make-appliance : groovy unresolved dependency: commons-cli

[mhabsaoui]

Hi, Is it normal to get this error about groovy with 'galaxy-appliance' on 'develop' branch ??

`# ./make-appliance -b -e ../galaxy-data testing masc oaqa stanford lingpipe opennlp gate option -b option -e ../galaxy-data org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: General error during conversion: Error grabbing Grapes -- [unresolved dependency: commons-cli#commons-cli;1.2: not found]

java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: commons-cli#commons-cli;1.2: not found] at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:71) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:81) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:54) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190) at groovy.grape.GrapeIvy.getDependencies(GrapeIvy.groovy:336) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:226) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:52) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:463) at groovy.grape.GrapeIvy$resolve$0.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:153) at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:432) at groovy.grape.GrapeIvy$resolve.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:149) at groovy.grape.GrapeIvy.grab(GrapeIvy.groovy:248) at groovy.grape.Grape.grab(Grape.java:141) at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:283) at org.codehaus.groovy.transform.ASTTransformationVisitor$3.call(ASTTransformationVisitor.java:302) at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:843) at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:548) at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:524) at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:501) at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:306) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:283) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:267) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:197) at groovy.lang.GroovyShell$2.run(GroovyShell.java:215) at groovy.lang.GroovyShell$2.run(GroovyShell.java:213) at java.security.AccessController.doPrivileged(Native Method) at groovy.lang.GroovyShell.run(GroovyShell.java:213) at groovy.lang.GroovyShell.run(GroovyShell.java:159) at groovy.ui.GroovyMain.processOnce(GroovyMain.java:550) at groovy.ui.GroovyMain.run(GroovyMain.java:337) at groovy.ui.GroovyMain.process(GroovyMain.java:323) at groovy.ui.GroovyMain.processArgs(GroovyMain.java:120) at groovy.ui.GroovyMain.main(GroovyMain.java:100) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:108) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)

1 error`

Thanks.

[ksuderman]

No this is not normal. Are you still experiencing the problem?

The error indicates that the Groovy script that builds the docker-compose.yml file was unable to download the Apache commons-cli module from Maven Central. Did you clean up your local Maven repository (~/.m2/repository) and/or Groovy's cache (~/.groovy/grapes)? Since you have used the make-appliance script before you should have those modules on your system already.

On Jun 27, 2017, at 10:02 AM, mhabsaoui notifications@github.com wrote:

Hi, Is it normal to get this error about groovy with 'galaxy-appliance' on 'develop' branch ??

https://user-images.githubusercontent.com/18755135/27591446-f447b5be-5b51-11e7-94c7-7398d830a99d.png `# ./make-appliance -b -e ../galaxy-data legotal masc oaqa stanford lingpipe opennlp gate option -b option -e ../galaxy-data org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: General error during conversion: Error grabbing Grapes -- [unresolved dependency: commons-cli#commons-cli;1.2: not found]

java.lang.RuntimeException: Error grabbing Grapes -- [unresolved dependency: commons-cli#commons-cli;1.2: not found] at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:71) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:81) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:54) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190) at groovy.grape.GrapeIvy.getDependencies(GrapeIvy.groovy:336) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSite.invoke(PogoMetaMethodSite.java:226) at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:52) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:463) at groovy.grape.GrapeIvy$resolve$0.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:153) at groovy.grape.GrapeIvy.resolve(GrapeIvy.groovy:432) at groovy.grape.GrapeIvy$resolve.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:149) at groovy.grape.GrapeIvy.grab(GrapeIvy.groovy:248) at groovy.grape.Grape.grab(Grape.java:141) at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:283) at org.codehaus.groovy.transform.ASTTransformationVisitor$3.call(ASTTransformationVisitor.java:302) at org.codehaus.groovy.control.CompilationUnit.applyToSourceUnits(CompilationUnit.java:843) at org.codehaus.groovy.control.CompilationUnit.doPhaseOperation(CompilationUnit.java:548) at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:524) at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:501) at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:306) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:283) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:267) at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:197) at groovy.lang.GroovyShell$2.run(GroovyShell.java:215) at groovy.lang.GroovyShell$2.run(GroovyShell.java:213) at java.security.AccessController.doPrivileged(Native Method) at groovy.lang.GroovyShell.run(GroovyShell.java:213) at groovy.lang.GroovyShell.run(GroovyShell.java:159) at groovy.ui.GroovyMain.processOnce(GroovyMain.java:550) at groovy.ui.GroovyMain.run(GroovyMain.java:337) at groovy.ui.GroovyMain.process(GroovyMain.java:323) at groovy.ui.GroovyMain.processArgs(GroovyMain.java:120) at groovy.ui.GroovyMain.main(GroovyMain.java:100) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:108) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:130)

1 error`

Thanks.

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Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman@cs.vassar.edu

[mhabsaoui]

Yep, tried already to clean groovy grapes. Installed Maven which was'nt. But same.

Now on my non-pro PC it's OK as below => it has to be a Proxy limitation...

[ksuderman]

Yes, it will be a proxy or something similar blocking Maven Central. You can try copying the ~/.groovy/grapes directory from the PC to the other machine and see if that helps. Once Groovy (Ivy actually) has downloaded the modules it should not need to access Maven Central again.

[ksuderman]

For further reference and documentation, I just received the same error on a fresh Ubuntu installation. Initially I tried creating a default ~/.groovy/grapeConfig.xml [1] and added Maven Central to the list of repositories, but that didn't fix the problem.

I then attempted to manually install the dependency with verbose logging enabled:

grape install -V common-cli commons-cli 1.2

That didn't work either, but I was able to see in the log that Groovy/Grape was complaining about a bizarre SSL error:

java.lang.RuntimeException: Unexpected error: java.security.InvalidAlgorithmParameterException: the trustAnchors parameter must be non-empty

This non-sensical error message seems to indicate that Java can not find a trustStore. In particular, "ca-certificates-java is not a dependency in the Oracle JDK/JRE so this must be explicitly installed." [2].

Running the following command [3] finally fixed the problem.

sudo /var/lib/dpkg/info/ca-certificates-java.postinst configure

References

1. https://github.com/apache/groovy/blob/master/src/resources/groovy/grape/defaultGrapeConfig.xml
2. https://stackoverflow.com/questions/6784463/error-trustanchors-parameter-must-be-non-empty
3. https://bugs.launchpad.net/ubuntu/+source/ca-certificates-java/+bug/1396760

[mhabsaoui]

Hi, thanks for feedback :+1:

Even if the last fixing executes properly (wheras the other commands didn't), it doesn't fixed the problem. Still non succeed with generating the appliance on Dev branch :/

I tried manually as follow, but the resources that it tries to access seem not found (Server access error, Connection timed out) ! Same for you ??

`$ grape install -V common-cli commons-cli 1.2 :: loading settings :: url = jar:file:/root/.sdkman/candidates/groovy/current/lib/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml :: resolving dependencies :: caller#all-caller;working41 confs: [default]

:: problems summary :: :::: WARNINGS module not found: -V#common-cli;commons-cli

==== cachedGrapes: tried

  /root/.groovy/grapes/-V/common-cli/ivy-commons-cli.xml

  -- artifact -V#common-cli;commons-cli!common-cli.jar:

  /root/.groovy/grapes/-V/common-cli/jars/common-cli-commons-cli-1.2.jar

==== localm2: tried

  file:/root/.m2/repository/-V/common-cli/commons-cli/common-cli-commons-cli.pom

  -- artifact -V#common-cli;commons-cli!common-cli.jar:

  file:/root/.m2/repository/-V/common-cli/commons-cli/common-cli-commons-cli-1.2.jar

==== jcenter: tried

  https://jcenter.bintray.com/-V/common-cli/commons-cli/common-cli-commons-cli.pom

  -- artifact -V#common-cli;commons-cli!common-cli.jar:

  https://jcenter.bintray.com/-V/common-cli/commons-cli/common-cli-commons-cli-1.2.jar

==== ibiblio: tried

  https://repo1.maven.org/maven2/-V/common-cli/commons-cli/common-cli-commons-cli.pom

  -- artifact -V#common-cli;commons-cli!common-cli.jar:

  https://repo1.maven.org/maven2/-V/common-cli/commons-cli/common-cli-commons-cli-1.2.jar

:::: ERRORS Server access error at url https://jcenter.bintray.com/-V/common-cli/commons-cli/common-cli-commons-cli.pom (java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out))

Server access error at url https://jcenter.bintray.com/-V/common-cli/commons-cli/common-cli-commons-cli-1.2.jar (java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out))

Server access error at url https://repo1.maven.org/maven2/-V/common-cli/commons-cli/common-cli-commons-cli.pom (java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out))

Server access error at url https://repo1.maven.org/maven2/-V/common-cli/commons-cli/common-cli-commons-cli-1.2.jar (java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out))

:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS`

The environment variables to go through our proxy are properly set in the shell, so no change here...

Thanks.

[ksuderman]

There appears to be something wrong with your grape install command as Ivy is looking for:

https://repo1.maven.org/maven2/-V/common-cli/commons-cli/common-cli-commons-cli.pom

note the -V in the repository path. However, the grape install is simply what allowed me to see the real error message. I suspect the underlying problem is the same; the trust store/certificate chain has not been correctly configured for Java so https connections don't work resulting in 404 errors.

What OS are you using?

[mhabsaoui]

Ubuntu 16.04 LTS.

sudo /var/lib/dpkg/info/ca-certificates-java.postinst configure

This command worked with no error.

sudo /var/lib/dpkg/info/ca-certificates-java.postinst configure Replacing debian:TeliaSonera_Root_CA_v1.pem Replacing debian:QuoVadis_Root_CA_3.pem Replacing debian:GlobalSign_Root_CA.pem Replacing debian:QuoVadis_Root_CA_2.pem Replacing debian:Security_Communication_RootCA2.pem Replacing debian:AddTrust_Qualified_Certificates_Root.pem Replacing debian:Network_Solutions_Certificate_Authority.pem Replacing debian:Deutsche_Telekom_Root_CA_2.pem Replacing debian:AddTrust_Low-Value_Services_Root.pem Replacing debian:AffirmTrust_Premium_ECC.pem Replacing debian:Equifax_Secure_eBusiness_CA_1.pem Replacing debian:ssl-cert-snakeoil.pem Replacing debian:DigiCert_Assured_ID_Root_G3.pem Replacing debian:Root_CA_Generalitat_Valenciana.pem Replacing debian:GeoTrust_Primary_Certification_Authority.pem Replacing debian:CA_Disig_Root_R1.pem Replacing debian:Izenpe.com.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R4.pem Replacing debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Replacing debian:AddTrust_External_Root.pem Replacing debian:Microsec_e-Szigno_Root_CA_2009.pem Replacing debian:RSA_Security_2048_v3.pem Replacing debian:Equifax_Secure_Global_eBusiness_CA.pem Replacing debian:Actalis_Authentication_Root_CA.pem Replacing debian:Comodo_Secure_Services_root.pem Replacing debian:certSIGN_ROOT_CA.pem Replacing debian:GlobalSign_Root_CA_-_R3.pem Replacing debian:T-TeleSec_GlobalRoot_Class_2.pem Replacing debian:Sonera_Class_2_Root_CA.pem Replacing debian:Atos_TrustedRoot_2011.pem Replacing debian:NetLock_Notary_=Class_A=_Root.pem Replacing debian:DigiCert_Global_Root_G2.pem Replacing debian:Baltimore_CyberTrust_Root.pem Replacing debian:TWCA_Global_Root_CA.pem Replacing debian:DigiCert_Global_Root_CA.pem Replacing debian:Secure_Global_CA.pem Replacing debian:Equifax_Secure_CA.pem Replacing debian:Certum_Trusted_Network_CA.pem Replacing debian:Certplus_Class_2_Primary_CA.pem Replacing debian:SecureTrust_CA.pem Replacing debian:CA_Disig_Root_R2.pem Replacing debian:Microsec_e-Szigno_Root_CA.pem Replacing debian:NetLock_Business_=Class_B=_Root.pem Replacing debian:Security_Communication_Root_CA.pem Replacing debian:QuoVadis_Root_CA_1_G3.pem Replacing debian:GlobalSign_Root_CA_-_R2.pem Replacing debian:Swisscom_Root_CA_2.pem Replacing debian:CA_Disig.pem Replacing debian:GeoTrust_Global_CA_2.pem Replacing debian:UTN_USERFirst_Hardware_Root_CA.pem Replacing debian:WoSign.pem Replacing debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Replacing debian:StartCom_Certification_Authority_2.pem Replacing debian:Swisscom_Root_CA_1.pem Replacing debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Replacing debian:TC_TrustCenter_Class_3_CA_II.pem Replacing debian:Camerfirma_Chambers_of_Commerce_Root.pem Replacing debian:TWCA_Root_Certification_Authority.pem Replacing debian:thawte_Primary_Root_CA_-_G2.pem Replacing debian:Sonera_Class_1_Root_CA.pem Replacing debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Replacing debian:Certum_Root_CA.pem Replacing debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Replacing debian:ePKI_Root_Certification_Authority.pem Replacing debian:S-TRUST_Universal_Root_CA.pem Replacing debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Replacing debian:DigiCert_Assured_ID_Root_G2.pem Replacing debian:EC-ACC.pem Replacing debian:AC_Raíz_Certicámara_S.A..pem Replacing debian:IdenTrust_Commercial_Root_CA_1.pem Replacing debian:DST_ACES_CA_X6.pem Replacing debian:AffirmTrust_Commercial.pem Replacing debian:EE_Certification_Centre_Root_CA.pem Replacing debian:DigiCert_Assured_ID_Root_CA.pem Replacing debian:Cybertrust_Global_Root.pem Replacing debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Replacing debian:CA_WoSign_ECC_Root.pem Replacing debian:USERTrust_RSA_Certification_Authority.pem Replacing debian:ApplicationCA_-_Japanese_Government.pem Replacing debian:Hongkong_Post_Root_CA_1.pem Replacing debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Replacing debian:IdenTrust_Public_Sector_Root_CA_1.pem Replacing debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Replacing debian:thawte_Primary_Root_CA.pem Replacing debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H6.pem Replacing debian:SwissSign_Silver_CA_-_G2.pem Replacing debian:WoSign_China.pem Replacing debian:Taiwan_GRCA.pem Replacing debian:OISTE_WISeKey_Global_Root_GB_CA.pem Replacing debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem Replacing debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Replacing debian:AddTrust_Public_Services_Root.pem Replacing debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_2009.pem Replacing debian:Certigna.pem Replacing debian:Go_Daddy_Class_2_CA.pem Replacing debian:XRamp_Global_CA_Root.pem Replacing debian:thawte_Primary_Root_CA_-_G3.pem Replacing debian:COMODO_Certification_Authority.pem Replacing debian:OISTE_WISeKey_Global_Root_GA_CA.pem Replacing debian:Chambers_of_Commerce_Root_-_2008.pem Replacing debian:StartCom_Certification_Authority.pem Replacing debian:Trustis_FPS_Root_CA.pem Replacing debian:Comodo_Trusted_Services_root.pem Replacing debian:Staat_der_Nederlanden_Root_CA.pem Replacing debian:DigiCert_High_Assurance_EV_Root_CA.pem Replacing debian:UTN_USERFirst_Email_Root_CA.pem Replacing debian:Swisscom_Root_EV_CA_2.pem Replacing debian:Entrust_Root_Certification_Authority_-_G2.pem Replacing debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Replacing debian:Staat_der_Nederlanden_EV_Root_CA.pem Replacing debian:DST_Root_CA_X3.pem Replacing debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Replacing debian:CFCA_EV_ROOT.pem Replacing debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Replacing debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Replacing debian:NetLock_Qualified_=Class_QA=_Root.pem Replacing debian:Juur-SK.pem Replacing debian:WellsSecure_Public_Root_Certificate_Authority.pem Replacing debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Replacing debian:AffirmTrust_Premium.pem Replacing debian:ACEDICOM_Root.pem Replacing debian:COMODO_ECC_Certification_Authority.pem Replacing debian:Buypass_Class_2_CA_1.pem Replacing debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Replacing debian:IGC_A.pem Replacing debian:DigiCert_Global_Root_G3.pem Replacing debian:Global_Chambersign_Root_-_2008.pem Replacing debian:Visa_eCommerce_Root.pem Replacing debian:QuoVadis_Root_CA_3_G3.pem Replacing debian:Entrust_Root_Certification_Authority_-_EC1.pem Replacing debian:Comodo_AAA_Services_root.pem Replacing debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Replacing debian:QuoVadis_Root_CA_2_G3.pem Replacing debian:DigiCert_Trusted_Root_G4.pem Replacing debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Replacing debian:AffirmTrust_Networking.pem Replacing debian:QuoVadis_Root_CA.pem Replacing debian:SwissSign_Platinum_CA_-_G2.pem Replacing debian:Certification_Authority_of_WoSign_G2.pem Replacing debian:GeoTrust_Global_CA.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R5.pem Replacing debian:SecureSign_RootCA11.pem Replacing debian:Certinomis_-_Root_CA.pem Replacing debian:Buypass_Class_2_Root_CA.pem Replacing debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem Replacing debian:Entrust_Root_Certification_Authority.pem Replacing debian:SwissSign_Gold_CA_-_G2.pem Replacing debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Replacing debian:Buypass_Class_3_Root_CA.pem Replacing debian:ComSign_CA.pem Replacing debian:Starfield_Class_2_CA.pem Replacing debian:E-Tugra_Certification_Authority.pem Replacing debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem Replacing debian:VeriSign_Universal_Root_Certification_Authority.pem Replacing debian:StartCom_Certification_Authority_G2.pem Replacing debian:NetLock_Express_=Class_C=_Root.pem Replacing debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Replacing debian:USERTrust_ECC_Certification_Authority.pem Replacing debian:Certinomis_-_Autorité_Racine.pem Replacing debian:ACCVRAIZ1.pem Replacing debian:Starfield_Root_Certificate_Authority_-_G2.pem Replacing debian:PSCProcert.pem Replacing debian:Camerfirma_Global_Chambersign_Root.pem Replacing debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Replacing debian:GeoTrust_Universal_CA.pem Replacing debian:CNNIC_ROOT.pem Replacing debian:GeoTrust_Universal_CA_2.pem Replacing debian:COMODO_RSA_Certification_Authority.pem Replacing debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Replacing debian:Security_Communication_EV_RootCA1.pem Replacing debian:T-TeleSec_GlobalRoot_Class_3.pem done.

About installed java/groovy :

java -v

openjdk version "1.8.0_131" OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11) OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)

javac -v

javac 1.8.0_131

grape -v

Groovy Version: 2.4.12 JVM: 1.8.0_131

Groovy was first installed from apt, then upgraded to latest with the SDKMAN.

Thanks !

[ksuderman]

This command worked with no error.

sudo /var/lib/dpkg/info/ca-certificates-java.postinst configure Replacing

And you're still getting the error? This is the command that fixed things for me...

We have slightly different version of things installed, but that shouldn't make a difference. I'm using Ubuntu: 14.04.3 Java: OpenJDK 1.8.0_111 Groovy: 2.4.7

I doubt it will help, but try using Groovy 2.4.7 and also check if you can use Java/Groovy to establish any https connections. The following should be sufficient for testing:

groovy -e "println new URL('https://google.com').text"

[mhabsaoui]

I doubt too that versions play a role here.

check if you can use Java/Groovy to establish any https connections.

So, the test gives me this (even with proxy env. variables set as parameters: -Dhttp.proxyHost=... -Dhttp.proxyPort=... )

groovy -e "println new URL('https://google.com').text"
Caught: java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out)
java.net.ConnectException: Connexion terminée par expiration du délai d'attente (Connection timed out)
    at script_from_command_line.run(script_from_command_line:1)

The connection seems not to go through...

[mhabsaoui]

Ok. I've seen with the admin => it seems that TCE ignores our env. proxy variables.

With the -Dhttps.proxyHost=... -Dhttps.proxyPort=... the https groovy command works. But make-appliance script still doesn't run, even if edited with env. params added inside the script :/

I've manually added the "commons-cli#commons-cli;1.2!commons-cli.jar" into the '~/.groovy/grapes/commons-cli/commons-cli/' path, but still same error.

[mhabsaoui]

The grape install command 'grape -Dhttps.proxyHost=... -Dhttps.proxyPort=... install -V common-cli commons-cli 1.2' still fails, as trying to access wrong repo's url (with the '-V' in url coming from nowhere).

The right url seems different :

What's going on O_O

[ksuderman]

I'm not sure why grape install is using the -V option as part of the group/artifact ID. Try running grape install without the -V option and see what happens.

[mhabsaoui]

Already tried, but the same.

BTW, isn't a bad command => commons-cli instead of common-cli ?

Removed the -V and modifed as above => it changes...

grape -Dhttps.proxyHost=...  -Dhttps.proxyPort=... install commons-cli commons-cli 1.2
:: loading settings :: url = jar:file:/root/.sdkman/candidates/groovy/current/lib/ivy-2.4.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
:: resolving dependencies :: caller#all-caller;working53
    confs: [default]
    found commons-cli#commons-cli;1.2 in localm2

:: problems summary ::
:::: WARNINGS
        [NOT FOUND  ] commons-cli#commons-cli;1.2!commons-cli.jar (0ms)

    ==== localm2: tried

      file:/root/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar

:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS

I will also paste the grapes folder from my PC to see if any better changes...

[mhabsaoui]

Now, after pasting grapes (copied from my non-pro PC) :

~/.groovy/grapes/ commons-cli/ org.apache/ org.apache.commons/ ~/.groovy/grapes/commons-cli/commons-cli/ ivy-1.2.xml ivy-1.2.xml.original ivydata-1.2.properties jars/ ~/.groovy/grapes/commons-cli/commons-cli/jars/commons-cli-1.2.jar

And now finally and only the 'make-appliance' works !

• BTW, there's an error in one Gate package name ==> it should be GateServices-2.2.0.tgz / GateServices-2.3.0.tgz => It has to be corrected in package_list.txt and Dockerfile.

• Is there a difference between GateServices-2.2.0.tgz =/= GateServices-2.3.0.tgz ??

• The GateConverter version is still GateConverter_2.0.0.tgz => change to GateConverter_2.1.0.tgz

• The names of gate services that are invoked from galaxy wrappers aren't correctly matched...

Thanks

[mhabsaoui]

Just wondering if TCE binary was coded so it takes in account proxy settings ?

Another solution I'm trying is adding proxy settings to Groovy ($HOME/.groovy/GrapeConfig.xml) in 'ivysettings', as grape install command still didn't worked.

[mhabsaoui]

Finally, I got it working Normally by adding our Nexus repository in the groovy settings (~/.groovy/grapeConfig.xml) as first repository => it works well :+1:

[ksuderman]

The TCE application builds the Galaxy tool_conf.xml file and doesn't do any network traffic, so no, it knows nothing about proxies. In any case, since it is a precompiled binary it would not be trying to download modules. I suspect the proxy problems are due to the YamlBuilder.groovy script which has a @Grab dependency on commons-cli.

Had I known that you were running your own Nexus repository, adding it to the grapeConfig.xml would have been one of my first suggestions!