Add Newick tree support

app/grandchallenge/components/form_fields.py

@@ -162,19 +162,16 @@ def get_file_field(self):
             type = "uuid"
 
         if type == "uuid":
-            ext = (
-                "json"
-                if self.instance.is_json_kind
-                else self.instance.kind.lower()
-            )
-            extra_help = f"{file_upload_text} .{ext}"
+            file_extensions = ", ".join(self.instance.file_extensions)
+            extra_help = f"{file_upload_text} {file_extensions}"
             return ModelChoiceField(
                 queryset=get_objects_for_user(
                     self.user,
                     "uploads.change_userupload",
                 ).filter(status=UserUpload.StatusChoices.COMPLETED),
                 widget=UserUploadSingleWidget(
-                    allowed_file_types=self.instance.file_mimetypes
+                    allowed_file_types=self.instance.file_mimetypes,
+                    allowed_file_extensions=self.instance.file_extensions,
                 ),
                 help_text=_join_with_br(self.help_text, extra_help),
                 **self.kwargs,

app/grandchallenge/components/migrations/0022_alter_componentinterface_kind_and_more.py

@@ -0,0 +1,108 @@
+# Generated by Django 4.2.16 on 2024-11-12 11:54
+
+from django.db import migrations, models
+
+import grandchallenge.components.models
+import grandchallenge.core.storage
+import grandchallenge.core.validators
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("components", "0021_alter_componentinterface_kind_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="componentinterface",
+            name="kind",
+            field=models.CharField(
+                choices=[
+                    ("STR", "String"),
+                    ("INT", "Integer"),
+                    ("FLT", "Float"),
+                    ("BOOL", "Bool"),
+                    ("JSON", "Anything"),
+                    ("CHART", "Chart"),
+                    ("2DBB", "2D bounding box"),
+                    ("M2DB", "Multiple 2D bounding boxes"),
+                    ("DIST", "Distance measurement"),
+                    ("MDIS", "Multiple distance measurements"),
+                    ("POIN", "Point"),
+                    ("MPOI", "Multiple points"),
+                    ("POLY", "Polygon"),
+                    ("MPOL", "Multiple polygons"),
+                    ("LINE", "Line"),
+                    ("MLIN", "Multiple lines"),
+                    ("ANGL", "Angle"),
+                    ("MANG", "Multiple angles"),
+                    ("ELLI", "Ellipse"),
+                    ("MELL", "Multiple ellipses"),
+                    ("3ANG", "Three-point angle"),
+                    ("M3AN", "Multiple three-point angles"),
+                    ("ATRG", "Affine transform registration"),
+                    ("CHOI", "Choice"),
+                    ("MCHO", "Multiple choice"),
+                    ("IMG", "Image"),
+                    ("SEG", "Segmentation"),
+                    ("HMAP", "Heat Map"),
+                    ("DSPF", "Displacement field"),
+                    ("PDF", "PDF file"),
+                    ("SQREG", "SQREG file"),
+                    ("JPEG", "Thumbnail jpg"),
+                    ("PNG", "Thumbnail png"),
+                    ("OBJ", "OBJ file"),
+                    ("MP4", "MP4 file"),
+                    ("NEWCK", "Newick tree-format file"),
+                    ("CSV", "CSV file"),
+                    ("ZIP", "ZIP file"),
+                ],
+                help_text="What is the type of this interface? Used to validate interface values and connections between components.",
+                max_length=5,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="componentinterfacevalue",
+            name="file",
+            field=models.FileField(
+                blank=True,
+                null=True,
+                storage=grandchallenge.core.storage.ProtectedS3Storage(),
+                upload_to=grandchallenge.components.models.component_interface_value_path,
+                validators=[
+                    grandchallenge.core.validators.ExtensionValidator(
+                        allowed_extensions=(
+                            ".json",
+                            ".zip",
+                            ".csv",
+                            ".png",
+                            ".jpg",
+                            ".jpeg",
+                            ".pdf",
+                            ".sqreg",
+                            ".obj",
+                            ".mp4",
+                            ".newick",
+                        )
+                    ),
+                    grandchallenge.core.validators.MimeTypeValidator(
+                        allowed_types=(
+                            "application/json",
+                            "application/zip",
+                            "text/plain",
+                            "application/csv",
+                            "text/csv",
+                            "application/pdf",
+                            "image/png",
+                            "image/jpeg",
+                            "application/octet-stream",
+                            "application/x-sqlite3",
+                            "application/vnd.sqlite3",
+                            "video/mp4",
+                        )
+                    ),
+                ],
+            ),
+        ),
+    ]

app/grandchallenge/components/models.py

@@ -52,6 +52,7 @@
     validate_docker_image,
 )
 from grandchallenge.components.validators import (
+    validate_newick_tree_format,
     validate_no_slash_at_ends,
     validate_safe_path,
 )
@@ -145,6 +146,7 @@ class InterfaceKindChoices(models.TextChoices):
     THUMBNAIL_PNG = "PNG", _("Thumbnail png")
     OBJ = "OBJ", _("OBJ file")
     MP4 = "MP4", _("MP4 file")
+    NEWICK = "NEWCK", _("Newick tree-format file")
 
     # Legacy support
     CSV = "CSV", _("CSV file")
@@ -270,6 +272,7 @@ def interface_type_file():
         * Thumbnail PNG
         * OBJ file
         * MP4 file
+        * Newick file
         """
         return {
             InterfaceKind.InterfaceKindChoices.CSV,
@@ -280,6 +283,7 @@ def interface_type_file():
             InterfaceKind.InterfaceKindChoices.THUMBNAIL_PNG,
             InterfaceKind.InterfaceKindChoices.OBJ,
             InterfaceKind.InterfaceKindChoices.MP4,
+            InterfaceKind.InterfaceKindChoices.NEWICK,
         }
 
     @staticmethod
@@ -300,6 +304,7 @@ def interface_type_undisplayable():
             InterfaceKind.InterfaceKindChoices.CSV,
             InterfaceKind.InterfaceKindChoices.ZIP,
             InterfaceKind.InterfaceKindChoices.OBJ,
+            InterfaceKind.InterfaceKindChoices.NEWICK,
         }
 
 
@@ -534,7 +539,7 @@ def default_field(self):
             return forms.JSONField
 
     @property
-    def file_mimetypes(self):
+    def file_mimetypes(self):  # noqa:C901
         if self.kind == InterfaceKind.InterfaceKindChoices.CSV:
             return (
                 "application/csv",
@@ -565,9 +570,32 @@ def file_mimetypes(self):
             )
         elif self.kind == InterfaceKind.InterfaceKindChoices.MP4:
             return ("video/mp4",)
+        elif self.kind == InterfaceKind.InterfaceKindChoices.NEWICK:
+            return ("text/x-nh", "application/octet-stream")
         else:
             raise RuntimeError(f"Unknown kind {self.kind}")
 
+    @property
+    def file_extensions(self):
+        exts = [self.file_extension]
+
+        if self.kind == InterfaceKind.InterfaceKindChoices.NEWICK:
+            exts.extend([".nwk", ".tree"])
+
+        return exts
+
+    @property
+    def file_extension(self):
+        if self.is_json_kind:
+            return ".json"
+
+        if self.is_file_kind:
+            if self.kind == InterfaceKind.InterfaceKindChoices.NEWICK:
+                return ".newick"
+            return f".{self.kind.lower()}"
+
+        raise RuntimeError(f"Unknown kind {self.kind}")
+
     def create_instance(self, *, image=None, value=None, fileobj=None):
         civ = ComponentInterfaceValue.objects.create(interface=self)
 
@@ -633,14 +661,11 @@ def _clean_overlay_segments(self):
             )
 
     def _clean_relative_path(self):
-        if self.is_json_kind:
-            if not self.relative_path.endswith(".json"):
-                raise ValidationError("Relative path should end with .json")
-        elif self.is_file_kind and not self.relative_path.endswith(
-            f".{self.kind.lower()}"
-        ):
+        if (
+            self.is_file_kind or self.is_json_kind
+        ) and not self.relative_path.endswith(self.file_extension):
             raise ValidationError(
-                f"Relative path should end with .{self.kind.lower()}"
+                f"Relative path should end with {self.file_extension}"
             )
 
         if self.is_image_kind:
@@ -1216,6 +1241,7 @@ class ComponentInterfaceValue(models.Model):
                     ".sqreg",
                     ".obj",
                     ".mp4",
+                    ".newick",
                 )
             ),
             MimeTypeValidator(
@@ -1431,6 +1457,9 @@ def validate_user_upload(self, user_upload):
             except JSONDecodeError as e:
                 raise ValidationError(e)
             self.interface.validate_against_schema(value=value)
+        elif self.interface.kind == InterfaceKindChoices.NEWICK:
+            validate_newick_tree_format(tree=user_upload.read_object())
+
         self._user_upload_validated = True
 
     def update_size_in_storage(self):

app/grandchallenge/components/validators.py

@@ -1,3 +1,4 @@
+from Bio import Phylo
 from django.core.exceptions import SuspiciousFileOperation, ValidationError
 from django.utils._os import safe_join
 
@@ -20,3 +21,17 @@ def validate_safe_path(value):
 def validate_no_slash_at_ends(value):
     if value[0] == "/" or value[-1] == "/":
         raise ValidationError("Path must not begin or end with '/'")
+
+
+def validate_newick_tree_format(tree):
+    """Validates a Newick tree by passing it through a validator"""
+    parser = Phylo.NewickIO.Parser.from_string(tree)
+
+    try:
+        has_tree = False
+        for _ in parser.parse():
+            has_tree = True
+        if not has_tree:
+            raise ValueError("No tree found")
+    except Exception as e:
+        raise ValidationError("Invalid Newick tree format:", e)

app/grandchallenge/components/views.py

@@ -458,7 +458,8 @@ def get(self, request, *args, **kwargs):
             UserUploadMultipleWidget.template_name,
             {
                 "widget": UserUploadMultipleWidget(
-                    allowed_file_types=self.interface.file_mimetypes
+                    allowed_file_types=self.interface.file_mimetypes,
+                    allowed_file_extensions=self.interface.file_extensions,
                 ).get_context(
                     name=widget_name,
                     value=None,

app/grandchallenge/uploads/widgets.py

@@ -5,17 +5,24 @@ class UserUploadWidgetMixin:
     template_name = "uploads/widget.html"
     input_type = None
 
-    def __init__(self, *args, allowed_file_types=None, **kwargs):
+    def __init__(
+        self,
+        *args,
+        allowed_file_types=None,
+        allowed_file_extensions=None,
+        **kwargs,
+    ):
         super().__init__(*args, **kwargs)
-        self.allowed_file_types = allowed_file_types
+        self.allowed_file_types = allowed_file_types or []
+        self.allowed_file_extensions = allowed_file_extensions or []
 
     def get_context(self, *args, **kwargs):
         context = super().get_context(*args, **kwargs)
         widget_id = f'X_{context["widget"]["attrs"]["id"]}'
         context["widget"]["attrs"]["id"] = widget_id
         context["widget"]["allowed_file_types"] = {
             "id": f"{widget_id}AllowedFileTypes",
-            "value": self.allowed_file_types,
+            "value": [*self.allowed_file_types, *self.allowed_file_extensions],
         }
         return context
 

app/tests/components_tests/test_models.py

@@ -157,6 +157,7 @@ def test_average_duration_filtering():
         (InterfaceKindChoices.THUMBNAIL_PNG, True, False),
         (InterfaceKindChoices.OBJ, True, False),
         (InterfaceKindChoices.MP4, True, False),
+        (InterfaceKindChoices.NEWICK, True, False),
     ),
 )
 def test_saved_in_object_store(kind, object_store_required, is_image):
@@ -220,6 +221,8 @@ def test_saved_in_object_store(kind, object_store_required, is_image):
         (InterfaceKindChoices.SQREG, True),
         (InterfaceKindChoices.THUMBNAIL_JPG, True),
         (InterfaceKindChoices.THUMBNAIL_PNG, True),
+        (InterfaceKindChoices.MP4, True),
+        (InterfaceKindChoices.NEWICK, True),
     ),
 )
 def test_clean_store_in_db(kind, object_store_required):
@@ -265,18 +268,21 @@ def test_no_uuid_validation():
 
 @pytest.mark.django_db
 @pytest.mark.parametrize(
-    "kind",
+    "kind, good_suffix",
     (
-        *InterfaceKind.interface_type_file(),
-        *InterfaceKind.interface_type_json(),
+        (InterfaceKind.InterfaceKindChoices.CSV, "csv"),
+        (InterfaceKind.InterfaceKindChoices.ZIP, "zip"),
+        (InterfaceKind.InterfaceKindChoices.PDF, "pdf"),
+        (InterfaceKind.InterfaceKindChoices.SQREG, "sqreg"),
+        (InterfaceKind.InterfaceKindChoices.THUMBNAIL_JPG, "jpeg"),
+        (InterfaceKind.InterfaceKindChoices.THUMBNAIL_PNG, "png"),
+        (InterfaceKind.InterfaceKindChoices.OBJ, "obj"),
+        (InterfaceKind.InterfaceKindChoices.MP4, "mp4"),
+        (InterfaceKind.InterfaceKindChoices.NEWICK, "newick"),
+        *((k, "json") for k in InterfaceKind.interface_type_json()),
     ),
 )
-def test_relative_path_file_ending(kind):
-    if kind in InterfaceKind.interface_type_json():
-        good_suffix = "json"
-    else:
-        good_suffix = kind.lower()
-
+def test_relative_path_file_ending(kind, good_suffix):
     i = ComponentInterfaceFactory(
         kind=kind,
         relative_path=f"foo/bar.{good_suffix}",