SIMSBIOHUB-647: Create Observations Page #1444

mauberti-bc · 2024-12-03T22:26:19Z

Links to Jira Tickets

{Include a link to all applicable Jira tickets}

Description of Changes

Allows observations to be added from a dedicated page

Testing Notes

{List any relevant testing considerations, necessary pre-reqs, and areas of the app to focus on. Specifically, include anything that will help the reviewers of this PR verify the code is functioning as expected.}

TODO

Check frontend tests
Check backend tests

github-actions · 2024-12-03T22:26:30Z

Openshift URLs for the PR Deployment:

codecov · 2024-12-03T22:27:55Z

Codecov Report

Attention: Patch coverage is 20.14028% with 797 lines in your changes missing coverage. Please review.

Project coverage is 45.35%. Comparing base (d1eb7b2) to head (bfa4367).

Files with missing lines	Patch %	Lines
...nts/sampling/hooks/useSamplingInformationCache.tsx	0.00%	76 Missing ⚠️
...veys/observations/create/CreateObservationPage.tsx	0.00%	69 Missing ⚠️
...ents/environments/environment/EnvironmentField.tsx	0.00%	69 Missing ⚠️
...onents/sampling/components/SamplingPeriodField.tsx	0.00%	57 Missing ⚠️
...nents/sampling/components/MethodTechniqueField.tsx	0.00%	55 Missing ⚠️
...mponents/sampling/components/SamplingSiteField.tsx	0.00%	45 Missing ⚠️
...s/observation-repository/observation-repository.ts	30.61%	32 Missing and 2 partials ⚠️
...i/src/repositories/observation-repository/utils.ts	60.25%	31 Missing ⚠️
...ations/form/components/subcounts/SubcountsForm.tsx	0.00%	29 Missing ⚠️
...ures/surveys/observations/form/ObservationForm.tsx	0.00%	28 Missing ⚠️
... and 49 more

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1444      +/-   ##
==========================================
- Coverage   45.92%   45.35%   -0.57%     
==========================================
  Files         907      946      +39     
  Lines       23537    24262     +725     
  Branches     3492     3639     +147     
==========================================
+ Hits        10809    11005     +196     
- Misses      12136    12649     +513     
- Partials      592      608      +16

☔ View full report in Codecov by Sentry.
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app/src/hooks/api/useObservationApi.ts

app/src/constants/i18n.ts

app/src/features/surveys/observations/create/CreateObservationPage.tsx

NickPhura · 2025-01-16T20:38:37Z

I pushed up a few misc changes. Mostly just some component cleanup and addressing a few react dependency complaints, etc.

wip wip: create location and date sections on form wip: style subcount form wip: adding measurements to subcounts add dual autocomplete subcount form subcount table on create observation page fix measurement search show measurement options in subcount table on create observation page wip: formik validation add subcount sign placeholder to create request wip: environments incorrectly formatted in handlesubmit fix incorrect key fix environments on create observations page fix measurement interfaces SIMSBIOHUB-659: Add Pagination to System Alerts on Admin Page (#1459) Add Pagination to System Alerts on Admin Page --------- Co-authored-by: Nick Phura <[email protected]> Update CSV Error Import Dialog Styling (#1456) - update csv import error dialog - replace failure snackbar & add frontend pagination to csv import errors BugFix: Fix Type for Capture Attachments (#1460) - modifying critter index file --------- Co-authored-by: Macgregor Aubertin-Young <[email protected]> Co-authored-by: Macgregor Aubertin-Young <[email protected]> BugFix: Method Attributes SQL (#1462) - fix sql Added DualAutocompleteUnitField.tsx to help reduce the size of the DualAutocompleteField.tsx. Renamed some of the dual autocomplete field props, just to make them more consistent/predictable. Fixed missing props in create/edit technique vantages (missing category data type prop). Add formik snackbar error component to observation form. Addressed a few react missing dependency warnings. Update missed jsdoc comments. Update missed jsdoc comments 2. WIP: Add create observation sampling fields. Working sampling fields. Enhancements to sampling fields

- WIP: observation db migrations. - Add database-models.

Fix subcount types. Fix existing unit tests.

…BIOHUB-647b

…nto SIMSBIOHUB-647b

api/src/repositories/observation-repository/observation-repository.ts

Remove console logs.

sonarqubecloud · 2025-02-04T01:45:22Z

Quality Gate failed

Failed conditions
10.1% Duplication on New Code (required ≤ 3%)
C Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

Catch issues before they fail your Quality Gate with our IDE extension SonarQube for IDE

api/src/repositories/observation-repository/observation-repository.ts

+      if (pagination.sort && pagination.order) {
+        if (pagination.sort === 'subcount') {
+          const knex = getKnex();
+          query.orderByRaw(knex.raw(`(subcount->>?)::numeric ${pagination.order}`, [pagination.sort]));


api/src/repositories/observation-repository/observation-repository.ts

+      if (pagination.sort && pagination.order) {
+        if (pagination.sort === 'subcount') {
+          const knex = getKnex();
+          query.orderByRaw(knex.raw(`(subcount->>?)::numeric ${pagination.order}`, [pagination.sort]));


To fix the problem, we need to ensure that the user-provided pagination.order value is safely embedded into the SQL query. This can be achieved by using parameterized queries or by explicitly validating and sanitizing the input before using it in the query.

The best way to fix this issue without changing existing functionality is to validate the pagination.order value to ensure it is either 'asc' or 'desc' before using it in the query. This can be done by using a conditional check and throwing an error if the value is invalid.

MacQSL · 2025-02-04T18:33:26Z

api/src/database-units/environment_unit.ts

question: Do you think we should name this directory database-units or something like database-types / database-enums. I see in the database there is an additional type / enum for alert_severity would this also be a database-unit?

Open to any name for the folder. Can't remember how I landed on unit. Probably just trying to pick something generic that could cover database enums (but also any other enum-like concept, if there are others?), and which aren't specifically table models.

MacQSL · 2025-02-04T18:34:30Z

api/src/openapi/schemas/observation.ts

+  ],
+  properties: {
+    observation_environment_qualitative_id: {
+      type: 'integer'


nit: minimum 1

MacQSL · 2025-02-04T18:34:44Z

api/src/openapi/schemas/observation.ts

+  required: ['observation_environment_quantitative_id', 'environment_quantitative_id', 'value'],
+  properties: {
+    observation_environment_quantitative_id: {
+      type: 'integer'


nit: minimum 1

MacQSL · 2025-02-04T18:35:18Z

api/src/openapi/schemas/observation.ts

+  required: ['observation_subcount_id', 'subcount', 'comment', 'qualitative_measurements', 'quantitative_measurements'],
+  properties: {
+    observation_subcount_id: {
+      type: 'integer'


nit: minimum 1

MacQSL · 2025-02-04T18:37:20Z

api/src/paths/observation/flattened/index.ts

+      schema: {
+        type: 'array',
+        items: {
+          type: 'integer'


nit: minimum 1 / 0?

MacQSL · 2025-02-04T18:37:39Z

api/src/paths/observation/flattened/index.ts

+      description: 'ITIS TSN number',
+      required: false,
+      schema: {
+        type: 'integer',


nit: minimum 1 / 0?

mauberti-bc added the Not Ready For Review Addressing feedback and/or refactoring label Dec 3, 2024

mauberti-bc added Early Feedback Welcome PR is not finished, but early review feedback is welcomed and removed Not Ready For Review Addressing feedback and/or refactoring labels Jan 8, 2025

mauberti-bc added Ready For Review PR is ready for review and removed Early Feedback Welcome PR is not finished, but early review feedback is welcomed labels Jan 16, 2025

NickPhura reviewed Jan 16, 2025

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app/src/hooks/api/useObservationApi.ts Show resolved Hide resolved

NickPhura reviewed Jan 16, 2025

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app/src/constants/i18n.ts Outdated Show resolved Hide resolved

NickPhura reviewed Jan 16, 2025

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app/src/features/surveys/observations/create/CreateObservationPage.tsx Outdated Show resolved Hide resolved

NickPhura force-pushed the SIMSBIOHUB-647b branch from a9ff7b5 to def7139 Compare January 17, 2025 00:51

NickPhura added Early Feedback Welcome PR is not finished, but early review feedback is welcomed and removed Ready For Review PR is ready for review labels Jan 20, 2025

mauberti-bc and others added 2 commits January 21, 2025 10:06

Tweaks

4683f3f

NickPhura force-pushed the SIMSBIOHUB-647b branch from e0b3dde to 4683f3f Compare January 21, 2025 18:07

NickPhura added 13 commits January 21, 2025 16:09

Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-647b

a24649d

Update create observation form components. Re-arrange folder structure.

d72a7aa

Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-647b

60f90ef

- Updated observation components.

167ea81

- WIP: observation db migrations. - Add database-models.

Fix migration, update seeds.

7bbc575

Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-647b

7daf2d3

Most of the backend is happy with the environment changes.

49e7e43

Fix existing unit tests

676df35

Initial: Split some interfaces into separate files for readability

397d54b

Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-647b

a0ccafc

Update/add database models

37747f6

Update interfaces

b2586f5

Change count back to subcount.

d3c0a11

Fix subcount types. Fix existing unit tests.

NickPhura and others added 8 commits January 31, 2025 20:37

Add get/find flattened observation service/repo functions

4db6afd

Remove console logs

bd8e33d

Fix sql

05ddb06

styling subcount card

24d01eb

Merge branch 'SIMSBIOHUB-647b' of github.com:bcgov/biohubbc into SIMS…

d11c591

…BIOHUB-647b

Update UI to fetch flattened observations

265fc1c

Merge branch 'SIMSBIOHUB-647b' of https://github.com/bcgov/biohubbc i…

ad03bf7

…nto SIMSBIOHUB-647b

Update observation comment column component.

2347bea

github-advanced-security bot found potential problems Feb 3, 2025

View reviewed changes

api/src/repositories/observation-repository/observation-repository.ts Fixed Show fixed Hide fixed

api/src/repositories/observation-repository/observation-repository.ts Fixed Show fixed Hide fixed

NickPhura added 3 commits February 3, 2025 16:27

Fix sampling styling

9073358

Merge remote-tracking branch 'origin/dev' into SIMSBIOHUB-647b

a4a8d03

Preload sites, techniques, and periods.

bfa4367

Remove console logs.

NickPhura added Ready For Review PR is ready for review and removed Early Feedback Welcome PR is not finished, but early review feedback is welcomed labels Feb 4, 2025

github-advanced-security bot found potential problems Feb 4, 2025

View reviewed changes

MacQSL reviewed Feb 4, 2025

View reviewed changes

api/src/paths/observation/flattened/index.ts

schema: {

type: 'array',

items: {

type: 'integer'

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nit: minimum 1 / 0?

MacQSL reviewed Feb 4, 2025

View reviewed changes

@@ -293,2 +293,5 @@
                       const knex = getKnex();
+                      if (pagination.order !== 'asc' && pagination.order !== 'desc') {
+                        throw new Error('Invalid order value');
+                      }
                       query.orderByRaw(knex.raw(`(subcount->>?)::numeric ${pagination.order}`, [pagination.sort]));

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SIMSBIOHUB-647: Create Observations Page #1444

SIMSBIOHUB-647: Create Observations Page #1444

mauberti-bc commented Dec 3, 2024 •

edited by NickPhura

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SIMSBIOHUB-647: Create Observations Page #1444

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SIMSBIOHUB-647: Create Observations Page #1444

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mauberti-bc commented Dec 3, 2024 • edited by NickPhura Loading

Links to Jira Tickets

Description of Changes

Testing Notes

TODO

github-actions bot commented Dec 3, 2024

codecov bot commented Dec 3, 2024 • edited Loading

Codecov Report

NickPhura commented Jan 16, 2025

sonarqubecloud bot commented Feb 4, 2025

Quality Gate failed

MacQSL Feb 4, 2025

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mauberti-bc commented Dec 3, 2024 •

edited by NickPhura

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edited

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