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Upload An Image Session

Introduced with XNAT 1.5, the import service is a customizable upload implementation for importing data into XNAT. XNAT comes with several pre-configured import implementations, but can be configured via java to meet any need.

The import is built to receive a zip, tar.gz, etc and place it into the prearchive or archive space. It has also been modified to import files from the user's cache space, which would have been previously uploaded.

POST - /data/services/import


Files

Files are attached in the body of the request. "inbody=true" must be set as a parameter. 


Select An Import Handler

Using the import-handler parameter, you can specify a specific implementation of the import logic. If this parameter is not specified, the default is "SI". 

OptionDescription
SIstandard session importer: Used to import individual DICOM or ECAT files or zips of DICOM or ECAT files.
gradual-DICOM

same implementation as XNAT's integrated DICOM receiver  Accepts individual DICOM files and follows the DICOM receiver mapping/archive logic

DICOM-zip

similar to the gradual-DICOM but accepts zipped collections of DICOM files. This is used by the XNAT Upload Assistant and XNAT Desktop Client. As of XNAT 1.8.3, .tar.gz and .tar archives are also supported. (NOTE: if your zip includes an erroneous file (e.g., non DICOM or invalid DICOM), DICOM-zip will return a 400 error, but any files uploaded prior to the erroneous one will still wind up in the prearchive, so you can wind up with a partial session if you have auto-archive enabled)

XAR

used to upload XAR files (zip files which include the session xml and the associated files)

inboxuses its own workflow, as documented here: Using DICOM Inbox to import an image session

All Parameters

All parameters are optional, though the 'dest' is highly encouraged


Parameter nameParameter descriptionSupporting import handlers
overwrite
  • none (DEFAULT): Do not overwrite existing xml or files
  • append: Add content to existing xml & file system, but do not overwrite existing files
  • delete: Upload new data, and overwrite any existing files. 
SI
overwrite_files
  • true: allow files to be overwritten for merges
  • false: do not allow files to be overwritten for merges
SI
quarantine
  • false (DEFAULT): follow project settings for whether new/modified archive content should go into quarantine
  • true: override project settings and place new/modified archive content in quarantine.
SI, inbox
triggerPipelines
  • true (DEFAULT): run the AutoRun pipeline for any archived sessions which are modified/created by this import
  • false: Do not run the AutoRun at this time
SI, inbox
src

Only used when attempting to import a previously uploaded file. You can specify multiple src attributes or separate them with commas. Example:

  • /user/cache/resources/X/files/X.zip
SI, gradual-DICOM, DICOM-zip, XAR
dest

Specifies intended destination. If it is empty, it will review the uploaded content and attempt to put it in the right place (or leave it in the prearchive Unassigned).

  • /prearchive
    • It will try to determine the proper project from the DICOM/ECAT headers.


  • /prearchive/projects/PROJECT
  • /prearchive/projects/PROJECT/timestamp
  • /prearchive/projects/PROJECT/timestamp/session
    • Importing to this url would allow you to merge additional content with previously uploaded content.


  • /archive
    • It will try to determine the proper project from the DICOM/ECAT headers.


  • /archive/projects/PROJECT
  • /archive/projects/PROJECT/subjects/SUBJECT
  • /archive/projects/PROJECT/subjects/SUBJECT/experiments/LABEL
    • Importing to this url would allow you to merge content with previously archived data.
SI, gradual-DICOM (archive destinations unsupported), DICOM-zip (archive destinations unsupported)
import-handler

Defaults to standard import logic ("SI"). Client can specify a key using free-form text which the server maps to a different implementation of the import logic. See above.

--
http-session-listener

Used by the web based zip uploader

  •  free-form text: which should uniquely identify this upload process. If this is used, an http-session variable will be created using this text as the attribute ID, and will contain process/status information.
SI, XAR
inbody

Used to tell the server that the body of the message is the actual file. This shouldn't be necessary if all upload tools set the Content-Type header appropriately.  But, many do not.  If your upload is failing and you can't figure out why, try setting this to true

  • true: the body of the message is the actual file
--
rename

Used with the gradual-DICOM importer, instructing XNAT to ignore the original dicom file name and rename it. Default is false.

  • true: renames each DICOM file in this pattern:
    ${StudyInstanceUID}-${SeriesNumber}-${InstanceNumber}-${HashSOPClassUIDWithSOPInstanceUID}.dcm

DICOM-zip, gradual-DICOM, inbox

PROJECT_ID

For use when not using dest attribute. If you're uploading ECAT data via SI and it's not working, try using project as the parameter name instead

SI, inbox, DICOM-zip, gradual-DICOM
SUBJECT_IDFor use when not using dest attributeSI, inbox, DICOM-zip, gradual-DICOM
EXPT_LABELFor use when not using dest attributeSI, inbox, DICOM-zip, gradual-DICOM
sessionAlternative property for EXPT_LABEL supported by some import handlersSI, inbox

Ignore-Unparsable

 XNAT 1.8.3+ only

  • true: silently discard files within zip/tar archive which are not readable as DICOM files
  • false (DEFAULT): reject upload when zip/tar archive contains non-DICOM files
DICOM-zip
Direct-Archive

XNAT 1.8.3+ only

DICOM-zip, gradual-DICOM




Refresh The Archive Catalog XML

Introduced with XNAT 1.6.2, the refresh catalog service is used to update catalog xmls that are out of sync with the file system.  This service can be used to store checksums for entries that are missing the, remove entries that no longer have valid files, or add new entries for files that have been manually added to the archive directory.

See: Catalog Refresh API

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