Feature/SUPeR expansion (expand other 13 DBs from NIE pseudobulk to other DBs for MVP)

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}

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}
 
 

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',

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 meiocyte'),('AT1G01020',0.0318393,0.28948,'Pollen'),('AT1G01020',0.0792938,0.40418,'Vascular'),('AT1G01020',0.0426172,0.292169,'Developing ovule'),('AT1G01020',0.03165,0.277587,'Mean_CTRL'),('AT1G01030',0.0345644,0.306613,'Unknown'),('AT1G01030',0.0224953,0.231296,'Tapetum'),('AT1G01030',0.0265322,0.225368,'Gynoecium and developing ovule'),('AT1G01030',0.0483986,0.335871,'Anther'),('AT1G01030',0.0118251,0.163059,'Epidermal'),('AT1G01030',0.0297713,0.270059,'Male meiocyte'),('AT1G01030',0.0856332,0.416266,'Pollen'),('AT1G01030',0.047488,0.339749,'Vascular'),('AT1G01030',0.0739971,0.359961,'Developing ovule'),('AT1G01030',0.0373011,0.306399,'Mean_CTRL');
+/*!40000 ALTER TABLE `sample_data` ENABLE KEYS */;
+UNLOCK TABLES;
+/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */;
+/*!40101 SET SQL_MODE=@OLD_SQL_MODE */;
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+-- Dump completed on 2026-07-30 00:24:07

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 */;
+
+--
+-- Dumping data for table `umap_coords`
+--
+
+LOCK TABLES `umap_coords` WRITE;
+/*!40000 ALTER TABLE `umap_coords` DISABLE KEYS */;
+INSERT INTO `umap_coords` VALUES (4,-3.454307,0.662751,'Unknown'),(45,-3.101461,1.666404,'Unknown'),(71,2.584931,-6.196103,'Gynoecium and developing ovule'),(157,-4.351600,1.759395,'Unknown'),(329,-0.016035,4.015458,'Male meiocyte'),(359,-4.663122,1.347665,'Unknown'),(685,-3.734362,1.471752,'Unknown'),(817,-3.904004,-0.424860,'Unknown');
+/*!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','{\"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 */;
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+/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
+/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
+-- Dump completed on 2026-07-30 01:27:00

config/databases/arabidopsis_root_shahan_umap.sql

@@ -0,0 +1,83 @@
+-- MySQL dump 10.13  Distrib 9.4.0, for Linux (x86_64)
+--
+-- Host: localhost    Database: arabidopsis_root_shahan_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_root_shahan_umap`
+--
+
+CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_root_shahan_umap` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */;
+
+USE `arabidopsis_root_shahan_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 (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;
+/*!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','{\"3\": 2.205624, \"16\": 0.762018, \"44\": 1.738013, \"159\": 0.902622}'),('AT1G01020','{\"36\": 1.82633, \"62\": 0.80323, \"82\": 0.967385, \"89\": 1.572109}'),('AT1G01030','{\"89\": 1.572109, \"159\": 0.549872}');
+/*!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 */;
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+/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */;
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+/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
+/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
+-- Dump completed on 2026-08-12 01:40:46