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barsnes-group / peptide-shaker-online

Web-based framework for interactive visual analysis of proteomics data
Apache License 2.0
7 stars 1 forks source link

No peptideshaker-online.war file available for download #28

Open dunecatnat opened 8 months ago

dunecatnat commented 8 months ago

Hello guys! First of all, thanks for the project! We are trying to have a go at it. I've configured and can run galaxy server, no issues there. However I don't find peptideshaker-online.war file following the link on the documentation page. It brings me to https://github.com/barsnes-group/peptide-shaker-online/wiki/ I tried to package the project myself, but there is a dependencty on compomics-utilities, which have as a dependency uk.ac.ebi.pride.archive:web-service-model which seems to not be available any more (although here the question is for EBI I suppose, not for you).

hbarsnes commented 8 months ago

Hello! Thanks for letting us know about the missing war file and the outdated EBI dependencies! I've already updated the EBI dependencies in the pom file such that you should now be able to build the project. However, for further assistance I will forward you to @yehiafarag. He's the main developer and knows more about the details of the implementation and how to set it up than me. Yehia will get back to you as soon as he's had the chance to look into the problem with the missing war file.

dunecatnat commented 7 months ago

Thanks a lot! Needed to downgrade my java version to 8 and then the build worked. Next step is to fiddle with the configs and try to run it!

yehiafarag commented 7 months ago

Oh great i was just on my way to write to you, please feel free to contact me if you need any help with the setup,

dunecatnat commented 7 months ago

@yehiafarag Sorry for radio silence, I was on vacation, but back to setting up the app now. I managed to run the build with all the configs, but I can't run the app in tomcat. I have tomcat 8.5 set up and running already another app, so the actual server setup is not an issue. I get a 505 error while trying to access the app at localhost:

java.nio.file.NoSuchFileException: /usr/local/Cellar/tomcat@8/8.5.93/libexec/temp/0-peptideshaker-online/WEB-INF/lib/xercesImpl-2.12.0.jar

I checked with tomcat@9 as well, the same story.

Checking the deployed directory, all the necessary jars are present. Logs don't show any errors either.

I thought maybe something was wrong with the db connection, as tomcat behaves weirdly without giving much info especially in that case. However I can connect to the db without any issue.

Am I missing some setup step? Did you have any similar issues?

yehiafarag commented 6 months ago

@dunecatnat hi Natalia, I guess the error came from one library in the utilities so I updated the app, just pull the new updated code and give it a try, let me know if the error is fixed :-)

dunecatnat commented 6 months ago

hi @yehiafarag Thank you for taking the time! Now I have a different package causing the same error java.nio.file.NoSuchFileException: /usr/local/Cellar/tomcat@9/9.0.88/libexec/temp/1-peptideshakeronline-1.0/WEB-INF/lib/javax.inject-2.2.0.jar I wonder if it is some tomcat config that I should set differently. As if the app doesn't find lib resources, while everything is in there.

yehiafarag commented 6 months ago

@dunecatnat umm... i am not sure why you get such errors but maybe i can send u the runnable war file and you can try to deploy it directly, u will just need to update the app configurations file

yehiafarag commented 6 months ago

peptideshakeronline-1.0.war https://drive.google.com/file/d/1a1lrrU-o0iJ-MefPV17swG0UwSmJewR2/view?usp=drive_web

On Mon, 22 Apr 2024 at 13:27, Natalia Tichshenko @.***> wrote:

hi @yehiafarag https://github.com/yehiafarag Thank you for taking the time! Now I have a different package causing the same error java.nio.file.NoSuchFileException: @.*** /9.0.88/libexec/temp/1-peptideshakeronline-1.0/WEB-INF/lib/javax.inject-2.2.0.jar I wonder if it is some tomcat config that I should set differently. As if the app doesn't find lib resources, while everything is in there.

— Reply to this email directly, view it on GitHub https://github.com/barsnes-group/peptide-shaker-online/issues/28#issuecomment-2069152480, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEPSRFVBFWO6LWXMZQ5F7LY6TX3RAVCNFSM6AAAAABFBVGZM2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGE2TENBYGA . You are receiving this because you were mentioned.Message ID: @.***>

-- Yehia Farag Department of Informatics University of Bergen

yehiafarag commented 6 months ago

please do not forget to update the configuration file " peptideshakeronline-1.0\WEB-INF\config.json" "galaxyServerUrl": "", "testUserAPIKey": "", "url": "jdbc:mysql://localhost:3306/", "driver": "com.mysql.jdbc.Driver", "password": "", "userName": "", "dbName": "", and let me know if you still having the same problem

On Mon, 22 Apr 2024 at 14:55, Yehia Farag @.***> wrote:

peptideshakeronline-1.0.war https://drive.google.com/file/d/1a1lrrU-o0iJ-MefPV17swG0UwSmJewR2/view?usp=drive_web

On Mon, 22 Apr 2024 at 13:27, Natalia Tichshenko @.***> wrote:

hi @yehiafarag https://github.com/yehiafarag Thank you for taking the time! Now I have a different package causing the same error java.nio.file.NoSuchFileException: @.*** /9.0.88/libexec/temp/1-peptideshakeronline-1.0/WEB-INF/lib/javax.inject-2.2.0.jar I wonder if it is some tomcat config that I should set differently. As if the app doesn't find lib resources, while everything is in there.

— Reply to this email directly, view it on GitHub https://github.com/barsnes-group/peptide-shaker-online/issues/28#issuecomment-2069152480, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEPSRFVBFWO6LWXMZQ5F7LY6TX3RAVCNFSM6AAAAABFBVGZM2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRZGE2TENBYGA . You are receiving this because you were mentioned.Message ID: @.***>

-- Yehia Farag Department of Informatics University of Bergen

-- Yehia Farag Department of Informatics University of Bergen

dunecatnat commented 6 months ago

Thanks for that! I can at least run the app now with the .war that you sent. Trying to run sample files now, although not seeing anything yet, maybe missing some packages for galaxy server, but I am not receiving any errors either.

The errors that I am having with running the app built on my machine are due to my setup and the way I build, I suppose. Out of curiosity, how do you build? maybe I am missing something here.

I am on Mac OS X 14.2.1 (latest) Had to downgrade to Java 1.8 to be able to run the build, otherwise it would give me errors. Tomcat 9.0.88 Galaxy server release 23.2