[MRG] Backport fix for receiving chunked datasets (#767)

docs/changelog/index.rst

@@ -7,6 +7,7 @@ Release Notes
 .. toctree::
    :maxdepth: 1
 
+   v2.0.2
    v2.0.1
    v2.0.0
    v1.5.7

docs/changelog/v2.0.2.rst

@@ -0,0 +1,10 @@
+.. _v2.0.2:
+
+2.0.2
+=====
+
+Fixes
+.....
+
+* Fixed datasets not transferring correctly when using
+  :attr:`~pynetdicom._config.STORE_RECV_CHUNKED_DATASET` (:issue:`765`)

docs/conf.py

@@ -123,9 +123,9 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"pynetdicom"
+project = "pynetdicom"
 year = datetime.now().strftime("%Y")
-copyright = u"2018-{}, pynetdicom contributors".format(year)
+copyright = "2018-{}, pynetdicom contributors".format(year)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -266,8 +266,8 @@
     (
         "index",
         "pynetdicom.tex",
-        u"pynetdicom Documentation",
-        u"pynetdicom contributors",
+        "pynetdicom Documentation",
+        "pynetdicom contributors",
         "manual",
     ),
 ]
@@ -316,5 +316,5 @@ def setup(app):
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
     "pynetdicom",
-    u"https://github.com/pydicom/pynetdicom/blob/{revision}/{package}/{path}#L{lineno}",
+    "https://github.com/pydicom/pynetdicom/blob/{revision}/{package}/{path}#L{lineno}",
 )

docs/index.rst

@@ -119,6 +119,7 @@ Applications
 Release Notes
 =============
 
+* :doc:`v2.0.2 </changelog/v2.0.2>`
 * :doc:`v2.0.1 </changelog/v2.0.1>`
 * :doc:`v2.0.0 </changelog/v2.0.0>`
 * :doc:`v1.5.7 </changelog/v1.5.7>`

pynetdicom/apps/qrscp/db.py

@@ -205,7 +205,7 @@ def add_instance(ds, session, fpath=None):
 
                 assert len(value) <= max_len
             else:
-                assert -(2 ** 31) <= value <= 2 ** 31 - 1
+                assert -(2**31) <= value <= 2**31 - 1
 
         setattr(instance, attr, value)
 
@@ -605,6 +605,9 @@ def _search_uid_list(elem, session, query=None):
     if not query:
         query = session.query(Instance)
 
+    if elem.VM == 1:
+        return query.filter(attr == elem.value)
+
     return query.filter(attr.in_(elem.value))
 
 

pynetdicom/apps/tests/test_qrscp_db.py

@@ -16,7 +16,7 @@
 except ImportError:
     HAVE_SQLALCHEMY = False
 
-from pydicom import dcmread
+from pydicom import dcmread, config as PYD_CONFIG
 import pydicom.config
 from pydicom.dataset import Dataset
 from pydicom.tag import Tag
@@ -30,6 +30,10 @@
     from pynetdicom.apps.qrscp import db
 
 
+if hasattr(PYD_CONFIG, "settings"):
+    PYD_CONFIG.settings.reading_validation_mode = 0
+
+
 TEST_DIR = os.path.dirname(__file__)
 DATA_DIR = os.path.join(TEST_DIR, "../", "../", "tests", "dicom_files")
 DATASETS = {

pynetdicom/dimse_messages.py

@@ -497,6 +497,7 @@ def decode_msg(
                 #   number of P-DATA primitives.
                 if self._data_set_file:
                     self._data_set_file.write(data[1:])
+                    self._data_set_file.file.flush()
                 else:
                     cast(BytesIO, self.data_set).write(data[1:])
 

pynetdicom/dimse_primitives.py

@@ -6,7 +6,7 @@
     in order for the DIMSE messages/primitives to be created correctly.
 """
 
-from collections.abc import MutableSequence
+from collections.abc import Sequence
 from io import BytesIO
 import logging
 from pathlib import Path
@@ -21,11 +21,13 @@
 
 
 if TYPE_CHECKING:  # pragma: no cover
+    from io import BufferedWriter
     from typing import Protocol  # Python 3.8+
 
     class NTF(Protocol):
         # Protocol for a NamedTemporaryFile
         name: str
+        file: BufferedWriter
 
         def write(self, data: bytes) -> bytes:
             ...
@@ -67,7 +69,7 @@ class DIMSEPrimitive:
     _action_type_id: Optional[int] = None
     _affected_sop_class_uid: Optional[UID] = None
     _affected_sop_instance_uid: Optional[UID] = None
-    _attribute_identifier_list: Optional[List[BaseTag]] = None
+    _attribute_identifier_list: Union[None, BaseTag, List[BaseTag]] = None
     _dataset: Optional[BytesIO] = None
     _event_type_id: Optional[int] = None
     _message_id: Optional[int] = None
@@ -206,7 +208,7 @@ def MessageID(self) -> Optional[int]:
     def MessageID(self, value: Optional[int]) -> None:
         """Set the *Message ID*."""
         if isinstance(value, int):
-            if 0 <= value < 2 ** 16:
+            if 0 <= value < 2**16:
                 self._message_id = value
             else:
                 raise ValueError("Message ID must be between 0 and 65535, inclusive")
@@ -230,7 +232,7 @@ def MessageIDBeingRespondedTo(self) -> Optional[int]:
     def MessageIDBeingRespondedTo(self, value: Optional[int]) -> None:
         """Set the *Message ID Being Responded To*."""
         if isinstance(value, int):
-            if 0 <= value < 2 ** 16:
+            if 0 <= value < 2**16:
                 self._message_id_being_responded_to = value
             else:
                 raise ValueError(
@@ -591,7 +593,7 @@ def MoveOriginatorMessageID(self, value: Optional[int]) -> None:
         """
         # Fix for peers sending a value consisting of nulls
         if isinstance(value, int):
-            if 0 <= value < 2 ** 16:
+            if 0 <= value < 2**16:
                 self._move_originator_message_id = value
             else:
                 raise ValueError(
@@ -1251,7 +1253,7 @@ def MessageIDBeingRespondedTo(self) -> Optional[int]:
     def MessageIDBeingRespondedTo(self, value: Optional[int]) -> None:
         """Set the *Message ID Being Responded To*."""
         if isinstance(value, int):
-            if 0 <= value < 2 ** 16:
+            if 0 <= value < 2**16:
                 self._message_id_being_responded_to = value
             else:
                 raise ValueError(
@@ -1502,13 +1504,13 @@ def AffectedSOPInstanceUID(self, value: OptionalUIDType) -> None:
         self._AffectedSOPInstanceUID = value  # type: ignore
 
     @property
-    def AttributeIdentifierList(self) -> Optional[List[BaseTag]]:
+    def AttributeIdentifierList(self) -> Optional[Union[BaseTag, List[BaseTag]]]:
         """Get or set the *Attribute Identifier List* as a :class:`list` of
         :class:`~pydicom.tag.BaseTag`.
 
         Parameters
         ----------
-        list of pydicom.tag.BaseTag
+        pydicom.tag.BaseTag or list of pydicom.tag.BaseTag
             The value to use for the *Attribute Identifier List* parameter.
             A list of pydicom :class:`pydicom.tag.BaseTag` instances or any
             values acceptable for creating them.
@@ -1524,20 +1526,22 @@ def AttributeIdentifierList(
             self._attribute_identifier_list = None
             return
 
-        # Singleton tags get put in a list
-        if not isinstance(value, (list, MutableSequence)):
-            value = [value]
-
-        # Empty list -> None
-        if not value:
-            self._attribute_identifier_list = None
-            return
-
         try:
-            # Convert each item in list to pydicom Tag
-            self._attribute_identifier_list = [Tag(tag) for tag in value]
+            if isinstance(value, Sequence):
+                if not value:
+                    self._attribute_identifier_list = None
+
+                if len(value) == 1:
+                    self._attribute_identifier_list = Tag(value[0])
+                else:
+                    self._attribute_identifier_list = [Tag(tag) for tag in value]
+            else:
+                self._attribute_identifier_list = Tag(value)
         except (TypeError, ValueError):
-            raise ValueError("Attribute Identifier List must be a list of pydicom Tags")
+            raise ValueError(
+                "Attribute Identifier List must be convertible to a pydicom "
+                "BaseTag or list of BaseTag"
+            )
 
     @property
     def AttributeList(self) -> Optional[BytesIO]:

pynetdicom/events.py

@@ -549,6 +549,9 @@ def attribute_identifiers(self) -> List[BaseTag]:
             if attr_list is None:
                 return []
 
+            if not isinstance(attr_list, list):
+                return [attr_list]
+
             return attr_list
         except AttributeError:
             pass

pynetdicom/sop_class.py

@@ -117,7 +117,7 @@ def __new__(cls: Type["SOPClass"], val: str) -> "SOPClass":
         if isinstance(val, SOPClass):
             return val
 
-        return super(SOPClass, cls).__new__(cls, val)
+        return cast("SOPClass", super().__new__(cls, val))
 
     def __getattribute__(self, name: str) -> Any:
         return super(SOPClass, self).__getattribute__(name)

pynetdicom/tests/test_ae.py

@@ -8,7 +8,7 @@
 
 import pytest
 
-from pydicom import read_file
+from pydicom import read_file, config as PYD_CONFIG
 from pydicom.dataset import Dataset
 from pydicom.uid import UID, ImplicitVRLittleEndian
 
@@ -29,6 +29,10 @@
 from pynetdicom.transport import AssociationServer, RequestHandler
 
 
+if hasattr(PYD_CONFIG, "settings"):
+    PYD_CONFIG.settings.reading_validation_mode = 0
+
+
 # debug_logger()
 
 

pynetdicom/tests/test_assoc_n.py

@@ -1059,7 +1059,7 @@ def handle(event):
             ds.Status = 0xFFF0
             ds.ErrorComment = "Some comment"
             ds.ErrorID = 12
-            ds.AttributeIdentifierList = [0x00100020]
+            ds.AttributeIdentifierList = 0x00100020
             return ds, None
 
         self.ae = ae = AE()
@@ -1081,7 +1081,7 @@ def handle(event):
         assert status.Status == 0xFFF0
         assert status.ErrorComment == "Some comment"
         assert status.ErrorID == 12
-        assert status.AttributeIdentifierList == [0x00100020]
+        assert status.AttributeIdentifierList == 0x00100020
         assert ds is None
         assoc.release()
         assert assoc.is_released

pynetdicom/tests/test_dimse_n.py

@@ -9,9 +9,10 @@
 
 import pytest
 
+from pydicom import config as PYD_CONFIG
 from pydicom.dataset import Dataset
 from pydicom.dataelem import DataElement
-from pydicom.tag import Tag
+from pydicom.tag import Tag, BaseTag
 from pydicom.uid import UID
 
 from pynetdicom import _config
@@ -63,6 +64,11 @@
     n_create_rsp_ds,
 )
 
+
+if hasattr(PYD_CONFIG, "settings"):
+    PYD_CONFIG.settings.reading_validation_mode = 0
+
+
 LOGGER = logging.getLogger("pynetdicom")
 LOGGER.setLevel(logging.CRITICAL)
 
@@ -375,14 +381,14 @@ def test_assignment(self):
             Tag(0x7FE0, 0x0010),
         ] == primitive.AttributeIdentifierList
         primitive.AttributeIdentifierList = [(0x7FE0, 0x0010)]
-        assert [Tag(0x7FE0, 0x0010)] == primitive.AttributeIdentifierList
+        assert Tag(0x7FE0, 0x0010) == primitive.AttributeIdentifierList
         primitive.AttributeIdentifierList = (0x7FE0, 0x0010)
-        assert [Tag(0x7FE0, 0x0010)] == primitive.AttributeIdentifierList
+        assert Tag(0x7FE0, 0x0010) == primitive.AttributeIdentifierList
 
         elem = DataElement((0x0000, 0x0005), "AT", [Tag(0x0000, 0x1000)])
-        assert isinstance(elem.value, MutableSequence)
+        assert isinstance(elem.value, BaseTag)
         primitive.AttributeIdentifierList = elem.value
-        assert [Tag(0x0000, 0x1000)] == primitive.AttributeIdentifierList
+        assert Tag(0x0000, 0x1000) == primitive.AttributeIdentifierList
 
         # MessageID
         primitive.MessageID = 11

pynetdicom/tests/test_events.py

@@ -479,6 +479,13 @@ def test_attr_identifiers(self):
         assert isinstance(tags[1], BaseTag)
         assert tags[1] == 0x00100020
 
+        request.AttributeIdentifierList = 0x00100010
+        event = Event(
+            None, evt.EVT_N_GET, {"request": request, "context": self.context.as_tuple}
+        )
+        tags = event.attribute_identifiers
+        assert tags == [0x00100010]
+
     def test_action_type(self):
         """Test with action_type."""
         request = N_ACTION()

pynetdicom/tests/test_pdu_items.py

@@ -6,6 +6,7 @@
 
 import pytest
 
+from pydicom import config as PYD_CONFIG
 from pydicom.uid import UID
 
 from pynetdicom import _config, debug_logger
@@ -85,6 +86,10 @@
 )
 
 
+if hasattr(PYD_CONFIG, "settings"):
+    PYD_CONFIG.settings.reading_validation_mode = 0
+
+
 # debug_logger()
 
 

pynetdicom/tests/test_primitives.py

@@ -4,6 +4,7 @@
 
 import pytest
 
+from pydicom import config as PYD_CONFIG
 from pydicom.uid import UID
 
 from pynetdicom import _config
@@ -26,6 +27,11 @@
 from pynetdicom.presentation import PresentationContext
 from pynetdicom.utils import pretty_bytes
 
+
+if hasattr(PYD_CONFIG, "settings"):
+    PYD_CONFIG.settings.reading_validation_mode = 0
+
+
 LOGGER = logging.getLogger("pynetdicom")
 LOGGER.setLevel(logging.CRITICAL)
 

pynetdicom/tests/test_service_storage.py

@@ -472,6 +472,7 @@ def handle(event):
         handlers = [(evt.EVT_C_STORE, handle)]
 
         self.ae = ae = AE()
+        ae.maximum_pdu_size = 256
         ae.add_supported_context(CTImageStorage)
         ae.add_requested_context(CTImageStorage)
         scp = ae.start_server(("localhost", 11112), block=False, evt_handlers=handlers)
@@ -492,6 +493,8 @@ def handle(event):
 
         ds = attrs["dataset"]
         assert "CompressedSamples^CT1" == ds.PatientName
+        assert "DataSetTrailingPadding" in ds
+        assert len(ds.DataSetTrailingPadding) == 126
 
         scp.shutdown()