Merge pull request #197 from BioAnalyticResource/dev

Update main branch

.github/workflows/bar-api.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.8, 3.9, 3.10.11, 3.11]
+        python-version: [3.8, 3.9, 3.10.13, 3.11, 3.12]
 
     services:
       redis:

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11.3-bullseye
+FROM python:3.12-bookworm
 
 WORKDIR /usr/src/app
 

api/__init__.py

@@ -61,6 +61,7 @@ def create_app():
     from api.resources.interactions import itrns
     from api.resources.gene_localizations import loc
     from api.resources.efp_image import efp_image
+    from api.resources.fastpheno import fastpheno
 
     bar_api.add_namespace(gene_information)
     bar_api.add_namespace(rnaseq_gene_expression)
@@ -72,6 +73,7 @@ def create_app():
     bar_api.add_namespace(itrns)
     bar_api.add_namespace(loc)
     bar_api.add_namespace(efp_image)
+    bar_api.add_namespace(fastpheno)
     bar_api.init_app(bar_app)
     return bar_app
 

api/models/fastpheno.py

@@ -0,0 +1,65 @@
+from api import db
+import enum
+from sqlalchemy.dialects.mysql import DECIMAL, ENUM
+from sqlalchemy.orm import relationship
+from sqlalchemy import ForeignKey
+from typing import List
+
+
+class Sites(db.Model):
+    __bind_key__ = "fastpheno"
+    __tablename__ = "sites"
+
+    sites_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    site_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False)
+    site_desc: db.Mapped[str] = db.mapped_column(db.String(99), nullable=True)
+    children: db.Mapped[List["Trees"]] = relationship()
+
+
+class Trees(db.Model):
+    __bind_key__ = "fastpheno"
+    __tablename__ = "trees"
+
+    trees_pk: db.Mapped[int] = db.mapped_column(db.Integer, nullable=False, primary_key=True)
+    sites_pk: db.Mapped[int] = db.mapped_column(ForeignKey("sites.sites_pk"))
+    longitude: db.Mapped[float] = db.mapped_column(db.Float, nullable=False)
+    latitude: db.Mapped[float] = db.mapped_column(db.Float, nullable=False)
+    genotype_id: db.Mapped[str] = db.mapped_column(db.String(5), nullable=True)
+    external_link: db.Mapped[str] = db.mapped_column(db.String(200), nullable=True)
+    tree_given_id: db.Mapped[str] = db.mapped_column(db.String(25), nullable=True)
+    children: db.Mapped[List["Band"]] = relationship()
+
+
+class MonthChoices(enum.Enum):
+    jan = "1"
+    feb = "2"
+    mar = "3"
+    apr = "4"
+    may = "5"
+    jun = "6"
+    jul = "7"
+    aug = "8"
+    sep = "9"
+    oct = "10"
+    nov = "11"
+    dec = "12"
+
+
+class Band(db.Model):
+    __bind_key__ = "fastpheno"
+    __tablename__ = "band"
+
+    trees_pk: db.Mapped[int] = db.mapped_column(ForeignKey("trees.trees_pk"), primary_key=True)
+    month: db.Mapped[str] = db.mapped_column(ENUM(MonthChoices), nullable=False, primary_key=True)
+    band: db.Mapped[float] = db.mapped_column(db.String(100), nullable=False, primary_key=True)
+    value: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)
+
+
+class Height(db.Model):
+    __bind_key__ = "fastpheno"
+    __tablename__ = "height"
+
+    trees_pk: db.Mapped[int] = db.mapped_column(ForeignKey("trees.trees_pk"), primary_key=True)
+    month: db.Mapped[str] = db.mapped_column(ENUM(MonthChoices), nullable=False, primary_key=True)
+    tree_height_proxy: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)
+    ground_height_proxy: db.Mapped[float] = db.mapped_column(DECIMAL(20, 15), nullable=False)

api/resources/fastpheno.py

@@ -0,0 +1,93 @@
+"""
+Date: Aug 2023
+Author: Vince L
+Fastpheno endpoint for retrieving tree data
+"""
+from flask_restx import Namespace, Resource
+from api import db
+from api.models.fastpheno import Sites, Trees, Band, Height
+from api.utils.bar_utils import BARUtils
+from markupsafe import escape
+
+
+fastpheno = Namespace("FastPheno", description="FastPheno API service", path="/fastpheno")
+
+
+@fastpheno.route("/get_bands/<string:site>/<string:month>/<string:band>")
+class FastPheno(Resource):
+    @fastpheno.param("site", _in="path", default="pintendre")
+    @fastpheno.param("month", _in="path", default="jan")
+    @fastpheno.param("band", _in="path", default="band_1")
+    def get(self, site, month, band):
+        """This end point returns band values for a specific site AND month-date"""
+        # Escape input data
+        site = escape(site).capitalize()
+        month = escape(month)
+        band = escape(band)
+
+        rows = db.session.execute(
+            db.select(Sites, Trees, Height, Band)
+            .select_from(Sites)
+            .join(Trees, Trees.sites_pk == Sites.sites_pk)  # don't need to use 2nd arg, for clarity... I set ORM rel
+            .join(Height, Height.trees_pk == Trees.trees_pk)
+            .join(Band, Band.trees_pk == Trees.trees_pk)
+            .where(Sites.site_name == site, Band.month == month, Height.month == month, Band.band == band)
+        ).all()
+        res = [
+            {
+                "site_name": s.site_name,
+                "tree_id": t.trees_pk,
+                "longitude": t.longitude,
+                "latitutde": t.latitude,
+                "genotype_id": t.genotype_id,
+                "tree_given_id": t.tree_given_id,
+                "external_link": t.external_link,
+                "band_value": float(b.value),
+                "tree_height_proxy": float(h.tree_height_proxy),
+                "ground_height_proxy": float(h.ground_height_proxy),
+                "band_month": b.month.name,
+            }
+            for s, t, h, b in rows
+        ]
+        if len(rows) == 0:
+            return (
+                BARUtils.error_exit("There are no data found for the given parameters"),
+                400,
+            )
+
+        return BARUtils.success_exit(res)
+
+
+@fastpheno.route("/get_trees/<string:genotype_id>")
+class FastPhenoTrees(Resource):
+    @fastpheno.param("genotype_id", _in="path", default="C")
+    def get(self, genotype_id):
+        """This end point returns trees for a given genotype_id across sites"""
+        # Escape input data
+        genotype_id = escape(genotype_id).capitalize()
+
+        rows = db.session.execute(
+            db.select(Sites, Trees)
+            .select_from(Sites)
+            .join(Trees, Trees.sites_pk == Sites.sites_pk)
+            .where(Trees.genotype_id == genotype_id)
+        ).all()
+        res = [
+            {
+                "site_name": s.site_name,
+                "tree_id": t.trees_pk,
+                "longitude": t.longitude,
+                "latitutde": t.latitude,
+                "genotype_id": t.genotype_id,
+                "tree_given_id": t.tree_given_id,
+                "external_link": t.external_link,
+            }
+            for s, t in rows
+        ]
+        if len(rows) == 0:
+            return (
+                BARUtils.error_exit("There are no data found for the given parameters"),
+                400,
+            )
+
+        return BARUtils.success_exit(res)

config/BAR_API.cfg

@@ -21,6 +21,7 @@ SQLALCHEMY_BINDS = {
     'eplant_rice' : 'mysql://root:root@localhost/eplant_rice',
     'eplant_soybean' : 'mysql://root:root@localhost/eplant_soybean',
     'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato',
+    'fastpheno' :  'mysql://root:root@localhost/fastpheno',
     'germination': 'mysql://root:root@localhost/germination',
     'kalanchoe': 'mysql://root:root@localhost/kalanchoe',
     'klepikova': 'mysql://root:root@localhost/klepikova',

config/databases/fastpheno.sql

@@ -0,0 +1,153 @@
+-- MySQL dump 10.13  Distrib 8.0.33, for Linux (x86_64)
+--
+-- Host: localhost    Database: cannabis
+-- ------------------------------------------------------
+-- Server version	8.0.33
+
+/*!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: `fastpheno`
+--
+
+DROP DATABASE IF EXISTS `fastpheno` ;
+
+CREATE DATABASE /*!32312 IF NOT EXISTS*/ `fastpheno` /*!40100 DEFAULT CHARACTER SET latin1 */ /*!80016 DEFAULT ENCRYPTION='N' */;
+
+USE `fastpheno`;
+
+--
+-- Table structure for table `sites`
+--
+
+DROP TABLE IF EXISTS `sites` ;
+/*!40101 SET @saved_cs_client     = @@character_set_client */;
+/*!50503 SET character_set_client = utf8mb4 */;
+CREATE TABLE IF NOT EXISTS `sites` (
+  `sites_pk` INT NOT NULL AUTO_INCREMENT,
+  `site_name` VARCHAR(45) UNIQUE NOT NULL,
+  `site_desc` VARCHAR(999) NULL,
+  PRIMARY KEY (`sites_pk`)) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `sites`
+--
+
+LOCK TABLES `sites` WRITE;
+/*!40000 ALTER TABLE `sites` DISABLE KEYS */;
+INSERT INTO `sites` VALUES (1,'Pintendre', 'Lorem ipsum dolor sit amet, consectetur adipiscing elit'),(2,'Pickering','Lorem ipsum dolor sit amet,');
+/*!40000 ALTER TABLE `sites` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `trees`
+--
+
+DROP TABLE IF EXISTS `trees` ;
+
+CREATE TABLE IF NOT EXISTS `trees` (
+  `trees_pk` INT NOT NULL AUTO_INCREMENT,
+  `sites_pk` INT NOT NULL,
+  `longitude` DECIMAL(10) NOT NULL,
+  `latitude` DECIMAL(10) NOT NULL,
+  `genotype_id` VARCHAR(5) NULL,
+  `external_link` VARCHAR(200) NULL,
+  `tree_given_id` VARCHAR(25) NULL,
+  PRIMARY KEY (`trees_pk`),
+  INDEX `sites_fk_idx` (`sites_pk` ASC),
+  CONSTRAINT `sites_fk`
+    FOREIGN KEY (`sites_pk`)
+    REFERENCES `sites` (`sites_pk`)
+    ON DELETE RESTRICT
+    ON UPDATE RESTRICT) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `trees`
+--
+
+LOCK TABLES `trees` WRITE;
+/*!40000 ALTER TABLE `trees` DISABLE KEYS */;
+INSERT INTO `trees` VALUES (1,1,336839,5178557,'C','example','11'),(2,1,336872,5178486,'C','example2','11'),(3,1,346872,5278486,'C','example3','B'),(4,2,330502,5262486,'XZ','example4','K123');
+/*!40000 ALTER TABLE `trees` ENABLE KEYS */;
+UNLOCK TABLES;
+
+--
+-- Table structure for table `band`
+--
+
+DROP TABLE IF EXISTS `band` ;
+
+CREATE TABLE IF NOT EXISTS `band` (
+  `trees_pk` INT NOT NULL,
+  `month` ENUM('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL,
+  `band` VARCHAR(100) NOT NULL,
+  `value` DECIMAL(20,15) NOT NULL,
+  INDEX `trees_fk_idx` (`trees_pk` ASC),
+  PRIMARY KEY (`trees_pk`, `month`, `band`),
+  CONSTRAINT `trees_fk`
+    FOREIGN KEY (`trees_pk`)
+    REFERENCES `trees` (`trees_pk`)
+    ON DELETE RESTRICT
+    ON UPDATE RESTRICT) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `band`
+--
+
+LOCK TABLES `band` WRITE;
+/*!40000 ALTER TABLE `band` DISABLE KEYS */;
+INSERT INTO `band` VALUES (1,'jan','band_1',0.025796278000000),(1,'jan','band_2',0.025796278000000),(1,'feb','band_1',0.025796278000000),(1,'mar','band_1',0.0234423232241),(1,'apr','band_1',0.089900613000000),(2,'feb','band_1',0.183586478000000),(4,'feb','band_1',0.223586478000000);
+/*!40000 ALTER TABLE `band` ENABLE KEYS */;
+UNLOCK TABLES;
+
+
+-- -----------------------------------------------------
+-- Table `height`
+-- -----------------------------------------------------
+DROP TABLE IF EXISTS `height` ;
+
+CREATE TABLE IF NOT EXISTS `height` (
+  `trees_pk` INT NOT NULL,
+  `month` ENUM('jan','feb','mar','apr','may','jun','jul','aug','sep','oct','nov','dec') NOT NULL,
+  `tree_height_proxy` DECIMAL(20,15) NOT NULL,
+  `ground_height_proxy` DECIMAL(20,15) NOT NULL,
+  INDEX `tree_fk_idx` (`trees_pk` ASC),
+  PRIMARY KEY (`trees_pk`, `month`),
+  CONSTRAINT `tree_fk`
+    FOREIGN KEY (`trees_pk`)
+    REFERENCES `trees` (`trees_pk`)
+    ON DELETE RESTRICT
+    ON UPDATE RESTRICT) ENGINE=InnoDB DEFAULT CHARSET=latin1;
+/*!40101 SET character_set_client = @saved_cs_client */;
+
+--
+-- Dumping data for table `height`
+--
+
+LOCK TABLES `height` WRITE;
+/*!40000 ALTER TABLE `height` DISABLE KEYS */;
+INSERT INTO `height` VALUES (1,'jan',2.23428942871000000,45.106719970000000),(1,'feb',3.478942871000000,49.106719970000000),(1,'mar',2.383630037000000,48.887859340000000),(1,'apr',1.376412749000000,49.052417760000000),(2,'feb',2.383630037000000,48.12341242131163),(4,'feb',2.623630037000000,45.22341242131163);
+/*!40000 ALTER TABLE `height` ENABLE KEYS */;
+UNLOCK TABLES;
+
+/*!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 2023-06-07 14:37:50

config/init.sh

@@ -20,6 +20,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_poplar.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_rice.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql
+mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql
 mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql

docker-compose.yml

@@ -3,7 +3,7 @@ version: "3.7"
 services:
 
   mysqldb:
-    image: mysql:8.0.33
+    image: mysql:8.1.0
     container_name: BAR_mysqldb
     # Must use this for mariadb client to connect
     command: --default-authentication-plugin=mysql_native_password
@@ -12,7 +12,7 @@ services:
       - MYSQL_ROOT_PASSWORD=root
 
   redis:
-    image: redis:7.0.11
+    image: redis:7.2.1
     container_name: BAR_redis
     restart: always
     ports: