OpenMRS Initializer module

• Introduction
• Goals
• Supported domains and default loading order
• Try it out
  • Runtime compatibility
  • Test your OpenMRS configs
  • Finer control of domains loading at runtime
  • Setting up and controlling logging
• Get in touch
• Releases notes
  • Version 2.7.0
  • Version 2.6.0
  • Version 2.5.2
  • Version 2.5.1
  • Version 2.5.0
  • Version 2.4.0
  • Version 2.3.0
  • Version 2.2.0
  • Version 2.1.0
  • Version 2.0.0
  • Version 1.1.0
  • Version 1.0.1

(Table of contents generated with markdown-toc)

Introduction

The Initializer module is an API-only module that processes the content of the configuration folder when it is found inside OpenMRS' application data directory:

.
├── modules/
├── openmrs.war
├── openmrs-runtime.properties
├── ...
└── configuration/

The configuration folder is subdivided into domain subfolders:

configuration/
  ├── addresshierarchy/
  ├── ampathforms/
  ├── ampathformstranslations/
  ├── appointmentspecialities/
  ├── appointmentservicedefinitions/
  ├── appointmentservicetypes/
  ├── attributetypes/
  ├── autogenerationoptions/
  ├── bahmniforms/
  ├── cohorttypes/
  ├── cohortattributetypes/
  ├── conceptclasses/
  ├── conceptsources/
  ├── concepts/
  ├── conceptsets/
  ├── datafiltermappings/
  ├── drugs/
  ├── encountertypes/
  ├── encounterroles/
  ├── fhirconceptsources/
  ├── fhirpatientidentifiersystems/
  ├── globalproperties/
  ├── htmlforms/
  ├── idgen/
  ├── jsonkeyvalues/
  ├── liquibase/
  ├── locations/
  ├── locationtagmaps/
  ├── locationtags/
  ├── messageproperties/
  ├── metadatasetmembers/ 
  ├── metadatasets/ 
  ├── metadatasharing/ 
  ├── metadatatermmappings/
  ├── ocl/
  ├── orderfrequencies/
  ├── ordertypes/
  ├── patientidentifiertypes/ 
  ├── personattributetypes/ 
  ├── privileges/ 
  ├── programs/ 
  ├── programworkflows/
  ├── programworkflowstates/
  ├── providerroles/
  ├── queues/
  ├── relationshiptypes/
  └── roles/
   

Each domain-specific subfolder contains OpenMRS metadata configuration files that pertains to the domain.

Goals

• This module loads an OpenMRS configuration consisting of OpenMRS metadata.
• CSV files are the preferred format, however a number of metadata domains rely on other file formats. See the list below for details.
• Initializer processes all configuration files upon starting up.
• Initializer produces a checksum file for each processed configuration file. A file will never be processed again until its checksum has changed.
  • See more info here about checksums.
• Each line of those CSV files represents an OpenMRS metadata entity to be created, edited or retired.
• Each line of those CSV files follows the WYSIWYG principle.

Supported domains and default loading order

We suggest to go through the following before looking at the specifics for each supported domain:

• Conventions for CSV files

This is the list of currently supported domains in their loading order:

1. Liquibase Changelog (XML file)
2. Localization Message Properties (.properties files)
3. Generic JSON key-values (JSON files)
4. Metadata Sharing Packages (ZIP files)
5. Visit Types (CSV files)
6. Patient Identifier Types (CSV files)
7. Relationship Types (CSV files)
8. Location Tags (CSV files)
9. Privileges (CSV files)
10. Encounter Types (CSV files)
11. Encounter Roles (CSV files)
12. Roles (CSV files)
13. Global Properties (XML files)
14. Attribute Types (CSV files)
15. Provider Roles (CSV files)
16. Locations (CSV files)
17. Location Tag Maps (CSV files)
18. Address Hierarchy (XML, CSV, .properties files)
19. Bahmni Forms (JSON Files)
20. Concept Classes (CSV files)
21. Concept Sources (CSV files)
22. Open Concept Lab (ZIP Files)
23. Concepts (CSV files)
24. Concept Sets and Answers (CSV files)
25. Programs (CSV files)
26. Program Worklows (CSV files)
27. Program Worklow States (CSV files)
28. Person Attribute Types (CSV files)
29. Identifier Sources (CSV files)
30. Autogeneration Options (CSV files)
31. Drugs (CSV files)
32. Order Frequencies (CSV files)
33. Order Types (CSV files)
34. Bahmni Appointment Specialities (CSV files)
35. Bahmni Appointment Service Definitions (CSV files)
36. Bahmni Appointment Service Types (CSV files)
37. Queues (CSV files)
38. Data Filter Entity-Basis Mappings (CSV files)
39. Metadata Sets (CSV files)
40. Metadata Set Members (CSV files)
41. Metadata Term Mappings (CSV files)
42. Cohort Types (CSV files)
43. Cohort Attribute Types (CSV files)
44. FHIR Concept Sources (CSV files)
45. FHIR Patient Identifier Systems (CSV Files)
46. AMPATH Forms (JSON files)
47. AMPATH Forms Translations (JSON files)
48. HTML Forms (XML files)

Try it out

Build the master branch and install the built OMOD to your OpenMRS instance:

git clone https://github.com/mekomsolutions/openmrs-module-initializer/tree/master
cd openmrs-module-initializer
mvn clean package

Runtime compatibility

• OpenMRS Core 2.1.1 (required)
• Bahmni Appointments 1.2.1 (compatible)
• Bahmni Core 0.93 (compatible)
• Bahmni I.e Apps 1.1.0 (compatible)
• Data Filter 1.0.0 (compatible)
• HTML Form Entry 4.0.0 (compatible)
• ID Gen 4.3 (compatible)
• Metadata Sharing 1.2.2 (compatible)
• Metadata Mapping 1.3.4 (compatible)
• Open Concept Lab 1.2.9 (compatible)

Test your OpenMRS configs

See the Initializer Validator README page.

Finer control of domains loading at runtime

See the documentation on Initializer's runtime properties.

Setting up and controlling logging

See the documentation on Initializer's logging properties.

Get in touch

• On OpenMRS Talk
  • Sign up, start a conversation and ping us with the mention @MekomSolutions in your post.
• On Slack:
  • Join the Initializer channel and ping us with a @Mekom mention.
• Report an issue:
  • https://github.com/mekomsolutions/openmrs-module-initializer/issues

---

Releases notes

Version 2.7.0

• Added support for 'queues' domain.
• Added support for 'addresshierarchy' domain.
• Fix for Liquibase Loader to ensure compatibility with OpenMRS versions 2.5.5+.
• Fix for OCL Loader to ensure it throws an Exception if the OCL import fails.
• Fix for Validator to not encounter failure upon repeated execution on the same JVM process.

Version 2.6.0

• Added support for 'cohorttypes' and 'cohortattributetypes' domains.

Version 2.5.2

• Updated versions of Validator's metadatamapping to 1.6.0 and metadatasharing to 1.9.0.

Version 2.5.1

• Enhanced Validator to prevent random failures because of LazyInitializationException, and better teardown cleanup for uses with Maven plugins such as openmrs-packager-maven-plugin 1.7.0.

Version 2.5.0

• Added support for AMPATH Forms translations, see #180 and #221
• Fix for Message Source when system default language is not English, see #212
• Logging now uses the configured level as a minimum.
• Added support for drug reference maps on the drugs domain.

Version 2.4.0

• Added support for 'fhirconceptsources' domain.
• Added support for 'fhirpatientidentifiersystems' domain.
• Enhancement to ensure that reloading Concept CSVs does not clear Members/Answers if those columns aren't part of CSV file.
• 'concepts' domain to support a new expandable MAPPINGS header, thereby discouraging the older Same as mappings.
• Concept references expanded to allow use of concept names in locales other than the default system locale.

Version 2.3.0

• Added configuration options for logging.
• Added support for OpenMRS 2.4.0+
• Added support for a 'liquibase' domain to support loading custom changesets.
• 'ocl' domain to support loading concepts, concept sets and answers from OCL export files in configuration/ocl.
• (Enhancement) Concept name UUIDs are seeded from 1) the concept UUID and 2) the concept name information, see here. This version runs a Liquibase changeset that forces a reload of the concept domain in order to update concept names accordingly.
• Backward-compatible overhaul of the concepts domain that provides full flexibility for managing concept names.
• Bulk loading of metadata entities i18n display messages specified under display:xy headers.
• (For devs.) Introduced a pre-loading mechanism to BaseFileLoader that allows checksums-independent loading of transient information out of the config files before the actual metadata are loaded. Each loader controls whether its pre-loader throws on error or is allowed to fail. By default pre-loaders are allowed to fail.
• Added support for setting the version property in the 'concepts' domain.
• Bulk creation and editing of concept set members and concept answers using CSV files in configuration/conceptsets.
• Added support enabling any Initializer runtime property value to also be specified from a system property.
• Bulk creation and edition of AMPATH forms provided as JSON schema definitions in configuration/ampathforms.
• Enhancement to Initializer's custom message source to support improved handling of fallback locales and overrides between messages properties file from core, modules, and Initializer 'messageproperties' domain files.
• Added support for remote sources and identifier pools to the 'idgen' domain.
• Enhancement to ensure predictable loading order of files within a domain if no explicit order is specified, based on alphabetical ordering of filenames.
• Enhancement to the 'messageproperties' domain to enable specifying the order in which two files in the same locale should be loaded.

Version 2.2.0

• 'attributetypes' domain to support Bahmni program attribute types.
• 'program' domain to support Name and Description headers.
• CSV parsers to actually fill new objects marked to be retired or voided before creating them as retired/voided entities.
• Added a runtime property to define the loading startup mode for the activator OpenMRS config loading process.
• Existing attributes and location tags which are not specified in CSV headers are no longer removed.
• Bulk creation and editing of concept sources provided as CSV files in configuration/conceptsources.
• Bulk creation and editing of encounter roles using CSV files in configuration/encounterroles.
• (For devs.) Domain directory names and loading orders are implied from the base Domain enum.
• Bulk creation and editing of relationship types provided through CSV files in configuration/relationshiptypes.
• Bulk creation and editing of provider roles using CSV files in configuration/providerroles.
• Bulk creation and editing of location tag maps using CSV files in configuration/locationtagmaps.

Version 2.1.0

• (Bug fix) Locations with invalid parent references to throw an IllegalArgumentException.
• (For devs.) Introduced CsvFailingLines for a better management of the outcome of CsvParser#process.
• Introduced safe and unsafe API modes to suit either app runtime loading or early failure loading for CI.
• (For devs.) Introduced BaseFileLoader and BaseInputStreamLoader as part of a better streamlined loading framework.
• Initialize Validator a standalone fatjar to make dry runs of OpenMRS configs.
• Nested structures of configuration files are supported.
• Added a runtime property to define an inclusion or exclusion list of domains.
• Added a runtime property to specify wildcard patterns filters for each domain.
• Added a runtime property to toggle off the generation of the checksums.
• Improved logging output with ASCII Tables for Java.
• Bulk creation and edition of ID Gen's autogeneration options provided through CSV files in configuration/autogenerationoptions.
• Support associating location tags to locations using boolean Tag| headers.
• Bulk creation and edition of location tags provided through CSV files in configuration/locationtags.
• Bulk creation and edition of Bahmni forms provided as JSON schema definitions in configuration/bahmniforms.
• Bulk creation and edition of htmlforms provided as XML schema definitions in configuration/htmlforms.
• Bulk creation and edition of Bahmni appointment service types provided through CSV files in configuration/appointmentservicetypes.
• Renaming domain: appointmentsservicesdefinitions → appointmentservicedefinitions.
• Renaming domain: appointmentsspecialities → appointmentspecialities.

Version 2.0.0

• (For devs.) Support for conditional loading of domains based on the runtime availability of OpenMRS modules.
• Bulk creation and edition of programs provided through CSV files in configuration/programs.
• Bulk creation and edition of program workflows provided through CSV files in configuration/programworkflows.
• Bulk creation and edition of program workflow states provided through CSV files in configuration/programworkflowstates.
• Bulk creation and edition of privileges provided through CSV files in configuration/privileges.
• Bulk creation and edition of roles provided through CSV files in configuration/roles.
• Bulk creation and edition of metadata terms mappings provided through CSV files in configuration/metadatatermmappings.
• Bulk creation and edition of encounter types provided through CSV files in configuration/encountertypes.
• Bulk creation and edition of Bahmni appointments specialities provided through CSV files in configuration/appointmentsspecialities.
• Bulk creation and edition of Bahmni appointments services definitions provided through CSV files in configuration/appointmentsservicesdefinitions.
• Bulk access management of Data Filter entity to basis mappings provided through CSV files in configuration/datafiltermappings.
• Bulk creation and edition of attribute types provided through CSV files in configuration/attributetypes.
• Support location attributes.
• Bulk creation and edition of patient identifier types provided through CSV files in configuration/patientidentifiertypes.
• Bulk creation and edition of metadata terms mappings provided through CSV files in configuration/metadatasets.
• Bulk creation and edition of metadata terms mappings provided through CSV files in configuration/metadatasetmembers.
• Bulk creation and edition of bahmni forms provided JSON files in configuration/bahmniforms.
• Support concept attributes.

Version 1.1.0

• Bulk creation and edition of drugs provided through CSV files in configuration/locations.

Version 1.0.1

• Loads i18n messages files from configuration/addresshierarchy and configuration/messageproperties.
• Bulk creation and edition of concepts provided through CSV files in configuration/concepts.
  This covers: basic concepts, concepts with nested members or answers and concepts with multiple mappings.
• Bulk creation and edition of drugs provided through CSV files in configuration/drugs.
• Overrides global properties provided through XML configuration files in configuration/globalproperties.
• Modifies (retire) or create ID Gen's identifier sources through CSV files in configuration/idgen.
• Exposes runtime key-values configuration parameters through JSON files in configuration/jsonkeyvalues.
• Bulk creation and edition of person attribute types provided through CSV files in configuration/personattributetypes.
• Imports MDS packages provided as .zip files in configuration/metadatasharing.
• Bulk creation and edition of order frequencies provided through CSV files in configuration/orderfrequencies.