Difference between revisions of "Connectathon Tool Installation"

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(FHIR Read-Write Server (HAPI FHIR Server))
(FHIR Read-Write Server (HAPI FHIR Server))
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=FHIR Read-Write Server (HAPI FHIR Server)=
=FHIR Read-Write Server (HAPI FHIR Server)=
The description for this section is quite long.
* Clone a copy of the HAPI-FHIR server
:<code>git clone https://github.com/jamesagnew/hapi-fhir.git</code>
* Checkout the appropriate branch or version. For NA 2020, we used v4.1.0. Your event may use a more recent version.
:<code>cd hapi-fhir</code>
:<code>git checkout v4.1.0</code>
* Modify source code
There are small changes necessary to configure the software. These are completed directly in the source code and not in a configuration file.
Please see [[HAPI FHIR Software for IHE Connectathons]]
Please see [[HAPI FHIR Software for IHE Connectathons]]
* Build the war file
Use the mvn command to build the war file. You want to use the flag -DskipTests unless you want to wait a long time for the unit tests to complete.
:<code>mvn -DskipTests install</code>
==Structure Sets and Other Test Data==
==Structure Sets and Other Test Data==

Revision as of 10:33, 16 February 2020


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.

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 Sets and Other 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