BHBC-1966: Push Dev To Test (#826)

* Fix/Enhancement: Port improved user access request functionality from Restoration, Adjust access request approval to account for existing bceid-basic-business identity sources (#771)

- Port improved user access request functionality from Restoration
  - Better/fixed handling for approving/denying user requests
  - Adjust access request approval to account for existing bceid-basic-business identity sources
- Existing access requests created before we accounted for bceid-basic-and-business identity sources should no longer throw an error when trying to approve/deny them.

* BHBC-1730: Use centerOfMass instead of centroid for project area center (#770)

* BHBC-1730: Use centerOfMass instead of centroid for project area center point.

* BHBC-1736: Fix Read More/Read Less idempotence bug (#772)

* BHBC-1736: Tighten qualification for string truncating

* BHBC-1736: Fix null coalesce

* BHBC-1736: Change variable name to be more descriptive

* Bugfix: Incorrect identity source enum (#776)

- account for the fact that openapi enums are case sensitive

* Create toDraft.yml (#779)

* Create toDraft.yml

* remove dependency

* Bump sqlite3 from 5.0.2 to 5.0.8 in /n8n (#773)

Bumps [sqlite3](https://github.com/TryGhost/node-sqlite3) from 5.0.2 to 5.0.8.
- [Release notes](https://github.com/TryGhost/node-sqlite3/releases)
- [Changelog](https://github.com/TryGhost/node-sqlite3/blob/master/CHANGELOG.md)
- [Commits](TryGhost/node-sqlite3@v5.0.2...v5.0.8)

---
updated-dependencies:
- dependency-name: sqlite3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nick Phura <[email protected]>

* Fixed horizontal autoscaler and consolidate deployment files (#781)

* Fixed horizontal autoscaler and consolidate deployment files

* Some config changes

* Forgot one

* fix

* Set utilization as portion of reques, not maximum

* BHBC-1778: Make resources page publicly viewable (#783)

* BHBC-1776: Update docker-compose and related env vars (#782)

* BHBC-1759: Fix cypress tests (#784)

- Fix cypress tests
- Update n8n version/config

* BHBC-1755: Add backbone api env var and platform-service. (#780)

* BHBC-1755: Add backbone api env var and platform-service.
- Remove clamav hardcoded default values
- Improve checking for required clamav env vars before initializing scanner
- Add missing clamav env vars to api deployment yaml

* Node upgrade as Cypress needs a newer version of node (#785)

* Bump convict from 6.2.2 to 6.2.3 in /n8n (#786)

Bumps [convict](https://github.com/mozilla/node-convict) from 6.2.2 to 6.2.3.
- [Release notes](https://github.com/mozilla/node-convict/releases)
- [Changelog](https://github.com/mozilla/node-convict/blob/master/CHANGELOG.md)
- [Commits](mozilla/node-convict@v6.2.2...v6.2.3)

---
updated-dependencies:
- dependency-name: convict
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Updates the HPAs for APP and API (#790)

* BHBC-1783: Error When Editing Purpose and Methodology (#787)

Fixed an error that occurred when attempting to edit the ‘Purpose and Methodology’ section of a survey.

 - Updated schema validation for GET on purpose_methodology update endpoint.
 - BHBC-1783: Add API response validation testing to update endpoint (work in progress).
 - BHBC-1783: Amend platform-service and its test file w 'dwc/submission/create' endpoint.

* BHBC-1775, BHBC-1809: Templates in prod are still downloaded from S3 Dev (#793)

 - Replace hardcoded URLs in Resources page by implementing env. vars (BHBC-1775)
 - Fix API response validation bugs for Project Drafts (BHBC-1809)

* BHBC-1796-1810 : bug fix - xlsx observation upload not completing (#792)

BHBC-1796: Bug fix - Observation points not displaying on map
BHBC-1810: Bug fix - Transformation of large template file crashes API in Openshift

* fix display of occurrences on full-screen view (#794)

* BHBC-1789: EML Updates + Survey Service (#766)

Tech debt: survey-service
EML: major updates to EML creation code

* BUGFIX: Strip null values from vantage code array in SQL response

* Tech Debt: Fix Cypress Tests (#800)

Tech Debt: Fix Cypress Tests (#800)

* BHBC-1837: Fix survey attachment metadata endpoint (#801)

Bug fix for survey attachment view details

* BHBC-1201: Push project/survey metadata (EML) to backbone on project/survey create/update (#803)

BHBC-1201: Push project/survey metadata (EML) to backbone on create/update

* BHBC-1841: Remove Project/Survey Publish Buttons And Related Code (#804)

 - Project and survey UI no longer include publish button
 - API no longer has endpoints for publishing

* BHBC-1868: Push Observation Data to BioHub (#805)

System admin button + endpoint to submit project and survey EML + Observation data to BioHub Backbone.

* BHBC-1868-2: Handle error popup for BioHub Submit, remove some old logs, enable biohub submission env var for dev. (#806)

- Handle error popup for BioHub Submit
- remove some old logs
- enable biohub submission env var for dev

* TechDebt: Update Keycloak config - add pkce method (#807)

- Update keycloak config to include pkce option

* TechDebt: Port latest version of DataLoader hook (and related hooks/tests) to SIMS (#809)

* TechDebt: Update Template apiVersion from "v1" to "template.openshift.io/v1" (#810)

* BHBC-1893/1880: Update the Composition and SRB Survey Template (#808)

* BHBC-1867: Cant delete a system user that has no system role (#811)

- Fix issue that prevented deleting system users that had no system role.
- Fix bug that was displaying non-human users in the manage users list.

* Update Sims Template Validations (#812)

* BHBC-1914, 1918, 1920 (#816)

Updated validation for summary templates

* BHBC-1923: Update Resource Page (#814)

* BHBC-1912:  Remove the Table Preview for Submitted Observations and Summary Results (#815)

* edits for moose srb and comp validation

* add transect validation

* add sheep pop comp validation survey (broken)

* sheep validation functioning

* goat validation functioning

* fix edits for validations

* trigger build

* initial commit

* remove Observation and Summary CSV table and ref

* trigger build

* fix merge conflict

* more merge conflicts

Co-authored-by: Anissa Agahchen <[email protected]>

* BHBC-1922: Add Attachments Datra To EML (#817)

* Include attachments metadata in EML
- adjusted EML pub date to short ISO format
- adjusted order of EML to conform with specification
- adjusted database smoke test script for usage as initial data population. while application now does not throw error, issues persist and have been documented in Jira

* added new elk summary template to resource page (#818)

Added Elk Summary Template to Resource Page

* BHBC-1930, 1931, 1932 (#820)- Elk Templates and summary results

* BHBC-1547: Create Project Improvements (#819)

Refactor create project page to a single form, removing the multi-step wizard

* BHBC-1925: Move Permits to Survey (#813)

- Adjusted permit model for model 1.2
- Adjusted db function project deletion routines
- Added smoke test file
- Purge old permit code from all project related components (frontend and backend)
- Add CustomFieldArray Component
- Move permit components/logic to Survey (from Project)

* BHBC-1966: Add 2 new items to the agency codes list (#825)

Add 2 new items to the agency codes list

Co-authored-by: Curtis Upshall <[email protected]>
Co-authored-by: Roland Stens <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Anissa Agahchen <[email protected]>
Co-authored-by: Kjartan <[email protected]>
Co-authored-by: AlfredRosenthal <[email protected]>
Co-authored-by: Charlie Garrett-Jones <[email protected]>

Makefile

@@ -9,9 +9,6 @@
 # Apply the contents of the .env to the terminal, so that the docker-compose file can use them in its builds
 export $(shell sed 's/=.*//' .env)
 
-.DEFAULT : help
-.PHONY : setup close clean build-backend run-backend build-web run-web database app api db-setup db-migrate db-rollback n8n-setup n8n-export clamav install test cypress lint lint-fix format format-fix help
-
 ## ------------------------------------------------------------------------------
 ## Alias Commands
 ## - Performs logical groups of commands for your convenience
@@ -57,6 +54,13 @@ clean: ## Closes and cleans (removes) all project containers
 	@echo "==============================================="
 	@docker-compose -f docker-compose.yml down -v --rmi all --remove-orphans
 
+prune: ## Deletes ALL docker artifacts (even those not associated to this project)
+	@echo -n "Delete ALL docker artifacts? [y/n] " && read ans && [ $${ans:-n} = y ]
+	@echo "==============================================="
+	@echo "Make: prune - deleting all docker artifacts
+	@echo "==============================================="
+	@docker system prune --all --volumes
+
 ## ------------------------------------------------------------------------------
 ## Build/Run Postgres DB Commands
 ## - Builds all of the SIMS postgres db projects (db, db_setup)

api/.pipeline/config.js

@@ -83,6 +83,8 @@ const phases = {
       (isStaticDeployment && (staticUrls.dev || defaultHostAPP)) ||
       `${appName}-${changeId}-af2668-dev.apps.silver.devops.gov.bc.ca`,
     backboneApiHost: 'https://api-dev-biohub-platform.apps.silver.devops.gov.bc.ca',
+    backboneIntakePath: '/api/dwc/submission/intake',
+    backboneIntakeEnabled: true,
     env: 'dev',
     elasticsearchURL: 'https://elasticsearch-af2668-dev.apps.silver.devops.gov.bc.ca',
     tz: config.timezone.api,
@@ -104,6 +106,8 @@ const phases = {
     host: staticUrlsAPI.test,
     appHost: staticUrls.test,
     backboneApiHost: 'https://api-test-biohub-platform.apps.silver.devops.gov.bc.ca',
+    backboneIntakePath: '/api/dwc/submission/intake',
+    backboneIntakeEnabled: false,
     env: 'test',
     elasticsearchURL: 'http://es01:9200',
     tz: config.timezone.api,
@@ -125,6 +129,8 @@ const phases = {
     host: staticUrlsAPI.prod,
     appHost: staticUrls.prod,
     backboneApiHost: 'https://api-biohub-platform.apps.silver.devops.gov.bc.ca',
+    backboneIntakePath: '/api/dwc/submission/intake',
+    backboneIntakeEnabled: false,
     env: 'prod',
     elasticsearchURL: 'http://es01:9200',
     tz: config.timezone.api,

api/.pipeline/lib/api.deploy.js

@@ -31,6 +31,8 @@ module.exports = (settings) => {
         CHANGE_ID: phases.build.changeId || changeId,
         APP_HOST: phases[phase].appHost,
         BACKBONE_API_HOST: phases[phase].backboneApiHost,
+        BACKBONE_INTAKE_PATH: phases[phase].backboneIntakePath,
+        BACKBONE_INTAKE_ENABLED: phases[phase].backboneIntakeEnabled,
         NODE_ENV: phases[phase].env || 'dev',
         ELASTICSEARCH_URL: phases[phase].elasticsearchURL,
         TZ: phases[phase].tz,

api/openshift/api.bc.yaml

@@ -1,4 +1,4 @@
-apiVersion: v1
+apiVersion: template.openshift.io/v1
 kind: Template
 metadata:
   creationTimestamp: null

api/openshift/api.dc.yaml

@@ -1,4 +1,4 @@
-apiVersion: v1
+apiVersion: template.openshift.io/v1
 kind: Template
 metadata:
   resourceVersion: ''
@@ -25,7 +25,14 @@ parameters:
     description: APP host for application frontend
     value: ''
   - name: BACKBONE_API_HOST
-    description: API host for BioHub Platform Backbone
+    required: true
+    description: API host for BioHub Platform Backbone. Example "https://platform.com".
+  - name: BACKBONE_INTAKE_PATH
+    required: true
+    description: API path for BioHub Platform Backbone DwCA submission intake endpoint. Example "/api/path/to/intake".
+  - name: BACKBONE_INTAKE_ENABLED
+    required: true
+    description: Controls whether or not SIMS will submit DwCA datasets to the BioHub Platform Backbone. Set to "true" to enable it, will be disabled by default otherwise.
   - name: CHANGE_ID
     description: Change id of the project. This will help to pull image stream
     required: true
@@ -161,6 +168,10 @@ objects:
                   value: ${APP_HOST}
                 - name: BACKBONE_API_HOST
                   value: ${BACKBONE_API_HOST}
+                - name: BACKBONE_INTAKE_PATH
+                  value: ${BACKBONE_INTAKE_PATH}
+                - name: BACKBONE_INTAKE_ENABLED
+                  value: ${BACKBONE_INTAKE_ENABLED}
                 - name: ENABLE_FILE_VIRUS_SCAN
                   value: ${ENABLE_FILE_VIRUS_SCAN}
                 - name: CLAMAV_HOST