def schema(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
extended: Optional[bool] = None,
attachments_only: Optional[bool] = None,
phi_namespace: Optional[str] = None,
) -> Box:
"""Get the schema of study.
URL: /study/{namespace}/{studyUid}/schema?sid={sid}&phi_namespace={phi_namespace}&extended={1,0}&attachments_only={0,1} # NOQA E501
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param extended: is an bool, when set to 1 will include
the optional phi_version and transfer_attributes
name/value pairs in the response.
:param attachments_only: is an bool, when set to 1
will only include a list of
the attachments in the study.
:param phi_namespace: A string, set to the UUID of the
namespace where the file was attached if it was
attached to a shared instance of the study
outside of the original storage namespace
:returns: study schema
"""
extended: int = bool_to_int(extended) # type: ignore
attachemtns_onlynt: int = bool_to_int(attachments_only) # type: ignore
url_template = '/study/{namespace}/{study_uid}/schema'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
}
request_arg_names = {'phi_namespace', 'extended', 'attachments_only'}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
response = self._storage.get(url, params=request_data)
response = check_response(response, url_arg_names=url_arg_names)
return Box(response.json())
def _dicom_payload(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
image_uid: str,
# In external api this is a hash parameter
image_version: str,
phi_namespace: Optional[str] = None,
pretranscode: Optional[bool] = None,
transfer_syntax: Optional[str] = None,
) -> PreparedRequest:
"""Gets dicom payload.
URL: {namespace}/{studyUid}/image/{imageUid}/version/{hash}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param image_uid: Image uid (Required).
:param image_version: image version (Required).
:param phi_namespace: A string, set to the UUID
If set, specifies the phi namespace from which to pull PHI.
Will overlay the values onto the phiSource.
:param pretranscode: Get pretranscoded dicom.
:param transfer_syntax: Transfer syntax.
:returns: dicom.
"""
pretranscode: int = bool_to_int( # type: ignore
pretranscode, )
url_template = '/study/{namespace}/{study_uid}/image/{image_uid}/version/{image_version}'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
'image_uid',
'image_version',
}
request_arg_names = {
'phi_namespace',
'pretranscode',
'transfer_syntax',
}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
return PreparedRequest(
storage=self._storage,
method=StorageMethod.get,
url=url,
params=request_data,
stream=True,
)
def count(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
image_uid: str,
images_only: Optional[bool] = None,
attachments_only: Optional[bool] = None,
count_files: Optional[bool] = None,
) -> Box:
"""Gets study file count.
URL: /study/{namespace}/{studyUid}/count?sid={sid}&images_only={1,0}&attachments_only={1,0}&count_files={1,0}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param image_uid: Image uid (Required).
:param images_only: an integer, zero or 1, returns the number
of images in the study with superseded images by way of study update not counted.
:param attachments_only: an integer, zero or 1, returns
the number of attachments which have been added to this study.
:param count_files: if present and set to 1 will count files stored
on-disk for images and/or attachments,
instead of counting from (possibly cached) meta data.
:returns: count obj
"""
images_only: int = bool_to_int(images_only) # type: ignore
attachments_only: int = bool_to_int(attachments_only) # type: ignore
count_files: int = bool_to_int(count_files) # type: ignore
url_template = '/study/{namespace}/{study_uid}/count'
url_arg_names = {'engine_fqdn', 'namespace', 'study_uid'}
request_arg_names = {'images_only', 'attachments_only', 'count_files'}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
response = self._storage.get(url, params=request_data)
response = check_response(response, url_arg_names=url_arg_names)
return Box(response.json())
def video(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
image_uid: str,
image_version: str,
reencode_video: Optional[bool] = None,
) -> Response:
"""Gets a study encapsulated video.
URL: /study/{namespace}/{studyUid}/image/{imageUid}/version/{imageVersion}/video?sid={sid}&reencode_video={0,1}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param image_uid: Image uid (Required).
:param image_version: Image version (Required).
:param reencode_video: An integer of value 1 or 0.
:returns: Video response
"""
reencode_video: int = bool_to_int(reencode_video) # type: ignore
url_template = '/study/{namespace}/{study_uid}/image/{image_uid}/version/{image_version}/video'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
'image_uid',
'image_version',
}
request_arg_names = {'reencode_video'}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
errors_mapping = {
415:
UnsupportedMediaType(
'Video was not found encapsulated in the DICOM file.'
) # NOQA: 997
}
response: Response = self._storage.get(
url,
params=request_data,
stream=True,
)
response = check_response(response, url_arg_names=url_arg_names)
return response
def wrap(
self,
engine_fqdn: str,
namespace: str,
opened_file: BufferedReader,
tags: Optional[str] = None,
render_wrapped_pdf: Optional[bool] = None,
) -> Box:
"""Upload a non DICOM image.
URL: /namespace/{namespace}/wrap?sid={sid}&render_wrapped_pdf={0,1}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param tags: Any DICOM tags to be overwrite or added should be provided as a form-data field.
:param opened_file: The multipart file to be uploaded should be provided as a form-data field.
:param render_wrapped_pdf: An integer value of either 0 or 1.
:returns: image object attributes
"""
render_wrapped_pdf: int = bool_to_int(render_wrapped_pdf) # type: ignore
url_template = '/namespace/{namespace}/wrap'
url_arg_names = {'engine_fqdn', 'namespace'}
request_arg_names: Set[str] = set()
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
files = {
'file': opened_file,
}
if tags is not None:
post_data = {
'tags': tags,
}
response = self._storage.post(
url,
params=request_data,
files=files,
data=post_data,
)
else:
response = self._storage.post(
url,
params=request_data,
files=files,
)
response = check_response(response, url_arg_names=url_arg_names)
return Box(response.json())
def delete(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
keep_attachments: Optional[bool] = None,
):
"""Deletes a study.
URL: /study/{namespace}/{study_uid}?sid={sid}&keep_attachments={1,0}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param keep_attachments: An integer value of 1 or 0.
If the optional parameter keep_attachments is set to 1, then:
all DICOM images will be deleted.
reports and attachments related to the study will be kept.
"""
keep_attachments: int = bool_to_int(keep_attachments) # type: ignore
url_template = '/study/{namespace}/{study_uid}'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
}
request_arg_names = {'keep_attachments'}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
response = self._storage.delete(url, params=request_data)
check_response(response, url_arg_names=url_arg_names)
def _wrap(
self,
engine_fqdn: str,
namespace: str,
opened_file: RequestsFileType,
tags: Optional[str] = None,
render_wrapped_pdf: Optional[bool] = None,
x_ambrahealth_job_id: Optional[str] = None,
) -> PreparedRequest:
"""Upload a non DICOM image.
URL: /namespace/{namespace}/wrap?sid={sid}&render_wrapped_pdf={0,1}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param tags: Any DICOM tags to be overwrite or added should be provided as a form-data field.
:param opened_file: The multipart file to be uploaded should be
provided as a form-data field.
File object, or may be 2-tuples (filename, fileobj),
3-tuples (filename, fileobj, contentype) or
4-tuples (filename, fileobj, contentype, custom_headers).
:param render_wrapped_pdf: An integer value of either 0 or 1.
:param x_ambrahealth_job_id: X-AmbraHealth-Job-Id headers argument
:raises ValueError: Multifiles uploading for wrap
:returns: image object attributes
"""
render_wrapped_pdf: int = bool_to_int( # type: ignore
render_wrapped_pdf, )
url_template = '/namespace/{namespace}/wrap'
url_arg_names = {'engine_fqdn', 'namespace'}
request_arg_names = {
'tags',
'render_wrapped_pdf',
}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
if isinstance(opened_file, tuple):
fp = opened_file[1]
elif isinstance(opened_file, FormData):
form_data_fields = opened_file._fields # NOQA:WPS437
if len(form_data_fields) != 1:
raise ValueError('Multifiles uploading for wrap.')
files_info = form_data_fields[0]
fp = files_info[2]
else:
fp = opened_file
file_size = os.fstat(fp.fileno()).st_size
if isinstance(opened_file, FormData):
files = opened_file
data_name = files._fields[0][0]['name'] # NOQA:WPS437
if data_name != 'file':
# In this case we have 404 error from storage
raise ValueError(
'For FormData use "file" field name. '
'Example f = fd.add_field("file", ...)', )
else:
files = {
'file': opened_file,
}
headers = {'X-File-Size': str(file_size)}
if x_ambrahealth_job_id is not None:
headers['X-AmbraHealth-Job-Id'] = x_ambrahealth_job_id
if tags is not None:
post_data = {
'tags': tags,
}
prepared_request = PreparedRequest(
storage=self._storage,
method=StorageMethod.post,
url=url,
params=request_data,
files=files,
headers=headers,
data=post_data,
)
else:
prepared_request = PreparedRequest(
storage=self._storage,
method=StorageMethod.post,
url=url,
params=request_data,
files=files,
headers=headers,
)
return prepared_request
def download(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
bundle: str,
phi_namespace: Optional[str] = None,
series_uid: Optional[str] = None,
image_uid: Optional[str] = None,
include_wrapped_dicoms: Optional[bool] = None,
stop_on_failure: Optional[bool] = None,
exclude_viewer: Optional[bool] = None,
) -> Response:
"""Downloads a study ZIP file.
URL: /study/{namespace}/{studyUid}/download?sid={sid}&phi_namespace={phi_namespace}&bundle={iso,dicom,osx,win}&include_wrapped_dicoms={0,1}&series_uid={series_uid[,series_uid...]}&image_uid={image_uid[,image_uid...]}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param bundle: A string with value "dicom", "iso", "osx" or "win" (Required).
:param phi_namespace: The shared-to namespace UUID
of a shared instance of a study (Optional)
:param include_wrapped_dicoms: When "1", will also
include the DICOM file of a wrapped DICOM.
Default is to only include the unwrapped file.
:param series_uid: One or more Series Instance UIDs,
comma-separated. Download will only include images
from these series.
:param image_uid: One or more SOP Instance UIDs,
comma-separated. Download will only include these images.
:param stop_on_failure: If "1", will not include the viewer
app if there are any errors generating the download.
:param exclude_viewer: If "1", viewer app will not be
included in the "iso", "osx", and "win" bundle.
The viewer app can be retrieved separately via /download/viewer
:raises ValueError: Wrong bundle value
:returns: study zip file response
"""
if bundle not in {'dicom', 'iso', 'osx', 'win'}:
raise ValueError('Boundle not in ("dicom", "iso", "osx", "win")')
include_wrapped_dicoms: int = bool_to_int(
include_wrapped_dicoms) # type: ignore
stop_on_failure: int = bool_to_int(stop_on_failure) # type: ignore
exclude_viewer: int = bool_to_int(exclude_viewer) # type: ignore
url_template = '/study/{namespace}/{study_uid}/download'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
}
request_arg_names = {
'bundle',
'phi_namespace',
'series_uid',
'image_uid',
'include_wrapped_dicoms',
'stop_on_failure',
'exclude_viewer',
}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
response: Response = self._storage.get(
url,
params=request_data,
stream=True,
)
response = check_response(response, url_arg_names=url_arg_names)
return response
def post_attachment(
self,
engine_fqdn: str,
namespace: str,
study_uid: str,
opened_file: BufferedReader,
phi_namespace: Optional[str] = None,
wrap_images: Optional[bool] = None,
return_html: Optional[bool] = None,
synchronous_wrap: Optional[bool] = None,
static_ids: Optional[bool] = None,
) -> Box:
"""Posts an attachment to a study.
URL: /study/{namespace}/{studyUid}/attachment?sid={sid}&phi_namespace={phi_namespace}&wrap_images={0,1}&return_html={0,1}&synchronous_wrap={0,1}&static_ids={0,1}
:param engine_fqdn: Engine FQDN (Required).
:param namespace: Namespace (Required).
:param study_uid: Study uid (Required).
:param opened_file: Opened file (Required).
:param phi_namespace: A string, set to the UUID of
the namespace where the file was attached if it
was attached to a shared instance of the study
outside of the original storage namespace
:param wrap_images: An integer of value 1 or 0.
For attachments that are images, or can be rendered
to an image, generate a new DICOM image in the study
containing (a rendered image of) the attachment
(also controlled by namespace setting auto_wrap_images).
:param synchronous_wrap: An integer of value 1 or 0.
If 1, do all processing for image wrapping before returning,
including Services notifications.
:param static_ids: An integer of value 1 or 0. If 1,
the attachment, series and any images rendered from PDF
are assigned (u)uids based on a hash of the attachment,
which will be the same if the attachment is re-uploaded.
The attachment is also allowed to be re-uploaded when set to 1.
:param return_html: An integer of value 1 or 0. Return results as
Content Type text html, instead of
application json (required for certain browsers)
:returns: posts attachments response
The request entity must contain
a single multipart/form-data element named
data containing the content to be attached.
If the optional parameter wrap_images or synchronous_wrap
is set to 1, or the uploading account has the setting
auto_wrap_images set to 1, then:
attachments of type image/jpeg or image/bmp are, asynchronously
(unless synchronous_wrap=1) to the Store Attachment request,
posted to the Wrap Attachment service, to be stored as a single
DICOM image in a new series within the specified study.
attachments of type application/pdf are, asynchronously
(unless synchronous_wrap=1) to the Store Attachment request,
rendered to DICOM images at a resolution of 200 ppi,
one image per page of the original PDF. The resulting are
stored in a new series within the specified study.
UIDs assigned to the series and images will be random unless static_ids=1
"""
wrap_images: int = bool_to_int(wrap_images) # type: ignore
synchronous_wrap: int = bool_to_int(synchronous_wrap) # type: ignore
static_ids: int = bool_to_int(static_ids) # type: ignore
return_html: int = bool_to_int(return_html) # type: ignore
files = {'data': opened_file}
url_template = '/study/{namespace}/{study_uid}/attachment'
url_arg_names = {
'engine_fqdn',
'namespace',
'study_uid',
}
request_arg_names = {
'phi_namespace',
'wrap_images',
'return_html',
'synchronous_wrap',
'static_ids',
}
url, request_data = self._storage.get_url_and_request(
url_template,
url_arg_names,
request_arg_names,
locals(),
)
response = self._storage.post(url, params=request_data, files=files)
check_response(response, url_arg_names=url_arg_names)
return Box(response.json())