The easiest way to remove the Queued pipelines from the project is by removing the rows from the database table, e.g. in psql:
delete from wrk_workflowdata where status = ‘Queued’;
Be careful with this because of course if you have a legitimate workflow queued this could cause problems.
The autorun pipeline runs because that’s just what it does: runs automatically. I *believe* that you can’t stop the autorun pipeline from running automatically, but you can modify what autorun does by editing the catalog/xnat_tools/AutoRun.xml file under your pipeline installation.
The recon-all.xml descriptor (and most everything else under the catalog folder) is NOT an actual pipeline configured to use the Freesurfer pipeline integration. Each file under catalog is actually a resource descriptor that configures a tool you can use within a pipeline definition.
Unfortunately, I don’t have any examples of a Freesurfer pipeline configuration. I was actually bemoaning my lack of knowledge about how to make that work this very morning. I know some people do have it configured and working though. If anyone has a sample configuration that they can post (stripping out any sensitive data, e.g. passwords or secure account data, etc.), that’d be great. If not, I’ll try to see if I can dig some stuff out and post up on the XNAT site.
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This is going to be a long reply so relax, sit back and enjoy the flight (!)
a) Issues with AutoRun - being Queued
Looks like AutoRun is being triggered by is not launched. Checklist:
i) Is Pipeline engine installed correctly? Does
PIPELINE_HOME/bin/XnatPipelineLauncher exist with execute permissions
for the user starting tomcat process? Does PIPELINE_HOME/logs folder
exist?
ii) Is the PIPELINE_HOME location correct in WEBAPP -> Administer ->
Default Settings - check Pipeline Installation Location. Typically
this would be XNAT_HOME/pipeline
iii) Check TOMCAT_HOME/webapps/YOUR_XNAT_APP_NAME/logs/application.log
- is there any error entry here of the type
org.nrg.pipeline.ProcessLauncher - Couldnt launch ......
iv) If there is, copy the string starting at
PIPELINE_HOME/bin/XnatPipelineLauncher and run it manually on the
command-prompt. What error message do you get?
v) What is in the folder PIPELINE_HOME/logs?
b) Use of AutoRun pipeline
As you have figured out, its supposed to run automatically on
archival. This pipeline generates the snapshots for each of the scans
in your imaging session. It also makes a REST call to launch all
pipelines associated with the project which are marked as "run
automatically on archival". It then sends email notification.
c) Pipeline 101:
When you write a shell script, you have:
i) Input parameters supplied as constants within the script, supplied
as command line arguments or you can source a file.
ii) There are steps in a particular order and logic (typically if
statements, loops) to invoke executables. For each executable that the
script invokes, the executable is located in a particular location,
there is an order in which the arguments are supplied and also a
possible prefix to the argument option (eg. -a MY_A_VALUE or --a
MY_A_VALUE or /a MY_A_VALUE etc).
iii) Its the responsibility of the shell to process a shell script.
XNAT Pipelines consist of a pipeline engine and a collection of XML
documents viz. pipeline XML, resource XML and parameter XML. The
pipeline XML and the resource XML typically are in
PIPELINE_HOME/catalog. XNAT pipeline engine is the interpreter which
processes a pipeline XML (ala shell script) and knows (using the
resource XML) how to construct a string which would result in
invocation of the executable. The input arguments to the Pipeline (ie
the pipeline XML) can be supplied in-line (ie constants within the
pipeline document) or through the parameter XML or name value pairs
as command line arguments to the pipeline engine.
So pipeline engine would need to know path to pipeline XML, input
parameters to the pipeline, path to parameter XML document (optional)
and path to the catalog folder. XNAT pipeline engine comes in two
flavors - one which updates XNAT workflow as each step is executed and
the other which processes the steps unaware of the presence of XNAT.
PIPELINE_HOME/bin/XnatPipelineLauncher is the pipeline engine with
XNAT workflow update capability
and
PIPELINE_HOME/bin/PipelineRunner is the engine unaware of XNAT.
iv) What does it take to create a XNAT pipeline:
Pipelines in XNAT would be triggered either by the user clicking
Action -> Build link or automatically on archival.
*) You need to identify which executable(s) (resource) you need to
invoke and in which order. You describe the executable in a resource
XML. You describe the order of invocation in the pipeline XML.
*) You need to provide the input parameters to the pipeline. Pipeline
engine can resolve XNAT XPATH statements and extract the input
parameters.
*) A pipeline would generate some data (a collection of images and
measures). You need to know how you would want to represent the
measures in XNAT. Do you need to create a new schema to model the
result of a pipeline? If yes, you create the schema.
v) Developer tasks for enabling XNAT pipeline
*) If input arguments to pipeline are to be selected using some logic,
you would need to create a velocity page (ui), a screen class and an
action class to launch the pipeline. The action class would write a
parameter document and invoke the XnatPipelineLauncher. The Site
administrator while adding the pipeline to the site repository, would
specify the velocity page which is to be rendered when the user clicks
Action -> Build -> Particular Pipeline
*) If the input arguments to pipeline can be extracted from the
session XML using XNAT XPATH statements, there wont be a need for a
velocity page, a screen class and an action class. A default page is
rendered to the user and an inbuilt action class would generate the
parameter XML and invoke XnatPipelineLauncher.
*) As a step in the pipeline, generate the XML instance of the new
schema representation and upload the XML and the associated data to
XNAT. We are the process of creating importer service which would be
capable of generating the XML and storing the data.
*) Create a page which would display the results of the pipeline and
create the display document which would show the results (aka listing)
in the project page.
e) Freesurfer pipeline:
At WashU, we have chosen to represent the data generated by Freesurfer
as an image assessor. The freesurfer pipeline used here at WashU,
contains input parameters which are specified (see input-parameter
section) using XNAT XPATH. So there is no velocity page, screen class
or action class required. I am attaching the required documents. You
will not be able to use the documents since you may not have all the
executables required. We could make these available if needed. Extract
the attached Freesurfer.zip in PIPELINE_HOME/templates/misc/catalog
and launch PIPELINE_HOME/setup.sh <ADMIN_EMAIL> <MAIL_SMTP_SERVER>.
I would advise you take a look at
PIPELINE_HOME/catalog/images/WebBasedQCImageCreator.xml and add that
to a project and launch the pipeline. Its easier to deal with this
pipeline, as it doesnt have an additional schema, additional
executables etc.
f) Finally:
There are lots of details that I have intentionally skipped to keep
things simple. Feel free to email if you have any doubts.
Regards
Mohana
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Try this solution:
http://www.digizol.org/2008/03/toolsjar-runtimeexception-no-compiler.html
Regards
Mohana
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