Connectathon Tool Installation

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Introduction

The sections below do not repeat the use of the tools. They assume the reader understands why the tool is needed for a Connectathon.

Central Archive

Central Archive Software

We use the DCM4CHEE Archive 5 that is described here: https://www.dcm4che.org. For January 2020, we installed and configured using the Docker version:

   git clone https://github.com/IHE-Tools/dicom-connectathon.git
   cd dicom-connectathon/dcm4chee/scripts

Review the file master_run.sh. It has a ROOT variable that points to a folder that should exist and will be used to hold files.

  • Change that value to match your installation
  • You might have to tell docker about that folder to provide access.
./master_run.sh

You now have this version of dcm4chee running:

  • dcm4che/dcm4chee-arc-psql:5.10.5

You could certainly modify the dcm4chee_run.sh script to use a different version. Note that we did not use Docker compose. The files in the docker-compose folder were not tested to completion.

Central Archive Data Files

The section Central Archive Software gave you a pointer to a git repository to pull configuration files. That same repository has scripts to retrieve DICOM files and place them on the Central Archive.

   git clone https://github.com/IHE-Tools/dicom-connectathon.git
   cd data-sets/scripts
   ./get_NA2020.sh [folder]

The last script retrieves a number of data sets (complete list below) and places them in the folder you specify. If you omit <folder>, the files are stored in /opt/connectathon-2020/data-sets.

Some of the data sets contain non-DICOM images. The get_NA2020.sh script removes those files in a hard coded way. If you extend the script, you will have to take this into consideration.

To store the images to the Central Archive:

./store_NA2020.sh [folder]

This script walks through all of the files stored in <folder> and sends them to the Central Archive using DICOM C-Store. If <folder> is not specified, the default value /opt/connectathon-2020/data-sets is used.

  • This script is hard coded to send to a PACS with these parameters: DCM4CHEE:localhost:11112. That is easy to change in one place.
  • The script assumes that all files under <folder> are DICOM files. It will abort if it runs into non-DICOM files.
  • This script assumes that the dcm4che command line tools are installed and are on the PATH of the current user. You can use a different command line tool by modifying store.sh.

Images Retrieved by the NA 2020 Scripts

Data Set Location
(3) GE Synocrystal Images ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/MAMMO_Samples/2019-EU-Samples/GE%20Senocrystal%20Images/STORE/51346117/70288881
(4) IMSGIOTTO Images ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/MAMMO_Samples/2018_EU_Samples/IMSGIOTTO_MOD_RAFFAELLO
(5) GE DBT samples ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2017-EU-Samples/GEHC/
(6) IMSGIOTTO Images ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2018-EU-Samples/
(7) Siemens images ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/DBT_samples/2017-EU-Samples/Siemens/
(8) GE samples ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/REM-NM_samples/GE_NM_830
(9) Toshiba samples ftp://ftp.ihe.net/Connectathon/samples/RAD-profiles/REM-NM_samples/MOD_TOSHIBA_1

FHIR Read-Write Server (HAPI FHIR Server)

The description for this section is quite long. Please see HAPI FHIR Software for IHE Connectathons

Structure Definitions and Other Test Data

The git repository https://github.com/IHE-Tools/fhir-known-resources contains scripts to load Structure Definitions and other test data (e.g., well known patients) into the FHIR Read/Write Server.

Clone the repository:

   git clone https://github.com/IHE-Tools/fhir-known-resources.git

POST Structure Definitions

The information you need to retrieve and POST the Structure definitions is found in fhir-known-resources/structure_definitions/README.txt.

You have to clone the IHE/fhir repository as it contains the structure definitions. Follow the directions in that README.txt file. There are scripts in the fhir-known-resources repository to help with the process.

POST Connectathon Test Patients

The information you need to retrieve and post the Connectathon test patients is found in fhir-known-resources/patients/README.txt. The README.txt references scripts in the fhir-known-resources repository that will help with the process.

POST mXDE / QEDm Test Data

XDS-I Software

Mitre Canary

The Mitre Canary software used during the NA 2020 Connectahon was managed using docker:

docker run --rm -p 18080:80 adammitre/canary:2.12.0

This provided a URL of the form: http://host:18080

Notes for NA 2020

  • The original suggestion was to run the latest version of the software. The authors discovered something and asked us to run the specific version listed above (2.12.0).
  • It will certainly be worth revisiting the versioning information in future years.

Other Data Sets