onyx-datomic

Onyx plugin providing read and write facilities for batch and stream processing on a Datomic database.

Installation

In your project file:

[org.onyxplatform/onyx-datomic "0.14.5.0"]

In your peer boot-up namespace:

(:require [onyx.plugin.datomic])

Datomic editions

Datomic Cloud edition was added in Jan. 2018 and the original Datomic was re-branded as Datomic On-Prem.

Datomic On-Prem can be accessed via Peer API and Client API, while Datomic Cloud is accessible only via Client API.

This plugin supports Datomic Peer API for Datomic On-Prem and Client API for Datomic Cloud. Client API is almost identical between On-Prem and Cloud other than connection mechanism, but some functions such as create-database is not supported for On-Prem. In addition to that, client API is not supported in Datomic On-Prem Free edition so it is not testable without a license and setting up of external transactor and peer-server.

For those reasons, client API is tested only against Datomic Cloud. Basic manual tests showed positive results on accessing to Datomic On-Prem Pro edition via Client API, but it is not continuously tested and may be broken.

Define Datomic dependency

The behavior is dynamically determined by looking up a datomic lib in classpath. Add one of peer, client, or cloud library in the classpath. Including multiple libs is not supported.

Peer lib

Add com.datomic/datomic-free or com.datomic/datomic-pro. Note that the registration to My Datomic is required to download Datomic Pro. The credential and repository needs to be set up in your project. See My Account page for the details.

[com.datomic/datomic-free "0.9.5544"]

Client lib for Datomic On-Prem

Add com.datomic/client-pro to your dependencies. See Project Configuration for the details.

Client lib for Datomic Cloud

Follow the instruction in Datomic Cloud documentation and add com.datomic/client-cloud to your project.

Attributes for Datomic Cloud Client API

Specify the following attributes to task map to connect Datomic Cloud.

key	type	description
:datomic-cloud/region	string	AWS region id where Datomic Cloud runs. e.g. us-east-1.
:datomic-cloud/system	string	System name chosen on setting up Datomic Cloud.
:datomic-cloud/query-group	string	Query group name if it is set up. Specify system name otherwise.
:datomic-cloud/endpoint	string	Optional. The default is http://entry.<system-name>.<region>.datomic.net:8182/
:datomic-cloud/proxy-port	string	Optional. Local port number for SSH tunnel to bastion. Default is 8182.
:datomic-cloud/db-name	string	Database name.

:datomic/uri is ignored.

Attributes for Datomic On-Prem Client API

Specify the following attributes to task map to connect Datomic On-Prem via Client API. Note that it is not tested due to the license and functional limitations described above.

key	type	description
:datomic-client/access-key	string	Access key specified in Peer-server command line options.
:datomic-client/secret	string	Secret specified in Peer-server command line options.
:datomic-client/endpoint	string	hostname:port-number of Peer-server.
:datomic-client/db-name	string	Database name.

:datomic/uri is ignored.

Functions

read-datoms

Reads datoms out of a Datomic database via datomic.api/datoms.

Catalog entry:

{:onyx/name :read-datoms
 :onyx/plugin :onyx.plugin.datomic/read-datoms
 :onyx/type :input
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/t t
 :datomic/datoms-index :eavt
 :datomic/datoms-components []
 :datomic/datoms-per-segment 20
 :onyx/max-peers 1
 :onyx/batch-size batch-size
 :onyx/doc "Reads a sequence of datoms from the d/datoms API"}

:datomic/datoms-components may be used to filter by a datomic index. See the Clojure Cookbook for examples.

Lifecycle entry:

{:lifecycle/task :read-datoms
 :lifecycle/calls :onyx.plugin.datomic/read-datoms-calls}

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/t	integer	The t-value of the database to read from
:datomic/datoms-index	keyword	datomic index to use in datomic.api/datoms call
:datomic/datoms-components	keyword	components of the datomic index to use (see datomic.api/datoms documentation)
:datomic/datoms-per-segment	integer	The number of datoms to compress into a single segment
:datomic/read-buffer	integer	The number of segments to buffer after partitioning, default is 1000

read-index-range

Reads datoms from an indexed attribute via datomic.api/index-range.

Catalog entry:

{:onyx/name :read-index-datoms
 :onyx/plugin :onyx.plugin.datomic/read-index-range
 :onyx/type :input
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/t t
 :datomic/index-attribute :your-indexed-attribute
 :datomic/index-range-start <<INDEX_START_VALUE>>
 :datomic/index-range-end <<INDEX_END_VALUE>>
 :datomic/datoms-per-segment 20
 :onyx/max-peers 1
 :onyx/batch-size batch-size
 :onyx/doc "Reads a range of datoms from the d/index-range API"}

Lifecycle entry:

{:lifecycle/task :read-index-datoms
 :lifecycle/calls :onyx.plugin.datomic/read-index-range-calls}

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/t	integer	The t-value of the database to read from
:datomic/index-attribute	keyword	datomic indexed attribute
:datomic/index-range-start	any	inclusive start value for the index range
:datomic/index-range-end	any	exclusive end value for the index range
:datomic/datoms-per-segment	integer	The number of datoms to compress into a single segment
:datomic/read-buffer	integer	The number of segments to buffer after partitioning, default is 1000

read-log

Reads the transaction log via repeated chunked calls of d/tx-range. Continues to read transactions until :datomic/log-end-tx is reached, or forever if :datomic/log-end-tx is nil.

Catalog entry:

{:onyx/name :read-log
 :onyx/plugin :onyx.plugin.datomic/read-log
 :onyx/type :input
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/log-start-tx <<OPTIONAL_TX_START_INDEX>>
 :datomic/log-end-tx <<OPTIONAL_TX_END_INDEX>>
 :onyx/max-peers 1
 :onyx/batch-size batch-size
 :onyx/doc "Reads a sequence of datoms from the d/log API"}

Lifecycle entry:

{:lifecycle/task :read-log
 :lifecycle/calls :onyx.plugin.datomic/read-log-calls}

Task will emit a sentinel :done when it reaches the tx log-end-tx (exclusive).

Segments will be read in the form {:t tx-id :data [[e a v t added] [e a v t added]]}.

To recover read-log offsets in a new job, please use the onyx resume points feature.

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/log-start-tx	integer	optional starting tx (inclusive) for log read
:datomic/log-end-tx	integer	optional ending tx (inclusive) for log read. Sentinel will emitted when this tx is passed.
:datomic/read-buffer	integer	The number of segments to buffer after partitioning, default is 1000

commit-tx

Writes new entity maps to datomic. Will automatically assign tempid's for the partition if a value for :datomic/partition is supplied and datomic transaction data is in map form.

Catalog entry:

{:onyx/name :write-datoms
 :onyx/plugin :onyx.plugin.datomic/write-datoms
 :onyx/type :output
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/partition :my.database/optional-partition-name
 :onyx/batch-size batch-size
 :onyx/doc "Transacts segments to storage"}

Lifecycle entry:

{:lifecycle/task :write-datoms
 :lifecycle/calls :onyx.plugin.datomic/write-tx-calls}

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/partition	keyword	Optional keyword. When supplied, :db/id tempids are added using this partition.

commit-bulk-tx (asynchronous)

Writes transactions via the :tx segment key to a Datomic database. The value of :tx should be as if it were ready for (d/transact uri tx). This lets you perform retractions and arbitrary db functions. Takes advantage of the Datomic transactor's ability to pipeline transactions by asynchronously transacting :onyx/batch-size transactions at once. Transaction futures are then derefed one by one after. Parallelism can thus be controlled by modifying the batch size appropriately. This is the recommended way to transact in bulk.

Catalog entry:

{:onyx/name :write-bulk-datoms-async
 :onyx/plugin :onyx.plugin.datomic/write-bulk-datoms-async
 :onyx/type :output
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/partition :my.database/partition
 :onyx/batch-size batch-size
 :onyx/doc "Transacts segments to storage"}

An example value of :tx would look like the following:

(require '[datomic.api :as d])

{:tx [[:db/add (d/tempid :db.part/user) :db/doc "Hello world"]]}

Lifecycle entry:

{:lifecycle/task :write-bulk-datoms-async
 :lifecycle/calls :onyx.plugin.datomic/write-bulk-tx-async-calls}

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/partition	keyword	Optional keyword. When supplied, :db/id tempids are added using this partition.

commit-bulk-tx (synchronous)

Exactly the same as commit-bulk-tx (asynchronous), but transacts each tx completely (blocking on the returned future) before proceeding to the next. You should generally prefer the async version.

Catalog entry:

{:onyx/name :write-bulk-datoms
 :onyx/plugin :onyx.plugin.datomic/write-bulk-datoms
 :onyx/type :output
 :onyx/medium :datomic
 :datomic/uri db-uri
 :datomic/partition :my.database/partition
 :onyx/batch-size batch-size
 :onyx/doc "Transacts segments to storage"}

An example value of :tx would look like the following:

(require '[datomic.api :as d])

{:tx [[:db/add (d/tempid :db.part/user) :db/doc "Hello world"]]}

Lifecycle entry:

{:lifecycle/task :write-bulk-datoms
 :lifecycle/calls :onyx.plugin.datomic/write-bulk-tx-calls}

Attributes

key	type	description
:datomic/uri	string	The URI of the datomic database to connect to
:datomic/partition	keyword	Optional keyword. When supplied, :db/id tempids are added using this partition.

Datomic Params Injection via Lifecycles

The datomic params lifecycles inject datomic dbs or conns into :onyx/fn params.

inject-conn

Injects a datomic conn into the event map. Will also inject as an :onyx/fn param if :onyx/param? is true.

{:lifecycle/task :use-conn-task
 :lifecycle/calls :onyx.plugin.datomic/inject-conn-calls
 :datomic/uri db-uri
 :onyx/param? true
 :lifecycle/doc "Initialises datomic conn as a :onyx.core/param"}

inject-db

Injects a datomic db into the event map. Will also inject as an :onyx/fn param if :onyx/param? is true.

:datomic/basis-t is optional, and if supplied it calls datomic.api/as-of on the db using :datomic/basis-t.

{:lifecycle/task :use-db-task
 :lifecycle/calls :onyx.plugin.datomic/inject-db-calls
 :datomic/uri db-uri
 :datomic/basis-t optional-basis-t
 :onyx/param? true
 :lifecycle/doc "Initialises datomic db as a :onyx.core/param"}

Development

Run tests against Datomic Cloud

1. Set up Datomic Cloud.
2. Allow inbound bastion traffic.
3. Start a socks proxy.
4. Update com.datomic/client-cloud version in project.clj if necessary.
5. Run tests compatible with Datomic cloud.

lein with-profile cloud test :cloud

Contributing

Pull requests into the master branch are welcomed.

License

Copyright © 2015 Michael Drogalis

Distributed under the Eclipse Public License, the same as Clojure.