# Problem uploading datasets with PyBIS API after migration (20.10.3 ---\> 20.10.12.5) **URL:** \ **Category:** Installation & maintenance\ **Created:** [1 October 2026 12:28 UTC](https://community.openbis.ch/t/problem-uploading-datasets-with-pybis-api-after-migration-20-10-3-20-10-12-5/685 "2026-10-01T12:28:59Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![farman](https://avatars.discourse-cdn.com/v4/letter/f/f14d63/32.png) [@farman](https://community.openbis.ch/u/farman)\ **Post date:** [1 October 2026 12:28 UTC](https://community.openbis.ch/t/problem-uploading-datasets-with-pybis-api-after-migration-20-10-3-20-10-12-5/685/1 "2026-10-01T12:28:59Z")
Hi all, I have an openbis instance that we recently migrated from 20.10.3 to 20.10.12.5 where most things went smoothly. However, uploading datasets with files from PyBIS (v 1.37.4) has stopped working due to some internal ATOMIC\_MOVE that fails moving the file from session-workspace to a mounted NFS data share. Here’s the error message: ```auto 2026-10-01 12:04:08,151 INFO \[qtp1377456236-45\] OPERATION.DataSetRegistrationTransaction - Start registration 2026-10-01 12:04:08,156 INFO \[qtp1377456236-45\] OPERATION.AbstractOmniscientTopLevelDataSetRegistrator - Start processing 2026-10-01 12:04:08,447 INFO \[qtp1377456236-45\] OPERATION.AbstractTransactionalCommand - Moving file '/data/openbis/session-workspace/user-XXXXTOKEN/6210282c-e527-46d4-a598-fab957c9e9cb/base.yaml' to '/data/openbis/store/4/staging/20261001120408183-1371880/base.yaml' 2026-10-01 12:04:08,449 ERROR \[Monitoring Proxy-T1::qtp1377456236-45::remote file operations\] OPERATION.IFileOperations - Java 7 ATOMIC_MOVE failed from '/data/openbis/session-workspace/user-XXXXTOKEN/6210282c-e527-46d4-a598-fab957c9e9cb/base.yaml' to '/data/openbis/store/4/staging/20261001120408183-1371880/base.yaml' java.nio.file.AtomicMoveNotSupportedException: /data/openbis/session-workspace/user-XXXXTOKEN/6210282c-e527-46d4-a598-fab957c9e9cb/base.yaml -> /data/openbis/store/4/staging/20261001120408183-1371880/base.yaml: Invalid cross-device link at java.base/sun.nio.fs.UnixCopyFile.move(UnixCopyFile.java:415) at java.base/sun.nio.fs.UnixFileSystemProvider.move(UnixFileSystemProvider.java:267) at java.base/java.nio.file.Files.move(Files.java:1422) at ch.systemsx.cisd.common.filesystem.FileOperations.rename(FileOperations.java:175) at ch.systemsx.cisd.common.filesystem.FileOperations.move(FileOperations.java:467) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at ch.systemsx.cisd.common.concurrent.MonitoringProxy$DelegatingInvocationHandler.invoke(MonitoringProxy.java:153) at ch.systemsx.cisd.common.concurrent.MonitoringProxy$MonitoringInvocationHandler$2.call(MonitoringProxy.java:347) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.lang.Thread.run(Thread.java:829) 2026-10-01 12:04:08,450 ERROR \[qtp1377456236-45\] OPERATION.IFileOperations - Call to method 'IFileOperations.move(File,File)'\[remote file operations\]: exception: Moving '/data/openbis/session-workspace/user-XXXSESSIONTOKEN/base.yaml' into directory '/data/openbis/store/4/staging/20261001120408183-1371880/base.yaml' failed. \[IOExceptionUnchecked\]. ``` We also have a generic dropbox that ingests data directly into one of the mounted NFS shares and it works without any problems. Uploading datasets using the GUI in ELN also works fine. It’s only the PyBIS uploads that fails like this. Would be happy for some inputs! Best, Filip ---
**Author:** ![farman](https://avatars.discourse-cdn.com/v4/letter/f/f14d63/32.png) [@farman](https://community.openbis.ch/u/farman)\ **Post date:** [2 October 2026 08:48 UTC](https://community.openbis.ch/t/problem-uploading-datasets-with-pybis-api-after-migration-20-10-3-20-10-12-5/685/2 "2026-10-02T08:48:08Z")
Hi again, I solved the problem. It turned out to be misconfigured symbolic links where **session-workspace** folder being in /data/openbis share and **staging** folder in a different share: Creating a symbolic link in /data/openbis share to the one defined in dss service.properties (in this case share 4) solved the problem: 1. Log in to the openbis-app docker container as root 2. If it doesn’t already exist, create session-workspace folder in destination share ```auto mkdir -m 770 /mnt/data4/session-workspace chown openbis:openbis /mnt/data4/session-workspace ``` 1. Standing in **/data/openbis** folder, create a symbolic link between it and the destination share ```auto ln -s /mnt/data4/session-workspace session-workspace ``` 1. Now you should have a symnolic link in /data/openbis folder to the destination share ```auto ls -la lrwxrwxrwx 1 openbis openbis 28 Oct 1 19:56 session-workspace -> /mnt/data4/session-workspace ``` In this way, the incoming files from PyBIS sessions land in the same share as they are destined to, and openbis internal ATOMIC\_MOVE function will work again. ---
**Author:** ![cbarillari](https://dub1.discourse-cdn.com/flex013/user_avatar/community.openbis.ch/cbarillari/32/10_2.png) [@cbarillari](https://community.openbis.ch/u/cbarillari)\ **Post date:** [20 October 2026 18:20 UTC](https://community.openbis.ch/t/problem-uploading-datasets-with-pybis-api-after-migration-20-10-3-20-10-12-5/685/3 "2026-10-20T18:20:19Z")