CTP Configuration for the Image Sharing Project

From MircWiki
Jump to navigation Jump to search

This article describes how the CTP application can be configured for use in the RSNA Image Sharing Project. This article is intended for Image Sharing Project developers. There are several CTP articles on the RSNA MIRC wiki that might be useful references when reading this article.

The Image Sharing Project is separated into two main use cases, one for the transfer of images for clinical use and one for transfer of anonymized research data. Each use case has a sender and a receiver.

  • The clinical sender is completely contained in the Edge Server and does not involve CTP.
  • The clinical receiver has two alternative configurations, one using both the Edge Server and CTP and the other using CTP stand-alone.
  • The research sender uses both the Edge Server and CTP together.
  • The research receiver uses CTP stand-alone.

The configuration of a CTP instance is specified by an XML file called config.xml. See CTP-The RSNA Clinical Trial Processor for detailed information about pipelines, pipeline stages, plugins, and the general processing model of the program.

This article presents a combined configuration file example including both of the research use cases and the clinical receiver, each implemented in its own pipeline. The configuration can be modified to remove pipelines that are not required in a specific installation.

In the configuration shown below, the server is put on port 80, and SSL is not enabled for access to the server itself, although communication with the Clearinghouse is always secure.

1 The Configuration File

This configuration example includes the separate pipelines for the research sender and research receiver: 

<Configuration log="yes">
    <Server port="1080"
    	ssl="no"
        keystore="keystore.jks"
        keystorePassword="edge1234"
        truststore="truststore.jks"
        truststorePassword="edge1234"/>
    <Pipeline name="Research Sender">
        <DicomImportService
            calledAETTag="00120010"
            class="org.rsna.ctp.stdstages.DicomImportService"
            logConnections="rejected"
            name="DicomImportService"
            port="1081"
            quarantine="quarantines/Sender/DicomImportService"
            root="roots/Sender/DicomImportService"
            servletContext="export" />
        <ObjectCache
            name="ObjectCache-RS"
            class="org.rsna.ctp.stdstages.ObjectCache"
            id="ObjectCache-RS"
            root="roots/Sender/ObjectCache-RS" />
        <DicomAnonymizer
            class="org.rsna.ctp.stdstages.DicomAnonymizer"
            lookupTable="scripts/lookup-table.properties"
            name="DicomAnonymizer"
            quarantine="quarantines/Sender/DicomAnonymizer"
            root="roots/Sender/DicomAnonymizer"
            script="scripts/Sender.script"/>
        <CachingXDSExportService
            servletContext="xds-export"
            name="CachingXDSExportService-RS"
            class="org.rsna.isn.ctp.xds.sender.CachingXDSExportService"
            root="roots/Sender/CachingXDSExportService-RS"
            objectCacheID="ObjectCache-RS"
            minAge="300"
            timeDepth="30"
            iti8Pix="mllps://clearinghouse.lifeimage.com:8888"
            iti8Reg="mllps://clearinghouse.lifeimage.com:8890"
            iti41="https://clearinghouse.lifeimage.com/services/xdsrepositoryb"
            iti41SrcId="1.3.6.1.4.1.19376.2.840.1.1.2.1"
            timeout="120000"
            quarantine="quarantines/Sender/CachingXDSExportService-RS">

            <Destination
                name="Trial S"
                key="9652fef890fe9b5de17f2116e971f153d7d655c3b57fef6012a2138239e34d20"
                token="fpzddg"
                dob="19460201"
                pw="quackquack"/>
            <Destination
                name="Trial T"
                key="e03c75ab7056c94335e3f06a6e81331a973413efc3474ff7a508ce842a3630ea"
                token="63x4ec"
                dob="19460201"
                pw="quackquack"/>

        </CachingXDSExportService>
    </Pipeline>
    <Pipeline name="Research Receiver">
        <PollingXDSImportService
            name="PollingXDSImportService-RR"
            class="org.rsna.isn.ctp.xds.receiver.PollingXDSImportService"
            root="roots/ResearchReceiver/PollingXDSImportService"
            interval="60"
            rad69URL="https://clearinghouse.lifeimage.com/ImagingDocumentSource_Service?wsdl"
            registryURL="https://clearinghouse.lifeimage.com/services/xdsregistryb"
            repositoryURL="https://clearinghouse.lifeimage.com/services/xdsrepositoryb"
            repositoryUniqueID="rsna.domain.repository"
            assigningAuthorityUniversalID="1.3.6.1.4.1.19376.2.840.1.1.1.1"
            assigningAuthorityUniversalIDType="ISO"
            homeCommunityID="rsna.domain</HomeCommunityId"
            siteID="9652fef890fe9b5de17f2116e971f153d7d655c3b57fef6012a2138239e34d20"
            imagesPerRequest="100"
            timeout="120000" />
        <ObjectLogger
            name="ObjectLogger-RR"
            class="org.rsna.ctp.stdstages.ObjectLogger"
            interval="1"
            verbose="yes" />
        <FileStorageService
            class="org.rsna.ctp.stdstages.FileStorageService"
            name="FileStorageService-RR"
            port="1086"
            quarantine="quarantines/ResearchReceiver/FileStorageService"
            root="roots/ResearchReceiver/FileStorageService"/>
<!--
        <DicomExportService
            name="DicomExportService-RR"
            class="org.rsna.ctp.stdstages.DicomExportService"
            root="roots/ResearchReceiver/DicomExportService"
            quarantine="quarantines/ResearchReceiver/DicomExportService"
            url="dicom://DestinationAET:ThisAET@ipaddress:port"
            interval="5000" />
-->
   </Pipeline>
    <Pipeline name="Clinical Receiver">
        <XDSImportService
            name="XDSImportService-CR"
            class="org.rsna.isn.ctp.xds.receiver.XDSImportService"
            root="roots/ClinicalReceiver/XDSImportService-CR"
            interval="60"
            rad69URL="https://clearinghouse.lifeimage.com/ImagingDocumentSource_Service?wsdl"
            registryURL="https://clearinghouse.lifeimage.com/services/xdsregistryb"
            repositoryURL="https://clearinghouse.lifeimage.com/services/xdsrepositoryb"
            repositoryUniqueID="rsna.domain.repository"
            assigningAuthorityUniversalID="1.3.6.1.4.1.19376.2.840.1.1.1.1"
            assigningAuthorityUniversalIDType="ISO"
            homeCommunityID="rsna.domain</HomeCommunityId"
            imagesPerRequest="100"
            timeout="120000"
            servletContext="xds-import" />
        <ObjectLogger
            name="ObjectLogger-CR"
            class="org.rsna.ctp.stdstages.ObjectLogger"
            interval="1"
            verbose="yes" />
        <FileStorageService
            class="org.rsna.ctp.stdstages.FileStorageService"
            name="FileStorageService"
            port="1087"
            quarantine="quarantines/ClinicalReceiver/FileStorageService"
            root="roots/ClinicalReceiver/FileStorageService"/>
<!--
        <DicomExportService
            name="DicomExportService-CR"
            class="org.rsna.ctp.stdstages.DicomExportService"
            root="roots/ClinicalReceiver/DicomExportService"
            quarantine="quarantines/ClinicalReceiver/DicomExportService"
            url="dicom://DestinationAET:ThisAET@ipaddress:port"
            interval="5000" />
-->
   </Pipeline>
</Configuration>

2 The Server Element

The Server element specifies the port of the web server. It also allows the specification of the keystore and truststore files. In the Image Sharing Network (ISN), these are special files and their names and passwords must be supplied. The ISN-installer.jar program installs the keystore.jks and keystore.jks files in the CTP directory. If other keystore or truststore files are to be used, be sure to specify their locations in the Server element.

3 The Research Sender Pipeline

The Research Sender Pipeline configuration assumes that unanonymized DICOM data objects are transmitted to CTP by an external application using the DICOM protocol. The objects are anonymized, removing PHI from both the text elements and the pixels. The objects are then cached until a user manually selects the study and assigns a destination, after which they are exported to the clearing house.

In this configuration, all the stages except the CachingXDSExportService are standard CTP stages. They are all documented in CTP-The RSNA Clinical Trial Processor.

Note: The DicomDecompressor and DicomPixelAnonymizer stages can be added to this pipeline if PHI is burned into the pixels of images received for transmission. If the DicomPixelAnonymizer is in the pipeline, the DicomDecompressor must also be present, and it must precede the DicomPixelAnonymizer.

3.1 CachingXDSExportService

The special attributes of the CachingXDSExportService are:

  • root is a directory within which the CachingXDSExportService caches objects and stores its indexing information.
  • cacheID specifies the ID of an ObjectCache stage that may be accessed by the CachingXDSExportService to obtain pre-anonyization information so it can index the objects by their PHI and make that information available to a user who accesses the servlet. If the cacheID attribute is not supplied, the CachingXDSExportService indexes the objects by the anonymized values.
  • servletContext specifies the context of a servlet that provides a user interface allowing as user to select cached studies and assign them destinations for export. The purpose of the servletContext attribute is to allow each CachingXDSExportService to have its own servlet in cases where multiple export pipelines are present in the same CTP instance.
  • minAge is the minimum age in seconds which defines the completion of a study. When the last object received for a study is at least minAge old, the study is considered complete and is available for selection for export. The default value is 300; the minimum accepted value is 60.
  • timeDepth specifies the length of time in days that studies are stored. The default value is 0, which means forever. If timeDepth is greater than zero, studies older than that value are automatically removed from the cache, making them no longer available for export.

3.1.1 The Destination Element

The CachingXDSExportService must have at least one Destination child element specifying both a name and key for the destination on the Clearinghouse.

3.1.2 The CachingXDSExportService Servlet

The servlet provided by the CachingXDSExportService is installed on the CTP servlet container at the context specified by the servletContext attribute. The servlet provides the following APIs:

  • /{servletContext} - GET returns an HTML page containing a form for selection of studies and destinations. The page also lists the studies that have already been transmitted and shows their status (number of images transmitted, total size of the study, success or failure of the transmission).
  • /{servletContext} - POST accepts a completed form and returns a new HTML page.

The servlet displays studies that are available for transmission. Each study has a status that is either OPEN or COMPLETE. A study is open is one for which an object an object has been received in the last number of seconds specified by the minAge attribute.

A study can be selected for transmission whether its status is OPEN or COMPLETE. Only those images that have been received by the time transmission starts will be included in the submission set.

When a study has been selected for transmission, it moves from the studies table to the Sent Studies table on the page. Once a study has been successfully transmitted to the selected destination, it remains visible in the Sent Studies table for one hour, after which the study is deleted from the table and from storage.

The servlet automatically provides an additional destination, Trash to allow studies to be deleted from the cached studies table and from storage.

4 The Research Receiver Pipeline

The Research Receiver Pipeline polls the Clearinghouse for submission sets, imports them, and passes the objects down the pipe. In the configuration shown above, the same key is used for both sending and receiving, so the objects that are transmitted will be very quickly be retrieved. This is just for testing; in a real installation, the configurations of the destination keys and siteID keys will be different.

4.1 PollingXDSImportService

The special attributes of the PollingXDSImportService are:

  • root is a directory within which the PollingXDSImportService stores its import queue.
  • interval specifies the time in seconds between polls of the Clearinghouse. The default value is 60. The minimum accepted value is 60.
  • siteID specifies the key or keys on which to poll the Clearinghouse. See the notes below for details.

Notes:

  • The siteID attribute can contain multiple keys, separated by whitespace, as in:
    siteID="9652fef890fe9b5de17f2116e971f153d7d655c3b57fef6012a2138239e34d20
            e03c75ab7056c94335e3f06a6e81331a973413efc3474ff7a508ce842a3630ea"
  • The PollingXDSImportService polls on the siteID keys, importing all the submission sets that are available. It then sleeps for the specified interval and then polls again. When multiple siteID keys are supplied, each key is polled during every interval.
  • The PollingXDSImportService tracks which studies it has imported, and it does not import the same study multiple times.

4.2 ObjectLogger

The ObjectLogger stage is included in the configuration just for testing. It logs information about every object that flows down the pipe to confirm what has been received. This stage should be removed in a operational installation.

4.3 FileStorageService

The FileStorageService stage is included for testing. It saves all the objects that are received. This stage may be useful in an operational installation as well. It is configured with a port (1086) on which it opens a web server to provide browser access to the studies received.

5 The Clinical Receiver Pipeline

The Clinical Receiver Pipeline provides a user interface for selecting studies to be downloaded from the Clearinghouse.

5.1 XDSImportService

The special attributes of the XDSImportService are:

  • root is a directory within which the XDSImportService stores its import queue.
  • interval specifies the time in seconds between polls of the Clearinghouse. The default value is 60. The minimum accepted value is 60.
  • servletContext specifies the context of a servlet that provides a user interface allowing a user to manually enter a key to import a submission set.

Notes:

  • The purpose of the servletContext attribute is to allow each XDSImportService to have its own servlet in cases where multiple import pipelines are present in the same CTP instance.

5.2 ObjectLogger

The ObjectLogger stage is included in the configuration just for testing. It logs information about every object that flows down the pipe to confirm what has been received. This stage should be removed in a operational installation.

5.3 FileStorageService

The FileStorageService stage is included for testing. It saves all the objects that are received. This stage may be useful in an operational installation as well. It is configured with a port (1087) on which it opens a web server to provide browser access to the studies received.

6 The ISN Tool Servlet

The system provides a useful servlet for creating destination keys. The servlet is accessed with the context /isn-tool. This servlet is installed automatically whenever a CachingXDSExportService or a PollingXDSImportService appears in the configuration.

7 Installation and Configuration

ISN is implemented as a set of CTP pipeline stages and servlets. The ISN-installer.jar program contains the installer for both CTP and the ISN stages and servlets. The installation procedure is identical to that of CTP. The CTP installation instructions are on the RSNA MIRC Wiki.

The installer can be used to upgrade an existing installation. When upgrading, the installer will not overwrite an existing config.xml file. It will also not modify any of the databases used by the program to track studies that have previously been downloaded.

After installation, the CTP/config.xml file must be edited to set the configuration for the site.

The Edge Server expects the CTP server to be on port 1080. This can be set during initial installation or by editing the config.cml file directly.

The standard configuration includes three pipelines. Those not required for the site should be deleted.

For sites that require either the Research Receiver or Clinical Receiver pipelines, the configuration of the pipeline may need to be modified if downloaded images are to be sent to another system. The initial configuration for both pipelines includes a DicomExportService, but the element is commented out. If a DicomImportService is required, remove the comment tags and set the correct values in the url attribute.

In operation, it will probably be desirable to remove all the ObjectLogger pipeline stages. They are included to assist in testing.

8 Notes for V&V Testing

8.1 Controlling the Logger

The log4j properties file installed in the program is located in the CTP directory. The contents are: 

# Logging Configuration

# set root logger level to ERROR and give it an appender
log4j.rootLogger = ERROR, RootAppender

# make the appender
log4j.appender.RootAppender = org.apache.log4j.DailyRollingFileAppender

# give it a layout
log4j.appender.RootAppender.layout = org.apache.log4j.PatternLayout
log4j.appender.RootAppender.layout.ConversionPattern = %d{HH:mm:ss} %-5p [%c{1}] %m%n

# set the filename
log4j.appender.RootAppender.File = logs/ctp.log

# set the datepattern
log4j.appender.RootAppender.DatePattern = '.'yyyy-MM-dd

#--------------------------------
# set the starting logger levels
#--------------------------------
log4j.logger.gov = WARN
log4j.logger.edu = WARN
log4j.logger.org = WARN
log4j.logger.org.rsna = INFO
log4j.logger.mirc = INFO
log4j.logger.org.openhealthtools.ihe.atna.auditor = OFF
log4j.logger.org.rsna.isn.ctp.xds.receiver = WARN
log4j.logger.org.rsna.isn.ctp.xds.sender = WARN

Either or both of the last two lines can be set to DEBUG to enable logging of all the polling and transmission activities.

8.2 Resetting the System

The configuration puts the root directories of all the pipeline stages under the CTP/roots directory. (Note: Just to be clear, the CTP/ROOT directory is the root of the server; the CTP/roots directory is the root of the pipeline stages.)

Each pipeline stage confines its persistent storage to its root directory.

To reset the system, stop CTP and delete the CTP/roots directory. When CTP starts again, it will recreate the directory and all the pipeline stages will create their root directories within it. This will have the effect of erasing all the history that indicates which studies have been downloaded. If the configuration has a PollingXDSImportService, it will then download everything on the Clearinghouse for the siteID keys that are in its configuration.

8.3 Clearing a Single PollingXDSImportService

A PollingXDSImportService tracks studies that it has previously download in a database contained in the database subdirectory of its root directory. The database consists of two files:

  • docsetIDs.db
  • docsetIDs.lg

To remove the download history, these files can be deleted. They will be recreated when they are required.

Retrieved from "http://mircwiki.rsna.org/index.php?title=CTP_Configuration_for_the_Image_Sharing_Project&oldid=6450"