Add support for predictions app

docs/CHANGELOG.rst

@@ -14,6 +14,16 @@ Added
   and propagate this change in ``Data`` resource
 
 
+==========
+Unreleased
+==========
+
+Added
+-----
+- Add support for predictions
+- Add version to annotation field
+
+
 ===================
 21.2.1 - 2024-10-08
 ===================

src/resdk/query.py

@@ -16,7 +16,7 @@
 
 import tqdm
 
-from resdk.resources import AnnotationField, DescriptorSchema, Process
+from resdk.resources import AnnotationField, DescriptorSchema, PredictionField, Process
 from resdk.resources.base import BaseResource
 
 
@@ -419,7 +419,48 @@ def _fetch(self):
         if missing:
             # Get corresponding annotation field details in a single query and attach it to
             # the values.
-            for field in self.resolwe.annotation_field.filter(id__in=missing.keys()):
+            for field in self.resolwe.annotation_field.filter(
+                id__in=missing.keys()
+            ).iterate():
+                for value in missing[field.id]:
+                    value._field = field
+                    value._original_values["field"] = field._original_values
+
+
+class PredictionFieldQuery(ResolweQuery):
+    """Add additional method to the prediction field query."""
+
+    def from_path(self, full_path: str) -> "PredictionField":
+        """Get the PredictionField from full path.
+
+        :raises LookupError: when field at the specified path does not exist.
+        """
+        group_name, field_name = full_path.split(".", maxsplit=1)
+        return self.get(name=field_name, group__name=group_name)
+
+
+class PredictionValueQuery(ResolweQuery):
+    """Populate prediction fields with a single query."""
+
+    def _fetch(self):
+        """Make request to the server and populate cache.
+
+        Fetch all values and their fields with 2 queries.
+        """
+        # Execute the query in a single request.
+        super()._fetch()
+
+        missing = collections.defaultdict(list)
+        for value in self._cache:
+            if value._field is None:
+                missing[value.field_id].append(value)
+
+        if missing:
+            # Get corresponding annotation field details in a single query and attach it to
+            # the values.
+            for field in self.resolwe.prediction_field.filter(
+                id__in=missing.keys()
+            ).iterate():
                 for value in missing[field.id]:
                     value._field = field
                     value._original_values["field"] = field._original_values

src/resdk/resolwe.py

@@ -33,7 +33,13 @@
 
 from .constants import CHUNK_SIZE
 from .exceptions import ValidationError, handle_http_exception
-from .query import AnnotationFieldQuery, AnnotationValueQuery, ResolweQuery
+from .query import (
+    AnnotationFieldQuery,
+    AnnotationValueQuery,
+    PredictionFieldQuery,
+    PredictionValueQuery,
+    ResolweQuery,
+)
 from .resources import (
     AnnotationField,
     AnnotationValue,
@@ -43,6 +49,8 @@
     Geneset,
     Group,
     Metadata,
+    PredictionField,
+    PredictionValue,
     Process,
     Relation,
     Sample,
@@ -106,26 +114,30 @@ class Resolwe:
     # Map between resource and Query map. Default in ResorweQuery, only overrides must
     # be listed here.
     resource_query_class = {
-        AnnotationValue: AnnotationValueQuery,
         AnnotationField: AnnotationFieldQuery,
+        AnnotationValue: AnnotationValueQuery,
+        PredictionField: PredictionFieldQuery,
+        PredictionValue: PredictionValueQuery,
     }
 
     # Map resource class to ResolweQuery name
     resource_query_mapping = {
         AnnotationField: "annotation_field",
         AnnotationValue: "annotation_value",
-        Data: "data",
         Collection: "collection",
-        Sample: "sample",
-        Relation: "relation",
-        Process: "process",
+        Data: "data",
         DescriptorSchema: "descriptor_schema",
-        User: "user",
-        Group: "group",
         Feature: "feature",
-        Mapping: "mapping",
         Geneset: "geneset",
+        Group: "group",
+        Mapping: "mapping",
         Metadata: "metadata",
+        PredictionField: "prediction_field",
+        PredictionValue: "prediction_value",
+        Process: "process",
+        Relation: "relation",
+        Sample: "sample",
+        User: "user",
     }
     # Map ResolweQuery name to it's slug_field
     slug_field_mapping = {

src/resdk/resources/__init__.py

@@ -54,6 +54,18 @@
    :members:
    :inherited-members:
 
+.. autoclass:: resdk.resources.PredictionValue
+   :members:
+   :inherited-members:
+
+.. autoclass:: resdk.resources.PredictionGroup
+   :members:
+   :inherited-members:
+
+.. autoclass:: resdk.resources.PredictionField
+   :members:
+   :inherited-members:
+
 .. autoclass:: resdk.resources.User
    :members:
    :inherited-members:
@@ -98,6 +110,7 @@
 from .descriptor import DescriptorSchema
 from .geneset import Geneset
 from .metadata import Metadata
+from .predictions import PredictionField, PredictionGroup, PredictionValue
 from .process import Process
 from .relation import Relation
 from .sample import Sample
@@ -113,6 +126,9 @@
     "Geneset",
     "Group",
     "Metadata",
+    "PredictionField",
+    "PredictionGroup",
+    "PredictionValue",
     "Sample",
     "Process",
     "Relation",

src/resdk/resources/annotations.py

@@ -51,6 +51,7 @@ class AnnotationField(BaseResource):
         "validator_regex",
         "vocabulary",
         "required",
+        "version",
     )
 
     def __init__(self, resolwe: "Resolwe", **model_data):