Refactoring for a cleaner api interface

pyorthanc/__init__.py

@@ -1,16 +1,17 @@
+from . import errors, util
+from ._filtering import build_patient_forest, find, trim_patients
+from ._find import find_instances, find_patients, find_series, find_studies, query_orthanc
+from ._modality import Modality, RemoteModality
+from ._resources import Instance, Patient, Series, Study
 from .async_client import AsyncOrthanc
 from .client import Orthanc
-from .filtering import build_patient_forest, find, trim_patients
-from .find import find_instances, find_patients, find_series, find_studies, query_orthanc
-from .remote import RemoteModality
-from .resources import Instance, Patient, Series, Study
 from .retrieve import retrieve_and_write_instance, retrieve_and_write_patient, retrieve_and_write_patients, \
     retrieve_and_write_series, retrieve_and_write_study
 
-
 __all__ = [
     'AsyncOrthanc',
     'Orthanc',
+    'Modality',
     'RemoteModality',
     'Patient',
     'Study',
@@ -29,4 +30,6 @@
     'retrieve_and_write_study',
     'retrieve_and_write_series',
     'retrieve_and_write_instance',
+    'util',
+    'errors',
 ]

pyorthanc/filtering.py → pyorthanc/_filtering.py

@@ -4,10 +4,10 @@
 
 from .async_client import AsyncOrthanc
 from .client import Orthanc
-from .resources.instance import Instance
-from .resources.patient import Patient
-from .resources.series import Series
-from .resources.study import Study
+from ._resources.instance import Instance
+from ._resources.patient import Patient
+from ._resources.series import Series
+from ._resources.study import Study
 from .util import async_to_sync
 
 

pyorthanc/find.py → pyorthanc/_find.py

@@ -1,11 +1,11 @@
 from typing import Dict, List, Union
 
 from .client import Orthanc
-from .resources.instance import Instance
-from .resources.patient import Patient
-from .resources.resource import Resource
-from .resources.series import Series
-from .resources.study import Study
+from ._resources.instance import Instance
+from ._resources.patient import Patient
+from ._resources.resource import Resource
+from ._resources.series import Series
+from ._resources.study import Study
 
 DEFAULT_RESOURCES_LIMIT = 1_000
 

pyorthanc/remote.py → pyorthanc/_modality.py

@@ -5,9 +5,8 @@
 from .client import Orthanc
 
 
-class RemoteModality:
-    """Wrapper around Orthanc API when dealing with a (remote) modality.
-    """
+class Modality:
+    """Wrapper around Orthanc API when dealing with a modality."""
 
     def __init__(self, client: Orthanc, modality: str) -> None:
         """Constructor
@@ -23,7 +22,7 @@ def __init__(self, client: Orthanc, modality: str) -> None:
         self.modality = modality
 
     def echo(self) -> bool:
-        """C-Echo to remote modality
+        """C-Echo to modality
 
         Returns
         -------
@@ -60,12 +59,12 @@ def query(self, data: Dict) -> Dict:
         ...         }
         ... }
 
-        >>> remote_modality = RemoteModality(
+        >>> modality = Modality(
         ...     client=Orthanc('http://localhost:8042'),
         ...     modality='sample'
         ... )
 
-        >>> remote_modality.query(data)
+        >>> modality.query(data)
         """
         return dict(self.client.post_modalities_id_query(self.modality, json=data))
 
@@ -88,13 +87,13 @@ def move(self, query_identifier: str, cmove_data: Dict) -> Dict:
 
         Examples
         --------
-        >>> remote_modality = RemoteModality(Orthanc('http://localhost:8042'), 'modality')
-        >>> query_id = remote_modality.query(
+        >>> modality = Modality(Orthanc('http://localhost:8042'), 'modality')
+        >>> query_id = modality.query(
         ...     data={'Level': 'Series',
         ...           'Query': {'PatientID': '',
         ...                     'Modality':'SR'}})
 
-        >>> remote_modality.move(
+        >>> modality.move(
         ...     query_identifier=query_id['ID'],
         ...     cmove_data={'TargetAet': 'TARGETAET'}
         ... )
@@ -103,7 +102,7 @@ def move(self, query_identifier: str, cmove_data: Dict) -> Dict:
         return dict(self.client.post_queries_id_retrieve(query_identifier, json=cmove_data))
 
     def store(self, instance_or_series_id: str) -> Dict:
-        """Store series or instance to remote modality.
+        """Store series or instance to modality.
 
         Parameters
         ----------
@@ -130,3 +129,4 @@ def get_query_answers(self) -> Dict:
         return answers
 
 
+RemoteModality = Modality

pyorthanc/retrieve.py

@@ -1,10 +1,10 @@
 import os
 from typing import List
 
-from .resources.instance import Instance
-from .resources.patient import Patient
-from .resources.series import Series
-from .resources.study import Study
+from ._resources.instance import Instance
+from ._resources.patient import Patient
+from ._resources.series import Series
+from ._resources.study import Study
 
 
 def retrieve_and_write_patients(patients: List[Patient], path: str) -> None:

tests/conftest.py

@@ -1,6 +1,6 @@
 import pytest
 
-from pyorthanc import AsyncOrthanc, Instance, Orthanc, Patient, RemoteModality, Series, Study
+from pyorthanc import AsyncOrthanc, Instance, Modality, Orthanc, Patient, Series, Study
 from .data import a_patient, a_series, a_study, an_instance
 from .setup_server import ORTHANC_1, ORTHANC_2, add_modality, clear_data, setup_data
 
@@ -68,7 +68,7 @@ def modality(client, second_client):
         add_modality(ORTHANC_1, ORTHANC_2.AeT, 'orthanc2', 4242)
         add_modality(ORTHANC_2, ORTHANC_1.AeT, 'orthanc1', 4242)
 
-    return RemoteModality(client, ORTHANC_2.AeT)
+    return Modality(client, ORTHANC_2.AeT)
 
 
 @pytest.fixture

tests/test_filtering.py

@@ -1,6 +1,6 @@
 import pytest
 
-from pyorthanc import Instance, Patient, Series, Study, filtering
+from pyorthanc import Instance, Patient, Series, Study, find
 from pyorthanc.util import make_datetime_from_dicom_date
 from tests.data import a_patient, a_series, a_study, an_instance
 
@@ -29,7 +29,7 @@
     ])
 def test_find(client_fixture, patient_filter, study_filter, series_filter, instance_filter, expected_nbr_of_patient,
               expected_nbr_of_series, request):
-    patients = filtering.find(
+    patients = find(
         orthanc=request.getfixturevalue(client_fixture),
         patient_filter=patient_filter,
         study_filter=study_filter,

tests/test_find.py

@@ -1,7 +1,7 @@
 import pytest
 
 from pyorthanc import find_instances, find_patients, find_series, find_studies, query_orthanc
-from pyorthanc.find import DEFAULT_RESOURCES_LIMIT
+from pyorthanc._find import DEFAULT_RESOURCES_LIMIT
 from .conftest import LABEL_INSTANCE, LABEL_PATIENT, LABEL_SERIES, LABEL_STUDY
 from .data import a_patient, a_series, a_study, an_instance