diff --git a/api/models/arabidopsis_NIE_umap.py b/api/models/arabidopsis_NIE_umap.py deleted file mode 100644 index d73edfa..0000000 --- a/api/models/arabidopsis_NIE_umap.py +++ /dev/null @@ -1,19 +0,0 @@ -from api import db - - -class UmapCoords(db.Model): - __bind_key__ = "arabidopsis_NIE_umap" - __tablename__ = "umap_coords" - - cell_id: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True) - umap_1: db.Mapped[float] = db.mapped_column(db.Float, nullable=False) - umap_2: db.Mapped[float] = db.mapped_column(db.Float, nullable=False) - cell_type: db.Mapped[str] = db.mapped_column(db.String(128), nullable=False) - - -class UmapExpression(db.Model): - __bind_key__ = "arabidopsis_NIE_umap" - __tablename__ = "umap_expression" - - gene_id: db.Mapped[str] = db.mapped_column(db.String(32), nullable=False, primary_key=True) - expression: db.Mapped[dict] = db.mapped_column(db.JSON, nullable=False) diff --git a/api/models/umap_dynamic.py b/api/models/umap_dynamic.py new file mode 100644 index 0000000..9073389 --- /dev/null +++ b/api/models/umap_dynamic.py @@ -0,0 +1,59 @@ +"""Every SUPeR Viewer UMAP database exposes the same umap_coords and umap_expression +tables, so instead of hand-writing a model file per database we generate them here.""" + +from api import db + +# Every UMAP database and the species its gene ids belong to. UMAP databases have no +# catalog entry, so the species that selects the gene id pattern is declared here. +UMAP_DATABASES = { + "arabidopsis_NIE_umap": "arabidopsis", + "arabidopsis_flower_lee_umap": "arabidopsis", + "arabidopsis_root_shahan_umap": "arabidopsis", + "arabidopsis_rosette_21d_lee_umap": "arabidopsis", + "arabidopsis_rosette_30d_lee_umap": "arabidopsis", + "arabidopsis_seed_0d_lee_umap": "arabidopsis", + "arabidopsis_seed_martin_umap": "arabidopsis", + "arabidopsis_seedling_12d_lee_umap": "arabidopsis", + "arabidopsis_seedling_3d_lee_umap": "arabidopsis", + "arabidopsis_seedling_6d_lee_umap": "arabidopsis", + "arabidopsis_shoot_zhang_umap": "arabidopsis", + "arabidopsis_silique_lee_umap": "arabidopsis", + "arabidopsis_stem_lee_umap": "arabidopsis", + "rice_OW_umap": "rice", +} + + +def _class_prefix(database): + return "".join(part.capitalize() for part in database.split("_")) + + +def _umap_coords_model(database): + return type( + _class_prefix(database) + "UmapCoords", + (db.Model,), + { + "__bind_key__": database, + "__tablename__": "umap_coords", + "cell_id": db.mapped_column(db.Integer, nullable=False, primary_key=True), + "umap_1": db.mapped_column(db.Float, nullable=False), + "umap_2": db.mapped_column(db.Float, nullable=False), + "cell_type": db.mapped_column(db.String(128), nullable=False), + }, + ) + + +def _umap_expression_model(database): + return type( + _class_prefix(database) + "UmapExpression", + (db.Model,), + { + "__bind_key__": database, + "__tablename__": "umap_expression", + "gene_id": db.mapped_column(db.String(32), nullable=False, primary_key=True), + "expression": db.mapped_column(db.JSON, nullable=False), + }, + ) + + +UMAP_COORDS_MODELS = {database: _umap_coords_model(database) for database in UMAP_DATABASES} +UMAP_EXPRESSION_MODELS = {database: _umap_expression_model(database) for database in UMAP_DATABASES} diff --git a/api/resources/umap_gene_expression.py b/api/resources/umap_gene_expression.py index 683d136..4a6c8ee 100644 --- a/api/resources/umap_gene_expression.py +++ b/api/resources/umap_gene_expression.py @@ -1,8 +1,7 @@ from flask_restx import Namespace, Resource from markupsafe import escape from api import db -from api.models.arabidopsis_NIE_umap import UmapCoords as ArabidopsisNIEUmapCoords -from api.models.arabidopsis_NIE_umap import UmapExpression as ArabidopsisNIEUmapExpression +from api.models.umap_dynamic import UMAP_COORDS_MODELS, UMAP_DATABASES, UMAP_EXPRESSION_MODELS from api.utils.bar_utils import BARUtils, load_combined_master umap_gene_expression = Namespace( @@ -20,14 +19,14 @@ def get_tables(database): :return: dict with the coordinates table, expression table and species """ # Set database - if database == "arabidopsis_NIE_umap": - coords_table = ArabidopsisNIEUmapCoords - expression_table = ArabidopsisNIEUmapExpression - species = "arabidopsis" - - else: + database = str(database) + if database not in UMAP_DATABASES: return {"success": False, "error": "Invalid database", "error_code": 400} + coords_table = UMAP_COORDS_MODELS[database] + expression_table = UMAP_EXPRESSION_MODELS[database] + species = UMAP_DATABASES[database] + return {"success": True, "coords_table": coords_table, "expression_table": expression_table, "species": species} diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index debbc6a..631fb2c 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -12,8 +12,32 @@ SQLALCHEMY_TRACK_MODIFICATIONS = False SQLALCHEMY_BINDS = { 'annotations_lookup': 'mysql://root:root@localhost/annotations_lookup', 'arabidopsis_ecotypes': 'mysql://root:root@localhost/arabidopsis_ecotypes', + 'arabidopsis_flower_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_flower_lee_pseudobulk', + 'arabidopsis_flower_lee_umap': 'mysql://root:root@localhost/arabidopsis_flower_lee_umap', 'arabidopsis_NIE_pseudobulk': 'mysql://root:root@localhost/arabidopsis_NIE_pseudobulk', 'arabidopsis_NIE_umap': 'mysql://root:root@localhost/arabidopsis_NIE_umap', + 'arabidopsis_root_shahan_pseudobulk': 'mysql://root:root@localhost/arabidopsis_root_shahan_pseudobulk', + 'arabidopsis_root_shahan_umap': 'mysql://root:root@localhost/arabidopsis_root_shahan_umap', + 'arabidopsis_rosette_21d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_rosette_21d_lee_pseudobulk', + 'arabidopsis_rosette_21d_lee_umap': 'mysql://root:root@localhost/arabidopsis_rosette_21d_lee_umap', + 'arabidopsis_rosette_30d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_rosette_30d_lee_pseudobulk', + 'arabidopsis_rosette_30d_lee_umap': 'mysql://root:root@localhost/arabidopsis_rosette_30d_lee_umap', + 'arabidopsis_seed_0d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seed_0d_lee_pseudobulk', + 'arabidopsis_seed_0d_lee_umap': 'mysql://root:root@localhost/arabidopsis_seed_0d_lee_umap', + 'arabidopsis_seed_martin_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seed_martin_pseudobulk', + 'arabidopsis_seed_martin_umap': 'mysql://root:root@localhost/arabidopsis_seed_martin_umap', + 'arabidopsis_seedling_12d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seedling_12d_lee_pseudobulk', + 'arabidopsis_seedling_12d_lee_umap': 'mysql://root:root@localhost/arabidopsis_seedling_12d_lee_umap', + 'arabidopsis_seedling_3d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seedling_3d_lee_pseudobulk', + 'arabidopsis_seedling_3d_lee_umap': 'mysql://root:root@localhost/arabidopsis_seedling_3d_lee_umap', + 'arabidopsis_seedling_6d_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_seedling_6d_lee_pseudobulk', + 'arabidopsis_seedling_6d_lee_umap': 'mysql://root:root@localhost/arabidopsis_seedling_6d_lee_umap', + 'arabidopsis_shoot_zhang_pseudobulk': 'mysql://root:root@localhost/arabidopsis_shoot_zhang_pseudobulk', + 'arabidopsis_shoot_zhang_umap': 'mysql://root:root@localhost/arabidopsis_shoot_zhang_umap', + 'arabidopsis_silique_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_silique_lee_pseudobulk', + 'arabidopsis_silique_lee_umap': 'mysql://root:root@localhost/arabidopsis_silique_lee_umap', + 'arabidopsis_stem_lee_pseudobulk': 'mysql://root:root@localhost/arabidopsis_stem_lee_pseudobulk', + 'arabidopsis_stem_lee_umap': 'mysql://root:root@localhost/arabidopsis_stem_lee_umap', 'arachis': 'mysql://root:root@localhost/arachis', 'cannabis': 'mysql://root:root@localhost/cannabis', 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', @@ -35,6 +59,8 @@ SQLALCHEMY_BINDS = { 'physcomitrella_db' : 'mysql://root:root@localhost/physcomitrella_db', 'poplar_nssnp' : 'mysql://root:root@localhost/poplar_nssnp', 'rice_interactions': 'mysql://root:root@localhost/rice_interactions', + 'rice_OW_pseudobulk': 'mysql://root:root@localhost/rice_OW_pseudobulk', + 'rice_OW_umap': 'mysql://root:root@localhost/rice_OW_umap', 'selaginella': 'mysql://root:root@localhost/selaginella', 'shoot_apex': 'mysql://root:root@localhost/shoot_apex', 'silique': 'mysql://root:root@localhost/silique', diff --git a/config/databases/arabidopsis_flower_lee_pseudobulk_dump.sql b/config/databases/arabidopsis_flower_lee_pseudobulk_dump.sql new file mode 100644 index 0000000..99ee154 --- /dev/null +++ b/config/databases/arabidopsis_flower_lee_pseudobulk_dump.sql @@ -0,0 +1,59 @@ +-- MySQL dump 10.13 Distrib 9.4.0, for Linux (x86_64) +-- +-- Host: localhost Database: arabidopsis_flower_lee_pseudobulk +-- ------------------------------------------------------ +-- Server version 9.4.0 + +/*!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: `arabidopsis_flower_lee_pseudobulk` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_flower_lee_pseudobulk` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_flower_lee_pseudobulk`; + +-- +-- 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` ( + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_signal_std` float DEFAULT '0', + `data_bot_id` varchar(64) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!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 ('AT1G01010',0.00849616,0.149845,'Unknown'),('AT1G01010',0.00382709,0.0747515,'Tapetum'),('AT1G01010',0.00555427,0.11437,'Gynoecium and developing ovule'),('AT1G01010',0.0165317,0.193183,'Anther'),('AT1G01010',0.0168979,0.204127,'Epidermal'),('AT1G01010',0.0129372,0.163582,'Male meiocyte'),('AT1G01010',0.00575536,0.116394,'Pollen'),('AT1G01010',0.0666808,0.380699,'Vascular'),('AT1G01010',0,0,'Developing ovule'),('AT1G01010',0.0116959,0.167702,'Mean_CTRL'),('AT1G01020',0.0269661,0.272391,'Unknown'),('AT1G01020',0.0461319,0.33191,'Tapetum'),('AT1G01020',0.0293728,0.20296,'Gynoecium and developing ovule'),('AT1G01020',0.0247412,0.224438,'Anther'),('AT1G01020',0.00594706,0.115624,'Epidermal'),('AT1G01020',0.0889595,0.422899,'Male 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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 2026-07-30 00:24:07 diff --git a/config/databases/arabidopsis_flower_lee_umap.sql b/config/databases/arabidopsis_flower_lee_umap.sql new file mode 100644 index 0000000..63a680d --- /dev/null +++ b/config/databases/arabidopsis_flower_lee_umap.sql @@ -0,0 +1,83 @@ +-- MySQL dump 10.13 Distrib 9.4.0, for Linux (x86_64) +-- +-- Host: localhost Database: arabidopsis_flower_lee_umap +-- ------------------------------------------------------ +-- Server version 9.4.0 + +/*!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: `arabidopsis_flower_lee_umap` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_flower_lee_umap` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_flower_lee_umap`; + +-- +-- Table structure for table `umap_coords` +-- + +DROP TABLE IF EXISTS `umap_coords`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_coords` ( + `cell_id` INT NOT NULL, + `umap_1` FLOAT NOT NULL, + `umap_2` FLOAT NOT NULL, + `cell_type` VARCHAR(128) NOT NULL, + PRIMARY KEY (`cell_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; 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data for table `umap_expression` +-- + +LOCK TABLES `umap_expression` WRITE; +/*!40000 ALTER TABLE `umap_expression` DISABLE KEYS */; +INSERT INTO `umap_expression` VALUES ('AT1G01010','{\"157\": 2.640544, \"685\": 2.787718, \"817\": 2.576473}'),('AT1G01020','{\"71\": 1.386144, \"329\": 2.122614, \"359\": 3.014546}'),('AT1G01030','{\"4\": 2.117453, \"45\": 3.218108}'); +/*!40000 ALTER TABLE `umap_expression` 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 2026-07-30 01:27:00 diff --git a/config/databases/arabidopsis_root_shahan_pseudobulk_dump.sql b/config/databases/arabidopsis_root_shahan_pseudobulk_dump.sql new file mode 100644 index 0000000..18f6687 --- /dev/null +++ b/config/databases/arabidopsis_root_shahan_pseudobulk_dump.sql @@ -0,0 +1,59 @@ +-- MySQL dump 10.13 Distrib 9.4.0, for Linux (x86_64) +-- +-- Host: localhost Database: arabidopsis_root_shahan_pseudobulk +-- ------------------------------------------------------ +-- Server version 9.4.0 + +/*!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: `arabidopsis_root_shahan_pseudobulk` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_root_shahan_pseudobulk` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `arabidopsis_root_shahan_pseudobulk`; + +-- +-- 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` ( + `data_probeset_id` varchar(16) NOT NULL, + `data_signal` float DEFAULT '0', + `data_signal_std` float DEFAULT '0', + `data_bot_id` varchar(64) NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!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 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*/; + +-- +-- Dumping data for table `umap_coords` +-- + +LOCK TABLES `umap_coords` WRITE; +/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */; +INSERT INTO `umap_coords` VALUES (3,-5.369063,13.085638,'col0_Root endodermis'),(16,-2.009994,7.254005,'col0_Phloem'),(36,-0.523138,2.255024,'col0_Phloem pole pericycle'),(44,-0.023207,2.463476,'col0_Phloem pole pericycle'),(62,6.431638,11.482953,'col0_Metaxylem'),(82,-4.284084,-11.077536,'col0_Root hair'),(89,5.733176,3.742696,'col0_Lateral root cap'),(159,-0.406075,15.254973,'col0_Root endodermis'); +/*!40000 ALTER TABLE `umap_coords` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `umap_expression` +-- + +DROP TABLE IF EXISTS `umap_expression`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_expression` ( + `gene_id` VARCHAR(32) NOT NULL, + `expression` JSON NOT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; 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NOT NULL, + `umap_2` FLOAT NOT NULL, + `cell_type` VARCHAR(128) NOT NULL, + PRIMARY KEY (`cell_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_coords` +-- + +LOCK TABLES `umap_coords` WRITE; +/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */; +INSERT INTO `umap_coords` VALUES (18,-0.423832,-0.107109,'Stele'),(19,-0.810030,2.770356,'Stele'),(31,1.540967,-4.477988,'Guard'),(56,3.173458,-0.707526,'Stele'),(71,6.609934,-0.060135,'Epidermal'),(84,0.063264,-6.048057,'Guard'),(169,-5.134893,-5.174132,'Guard'),(443,6.784662,-4.711861,'Guard'); +/*!40000 ALTER TABLE `umap_coords` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `umap_expression` +-- + +DROP TABLE IF EXISTS `umap_expression`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_expression` ( + `gene_id` VARCHAR(32) NOT NULL, + `expression` JSON NOT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_expression` +-- + +LOCK TABLES `umap_expression` WRITE; +/*!40000 ALTER TABLE `umap_expression` DISABLE KEYS */; +INSERT INTO `umap_expression` VALUES ('AT1G01010','{\"71\": 1.098612, \"169\": 0.693147, \"443\": 0.693147}'),('AT1G01020','{\"18\": 0.693147, \"31\": 0.693147, \"56\": 1.098612}'),('AT1G01030','{\"19\": 0.693147, \"31\": 0.693147, \"84\": 0.693147}'); +/*!40000 ALTER TABLE `umap_expression` 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 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(`data_probeset_id`,`data_bot_id`), + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!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 ('AT1G01010',0.00325586,0.0479114,'Epidermal'),('AT1G01010',0.00541272,0.06101,'Stele'),('AT1G01010',0.00597775,0.0640906,'Meristematic'),('AT1G01010',0.00476521,0.0575352,'Unannotated'),('AT1G01010',0.00237031,0.0404645,'Mesophyll'),('AT1G01010',0.00132533,0.0302802,'Guard'),('AT1G01010',0.00445705,0.0556244,'Mean_CTRL'),('AT1G01020',0.0292335,0.14248,'Epidermal'),('AT1G01020',0.0279543,0.139355,'Stele'),('AT1G01020',0.0333544,0.150104,'Meristematic'),('AT1G01020',0.0232038,0.127067,'Unannotated'),('AT1G01020',0.0189625,0.113069,'Mesophyll'),('AT1G01020',0.0331332,0.147879,'Guard'),('AT1G01020',0.0263362,0.135038,'Mean_CTRL'),('AT1G01030',0.013915,0.101089,'Epidermal'),('AT1G01030',0.0150714,0.106465,'Stele'),('AT1G01030',0.0143343,0.103106,'Meristematic'),('AT1G01030',0.0211872,0.126206,'Unannotated'),('AT1G01030',0.0110338,0.088,'Mesophyll'),('AT1G01030',0.0303829,0.165249,'Guard'),('AT1G01030',0.017151,0.113482,'Mean_CTRL'); +/*!40000 ALTER TABLE `sample_data` ENABLE KEYS */; 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utf8mb4 */; +CREATE TABLE `umap_expression` ( + `gene_id` VARCHAR(32) NOT NULL, + `expression` JSON NOT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_expression` +-- + +LOCK TABLES `umap_expression` WRITE; +/*!40000 ALTER TABLE `umap_expression` DISABLE KEYS */; +INSERT INTO `umap_expression` VALUES ('AT1G01010','{\"63\": 0.693147, \"92\": 1.098612, \"112\": 0.693147}'),('AT1G01020','{\"1\": 0.693147, \"166\": 0.693147, \"354\": 0.693147}'),('AT1G01030','{\"32\": 0.693147, \"381\": 0.693147}'); +/*!40000 ALTER TABLE `umap_expression` 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 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NOT NULL, + PRIMARY KEY (`cell_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_coords` +-- + +LOCK TABLES `umap_coords` WRITE; +/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */; +INSERT INTO `umap_coords` VALUES (1,-1.624959,-3.549993,'Stele'),(14,-3.982634,-0.261779,'Epidermal'),(19,3.092637,-4.230665,'Meristematic'),(50,-7.398050,-0.084165,'Meristematic'),(106,-2.365161,0.405073,'Stele'),(118,-3.922566,4.035084,'Epidermal'),(119,1.429272,0.170757,'Epidermal'),(269,-3.150418,1.525333,'Epidermal'); +/*!40000 ALTER TABLE `umap_coords` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `umap_expression` +-- + +DROP TABLE IF EXISTS `umap_expression`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_expression` ( + `gene_id` VARCHAR(32) NOT NULL, + `expression` JSON NOT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_expression` +-- + +LOCK TABLES `umap_expression` WRITE; +/*!40000 ALTER TABLE `umap_expression` DISABLE KEYS */; +INSERT INTO `umap_expression` VALUES ('AT1G01010','{\"106\": 1.420628, \"118\": 1.558638, \"269\": 2.512673}'),('AT1G01020','{\"1\": 1.292535, \"50\": 0.895021, \"119\": 2.362304}'),('AT1G01030','{\"14\": 2.626154, \"19\": 2.423746}'); +/*!40000 ALTER TABLE `umap_expression` 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 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(`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!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 ('AT1G01010',0.0118031,0.117995,'Proliferating cell'),('AT1G01010',0.00625838,0.0816509,'Unknown'),('AT1G01010',0.00710315,0.0839763,'Shoot system epidermis'),('AT1G01010',0.0307755,0.237696,'Shoot system vascular system'),('AT1G01010',0.00195312,0.044151,'Shoot system endodermis'),('AT1G01010',0.0153229,0.162467,'Mesophyll cell'),('AT1G01010',0.00417537,0.0644818,'Leaf guard cell'),('AT1G01010',0.0108696,0.116056,'Companion cell'),('AT1G01010',0.00943396,0.0966693,'Shoot apical meristem'),('AT1G01010',0.011989,0.13384,'Mean_CTRL'),('AT1G01020',0.0889001,0.315935,'Proliferating cell'),('AT1G01020',0.0449262,0.225724,'Unknown'),('AT1G01020',0.0600679,0.253937,'Shoot 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NOT NULL, + KEY `data_probeset_id` (`data_probeset_id`,`data_bot_id`,`data_signal`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!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 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SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_coords` ( + `cell_id` INT NOT NULL, + `umap_1` FLOAT NOT NULL, + `umap_2` FLOAT NOT NULL, + `cell_type` VARCHAR(128) NOT NULL, + PRIMARY KEY (`cell_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_coords` +-- + +LOCK TABLES `umap_coords` WRITE; +/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */; +INSERT INTO `umap_coords` VALUES (100,-7.012577,2.260986,'Xylem'),(144,-9.243169,-1.838689,'Cambium'),(162,-7.496518,2.218189,'Xylem'),(522,-7.903540,-2.617334,'Cambium'),(598,-4.392389,2.060507,'Epidermal'),(814,-7.459464,0.766465,'Cambium'),(9526,-6.040127,-1.044228,'Cambium'),(9544,0.872937,-2.713217,'Guard'); +/*!40000 ALTER TABLE `umap_coords` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `umap_expression` +-- + +DROP TABLE IF EXISTS `umap_expression`; +/*!40101 SET @saved_cs_client = @@character_set_client */; 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ht_Fibre'),('Os01g0100400',0.0211561,0.192842,'Mild.Salinity_Epidermis'),('Os01g0100400',0.0194,0.19279,'Mild.Salinity_Large.Parenchyma'),('Os01g0100400',0.0353049,0.255794,'Mild.Salinity_Mesophyll'),('Os01g0100400',0.0348313,0.264582,'Mild.Salinity_Mesophyll.Precursor'),('Os01g0100400',0.0238516,0.205391,'Mild.Salinity_Epidermal.Precursor'),('Os01g0100400',0.030989,0.25445,'Mild.Salinity_Fibre'),('Os01g0100400',0.0678461,0.336451,'Mild.Salinity_Meristem'),('Os01g0100400',0.0474255,0.303938,'Mild.Salinity_Procambium'),('Os01g0100400',0.0399301,0.315842,'Mild.Salinity_Xylem.Parenchyma'),('Os01g0100400',0.0871675,0.393361,'Mild.Salinity_Bundle.Sheath'),('Os01g0100400',0.139002,0.515538,'Mild.Salinity_Phloem.CC'),('Os01g0100400',0.0960242,0.422965,'Mild.Salinity_Phloem.SE'),('Os01g0100400',0.0205265,0.191488,'Mild.Salinity_Xylem'),('Os01g0100400',0.0214002,0.192602,'Mild.Salinity_Mestome.Sheath'),('Os01g0100400',0.0664962,0.335898,'Moderate.Drought_Meristem'),('Os01g0100400',0.0273033,0.220303,'Moderate.Drought_Mesophyll'),('Os01g0100400',0.0222782,0.203386,'Moderate.Drought_Epidermal.Precursor'),('Os01g0100400',0.0259845,0.228898,'Moderate.Drought_Mesophyll.Precursor'),('Os01g0100400',0.0186042,0.185566,'Moderate.Drought_Large.Parenchyma'),('Os01g0100400',0.0147004,0.170015,'Moderate.Drought_Fibre'),('Os01g0100400',0.0468147,0.292589,'Moderate.Drought_Procambium'),('Os01g0100400',0.0221867,0.200224,'Moderate.Drought_Epidermis'),('Os01g0100400',0.0524078,0.309226,'Moderate.Drought_Bundle.Sheath'),('Os01g0100400',0.125287,0.466678,'Moderate.Drought_Phloem.SE'),('Os01g0100400',0.030251,0.210608,'Moderate.Drought_Xylem'),('Os01g0100400',0.0601601,0.327276,'Moderate.Drought_Phloem.CC'),('Os01g0100400',0.0201403,0.200191,'Moderate.Drought_Xylem.Parenchyma'),('Os01g0100400',0.0628024,0.354985,'Moderate.Drought_Mestome.Sheath'),('Os01g0100400',0.0354411,0.260916,'Moderate.Salinity_Mesophyll.Precursor'),('Os01g0100400',0.0549155,0.317356,'Moderate.Salinity_Procambium'),('Os01g0100400',0.0312315,0.241889,'Moderate.Salinity_Large.Parenchyma'),('Os01g0100400',0.0241878,0.214254,'Moderate.Salinity_Epidermis'),('Os01g0100400',0.0376156,0.256783,'Moderate.Salinity_Mesophyll'),('Os01g0100400',0.0740645,0.348506,'Moderate.Salinity_Meristem'),('Os01g0100400',0.033431,0.244942,'Moderate.Salinity_Epidermal.Precursor'),('Os01g0100400',0.0323639,0.234487,'Moderate.Salinity_Xylem'),('Os01g0100400',0.115759,0.453403,'Moderate.Salinity_Bundle.Sheath'),('Os01g0100400',0.138389,0.465301,'Moderate.Salinity_Phloem.SE'),('Os01g0100400',0.079379,0.385696,'Moderate.Salinity_Phloem.CC'),('Os01g0100400',0.0175796,0.171397,'Moderate.Salinity_Fibre'),('Os01g0100400',0.0438501,0.265154,'Moderate.Salinity_Mestome.Sheath'),('Os01g0100400',0.0144441,0.158227,'Moderate.Salinity_Xylem.Parenchyma'),('Os01g0100400',0.0302499,0.236497,'Well.Watered_Epidermal.Precursor'),('Os01g0100400',0.0505523,0.314985,'Well.Watered_Procambium'),('Os01g0100400',0.0391295,0.287743,'Well.Watered_Mesophyll.Precursor'),('Os01g0100400',0.0423554,0.275996,'Well.Watered_Large.Parenchyma'),('Os01g0100400',0.0260048,0.225352,'Well.Watered_Epidermis'),('Os01g0100400',0.0710863,0.377935,'Well.Watered_Fibre'),('Os01g0100400',0.0441145,0.290909,'Well.Watered_Mesophyll'),('Os01g0100400',0.0771836,0.364403,'Well.Watered_Meristem'),('Os01g0100400',0.128817,0.477777,'Well.Watered_Phloem.SE'),('Os01g0100400',0.093579,0.432103,'Well.Watered_Phloem.CC'),('Os01g0100400',0.0731546,0.363258,'Well.Watered_Bundle.Sheath'),('Os01g0100400',0.0455864,0.296806,'Well.Watered_Xylem'),('Os01g0100400',0.0479942,0.323023,'Well.Watered_Xylem.Parenchyma'),('Os01g0100400',0.0387572,0.291312,'Well.Watered_Mestome.Sheath'),('Os01g0100400',0.0413686,0.279097,'Mean_CTRL'); 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+/*!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: `rice_OW_umap` +-- + +CREATE DATABASE /*!32312 IF NOT EXISTS*/ `rice_OW_umap` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */; + +USE `rice_OW_umap`; + +-- +-- Table structure for table `umap_coords` +-- + +DROP TABLE IF EXISTS `umap_coords`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_coords` ( + `cell_id` INT NOT NULL, + `umap_1` FLOAT NOT NULL, + `umap_2` FLOAT NOT NULL, + `cell_type` VARCHAR(128) NOT NULL, + PRIMARY KEY (`cell_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_coords` +-- + +LOCK TABLES `umap_coords` WRITE; +/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */; +INSERT INTO `umap_coords` VALUES (28,4.169194,-0.093138,'Mild.Drought_Mestome.Sheath'),(36,1.489732,-4.531291,'Mild.Drought_Phloem.SE'),(38,5.240719,5.009850,'Mild.Drought_Large.Parenchyma'),(40,-1.985161,7.215361,'Mild.Drought_Mesophyll'),(82,3.058005,-1.310818,'Mild.Drought_Bundle.Sheath'),(123,5.759590,1.726379,'Mild.Drought_Phloem.CC'),(180,1.011132,-2.744384,'Mild.Drought_Phloem.SE'),(279,3.111691,-1.251301,'Mild.Drought_Bundle.Sheath'); +/*!40000 ALTER TABLE `umap_coords` ENABLE KEYS */; +UNLOCK TABLES; + +-- +-- Table structure for table `umap_expression` +-- + +DROP TABLE IF EXISTS `umap_expression`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `umap_expression` ( + `gene_id` VARCHAR(32) NOT NULL, + `expression` JSON NOT NULL, + PRIMARY KEY (`gene_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `umap_expression` +-- + +LOCK TABLES `umap_expression` WRITE; +/*!40000 ALTER TABLE `umap_expression` DISABLE KEYS */; +INSERT INTO `umap_expression` VALUES ('Os01g0100100','{\"36\": 1.978312, \"38\": 2.48399, \"40\": 2.624965}'),('Os01g0100200','{\"82\": 1.976703, \"180\": 1.763575, \"279\": 1.730714}'),('Os01g0100400','{\"28\": 1.847175, \"123\": 1.959751}'); +/*!40000 ALTER TABLE `umap_expression` 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 2026-08-12 01:41:39 diff --git a/config/init.sh b/config/init.sh index 1e92e5c..5ebc661 100755 --- a/config/init.sh +++ b/config/init.sh @@ -11,8 +11,32 @@ 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/arabidopsis_flower_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_flower_lee_umap.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_NIE_pseudobulk_dump.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_NIE_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_root_shahan_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_root_shahan_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_rosette_21d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_rosette_21d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_rosette_30d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_rosette_30d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_0d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_0d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_martin_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seed_martin_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_12d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_12d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_3d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_3d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_6d_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_seedling_6d_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_shoot_zhang_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_shoot_zhang_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_silique_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_silique_lee_umap.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_stem_lee_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_stem_lee_umap.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql @@ -34,6 +58,8 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/phelipanche.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/physcomitrella_db.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/poplar_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/rice_interactions.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/rice_OW_pseudobulk_dump.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/rice_OW_umap.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/selaginella.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/shoot_apex.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/silique.sql diff --git a/data/efp_info/combined_master.json b/data/efp_info/combined_master.json index e8b1530..be7361a 100644 --- a/data/efp_info/combined_master.json +++ b/data/efp_info/combined_master.json @@ -708,7 +708,7 @@ } }, "pseudobulk_std": { - "assigned_databases": 1, + "assigned_databases": 14, "tables": { "sample_data": { "columns": { @@ -1609,6 +1609,258 @@ "schema_source": "prod_information_schema", "status": "active" }, + "arabidopsis_flower_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_root_shahan_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_rosette_21d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_rosette_30d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_seed_0d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_seed_martin_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_seedling_12d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_seedling_3d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_seedling_6d_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_shoot_zhang_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_silique_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, + "arabidopsis_stem_lee_pseudobulk": { + "species": "arabidopsis", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "arabidopsis", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, "arachis": { "species": "arachis", "source": "efp", @@ -30252,6 +30504,27 @@ "schema_source": "prod_information_schema", "status": "inactive" }, + "rice_OW_pseudobulk": { + "species": "rice", + "source": "super_viewer", + "platform": "rna_seq", + "schema_variant": "pseudobulk_std", + "schema_verified": true, + "value_semantics": { + "quantity": null, + "unit": null, + "scale": null + }, + "identifier_type": "gene_model", + "gene_id_pattern": "rice", + "used_by": [], + "views": {}, + "tables_present": [ + "sample_data" + ], + "schema_source": "prod_information_schema", + "status": "active" + }, "rice_abiotic_stress_sc_pseudobulk": { "species": "rice", "source": "efp", diff --git a/tests/resources/test_gene_expression.py b/tests/resources/test_gene_expression.py index 0b0e164..ed59da2 100644 --- a/tests/resources/test_gene_expression.py +++ b/tests/resources/test_gene_expression.py @@ -62,7 +62,25 @@ def setUp(self): def test_only_the_pseudobulk_model_maps_data_signal_std(self): """The variant-aware model generator has to stay a no-op for every other database.""" with_std = {name for name, model in SAMPLE_DATA_MODELS.items() if hasattr(model, "data_signal_std")} - self.assertEqual(with_std, {"arabidopsis_NIE_pseudobulk"}) + self.assertEqual( + with_std, + { + "arabidopsis_NIE_pseudobulk", + "arabidopsis_flower_lee_pseudobulk", + "arabidopsis_root_shahan_pseudobulk", + "arabidopsis_rosette_21d_lee_pseudobulk", + "arabidopsis_rosette_30d_lee_pseudobulk", + "arabidopsis_seed_0d_lee_pseudobulk", + "arabidopsis_seed_martin_pseudobulk", + "arabidopsis_seedling_12d_lee_pseudobulk", + "arabidopsis_seedling_3d_lee_pseudobulk", + "arabidopsis_seedling_6d_lee_pseudobulk", + "arabidopsis_shoot_zhang_pseudobulk", + "arabidopsis_silique_lee_pseudobulk", + "arabidopsis_stem_lee_pseudobulk", + "rice_OW_pseudobulk", + }, + ) def test_pseudobulk_rows_carry_value_std(self): response = self.client.get("/gene_expression/expression/arabidopsis_NIE_pseudobulk/AT1G01010") diff --git a/tests/resources/test_superviewer_databases.py b/tests/resources/test_superviewer_databases.py new file mode 100644 index 0000000..d34710e --- /dev/null +++ b/tests/resources/test_superviewer_databases.py @@ -0,0 +1,297 @@ +from api import app +from unittest import TestCase + + +# Each database, its rows per gene, and each fixture gene's stored Mean_CTRL row as the +# endpoint renders it. Several databases share a rows per gene, so the Mean_CTRL values +# are what catch a bind pointing at the wrong database. +PSEUDOBULK_DATABASES = [ + ( + "arabidopsis_flower_lee_pseudobulk", + 10, + { + "AT1G01010": ("0.0116959", "0.167702"), + "AT1G01020": ("0.03165", "0.277587"), + "AT1G01030": ("0.0373011", "0.306399"), + }, + ), + ( + "arabidopsis_root_shahan_pseudobulk", + 100, + { + "AT1G01010": ("0.157898", "0.422084"), + "AT1G01020": ("0.0793918", "0.261753"), + "AT1G01030": ("0.010148", "0.0959647"), + }, + ), + ( + "arabidopsis_rosette_21d_lee_pseudobulk", + 6, + { + "AT1G01010": ("0.00284308", "0.0456808"), + "AT1G01020": ("0.0439676", "0.175693"), + "AT1G01030": ("0.0212323", "0.126861"), + }, + ), + ( + "arabidopsis_rosette_30d_lee_pseudobulk", + 7, + { + "AT1G01010": ("0.00445705", "0.0556244"), + "AT1G01020": ("0.0263362", "0.135038"), + "AT1G01030": ("0.017151", "0.113482"), + }, + ), + ( + "arabidopsis_seed_0d_lee_pseudobulk", + 7, + { + "AT1G01010": ("0.00980994", "0.0833147"), + "AT1G01020": ("0.031434", "0.148299"), + "AT1G01030": ("0.0182901", "0.115757"), + }, + ), + ( + "arabidopsis_seed_martin_pseudobulk", + 35, + { + "AT1G01010": ("0.0171608", "0.176218"), + "AT1G01020": ("0.0557825", "0.343745"), + "AT1G01030": ("0.00160503", "0.0590966"), + }, + ), + ( + "arabidopsis_seedling_12d_lee_pseudobulk", + 6, + { + "AT1G01010": ("0.0295017", "0.263786"), + "AT1G01020": ("0.0487004", "0.339183"), + "AT1G01030": ("0.0595717", "0.380804"), + }, + ), + ( + "arabidopsis_seedling_3d_lee_pseudobulk", + 9, + { + "AT1G01010": ("0.00687618", "0.0697902"), + "AT1G01020": ("0.0117318", "0.0909308"), + "AT1G01030": ("0.00505709", "0.0598023"), + }, + ), + ( + "arabidopsis_seedling_6d_lee_pseudobulk", + 6, + { + "AT1G01010": ("0.0379364", "0.27957"), + "AT1G01020": ("0.0864976", "0.41424"), + "AT1G01030": ("0.0899645", "0.426446"), + }, + ), + ( + "arabidopsis_shoot_zhang_pseudobulk", + 10, + { + "AT1G01010": ("0.011989", "0.13384"), + "AT1G01020": ("0.0622745", "0.262763"), + "AT1G01030": ("0.038467", "0.251784"), + }, + ), + ( + "arabidopsis_silique_lee_pseudobulk", + 8, + { + "AT1G01010": ("0.00496354", "0.0593082"), + "AT1G01020": ("0.0222446", "0.124802"), + "AT1G01030": ("0.00131167", "0.0306192"), + }, + ), + ( + "arabidopsis_stem_lee_pseudobulk", + 9, + { + "AT1G01010": ("0.00751716", "0.131966"), + "AT1G01020": ("0.0695734", "0.401791"), + "AT1G01030": ("0.00053516", "0.0321555"), + }, + ), + ( + "rice_OW_pseudobulk", + 71, + { + "Os01g0100100": ("0.136496", "0.502172"), + "Os01g0100200": ("0.00848389", "0.12733"), + "Os01g0100400": ("0.0413686", "0.279097"), + }, + ), +] + +# Each database, its fixture cells, and the cells that carry an expression value for each +# fixture gene. The cells left out are the gaps: an absent key means zero expression. +UMAP_DATABASES = [ + ( + "arabidopsis_flower_lee_umap", + [4, 45, 71, 157, 329, 359, 685, 817], + { + "AT1G01010": [157, 685, 817], + "AT1G01020": [71, 329, 359], + "AT1G01030": [4, 45], + }, + ), + ( + "arabidopsis_root_shahan_umap", + [3, 16, 36, 44, 62, 82, 89, 159], + { + "AT1G01010": [3, 16, 44, 159], + "AT1G01020": [36, 62, 82, 89], + "AT1G01030": [89, 159], + }, + ), + ( + "arabidopsis_rosette_21d_lee_umap", + [18, 19, 31, 56, 71, 84, 169, 443], + { + "AT1G01010": [71, 169, 443], + "AT1G01020": [18, 31, 56], + "AT1G01030": [19, 31, 84], + }, + ), + ( + "arabidopsis_rosette_30d_lee_umap", + [3, 52, 76, 77, 114, 116, 775, 783], + { + "AT1G01010": [52, 775, 783], + "AT1G01020": [76, 77, 116], + "AT1G01030": [3, 114], + }, + ), + ( + "arabidopsis_seed_0d_lee_umap", + [0, 3, 21, 31, 56, 125, 154, 208], + { + "AT1G01010": [125, 154, 208], + "AT1G01020": [21, 31, 56], + "AT1G01030": [0, 3], + }, + ), + ( + "arabidopsis_seed_martin_umap", + [10, 143, 145, 155, 171, 233, 1593, 1723], + { + "AT1G01010": [10, 143, 171], + "AT1G01020": [145, 155, 233], + "AT1G01030": [1593, 1723], + }, + ), + ( + "arabidopsis_seedling_12d_lee_umap", + [19, 98, 141, 157, 237, 241, 489, 557], + { + "AT1G01010": [19, 489, 557], + "AT1G01020": [98, 157, 237], + "AT1G01030": [141, 241], + }, + ), + ( + "arabidopsis_seedling_3d_lee_umap", + [1, 32, 63, 92, 112, 166, 354, 381], + { + "AT1G01010": [63, 92, 112], + "AT1G01020": [1, 166, 354], + "AT1G01030": [32, 381], + }, + ), + ( + "arabidopsis_seedling_6d_lee_umap", + [1, 14, 19, 50, 106, 118, 119, 269], + { + "AT1G01010": [106, 118, 269], + "AT1G01020": [1, 50, 119], + "AT1G01030": [14, 19], + }, + ), + ( + "arabidopsis_shoot_zhang_umap", + [5, 8, 13, 18, 23, 30, 36, 37], + { + "AT1G01010": [23, 30, 36], + "AT1G01020": [5, 8, 18, 30], + "AT1G01030": [13, 37], + }, + ), + ( + "arabidopsis_silique_lee_umap", + [28, 34, 104, 120, 278, 370, 799, 987], + { + "AT1G01010": [28, 278, 370], + "AT1G01020": [34, 104, 120], + "AT1G01030": [799, 987], + }, + ), + ( + "arabidopsis_stem_lee_umap", + [100, 144, 162, 522, 598, 814, 9526, 9544], + { + "AT1G01010": [522, 598, 814], + "AT1G01020": [100, 144, 162], + "AT1G01030": [9526, 9544], + }, + ), + ( + "rice_OW_umap", + [28, 36, 38, 40, 82, 123, 180, 279], + { + "Os01g0100100": [36, 38, 40], + "Os01g0100200": [82, 180, 279], + "Os01g0100400": [28, 123], + }, + ), +] + + +class TestIntegrations(TestCase): + def setUp(self): + self.app_client = app.test_client() + + def test_get_superviewer_pseudobulk_expression(self): + """This tests the pseudobulk expression data returned for every SUPeR Viewer database + :return: + """ + for database, rows_per_gene, mean_ctrl in PSEUDOBULK_DATABASES: + for gene, (value, value_std) in mean_ctrl.items(): + with self.subTest(database=database, gene=gene): + response = self.app_client.get("/gene_expression/expression/{}/{}".format(database, gene)) + self.assertEqual(response.status_code, 200) + data = response.json["data"] + + # Every gene carries all of its database's rows, Mean_CTRL included + self.assertEqual(data["record_count"], rows_per_gene) + self.assertEqual(len(data["data"]), rows_per_gene) + for row in data["data"]: + self.assertEqual(set(row), {"name", "value", "value_std"}) + + # Mean_CTRL comes back inline, exactly once, with its stored values + controls = [row for row in data["data"] if row["name"] == "Mean_CTRL"] + self.assertEqual(len(controls), 1) + self.assertEqual(controls[0]["value"], value) + self.assertEqual(controls[0]["value_std"], value_std) + + def test_get_superviewer_umap_coordinates(self): + """This tests the UMAP coordinates returned for every SUPeR Viewer database + :return: + """ + for database, cells, _expression_cells in UMAP_DATABASES: + with self.subTest(database=database): + response = self.app_client.get("/umap_gene_expression/{}".format(database)) + self.assertEqual(response.status_code, 200) + self.assertEqual(sorted(int(cell) for cell in response.json["data"]), cells) + + def test_get_superviewer_umap_expression(self): + """This tests that UMAP expression stays sparse: gap cells have no key + :return: + """ + for database, _cells, expression_cells in UMAP_DATABASES: + for gene, cells in expression_cells.items(): + with self.subTest(database=database, gene=gene): + response = self.app_client.get("/umap_gene_expression/{}/{}".format(database, gene)) + self.assertEqual(response.status_code, 200) + self.assertEqual(sorted(int(cell) for cell in response.json["data"]), cells)