…zation-role, remove not needed type information from test organizations

… test setup readme, increase dsf version in test setup to 0.5.2, use organization-role instead of organization-type

…r test setup

'origin/issues/54_Start_New_Development_Cycle' into develop

upgrades DSF dependency to 0.6.0(-SNAPSHOT), closes #56

'origin/issues/54_Start_New_Development_Cycle' into develop

issues/56_connection_test_onProcessesDeployed

Defines a release version via the PluginDefinition class and adds
#{date} to the fhir resources. Switches fhir files to the new #{...}
pattern. Adds the #{version} place holder to the bpmn files.

Closes #59

'origin/issues/49_codesystem-organization-type-role' into develop

'origin/issues/56_connection_test_onProcessesDeployed' into develop

issues/59_property_placeholders

into develop

develop

issues/51_crr-pseudonym-type-information

In method setSubjectOrIdentifier of ReadData all identifiers of the
patient removed and a single identifier with the correct type is set.

'origin/issues/51_crr-pseudonym-type-information' into develop

into develop

into develop

Search bundle urls are now "url encoded" based uri templates from the
spring framework. Adds some test cases to validate search bundle
creation and query parameter replacement.

restart policy "no" makes it easier to debug issues related to crashing
containers

This initial process validation task implementation requires 29
additional jars to be added to the BPE as regular (non-process) plugins.
Alternatively we could release the process plugin as a tar.gz/zip or we
might want to add the needed HAPI dependencies into the DSF BPE itself.
This implementation  contains some workarounds due to limitations of
some classes in the dsf-fhir-validation module.

The maven build produces a
codex-process-data-transfer-0.5.0-SNAPSHOT.zip containing the
codex-process-data-transfer-0.5.0-SNAPSHOT.jar and all dependency needed
to start a stand-alone bundle/resource validator.

Windows:
java -cp codex-process-data-transfer-0.5.0-SNAPSHOT.jar;lib/*
de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain
some-bundle.json some-resource.xml

Unix:
java -cp codex-process-data-transfer-0.5.0-SNAPSHOT.jar:lib/*
de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain
some-bundle.json some-resource.xml

The stand-alone validator outputs debug infos to System.err and the
validation result to System.out. For a given single resource a
OperationOutcome resource is produced and for a given Bundle, a bundle
with added response.outcome per entry with be printed to System.out.
The validator validates every json or xml file defined as command line
argument.
The validator can be configured using a application.properties file
within the execution folder or via java system properties, meaning java
command line parameters -Dfoo=bar. For configuration properties see
classes
de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.spring.config.ValidationConfig
and
de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.ValidationMain.TestConfig.

clients only initialize a trust store only ssl context, if key store and
key store password are null.

Jersey based clients not use the ApacheConnectorProvider. Standard
connector provider has no support for forwarding proxies. Added a
ontology server connection test to the ValueSetExpansionClient and usage
of to ValidatorMain.

The GECCO 1.0.5 radiology-procedures profile needs a min=0 config in the
rule Procedure.code.coding:dicom in order for the HAPI Snapshot
Generator to generate the correct StructureDefinition snapshot.

The contructor of ValidationPackageManagerImpl used in the
ValidateDataLearningTest was missing the "dicom" fix, aka
GeccoRadiologyProceduresCodingSliceMinFixer

'origin/issues/53_timestamp_encoding_in_search_bundle' into develop

issues/39_internal_bundle_validation

issues/39_internal_bundle_validation

Removed "-type" suffix from the error code CodeSystem/ValueSet.

Removed not needed TODO comments.

Changed log level from error to warning for first try ValueSet expansion
errors (errors resulting in trying to expand via external terminology
server next).

Changed external terminology server for the test setup.

To start the dic-fhir service with a locally build DSF image use:
docker-compose -f docker-compose.yml -f
docker-compose.local-dsf-build.yml up dic-fhir

These changes depend on highmed/highmed-dsf#354 being merged.

Increased version numbers of log42-utils and crypto-utils dependencies
to the latest versions.

Snapshots are only generate for StructureDefinitions from the root
validation package and its dependencies. ValueSet are only expanded if
they are part of binding rules from these StructureDefinitions. The
binding strength can be configured.

change log level for errors during internal ValueSet expansion

Added getServerBase Method to GeccoClient interface and implementing
classes. Removed geccoServerBase field from ReadData service, since it
may not be configured (when testing without GECCO FHIR Server or at the
GTH), resulting in a NullPointerException.

The file codex-processes-ap1-docker-test-setup/docker-compose.override.yml
has been added to .gitignore and can now be used to defined local
overrides. See https://docs.docker.com/compose/extends on how to use
override files.

Added new environment variable to disable FHIR validation. Added new
functionality to test if all resources are declaring at least on
supported profile. A validation error is raised if no supported profile
is defined. Profiles are supported if they are declared in the root
validation package (currently de.gecco | 1.0.5) or are dependencies of
the StructureDefinitions. Only profile with abstract = false and kind =
resource are supported as claimed profiles by resources beeing
validated.

'origin/issues/39_internal_bundle_validation' into develop

issues/36_feedback_messages_binary_delete

Spring config for processes now in separate classes.

See http://hl7.org/fhir/R4/activitydefinition-definitions.html#ActivityDefinition.name

Name should be usable as an identifier for the module by machine
processing applications such as code generation:
[A-Z]([A-Za-z0-9_]){0,254}

A failed delete should not fail the process. Now same behavior as
translate process DeleteDataForCrr.

For this to work, the DSF needs a mechanism to ignore unknown references
when updating task resources after deleting a referenced binary or we
need to delete the binaries after all Task resource have been updated.

This is needed in order to be able to correlate continue process
messages from the GTH to a single process instance.

'origin/issues/36_feedback_messages_binary_delete' into develop

Fixed bad error handling, Added error cases for failed decryption at
CRR. Switched from intermediate message throw events to message send
task for startDataTranslate and startDataReceice messages to add error
boundary events in case GTH or CRR is not reachable or throws error
during post of Task.