diff --git a/api/models/brassica_rapa.py b/api/models/brassica_rapa.py deleted file mode 100644 index d2c7c73..0000000 --- a/api/models/brassica_rapa.py +++ /dev/null @@ -1,12 +0,0 @@ -from api import db - - -class SampleData(db.Model): - __bind_key__ = "brassica_rapa" - __tablename__ = "sample_data" - - proj_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=False) - sample_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False) - data_probeset_id: db.Mapped[str] = db.mapped_column(db.String(16), nullable=False, primary_key=True) - data_signal: db.Mapped[float] = db.mapped_column(db.Float, primary_key=True) - data_bot_id: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False, primary_key=True) diff --git a/api/resources/rnaseq_gene_expression.py b/api/resources/rnaseq_gene_expression.py index fb15f30..79cde39 100644 --- a/api/resources/rnaseq_gene_expression.py +++ b/api/resources/rnaseq_gene_expression.py @@ -7,7 +7,6 @@ from api import db from api.models.arachis import SampleData as Arachis from api.models.cannabis import SampleData as Cannabis -from api.models.brassica_rapa import SampleData as BrassicaRapa from api.models.dna_damage import SampleData as DNADamage from api.models.embryo import SampleData as Embryo from api.models.germination import SampleData as Germination @@ -79,9 +78,6 @@ def get_data(species, database, gene_id, sample_ids=None): elif species == "arachis": if not BARUtils.is_arachis_gene_valid(gene_id): return {"success": False, "error": "Invalid gene id", "error_code": 400} - elif species == "brassica_rapa": - if not BARUtils.is_brassica_rapa_gene_valid(gene_id): - return {"success": False, "error": "Invalid gene id", "error_code": 400} elif species == "cannabis": if not BARUtils.is_cannabis_gene_valid(gene_id): return {"success": False, "error": "Invalid gene id", "error_code": 400} @@ -121,11 +117,6 @@ def get_data(species, database, gene_id, sample_ids=None): # Example: PK-PFLW sample_regex = re.compile(r"^PK-\D{1,4}|MED_CTRL$", re.I) - elif database == "brassica_rapa": - table = BrassicaRapa - # Example: E1 - sample_regex = re.compile(r"^\D{1,2}\d{0,2}|MED_CTRL$", re.I) - elif database == "dna_damage": table = DNADamage # Another insane regex! diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index 92b0571..a7f2cbf 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -13,7 +13,6 @@ SQLALCHEMY_BINDS = { 'annotations_lookup': 'mysql://root:root@localhost/annotations_lookup', 'arabidopsis_ecotypes': 'mysql://root:root@localhost/arabidopsis_ecotypes', 'arachis': 'mysql://root:root@localhost/arachis', - 'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa', 'cannabis': 'mysql://root:root@localhost/cannabis', 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', 'dna_damage': 'mysql://root:root@localhost/dna_damage', diff --git a/config/databases/brassica_rapa.sql b/config/databases/brassica_rapa.sql deleted file mode 100644 index 4effbc3..0000000 --- a/config/databases/brassica_rapa.sql +++ /dev/null @@ -1,62 +0,0 @@ --- MySQL dump 10.13 Distrib 8.4.2, for Linux (x86_64) --- --- Host: localhost Database: brassica_rapa --- ------------------------------------------------------ --- Server version 8.4.2 - -/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; -/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; -/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; -/*!50503 SET NAMES utf8mb4 */; -/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; -/*!40103 SET TIME_ZONE='+00:00' */; -/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; -/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; -/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; -/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; - --- --- Current Database: `brassica_rapa` --- - -CREATE DATABASE /*!32312 IF NOT EXISTS*/ `brassica_rapa` /*!40100 DEFAULT CHARACTER SET utf8mb4 COLLATE utf8mb4_0900_ai_ci */ /*!80016 DEFAULT ENCRYPTION='N' */; - -USE `brassica_rapa`; - --- --- Table structure for table `sample_data` --- - -DROP TABLE IF EXISTS `sample_data`; -/*!40101 SET @saved_cs_client = @@character_set_client */; -/*!50503 SET character_set_client = utf8mb4 */; -CREATE TABLE `sample_data` ( - `sample_id` int unsigned NOT NULL DEFAULT '0', - `proj_id` varchar(5) NOT NULL DEFAULT '0', - `data_probeset_id` varchar(16) NOT NULL, - `data_signal` float NOT NULL DEFAULT '0', - `data_bot_id` varchar(10) DEFAULT NULL, - KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; -/*!40101 SET character_set_client = @saved_cs_client */; - --- --- Dumping data for table `sample_data` --- - -LOCK TABLES `sample_data` WRITE; -/*!40000 ALTER TABLE `sample_data` DISABLE KEYS */; -INSERT INTO `sample_data` VALUES (1,'1','BraA01g000010',7.93926,'UO'); -/*!40000 ALTER TABLE `sample_data` ENABLE KEYS */; -UNLOCK TABLES; -/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; - -/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; -/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; -/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; -/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; -/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; -/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; -/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; - --- Dump completed on 2024-07-29 11:30:25 diff --git a/config/init.sh b/config/init.sh index dbfc82a..8da8309 100755 --- a/config/init.sh +++ b/config/init.sh @@ -12,7 +12,6 @@ echo "Welcome to the BAR API. Running init!" mysql -u $DB_USER -p$DB_PASS < ./config/databases/annotations_lookup.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql -mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql diff --git a/tests/resources/test_rnaseq_gene_expression.py b/tests/resources/test_rnaseq_gene_expression.py index 4730866..cde2c88 100644 --- a/tests/resources/test_rnaseq_gene_expression.py +++ b/tests/resources/test_rnaseq_gene_expression.py @@ -187,17 +187,6 @@ def test_get_rna_expression_data(self): expected = {"wasSuccessful": False, "error": "Invalid gene id"} self.assertEqual(response.json, expected) - # Brassica rapa - # Valid data - response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/brassica_rapa/BraA01g000010/UO") - expected = {"wasSuccessful": True, "data": {"UO": 7.93926}} - self.assertEqual(response.json, expected) - - # Invalid gene id - response = self.app_client.get("/rnaseq_gene_expression/brassica_rapa/abc/UO") - expected = {"wasSuccessful": False, "error": "Invalid gene id"} - self.assertEqual(response.json, expected) - # Cannabis # Valid data response = self.app_client.get("/rnaseq_gene_expression/cannabis/cannabis/AGQN03009284/PK-RT")