Giga Chokheli

Posted on 9th August 2023

Side by side: Datomic and PostgreSQL, Part 1

news-paper Clojure | News | Software Development |

Greetings fellow Cojurians, to clarify from the outset, the objective of this article (or series of articles) is to highlight the differences in data modeling between SQL and Datomic. The conclusion will be yours to draw; I will merely present the facts.

Datomic was once considered a luxury product in the realm of parentheses, causing many companies and projects to avoid it. Eventually, NuBank decided to acquire Cognitect. Perhaps it was cheaper to buy the company than to continue paying licensing fees in the long term. A few months later, Datomic was released as a free-to-use product.

What makes Datomic special? In my experience, it’s an entirely different type of database compared to what I, and possibly you, have used in production before. It’s a refreshing change in terms of developer experience and code organization. One particular feature that may seem alien to those in the SQL world is Datomic’s time-oriented design.

What does it mean to be time-oriented? In Datomic, the database does not only contain the current state of the data, but it also retains a complete history of changes made to that data. In other words, Datomic stores not only the present state but also the past states of the data. However, before we delve into this, we will take a thorough tour of Datomic and SQL, comparing these two paradigms.

While there’s much to discuss, I prefer to demonstrate through examples. The context will be simple data modeling and execution to provide examples of both approaches, enabling readers to draw their own conclusions. —


To kick off our exploration, let’s define a simple Entity Relationship Model: 

The path ahead of us is straightforward; it’s a diagram illustrating ERD in an SQL database. Our SQL choice is the well-known Postgres. Within the Clojure ecosystem, we have a number of libraries that deal with SQL, such as HugSQL, HoneySQL, and plain SQL migration scripts. When dealing with database migration, my personal preference is the combination of plain SQL and migratus, a pair endorsed by our dear friend, exceptional individual, and veteran of Clojure open-source software – Sean Corfield, the author of our beloved HoneySQL and many other libraries.



    Title TEXT NOT NULL,
    Author TEXT NOT NULL,
    Genre TEXT,
    Publication_Date DATE
    First_Name TEXT NOT NULL,
    Last_Name TEXT NOT NULL,
    Email TEXT
    Book_ID INT,
    Patron_ID INT,
    Borrower_ID INT,
    Borrow_Date DATE,
    Due_Date DATE,
    FOREIGN KEY (Patron_ID) REFERENCES Person(id),
    FOREIGN KEY (Borrower_ID) REFERENCES Person(id),

--;; is Migratus specific comment to distinguish between SQL statements.


;; Book
 {:db/ident       :book/title
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The title of a book."}

 {:db/ident       :book/author
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The author of a book."}

 {:db/ident       :book/genre
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The genre of a book."}

 {:db/ident       :book/publication-date
  :db/valueType   :db.type/instant
  :db/cardinality :db.cardinality/one
  :db/doc         "The publication date of a book."}

 ;; Person
 {:db/ident       :person/first-name
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The first name of a person."}

 {:db/ident       :person/last-name
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The last name of a person."}

 {:db/ident       :person/email
  :db/valueType   :db.type/string
  :db/cardinality :db.cardinality/one
  :db/doc         "The email of a person."}

 ;; Registry
 {:db/ident       :registry/book
  :db/valueType   :db.type/ref
  :db/cardinality :db.cardinality/one
  :db/doc         "The book being borrowed."}

 {:db/ident       :registry/patron
  :db/valueType   :db.type/ref
  :db/cardinality :db.cardinality/one
  :db/doc         "The patron lending a book."}

 {:db/ident       :registry/borrower
  :db/valueType   :db.type/ref
  :db/cardinality :db.cardinality/one
  :db/doc         "The borrower of a book."}

 {:db/ident       :registry/borrow-date
  :db/valueType   :db.type/instant
  :db/cardinality :db.cardinality/one
  :db/doc         "Borrowed date."}

 {:db/ident       :registry/due-date
  :db/valueType   :db.type/instant
  :db/cardinality :db.cardinality/one
  :db/doc         "The due date for returning the book."}]
  • :db/ident: Unique identifier for an entity, which is typically used to provide a human-readable, namespace-qualified name for an entity, and once set, it cannot be changed. Namespace in our context is :book and title is its attribute.
  • :db/valueType: The type of value that can be associated with an entity. For instance, it could be used to specify that an attribute must be of type :db.type/string:db.type/long:db.type/boolean, etc.
    • db.type/ref means it would refer to another entity, fact (datum)
      Important different compared to SQL is a lack of direct connection with any specific entity. There’s no concept of foreign key in Datomic.
  • :db/cardinality: Is used to specify whether an attribute of an entity can have one or multiple values. If it is set to :db.cardinality/one, then each entity can have at most one value for the attribute. If it is set to :db.cardinality/many, then each entity can have many values for the attribute.
  • :db/doc: Is used to store a human-readable documentation string for an entity. It’s a good practice to provide documentation for all the entities and attributes in the database, to make it clear what they represent and how they should be used.

Database setup and Migrations

The next step in line is to start the database and migrate the schema.


Create role and corresponding database (I assume we have PostgreSQL running and console available):



Add these dependencies to deps.edn under :deps key

;; migrations
migratus/migratus {:mvn/version "1.5.1"}
;; SQL DSL for Clojure
com.github.seancorfield/honeysql {:mvn/version "2.4.1045"}
;; PostgreSQL Driver
org.postgresql/postgresql {:mvn/version "42.6.0"}}
;; JDBC access layer
com.github.seancorfield/next.jdbc {:mvn/version "1.3.883"}}


(ns gig.sql
  (:require [migratus.core :as migratus]))

;; Initialize database
(def config {:store                :database
             :migration-dir        "resources/migrations/"
             :init-script          "schema.sql"
             :migration-table-name "booky"
             :db {:port       5432
                  :dbname     "booky"
                  :host       "localhost"
                  :dbtype     "postgresql"
                  :user       "booker"
                  :password   "dev"}})

;initialize the database using the 'schema.sql' script
(migratus/init config)
  1. import migratus library
  2. Read config
    • The important step is to manually create dir resources/migrations and SQL file schema.sql with SQL schema mentioned above
  3. init function performs database initialization through provided configuration


In this case things a little different as Datomic relies on other different types of storage for persistence. In our case, we’ll be using in memory for the demonstration purposes.1


com.datomic/peer {:mvn/version "1.0.6735"}


(ns gig.datomic
  (:require [datomic.api :as d]))

(def db-uri "datomic:mem://booky")

(d/create-database db-uri)

(def conn (d/connect db-uri))

(def schema (edn/read-string (slurp "resources/schema.edn")))

@(d/transact conn schema)
  • To avoid polluting namespace, I’d rather keep schema into a separate file – resources/schema.edn
  • d/transact submits transaction to the database

Save data into database


Sample data

(def book
  {:title "The Man Without Qualities"
   :author "Robert Musil"
   :genre "Philosophical Fiction"
   :publication-date (t/date "1943-11-06")})

(def patron
  {:first-name "Ulrich"
   :last-name ""
   :email "ulrich@kakania.at"})

(def borrower
  {:first-name "Agatha"
   :last-name ""
   :email "agatha@kakania.at"})

(def registry
  {:book-id 1
   :patron-id 2
   :borrower-id 3
   :borrow-date (t/date "2023-07-28")
   :due-date (t/date "2023-10-28")})

Create a connection to database

(def db (jdbc/get-connection (:db config)))


  {:insert-into :book
   :values [book]})
 {:return-keys true})
  1. jdbc/execut! takes in datasource and query, performs execution and returns the result
  2. sql/format is responsible for processing Clojure map into SQL query
  3. The map is the example of HoneySQL map syntax
  4. An option to return inserted data

The result

[#:book{:id 14,
        :title "The Man Without Qualities",
        :author "Robert Musil",
        :genre "Philosophical Fiction",
        :publication_date #inst "1943-11-05T23:00:00.000-00:00"}]
sql/format and honeysql

The query above results in:

["INSERT INTO book (title, author, genre, publication_date) VALUES (?, ?, ?, ?)"
 "The Man Without Qualities"
 "Robert Musil"
 "Philosophical Fiction"
 #time/date "1943-11-06"]
Perform the rest of insertions

At this point, I’d rather compose a handy function for execution

(defn execute [q]
  (jdbc/execute! db (sql/format q)
                  {:return-keys true}))

Hence insertion of remaining data is simplified

 {:insert-into :person
  :values [patron

 {:insert-into :registry
  :values [registry]})


Sample data

In case of Datomic, sample data looks a bit different, instead of separate definitions, we have all data in a single var:

(def data
  [{:db/id "musil"
    :book/title "The Man Without Qualities"
    :book/author "Robert Musil"
    :book/genre "Philosophical Fiction"
    :book/publication-date (instant/read-instant-date "1943-11-06")}

   {:db/id "ulrich"
    :person/first-name "Ulrich"
    :person/last-name ""
    :person/email "ulrich@kakania.at"}

   {:db/id "agatha"
    :person/first-name "Agatha"
    :person/last-name ""
    :person/email "agatha@kakania.at"}

   {:registry/book "musil"
    :registry/patron "ulrich"
    :registry/borrower "agatha"
    :registry/borrow-date (instant/read-instant-date "2023-07-28")
    :registry/due-date (instant/read-instant-date "2023-10-28")}])

Save (transact)

(d/transact conn data)
  • :db/id is a temporary id used in the context of transaction to actually create a relationship. Example from the execution {"musil" 17592186045418, "ulrich" 17592186045419, "agatha" 17592186045420}
  • Hence we don’t explicitly force relationship on the schema level, but during transaction. If we try to transact without temporary id the REPL will greet we with error – :db.error/tempid-not-an-entity tempid 'whatever' used only as value in transaction

Querying data from database

I wouldn’t say that we’ve been sailing into much familiar waters until now, but at this point things do actually get quite different, challenging at some extent, but I do usually hold myself from jumping to conclusions till the moment I comprehend the technology and reasoning behind design decisions. Down the down you’ll see what I mean.

Querying through (Honey)SQL

Run a simple query first, fetch all data from person table

 {:select [:*]
  :from :person})

The result:

[#:person{:id 1,
          :first_name "Ulrich",
          :last_name "",
          :email "ulrich@kakania.at"}
 #:person{:id 2,
          :first_name "Agatha",
          :last_name "",
          :email "agatha@kakania.at"}]

Borrower Agatha

Now, let’s make things a little complicated and fetch books from registry where the borrower is Agatha.2 A regular SQL:

SELECT book.title, 
       borrower.first_name AS borrower,
       patron.first_name AS patron
FROM registry
         INNER JOIN book ON registry.book_id = book.id
         INNER JOIN person AS borrower ON registry.borrower_id = borrower.id
         INNER JOIN person AS patron ON registry.patron_id = patron.id
WHERE borrower.email = 'agatha@kakania.at';


 {:select [:book.title
           [:borrower.first-name :borrower]
           [:patron.first-name :patron]]
  :from [:registry]
  :join [:book [:= :registry.book-id :book.id]
        [:person :borrower] [:= :registry.borrower-id :borrower.id]
        [:person :patron] [:= :registry.patron-id :patron.id]]
  :where [:= :borrower.email "agatha@kakania.at"]})


[{:book/title = "The Man Without Qualities"
  :registry/borrow_date = 2023-07-28
  :person/borrower = "Agatha"
  :person/patron = "Ulrich"}]

Querying through Datalog (Datomic)

Datalog is the querying language supported here, nonetheless Datomic provides 3 ways of pulling data:

  1. Pull API: The pull API in Datomic is a powerful, declarative way to retrieve an entity and its associated attributes in one call, letting us shape the returned data to fit our needs.
  2. Datalog Queries: Datomic uses Datalog, a declarative logic programming language, enabling expressive relational queries including joins, recursion, negation, and more, where we specify a pattern to match in the database and get back a set of tuples matching the pattern.
  3. Entity API: The Entity API in Datomic is a simpler method to access the attributes of a single entity given its entity ID, offering a less flexible but straightforward alternative to the Pull API for accessing multiple attributes of a single entity.

A regular Datalog query

The first and utmost important step is to capture the current state of the database in Clojure, the usual step is:

(def db (d/db conn))

The d/db function is used to get a value of the database from the connection. The value represents the entire database at a specific point in time.

Then we can perform queries:

(d/q '[:find ?e ?first-name ?email
       [?e :person/first-name ?first-name]
       [?e :person/email ?email]]
  • q/q is a query execution function
  • :find receives one or more attributes, SQL analog is SELECT
  • :where is core of the query
    • ?e is a variable that will hold the entity ID. In Datalog, variables are represented by symbols that start with a ?
    • :person/first-name is an attribute in the database. In this case, it represents the first name of a person
    • ?first-name is another variable that will hold the value of the :person/first-name attribute for the entity ?e in the following queries if we need to narrow it down.
    The clause [?e :person/first-name ?first-name]  can be read as for the entity ?e, find the value of the :person/first-name attribute and bind it to the ?first-name variable.In more simple terms: Find me the first name of a person, and let’s refer to this person as ?e and their first name as ?first-name.


#{[17592186045421 "Agatha" "" "agatha@kakania.at"]
  [17592186045420 "Ulrich" "" "ulrich@kakania.at"]}

A regular Datalog query returns a set of tuples without corresponding keys. If we need to return maps, then :keys is require alongside corresponding arguments:

(d/q '[:find ?e ?first-name ?last-name ?email
       :keys id first-name last-name email
       [?e :person/first-name ?first-name]
       [?e :person/last-name ?last-name]
       [?e :person/email ?email]]


[{:id 17592186045421,
  :first-name "Agatha",
  :last-name "",
  :email "agatha@kakania.at"}
 {:id 17592186045420,
  :first-name "Ulrich",
  :last-name "",
  :email "ulrich@kakania.at"}]

Pull API

(d/q '[:find [(pull ?e [*]) ...]
       :where [?e :person/first-name]]
  • pull is a function provided by Datomic that retrieves entities from the database along with their attributes.
  • ?e is a variable that represents an entity ID. This variable should have been bound to a value in a previous clause of the query.
  • [*] is a pull pattern that specifies which attributes to retrieve. The asterisk (*) is a wildcard that means all attributesSQL equivalent is SELECT *

So, (pull ?e [*]) can be read as retrieve the entity with the ID ?e and all of its attributes.

In simple terms, it’s like asking the database: Give me everything you know about the entity identified by ?e.


[{:db/id 17592186045420,
  :person/first-name "Ulrich",
  :person/last-name "",
  :person/email "ulrich@kakania.at"}
 {:db/id 17592186045421,
  :person/first-name "Agatha",
  :person/last-name "",
  :person/email "agatha@kakania.at"}]
Entity API
(d/entity db entity-id)
  • d/entity is a function provided by Datomic that retrieves an entity from the database. It returns an entity map, which is a lazy, dynamic view of the entity’s attributes at the point in time represented by the database value.
  • db let’s repeat – db is the Datomic database value, representing a particular point in time in the database.
  • entity-id is the unique identifier of the entity that we want to retrieve. This identifier is typically a number that Datomic automatically assigns when the entity is first created, but it can also be a lookup ref or a tempid, depending on the context.

(d/entity db entity-id) can be read as retrieve the entity with the ID entity-id from the database db.

In simple terms – Give me the thing (entity) identified by entity-id, as it was at the point in time represented by db.

(let [entity (d/entity db 17592186045420)]
  (select-keys entity [:person/first-name


#:person{:first-name "Ulrich",
         :last-name "",
         :email "ulrich@kakania.at"}

In the context of the real-world application we usually hold the id and Entity API is certainly a unique and beneficial feature, particularly in the scenarios where the performance is critical.

Borrower – Agatha

We had the first glance at Datomic query engine and it’s variations, at this point we’re ready to compose a bit more complex query and fetch registry record that corresponds agatha as the borrower.

(d/q '[:find ?title ?borrow-date ?borrower-name ?patron-name
       :keys title borrow-date borrower patron
       [?registry :registry/book ?book]
       [?registry :registry/borrow-date ?borrow-date]
       [?registry :registry/borrower ?borrower]
       [?registry :registry/patron ?patron]
       [?book :book/title ?title]
       [?borrower :person/first-name ?borrower-name]
       [?borrower :person/email "agatha@kakania.at"]
       [?patron :person/first-name ?patron-name]]
  1. The first 4 clauses, regarding :registry identify an entry – the associated book, the borrow date, and both the borrower and patron involved
  2. [?book :book/title ?title] retrieves the title of the associated book
  3. [?borrower :person/first-name ?borrower-name] finds the first name of the borrower
  4. [?borrower :person/email "agatha@kakania.at"] ensures that the borrower’s email is agatha@kakania.at
  5. [?patron :person/first-name ?patron-name]: Retrieves the first name of the patron

:find is complemented with a list of data variables we are interested in.


[{:title "The Man Without Qualities",
  :borrow-date #inst "2023-07-28T00:00:00.000-00:00",
  :borrower "Agatha",
  :patron "Ulrich"}]

— At this point in time and space, our little journey has come to an end. In the next article we’ll talk about Datomic Specific features, that would improve the processes we have talked about.

The repository with the code is available at the following link – booky.

Cheers, Giga