Feature/nie pseudobulk umap (Pseudobulk expression and UMAP for SUPeR viewer)

api/__init__.py

@@ -81,6 +81,7 @@ def create_app():
     from api.resources.gaia import gaia
     from api.resources.rnaseq_gene_expression import rnaseq_gene_expression
     from api.resources.microarray_gene_expression import microarray_gene_expression
+    from api.resources.umap_gene_expression import umap_gene_expression
     from api.resources.proxy import bar_proxy
     from api.resources.thalemine import thalemine
     from api.resources.snps import snps
@@ -98,6 +99,7 @@ def create_app():
     bar_api.add_namespace(gaia)
     bar_api.add_namespace(rnaseq_gene_expression)
     bar_api.add_namespace(microarray_gene_expression)
+    bar_api.add_namespace(umap_gene_expression)
     bar_api.add_namespace(bar_proxy)
     bar_api.add_namespace(thalemine)
     bar_api.add_namespace(snps)

api/models/arabidopsis_NIE_umap.py

@@ -0,0 +1,19 @@
+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)

api/models/efp_dynamic.py

@@ -4,20 +4,43 @@
 from api import db
 from api.utils.bar_utils import load_combined_master
 
+# Optional sample_data columns, keyed by the schema_variants role that declares them.
+# A database only gets one of these if its assigned variant declares a column with that
+# role, so every variant predating this mapping generates exactly the columns it did
+# before. Each value is a factory: mapped_column objects cannot be shared between models.
+_OPTIONAL_COLUMNS_BY_ROLE = {
+    "value_std": lambda: db.mapped_column(db.Float, nullable=True),
+}
 
-def _sample_data_model(database):
+
+def _optional_columns(variant):
+    """Extra mapped columns this variant's sample_data declares, keyed by column name."""
+    columns = variant.get("tables", {}).get("sample_data", {}).get("columns", {})
+    return {
+        column: _OPTIONAL_COLUMNS_BY_ROLE[spec["role"]]()
+        for column, spec in columns.items()
+        if spec.get("role") in _OPTIONAL_COLUMNS_BY_ROLE
+    }
+
+
+def _sample_data_model(database, variant):
     class_name = "".join(part.capitalize() for part in database.split("_")) + "SampleData"
-    return type(
-        class_name,
-        (db.Model,),
-        {
-            "__bind_key__": database,
-            "__tablename__": "sample_data",
-            "data_probeset_id": db.mapped_column(db.String(255), primary_key=True),
-            "data_bot_id": db.mapped_column(db.String(255), primary_key=True),
-            "data_signal": db.mapped_column(db.Float, primary_key=True),
-        },
-    )
-
-
-SAMPLE_DATA_MODELS = {database: _sample_data_model(database) for database in load_combined_master()["databases"]}
+    attributes = {
+        "__bind_key__": database,
+        "__tablename__": "sample_data",
+        "data_probeset_id": db.mapped_column(db.String(255), primary_key=True),
+        "data_bot_id": db.mapped_column(db.String(255), primary_key=True),
+        "data_signal": db.mapped_column(db.Float, primary_key=True),
+    }
+    attributes.update(_optional_columns(variant))
+    return type(class_name, (db.Model,), attributes)
+
+
+_MASTER = load_combined_master()
+
+# A few catalogued databases name a schema_variant that is not in schema_variants; they
+# fall back to {} and so generate the three required columns only, exactly as before.
+SAMPLE_DATA_MODELS = {
+    database: _sample_data_model(database, _MASTER["schema_variants"].get(info["schema_variant"], {}))
+    for database, info in _MASTER["databases"].items()
+}

api/resources/gene_expression.py

@@ -54,19 +54,31 @@ def get(self, database, gene_id):
 
             query_id = rows[0][0]
 
+        # only databases whose schema_variant declares a standard deviation column have
+        # data_signal_std mapped; every other database keeps the two-key row shape
+        has_signal_std = hasattr(model, "data_signal_std")
+        columns = [model.data_bot_id, model.data_signal]
+        if has_signal_std:
+            columns.append(model.data_signal_std)
+
         rows = db.session.execute(
-            db.select(model.data_bot_id, model.data_signal).where(func.upper(model.data_probeset_id) == query_id.upper())
+            db.select(*columns).where(func.upper(model.data_probeset_id) == query_id.upper())
         ).all()
 
         if len(rows) == 0:
             return BARUtils.error_exit("There are no data found for the given gene"), 400
 
+        if has_signal_std:
+            data = [{"name": name, "value": str(value), "value_std": str(std)} for name, value, std in rows]
+        else:
+            data = [{"name": name, "value": str(value)} for name, value in rows]
+
         res = {
             "gene_id": gene_id,
             "probset_id": query_id,
             "database": database,
             "record_count": len(rows),
-            "data": [{"name": name, "value": str(value)} for name, value in rows],
+            "data": data,
         }
 
         return BARUtils.success_exit(res)

api/resources/umap_gene_expression.py

@@ -0,0 +1,78 @@
+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.utils.bar_utils import BARUtils, load_combined_master
+
+umap_gene_expression = Namespace(
+    "UMAP Gene Expression",
+    description="UMAP coordinates and single cell gene expression data from the BAR Databases",
+    path="/umap_gene_expression",
+)
+
+
+class UMAPUtils:
+    @staticmethod
+    def get_tables(database):
+        """This function sets the tables and species for a UMAP database
+        :param database: name of BAR 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:
+            return {"success": False, "error": "Invalid database", "error_code": 400}
+
+        return {"success": True, "coords_table": coords_table, "expression_table": expression_table, "species": species}
+
+
+@umap_gene_expression.route("/<string:database>")
+class GetUMAPCoordinates(Resource):
+    @umap_gene_expression.param("database", _in="path", default="arabidopsis_NIE_umap")
+    def get(self, database=""):
+        """This end point returns the UMAP coordinates of every cell"""
+        database = escape(database)
+
+        tables = UMAPUtils.get_tables(database)
+        if not tables["success"]:
+            return BARUtils.error_exit(tables["error"]), tables["error_code"]
+
+        table = tables["coords_table"]
+        rows = db.session.execute(db.select(table.cell_id, table.umap_1, table.umap_2, table.cell_type)).all()
+
+        data = {}
+        for row in rows:
+            data[row[0]] = {"umap_1": row[1], "umap_2": row[2], "cell_type": row[3]}
+
+        return BARUtils.success_exit(data)
+
+
+@umap_gene_expression.route("/<string:database>/<string:gene_id>")
+class GetUMAPGeneExpression(Resource):
+    @umap_gene_expression.param("database", _in="path", default="arabidopsis_NIE_umap")
+    @umap_gene_expression.param("gene_id", _in="path", default="At1g01010")
+    def get(self, database="", gene_id=""):
+        """This end point returns the sparse UMAP gene expression data, keyed by cell id"""
+        database = escape(database)
+        gene_id = escape(gene_id)
+
+        tables = UMAPUtils.get_tables(database)
+        if not tables["success"]:
+            return BARUtils.error_exit(tables["error"]), tables["error_code"]
+
+        pattern = load_combined_master()["gene_id_patterns"][tables["species"]]
+        if not BARUtils.is_valid_gene_id(pattern, gene_id):
+            return BARUtils.error_exit("Invalid gene id"), 400
+
+        table = tables["expression_table"]
+        rows = db.session.execute(db.select(table.expression).where(table.gene_id == gene_id)).scalars().all()
+
+        if len(rows) == 0:
+            return BARUtils.error_exit("There are no data found for the given gene"), 400
+
+        return BARUtils.success_exit(rows[0])

config/BAR_API.cfg

@@ -12,6 +12,8 @@ SQLALCHEMY_TRACK_MODIFICATIONS = False
 SQLALCHEMY_BINDS = {
     'annotations_lookup': 'mysql://root:root@localhost/annotations_lookup',
     'arabidopsis_ecotypes': 'mysql://root:root@localhost/arabidopsis_ecotypes',
+    'arabidopsis_NIE_pseudobulk': 'mysql://root:root@localhost/arabidopsis_NIE_pseudobulk',
+    'arabidopsis_NIE_umap': 'mysql://root:root@localhost/arabidopsis_NIE_umap',
     'arachis': 'mysql://root:root@localhost/arachis',
     'cannabis': 'mysql://root:root@localhost/cannabis',
     'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp',

config/databases/arabidopsis_NIE_pseudobulk_dump.sql

@@ -0,0 +1,64 @@
+-- MySQL dump 10.13  Distrib 9.4.0, for Linux (x86_64)
+--
+-- Host: localhost    Database: arabidopsis_NIE_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_NIE_pseudobulk`
+--
+
+CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_NIE_pseudobulk` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */;
+
+USE `arabidopsis_NIE_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',0.0346533,0.224356,'D0_Mesophyll'),('AT1G01010',0.0251518,0.185286,'D0_Sieve element_responsive'),('AT1G01010',0.0297745,0.203837,'D0_Guard'),('AT1G01010',0.0550332,0.260401,'D0_Defense state'),('AT1G01010',0.0424581,0.239094,'D0_Epidermal'),('AT1G01010',0.0163655,0.146177,'D0_Phloem Parenchyma'),('AT1G01010',0.0389615,0.234467,'D0_Metabolic stress state'),('AT1G01010',0.0292404,0.198967,'D0_Phloem companion'),('AT1G01010',0.0510094,0.226118,'D0_Trichome'),('AT1G01010',0.027103,0.181704,'D0_Dividing'),('AT1G01010',0.0692417,0.276578,'D0_Stress responsive'),('AT1G01010',0.0110158,0.119154,'D0_Sugar metabolic state'),('AT1G01010',0.0565404,0.272046,'D0_Immune active'),('AT1G01010',0.0513775,0.273271,'D0_Hydathode'),('AT1G01010',0.045102,0.247266,'D0_Vascular'),('AT1G01010',0.0256331,0.169289,'D0_Myrosin'),('AT1G01010',0.0274436,0.177235,'W0_Vascular'),('AT1G01010',0.024174,0.172252,'W0_Mesophyll'),('AT1G01010',0.0213485,0.15354,'W0_Phloem Parenchyma'),('AT1G01010',0.0286998,0.178188,'W0_Dividing'),('AT1G01010',0.0278313,0.182473,'W0_Epidermal'),('AT1G01010',0.0563447,0.251333,'W0_Immune active'),('AT1G01010',0.0343054,0.201204,'W0_Sieve element_responsive'),('AT1G01010',0.0574457,0.253535,'W0_Defense state'),('AT1G01010',0.0136855,0.12117,'W0_Guard'),('AT1G01010',0.0272221,0.169833,'W0_Phloem companion'),('AT1G01010',0.0715313,0.271057,'W0_Stress responsive'),('AT1G01010',0.00820466,0.0673068,'W0_Myrosin'),('AT1G01010',0.0393423,0.199799,'W0_Sugar metabolic state'),('AT1G01010',0.0339956,0.217678,'W0_Metabolic stress state'),('AT1G01010',0.0214199,0.133693,'W0_Trichome'),('AT1G01010',0.0571251,0.236552,'W0_Hydathode'),('AT1G01010',0.0422542,0.250415,'W15_Dividing'),('AT1G01010',0.0446,0.254963,'W15_Mesophyll'),('AT1G01010',0.037824,0.236808,'W15_Phloem Parenchyma'),('AT1G01010',0.0420744,0.251218,'W15_Immune active'),('AT1G01010',0.0387755,0.241218,'W15_Epidermal'),('AT1G01010',0.104241,0.43291,'W15_Hydathode'),('AT1G01010',0.104467,0.324257,'W15_Stress responsive'),('AT1G01010',0.03282,0.228891,'W15_Guard'),('AT1G01010',0.0783275,0.325689,'W15_Defense state'),('AT1G01010',0.0205945,0.15169,'W15_Myrosin'),('AT1G01010',0.0290853,0.203305,'W15_Phloem companion'),('AT1G01010',0.0409241,0.246531,'W15_Vascular'),('AT1G01010',0,0,'W15_Trichome'),('AT1G01010',0.0304135,0.206024,'W15_Sieve element_responsive'),('AT1G01010',0,0,'W15_Sugar metabolic state'),('AT1G01010',0.0573618,0.262866,'W15_Metabolic stress state'),('AT1G01010',0.0187317,0.156752,'R15_Sieve element_responsive'),('AT1G01010',0.0287312,0.191696,'R15_Immune active'),('AT1G01010',0.0329913,0.213788,'R15_Mesophyll'),('AT1G01010',0.0130775,0.14382,'R15_Guard'),('AT1G01010',0.0547408,0.257222,'R15_Defense state'),('AT1G01010',0.0541722,0.243631,'R15_Stress responsive'),('AT1G01010',0.02531,0.180358,'R15_Phloem Parenchyma'),('AT1G01010',0.0400045,0.239473,'R15_Epidermal'),('AT1G01010',0.0300884,0.196556,'R15_Vascular'),('AT1G01010',0.0282214,0.199286,'R15_Dividing'),('AT1G01010',0.034919,0.214859,'R15_Phloem companion'),('AT1G01010',0.018792,0.157063,'R15_Metabolic stress state'),('AT1G01010',0.0528136,0.261553,'R15_Trichome'),('AT1G01010',0,0,'R15_Myrosin'),('AT1G01010',0.0564275,0.281679,'R15_Hydathode'),('AT1G01010',0.0462055,0.222434,'R15_Sugar metabolic state');
+INSERT INTO `sample_data` VALUES ('AT1G01010',0.0242853,0.114475,'W0_Phloem average');
+INSERT INTO `sample_data` VALUES ('AT1G01010',0.0228029,0.123446,'D0_Phloem average');
+INSERT INTO `sample_data` VALUES ('AT1G01010',0.0301145,0.140262,'R15_Phloem average');
+INSERT INTO `sample_data` VALUES ('AT1G01010',0.0334546,0.156053,'W15_Phloem average');
+INSERT INTO `sample_data` VALUES ('AT1G01010',0.036322,0.224118,'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 */;
+/*!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 2026-07-17 01:32:31

config/databases/arabidopsis_NIE_umap.sql

@@ -0,0 +1,83 @@
+-- MySQL dump 10.13  Distrib 9.4.0, for Linux (x86_64)
+--
+-- Host: localhost    Database: arabidopsis_NIE_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_NIE_umap`
+--
+
+CREATE DATABASE /*!32312 IF NOT EXISTS*/ `arabidopsis_NIE_umap` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */;
+
+USE `arabidopsis_NIE_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 (43,-6.89231,7.56863,'Metabolic stress state'),(44,2.87577,-4.82349,'Dividing'),(45,-0.262505,-8.55344,'Guard'),(46,-4.5876,6.05261,'Defense state');
+/*!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','{\"43\": 1.152292, \"44\": 1.546603, \"46\": 1.392931}'),('AT3G18780','{\"43\": 1.673516, \"44\": 3.142986, \"45\": 1.490115, \"46\": 1.953491}');
+/*!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 2026-07-17 01:12:53

config/init.sh

@@ -11,6 +11,8 @@ 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_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/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