Transcriptomic POC

ensembl-track-api.openapi.yaml

@@ -26,13 +26,73 @@ servers:
   - url: http://www.ensembl.org/api/tracks
     description: Production server
 paths:
+  /transcriptomic/{genome_id}/configuration:
+    get:
+      summary: Returns prepared transcriptomic selections and static filter counts.
+      description: >
+        Resolved through the same dataset/release selection as track_categories, or
+        pinned with dataset_id. Counts are occurrences across
+        handover records, grouped case-insensitively, and do not change with
+        selection. Selections contain display and filtering metadata. Each product includes
+        a track_id referencing the registered track. File locations are returned
+        by /track/{track_id}, not by this configuration endpoint. Rendering settings may not yet be configured.
+      parameters:
+        - name: genome_id
+          in: path
+          required: true
+          schema:
+            type: string
+            format: uuid
+        - name: dataset_id
+          in: query
+          description: Pin a registered dataset for this genome; mutually exclusive with release.
+          schema:
+            type: string
+            format: uuid
+        - name: release
+          in: query
+          description: Select the catalogue as of this release; defaults to latest when neither parameter is given.
+          schema:
+            type: string
+            format: date
+      responses:
+        '400':
+          description: Invalid dataset UUID or conflicting query parameters.
+        '200':
+          description: Prepared coverage catalogue.
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  track_count:
+                    type: integer
+                  filters:
+                    type: object
+                    additionalProperties:
+                      type: array
+                      items:
+                        type: object
+                        properties:
+                          value:
+                            type: string
+                          count:
+                            type: integer
+                  selections:
+                    type: array
+                    items:
+                      $ref: '#/components/schemas/TranscriptomicSelection'
+        '404':
+          description: No coverage configuration for the requested genome.
   /track_categories/{genome_id}:
     get:
       summary: Returns all track categories (and tracks) for a given genome at a specific release.
       description: >
         Returns tracks filtered by release date and browser type. 
         Automatically deduplicates tracks with overlapping specifications, 
         keeping only the most recent version of each track type.
+        Configured transcriptomic categories use the same release selection and
+        return an empty track_list.
       parameters:
         - name: genome_id
           in: path
@@ -264,6 +324,55 @@ components:
             - Variation
             - Regulation
 
+    TranscriptomicSelection:
+      type: object
+      additionalProperties: false
+      required:
+        - selection_id
+        - parent_sample_id
+        - display_label
+        - selection_level
+        - data_type
+        - metadata
+        - track_products
+      properties:
+        selection_id:
+          type: string
+        parent_sample_id:
+          type: string
+        display_label:
+          type: string
+        selection_level:
+          type: string
+          enum: [run]
+        data_type:
+          type: string
+          enum: [rnaseq]
+        metadata:
+          type: object
+          additionalProperties:
+            type: string
+        track_products:
+          type: array
+          minItems: 1
+          maxItems: 1
+          items:
+            $ref: '#/components/schemas/TranscriptomicTrackProduct'
+
+    TranscriptomicTrackProduct:
+      type: object
+      additionalProperties: false
+      required:
+        - track_type
+        - track_id
+      properties:
+        track_type:
+          type: string
+          enum: [rnaseq_coverage]
+        track_id:
+          type: string
+          format: uuid
+
     TrackList:
       type: object
       properties:

tracks/management/commands/seed_transcriptomic_configuration.py

@@ -0,0 +1,178 @@
+"""Register the coverage pilot and its prepared discovery configuration."""
+
+import json
+import re
+import uuid
+from datetime import date
+from pathlib import Path
+
+from django.core.management.base import BaseCommand, CommandError
+from django.db import transaction
+
+from tracks.models import (
+    Category,
+    DatasetRelease,
+    Specifications,
+    Track,
+    TranscriptomicConfiguration,
+)
+from tracks.transcriptomic import prepare_configuration
+
+
+class Command(BaseCommand):
+    help = "Seed run-level coverage tracks and static counts from the Genebuild JSON."
+
+    def add_arguments(self, parser):
+        parser.add_argument("--genome-id", required=True, type=uuid.UUID)
+        parser.add_argument("--records", required=True, type=Path)
+        parser.add_argument(
+            "--release", required=True, help="Release label, YYYY-MM-DD"
+        )
+        parser.add_argument(
+            "--dataset-id",
+            type=uuid.UUID,
+            help="Existing dataset for an identical retry; omit to create a new version.",
+        )
+
+    def handle(self, *args, **options):
+        try:
+            records = json.loads(options["records"].read_text(encoding="utf-8-sig"))
+            prepared = prepare_configuration(records)
+        except (OSError, ValueError) as error:
+            raise CommandError(str(error)) from error
+
+        # Validate options
+        genome_id = options["genome_id"]
+
+        release = options["release"]
+        if not re.fullmatch(r"[0-9]{4}-[0-9]{2}(?:-[0-9]{2})?", release):
+            raise CommandError("--release must use YYYY-MM or YYYY-MM-DD.")
+
+        try:
+            # Add a day only for calendar validation; preserve the release label.
+            date.fromisoformat(release if len(release) == 10 else f"{release}-01")
+        except ValueError as error:
+            raise CommandError(
+                "--release must contain a valid year, month and optional day."
+            ) from error
+
+        dataset_id = options.get("dataset_id") or uuid.uuid4()
+        for record in records:
+            supplied_uuid = record["target_genome"].get("genome_uuid")
+            if supplied_uuid and supplied_uuid != str(genome_id):
+                raise CommandError(
+                    "The supplied genome UUID conflicts with the handover."
+                )
+
+        # Seed the configuration and tracks
+        with transaction.atomic():
+            category, _ = Category.objects.get_or_create(
+                track_category_id="transcriptomic",
+                defaults={"label": "Transcriptomic data", "type": "Genomic"},
+            )
+
+            spec, _ = Specifications.objects.get_or_create(
+                name="rnaseq-coverage-genomebrowser",
+                defaults={
+                    "label": "RNA-seq coverage",
+                    "category": category,
+                    "browser": "GenomeBrowser",
+                    "type": "regular",
+                    "discovery_mode": "configured",
+                    "files": ["rnaseq_coverage"],
+                    "trigger": [],
+                    "settings": {},
+                    "on_by_default": False,
+                    "description": "Run-level RNA-seq coverage supplied by Genebuild.",
+                },
+            )
+            if (
+                spec.category_id != category.pk
+                or spec.browser != "GenomeBrowser"
+                or spec.discovery_mode != "configured"
+                or spec.files != ["rnaseq_coverage"]
+            ):
+                raise CommandError(
+                    "Existing coverage specification conflicts with this importer."
+                )
+
+            config, _ = TranscriptomicConfiguration.objects.get_or_create(
+                genome_id=genome_id,
+                dataset_id=dataset_id,
+                defaults={"specification": spec},
+            )
+            if config.specification_id != spec.pk:
+                raise CommandError(
+                    "This genome already has a different configured specification."
+                )
+
+            # The existing selector has no tie-breaker for competing versions in one release.
+            competing = DatasetRelease.objects.filter(
+                genome_id=genome_id,
+                release_label=release,
+                dataset_id__in=Track.objects.filter(
+                    genome_id=genome_id,
+                    specifications=spec,
+                ).values("dataset_id"),
+            ).exclude(dataset_id=dataset_id)
+            if competing.exists():
+                raise CommandError(
+                    "A coverage dataset already exists for this release; retry with its --dataset-id."
+                )
+
+            for record in prepared["selections"]:
+                record["track_products"][0]["track_id"] = str(
+                    uuid.uuid5(
+                        config.dataset_id, record["selection_id"] + ":rnaseq_coverage"
+                    )
+                )
+
+            if config.configuration and config.configuration != prepared:
+                raise CommandError(
+                    "Dataset content differs. Omit --dataset-id to create a new version at a new release."
+                )
+
+            created_count = 0
+            for record in records:
+                product = record["track_products"][0]
+
+                # Retained catalogue UUID gives stable track IDs across repeated seeds.
+                track_id = uuid.uuid5(
+                    config.dataset_id, record["selection_id"] + ":rnaseq_coverage"
+                )
+
+                existing_track = Track.objects.filter(track_id=track_id).first()
+                if existing_track is not None and existing_track.datafiles != {
+                    "rnaseq_coverage": product["track_file"]
+                }:
+                    raise CommandError(
+                        f"Track {track_id} already exists with a different file path. Omit --dataset-id to create a new version at a new release."
+                    )
+
+                track, created = Track.objects.update_or_create(
+                    track_id=track_id,
+                    defaults={
+                        "genome_id": genome_id,
+                        "dataset_id": config.dataset_id,
+                        "datafiles": {"rnaseq_coverage": product["track_file"]},
+                    },
+                )
+                track.specifications.add(spec)
+                created_count += int(created)
+
+            config.configuration = prepared
+            config.track_count = prepared["track_count"]
+            config.save(update_fields=["configuration", "track_count"])
+            DatasetRelease.objects.get_or_create(
+                genome_id=genome_id,
+                dataset_id=config.dataset_id,
+                release_label=release,
+            )
+
+        self.stdout.write(
+            self.style.SUCCESS(
+                f"Seeded {config.track_count} tracks for genome {genome_id} "
+                f"({created_count} created); dataset {config.dataset_id}; release {release}. "
+                "File paths are preserved; trigger/settings remain unchanged."
+            )
+        )