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Updated bcprov to the latest 1.5 beta that already has the manifest changes necessary and is signed by BC.

Issue: MIRTH-2963

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Committed an already signed bcprov with a modified manfiest. Exclude bcprov from being signed and having its manifest modified during the build process. bcprov 1.5 will not need to be modified, and could be used instead when it is released.

Issue: MIRTH-2963

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Updated the build to automatically add the following to all client-lib and extension jars:

Permissions: all-permissions

Codebase: *

Application-Name: Mirth Connect

Also unsigned bcprov-jdk16-144.jar and not-yet-commons-ssl-0.3.11.jar since we modify the manifest and the signatures are no longer valid. We re-sign the jar after modifying the manifest during the build process.

Issue: MIRTH-2963

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MIRTH-2849 and MIRTH-2915 - Auto generate javadocs for userutil packages during the build process. Include the user-api javadocs on the file system in docs/javadocs/user-api and host the javadocs under the root http context path /javadocs. Allow directory listing for this directory. Also disable serving the default Jetty favicon in the DefaultHandler.
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Fixed build reference to beta version of derby. The target this reference was in was only called manually.

Issue: MIRTH-2706

MIRTH-2636: Moved user-specific APIs into designated wrapper classes in the server/userutil and connect/userutil packages. The only classes which should reference anything in these userutil packages are JavaScriptScopeUtil and ValueReplacer. Nearly all non-deprecated method signatures from 2.x have been preserved in the 3.0 userutil wrappers, and deprecated as necessary. To that end, the MessageObject class has been added back as a wrapper class, and JSSU adds "messageObject" back into JavaScript scopes, to keep legacy compatibility. Every deprecated method also logs an error entry to the server log as well.
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Moved license file to /docs folder

Renamed /lib to /server-lib

Moved mirth-server.jar to /server-lib

Moved mirth-cli.jar to /cli-lib

Removed mirthdb automatic creation on build.

Changed default mirthdb path to /appdata/mirthdb

Renamed mirth-manager.jar to mirth-manager-launcher.jar

Issue: MIRTH-1713

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MIRTH-1700, MIRTH-2552: Updated the migration controller to call custom classes/code to handle server/schema migration, instead of just executing each delta script. The concept of a separate "schema version" is now gone; now SCHEMA_INFO.VERSION stores the product version (e.g. 3.0.0). Instead of simply iterating through the schema versions and calling each delta script, the migration controller now delegates that to custom Java classes (for now, just Migrate2_0_0 and Migrate3_0_0) that can call their respective delta scripts -and- do whatever other custom code may be necessary.

The channel table has been changed so that the entire serialized channel is stored in a single column. The ID, name, and revision columns remain, however. This is an example of where "custom code" is needed on server migration. Migrate3_0_0 executes all the delta scripts up to the 3.0.0 script (which renames the old channel table and creates the new one). Then it manually selects data out from the old table, builds up the 2.x model XML as a document, and stores the serialized data in the new table.

The migrateContents and migrateServerProperties functions that were in the migration controller have been moved to Migrate2_0_0, since the upgrade from 1.8.2 to 2.0.0 is the only place they were necessary anyway.

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MIRTH-2241

Added event pruning capability to the message pruner.

Renamed the message pruner plugin to "Data Pruner".

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Moved xstream converters that were overriding xstream classes into our own package and register the converters in ObjectXMLSerializer. Removed unused DateConverter and the com.thoughtworks packages.

Issue: MIRTH-1793

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MIRTH-2445, MIRTH-2346, MIRTH-2444: Completely changed how moving/renaming/deleting works in the File Reader.

Instead of "Delete After Read", there is now an "After Processing Action". You can select "None", "Move", or "Delete", depending on what you want to do after a message has been successfully processed through the channel. The Move-to Directory / File Name are still there, and apply to this action.

There are now two different error actions. The first, "Error Reading Action", determines what should happen when the file failed to be read in and processed by the channel.

The other one is "Error in Response Action", which determines what to do when the message was successfully processed, but the status of the selected response is ERROR. In this case, you can choose "After Processing Action", "Move", or "Delete". If "After Processing Action" is chosen (the default), ERROR responses will just cause the After Processing Action to be performed, and not do anything different.

In addition to the error move-to directory, there is also an error move-to file name. Both of these fields apply only to the Error Reading and Error in Response actions.

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Added Raw data type

Added two SerializationTypes that each data type must define (RAW or XML). Currently, the raw datatype uses RAW, and all other data types use XML. The SerializationType determines what datatype the transformed content is stored as, as well as what type of object msg and tmp will be in the transformer scripts.

DataType now stores the SerializationType so the transformer executors can utilize them.

Issue: MIRTH-2275

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BatchAdaptor has now been isolated from the Serializers.

DataType now contains a BatchAdaptor.

Plugin classes have been updated to accommodate this change.

DataType (and related) have been moved from model to server since they are not used by the client.

AutoResponder (and related) have been moved from model to server since they are not used by the client.

Issue: MIRTH-2357

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Rewrote the JMS connectors for Mirth Connect 3.0

Highlights:

- The JMS connectors now have the ability to automatically reconnect to the JMS broker if the connection goes down.

- JMS message acknowledgments are sent only after the message has been persisted by Mirth Connect, for guaranteed delivery.

Issue: MIRTH-1945

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Data Types now have separate inbound and outbound properties.

Inbound properties consist of SerializationProperties, BatchProperties, and ResponseGenerationProperties.

Outbound properties consist of DeserializationProperties, ResponseValidationProperties, and Template SerializationProperties.

The data types dialog has been completely revamped.

The "Properties" button is gone.

Both inbound and outbound properties are now visible once a connector is selected.

The property editor panel (tree and description) has been written from scratch.

The old editor (bean version) and beaninfo classes have been removed. The property descriptor information now comes from the respective Property Group object.

X12 data type has been combined with EDI. They are now referenced as "EDI / X12".

Updated DataType client and server plugins.

Moved getDefaultProperties from DataTypeDelegate to DataTypeClientPlugin since the server doesn't use it.

Serializers now take in SerializerProperties (which contains Serialization, Deserialization, and Batch properties).

MIRTH-2274

Issue: MIRTH-2273

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Moved the DataTypeServerPlugin implementations into the server jars instead of the shared jars so they will not be accessible by the model.

Issue: MIRTH-2325

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Fix zip file paths in build file.

Issue: MIRTH-2325

Data Types have been converted to plugins.

Delimited, DICOM, EDI, HL7v2, HL7v3, NCPDP, X12, XML have been implemented.

Removed static data type names from DataTypeFactory. These names are now retrieved from the loaded extensions.

Added DataTypeClientPlugin map to LoadedExtensions on the client. Check this class for client side methods.

Added DataTypeServerPlugin map to ExtensionController on the server. Check this class for server side methods.

Check DataTypeDelegate for shared methods.

Moved data type specific classes into the appropriate plugin package/jar

Changed "dataType" map in Frame to "dataTypeToDisplayName" to be more descriptive

Added a "displayNameToDataType" map for revese lookups.

NCPDP now has its own token marker instead of using HL7v2's

Added plugins/datatypes package to accessible rules on client classpath

Moved dicomobject/byte array conversion methods from DicomSerializer to DicomConvertor so it is not part of a plugin package.

Issue: MIRTH-2325

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MIRTH-2322: Added transmission mode plugin architecture to Mirth Connect.

The "Basic TCP" transmission mode is technically a plugin, but it's hard-coded and can't be removed by the Extension Manager.

"MLLP" was refactored as a separate plugin.

StreamHandler classes were moved from tcp.stream to model.transmission because they can potentially be used by more than just TCP connectors (e.g. RS-232).

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Fixed bug in the Server build that caused FileScheme to be included twice.

Issue: MIRTH-2250

Changed the Command project to include the Server project source directly instead of the jar because it requires new connector properties classes that aren't in the shared jar.

Changed the access rules in all projects that include Server so that they can't access anything that isn't in mirth-client-core.jar or any connector-shared.jar

Cleaned up the classpath orders and build connector orders.

Issue: MIRTH-2250

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Renamed VmListener to VmReceiver

Renamed VmListenerProperties to VmReceiverProperties

Renamed VmSender to VmDispatcher

Renamed VmSenderProperties to VmDispatcher

Updated build references. Please rebuild and recreate database.

Issue: MIRTH-2250

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Added Derby support.

Separated coupling between JdbcDao and ChannelController so that JdbcDao no longer calls ChannelController to lookup the localChannelId for a channelId, which in turn called JdbcDao again. The map of channelIds to localChannelIds is now stored in JdbcDao.

Donkey's channel storage is now initialized on channel deploy.

Modified channel deploy to check if a ResponseSelector has been defined and if not, create one using the source connector's inbound data type.

Fixed some potential problems with error handling in donkey Channel/DestinationChain.

Changed XmlQuerySource.getQuery() and CachedPreparedStatementSource.getPreparedStatement() so that they return null if there is no query for the given queryId, rather than throwing an exception. This was done since some queries are only defined for specific databases.

Cleaned up donkey's unit tests and ensured that database connections, statements, and result sets are only opened when needed and are closed as soon as possible in finally blocks.

Removed the com.mirth.connect.server.tasks package and the classes within it, which are unused.

Added / cleaned up indexes on donkey tables.

Added debug log output to JdbcDao.

Made the custom meta-data columns case-insensitive by automatically converting them to uppercase.

Issue: MIRTH-2250

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Removed old MLLP connector code.

Issue: MIRTH-2263

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Added build changes that were accidentally reverted by the initial Mirth Connect 3.0 commit.

Issue: MIRTH-2250

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Initial Mirth Connect 3.0 commit. Updated Server to use Donkey.

Issue: MIRTH-2250

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Disabling SNI for jarsigner's timestamp service.
Added not-yet-commons-ssl to server setup lib.

Issue: MIRTH-2050

Added mirth-crypto to server setup lib.

Issue: MIRTH-2050

Updated Derby 10.8.1.2 to 10.8.2.2