Seattle tutorial - with molecules

Credits: This tutorial is based on the original Datomic Seattle tutorial (there is also a new tutorial) and some text passages have been quoted as-is or been slightly modified to describe how Molecule works.


After setting up the database and populating it with data we can start making queries. We make queries by building “molecules” which are chains of attributes put together with the builder pattern. We can imagine this as a 3-dimensional data structure of atoms bound together in various patterns to build molecules…

Molecule builder pattern

The first thing you do with Molecule is to define your domain namespaces and attributes in a trait that defines namespaces with attributes for your domain:

trait Community {
  val name = oneString.fullTextSearch
  val url  = oneString

The name field defines an attribute of type String with cardinality one. Adding the fullTextSearch option will tell Datomic that we want to be able to make fulltext searches on the values of this attribute.

After defining the schema like this, we run sbt compile and Molecule will generate some boilerplate traits that allow us to build molecules of our attributes:

val nameUrls = m(

Since the m method is implicit we can generally just write

val nameUrls =

If you look at the generated namespace code you’ll see that it is a little more complex behind the scenes. That’s because we want our IDE to be able to infer the type of each attribute. If we for instance had an age attribute of type Int we could infer the return types of calling the get method on a molecule. That would return a List of name/age tuples of type Iterable[(String, Int)]:

val nameAges: Iterable[(String, Int)] =

A feature of Molecule is to omit the values of an attribute from the result set by adding an underscore to the attribute name:

val names: Iterable[String] =

This is handy if we want to query for entities that we want to be sure have an age and where we at the same time don’t need the age returned.

Now let’s follow along the Datomic Seattle tutorial and see how Molecule can perform the same queries.

☝︎ A first query

To find communities we can make a communities molecule looking for entities with Community name:

val communities = m(

With this molecule at hand we can get the community names: Or we can ask for the size of our returned data set:

communities.get === // List of community names...

or we could check how many communities we have

communities.get.size === 150

If we want the entity ids of our communities we can add the generic attribute e to our molecule. We might not be interested in the names but we want to make sure that we find entities having a name, so we add the name attribute with an underscore (to omit it from the result set):

Community.e.name_.get(3) === List(17592186045518L, 17592186045516L, 17592186045514L)

☝︎ Getting an entity’s attribute values

A way to get additional attribute values once we have an entity id is to touch it:

val communityId = Community.e.name_.get.head

// Use the community id to touch all the entity's attribute values
communityId.touch === Map(
  ":community/type" -> ":community.type/website",
  ":community/url" -> "",
  ":community/category" -> List("community council"),
  ":community/orgtype" -> ":community.orgtype/community",
  ":db/id" -> 17592186045665L,
  ":community/name" -> "Greenlake Community Council",
  ":community/neighborhood" -> Map(
    ":db/id" -> 17592186045666L,
    ":neighborhood/district" -> Map(
      ":db/id" -> 17592186045667L,
      ":district/name" -> "Northwest",
      ":district/region" -> ":district.region/sw"),
    ":neighborhood/name" -> "Green Lake"))

We can also retrive attribute values one by one by simply applying an attribute name to the entity id:

communityId(":community/name") === Some("Greenlake Community Council")
communityId(":community/url") === Some("")
communityId(":community/category") === Some(Set("community council"))
communityId(":community/emptyOrBogusAttribute") === None

☝︎ Querying for an attribute’s value

After defining a molecule like we can call the get method on it to retrieve values that matches it. When there’s only one attribute defined in the molecule we’ll get a list of this attribute’s value back. === List(
  "KOMO Communities - Ballard",
  "Ballard Blog",
  "Ballard Historical Society")

If our molecule defines two or more attributes we’ll get tuples of values back. === List(
  ("Broadview Community Council", ""),
  ("KOMO Communities - Wallingford", ""),
  ("Aurora Seattle", ""))

☝︎ Querying by attribute values

When applying a value to an attribute we narrow the selection of entities that will match our molecule data structure. Let’s find communities of type “twitter”:`type`("twitter").get(3) === List(
  ("Columbia Citizens", "twitter"),
  ("Discover SLU", "twitter"),
  ("Fremont Universe", "twitter"))

(We use the back-ticks to avoid having Scala to think of type as a Scala keyword)

Since the type will always be “twitter” we could omit it from the result set by adding an underscore to the type attribute (and we don’t need the back-ticks anymore)."twitter").get(3) === List(
  "Magnolia Voice", "Columbia Citizens", "Discover SLU")

Notice that we get some different communities. We are not guaranteed a specific order of returned values and the first 3 values can therefore vary as we see here even though the molecules/queries are similar.

In most of our examples we supply static data like “twitter” but even though our molecules are created at compile time we can even supply data as variables like we would do with user input from forms etc. So we could as well write the following and get the same result.

val tw = "twitter" === List(
  "Magnolia Voice", "Columbia Citizens", "Discover SLU")

Retrieving values of many-attributes like category gives us sets of values back

Community.name_("belltown").category.get.head === Set("events", "news")

Since we often want a single result back, Molecule supplies a one convenience method that calls get.head.

We can apply multiple values to many-attributes like category and it will match entities having any of those values (OR-semantics)."news", "arts").get(3) === List(
  "Beach Drive Blog",
  "KOMO Communities - Ballard",
  "Ballard Blog")

☝︎ Querying across references

The sample data model includes three main entity types communities, neighborhoods and districts that are related to each other with references. Molecule lets you traverse those references by going from one namespace to the next. Let’s find communities in the noth-eastern region:"ne").get(3) === List(
  "Maple Leaf Community Council",
  "Hawthorne Hills Community Website",
  "KOMO Communities - View Ridge")

Or comunity names and their region: === List(
  ("KOMO Communities - North Seattle","n"),
  ("Morgan Junction Community Association","sw"),
  ("Friends of Seward Park","se"))

☝︎ Parameterizing queries - input molecules

When you apply values to molecules, the resulting query string is cached by Datomic. If you keep varying the string content, the cache is not effective. To take advantage of query caching it is recommended to make parameterized queries that can be cached once and used with varying input parameters.

Single input value for an attribute

Instead of applying the constant value “twitter” to a molecule Community.type("twitter") we can use the ? input placeholder in an “input molecule” telling us that it waits for an input value.

val communitiesOfType = m(

When can then apply different input values to our input molecule:

val twitterCommunities = communitiesOfType("twitter")
val facebookCommunities = communitiesOfType("facebook_page")

Those two molecules re-use the same cached query and just apply different input values. Now we can more efficiently get out results.

twitterCommunities.get(3) === List(
  "Magnolia Voice", "Columbia Citizens", "Discover SLU")
facebookCommunities.get(3) === List(
  "Magnolia Voice", "Columbia Citizens", "Discover SLU")

If we omit the underscore we can get the type too

val communitiesWithType = m(`type`(?))

communitiesWithType("twitter").get(3) === List(
  ("Discover SLU", "twitter"),
  ("Fremont Universe", "twitter"),
  ("Columbia Citizens", "twitter"))

Multiple input values for an attribute - logical OR

Find communities of type “facebook_page” OR “twitter”:

communitiesWithType("facebook_page" or "twitter").get(3) === List(
  ("Eastlake Community Council", "facebook_page"),
  ("Discover SLU", "twitter"),
  ("MyWallingford", "facebook_page"))

Alternative syntaxes where comma-separations act as logical OR:

communitiesWithType("facebook_page", "twitter")
communitiesWithType(Seq("facebook_page", "twitter"))

Tuple of input values for multiple attributes - logical AND

In addition to passing multiple values for a single attribute, you can pass a tuple of values for multiple attributes ensuring that both values are present.

val typeAndOrgtype = m(

With this input molecule we can find communities that are of type “email_list” AND orgtype “community”.

typeAndOrgtype("email_list" and "community").get(3) === List(
  "Ballard Moms",
  "Admiral Neighborhood Association",
  "15th Ave Community")

The order of arguments in the logical AND expression will correspond to the order of the input placeholders in the input molecule so that “email_list” corresponds to type_(?) and “community” corresponds to community_(?).

Arguments in expressions are also type-checked against the expected types of the corresponding attributes. Our IDE would infer that the orgtype attribute doesn’t expect an Int as the second argument if we were to pass the expression “email_list and 42”. This helps us avoid populating our database with unexpected data.

We can express logical AND expressions with a list of arguments too:

// AND-semantics given an input molecule expecting 2 inputs!
typeAndOrgtype("email_list", "community")

Or we can pass a list of arguments. IMPORTANT: note how the semantics of a list of arguments change compared to the OR semantics that we saw with the single-input molecule above that had OR-semantics. When we have multiple inputs the semantics change to AND-semantics!

// AND-semantics given an input molecule expecting 2 inputs!
typeAndOrgtype(Seq(("email_list", "community")))

Multiple tuples of input values for multiple attributes - logical AND/OR

We can also ask for alternative tuples of data structures. Since the input values can then vary, we could ask our molecule to return the input values too.

val typeAndOrgtype2 = m(`type`(?).orgtype(?))

Now let’s ask for email-list communities OR commercial website communities. Note how this combines logical AND and OR.

  ("email_list" and "community") or 
  ("website" and "commercial")
).get(5) === List(
  ("Fremont Arts Council", "email_list", "community"),
  ("Greenwood Community Council Announcements", "email_list", "community"),
  ("Broadview Community Council", "email_list", "community"),
  ("Alki News", "email_list", "community"),
  ("Beacon Hill Burglaries", "email_list", "community"))

As usual we can use alternative syntaxes as well. Here we group the AND expression arguments as tuple values. Comma-separations between the tuples act as logical OR.

// ((a AND b) OR (c AND d))
typeAndOrgtype2(("email_list", "community"), ("website", "commercial"))
typeAndOrgtype2(Seq(("email_list", "community"), ("website", "commercial")))

☝︎ Invoking functions in queries

Datomic lets you invoke functions in queries. Molecule use this to apply comparison operations on attribute values. Here we can for instance find communities whose name come before “C” in alphabetical order.

m( < "C").get(3) === List(
  "Ballard Blog", "Beach Drive Blog", "Beacon Hill Blog")

Note how we use the m method here to allow the postfix notation (spaces around <). Alternatively you can call the < method explicitly if you prefer this syntax:<("C").get(3) === List(
  "Ballard Blog", "Beach Drive Blog", "Beacon Hill Blog")

We can also parameterize the molecule.

val communitiesBefore = m( < ?)

communitiesBefore("C").get(3) === List(
  "Ballard Blog", "Beach Drive Blog", "Beacon Hill Blog")
communitiesBefore("A").get(3) === List("15th Ave Community")

☝︎ Querying with fulltext search

Datomic supports fulltext searching. When you define an attribute of string value, you can indicate whether it should be indexed for fulltext search. For instance Community name and category have the fulltextSearch option defined in the Seattle schema. Let’s find communities with “Wallingford” in the name.

( contains "Wallingford" take 3) === List(
  "KOMO Communities - Wallingford")

And we can parameterize fulltext searches too:

val communitiesWith = m( contains ?)

(communitiesWith("Wallingford") take 3) === List(
  "KOMO Communities - Wallingford")

Fulltext search on many-cardinality attributes

The category attribute can have several values so when we do a fulltext search on its values we’ll get back a set of its values that match our seed. We can also combine fulltext search with other constraints. Here we look for website communities with a category containing the word “food”:

m("website").category contains "food").get(3) === List(
  ("Community Harvest of Southwest Seattle", Set("sustainable food")),
  ("InBallard", Set("food")))

And parameterized:

val typeAndCategory = m( contains ?)

typeAndCategory("website", Set("food")).get(3) === List(
  ("Community Harvest of Southwest Seattle", Set("sustainable food")),
  ("InBallard", Set("food")))

Note how the values of the category attribute are now returned since they can vary across the result set contrary to the type attribute which is not since it will have the same value for all matches.

☝︎ Querying with rules - logical OR

Datomic rules are named groups of Datomic clauses that can be plugged into Datomic queries. As a Molecule user you don’t need to know about rules since Molecule automatically translates your logic to Datomic rules.

We can for instance find social media communities with a logical OR expresion:"twitter" or "facebook_page").get(3) === List(
  "Magnolia Voice", "Columbia Citizens", "Discover SLU")

… or find communities in the NE or SW regions."ne" or "sw").get(3) === List(
  "Beach Drive Blog", 
  "KOMO Communities - Green Lake", 
  "Delridge Produce Cooperative")

And we can combine them to find social-media communities in southern regions.

val southernSocialMedia = List(
  "Columbia Citizens",
  "Fauntleroy Community Association",
  "Blogging Georgetown")"twitter" or "facebook_page")
  .District.region_("sw" or "s" or "se").get === southernSocialMedia

Let’s parameterized the same query:

val typeAndRegion = m(

  ("twitter" or "facebook_page") and 
  ("sw" or "s" or "se")
).get === southernSocialMedia

// or
  Seq("twitter", "facebook_page"), 
  Seq("sw", "s", "se")
).get === southernSocialMedia

Note how this syntax for the ((a OR b) AND (c OR d)) expression is different from the syntax we had earlier in the section “Multiple tuples of input values for multiple attributes” where we had a ((a AND b) OR (c AND d)) expression.

☝︎ Working with time

All of the query results shown in the previous two sections were based on the initial seed data we loaded into our database. The data hasn’t changed since then. In this section we’ll load some more data, and explain how to work with database values from different moments in time.

Time is built in

One of the key concepts in Datomic is that new facts don’t replace old facts. Instead, by default, the system keeps track of all the facts, forever. This makes it possible to look at the database as it was at a certain point in time, or at the changes since a certain point in time.

When you submit a transaction to a database, Datomic keeps track of the entities, attributes and values you add or retract. It also keeps track of the transaction itself. Transactions are entities in their own right, and you can write queries to find them. The system associates one attribute with each transaction entity, Db.txInstant, which records the time the transaction was processed.

Molecule has a Db namespace with a txInstant attribute that we can use to query for transactions instants (represented as java.util.Date instances) that has been created. We’ve only executed two transactions, but the earlier system executed a few as part of its bootstrapping process. We know, though, that our two are the most recent. The code below uses a Db.txInstant molecule to retrieve transaction times, sort them into reverse chronological order, and store the most recent two as dataTxDate and schemaTxDate, when we added our data and our schema, respectively.

val txDates = Db.txInstant.get.toSeq.sorted.reverse
val dataTxDate = txDates(0)
val schemaTxDate = txDates(1)

Revisiting the past - getAsOf(PastDate)

Once we have the relevant transaction times, we can look at the database as of that point in time. To do this, we retrieve the current database value by calling the molecule method getAsOf, passing in the Date we’re interested in. The getAsOf method returns a new molecule based on the database value that is “rewound” back to the requested date.

An example will help make this clear. The code below gets the value of the database as of our schema transaction. Then it runs our very first query, which retrieves entities representing communities, and prints the size of the results. Because we’re using a database value from before we ran the transaction to load seed data, the size is 0.

// Take all Community entities
val communities = m(Community.e.name_)
communities.getAsOf(schemaTxDate).size === 0

If we do the same thing using the date of our seed data transaction, the query returns 150 results, because as of that moment, the seed data is there.

communities.getAsOf(dataTxDate).size === 150

Changes since a date - getSince(compareDate)

The getAsOf method allows us to look at a database value containing data changes up to a specific point in time. There is another method getSince that allows us to look at a database value containing data changes since a specific point in time.

The code below gets the value of the database since our schema transaction and counts the number of communities. Because we’re using a database value containing changes made since we ran the transaction to load our schema - including the changes made when we loaded our seed data - the size is 150.

communities.getSince(schemaTxDate).size === 150

If we do the same thing using the date of our seed data transaction, the query returns 0 results, because we haven’t added any communities since that time.

communities.getSince(dataTxDate).size === 0

While we passed specific transaction dates to getAsOf and getSince, you can pass any date. The system find the closest relevant transaction and use that as the basis for filtering.

Keeping track of data over time is a very powerful feature. However, there may be some data you don’t want to keep old versions of. You can control whether old versions are kept on a per-attribute basis by adding noHistory to your attribute definition when you create your schema. If you choose not to keep history for a given attribute and you look at a database as of a time before the most recent change to a given entity’s value for that attribute, you will not find any value for it.

Imagining the future - getWith(TestTxData)

Revisiting the past is a very powerful feature. It’s also possible to imagine the future. The getAsOf and getSince methods work by removing data from the current database value. You can also add data to a database value, using the Molecule method getWith. The result is a database value that’s been modified without submitting a transaction and changing the data stored in the system. The modified database value can be used to execute queries, allowing you to perform “what if” calculations before committing to data changes.

When a getWith(TestTxData) database object goes out of scope it is simply garbage collected. So we don’t need to do any tear down of some state as is common with normal database mockups.

We can explore this feature using a second seed data file provided with the sample application, “samples/seattle/seattle-data1.edn”. The code below reads it into a list.

val data_rdr2 = new FileReader("examples/resources/seattle/seattle-data1a.dtm")
val newDataTx = Util.readAll(data_rdr2).get(0).asInstanceOf[java.util.List[Object]]

Once we have this new data transaction, we can build a database value that includes it. To do that, we simply get the current database value (or one as of or since a point in time) and call getWith, passing in the transaction data. getWith returns a molecule based on the new value of the database after the new data is added. If we execute our community counting query against it, we get 258 results.

// test db
communities.getWith(newDataTx).get.size === 258

The actual data hasn’t changed yet, so if we query the current database value, we still get 150 results. We won’t see a change in the current database value until we submit the new transaction. After that, querying the current database value returns 258 results. Finally, if we get another database value containing data since our first seed data transaction ran, and query for communities we get 108 results, the number added by new data transaction.

// existing db
communities.get.size === 150

// transact

// updated db
communities.get.size === 258

// number of new transactions
communities.getSince(dataTxDate).size === 108

☝︎ Insert data

You can add data in two ways with Molecule:

  1. Build a molecule with data and insert
  2. Use a molecule template to insert matching data

“Data-molecule” with values

To insert a single data structure you can populate a molecule with values and then add it:

  .category("my", "favorites")"myNeighborhood")"myDistrict").region("nw").save.eids === List(
    17592186045891L, 17592186045892L, 17592186045893L)

Note how we can add values for referenced namespaces and multiple values for cardinality-many attributes like category - all in one go!

Apart from the new Community entity two more entities are also added. Since neither “myNeighborhood” nor “myDistrict” exist they are created to so that we can reference them.

In Datomic there is no requirement that we add a “complete” set of namespace attributes to create an entity. For instance, we could add a community only with"My community").add.

“Insert-molecule” + matching values

A more efficient way to add larger sets of data is to define an “Insert-Molecule” that models the data structure we want to insert into the database. Note how we call the insert method to define it as an Input-Molecule:

val insertCommunity = m(`type`.orgtype.category
) insert

We can then create a new Community by applying a matching set of attribute values:

  "BBB", "url B", "twitter", "personal", Set("some", "cat B"), 
    "neighborhood B", 
    "district B", "s"
).eids === List(17592186045895L, 17592186045896L, 17592186045897L)

As before, three entities are created here since we reference a new Neighborhood and District.

All values are type checked against the expected type of each attribute!

Insert-Molecule + multiple data tuples

With our insert-molecule at hand we can insert large numbers of data tuples. As an example we can insert 3 communities and referenced neighborhoods/district/regions in one go:

val newCommunitiesData = List(
  ("DDD Blogging Georgetown", "", 
    "blog", "commercial", Set("DD cat 1", "DD cat 2"), 
    "DD Georgetown", "Greater Duwamish", "s"),
  ("DDD Interbay District Blog", "", 
    "blog", "community", Set("DD cat 3"), 
    "DD Interbay", "Magnolia/Queen Anne", "w"),
  ("DDD KOMO Communities - West Seattle", "", 
    "blog", "commercial", Set("DD cat 4"), 
    "DD West Seattle", "Southwest", "sw")

// Insert 3 new communities with 3 new neighborhoods
insertCommunity(newCommunitiesData) === List(
  17592186045909L, 17592186045910L, 17592186045911L,
  17592186045912L, 17592186045913L, 17592186045914L,
  17592186045915L, 17592186045916L, 17592186045917L)

This approach gives us a clean way of populating a database where we can supply raw data from any source easily as long as we can format it as a list of tuples of values each matching our template molecule.

We use an insert-molecule also when we initially populate the Seattle database.

Optional attribute values

We might have a data set with some optional attribute values. We can append a $ to such attribute names to tell Molecule that this is an optional value:

val insertCommunity = m(`type`.orgtype$.category
) insert

If for instance some row has no orgtype we can use None (and likewise Some(<value>)):

("community4", "url2", "blog", None, Set("cat3", "cat1"), "NbhName4", "DistName4", "ne")

In an sql table we would “insert a null value” for such column. But with Molecule/Datomic we just simply don’t assert any orgtype value for that entity at all! In other words: there is no orgtype fact to be asserted.

Type safety

In this example we have only inserted text strings. But all input is type checked against the selectedattributes of the molecule which makes the insert operation type safe. We even infer the expected type so that our IDE will bark if it finds for instance an Integer somewhere in our input data:

("community2", "url2", "type2", 42, Set("cat3", "cat1"), "NbhName2", "DistName2", "DistReg2")

A data set having the value 42 as a value for the orgtype attribute won’t compile and our IDE will infer that we have an invalid data set.

☝︎ Update and/or delete data

To update data with Molecule, we first need the id of the entity that we want to update.

val belltown = Community.e.name_("belltown").get.head

Then we can “replace” some attributes

Community(belltown).name("belltown 2").url("url 2").update

What really happens is not a mutation of data since no data is ever deleted or over-written in Datomic. Instead a new fact for the attribute is asserted. The new fact will turn up when queried for. But if we go back in time we can see the previous value at that point in time - many updates could have been performed over time, and all previous values are stored.

Updating cardinality-many attributes

When updating cardinality-many attributes we need to tell which of the values we want to update:

Community(belltown).category("news" -> "Cool news").update

This syntax causes Molecule to first retract the old value “news” and then assert/add the new value “Cool news”. Note that if the before-value doesn’t exist the new value will still be inserted, so you might be sure what the current value is by querying for it first.

We can even update several values of a cardinality-many attribute in one go:

  "Cool news" -> "Super cool news",
  "events" -> "Super cool events").update

Adding/removing values of cardinality-many attributes

If we want to add or remove values of a cardinality-many attribute we can use the following mehtods:

// add
Community(belltown).category.add("extra category").update

// remove
Community(belltown).category.remove("Super cool events").update

Delete/retract values

When you update a molecule you can apply an empty value apply() or simply () after an attribute name to delete/retract the attributes value(s). We can mix updates and retractions:

Community(belltown).name("belltown 3").url().category().update

name gets the new value “belltown 3” and both the url and category attributes have their values retracted.

There are a couple of important things to know about retracting data. The first is that we must specify the value of the attribute being retracted. When applying the empty value, Molecule therefore first looks up the current value in order to be able to retract it.

The other thing to know is that, because we can access database values as they existed at specific points in time, we can retrieve retracted data by looking in the past. In other words, the data isn’t really gone. If we want data to really be gone after we retract it, we have to disable history for the specific attribute, as described in Database setup.