I’m executing Strategus based on the instructions in the SOS video given by @anthonysena. KeyringSetup.R executes without any issues (with the modifications I’ve made for my configuration).
When I run StrategusCodeToRun.R I get the error shown below for the execute function.
However, when I test the connectionDetails I do not get this error (see output below).
I’m guessing that maybe the execute function does not use the connectionDetails object directly but pulls parameters out of it (and maybe also from the keyring?).
What do I need to do to get execute to connect to my Databricks instance?
Is there a way I can step through the execute function in the StrategusCodeToRun.R script to see how the connection is being made and why it is failing (I’m new(ish) to R and R-Studio)?
Scripts and output are attachd.
KeyringSetup.R.txt (3.9 KB)
StrategusCodeToRun.R.txt (2.7 KB)
output.txt (12.7 KB)
Error Seen for execute function in StrategusCodeToRun.R
>
> execute(
+ analysisSpecifications = analysisSpecifications,
+ executionSettings = executionSettings,
+ executionScriptFolder = file.path(outputLocation, connectionDetailsReference, "strategusExecution"),
+ keyringName = "sos-challenge"
+ )
Connecting using Spark JDBC driver
Error in rJava::.jcall(jdbcDriver, "Ljava/sql/Connection;", "connect", :
java.sql.SQLException: [Databricks][DatabricksJDBCDriver](500593) Communication link failure. Failed to connect to server. Reason: HTTP Response code: 401, Error message: Unknown.
>
Output from test of connection
> # --- start test of connectionDetails -----------------------------------------------------------
> testConnection <- DatabaseConnector::connect(connectionDetails)
Connecting using Spark JDBC driver
> testConnection
<DatabaseConnectorConnection> nachc-databricks.cloud.databricks.com>
DatabaseConnector::querySql(testConnection, "show tables in demo_cdm")
DATABASE TABLENAME ISTEMPORARY
1 demo_cdm attribute_definition 0
2 demo_cdm care_site 0
3 demo_cdm cdm_source 0
4 demo_cdm cohort 0
5 demo_cdm cohort_censor_stats 0
6 demo_cdm cohort_definition 0
7 demo_cdm cohort_inclusion 0
8 demo_cdm cohort_inclusion_result 0
9 demo_cdm cohort_inclusion_stats 0
10 demo_cdm cohort_summary_stats 0
11 demo_cdm concept 0
12 demo_cdm concept_ancestor 0
13 demo_cdm concept_class 0
14 demo_cdm concept_relationship 0
15 demo_cdm concept_synonym 0
16 demo_cdm condition_era 0
17 demo_cdm condition_occurrence 0
18 demo_cdm cost 0
19 demo_cdm death 0
20 demo_cdm device_exposure 0
21 demo_cdm domain 0
22 demo_cdm dose_era 0
23 demo_cdm drug_era 0
24 demo_cdm drug_exposure 0
25 demo_cdm drug_strength 0
26 demo_cdm fact_relationship 0
27 demo_cdm location 0
28 demo_cdm measurement 0
29 demo_cdm metadata 0
30 demo_cdm note 0
31 demo_cdm note_nlp 0
32 demo_cdm observation 0
33 demo_cdm observation_period 0
34 demo_cdm payer_plan_period 0
35 demo_cdm person 0
36 demo_cdm procedure_occurrence 0
37 demo_cdm provider 0
38 demo_cdm relationship 0
39 demo_cdm source_to_concept_map 0
40 demo_cdm specimen 0
41 demo_cdm visit_detail 0
42 demo_cdm visit_occurrence 0
43 demo_cdm vocabulary 0
> DatabaseConnector::disconnect(testConnection)
> # --- end test of connectionDetails -------------------------------------------------------------
>
Thanks,
John