Installation issue with Fruit_Struct test data

[John Watts]

Hi All,

I'm a newbie trying to do the XNAT Admin 101 course and I've hit a problem early on with the following error. I've also just re-run this un my Unbuntu 20.04 server  (rather than an Ubuntu Shell on windows) and get the same problem. Anyone had this and/ or point me at a fix?

Cheers

John 

xnat@Ubu:~/xnat_populate$ groovy PopulateXnat.groovy -s http://ubu:8080/xnat_app/app/template/Login.vm#! -u admin -p [password removed!] -d Fruit_Struct

Data file not found. Interpretting data input as uploading comma-separated list of projects: Fruit_Struct...

Metadata YAML for Fruit_Struct not found in: data/Fruit_Struct_metadata.yaml...

Metadata YAML for Fruit_Struct found in: sample_projects/Fruit_Struct_metadata.yaml

Parsed YAML for project Fruit_Struct.

Data zip for Fruit_Struct not found. Download from NRG download site will be attempted.

Downloading data for Fruit_Struct...

    [unzip] Expanding: /home/xnat/xnat_populate/data/Fruit_Struct.zip into /home/xnat/xnat_populate/data

XNAT site initialized...

None of the XNAT projects selected require XNAT plugins. Skipping plugin checks...

Caught: com.jayway.restassured.path.json.exception.JsonPathException: Failed to parse the JSON document

com.jayway.restassured.path.json.exception.JsonPathException: Failed to parse the JSON document

        at com.jayway.restassured.path.json.JsonPath$ExceptionCatcher.invoke(JsonPath.java:917)

        at com.jayway.restassured.path.json.JsonPath$4.doParseWith(JsonPath.java:882)

        at com.jayway.restassured.path.json.JsonPath$JsonParser.parseWith(JsonPath.java:961)

        at com.jayway.restassured.path.json.JsonPath.getJsonObject(JsonPath.java:924)

        at com.jayway.restassured.path.json.JsonPath.getObject(JsonPath.java:522)

        at com.jayway.restassured.path.json.JsonPath$getObject$0.call(Unknown Source)

        at org.nrg.xnat.interfaces.XnatInterface.listProjects(XnatInterface.groovy:660)

        at org.nrg.xnat.interfaces.XnatInterface$listProjects$4.call(Unknown Source)

        at org.nrg.populate.XnatDriver.postData(XnatDriver.groovy:159)

        at org.nrg.populate.XnatDriver$postData$2.call(Unknown Source)

        at PopulateXnat.run(PopulateXnat.groovy:88)

Caused by: groovy.json.JsonException: Lexing failed on line: 1, column: 1, while reading '<', no possible valid JSON value or punctuation could be recognized.

        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper.parse(ConfigurableJsonSlurper.groovy:96)

        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper$parse.callCurrent(Unknown Source)

        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper.parseText(ConfigurableJsonSlurper.groovy:82)

        at com.jayway.restassured.path.json.JsonPath$4$1.method(JsonPath.java:880)

        at com.jayway.restassured.path.json.JsonPath$ExceptionCatcher.invoke(JsonPath.java:915)

        ... 10 more

xnat@Ubu:~/xnat_populate$

[Moore, Charlie]

Hello there,

That URL doesn't look like the URL to your XNAT instance, but rather the URL to the Login​ page of your XNAT. Assuming that xnat_app is the tomcat application context, try using http://ubu:8080/xnat_app as your URL instead.

Thanks,

Charlie

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Subject: [XNAT Discussion] Installation issue with Fruit_Struct test data

 

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[Herrick, Rick]

Also, have you logged into your XNAT yet? That is, gone to http://ubu:8080/xnat_app, logged in, and initialized the instance (specifically, set the site URL to http://ubu:8080/xnat_app)?

 

-- 

Rick Herrick

XNAT Architect/Developer

Computational Imaging Laboratory

Washington University School of Medicine

To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/CH2PR02MB67107F4A3E6C270F38A147F8FEA99%40CH2PR02MB6710.namprd02.prod.outlook.com.

[John Watts]

Hi Rick and Charlie, 

thank you! was using UI login URL and now working with your help! 

I have successfully installed XNAT and now looking back at the admin screen its clear!

Thanks both, much appreciated!

John 

[Thomas Guiot]

Dear all,

also a newbie here, following the Admin 101 course, and having the same problem.

I have xnat 1.8.5 build 12, running on Debian 11 with tomcat9 and jre1.8

here's the log :

guiot@XNAAMP1:~/xnat_populate$ groovy PopulateXnat.groovy -s http://xnaamp1.bordet.be:8080/xnat -u admin -p admin -d QC_Review
Data file not found. Interpretting data input as uploading comma-separated list of projects: QC_Review...
Metadata YAML for QC_Review not found in: data/QC_Review_metadata.yaml...
Metadata YAML for QC_Review found in: sample_projects/QC_Review_metadata.yaml
Parsed YAML for project QC_Review.
Data zip for QC_Review not found. Download from NRG download site will be attempted.
Downloading data for QC_Review...
    [unzip] Expanding: /home/gu...@bordet.be/xnat_populate/data/QC_Review.zip into /home/gu...@bordet.be/xnat_populate/data
XNAT instance has been initialized previously

None of the XNAT projects selected require XNAT plugins. Skipping plugin checks...

XNAT user 'owner' already exists...
XNAT user 'member' already exists...
XNAT user 'collaborator' already exists...
Project 'QC_Review' successfully created
Subject 'RIQ_AA' successfully created.
Imaging session 'RIQ_AA_MR1' successfully created
A subsequent operation requires that the AutoRun pipeline complete on this session (RIQ_AA_MR1) before continuing. If this step appears to be hanging, it likely means that the pipeline engine is not configured correctly on the XNAT server. Waiting for AutoRun completion for up to 600 seconds...

Caught: com.jayway.restassured.path.json.exception.JsonPathException: Failed to parse the JSON document
com.jayway.restassured.path.json.exception.JsonPathException: Failed to parse the JSON document
        at com.jayway.restassured.path.json.JsonPath$ExceptionCatcher.invoke(JsonPath.java:917)
        at com.jayway.restassured.path.json.JsonPath$4.doParseWith(JsonPath.java:882)
        at com.jayway.restassured.path.json.JsonPath$JsonParser.parseWith(JsonPath.java:961)

        at com.jayway.restassured.path.json.JsonPath.get(JsonPath.java:201)
        at com.jayway.restassured.path.json.JsonPath.getString(JsonPath.java:351)
        at com.jayway.restassured.path.json.JsonPath$getString$0.call(Unknown Source)
        at org.nrg.xnat.interfaces.XnatInterface.waitForAutoRun(XnatInterface.groovy:278)
        at org.nrg.xnat.interfaces.XnatInterface$waitForAutoRun$19.callCurrent(Unknown Source)
        at org.nrg.xnat.interfaces.XnatInterface.createSubjectAssessor(XnatInterface.groovy:964)
        at org.nrg.xnat.interfaces.XnatInterface.createSubjectAssessor(XnatInterface.groovy)
        at org.nrg.xnat.interfaces.XnatInterface$_createSubject_closure24.doCall(XnatInterface.groovy:878)
        at org.nrg.xnat.interfaces.XnatInterface.createSubject(XnatInterface.groovy:877)
        at org.nrg.xnat.interfaces.XnatInterface.createSubject(XnatInterface.groovy)
        at org.nrg.xnat.interfaces.XnatInterface$createSubject$13.callCurrent(Unknown Source)
        at org.nrg.xnat.interfaces.XnatInterface.createSubject(XnatInterface.groovy:906)
        at org.nrg.xnat.interfaces.XnatInterface$_createProject_closure20.doCall(XnatInterface.groovy:838)
        at org.nrg.xnat.interfaces.XnatInterface.createProject(XnatInterface.groovy:837)
        at org.nrg.xnat.interfaces.XnatInterface$createProject$6.call(Unknown Source)
        at org.nrg.populate.XnatDriver$_postData_closure13.doCall(XnatDriver.groovy:175)
        at org.nrg.populate.XnatDriver.postData(XnatDriver.groovy:174)

        at org.nrg.populate.XnatDriver$postData$2.call(Unknown Source)
        at PopulateXnat.run(PopulateXnat.groovy:88)
Caused by: groovy.json.JsonException: Lexing failed on line: 1, column: 1, while reading '<', no possible valid JSON value or punctuation could be recognized.
        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper.parse(ConfigurableJsonSlurper.groovy:96)
        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper$parse.callCurrent(Unknown Source)
        at com.jayway.restassured.internal.path.json.ConfigurableJsonSlurper.parseText(ConfigurableJsonSlurper.groovy:82)
        at com.jayway.restassured.path.json.JsonPath$4$1.method(JsonPath.java:880)
        at com.jayway.restassured.path.json.JsonPath$ExceptionCatcher.invoke(JsonPath.java:915)

        ... 21 more

I know the URL is correct as I used it successfully in the previous populateXnat demo with Fruit_Struct. but here, with QC_Review, I'm getting this error.

any idea ?

thanks

Thomas

[Will Horton]

Hello Thomas, I believe what's happening here is that you are running into an AutoRun pipeline dependency that was baked into the project definition in the pre-XNAT 1.8 world. There are changes in the dev branch of the xnat_populate repo that can address this. Try the following and see if that resolves the issue: 

$ git checkout dev

$ git pull

$ groovy PopulateXnat.groovy -s [SERVER] -u admin -p admin -d QC_Review

We are hoping to release an updated branch of the xnat-academy branch that incorporates these changes in the near future. 

[Will Horton]

To make things simpler, I have created an xnat-academy-dev branch within the repo. Let's use that instead of dev. So the instructions should now be: 

$ git checkout xnat-academy-dev

$ git pull

$ groovy PopulateXnat.groovy -s [SERVER] -u admin -p admin -d QC_Review

Regards,

Will