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Issue compiling circe-be repository

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#1

Hi I’m new to OHDSI, and I’m having issues compiling the circe-be repository

repo: https://github.com/OHDSI/circe-be
master branch / tag: v1.9.5

$ mvn --version
Apache Maven 3.8.5 (3599d3414f046de2324203b78ddcf9b5e4388aa0)
Maven home: /usr/local/Cellar/maven/3.8.5/libexec
Java version: 18.0.1, vendor: Homebrew, runtime: /usr/local/Cellar/openjdk/18.0.1/libexec/openjdk.jdk/Contents/Home
Default locale: en_US, platform encoding: UTF-8
OS name: “mac os x”, version: “12.5”, arch: “x86_64”, family: “mac”

Running mvn compile gave me this error

$ mvn clean compile

[INFO] Scanning for projects…

[INFO]

[INFO] --------------------------< org.ohdsi:circe >---------------------------

[INFO] Building circe 1.9.5-SNAPSHOT

[INFO] --------------------------------[ jar ]---------------------------------

Downloading from central: https]://repo.maven.apache.org/maven2/org/ohdsi/standardized-analysis-utils/1.3.0/standardized-analysis-utils-1.3.0.pom

Downloading from central: https]://repo.maven.apache.org/maven2/org/ohdsi/sql/SqlRender/1.6.8/SqlRender-1.6.8.pom

[INFO] ------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 1.820 s

[INFO] Finished at: 2022-08-17T14:44:19-07:00

[INFO] ------------------------------------------------------------------------

[ERROR] Failed to execute goal on project circe: Could not resolve dependencies for project org.ohdsi:circe:jar:1.9.5-SNAPSHOT: Failed to collect dependencies at org.ohdsi:standardized-analysis-utils:jar:1.3.0: Failed to read artifact descriptor for org.ohdsi:standardized-analysis-utils:jar:1.3.0: Could not transfer artifact org.ohdsi:standardized-analysis-utils:pom:1.3.0 from/to maven-default-http-blocker (http]://0.0.0.0/): Blocked mirror for repositories: [ohdsi (http://repo.ohdsi.org:8085/nexus/content/repositories/releases, default, releases+snapshots), ohdsi.thirdparty (http]://repo.ohdsi.org:8085/nexus/content/repositories/thirdparty, default, releases+snapshots), ohdsi.snapshots (http]://repo.ohdsi.org:8085/nexus/content/repositories/snapshots, default, snapshots)] → [Help 1]

From what I understand mvn requires ‘https’ for the repository url for security reasons. Anyone else have this issue? Any insight is appreciated.

#2

Current versions of maven have a default http blocker for downloading from insecure repositories. You can either configure a specific mirror exception for the ohdsi repository or in the main maven settings remove the default blocker mirror which looks like this:

<mirror>
  <id>maven-default-http-blocker</id>
  <mirrorOf>external:http:*</mirrorOf>
  <name>Pseudo repository to mirror external repositories initially using HTTP.</name>
  <url>http://0.0.0.0/</url>
  <blocked>true</blocked>
</mirror>

Either solution should allow you to build the library.

#3

Thanks for the reply. I was able to get past the error using the mirror trick.

However I got errors from the test suite while trying to build the project

Results :

Tests in error:
CohortGeneration_5_2_0_Test.org.ohdsi.circe.cohortdefinition.CohortGeneration_5_2_0_Test » IllegalState
WindowCriteria_5_0_0_Test.org.ohdsi.circe.cohortdefinition.builders.WindowCriteria_5_0_0_Test » IllegalState
CorelatedCriteria_5_0_0_Test.org.ohdsi.circe.cohortdefinition.builders.CorelatedCriteria_5_0_0_Test » IllegalState
…

In my case it looks like there’s some failure setting up the embedded postgres server

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.016 sec <<< FAILURE! - in org.ohdsi.circe.cohortdefinition.CohortGeneration_5_0_0_Test
org.ohdsi.circe.cohortdefinition.CohortGeneration_5_0_0_Test Time elapsed: 0.016 sec <<< ERROR!
java.lang.IllegalStateException: Process [/var/folders/lb/hlcdhxzd5bx2pctsmrs5p6dw0000gq/T/embedded-pg/PG-73dc0043fe7bdb624d5e8726bc457b7e/bin/initdb, -A, trust, -U, postgres, -D, /var/folders/lb/hlcdhxzd5bx2pctsmrs5p6dw0000gq/T/epg14979164187153190101, -E, UTF-8] failed

at com.opentable.db.postgres.embedded.EmbeddedPostgres.system(EmbeddedPostgres.java:602)
at com.opentable.db.postgres.embedded.EmbeddedPostgres.initdb(EmbeddedPostgres.java:221)
at com.opentable.db.postgres.embedded.EmbeddedPostgres.(EmbeddedPostgres.java:142)
at com.opentable.db.postgres.embedded.EmbeddedPostgres$Builder.start(EmbeddedPostgres.java:554)
at org.ohdsi.circe.PostgresSingletonRule.pg(PostgresSingletonRule.java:67)
at org.ohdsi.circe.PostgresSingletonRule.before(PostgresSingletonRule.java:59)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:50)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:264)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:153)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:124)
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:200)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:153)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:103)

It’s not blocking me at the moment, but out of curiosity I’m wondering if there’s some setup steps I’m missing.

#4

Hi, sorry for the problems.

On the note of the maven problem, we’ll update the repository references to be compatible with Maven 3.6+

As far as your problem with the embedded postgresql instance, there shouldn’t be any setup necessary (it works out of the box on my windows box, but I think you’re running under linux). We were running on TravisCI for a while, but I just found out that TravisCI was disconnected from the circe repo, and I will have to invoke the tests and codecov via git actions. I’ll put that on my to-do to get that running.

I did some searching and if you’re actually on MacOs and not linux, you may find some guidance here: java - Tests using embedded postgres fail with Illegal State Exception - Stack Overflow.

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