Re: [galaxy-dev] Implementing blend4j
Just to close this e-mail thread out, blend4j is now available in the maven central repository. You can add it to your maven project with the following dependency definition: dependency groupIdcom.github.jmchilton.blend4j/groupId artifactIdblend4j/artifactId version0.1-alpha-1/version /dependency -John On Mon, Jul 15, 2013 at 6:17 PM, John Chilton chil...@msi.umn.edu wrote: Fantastic. blend4j definitely should be in a public repository, just don't know how and have not had the time. Any help in that process would be most welcome. -John On Jul 15, 2013 10:43 AM, Eric Kuyt eric.ku...@wur.nl wrote: Nice, this works! Maybe after some testing we can try to get the package in the central maven repositories. I think for now all the functionality I need is in your version of blend4j. But if I think of something new I'll try to participate. Thanks On 13 July 2013 08:58, John Chilton chil...@msi.umn.edu wrote: So you have packaged blend4j and all of its dependencies into one jar file? I don't have any experience doing that. I could imagine potentially some files conflicting and only one version being written and so jersey-json breaks? Is this a possibility, some of the jar metadata sort of files? I have used blend4j a few different ways (in a war, as a Java web start application, and as a standalone application) but always with applications where it is in its own jar file and all of its dependencies are in their own and original jar files. So I would recommend using it in that mode, if that is not possible however I would search the web for others having problems repackaging jersey-json. As for development, you can use my artifactory server to grab the canonical blend4j, by adding the following to your pom.xml file: repositories repository idmsi-artifactory/id nameMSI Artifactory/name urlhttp://artifactory.msi.umn.edu/libs-snapshot/url /repository /repositories dependencies dependency groupIdcom.github.jmchilton.blend4j/groupId artifactIdblend4j/artifactId version0.1-SNAPSHOT/version /dependency If instead you want to test your own changes to blend4j, I believe you can just do a mvn install or something like that from the blend4j fork directory on your development server to install a local copy into your maven cache. blend4j is the first project I have used maven with, so some of my terminology could be wrong there, but hopefully the idea makes sense. Also happy to look at pull requests if it helps to push changes upstream. Sorry if this response is not more helpful, let me know if there is anything else I can do or answer. -John On Thu, Jul 11, 2013 at 4:37 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Implementing blend4j
Nice, this works! Maybe after some testing we can try to get the package in the central maven repositories. I think for now all the functionality I need is in your version of blend4j. But if I think of something new I'll try to participate. Thanks On 13 July 2013 08:58, John Chilton chil...@msi.umn.edu wrote: So you have packaged blend4j and all of its dependencies into one jar file? I don't have any experience doing that. I could imagine potentially some files conflicting and only one version being written and so jersey-json breaks? Is this a possibility, some of the jar metadata sort of files? I have used blend4j a few different ways (in a war, as a Java web start application, and as a standalone application) but always with applications where it is in its own jar file and all of its dependencies are in their own and original jar files. So I would recommend using it in that mode, if that is not possible however I would search the web for others having problems repackaging jersey-json. As for development, you can use my artifactory server to grab the canonical blend4j, by adding the following to your pom.xml file: repositories repository idmsi-artifactory/id nameMSI Artifactory/name urlhttp://artifactory.msi.umn.edu/libs-snapshot/url /repository /repositories dependencies dependency groupIdcom.github.jmchilton.blend4j/groupId artifactIdblend4j/artifactId version0.1-SNAPSHOT/version /dependency If instead you want to test your own changes to blend4j, I believe you can just do a mvn install or something like that from the blend4j fork directory on your development server to install a local copy into your maven cache. blend4j is the first project I have used maven with, so some of my terminology could be wrong there, but hopefully the idea makes sense. Also happy to look at pull requests if it helps to push changes upstream. Sorry if this response is not more helpful, let me know if there is anything else I can do or answer. -John On Thu, Jul 11, 2013 at 4:37 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Implementing blend4j
Fantastic. blend4j definitely should be in a public repository, just don't know how and have not had the time. Any help in that process would be most welcome. -John On Jul 15, 2013 10:43 AM, Eric Kuyt eric.ku...@wur.nl wrote: Nice, this works! Maybe after some testing we can try to get the package in the central maven repositories. I think for now all the functionality I need is in your version of blend4j. But if I think of something new I'll try to participate. Thanks On 13 July 2013 08:58, John Chilton chil...@msi.umn.edu wrote: So you have packaged blend4j and all of its dependencies into one jar file? I don't have any experience doing that. I could imagine potentially some files conflicting and only one version being written and so jersey-json breaks? Is this a possibility, some of the jar metadata sort of files? I have used blend4j a few different ways (in a war, as a Java web start application, and as a standalone application) but always with applications where it is in its own jar file and all of its dependencies are in their own and original jar files. So I would recommend using it in that mode, if that is not possible however I would search the web for others having problems repackaging jersey-json. As for development, you can use my artifactory server to grab the canonical blend4j, by adding the following to your pom.xml file: repositories repository idmsi-artifactory/id nameMSI Artifactory/name urlhttp://artifactory.msi.umn.edu/libs-snapshot/url /repository /repositories dependencies dependency groupIdcom.github.jmchilton.blend4j/groupId artifactIdblend4j/artifactId version0.1-SNAPSHOT/version /dependency If instead you want to test your own changes to blend4j, I believe you can just do a mvn install or something like that from the blend4j fork directory on your development server to install a local copy into your maven cache. blend4j is the first project I have used maven with, so some of my terminology could be wrong there, but hopefully the idea makes sense. Also happy to look at pull requests if it helps to push changes upstream. Sorry if this response is not more helpful, let me know if there is anything else I can do or answer. -John On Thu, Jul 11, 2013 at 4:37 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Implementing blend4j
So you have packaged blend4j and all of its dependencies into one jar file? I don't have any experience doing that. I could imagine potentially some files conflicting and only one version being written and so jersey-json breaks? Is this a possibility, some of the jar metadata sort of files? I have used blend4j a few different ways (in a war, as a Java web start application, and as a standalone application) but always with applications where it is in its own jar file and all of its dependencies are in their own and original jar files. So I would recommend using it in that mode, if that is not possible however I would search the web for others having problems repackaging jersey-json. As for development, you can use my artifactory server to grab the canonical blend4j, by adding the following to your pom.xml file: repositories repository idmsi-artifactory/id nameMSI Artifactory/name urlhttp://artifactory.msi.umn.edu/libs-snapshot/url /repository /repositories dependencies dependency groupIdcom.github.jmchilton.blend4j/groupId artifactIdblend4j/artifactId version0.1-SNAPSHOT/version /dependency If instead you want to test your own changes to blend4j, I believe you can just do a mvn install or something like that from the blend4j fork directory on your development server to install a local copy into your maven cache. blend4j is the first project I have used maven with, so some of my terminology could be wrong there, but hopefully the idea makes sense. Also happy to look at pull requests if it helps to push changes upstream. Sorry if this response is not more helpful, let me know if there is anything else I can do or answer. -John On Thu, Jul 11, 2013 at 4:37 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Implementing blend4j
Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Implementing blend4j
Sorry forgot, root cause = A message body writer for Java type, class com.github.jmchilton.blend4j.galaxy.beans.History, and MIME media type, application/json, was not found On 11 July 2013 11:37, Eric Kuyt eric.ku...@wur.nl wrote: Hello all, I'm trying to implement blend4j in a java application. for this I cloned the source, fetched the dependencies and added a maven assembly plugin to assemble a jar file with dependencies. This jar I put in my classpath. Now fetching histories works, but creating a new one fails. Online I see a lot of jersey users have this problem and it seems like jersey-json is not available, but jersey-json is packaged in the jar. Anyone else have this problem? @John maybe you have better practices? I would like to have blend4j in my maven dependencies, but not build my own nexus. Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
