large_image_source_dicom.assetstore package

Submodules

large_image_source_dicom.assetstore.dicomweb_assetstore_adapter module

class large_image_source_dicom.assetstore.dicomweb_assetstore_adapter.DICOMwebAssetstoreAdapter(assetstore)

Bases: AbstractAssetstoreAdapter

This defines the interface to be used by all assetstore adapters.

property assetstore_meta

property auth_session

deleteFile(file)

This is called when a File is deleted to allow the adapter to remove the data from within the assetstore. This method should not modify or delete the file object, as the caller will delete it afterward.

Parameters:

file (dict) – The File document about to be deleted.

downloadFile(file, offset=0, headers=True, endByte=None, contentDisposition=None, extraParameters=None, **kwargs)

This method is in charge of returning a value to the RESTful endpoint that can be used to download the file. This should either return a generator function that yields the bytes of the file (which will stream the file directly), or modify the response headers and raise a cherrypy.HTTPRedirect.

Parameters:

• file (dict) – The file document being downloaded.

• offset (int) – Offset in bytes to start the download at.

• headers (bool) – Flag for whether headers should be sent on the response.

• endByte (int or None) – Final byte to download. If None, downloads to the end of the file.

• contentDisposition (str or None) – Value for Content-Disposition response header disposition-type value.

finalizeUpload(upload, file)

Call this once the last chunk has been processed. This method does not need to delete the upload document as that will be deleted by the caller afterward. This method may augment the File document, and must return the File document.

Parameters:

• upload (dict) – The upload document.

• file (dict) – The file document that was created.

Returns:

The file document with optional modifications.

getFileSize(file)

Get the file size (computing it, if necessary). Default behavior simply returns file.get(‘size’, 0). This method exists because some assetstores do not compute the file size immediately, but only when it is actually needed. The assetstore may also need to update the file size after some changes.

importData(parent, parentType, params, progress, user, **kwargs)

Import DICOMweb WSI instances from a DICOMweb server.

Parameters:

• parent – The parent object to import into.

• parentType (str) – The model type of the parent object.

• params (dict) –

  Additional parameters required for the import process. This dictionary may include the following keys:

  limit:

  (optional) limit the number of studies imported.

  filters:

  (optional) a dictionary/JSON string of additional search filters to use with dicomweb_client’s search_for_series() function.

• progress (girder.utility.progress.ProgressContext) – Object on which to record progress if possible.

• user (dict or None) – The Girder user performing the import.

Returns:

a list of items that were created

initUpload(upload)

This must be called before any chunks are uploaded to do any additional behavior and optionally augment the upload document. The method must return the upload document. Default behavior is to simply return the upload document unmodified.

Parameters:

upload (dict) – The upload document to optionally augment.

setContentHeaders(file, offset, endByte, contentDisposition=None)

Sets the Content-Length, Content-Disposition, Content-Type, and also the Content-Range header if this is a partial download.

Parameters:

• file – The file being downloaded.

• offset (int) – The start byte of the download.

• endByte (int or None) – The end byte of the download (non-inclusive).

• contentDisposition (str or None) – Content-Disposition response header disposition-type value, if None, Content-Disposition will be set to ‘attachment; filename=$filename’.

static validateInfo(doc)

Adapters may implement this if they need to perform any validation steps whenever the assetstore info is saved to the database. It should return the document with any necessary alterations in the success case, or throw an exception if validation fails.

large_image_source_dicom.assetstore.rest module

class large_image_source_dicom.assetstore.rest.DICOMwebAssetstoreResource

Bases: Resource

importData(assetstore, destinationId, destinationType, limit, filters, progress)

Module contents

class large_image_source_dicom.assetstore.DICOMwebAssetstoreAdapter(assetstore)

Bases: AbstractAssetstoreAdapter

This defines the interface to be used by all assetstore adapters.

property assetstore_meta

property auth_session

deleteFile(file)

This is called when a File is deleted to allow the adapter to remove the data from within the assetstore. This method should not modify or delete the file object, as the caller will delete it afterward.

Parameters:

file (dict) – The File document about to be deleted.

downloadFile(file, offset=0, headers=True, endByte=None, contentDisposition=None, extraParameters=None, **kwargs)

This method is in charge of returning a value to the RESTful endpoint that can be used to download the file. This should either return a generator function that yields the bytes of the file (which will stream the file directly), or modify the response headers and raise a cherrypy.HTTPRedirect.

Parameters:

• file (dict) – The file document being downloaded.

• offset (int) – Offset in bytes to start the download at.

• headers (bool) – Flag for whether headers should be sent on the response.

• endByte (int or None) – Final byte to download. If None, downloads to the end of the file.

• contentDisposition (str or None) – Value for Content-Disposition response header disposition-type value.

finalizeUpload(upload, file)

Call this once the last chunk has been processed. This method does not need to delete the upload document as that will be deleted by the caller afterward. This method may augment the File document, and must return the File document.

Parameters:

• upload (dict) – The upload document.

• file (dict) – The file document that was created.

Returns:

The file document with optional modifications.

getFileSize(file)

Get the file size (computing it, if necessary). Default behavior simply returns file.get(‘size’, 0). This method exists because some assetstores do not compute the file size immediately, but only when it is actually needed. The assetstore may also need to update the file size after some changes.

importData(parent, parentType, params, progress, user, **kwargs)

Import DICOMweb WSI instances from a DICOMweb server.

Parameters:

• parent – The parent object to import into.

• parentType (str) – The model type of the parent object.

• params (dict) –

  Additional parameters required for the import process. This dictionary may include the following keys:

  limit:

  (optional) limit the number of studies imported.

  filters:

  (optional) a dictionary/JSON string of additional search filters to use with dicomweb_client’s search_for_series() function.

• progress (girder.utility.progress.ProgressContext) – Object on which to record progress if possible.

• user (dict or None) – The Girder user performing the import.

Returns:

a list of items that were created

initUpload(upload)

This must be called before any chunks are uploaded to do any additional behavior and optionally augment the upload document. The method must return the upload document. Default behavior is to simply return the upload document unmodified.

Parameters:

upload (dict) – The upload document to optionally augment.

setContentHeaders(file, offset, endByte, contentDisposition=None)

Sets the Content-Length, Content-Disposition, Content-Type, and also the Content-Range header if this is a partial download.

Parameters:

• file – The file being downloaded.

• offset (int) – The start byte of the download.

• endByte (int or None) – The end byte of the download (non-inclusive).

• contentDisposition (str or None) – Content-Disposition response header disposition-type value, if None, Content-Disposition will be set to ‘attachment; filename=$filename’.

static validateInfo(doc)

Adapters may implement this if they need to perform any validation steps whenever the assetstore info is saved to the database. It should return the document with any necessary alterations in the success case, or throw an exception if validation fails.

large_image_source_dicom.assetstore.load(info)

Load the plugin into Girder.

Parameters:

info – a dictionary of plugin information. The name key contains the name of the plugin according to Girder.