trait_ctp

info

CTMM-TraIT CTP repository to:

• store collection and site specific CTP configurations
• store the supported CTP client version
• generate a standard CTP configurationfor a new collection and site (scripted)

requirements

to run CTP and the generation scripts the following libraries are required

• java 8
• jq (to parse json, https://stedolan.github.io/jq/download/)
• dcmtk (to test the dicom transfer, https://dicom.offis.de/dcmtk.php.en)

generation manual

follow these steps to generate a new configuration:

1. git pull (to get the latest repository changes)
2. edit the pipeline_config.json
   • name: this should be the exact same name as in XNAT (case-sensitve)
   • site: identifier or name for the contributing site
   • uid: the DICOM root UID generated by the trait servicedesk
   • webport: 8080 default
   • dicomport: 104 default
3. run "sh generate_pipeline.sh" (the configuration will show up in ../site_configurations)
4. run "sh start_ctp.sh" (this will start the generated configuration)
   • this script will also add a lookup.properties so the test data will not go to quarantine, the patient id will be "_trait_admin_test"
5. open a new terminal, run "sh send_test_files.sh"
   • login to xnat, the prearchive should have a new study with 10 CT-slices for patient "_trait_admin_test"
6. if the configuration is correct:
   • run "sh clean_ctp.sh", this is the same script will clean the ./scr/CTP folder
   • add the ./src/"CTP_[COLLECTION_NAME] [SITE_NAME].zip" to topdesk for redistribution
   • git commit/push

building custimized pipelines

if the standard pipeline does not fulfill the requirements for a collection/site use these steps to create custom pipelines:

• go to /site_configurations/[COLLECTION_NAME]/[SITE_NAME] and alter the config.xml or the anonymizer.properties
• make sure the pipeline_config.json matches the settings of the pipeline you want to test
• after changes redo step 4.to 6.