Simsbiohub 496 bctw deployments script

Makefile

@@ -23,7 +23,7 @@ env: | setup ## Copies the default ./env_config/env.docker to ./.env
 
 postgres: | close build-postgres run-postgres ## Performs all commands necessary to run the postgres project (db) in docker
 backend: | close build-backend run-backend ## Performs all commands necessary to run all backend projects (db, api) in docker
-web: | close build-web run-web ## Performs all commands necessary to run all backend+web projects (db, api, app) in docker
+web: | close build-web check-env run-web ## Performs all commands necessary to run all backend+web projects (db, api, app) in docker
 
 db-setup: | build-db-setup run-db-setup ## Performs all commands necessary to run the database migrations and seeding
 db-migrate: | build-db-migrate run-db-migrate ## Performs all commands necessary to run the database migrations
@@ -62,6 +62,12 @@ prune: ## Deletes ALL docker artifacts (even those not associated to this projec
 	@docker system prune --all --volumes -f
 	@docker volume prune --all -f
 
+check-env: ## Check for missing env vars
+	@echo "==============================================="
+	@echo "Make: check-env - check for missing env vars"
+	@echo "==============================================="
+	@awk_output=$$(awk -F= 'NR==FNR{a[$$1]; next} !($$1 in a)' .env env_config/env.docker); if [ -z "$$awk_output" ]; then echo "Up to date"; else echo "Missing ENV variables!\n$$awk_output"; fi
+
 ## ------------------------------------------------------------------------------
 ## Build/Run Postgres DB Commands
 ## - Builds all of the SIMS postgres db projects (db, db_setup)

scripts/bctw-deployments/.gitignore

@@ -0,0 +1,5 @@
+# Ignore all files in this directory
+files/*
+
+!files/input.dev.json
+

scripts/bctw-deployments/README.md

@@ -0,0 +1,104 @@
+# Generate SQL from existing BCTW Caribou deployments
+
+## Purpose
+SIMS needs to be updated to include existing BCTW deployments. This script combines BCTW deployments with
+matching critters and injects Caribou region herd geometries.
+
+## Pre requisites
+1. BCTW SQL - Export valid telemetry collar deployments as JSON.
+```sql
+SELECT
+  deployment_id,
+  critter_id,
+  attachment_start
+FROM collar_animal_assignment
+WHERE bctw.is_valid(valid_to)
+AND attachment_start IS NOT NULL;
+```
+2. Critterbase SQL - Export all caribou as JSON.
+```sql
+SELECT
+	c.critter_id,
+	u.unit_name
+FROM
+	critter c
+JOIN critter_collection_unit cc
+ON
+	c.critter_id = cc.critter_id
+JOIN xref_collection_unit u
+ON
+	cc.collection_unit_id = u.collection_unit_id
+WHERE
+	c.itis_tsn = 180701;
+```
+3. Create JSON file from previous outputs as single array.
+
+- critter_deployments.json
+```json
+[
+  {
+    "critter_id": "A",
+    "unit_name": "Atlin"
+  },
+  {
+    "critter_id": "B",
+    "unit_name": "Atlin"
+  },
+  {
+    "deployment_id": "C",
+    "critter_id": "A",
+    "attachment_start": "2024-01-01",
+  },
+  {
+    "deployment_id": "D",
+    "critter_id": "B",
+    "attachment_start": "2024-01-01",
+  },
+  ...
+]
+
+```
+
+## How to run
+1. Create input file.
+2. Call run.sh with input file as argument.
+
+```bash
+./run.sh {input-filename}.json
+
+# Dev example
+./run.sh input.dev.json
+```
+
+## Requirements
+- Ticket: [SIMSBIOHUB-496](https://apps.nrs.gov.bc.ca/int/jira/browse/SIMSBIOHUB-496)
+
+As a biologist who had uploaded telemetry deployments to BCTW through the BCTW UI, I want to see those deployment IDs in a SIMS Survey.
+
+When deciding what Survey to put a deployment ID in, group by deployment year and caribou herd.
+
+For example,
+
+- Telkwa herd 2021 would be a Survey
+- Telkwa herd 2022 would be a Survey
+- Porcupine herd 2022 would be a Survey
+
+#### For every Survey, make a new Project with the following values:
+
+- Name: Caribou herd name - telemetry
+- Program: Wildlife
+- Dates: Jan. 1 - Dec. 31 of {year}
+- Objectives: Telemetry deployments for Caribou herd name in year.
+
+#### For each Survey, include these values:
+
+- Name: Caribou herd name - Year - telemetry
+- Type: Monitoring
+- Start date: Date of the earliest telemetry deployment in the Survey
+- End date: Date of the last telemetry deployment in the Survey
+- Species: Caribou
+- Ecological Variables: Mortality, Distribution
+- Site selection strategy: "Oportunistic" (have to add this as an option)
+- Study area: Relevant herd's boundary
+
+