update

Author: Hoeze

…rename_submission_date_to_submission_.py …sion_date_to_submission_uploaded_date.pypackages/grz-db/src/grz_db/migrations/versions/66f36abbea34_rename_submission_date_to_submission_.py renamed to packages/grz-db/src/grz_db/migrations/versions/66f36abbea34_rename_submission_date_to_submission_uploaded_date.py packages/grz-db/src/grz_db/migrations/versions/66f36abbea34_rename_submission_date_to_submission_.py renamed to packages/grz-db/src/grz_db/migrations/versions/66f36abbea34_rename_submission_date_to_submission_uploaded_date.py

@@ -1,4 +1,4 @@
-"""rename submission_date to submission_finished_date
+"""rename submission_date to submission_uploaded_date
 
 Revision ID: 66f36abbea34
 Revises: 09602efd9105
@@ -19,7 +19,7 @@
 
 def upgrade() -> None:
     """Upgrade schema."""
-    op.alter_column("submissions", "submission_date", new_column_name="submission_finished_date")
+    op.alter_column("submissions", "submission_date", new_column_name="submission_uploaded_date")
 
 
 def downgrade() -> None:

packages/grz-db/src/grz_db/models/submission/__init__.py

@@ -143,7 +143,7 @@ class SubmissionBase(SQLModel):
     pseudonym: str | None = Field(default=None, index=True)
 
     # fields from Prüfbericht
-    submission_finished_date: datetime.date | None = None
+    submission_uploaded_date: datetime.date | None = None
     submission_type: SubmissionType | None = None
     submitter_id: SubmitterId | None = None
     data_node_id: GenomicDataCenterId | None = None
@@ -206,7 +206,7 @@ def diff(
             new_value = getattr(other, key)
 
             # Ensure fields are cast to date
-            if key == "submission_finished_date":
+            if key == "submission_uploaded_date":
                 if isinstance(old_value, datetime.datetime):
                     old_value = old_value.date()
                 if isinstance(new_value, datetime.datetime):
@@ -228,7 +228,7 @@ def from_metadata(
         cls,
         submission_id: str,
         metadata: GrzSubmissionMetadata,
-        submission_finished_date: datetime.date,
+        submission_uploaded_date: datetime.date,
     ) -> Self:
         """Construct a Submission populated with values derived from parsed metadata.
 
@@ -241,8 +241,8 @@ def from_metadata(
         if isinstance(metadata_submission_date, datetime.datetime):
             metadata_submission_date = metadata_submission_date.date()
 
-        if isinstance(submission_finished_date, datetime.datetime):
-            submission_finished_date = submission_finished_date.date()
+        if isinstance(submission_uploaded_date, datetime.datetime):
+            submission_uploaded_date = submission_uploaded_date.date()
 
         return cls.model_validate(
             {
@@ -258,7 +258,7 @@ def from_metadata(
                 "data_node_id": metadata.submission.genomic_data_center_id,
                 "consented": metadata.consents_to_research(date=metadata_submission_date),
                 "submission_size": metadata.get_submission_size(),
-                "submission_finished_date": submission_finished_date,
+                "submission_uploaded_date": submission_uploaded_date,
                 "submission_metadata": metadata.to_redacted_dict(),
             }
         )
@@ -735,7 +735,7 @@ def _list_submitter_qc_candidates(
                 .join(QCQueueEntry, QCQueueEntry.submission_id == Submission.id)  # type: ignore[arg-type]
                 .where(Submission.submission_type == SubmissionType.initial)
                 .where(Submission.basic_qc_passed)  # type: ignore[arg-type]
-                .where(Submission.submission_finished_date.between(start_date, end_date))  # type: ignore[union-attr]
+                .where(Submission.submission_uploaded_date.between(start_date, end_date))  # type: ignore[union-attr]
                 .where(Submission.submitter_id == submitter_id)
                 .order_by(QCQueueEntry.basic_qc_passed_at, Submission.id)  # type: ignore[arg-type]
             ).all()
@@ -780,7 +780,7 @@ def _is_randomly_selected_for_qc(
 
         block_size = math.floor(1 / target_proportion)
         block_index = absolute_index // block_size
-        submission_quarter, submission_year = date_to_quarter_year(submission.submission_finished_date)  # type: ignore[arg-type]
+        submission_quarter, submission_year = date_to_quarter_year(submission.submission_uploaded_date)  # type: ignore[arg-type]
         seed = f"{submission.submitter_id}-{submission_year}-{submission_quarter}-{block_index}-{salt}"
         rng = random.Random(seed)  # noqa: S311
 
@@ -1033,7 +1033,7 @@ def list_submissions(
                     isouter=True,
                 )
                 .order_by(
-                    sqlfn.coalesce(latest_state_per_submission.c.timestamp, Submission.submission_finished_date)
+                    sqlfn.coalesce(latest_state_per_submission.c.timestamp, Submission.submission_uploaded_date)
                     .desc()
                     .nulls_first()
                 )
@@ -1117,7 +1117,7 @@ def should_qc(self, submission_id: str, target_percentage: float, salt: str | No
 
         if submission is None:
             raise SubmissionNotFoundError(submission_id)
-        submission_date = submission.submission_finished_date
+        submission_date = submission.submission_uploaded_date
         if submission_date is None:
             raise SubmissionDateIsNoneError()
         submission_type = submission.submission_type
@@ -1181,14 +1181,14 @@ def _diff_metadata(
         self,
         submission_id: str,
         metadata: GrzSubmissionMetadata,
-        submission_finished_date: datetime.date,
+        submission_uploaded_date: datetime.date,
         ignore_fields: set[str] | None = None,
     ) -> SubmissionDiffCollection:
         """Compare a submission's current database state against fresh metadata.
 
         :param submission_id: Submission ID to look up.
         :param metadata: Parsed metadata from the submission's ``metadata.json``.
-        :param submission_finished_date: Date of submission upload finish
+        :param submission_uploaded_date: Date of submission upload finish
         :param ignore_fields: Field names to skip entirely during the comparison.
         :returns: A :class:`SubmissionDiffCollection` instance summarising all detected differences.
         """
@@ -1199,10 +1199,10 @@ def _diff_metadata(
         if ignore_fields is None:
             ignore_fields = set()
 
-        if isinstance(submission_finished_date, datetime.datetime):
-            submission_finished_date = submission_finished_date.date()
+        if isinstance(submission_uploaded_date, datetime.datetime):
+            submission_uploaded_date = submission_uploaded_date.date()
 
-        new_submission = Submission.from_metadata(submission_id, metadata, submission_finished_date)
+        new_submission = Submission.from_metadata(submission_id, metadata, submission_uploaded_date)
 
         return current_submission.diff(new_submission, ignore_fields)
 
@@ -1242,7 +1242,7 @@ def diff(
         self,
         submission_id: str,
         metadata: GrzSubmissionMetadata,
-        submission_finished_date: datetime.date | None,
+        submission_uploaded_date: datetime.date | None,
         ignore_fields: set[str] | None = None,
     ) -> tuple[SubmissionDiffCollection, DonorsDiffCollection]:
         """
@@ -1255,20 +1255,20 @@ def diff(
 
         :param submission_id: The unique identifier of the submission to be compared.
         :param metadata: The metadata of the submission to compare against.
-        :param submission_finished_date: The date when the submission process was finished.
+        :param submission_uploaded_date: The date when the submission process was finished.
             If None, the field will not be included in the comparison.
         :param ignore_fields: Optional set of field names to be ignored during the metadata comparison.
         :returns: A tuple containing the differences in the submission metadata and the corresponding donor entries.
         """
-        if submission_finished_date is None:
+        if submission_uploaded_date is None:
             # set arbitrary date if not provided
-            submission_finished_date = metadata.submission.submission_date
+            submission_uploaded_date = metadata.submission.submission_date
 
             # Add submission date to ignore fields
             ignore_fields = ignore_fields or set()
-            ignore_fields.add("submission_finished_date")
+            ignore_fields.add("submission_uploaded_date")
 
-        submission_diff = self._diff_metadata(submission_id, metadata, submission_finished_date, ignore_fields)
+        submission_diff = self._diff_metadata(submission_id, metadata, submission_uploaded_date, ignore_fields)
         donor_diff = self._diff_donors(submission_id, metadata)
         return submission_diff, donor_diff
 

packages/grz-db/tests/test_should_qc.py

@@ -79,7 +79,7 @@ def _add_submission_with_history(
     """
     db.add_submission(submission_id)
 
-    db.modify_submission(submission_id, "submission_finished_date", str(submission_date.isoformat()))
+    db.modify_submission(submission_id, "submission_uploaded_date", str(submission_date.isoformat()))
     db.modify_submission(submission_id, "submission_type", SubmissionType.initial)
     db.modify_submission(submission_id, "submitter_id", submitter_id)
     db.modify_submission(submission_id, "basic_qc_passed", "true")
@@ -488,7 +488,7 @@ def test_should_qc_raises_on_missing_submission_type(self, db: SubmissionDb):
         """Verify SubmissionTypeIsNoneError when submission_type is None."""
         submission_id = f"{SUBMITTER_ID}_2025-12-01_00000000"
         db.add_submission(submission_id)
-        db.modify_submission(submission_id, "submission_finished_date", "2025-12-01")
+        db.modify_submission(submission_id, "submission_uploaded_date", "2025-12-01")
         db.modify_submission(submission_id, "basic_qc_passed", "true")
 
         with pytest.raises(SubmissionTypeIsNoneError):

packages/grz-db/tests/test_submission.py

@@ -83,7 +83,7 @@ def test_from_metadata_sets_fields_from_metadata(metadata: GrzSubmissionMetadata
     assert submission.genomic_study_subtype == metadata.submission.genomic_study_subtype
     assert submission.pseudonym == metadata.submission.local_case_id
     assert submission.data_node_id == metadata.submission.genomic_data_center_id
-    assert submission.submission_finished_date == explicit_date  # explicit date takes precedence
+    assert submission.submission_uploaded_date == explicit_date  # explicit date takes precedence
     assert submission.submission_size == metadata.get_submission_size()
     assert submission.submission_metadata == metadata.to_redacted_dict()
 

packages/grzctl/src/grzctl/commands/db/cli.py

@@ -54,7 +54,7 @@
     SequenceSubtype,
     SequenceType,
 )
-from pydantic import Field
+from pydantic import Field, ValidationError
 from tqdm.auto import tqdm
 
 from ... import get_versions
@@ -698,20 +698,20 @@ def populate(  # noqa: C901, PLR0913
             "or use 'grzctl db submission modify' directly."
         ) from e
 
-    submission_finished_date = (
-        submission_date.date() if submission_date is not None else submission.submission_finished_date
+    submission_uploaded_date = (
+        submission_date.date() if submission_date is not None else submission.submission_uploaded_date
     )
     if submission_date is None:
         log.warning(
             "No submission date provided and submission date is missing in the database. "
             "Will use submission date from metadata.json..."
         )
-        submission_finished_date = metadata.submission.submission_date
+        submission_uploaded_date = metadata.submission.submission_date
 
     submission_diff, donors_diff = db_service.diff(
         submission_id,
         metadata,
-        submission_finished_date=submission_finished_date,
+        submission_uploaded_date=submission_uploaded_date,
         ignore_fields=set(ignore_field),
     )
 
@@ -941,6 +941,69 @@ def change_request(ctx: click.Context, submission_id: str, change_str: str, data
         raise click.ClickException(f"Failed to update submission state: {e}") from e
 
 
+def _research_consented_today(submission: Submission) -> bool | None:
+    """Research consent for the submission re-evaluated as of today.
+
+    Unlike the persisted ``consented`` field (evaluated at the submission date),
+    this recomputes consent from the stored redacted metadata using today's date.
+
+    :param submission: Submission whose stored metadata to evaluate.
+    :returns: ``True``/``False`` for the consent decision today, or ``None`` when
+        no metadata is stored (e.g. rows migrated without backpopulated metadata)
+        or when the stored metadata cannot be parsed.
+    """
+    if not submission.submission_metadata:
+        return None
+    try:
+        metadata = GrzSubmissionMetadata.model_validate(submission.submission_metadata)
+    except ValidationError:
+        log.debug("Could not parse stored metadata for submission %s to evaluate consent today.", submission.id)
+        return None
+    return metadata.consents_to_research(date=date.today())
+
+
+def _build_attribute_table(submission: Submission, research_consented_today: bool | None) -> rich.table.Table:
+    """Build the attribute table shown by ``submission show``.
+
+    :param submission: Submission to render.
+    :param research_consented_today: Research consent re-evaluated as of today
+        (see :func:`_research_consented_today`), or ``None`` when unavailable.
+    :returns: A populated rich table of submission attributes.
+    """
+    attribute_table = rich.table.Table(box=None)
+    attribute_table.add_column("Attribute", justify="right")
+    attribute_table.add_column("Value")
+    for label, attr_name in (
+        ("tanG", "tan_g"),
+        ("Pseudonym", "pseudonym"),
+        ("Submission Uploaded Date", "submission_uploaded_date"),
+        ("Submission Size", "submission_size"),
+        ("Submission Type", "submission_type"),
+        ("Submitter ID", "submitter_id"),
+        ("Data Node ID", "data_node_id"),
+        ("Disease Type", "disease_type"),
+        ("Genomic Study Type", "genomic_study_type"),
+        ("Genomic Study Subtype", "genomic_study_subtype"),
+        ("Basic QC Passed", "basic_qc_passed"),
+        ("Research consent (at submission)", "consented"),
+        ("Selected For QC", "selected_for_qc"),
+        ("Detailed QC Passed", "detailed_qc_passed"),
+    ):
+        attr = getattr(submission, attr_name)
+        attribute_table.add_row(
+            rich.text.Text(f"{label}", style="cyan"), rich.text.Text(str(attr)) if attr is not None else _TEXT_MISSING
+        )
+        if attr_name == "consented":
+            # Adjacent row: research consent re-evaluated as of today (recomputed from stored metadata).
+            attribute_table.add_row(
+                rich.text.Text("Research consent (today)", style="cyan"),
+                rich.text.Text(str(research_consented_today))
+                if research_consented_today is not None
+                else _TEXT_MISSING,
+            )
+    return attribute_table
+
+
 @submission.command("show")
 @click.argument("submission_id", type=str)
 @output_json
@@ -956,8 +1019,11 @@ def show(ctx: click.Context, submission_id: str, output_json: bool):
         console_err.print(f"[red]Error: Submission with ID '{submission_id}' not found.[/red]")
         raise click.Abort()
 
+    research_consented_today = _research_consented_today(submission)
+
     if output_json:
         submission_dict = submission.model_dump(mode="json")
+        submission_dict["research_consented_today"] = research_consented_today
         submission_dict["states"] = []
 
         for state_log in sorted(submission.states, key=lambda s: s.timestamp):
@@ -977,29 +1043,7 @@ def show(ctx: click.Context, submission_id: str, output_json: bool):
         sys.stdout.write("\n")
         return
 
-    attribute_table = rich.table.Table(box=None)
-    attribute_table.add_column("Attribute", justify="right")
-    attribute_table.add_column("Value")
-    for label, attr_name in (
-        ("tanG", "tan_g"),
-        ("Pseudonym", "pseudonym"),
-        ("Submission Date", "submission_finished_date"),
-        ("Submission Size", "submission_size"),
-        ("Submission Type", "submission_type"),
-        ("Submitter ID", "submitter_id"),
-        ("Data Node ID", "data_node_id"),
-        ("Disease Type", "disease_type"),
-        ("Genomic Study Type", "genomic_study_type"),
-        ("Genomic Study Subtype", "genomic_study_subtype"),
-        ("Basic QC Passed", "basic_qc_passed"),
-        ("Consented", "consented"),
-        ("Selected For QC", "selected_for_qc"),
-        ("Detailed QC Passed", "detailed_qc_passed"),
-    ):
-        attr = getattr(submission, attr_name)
-        attribute_table.add_row(
-            rich.text.Text(f"{label}", style="cyan"), rich.text.Text(str(attr)) if attr is not None else _TEXT_MISSING
-        )
+    attribute_table = _build_attribute_table(submission, research_consented_today)
 
     renderables: list[rich.console.RenderableType] = [rich.padding.Padding(attribute_table, (1, 0))]
     if submission.states:
@@ -1110,18 +1154,18 @@ def _backfill_submission(  # noqa: PLR0911, PLR0913
         return _BackfillResult.ERROR
 
     try:
-        # If submission_finished_date is not set in the DB, replace it with the one from metadata.json.
+        # If submission_uploaded_date is not set in the DB, replace it with the one from metadata.json.
         # This case is expected for submissions that were created before the submission_date field was added.
-        submission_finished_date = (
-            current_submission.submission_finished_date
-            if current_submission.submission_finished_date
+        submission_uploaded_date = (
+            current_submission.submission_uploaded_date
+            if current_submission.submission_uploaded_date
             else metadata.submission.submission_date
         )
 
         submission_diff, donors_diff = db_service.diff(
             submission_id,
             metadata,
-            submission_finished_date=submission_finished_date,
+            submission_uploaded_date=submission_uploaded_date,
             ignore_fields=ignore_fields or None,
         )
     except Exception as exc:
@@ -1223,7 +1267,7 @@ def backfill(  # noqa: PLR0913
         raise click.UsageError("--submission-id and --start-date/--end-date are mutually exclusive.")
 
     ignore_fields = set(ignore_field) | {
-        "submission_finished_date",
+        "submission_uploaded_date",
         "tan_g",
         "local_case_id",
     }

packages/grzctl/src/grzctl/commands/db/tui.py

@@ -120,7 +120,7 @@ async def load(self, database: SubmissionDb, quarter: int | None = None, year: i
         with database._get_session() as session:
             statement = (
                 select(  # type: ignore[type-var]
-                    Submission.submitter_id, Submission.submission_finished_date, Submission.detailed_qc_passed
+                    Submission.submitter_id, Submission.submission_uploaded_date, Submission.detailed_qc_passed
                 )
                 .where(Submission.submission_type == SubmissionType.initial)
                 .where(Submission.basic_qc_passed)  # type: ignore[arg-type]
@@ -238,7 +238,7 @@ async def search(
                 Submission.id == latest_state_per_submission.c.submission_id,  # type: ignore[arg-type]
                 isouter=True,
             ).order_by(
-                sqlfn.coalesce(latest_state_per_submission.c.timestamp, Submission.submission_finished_date)
+                sqlfn.coalesce(latest_state_per_submission.c.timestamp, Submission.submission_uploaded_date)
                 .desc()
                 .nulls_first()
             )