upload failure on zip file containing dcm

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Hassan Heydari N.

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Dec 9, 2020, 11:07:48 AM12/9/20
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Hi everybody
I'm trying to convert a video file to a zip file containing dcm files, then I upload it to xnat.
here is my code https://gitlab.com/HassanHeydariNasab/atom360-video2dcm
when I upload the zip file to xnat using "XNAT Compressed Uploader" page I get this error:
```Extraction / Review summary:
Importing file (test.zip)
Uploading to /data/xnat/cache/USERS/1/uploads/20201202_181550351/test.zip ...
file uploaded
mkdir /data/xnat/prearchive/mp7/20201202_181550351
Importing to /data/xnat/prearchive/mp7/20201202_181550351
processing
looking for DICOM files
found 5 DICOM files
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.13400.1606931882.432269)
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.13402.1606931882.468427)
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.13401.1606931882.450547)
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.13403.1606931882.486379)
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.13404.1606931882.503803)
done finding DICOM
looking for ECAT files
found 0 ECAT files
done finding ECAT
done
Setting additional values for '_1'
failed to set appropriate field(s) for '_1'. Data may be publicly accessible until archived.
Setting additional values for '_2'
failed to set appropriate field(s) for '_2'. Data may be publicly accessible until archived.
Setting additional values for '_3'
failed to set appropriate field(s) for '_3'. Data may be publicly accessible until archived.
Setting additional values for '_4'
failed to set appropriate field(s) for '_4'. Data may be publicly accessible until archived.
Setting additional values for '_5'
failed to set appropriate field(s) for '_5'. Data may be publicly accessible until archived.
An error occurred adding the session to the prearchive database```
Does it complain of dcm metadata?

Moore, Charlie

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Dec 9, 2020, 11:27:01 AM12/9/20
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Hello,

The compressed uploader expects to receive a single DICOM study. Your zip appears to have 5 separate DICOM studies (as determined by having 5 different Study Instance UIDs). If there are other issues, they may be captured in the XNAT logs.

Thanks,
Charlie
From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Hassan Heydari N. <hac...@gmail.com>
Sent: Tuesday, December 8, 2020 1:07 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] upload failure on zip file containing dcm
 

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Hassan Heydari N.

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Dec 9, 2020, 12:55:18 PM12/9/20
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the same result with zip file containing 1 dcm file:


Importing file (series-000001.zip)
Uploading to /data/xnat/cache/USERS/1/uploads/20201209_173508986/series-000001.zip ...
file uploaded
mkdir /data/xnat/prearchive/mp7/20201209_173508986
Importing to /data/xnat/prearchive/mp7/20201209_173508986

processing
looking for DICOM files

found 1 DICOM files
found DICOM study (1.2.276.0.7230010.3.1.2.8323329.10922.1607438981.40472)

done finding DICOM
looking for ECAT files
found 0 ECAT files
done finding ECAT
done
Setting additional values for '_1'
failed to set appropriate field(s) for '_1'. Data may be publicly accessible until archived.

An error occurred adding the session to the prearchive database

Moore, Charlie

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Dec 9, 2020, 1:24:58 PM12/9/20
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Is there anything captured in the XNAT logs?

Thanks,
Charlie
Sent: Wednesday, December 9, 2020 11:55 AM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: Re: [XNAT Discussion] upload failure on zip file containing dcm
 

Hassan Heydari N.

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Dec 10, 2020, 12:11:41 AM12/10/20
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There is no related logs at Administrator panel and xnat-web (running via docker)

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Moore, Charlie

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Dec 10, 2020, 11:19:11 AM12/10/20
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XNAT's logs can be accessed from $XNAT_URL/xapi/logs/download in your browser if you're an admin or within $xnat.home/logs in the VM/container where tomcat is running.

Thanks,
Charlie
Sent: Wednesday, December 9, 2020 11:11 PM
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KK Mehta

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Jan 7, 2021, 1:28:44 AM1/7/21
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Hi Charlie,

I'm facing the same issue and I checked the logs as well, but there's no mention of the upload issue. 
In my case, it doesn't even show up on the pre-archive. 

What I'm trying to achieve is use jpg2dcm tool from dcm4che to convert images to DICOM and have them uploaded to xnat. 
This is where I'm stuck as well. Is there any other way to find out what exactly is going wrong? 
The error message isn't clear enough.

Thanks! 

Moore, Charlie

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Jan 7, 2021, 10:14:48 AM1/7/21
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Hello,

You could post one of the problematic images here (provided it's not sensitive) and I could take a look at it..

Thanks,
Charlie
From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of KK Mehta <meht...@gmail.com>
Sent: Thursday, January 7, 2021 12:28 AM

KK Mehta

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Jan 7, 2021, 11:59:37 AM1/7/21
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Sure
Here's the error message I'm getting: 
``` 
Extraction / Review summary:
Importing file (converted_dicom_from_jpg.dcm.zip)
Uploading to /data/xnat/cache/USERS/4/uploads/20210107_165041637/converted_dicom_from_jpg.dcm.zip ...
file uploaded
mkdir /data/xnat/prearchive/1/20210107_165041637
Importing to /data/xnat/prearchive/1/20210107_165041637
processing
looking for DICOM files
found 1 DICOM files
found DICOM study (2.25.1681113358660985660803568400256456253)
done finding DICOM
looking for ECAT files
found 0 ECAT files
done finding ECAT
done
Setting additional values for '_1'
failed to set appropriate field(s) for '_1'. Data may be publicly accessible until archived.
An error occurred adding the session to the prearchive database
```
I used jpg2dcm tool from dcm4che and converted the below image to dcm, compressed it and tried uploading it on XNAT.

issue_3.jpg

Moore, Charlie

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Jan 7, 2021, 12:44:15 PM1/7/21
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I meant the converted DICOM image, not the source JPEG.

Thanks,
Charlie
Sent: Thursday, January 7, 2021 10:59 AM

KK Mehta

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Jan 7, 2021, 1:13:30 PM1/7/21
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Oh sure, I'm attaching it here
converted_dicom_from_jpg.dcm

Moore, Charlie

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Jan 7, 2021, 1:46:16 PM1/7/21
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When I upload zip the DICOM file and upload it with the compressed uploader, I get the same error, but the cause is logged in the XNAT logs in dicom.log:
2021-01-07 18:37:36,306 [pool-3-thread-1] WARN  org.nrg.dcm.xnat.DICOMSessionBuilder - Session builder not implemented for SOP class(es) [1.2.840.10008.5.1.4.1.1.7] or modality(ies) [null], trying default session builder factory


XNAT doesn't support DICOM instances without a value for (0008,0060) Modality.

Thanks,
Charlie
Sent: Thursday, January 7, 2021 12:13 PM
To: xnat_discussion <xnat_di...@googlegroups.com>

KK Mehta

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Jan 8, 2021, 7:47:56 AM1/8/21
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Hey Charlie,
Thanks a lot for your insight.
Can you guide me to any relevant documentation for adding modality appropriately using jpg2dcm tool?

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Moore, Charlie

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Jan 8, 2021, 10:40:46 AM1/8/21
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The README.md for the repo you linked earlier says you can use the -m flag to set DICOM headers on the converted files. Note that if you are attempting to have these converted DICOM objects stand alone as their own session, you will probably need to use a modality from the list here: https://groups.google.com/g/xnat_discussion/c/aK8R4rzLRSs/m/mdL2EEuqAAAJ .

Thanks,
Charlie
Sent: Friday, January 8, 2021 6:47 AM
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