dcm4che / dcm4chee-arc-cdi Goto Github PK

Full-featured DICOM Archive based on Java Enterprise

Java 95.51% XSLT 1.53% Shell 0.02% Awk 0.01% HTML 0.11% JavaScript 2.44% CSS 0.38%

dcm4chee-arc-cdi's Introduction

dcm4che DICOM Toolkit & Library

Sources: https://github.com/dcm4che/dcm4che
Binaries: https://sourceforge.net/projects/dcm4che/files/dcm4che3
Issue Tracker: https://github.com/dcm4che/dcm4che/issues
Build Status:

This is a complete rewrite of dcm4che-2.x.

One main focus was to minimize the memory footprint of the DICOM data sets. It already provides modules to store/fetch configuration data to/from LDAP, compliant to the DICOM Application Configuration Management Profile, specified in DICOM PS 3.15, Annex H.

dcm4che uses a native library for the compression and decompression of images. Here is the list of supported systems and architectures:

System	Architecture	Package	Requirement
Linux	x86 64-bit	linux-x86-64	GLIBC_2.17
Linux	ARM 64-bit	linux-aarch64	GLIBC_2.27
Linux	ARM 32-bit	linux-armv7a	GLIBC_2.28
Windows	x86 64-bit	windows-x86-64	Windows 7 or higher
Windows	x86 32-bit	windows-x86	Windows 7 or higher
Mac OS	x86 64-bit	macosx-x86-64	Mac OS 10.13 or higher
Mac OS	ARM 64-bit	macosx-aarch64	Mac OS 11 or higher

Build

Make sure you have Java 17 (JDK) or newer installed.

Run the Maven Wrapper script for building:

./mvnw install

or on Windows:

.\mvnw install

Modules

dcm4che-audit
dcm4che-audit-keycloak
dcm4che-conf
- dcm4che-conf-api
- dcm4che-conf-api-hl7
- dcm4che-conf-json
- dcm4che-conf-json-schema
- dcm4che-conf-ldap
- dcm4che-conf-ldap-audit
- dcm4che-conf-ldap-hl7
- dcm4che-conf-ldap-imageio
- dcm4che-conf-ldap-schema
dcm4che-core
dcm4che-dcmr
dcm4che-deident
dcm4che-dict
dcm4che-dict-priv
dcm4che-emf
dcm4che-hl7
dcm4che-image
dcm4che-imageio
dcm4che-imageio-opencv
dcm4che-imageio-rle
dcm4che-js-dict
dcm4che-json
dcm4che-mime
dcm4che-net
dcm4che-net-audit
dcm4che-net-hl7
dcm4che-net-imageio
dcm4che-soundex
dcm4che-ws-rs
dcm4che-xdsi
dcm4che-jboss-modules

Utilities

agfa2dcm: Extract DICOM files from Agfa BLOB file
agfa2sr: Extract concatenated XML Agfa Reports and convert them to DICOM SR Documents
dcm2dcm: Transcode DICOM file according the specified Transfer Syntax
dcm2jpg: Convert DICOM image to JPEG or other image formats
dcm2json: Convert DICOM file in JSON presentation
dcm2pdf: Extract encapsulated PDF, CDA or STL from DICOM file
dcm2str: Apply Attributes Format Pattern to dicom file or command line parameters.
dcm2xml: Convert DICOM file in XML presentation
dcmbenchmark: Parse a DICOM file repetitively, measuring time and used memory
dcmdir: Dump, create or update DICOMDIR file
dcmdump: Dump DICOM file in textual form
dcmldap: Insert/remove configuration entries for Network AEs into/from LDAP server
dcmqrscp: Simple DICOM archive
dcmvalidate: Validate DICOM object according a specified Information Object Definition
deidentify: De-identify one or several DICOM files
emf2sf: Convert DICOM Enhanced Multi-frame image to legacy DICOM Single-frame images
findscu: Invoke DICOM C-FIND Query Request
fixlo2un: Fixes length of private tags truncated to 2 bytes on conversion from implicit VR to explicit VR Transfer Syntax
getscu: Invoke DICOM C-GET Retrieve Request
hl72xml: Convert HL7 v2.x message in XML presentation
hl7pdq: Query HL7 v2.x Patient Demographics Supplier
hl7pix: Query HL7 v2.x PIX Manager
hl7rcv: HL7 v2.x Receiver
hl7snd: Send HL7 v2.x message
ianscp: DICOM Instance Availability Notification receiver
ianscu: Send DICOM Instance Availability Notification
jpg2dcm: Convert JPEG images or MPEG videos in DICOM files
json2dcm: Converts JSON file to DICOM file
json2index: Creates search index for UI configuration from JSON schema files
json2props: Convert Archive configuration schema JSON files to key/value properties files and vice versa
json2rst: Generate ReStructuredText files from Archive configuration schema JSON files
maskpxdata: Mask information burned into the Pixel Data
mkkos: Make DICOM Key Object Selection Document
modality: Simulates DICOM Modality
movescu: Invoke DICOM C-MOVE Retrieve request
mppsscp: DICOM Modality Performed Procedure Step Receiver
mppsscu: Send DICOM Modality Performed Procedure Step
pdf2dcm: Convert PDF file into DICOM file
planarconfig: Detects the actual planar configuration of uncompressed pixel data of color images with Photometric Interpretation RGB or YBR_FULL and optionally correct non matching values of attribute Planar Configuration of the image
qstar: QStar SOAP Client to prefetch/retrieve or fetch file information of specified files
stgcmtscu: Invoke DICOM Storage Commitment Request
storescp: DICOM Composite Object Receiver
storescu: Send DICOM Composite Objects
stowrs: Send DICOM Composite Objects or Bulkdata file over Web
stowrsd: STOW-RS Server
swappxdata: Swaps bytes of uncompressed pixel data in DICOM files
syslog: Send Syslog messages via TCP/TLS or UDP to a Syslog Receiver
syslogd: Receives RFC 5424 Syslog messages via TCP/TLS or UDP
tpl2xml: Converts private dictionaries present in template file(s) to xml file(s).
upsscu: Invokes services of Unified Procedure Step Service Class
wadors: Wado RS Client Simulator
wadows: Wado WS Client Simulator
xml2dcm: Create/Update DICOM file from/with XML presentation
xml2hl7: Create HL7 v2.x message from XML presentation
xroad: XRoad SOAP Client to query Estonia National Patient Registry for Patient Demographics

License

Mozilla Public License Version 1.1

dcm4chee-arc-cdi's People

Contributors

Stargazers

Watchers

Forkers

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dcm4chee-arc-cdi's Issues

auto-routing implementation

Hello again,
As stated in the README.md, auto-routing is not yet implemented.
The company I work for is very interested in this feature and would be willing to invest person-hours on implementing it.
Is somebody working already on this feature, that I could contact in order to coordinate our efforts?

Attempt to view an image from qido web interface throws exception

Using the web interface at http://localhost:8080/dcm4chee-web/#

Now there is no exception being thrown when running from eclipse and searching. Thanks!

But, now I get the following error when pressing "V" to view an image:

java.lang.IllegalStateException: Input not set
at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.readMetadata(DicomImageReader.java:463) [dcm4che-imageio-3.3.4-SNAPSHOT.jar:3.3.4-SNAPSHOT]
at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.getStreamMetadata(DicomImageReader.java:212) [dcm4che-imageio-3.3.4-SNAPSHOT.jar:3.3.4-SNAPSHOT]
at org.dcm4chee.archive.wado.WadoURI.readImage(WadoURI.java:333) [dcm4chee-arc-wado-4.4.0-SNAPSHOT.jar:]
at org.dcm4chee.archive.wado.WadoURI.access$000(WadoURI.java:96) [dcm4chee-arc-wado-4.4.0-SNAPSHOT.jar:]
at org.dcm4chee.archive.wado.WadoURI$1.write(WadoURI.java:313) [dcm4chee-arc-wado-4.4.0-SNAPSHOT.jar:]
at org.jboss.resteasy.plugins.providers.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:32) [resteasy-jaxrs-3.0.6.Final.jar:]
at org.jboss.resteasy.plugins.providers.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:17) [resteasy-jaxrs-3.0.6.Final.jar:]
at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.writeTo(AbstractWriterInterceptorContext.java:129) [resteasy-jaxrs-3.0.6.Final.jar:]

Pressing search button on web interface with no search criteria gives: Internal Server Error

After deploying dcm4chee-arc-web, and going to:

http://localhost:8080/dcm4chee-web/

and pressing the S key, I get this error. It is due to an exception being thrown in QuidoRS class:

22:04:36,519 INFO [org.dcm4chee.archive.qido.QidoRS](default task-16) searchForStudiesJSON: 17 Matches
22:04:36,520 WARN [org.jboss.resteasy.core.ExceptionHandler](default task-16) failed to execute: javax.ws.rs.WebApplicationException: HTTP 500 Internal Server Error
at org.dcm4chee.archive.qido.QidoRS$2.write(QidoRS.java:605) [dcm4chee-arc-qido-4.4.0-SNAPSHOT.jar:]
at org.jboss.resteasy.plugins.providers.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:32) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.plugins.providers.StreamingOutputProvider.writeTo(StreamingOutputProvider.java:17) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.writeTo(AbstractWriterInterceptorContext.java:129) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.interception.ServerWriterInterceptorContext.writeTo(ServerWriterInterceptorContext.java:62) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:118) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.security.doseta.DigitalSigningInterceptor.aroundWriteTo(DigitalSigningInterceptor.java:143) [resteasy-crypto-3.0.8.Final.jar:]
at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:122) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.plugins.interceptors.encoding.GZIPEncodingInterceptor.aroundWriteTo(GZIPEncodingInterceptor.java:100) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:122) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.ServerResponseWriter.writeNomapResponse(ServerResponseWriter.java:99) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.SynchronousDispatcher.writeResponse(SynchronousDispatcher.java:427) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:376) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:179) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:220) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:56) [resteasy-jaxrs-3.0.8.Final.jar:]
at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:51) [resteasy-jaxrs-3.0.8.Final.jar:]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) [jboss-servlet-api_3.1_spec-1.0.0.Final.jar:1.0.0.Final]
at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:85) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:61) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at org.wildfly.extension.undertow.security.SecurityContextAssociationHandler.handleRequest(SecurityContextAssociationHandler.java:78)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:25) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:113) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:56) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:45) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:61) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:58) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:70) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.security.handlers.SecurityInitialHandler.handleRequest(SecurityInitialHandler.java:76) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:25) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at org.wildfly.extension.undertow.security.jacc.JACCContextIdHandler.handleRequest(JACCContextIdHandler.java:61)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:25) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:25) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:240) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:227) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:73) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:146) [undertow-servlet-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.server.Connectors.executeRootHandler(Connectors.java:168) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:727) [undertow-core-1.0.10.Final.jar:1.0.10.Final]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [rt.jar:1.7.0_51]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [rt.jar:1.7.0_51]
at java.lang.Thread.run(Thread.java:744) [rt.jar:1.7.0_51]
Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
at com.sun.org.apache.xalan.internal.xsltc.trax.TemplatesImpl.getTransletInstance(TemplatesImpl.java:387) [rt.jar:1.7.0_51]
at com.sun.org.apache.xalan.internal.xsltc.trax.TemplatesImpl.newTransformer(TemplatesImpl.java:418) [rt.jar:1.7.0_51]
at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl.newTransformerHandler(TransformerFactoryImpl.java:1062) [rt.jar:1.7.0_51]
at __redirected.__TransformerFactory.newTransformerHandler(__TransformerFactory.java:193) [jboss-modules.jar:1.3.3.Final]
at org.dcm4che3.io.SAXTransformer.getSAXWriter(SAXTransformer.java:70) [dcm4che-core-3.3.4-SNAPSHOT.jar:3.3.4-SNAPSHOT]
at org.dcm4chee.archive.qido.QidoRS$2.write(QidoRS.java:600) [dcm4chee-arc-qido-4.4.0-SNAPSHOT.jar:]
... 42 more

Failed to install the 4.4.0 beta 1 for dependency missed

Creating archiving rules

Please provide with an example configuration Json file or instructions ,how to add a new archiving rule ,to archive and QR to and from a external DICOM entity .

audit logger still tries to log to localhost after audit dicomHostname is set to actual host name

Hello,

I am using the ldap configuration for settings management.
I have changed the dicomHostname in apache directory studio to point to my actual
host name, but I still see message like:

 Send audit message to localhost/127.0.0.1:514 
 Error: failed to write audit log message.........

Is there another place where I have to change localhost?

Thanks!
Aaron

Cannot build project

Hi guys,
It seems that the release repository (http://www.dcm4che.org/maven2/) is not holding the expected versions causing errors when attempting to build the project

best regards
Alexis

deploy error

any help about the following error

Request
{
"address" => [("deployment" => "dcm4chee-arc-ear-4.5.0-SNAPSHOT-mysql.ear")],
"operation" => "deploy"
}

Response

Internal Server Error
{
"outcome" => "failed",
"failure-description" => {"JBAS014771: Services with missing/unavailable dependencies" => [
"jboss.naming.context.java.comp."dcm4chee-arc-ear-4.5.0-SNAPSHOT-mysql"."dcm4chee-arc-noneiocm-4.5.0-SNAPSHOT".NoneIOCMChangeRequestorServiceEJB.env."org.dcm4chee.archive.noneiocm.impl.NoneIOCMChangeRequestorServiceEJB".noneiocmQueue is missing [jboss.naming.context.java.queue.noneiocm]",
"jboss.naming.context.java.comp."dcm4chee-arc-ear-4.5.0-SNAPSHOT-mysql"."dcm4chee-arc-store-remember-4.5.0-SNAPSHOT".StoreAndRememberEJB.env."org.dcm4chee.archive.store.remember.impl.StoreAndRememberEJB".storeAndRememberQueue is missing [jboss.naming.context.java.queue.storeremember]"
]},
"rolled-back" => true
}

Getting WELD-001408: Unsatisfied dependencies for type Hooks<DefaultPersonNameManager> with qualifiers @Default

I have taken the code from GITHUB for dcm4chee-arc-cdi project,i have built the code using Maven as specified in the link.it successfully generated the dcm4chee-arc-ear file.

Now when i try to deploy the ear file into JBOSS wildfly server version( wildfly-8.2.0.Final) iam getting the dependencies issue.

19:48:29,958 ERROR [org.jboss.msc.service.fail](MSC service thread 1-4) MSC000001: Failed to start service jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService: org.jboss.msc.service.StartException in service jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService: Failed to start service
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1904) [jboss-msc-1.2.2.Final.jar:1.2.2.Final]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [rt.jar:1.7.0_79]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [rt.jar:1.7.0_79]
at java.lang.Thread.run(Thread.java:745) [rt.jar:1.7.0_79]
Caused by: org.jboss.weld.exceptions.DeploymentException: WELD-001408: Unsatisfied dependencies for type Hooks with qualifiers @default
at injection point [BackedAnnotatedField] @Inject @limit private org.dcm4chee.archive.store.impl.StoreServiceEJB.personNameSelector
at org.dcm4chee.archive.store.impl.StoreServiceEJB.personNameSelector(StoreServiceEJB.java:0)

at org.jboss.weld.bootstrap.Validator.validateInjectionPointForDeploymentProblems(Validator.java:372)
at org.jboss.weld.bootstrap.Validator.validateInjectionPoint(Validator.java:293)
at org.jboss.weld.bootstrap.Validator.validateGeneralBean(Validator.java:134)
at org.jboss.weld.bootstrap.Validator.validateRIBean(Validator.java:167)
at org.jboss.weld.bootstrap.Validator.validateBean(Validator.java:531)
at org.jboss.weld.bootstrap.ConcurrentValidator$1.doWork(ConcurrentValidator.java:68)
at org.jboss.weld.bootstrap.ConcurrentValidator$1.doWork(ConcurrentValidator.java:66)
at org.jboss.weld.executor.IterativeWorkerTaskFactory$1.call(IterativeWorkerTaskFactory.java:60)
at org.jboss.weld.executor.IterativeWorkerTaskFactory$1.call(IterativeWorkerTaskFactory.java:53)
at java.util.concurrent.FutureTask.run(FutureTask.java:262) [rt.jar:1.7.0_79]
... 3 more

19:48:30,042 ERROR [org.jboss.as.controller.management-operation](Controller Boot Thread) JBAS014613: Operation ("deploy") failed - address: ([("deployment" => "dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear")]) - failure description: {"JBAS014671: Failed services" => {"jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService" => "org.jboss.msc.service.StartException in service jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService: Failed to start service
Caused by: org.jboss.weld.exceptions.DeploymentException: WELD-001408: Unsatisfied dependencies for type Hooks with qualifiers @default
at injection point [BackedAnnotatedField] @Inject @limit private org.dcm4chee.archive.store.impl.StoreServiceEJB.personNameSelector
at org.dcm4chee.archive.store.impl.StoreServiceEJB.personNameSelector(StoreServiceEJB.java:0)
"}}
19:48:30,090 INFO [org.jboss.as.server](ServerService Thread Pool -- 31) JBAS018559: Deployed "postgresql-9.4-1201-jdbc41.jar" (runtime-name : "postgresql-9.4-1201-jdbc41.jar")
19:48:30,091 INFO [org.jboss.as.server](ServerService Thread Pool -- 31) JBAS018559: Deployed "dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear" (runtime-name : "dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear")
19:48:30,104 INFO [org.jboss.as.controller](Controller Boot Thread) JBAS014774: Service status report
JBAS014777: Services which failed to start: service jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService: org.jboss.msc.service.StartException in service jboss.deployment.unit."dcm4chee-arc-ear-4.5.0-SNAPSHOT-psql.ear".WeldStartService: Failed to start service