Initial/models schemas

.gitignore

@@ -160,3 +160,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+
+# vscode
+.vscode/

docker-compose.yaml

@@ -6,7 +6,7 @@ services:
     depends_on:
       - tds-db
     environment:
-      - DATABASE_URI=postgres://reference-db:5432
+      - DATABASE_URI=postgres://tds-db:5432
       - CORS_ORIGINS="*"
       - BENTO_AUTHZ_SERVICE_URL=""
     ports:

transcriptomics_data_service/models.py

@@ -0,0 +1,21 @@
+from pydantic import BaseModel
+
+__all__ = [
+    "ExperimentResult",
+    "GeneExpression",
+]
+
+
+class ExperimentResult(BaseModel):
+    experiment_result_id: str
+    assembly_id: str | None = None
+    assembly_name: str | None = None
+
+
+class GeneExpression(BaseModel):
+    gene_code: str
+    sample_id: str
+    experiment_result_id: str
+    raw_count: int
+    tpm_count: float | None = None
+    tmm_count: float | None = None

transcriptomics_data_service/sql/schema.sql

@@ -0,0 +1,15 @@
+CREATE TABLE IF NOT EXISTS experiment_results (
+    experiment_result_id VARCHAR(31) NOT NULL PRIMARY KEY,
+    assembly_id VARCHAR(63),
+    assembly_name VARCHAR(63)
+);
+
+CREATE TABLE IF NOT EXISTS gene_expressions (
+    gene_code VARCHAR(31) NOT NULL,
+    sample_id VARCHAR(31) NOT NULL,
+    experiment_result_id VARCHAR(31) NOT NULL REFERENCES experiment_results ON DELETE CASCADE,
+    raw_count INTEGER NOT NULL,
+    tpm_count FLOAT,
+    tmm_count FLOAT,
+    PRIMARY KEY (gene_code, sample_id, experiment_result_id)
+);