Bug Fixes and Unit Tests for BLANK & REPLACE Actions & Sequences (#242)

* Expand BLANK Action to other VRs

1. Expanded BLANK Action to other VRs.
2. Added unit tests for validating action interaction.
3. Added table of action interactions to help docs.

* Update recipe-headers.md
* Update test_action_interaction.py
Correcting bad test method names.
* Update deid-data install version
* Update parser.py

Reverted expand_field_expression to always return desired as a Tag.  Instead convert to DataElement in blank_field.

* Expanding blank to all VRs
Updating BLANK test coverage to all VRs.
* Updating field counts in unit tests.
Updating unit tests failing due to field count changes in test image.
* Update test_blank_action.py
Restructured blank_action unit tests.
* Fix for #244 - Replace fails for numeric VR
Removing deid-data pin.
* Update actions.py
Committing review suggestions.
* Header Sequence Updates
Corrected issue #243 which prevented tags within sequences from being acted upon.   Added unit tests for sequence processing

* Update test_replace_identifiers.py
Updated test_replace_identifiers to target ctbrain1.dcm by name.
* Update test_dicom_funcs.py

Updated test_user_provided_func to target ctbrain1.dcm

.github/workflows/main.yaml

@@ -40,5 +40,5 @@ jobs:
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate testing
-          pip install deid-data==0.0.17
+          pip install deid-data
           python -m unittest discover -s deid/tests/ -p '[t|T]est*.py'

CHANGELOG.md

@@ -14,7 +14,9 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
-
+- Expand BLANK Action to additional VRs [#241](https://github.com/pydicom/deid/issues/241) (0.3.2)
+  - Correct issues with REPLACE action on numeric VRs [#244](https://github.com/pydicom/deid/issues/244)
+  - Correct issue with actions on fields within sequences [#243](https://github.com/pydicom/deid/issues/243)
 - pre-commit for linting and formatting (0.3.1)
 - Add `ctpcoordinates` and `ctpkeepcoordinates` to handle different formats (0.3.0)
   - Minimum Python required is 3.7, numpy 1.20

deid/dicom/parser.py

@@ -160,8 +160,9 @@ def get_nested_field(self, field, return_parent=False):
             # Otherwise it's an index into a sequence
             else:
 
-                # If the parent has been removed, we can't continue
-                if not int(uid) in parent:
+                # If the sequence is outside the bounds of the array of items
+                # within the sequence, we can't continue.
+                if int(uid) < 0 or int(uid) >= len(parent.value):
                     return None, desired
                 parent = parent[int(uid)]
 
@@ -186,16 +187,10 @@ def blank_field(self, field):
         """
         Blank a field
         """
-        element = self.get_nested_field(field)
-
-        # Assert we have a data element, and can blank a string
-        if element:
-            if not isinstance(element, DataElement):
-                bot.warning("Issue parsing %s as a DataElement, not blanked." % field)
-            elif element.VR in ["US", "SS"]:
-                element.value = ""
-            else:
-                bot.warning("Unrecognized VR for %s, skipping blank." % field)
+        # Returns the parent, and a DataElement (indexes into parent by tag)
+        parent, desired = self.get_nested_field(field, return_parent=True)
+        if parent and desired in parent:
+            parent[desired].value = None
 
     def replace_field(self, field, value):
         """