Rick Herrick rherrick
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| -- Change 'xnat' to the database user that owns the XNAT tables. | |
| -- You need to stop Tomcat before running this query. | |
| SELECT drop_user_views('xnat'); |
rherrick
/ create_recon.sh
Last active
July 24, 2017 17:09
Create XNAT image reconstruction then update to include manually added files
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| # Get a session | |
| http --auth admin:minda --session=admin xnat164.xnat.org/data/projects | |
| # Create the reconstruction and resource folder | |
| http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001 xnat:reconstructedImageData/type==RECON_A | |
| http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001/resources/NIFTI format==NIFTI | |
| # Upload NIFTI and JSON to the reconstruction resource | |
| for SERIES in t1_mpr_1mm_p2_pos50_20061214091206_4 t1_mpr_1mm_p2_pos50_20061214091206_5 t2_spc_1mm_p2_20061214091206_6; do | |
| http --session=admin PUT xnat164.xnat.org/data/archive/projects/prj001/subjects/prj001_001/experiments/prj001_001_MR2/reconstructions/prj001_001_MR2_recon_001/resources/NIFTI/files/${SERIES}.nii.gz inbody==true < ${SERIES}.nii.gz |
rherrick
/ xnat-ext-1.7.4-SNAPSHOT.gradle
Last active
August 17, 2017 18:06
External Gradle configuration
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| apply plugin: "jacoco" | |
| ext.propertyWithDefault = { String name, def value -> | |
| hasProperty(name) ? property(name) : value | |
| } | |
| dependencyManagement.imports { | |
| mavenBom "org.nrg:parent:${vXnat}" | |
| } |
rherrick
/ build.gradle
Created
December 8, 2017 01:07
Simple configuration of Javadoc coverage doclet for Gradle
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| configurations { | |
| // Other configuration lines might be in here | |
| javadocCoverage | |
| } | |
| dependencies { | |
| // Your application's other dependencies go here. | |
| javadocCoverage "com.manoelcampos:javadoc-coverage:1.1.0" | |
| } |
rherrick
/ build.gradle
Last active
February 27, 2018 18:58
Repositories element without dcm4che repo for XNAT pom.xml and build.gradle files. Note that the repositories block in build.gradle should _not_ be applied to a repositories block inside a buildscript block, only to the standard repositories block.
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| repositories { | |
| mavenLocal() | |
| maven { | |
| url "http://maven.imagej.net/content/groups/public" | |
| name "ImageJ Maven Repository" | |
| } | |
| jcenter() | |
| mavenCentral() | |
| maven { | |
| url "https://nrgxnat.jfrog.io/nrgxnat/libs-release" |
rherrick
/ add-to-java-cacerts.sh
Created
May 10, 2018 01:29
Shows failure to install Charles proxy cert on Java 10 JDK on OS X
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| decker:Internet Plug-Ins root# JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home $(find /Applications/Charles.app/Contents/ -name "*.command") | |
| ############################################ | |
| Charles Root Certificate Java VM Import Tool | |
| ############################################ | |
| This tool imports your Charles Root Certificate into the Java VMs that it finds on | |
| your computer, so that Java applications trust your Charles Root Certificate for | |
| SSL Proxying. |
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| package com.nerdnetworks; | |
| import java.io.IOException; | |
| import java.nio.file.Files; | |
| import java.nio.file.Paths; | |
| import java.util.HashSet; | |
| import java.util.Set; | |
| import java.util.concurrent.atomic.AtomicInteger; | |
| public class Main { |
rherrick
/ 2019-03-28T18_22_05_888Z-debug.log
Created
March 28, 2019 18:48
Failure when launching test node app
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| 0 info it worked if it ends with ok | |
| 1 verbose cli [ '/Users/username/.nvm/versions/node/v10.15.3/bin/node', | |
| 1 verbose cli '/Users/username/.nvm/versions/node/v10.15.3/bin/npm', | |
| 1 verbose cli 'run', | |
| 1 verbose cli 'dev' ] | |
| 2 info using [email protected] | |
| 3 info using [email protected] | |
| 4 verbose run-script [ 'predev', 'dev', 'postdev' ] | |
| 5 info lifecycle @~predev: @ | |
| 6 info lifecycle @~dev: @ |
rherrick
/ get-resources.sh
Created
September 20, 2020 21:49
Get resource files from XNAT dataset collection
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| #!/usr/bin/env bash | |
| showHelp() { | |
| echo | |
| echo "Usage: ${0} --server <URL> --username <USER> --password <PASSWORD> --project <PROJECT> --collection <COLLECTION_ID>" | |
| echo | |
| echo "Note: all options are required, with the exception of --password. If --password" | |
| echo " is omitted, you must enter your password when the script runs." | |
| echo | |
| exit 255 |
rherrick
/ Anonymizer.groovy
Created
September 21, 2020 18:00
A script that pulls in the XNAT Mizer library and DicomEdit 4 and 6 and applies an anonymization script to DICOM files. Requires Groovy installation. Save this file as Anonymizer.groovy, make it executable (e.g. chmod +x Anonymizer.groovy), then run it.
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| #!/usr/bin/env groovy | |
| @GrabConfig(systemClassLoader = true) | |
| @GrabResolver(name = "NRG Release Repo", root = "https://nrgxnat.jfrog.io/nrgxnat/libs-release") | |
| @GrabResolver(name = "NRG Snapshot Repo", root = "https://nrgxnat.jfrog.io/nrgxnat/libs-snapshot") | |
| @Grapes([ | |
| @GrabExclude("org.slf4j:slf4j-simple"), | |
| @GrabExclude("org.slf4j:slf4j-log4j12"), | |
| @Grab("info.picocli:picocli:4.5.1"), | |
| @Grab("ch.qos.logback:logback-classic:1.2.3"), | |
| @Grab("org.nrg.dicom:mizer:1.2.0-SNAPSHOT"), |