionPoolAdminServiceImpl.createConnectorConnectionPool(ConnectorConnectionPoolAdminServiceImpl.java:195)
        at com.sun.enterprise.connectors.ConnectorRuntime.createConnectorConnectionPool(ConnectorRuntime.java:331)
        at org.glassfish.jdbc.deployer.JdbcConnectionPoolDeployer.actualDeployResource(JdbcConnectionPoolDeployer.java:201)
        at org.glassfish.jdbc.deployer.JdbcConnectionPoolDeployer.deployResource(JdbcConnectionPoolDeployer.java:170)
        at com.sun.enterprise.connectors.service.ConnectorService.loadDeferredResources(ConnectorService.java:233)
        at com.sun.enterprise.connectors.service.ConnectorService$1.run(ConnectorService.java:153)
        at java.security.AccessController.doPrivileged(Native Method)
Those two dependencies now remove, they are not needed and more, they are not compatible.

Look into the Payara sources and think

 ... and create this issue: https://github.com/payara/Payara/issues/1967 Oh, by the way, why I did not think it before? ORB factory is simply initialized after the prebootcommandfile execution! Ok, let's move the ping to a new file postboot.txt and add another commandLineOption to pom.xml:
<commandLineOption>
  <key>--postbootcommandfile</key>
  <value>${project.build.outputDirectory}/postboot.txt</value>
</commandLineOption>

MySQL and time zones 

Pool ping was still failing with some weird error message about unknown CEST timezone. StackOverflow advices did not work, neither one about configuring the JDBC driver. I have found several bugs reported to MySQL devs: https://bugs.mysql.com/bug.php?id=86425
I tried to change the server's default-time-zone via the MySql Workbench with no success until I noted that it updates incorrect file in my user's home directory. Finally I added these lines into /etc/mysql/my.cnf and restarted the mysql service ... and it worked.
[mysqld]
default-time-zone = +00:00

Success 

Yes, that was all. But ... there is nothing interesting in the log output, no logging about asadmin commands, no logging about their success. I was lazy to create my own logging.properties and to add path as another commandLineOption so I hacked the jar in maven repository (please, don't do this, don't be lazy!) ... the nearest usable loggers and logs was these:

[2017-09-12T22:23:53.622+0200] [] [FINE] [] [javax.enterprise.resource.resourceadapter.org.glassfish.jdbcruntime] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505247833622] [levelValue: 500] [CLASSNAME: org.glassfish.jdbcruntime.JdbcRuntimeExtension] [METHODNAME: isConnectionPoolReferredInServerInstance] JDBC resource jdbc/experiment-jta refers experiment-mysql in this server instance and is enabled
 

[2017-09-12T22:23:54.398+0200] [] [FINE] [] [org.glassfish.naming] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1505247834398] [levelValue: 500] [CLASSNAME: com.sun.enterprise.naming.util.NamingUtilsImpl] [METHODNAME: makeCopyOfObject] [[
  ** makeCopyOfObject:: ConnectorConnectionPool :: experiment-mysql
steady size: 5
max pool size: 20
max wait time: 60000
pool resize qty: 2
Idle timeout: 300
failAllConnections: true
Transaction Support Level: 1
isConnectionValidationRequired_ true
preferValidateOverRecreate_ false
matchConnections_ false
associateWithThread_ false
lazyConnectionAssoc_ false
lazyConnectionEnlist_ false
maxConnectionUsage_ 0
pingPoolDuringCreation_ false
poolingOn_ true
validateAtmostOncePeriod_ 0
connectionLeakTracingTimeout_0
connectionReclaim_false
connectionCreationRetryAttempts_0
connectionCreationRetryIntervalInMilliSeconds_10
nonTransactional_ false
nonComponent_ false
ConnectorDescriptorInfo ->
rarName: __ds_jdbc_ra
resource adapter class: com.sun.gjc.spi.ResourceAdapterImpl
connection def name: javax.sql.DataSource
MCF Config properties-> ClassName:com.mysql.cj.jdbc.MysqlDataSource
ConnectionValidationRequired:true
ValidationMethod:auto-commit
ValidationTableName:
ValidationClassName:
TransactionIsolation:
GuaranteeIsolationLevel:true
StatementWrapping:true
LogJdbcCalls:false
SlowQueryThresholdInSeconds:-1
StatementTimeout:-1
PoolMonitoringSubTreeRoot:resources/experiment-mysql
PoolName:experiment-mysql
StatementCacheSize:0
StatementCacheType:
InitSql:null
SqlTraceListeners:fish.payara.jdbc.SilentSqlTraceListener
StatementLeakTimeoutInSeconds:0
StatementLeakReclaim:false
DatabaseName:iqhouse_experiment
User:test
Password:****
ServerName:localhost
DriverProperties:setcharacterEncoding#UTF-8##setport#3306##setuseJDBCCompliantTimezoneShift#true##setuseLegacyDatetimeCode#true##setuseUnicode#true##setserverTimezone#UTC##setzeroDateTimeBehavior#convertToNull##
Delimiter:#
EscapeCharacter:\
]]  
Now I can continue to level 2: Good REST services ... to be continued ;)