✅ acq2sqlite.py:none_to_null so template and input missingness matches

Makefile

@@ -34,7 +34,7 @@ docs/_static/mrqart/main.css: static/main.css
 ##
 
 .lint: $(wildcard *.py) $(wildcard sphinx/*.rst) | venv-dev
-	$(source_venv) && black . > .lint && isort . >> .lint && codespell -w >> .lint
+	$(source_venv) && black . > .lint && isort --skip-gitignore . >> .lint && codespell -w >> .lint
 
 test: .test.doctest .test.pytest
 .test.doctest: change_header.py acq2sqlite.py dcmmeta2tsv.py | venv-program venv-dev  #$(wildcard *py)

acq2sqlite.py

@@ -15,6 +15,19 @@
 logging.basicConfig(level=os.environ.get("LOGLEVEL", logging.INFO))
 
 
+def none_to_null(row: Optional[sqlite3.Row]):
+    """
+    Template should match get_header. This changes all ``None``s to ``"null"``
+    :param row: single row from a sqlite query (likely :py:func:`get_template`)
+    """
+    if not row:
+        return row
+    res = {}
+    for k in row.keys():
+        res[k] = row[k] if row[k] else NULLVAL.value
+    return res
+
+
 def column_names():
     """
     These names match what's used by dcmmeta2tsv.py and 00_build_db.bash
@@ -289,6 +302,7 @@ def get_template(self, pname: str, seqname: str) -> sqlite3.Row:
             (pname, seqname),
         )
         res = cur.fetchone()
+        res = none_to_null(res)
         logging.debug("found template: %s", res)
         return res
 

template_checker.py

@@ -39,8 +39,8 @@ def find_errors(template: TagValues, current_hdr: TagValues) -> dict[str, ErrorC
     """
     errors = {}
     for k in DBQuery.CONSTS:
-        t_k = template.get(k, "0")
-        h_k = current_hdr.get(k, "0")
+        t_k = template.get(k, "null")
+        h_k = current_hdr.get(k, "null")
 
         # TODO: more checks for specific headers
         #: TR is in milliseconds. no need to keep decimals precision
@@ -66,11 +66,13 @@ class TemplateChecker:
     read a dicom file and report if it conforms to the expected template
     """
 
-    def __init__(self):
+    def __init__(self, db=None):
         """
         db connection and tag reader (from taglist.txt)
+        :param db: sql connection passed on to :py:class:`DBQuery`.
+            ``None`` (default) is local sqlite3.
         """
-        self.db = DBQuery()
+        self.db = DBQuery(db)
         self.reader = DicomTagReader()
 
     def check_file(self, dcm_path) -> CheckResult:

tests/test_html.py

@@ -3,7 +3,8 @@
 from jinja2 import Template
 
 from compliance_check_html import generate_html_report
-#from template_checker import CheckResult, TemplateChecker
+
+# from template_checker import CheckResult, TemplateChecker
 
 
 @pytest.fixture

tests/test_sql.py

@@ -6,7 +6,7 @@
 
 from acq2sqlite import DBQuery
 from dcmmeta2tsv import DicomTagReader, TagDicts
-from template_checker import TemplateChecker, CheckResult
+from template_checker import CheckResult, TemplateChecker
 
 #: Example template to test against. Previously used within test like::
 #:   mocker.patch.object(template_checker.db, "get_template", return_value=mock_template)
@@ -25,24 +25,29 @@
     # Other relevant fields can be added as well if seen as necessary
 }
 
+
 @pytest.fixture
 def db():
     """create an in memory database handler"""
     mem_db = DBQuery(sqlite3.connect(":memory:"))
     with open("schema.sql") as f:
         _ = [mem_db.sql.execute(c) for c in f.read().split(";")]
     # create template table. also see ../make_template_by_count.sql
-    mem_db.sql.execute("""
+    mem_db.sql.execute(
+        """
       create table template_by_count (
           n int, Project text, SequenceName text,
-          param_id int, first text, last text)""")
+          param_id int, first text, last text)"""
+    )
     vals = [x for x in MOCK_TEMPLATE.values()]
     cols = ",".join(MOCK_TEMPLATE.keys())
     qs = ",".join(["?" for x in vals])
     sql = f"INSERT INTO acq_param ({cols}) VALUES ({qs})"
     mem_db.sql.execute(sql, vals)
-    sql = "INSERT INTO template_by_count (Project, SequenceName, param_id)" + \
-          f"VALUES ('{MOCK_TEMPLATE['Project']}', '{MOCK_TEMPLATE['SequenceName']}', 1)"
+    sql = (
+        "INSERT INTO template_by_count (Project, SequenceName, param_id)"
+        + f"VALUES ('{MOCK_TEMPLATE['Project']}', '{MOCK_TEMPLATE['SequenceName']}', 1)"
+    )
     mem_db.sql.execute(sql)
 
     return mem_db
@@ -142,7 +147,7 @@ def test_find_acquisitions_since(db):
 
 @pytest.fixture
 def template_checker(db):
-    return TemplateChecker(db)
+    return TemplateChecker(db.sql)
 
 
 def test_check_header_notemplate(template_checker):
@@ -159,8 +164,9 @@ def test_check_header_notemplate(template_checker):
         "Comments": "Unaliased MB3/PE4/LB SENSE1",
     }
     result = template_checker.check_header(test_row)
-    assert result['errors'] == {}
-    assert result['conforms']
+    assert result["errors"] == {}
+    assert result["conforms"]
+
 
 def test_check_header(template_checker):
     """
@@ -190,7 +196,8 @@ def test_check_header(template_checker):
     assert result["input"] == test_row
     assert result["template"]["TR"] == MOCK_TEMPLATE["TR"]
 
-def test_check_header_matches(db, template_checker):
+
+def test_check_header_matches(template_checker):
     result: CheckResult = template_checker.check_header(MOCK_TEMPLATE)
-    assert result["conforms"] == True
     assert result["errors"] == {}
+    assert result["conforms"] == True