Add support for download

pyorthanc/_resources/instance.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from datetime import datetime
-from typing import Any, Dict, List, TYPE_CHECKING
+from typing import Any, BinaryIO, Dict, List, TYPE_CHECKING, Union
 
 import pydicom
 
@@ -42,6 +42,9 @@ def get_dicom_file_content(self) -> bytes:
         """
         return self.client.get_instances_id_file(self.id_)
 
+    def download(self, target_path: Union[str, BinaryIO], with_progres: bool = False) -> None:
+        self._download_file(f'{self.client.url}/instances/{self.id_}/file', target_path, with_progres)
+
     @property
     def uid(self) -> str:
         """Get SOPInstanceUID"""

pyorthanc/_resources/patient.py

@@ -1,6 +1,6 @@
 import warnings
 from datetime import datetime
-from typing import Dict, List
+from typing import BinaryIO, Dict, List, Union
 
 from httpx import ReadTimeout
 
@@ -107,6 +107,9 @@ def get_zip(self) -> bytes:
         """
         return self.client.get_patients_id_archive(self.id_)
 
+    def download(self, target_path: Union[str, BinaryIO], with_progres: bool = False) -> None:
+        self._download_file(f'{self.client.url}/patients/{self.id_}/archive', target_path, with_progres)
+
     def get_patient_module(self, simplify: bool = False, short: bool = False) -> Dict:
         """Get patient module in a simplified version
 

pyorthanc/_resources/resource.py

@@ -1,4 +1,7 @@
-from typing import Any, Dict, List, Optional
+import abc
+from typing import Any, BinaryIO, Dict, List, Optional, Union
+
+from httpx._types import QueryParamTypes
 
 from .. import errors, util
 from ..client import Orthanc
@@ -41,6 +44,7 @@ def identifier(self) -> str:
         """
         return self.id_
 
+    @abc.abstractmethod
     def get_main_information(self):
         raise NotImplementedError
 
@@ -62,6 +66,44 @@ def _make_response_format_params(self, simplify: bool = False, short: bool = Fal
 
         return params
 
+    def _download_file(
+            self, url: str,
+            path: Union[str, BinaryIO],
+            with_progress: bool = False,
+            params: Optional[QueryParamTypes] = None):
+        if isinstance(path, str):
+            file = open(path, 'wb')
+        elif isinstance(path, BinaryIO):
+            file = path
+        else:
+            raise TypeError(f'"path" must be a file-like object or a file path, got "{type(path)}".')
+
+        try:
+            with self.client.stream('GET', url, params=params) as response:
+                if with_progress:
+                    try:
+                        from tqdm import tqdm
+                    except ModuleNotFoundError:
+                        raise ModuleNotFoundError(
+                            'Optional dependency tqdm have to be installed for the progress indicator. '
+                            'Install with `pip install pyorthanc[progress]` or `pip install pyorthanc[all]'
+                        )
+
+                    last_num_bytes_downloaded = response.num_bytes_downloaded
+
+                    with tqdm(unit='B', unit_scale=True, desc=self.__repr__()) as progress:
+                        for chunk in response.iter_bytes():
+                            file.write(chunk)
+                            progress.update(response.num_bytes_downloaded - last_num_bytes_downloaded)
+                            last_num_bytes_downloaded = response.num_bytes_downloaded
+
+                else:
+                    for chunk in response.iter_bytes():
+                        file.write(chunk)
+
+        finally:
+            file.close()
+
     def __eq__(self, other: 'Resource') -> bool:
         return self.id_ == other.id_
 

pyorthanc/_resources/series.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from datetime import datetime
-from typing import Dict, List, TYPE_CHECKING
+from typing import BinaryIO, Dict, List, TYPE_CHECKING, Union
 
 from httpx import ReadTimeout
 
@@ -570,6 +570,9 @@ def get_zip(self) -> bytes:
         """
         return self.client.get_series_id_archive(self.id_)
 
+    def download(self, target_path: Union[str, BinaryIO], with_progres: bool = False) -> None:
+        self._download_file(f'{self.client.url}/series/{self.id_}/archive', target_path, with_progres)
+
     def get_shared_tags(self, simplify: bool = False, short: bool = False) -> Dict:
         """Retrieve the shared tags of the series"""
         params = self._make_response_format_params(simplify, short)

pyorthanc/_resources/study.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from datetime import datetime
-from typing import Dict, List, TYPE_CHECKING
+from typing import BinaryIO, Dict, List, TYPE_CHECKING, Union
 
 from httpx import ReadTimeout
 
@@ -528,6 +528,9 @@ def get_zip(self) -> bytes:
         """
         return self.client.get_studies_id_archive(self.id_)
 
+    def download(self, target_path: Union[str, BinaryIO], with_progres: bool = False) -> None:
+        self._download_file(f'{self.client.url}/studies/{self.id_}/archive', target_path, with_progres)
+
     def get_shared_tags(self, simplify: bool = False, short: bool = False) -> Dict:
         """Retrieve the shared tags of the study"""
         params = self._make_response_format_params(simplify, short)

pyproject.toml

@@ -17,10 +17,17 @@ keywords = ["Orthanc", "DICOM", "Medical-Imaging"]
 python = "^3.8"
 httpx = ">=0.24.1,<1.0.0"
 pydicom = "^2.3.0"
+tqdm = { version = "^4.66.1", optional = true }
+
+
+[tool.poetry.extras]
+progress = ["tqdm"]
+all = ["progress"]
+
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "^1.5.3"
-mkdocstrings = {extras = ["python"], version = "^0.23.0"}
+mkdocstrings = { extras = ["python"], version = "^0.23.0" }
 mkdocs-material = "^9.4.6"
 jinja2 = "^3.1.2"
 
@@ -29,6 +36,9 @@ jinja2 = "^3.1.2"
 pytest = "^7.4.3"
 simple-openapi-client = "^0.5.3"
 
+
+
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

tests/conftest.py

@@ -1,3 +1,5 @@
+import tempfile
+
 import pytest
 
 from pyorthanc import AsyncOrthanc, Instance, Modality, Orthanc, Patient, Series, Study
@@ -89,3 +91,9 @@ def series(client_with_data_and_labels):
 @pytest.fixture
 def instance(client_with_data_and_labels):
     return Instance(client=client_with_data_and_labels, id_=an_instance.IDENTIFIER)
+
+
+@pytest.fixture
+def tmp_dir():
+    with tempfile.TemporaryDirectory() as dir_path:
+        yield dir_path

tests/test_instance.py

@@ -1,3 +1,4 @@
+import io
 from datetime import datetime
 
 import pydicom
@@ -21,7 +22,7 @@ def test_attributes(instance):
     assert instance.get_main_information().keys() == an_instance.INFORMATION.keys()
 
     assert instance.uid == an_instance.INFORMATION['MainDicomTags']['SOPInstanceUID']
-    assert type(instance.file_size) == int
+    assert isinstance(instance.file_size, int)
     assert instance.creation_date == EXPECTED_DATE
     assert instance.labels == [LABEL_INSTANCE]
     assert instance.series_identifier == a_series.IDENTIFIER
@@ -65,13 +66,13 @@ def test_get_tag_content(instance):
 def test_anonymize(instance):
     anonymized_instance = instance.anonymize(remove=['InstanceCreationDate'])
 
-    assert type(anonymized_instance) == bytes
+    assert isinstance(anonymized_instance, bytes)
 
 
 def test_modify(instance):
     modified_instance = instance.modify(replace={'NumberOfFrames': '10'})
 
-    assert type(modified_instance) == bytes
+    assert isinstance(modified_instance, bytes)
 
 
 def test_pydicom(instance):
@@ -88,3 +89,28 @@ def test_label(instance, label):
 
     instance.remove_label(label)
     assert label not in instance.labels
+
+
+def test_get_dicom_file_content(instance):
+    result = instance.get_dicom_file_content()
+
+    assert isinstance(result, bytes)
+    pydicom.dcmread(io.BytesIO(result))  # Assert not raised
+
+
+def test_download(instance, tmp_dir):
+    # Test with buffer
+    buffer = io.BytesIO()
+    instance.download(buffer)
+    pydicom.dcmread(buffer)  # Assert not raised
+
+    # Test with filepath
+    instance.download(f'{tmp_dir}/file.dcm')
+    pydicom.dcmread(f'{tmp_dir}/file.dcm')  # Assert not raised
+
+    # Test with progress enable
+    buffer = io.BytesIO()
+    instance.download(buffer, with_progres=True)
+    pydicom.dcmread(buffer)  # Assert not raised
+
+

tests/test_patient.py

@@ -36,11 +36,20 @@ def test_attributes(patient):
 def test_zip(patient):
     result = patient.get_zip()
 
-    assert type(result) is bytes
+    assert isinstance(result, bytes)
     zipfile = ZipFile(io.BytesIO(result))
     assert zipfile.testzip() is None  # Verify that zip files are valid (if it is, returns None)
 
 
+def test_download(patient: Patient, tmp_dir: str):
+    buffer = io.BytesIO()
+    patient.download(buffer)
+    assert ZipFile(buffer).testzip() is None  # Verify that zip files are valid (if it is, returns None)
+
+    patient.download(f'{tmp_dir}/file.zip')
+    assert ZipFile(f'{tmp_dir}/file.zip').testzip() is None
+
+
 def test_patient_module(patient):
     result = patient.get_patient_module()
     assert result == a_patient.MODULE
@@ -77,7 +86,7 @@ def test_anonymize(patient):
     assert anonymize_patient.name == a_patient.NAME
 
 
-def test_anonymize_as_job(patient):
+def test_anonymize_as_job(patient: Patient):
     job = patient.anonymize_as_job(remove=['PatientName'])
     job.wait_until_completion()
     anonymize_patient = Patient(job.content['ID'], patient.client)
@@ -145,7 +154,7 @@ def test_modify_as_job_remove(patient):
     assert 'ID' not in job.content  # Has no effect because PatientID can't be removed
 
 
-def test_modify_as_job_replace(patient):
+def test_modify_as_job_replace(patient: Patient):
     job = patient.modify_as_job(replace={'PatientName': 'NewName'})
     assert patient.name == a_patient.NAME
 

tests/test_series.py

@@ -10,7 +10,7 @@
 from .data import a_patient, a_series, a_study
 
 
-def test_attributes(series):
+def test_attributes(series: Series):
     assert series.get_main_information().keys() == a_series.INFORMATION.keys()
 
     assert series.identifier == a_series.IDENTIFIER
@@ -54,7 +54,16 @@ def test_zip(series):
     assert zipfile.testzip() is None  # Verify that zip files are valid (if it is, returns None)
 
 
-def test_anonymize(series):
+def test_download(series: Series, tmp_dir: str):
+    buffer = io.BytesIO()
+    series.download(buffer)
+    assert ZipFile(buffer).testzip() is None  # Verify that zip files are valid (if it is, returns None)
+
+    series.download(f'{tmp_dir}/file.zip')
+    assert ZipFile(f'{tmp_dir}/file.zip').testzip() is None
+
+
+def test_anonymize(series: Series):
     anonymized_series = series.anonymize(remove=['Modality'])
     assert anonymized_series.uid != a_series.INFORMATION['MainDicomTags']['SeriesInstanceUID']
     with pytest.raises(errors.TagDoesNotExistError):
@@ -71,7 +80,7 @@ def test_anonymize(series):
            a_series.INFORMATION['MainDicomTags']['StationName']
 
 
-def test_anonymize_as_job(series):
+def test_anonymize_as_job(series: Series):
     job = series.anonymize_as_job(remove=['Modality'])
     job.wait_until_completion()
     anonymized_series = Series(job.content['ID'], series.client)
@@ -94,7 +103,7 @@ def test_anonymize_as_job(series):
            a_series.INFORMATION['MainDicomTags']['StationName']
 
 
-def test_modify_remove(series):
+def test_modify_remove(series: Series):
     assert series.manufacturer == a_series.MANUFACTURER
 
     modified_series = series.modify(remove=['Manufacturer'])
@@ -120,7 +129,7 @@ def test_modify_remove(series):
         series.modify(remove=['SeriesInstanceUID'], force=True)
 
 
-def test_modify_replace(series):
+def test_modify_replace(series: Series):
     assert series.manufacturer == a_series.MANUFACTURER
 
     modified_series = series.modify(replace={'Manufacturer': 'new-manufacturer'})
@@ -150,7 +159,7 @@ def test_modify_replace(series):
     assert modified_series.id_ != series.id_
 
 
-def test_modify_as_job_remove(series):
+def test_modify_as_job_remove(series: Series):
     # Create new modified series
     job = series.modify_as_job(remove=['Manufacturer'])
     job.wait_until_completion()
@@ -184,7 +193,7 @@ def test_modify_as_job_remove(series):
     assert 'ID' not in job.content  # Has no effect because SeriesInstanceUID can't be removed
 
 
-def test_modify_as_job_replace(series):
+def test_modify_as_job_replace(series: Series):
     job = series.modify_as_job(replace={'Manufacturer': 'new-manufacturer'})
     job.wait_until_completion()
     modified_series = Series(job.content['ID'], series.client)