dcm4chee (in docker) wants to write home dir?

[stbender]

Hello,

I tried to deploy dcm4chee via docker-compose as described here:
https://github.com/dcm4che/dcm4chee-arc-light/wiki/Run-minimum-set-of-archive-services-on-a-single-host

I used the exact docker-compose.yml and docker-compose.env as listed on the page named above.

I start the system with this command:
sudo docker-compose -p dcm4chee up -d
as user radswz in the folder /home/radswz.

The system starts fine.
But soon as I send some images I get these errors:
`2022-09-05 18:07:27,288 INFO [org.dcm4che3.net.Dimse] (EE-ManagedExecutorService-default-Thread-97) DCM4CHEE<-MBP-SB(6) >> 1:C-STORE-RQ[pcid=45, prior=2
cuid=1.2.840.10008.5.1.4.1.1.2 - CT Image Storage
iuid=1.3.12.2.1107.5.1.4.95211.30000022030611181393500004150 - ?
tsuid=1.2.840.10008.1.2.1 - Explicit VR Little Endian]
2022-09-05 18:07:27,294 WARN [org.dcm4chee.arc.store.impl.StoreServiceImpl] (EE-ManagedExecutorService-default-Thread-97) DCM4CHEE<-MBP-SB(6): Failed to store received object:
: java.nio.file.AccessDeniedException: /home/radswz
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:389)
at java.base/java.nio.file.Files.createDirectory(Files.java:690)
at java.base/java.nio.file.Files.createAndCheckIsDirectory(Files.java:797)
at java.base/java.nio.file.Files.createDirectories(Files.java:783)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.filesystem.FileSystemStorage.createDirectories(FileSystemStorage.java:165)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.filesystem.FileSystemStorage.openOutputStreamA(FileSystemStorage.java:183)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.AbstractStorage.openOutputStream(AbstractStorage.java:122)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.openOutputStream(StoreServiceImpl.java:754)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.access$200(StoreServiceImpl.java:107)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl$TranscoderHandler.newOutputStream(StoreServiceImpl.java:738)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.initDicomOutputStream(Transcoder.java:919)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.access$700(Transcoder.java:71)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder$1.readValue(Transcoder.java:465)
at org.dcm4che.core@5.27.0//org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:681)
at org.dcm4che.core@5.27.0//org.dcm4che3.io.DicomInputStream.readAllAttributes(DicomInputStream.java:568)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.transcode(Transcoder.java:440)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.writeToStorage(StoreServiceImpl.java:248)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:199)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:190)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl$Proxy$_$$WeldClientProxy.store(Unknown Source)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.store.scp.CStoreSCP.store(CStoreSCP.java:36)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.service.BasicCStoreSCP.onDimseRQ(BasicCStoreSCP.java:72)
at jdk.internal.reflect.GeneratedMethodAccessor87.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.jboss.weld.core@3.1.9.Final//org.jboss.weld.bean.proxy.AbstractBeanInstance.invoke(AbstractBeanInstance.java:38)
at org.jboss.weld.core@3.1.9.Final//org.jboss.weld.bean.proxy.ProxyMethodHandler.invoke(ProxyMethodHandler.java:106)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4che3.net.service.DicomService$507164635$Proxy$$$_WeldClientProxy.onDimseRQ(Unknown Source)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.service.DicomServiceRegistry.onDimseRQ(DicomServiceRegistry.java:86)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.ApplicationEntity.onDimseRQ(ApplicationEntity.java:491)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.onDimseRQ(Association.java:750)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.PDUDecoder.decodeDIMSE(PDUDecoder.java:466)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.handlePDataTF(Association.java:733)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.State$4.onPDataTF(State.java:108)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.onPDataTF(Association.java:729)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.PDUDecoder.nextPDU(PDUDecoder.java:177)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association$2.run(Association.java:566)
at org.jboss.as.ee@26.1.1.Final//org.jboss.as.ee.concurrent.ControlPointUtils$ControlledRunnable.run(ControlPointUtils.java:125)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.SecurityIdentity.runAsConsumer(SecurityIdentity.java:376)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.Scoped.runAsConsumer(Scoped.java:112)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.Scoped.runAs(Scoped.java:60)
at org.jboss.as.ee@26.1.1.Final//org.jboss.as.ee.concurrent.SecurityIdentityUtils.lambda$doIdentityWrap$1(SecurityIdentityUtils.java:63)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.internal.ManagedFutureTask.run(ManagedFutureTask.java:117)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.ManagedThreadFactoryImpl$ManagedThread.run(ManagedThreadFactoryImpl.java:227)

2022-09-05 18:07:27,297 INFO [org.dcm4che3.net.Association] (EE-ManagedExecutorService-default-Thread-97) DCM4CHEE<-MBP-SB(6): processing 1:C-STORE-RQ[pcid=45, prior=2
cuid=1.2.840.10008.5.1.4.1.1.2 - CT Image Storage
iuid=1.3.12.2.1107.5.1.4.95211.30000022030611181393500004150 - ?
tsuid=1.2.840.10008.1.2.1 - Explicit VR Little Endian] failed. Caused by: : org.dcm4che3.net.service.DicomServiceException: java.nio.file.AccessDeniedException: /home/radswz
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.writeToStorage(StoreServiceImpl.java:257)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:199)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:190)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl$Proxy$_$$WeldClientProxy.store(Unknown Source)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.store.scp.CStoreSCP.store(CStoreSCP.java:36)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.service.BasicCStoreSCP.onDimseRQ(BasicCStoreSCP.java:72)
at jdk.internal.reflect.GeneratedMethodAccessor87.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.jboss.weld.core@3.1.9.Final//org.jboss.weld.bean.proxy.AbstractBeanInstance.invoke(AbstractBeanInstance.java:38)
at org.jboss.weld.core@3.1.9.Final//org.jboss.weld.bean.proxy.ProxyMethodHandler.invoke(ProxyMethodHandler.java:106)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4che3.net.service.DicomService$507164635$Proxy$$$_WeldClientProxy.onDimseRQ(Unknown Source)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.service.DicomServiceRegistry.onDimseRQ(DicomServiceRegistry.java:86)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.ApplicationEntity.onDimseRQ(ApplicationEntity.java:491)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.onDimseRQ(Association.java:750)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.PDUDecoder.decodeDIMSE(PDUDecoder.java:466)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.handlePDataTF(Association.java:733)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.State$4.onPDataTF(State.java:108)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association.onPDataTF(Association.java:729)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.PDUDecoder.nextPDU(PDUDecoder.java:177)
at org.dcm4che.net@5.27.0//org.dcm4che3.net.Association$2.run(Association.java:566)
at org.jboss.as.ee@26.1.1.Final//org.jboss.as.ee.concurrent.ControlPointUtils$ControlledRunnable.run(ControlPointUtils.java:125)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.SecurityIdentity.runAsConsumer(SecurityIdentity.java:376)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.Scoped.runAsConsumer(Scoped.java:112)
at org.wildfly.security.elytron-base@1.19.0.Final//org.wildfly.security.auth.server.Scoped.runAs(Scoped.java:60)
at org.jboss.as.ee@26.1.1.Final//org.jboss.as.ee.concurrent.SecurityIdentityUtils.lambda$doIdentityWrap$1(SecurityIdentityUtils.java:63)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.internal.ManagedFutureTask.run(ManagedFutureTask.java:117)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.ManagedThreadFactoryImpl$ManagedThread.run(ManagedThreadFactoryImpl.java:227)
Caused by: java.nio.file.AccessDeniedException: /home/radswz
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:389)
at java.base/java.nio.file.Files.createDirectory(Files.java:690)
at java.base/java.nio.file.Files.createAndCheckIsDirectory(Files.java:797)
at java.base/java.nio.file.Files.createDirectories(Files.java:783)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.filesystem.FileSystemStorage.createDirectories(FileSystemStorage.java:165)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.filesystem.FileSystemStorage.openOutputStreamA(FileSystemStorage.java:183)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear//org.dcm4chee.arc.storage.AbstractStorage.openOutputStream(AbstractStorage.java:122)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.openOutputStream(StoreServiceImpl.java:754)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.access$200(StoreServiceImpl.java:107)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl$TranscoderHandler.newOutputStream(StoreServiceImpl.java:738)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.initDicomOutputStream(Transcoder.java:919)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.access$700(Transcoder.java:71)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder$1.readValue(Transcoder.java:465)
at org.dcm4che.core@5.27.0//org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:681)
at org.dcm4che.core@5.27.0//org.dcm4che3.io.DicomInputStream.readAllAttributes(DicomInputStream.java:568)
at org.dcm4che.imageio@5.27.0//org.dcm4che3.imageio.codec.Transcoder.transcode(Transcoder.java:440)
at deployment.dcm4chee-arc-ear-5.27.0-psql.ear.dcm4chee-arc-store-5.27.0.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.writeToStorage(StoreServiceImpl.java:248)
... 32 more`

Why does the system try to write to my home directory?
Thank your in advance for your help!

[vrindanayak]

@stbender Can you show your archive service / container definition from docker-compose.yml? Also, verify the file owner permissions of the mapped out volumes.

[stbender]

Sure!

docker-compose.yml

version: "3"
services:
ldap:
image: dcm4che/slapd-dcm4chee:2.6.2-27.0
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "389:389"
env_file: docker-compose.env
volumes:
- /var/local/dcm4chee-arc/ldap:/var/lib/openldap/openldap-data
- /var/local/dcm4chee-arc/slapd.d:/etc/openldap/slapd.d
db:
image: dcm4che/postgres-dcm4chee:14.4-27
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "5432:5432"
env_file: docker-compose.env
volumes:
- /etc/localtime:/etc/localtime:ro
- /etc/timezone:/etc/timezone:ro
- /var/local/dcm4chee-arc/db:/var/lib/postgresql/data
arc:
image: dcm4che/dcm4chee-arc-psql:5.27.0
logging:
driver: json-file
options:
max-size: "10m"
ports:
- "8080:8080"
- "8443:8443"
- "9990:9990"
- "9993:9993"
- "11112:11112"
- "2762:2762"
- "2575:2575"
- "12575:12575"
env_file: docker-compose.env
environment:
WILDFLY_CHOWN: /opt/wildfly/standalone /storage
WILDFLY_WAIT_FOR: ldap:389 db:5432
depends_on:
- ldap
- db
volumes:
- /etc/localtime:/etc/localtime:ro
- /etc/timezone:/etc/timezone:ro
- /var/local/dcm4chee-arc/wildfly:/opt/wildfly/standalone
- /var/local/dcm4chee-arc/storage:/storage

docker-compose.env

STORAGE_DIR=/storage/fs1
POSTGRES_DB=pacsdb
POSTGRES_USER=pacs
POSTGRES_PASSWORD=pacs

initially, I wanted the images to be stored in /home/radswz/images, so the first line of docker-compose.env was
STORAGE_DIR=/home/radswz/images
But of course this did not work, so I switched back to the original .env content.
I thought maybe there's some cached parameters in docker-compose so the STORAGE_DIR parameter change was not applied. So I did sudo docker system prune -a and a system reboot. On the next start of dcm4chee all the files were downloaded again, but the error still is the same.

This is the folder content /var/local/dcm4chee-arc:

drwx------ 19 lxd root 4096 Sep 5 17:45 db
drwxr-sr-x 2 1021 1021 4096 Sep 5 17:45 ldap
drwxr-sr-x 3 1021 1021 4096 Sep 2 20:16 slapd.d
drwxr-sr-x 2 1023 1023 4096 Sep 2 20:24 storage
drwxr-sr-x 7 1023 1023 4096 Sep 2 20:24 wildfly

[vrindanayak]

That's because STORAGE_DIR is also used in initializing ldap image to set the URI of storage system. Verify in your ldap content (using Apache DS) the config of fs1 storage descriptor.
If this was a complete new installation, you may just purge the mapped out ldap volumes and restart the services for the default values in .env to take effect. Else, you may also update the storage descriptor URI after the ldap container has started and retry sending studies

[stbender]

Indeed, this is a complete new installation. I need to get the base installation running before I customize some settings like the AET.
How should I

purge the mapped out ldap volumes and restart the services

?
As I wrote, I already did a sudo docker system prune -a and a system reboot.

[vrindanayak]

Just delete

/var/local/dcm4chee-arc/ldap
/var/local/dcm4chee-arc/slapd.d

[stbender]

ok, this is what I did:
sudo docker system prune -a
sudo rm -rf /var/local/dcm4chee-arc
reboot
sudo docker-compose -p dcm4chee up -d
(all files were downloaded)
archive starts
--> it works!
Thank you very much for your help!