Category: Database

NEO4J: WITH and Scope

I have encountered another manual reading failure error — if you actually read the Cypher documentation for WITH, it clearly states that entering a WITH block creates a new scope into which previous variables are not imported. Unless you specifically include them. You can individually include variables in this new scope (WITH oldvariable1, oldvariable2, newSomething as newvariable1) or just use * to include all previous variables.

Doing neither will produce an error that a variable that you are absolutely positive exists does not, in fact, exist.

NEO4J: Union Sets

There are a lot of places where cypher queries don’t seem to have an “OR” type of functionality … but you can union two returned sets provided they have the same properties list
MATCH z=(:TOMATO {name: ‘Black Krim’})
RETURN z
UNION
MATCH z=(:TOMATO {name: ‘Cherokee Purple’})
RETURN z;

NEO4J: Debugging a Cypher Query

It is somewhat ironic that I continue to use print statements as my debugging tool of choice when programming but spent a decent bit of time trying to find a cypher query debugger. Just use a print statement — or, in this case, return.

When my query returned an error indicating that the variable isn’t defined even though I copy/pasted the variable name from whence I defined it:

I could just omit the component of the query with the error and try returning this variable

And performing operations on null values may not get me anywhere. Adding a replacement command to drop the commas produces integer values:

NEO4J: Installing Plugins

Since I have the /plugins directory persisted, I can use wget <URL> to grab a JAR file and place it into the plugins folder. Restart the container and the plugin is active.

Example installing APOC extended plugin:

cd /docker/neo4j/plugins;wget https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/5.11.0/apoc-5.11.0-extended.jar;docker stop neo4j;docker start neo4j

NEO4J: APOC Plugin in Docker Container

I wanted to test some of the Awesome Procedures on Cypher (APOC) functions, but first I needed to install the plugins. I needed to modify my docker run statement slightly to persist the /plugins directory and install APOC core:

 

docker run -dit -p 7474:7474 -p 7687:7687 --volume=/docker/neo4j/data:/data --volume=/docker/neo4j/conf:/var/lib/neo4j/conf --volume=/docker/neo4j/plugins:/plugins -e NEO4J_AUTH=none -e NEO4J_apoc_export_file_enabled=true -e NEO4J_apoc_import_file_enabled=true -e NEO4J_apoc_import_file_use__neo4j__config=true -e NEO4J_PLUGINS=\[\"apoc\"\] --name neo4j neo4j

NEO4J: Adding Indices

Like SQL-based databases, you can create indices in Neo4j to optimize frequently performed searches. In my particular case, I am usually searching by the plant name. Adding an index on the plant’s name, therefore, makes sense:

CREATE INDEX index_tomato_name IF NOT EXISTS
FOR (n:TOMATO)
ON (n.name)

I am also interested in mapping the genetic lineage, so I’ve added indices for the male and female parent plants:

CREATE INDEX index_tomato_parentm IF NOT EXISTS
for ()-[r:PARENT_M]-()
on (r.name)

CREATE INDEX index_tomato_parentf IF NOT EXISTS
for ()-[r:PARENT_F]-()
on (r.name)

 

Hypothetically, you can use the procedure CALL db.indexes(); to view all of the indices in a database, but SHOW PROCEDURES; shows me that procedure isn’t registered in the community edition.

╒═════════════════════════════════════════════════════════╤══════════════════════════════════════════════════════════════════════╤═══════╤═════════════╕
│name                                                     │description                                                           │mode   │worksOnSystem│
╞═════════════════════════════════════════════════════════╪══════════════════════════════════════════════════════════════════════╪═══════╪═════════════╡
│"db.awaitIndex"                                          │"Wait for an index to come online (for example: CALL db.awaitIndex(\"M│"READ" │true         │
│                                                         │yIndex\", 300))."                                                     │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.awaitIndexes"                                        │"Wait for all indexes to come online (for example: CALL db.awaitIndexe│"READ" │true         │
│                                                         │s(300))."                                                             │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.clearQueryCaches"                                    │"Clears all query caches."                                            │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.createLabel"                                         │"Create a label"                                                      │"WRITE"│false        │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.createProperty"                                      │"Create a Property"                                                   │"WRITE"│false        │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.createRelationshipType"                              │"Create a RelationshipType"                                           │"WRITE"│false        │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.index.fulltext.awaitEventuallyConsistentIndexRefresh"│"Wait for the updates from recently committed transactions to be appli│"READ" │true         │
│                                                         │ed to any eventually-consistent full-text indexes."                   │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.index.fulltext.listAvailableAnalyzers"               │"List the available analyzers that the full-text indexes can be config│"READ" │true         │
│                                                         │ured with."                                                           │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.index.fulltext.queryNodes"                           │"Query the given full-text index. Returns the matching nodes, and thei│"READ" │true         │
│                                                         │r Lucene query score, ordered by score. Valid keys for the options map│       │             │
│                                                         │ are: 'skip' to skip the top N results; 'limit' to limit the number of│       │             │
│                                                         │ results returned; 'analyzer' to use the specified analyzer as search │       │             │
│                                                         │analyzer for this query."                                             │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.index.fulltext.queryRelationships"                   │"Query the given full-text index. Returns the matching relationships, │"READ" │true         │
│                                                         │and their Lucene query score, ordered by score. Valid keys for the opt│       │             │
│                                                         │ions map are: 'skip' to skip the top N results; 'limit' to limit the n│       │             │
│                                                         │umber of results returned; 'analyzer' to use the specified analyzer as│       │             │
│                                                         │ search analyzer for this query."                                     │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.info"                                                │"Provides information regarding the database."                        │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.labels"                                              │"List all available labels in the database."                          │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.ping"                                                │"This procedure can be used by client side tooling to test whether the│"READ" │true         │
│                                                         │y are correctly connected to a database. The procedure is available in│       │             │
│                                                         │ all databases and always returns true. A faulty connection can be det│       │             │
│                                                         │ected by not being able to call this procedure."                      │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.prepareForReplanning"                                │"Triggers an index resample and waits for it to complete, and after th│"READ" │true         │
│                                                         │at clears query caches. After this procedure has finished queries will│       │             │
│                                                         │ be planned using the latest database statistics."                    │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.propertyKeys"                                        │"List all property keys in the database."                             │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.relationshipTypes"                                   │"List all available relationship types in the database."              │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.resampleIndex"                                       │"Schedule resampling of an index (for example: CALL db.resampleIndex(\│"READ" │true         │
│                                                         │"MyIndex\"))."                                                        │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.resampleOutdatedIndexes"                             │"Schedule resampling of all outdated indexes."                        │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.schema.nodeTypeProperties"                           │"Show the derived property schema of the nodes in tabular form."      │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.schema.relTypeProperties"                            │"Show the derived property schema of the relationships in tabular form│"READ" │true         │
│                                                         │."                                                                    │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.schema.visualization"                                │"Visualizes the schema of the data based on available statistics. A ne│"READ" │true         │
│                                                         │w node is returned for each label. The properties represented on the n│       │             │
│                                                         │ode include: `name` (label name), `indexes` (list of indexes), and `co│       │             │
│                                                         │nstraints` (list of constraints). A relationship of a given type is re│       │             │
│                                                         │turned for all possible combinations of start and end nodes. The prope│       │             │
│                                                         │rties represented on the relationship include: `name` (type name). Not│       │             │
│                                                         │e that this may include additional relationships that do not exist in │       │             │
│                                                         │the data due to the information available in the count store. "       │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.clear"                                         │"Clear collected data of a given data section. Valid sections are 'QUE│"READ" │true         │
│                                                         │RIES'"                                                                │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.collect"                                       │"Start data collection of a given data section. Valid sections are 'QU│"READ" │true         │
│                                                         │ERIES'"                                                               │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.retrieve"                                      │"Retrieve statistical data about the current database. Valid sections │"READ" │true         │
│                                                         │are 'GRAPH COUNTS', 'TOKENS', 'QUERIES', 'META'"                      │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.retrieveAllAnonymized"                         │"Retrieve all available statistical data about the current database, i│"READ" │true         │
│                                                         │n an anonymized form."                                                │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.status"                                        │"Retrieve the status of all available collector daemons, for this data│"READ" │true         │
│                                                         │base."                                                                │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"db.stats.stop"                                          │"Stop data collection of a given data section. Valid sections are 'QUE│"READ" │true         │
│                                                         │RIES'"                                                                │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.cluster.routing.getRoutingTable"                   │"Returns the advertised bolt capable endpoints for a given database, d│"DBMS" │true         │
│                                                         │ivided by each endpoint's capabilities. For example an endpoint may se│       │             │
│                                                         │rve read queries, write queries and/or future getRoutingTable requests│       │             │
│                                                         │."                                                                    │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.components"                                        │"List DBMS components and their versions."                            │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.info"                                              │"Provides information regarding the DBMS."                            │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.killConnection"                                    │"Kill network connection with the given connection id."               │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.killConnections"                                   │"Kill all network connections with the given connection ids."         │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.listCapabilities"                                  │"List capabilities"                                                   │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.listConfig"                                        │"List the currently active config of Neo4j."                          │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.listConnections"                                   │"List all accepted network connections at this instance that are visib│"DBMS" │true         │
│                                                         │le to the user."                                                      │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.queryJmx"                                          │"Query JMX management data by domain and name. For instance, \"*:*\"" │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.routing.getRoutingTable"                           │"Returns the advertised bolt capable endpoints for a given database, d│"DBMS" │true         │
│                                                         │ivided by each endpoint's capabilities. For example an endpoint may se│       │             │
│                                                         │rve read queries, write queries and/or future getRoutingTable requests│       │             │
│                                                         │."                                                                    │       │             │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.upgrade"                                           │"Upgrade the system database schema if it is not the current schema." │"WRITE"│true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"dbms.upgradeStatus"                                     │"Report the current status of the system database sub-graph schema."  │"READ" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"tx.getMetaData"                                         │"Provides attached transaction metadata."                             │"DBMS" │true         │
├─────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────┼───────┼─────────────┤
│"tx.setMetaData"                                         │"Attaches a map of data to the transaction. The data will be printed w│"DBMS" │false        │
│                                                         │hen listing queries, and inserted into the query log."                │       │             │
└─────────────────────────────────────────────────────────┴──────────────────────────────────────────────────────────────────────┴

NEO4J: Searching

Returning data from NEO4J is matching — we can match a node using MATCH p=(a:TOMATO {name: 'Black Krim'}) return p;

where the object “p” becomes a set of nodes labeled with ‘TOMATO’ where the value of ‘name’ is ‘Black Krim’

More advanced matches set the return object to a set of nodes and relationships — here we set p to the set of items starting at the node labeled TOMATO with name ‘PLANT0’ with relationships and nodes until you get to a node labeled TOMATO with name ‘Tomato0000007’

MATCH p=(a:TOMATO {name: 'PLANT0'})-[*]->(b:TOMATO {name: 'Tomato0000007'}) RETURN p

NEO4J: Relational Databases

I always found it odd that relational databases didn’t really have relationships as part of the stored data. Technically, they could if you had a view or stored procedure with a bunch of JOIN’s in there. But relational databases stored data about which you could build relationships. And people using the data may not even know about relationships that other people saw within that data. Some of our databases at work have amazing documentation — a hundred meg of PDF files detailing the relationships that the database creator wanted people to use. Other databases? No such luck!

To me, that’s the big advantage of a Graph database — the relationships are stored within the data, so anyone viewing it for the first time doesn’t need to poke around, see where values could be correlated across tables, and create their own JOIN statements to build out the relationship. Recording data in the database means defining those relationships. It would still be good to document a graph model (we have ‘people’ nodes who ‘act in’, ‘cast’, ‘produce’, or ‘direct’ ‘movie’ nodes), but you could figure all of those things out by perusing the database content.

NEO4J: Applications

I remember a friend of mine who taught introductory computer programming classes in University. One test question he always used was essentially ‘do something that people can do easily’. The exact details would change year to year, but the important thing is that the instructions simply stated “Sort the following list in alphabetical order”. Not write a program that sorts an arbitrary list into alphabetical order — sort this list. And, sure, you could write a program to do it. A program that would successfully accomplish the goal got an A grade. But so did someone who just took the list, sorted it alphabetically in their head, and wrote the list in alphabetical order. That answer? Would get extra credit. Because knowing when not to program is really important too. From a business standpoint, it’s a waste of money for someone to write a program to perform some easy one-off task that is never going to be done again.

I think about that a lot when I see “new” technologies getting picked up. I call it the “CIO magazine” approach to technology adoption. You see some new thing, have a very basic understanding of how it works, and decide we need to use one of these. And fail to consider if your use case is reasonable or if you’re willing to do the extra work for the “new” thing. The biggest example I experience of “not reasonable” is the prevalence of Java programming. If I am selling software, cross-platform compilation is A Very Good Thing. If I can maintain a single pipeline and a single release that all of my customers can use? Score! Internally developed software, though? We requisition specific platforms. Our Linux servers are not going to be Windows servers next Tuesday. I can write code, compile it for Linux, and be fine even if it doesn’t run under Windows. Because it doesn’t need to run under Windows. The extra work — our internal support groups adopted Agile. Except no one was willing to prioritize the ticket queue — so there’s no prioritized list of work to select from. Everyone has two “issues” for their sprint — “incident support” and “admin time”. A few people might get involved in a specific project and add “dns decom” or “nextgen vpn testing”. But sprint planning is repetitive (I’ve got incident support & admin time, too!), daily standups were a joke (I did tickets yesterday & had a meeting), and techs still didn’t know what ticket was the priority that should be pulled next. Which doesn’t make Java or Agile a bad idea — it just makes them overly complicated for the situation in which they are being used.

I think of all of this when I see Graph databases being implemented — step #0 is does a graph database make sense for my data? What would that mean? It would mean that the data elements are interconnected somehow — if you’d be using a lot of JOIN queries to interact with the stored data, then a graph model might make sense. If you’re just selecting items from individual tables where values are whatever? Then a graph database is a complex way of storing and accessing that data.