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macarthur-lab / matchbox

matchbox server for the Matchmaker Exchange
BSD 3-Clause "New" or "Revised" License
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Error while deploying using Docker (both methods) #53

Closed northwestwitch closed 5 years ago

northwestwitch commented 5 years ago

Hi! We had a short exchange about this on another issue (#51). Don't know if you are working on this but I tested today and the installation with Docker (with data in container) still gives this error:

[INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7.643 s [INFO] Finished at: 2018-10-15T08:36:26+00:00 [INFO] Final Memory: 17M/165M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project matchbox: Could not resolve dependencies for project org.broadinstitute.macarthurlab:matchbox:jar:0.1.0: The following artifacts could not be resolved: org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:10.1.0, org.monarchinitiative.exomiser:exomiser-spring-boot-test:jar:10.1.0: Could not find artifact org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:10.1.0 in central (https://repo.maven.apache.org/maven2) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException The command '/bin/sh -c $MVN -Dmaven.test.skip=true clean install package' returned a non-zero code: 1

I'll test with other Docker method now!

northwestwitch commented 5 years ago

Nope. Using the "with_data_mounted_to_container" option I get these errors:

Downloaded: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.9/maven-project-2.0.9.jar (119 KB at 424.7 KB/sec) [INFO] Changes detected - recompiling the module! [INFO] Compiling 42 source files to /Exomiser/matchbox/target/classes [INFO] ------------------------------------------------------------- [WARNING] COMPILATION WARNING : [INFO] ------------------------------------------------------------- [WARNING] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/network/Communication.java:[60,98] sun.net.www.protocol.https.Handler is internal proprietary API and may be removed in a future release [WARNING] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/network/Communication.java:[153,83] sun.net.www.protocol.http.Handler is internal proprietary API and may be removed in a future release [WARNING] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/match/PhenotypeSimilarityScorerImpl.java: /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/match/PhenotypeSimilarityScorerImpl.java uses unchecked or unsafe operations. [WARNING] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/match/PhenotypeSimilarityScorerImpl.java: Recompile with -Xlint:unchecked for details. [INFO] 4 warnings [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[3,19] package org.mockito does not exist [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[23,17] cannot find symbol symbol: variable Mockito location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[24,17] cannot find symbol symbol: variable Mockito location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[25,17] cannot find symbol symbol: variable Mockito location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [INFO] 4 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 11.322 s [INFO] Finished at: 2018-10-15T10:22:25+00:00 [INFO] Final Memory: 37M/176M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project matchbox: Compilation failure: Compilation failure: [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[3,19] package org.mockito does not exist [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[23,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[24,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[25,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException The command '/bin/sh -c $MVN -Dmaven.test.skip=true clean install package' returned a non-zero code: 1

northwestwitch commented 5 years ago

Additionally, the address where to download the seqr reference data has changed, so I think the link the readme of the installer with data mounted to container should be changed from:

wget https://storage.googleapis.com/seqr-reference-data/1711_phenotype.tar.gz to

wget https://storage.googleapis.com/seqr-reference-data/1807_phenotype.tar.gz

DSRYU commented 5 years ago

@northwestwitch

Hello.

I also got same error message during updating to new release matchbox.

The used matchbox version is with_data_mounted_to_container and the reference directory details are as follows: ls -al /data/reference_data/ total 16 drwxr-xr-x 4 rarebird rarebird 4096 11월 8 18:08 . drwxr-xr-x 3 root root 4096 11월 8 18:13 .. drwxrwx--- 3 rarebird rarebird 4096 7월 27 12:40 1807_phenotype drwxrwxrwx 3 rarebird rarebird 4096 8월 7 2017 exomiser-cli-8.0.0

When docker image is building, I got the same error, "cannot find symbol , symbol: variable Mockito" as follows. I also got same error when I tried to install matchbox using another docker version image.

[INFO] 4 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 59.763 s [INFO] Finished at: 2018-11-08T09:28:36+00:00 [INFO] Final Memory: 40M/329M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project matchbox: Compilation failure: Compilation failure: [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[3,19] package org.mockito does not exist [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[23,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[24,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] /Exomiser/matchbox/src/main/java/org/broadinstitute/macarthurlab/matchbox/config/ExomiserConfig.java:[25,17] cannot find symbol [ERROR] symbol: variable Mockito [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.config.ExomiserConfig [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException The command '/bin/sh -c $MVN -Dmaven.test.skip=true clean install package' returned a non-zero code: 1

northwestwitch commented 5 years ago

Hi! This has not been fixed yet, but I've found a workaround to get a functioning version of the server:

<!-- https://mvnrepository.com/artifact/org.mockito/mockito-core -->
    <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-all</artifactId>
       <version>2.0.2-beta</version>
   </dependency>

The problem is that the specific created query is not recognized by the API, so it's used a generic query that returns another number instead. I didn't want to enter into the specifics of the API so I've just fixed the test to match the result of the general query.

To fix it in this way you should change the last line in testGeneSymbolWithNoVariantInfoMatchOnly test into:

assertThat(df.format(genotypeSimilarityScore.getScore()), equalTo("0.94"));

After these fixes Maven compiles and the server runs as it should!

northwestwitch commented 5 years ago

Ah and remember to use the reference data 1807 when you set up Exomiser (look above in this issue). Good luck!

DSRYU commented 5 years ago

Thank you.

I'll try it. ^^