Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

SIMSBIOHUB-459 - Update SIMS To Use ITIS and BioHub Taxonomy #1210

Merged
merged 44 commits into from
Feb 14, 2024
Merged

SIMSBIOHUB-459 - Update SIMS To Use ITIS and BioHub Taxonomy #1210

merged 44 commits into from
Feb 14, 2024

Conversation

curtisupshall
Copy link
Contributor

@curtisupshall curtisupshall commented Feb 6, 2024 •
edited
Loading

Links to Jira Tickets

Quickstart for the new .env variables

Paste these into your .env, replacing the old BACKBONE_API_HOST:

# BACKBONE_INTERNAL_API_HOST=http://host.docker.internal:6200
BACKBONE_INTERNAL_API_HOST=https://api-dev-biohub-platform.apps.silver.devops.gov.bc.ca

# BACKBONE_PUBLIC_API_HOST=http://localhost:6200
BACKBONE_PUBLIC_API_HOST=https://api-dev-biohub-platform.apps.silver.devops.gov.bc.ca

Description of Changes

  • .env and pipeline changes to reflect new environment variables:
    • BACKBONE_INTERNAL_API_HOST: The internal host used by the SIMS API to talk to BioHub
    • BACKBONE_PUBLIC_API_HOST: The public host used by the SIMS frontend (and other services) to talk to BioHub
  • Removes code associated with elasticsearch;
  • Replaces taxonomy-related API calls with BioHub taxonomy endpoint calls;
  • Shows error dialog whenever observation import fails;
  • Adds new Species column alias support for observation importing:
    • Species
    • Tsn
    • Itis_tsn
    • Taxon
  • Minor edits to the ErrorDialog;
  • Updates database seeds to use ITIS TSN instead of elasticsearch;
  • Updates the survey_observation and study_species tables to support ITIS TSN/scientific name.

Testing Notes

You should be able to:

  • Import observations, supporting allowed column aliases;
  • Edit observations;
  • Insert new observations;
  • Create/edit a survey with focal species + ancillary species.

@curtisupshall curtisupshall added the Not Ready For Review Addressing feedback and/or refactoring label Feb 6, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 6, 2024

Openshift URLs for the PR Deployment:

@curtisupshall curtisupshall changed the title SIMSBIOHUB-459 SIMSBIOHUB-459 - Update SIMS To Use ITIS and BioHub Taxonomy Feb 7, 2024
KjartanE and others added 15 commits February 7, 2024 12:44
@KjartanE
fix project and survey page taxon display
5ea43df
@curtisupshall
SIMSBIOHUB-459: Updated db seeder for observation records.
237950e
@curtisupshall
SIMSBIOHUB-459: TSN fetching refactor WIP
f73e077
@KjartanE
observations view functioning, save wip
1d1193d
@curtisupshall @KjartanE
SIMSBIOHUB-414: Show Feature Popup on Survey Page (#1206)
ae4c007 
* Adds survey sampling sites and study areas back to the Survey Map (since being removed by #1202);
* Adds various popups to survey map features, showing various point/polygon metadata;
* Removes extraneous observation table hook call;
* Updates method names and documentation for telemetry API hooks.
@NickPhura @KjartanE
SIMSBIOHUB-462: Observation Subcount Schema (#1207)
6180975 
SIMSBIOHUB-462: Observation Subcount Schema
@curtisupshall @KjartanE
SIMSBIOHUB-460, 475 - Study Area + Observations Import bugs (#1209)
4f2bb8e 
* Fixed a bug where newly added Study Areas were not shown until page reload
* Fixed a bug where users could not import survey observations
@KjartanE
Merge branch 'dev' into SIMSBIOHUB-459
9a1a9a1
@curtisupshall
SIMSBIOHUB-459: Removed useItisApi and moved logic to useTaxonomyApi;…
4f2bdc4 
… Added useTaxonomyApi.interface
@curtisupshall
Merge branch 'SIMSBIOHUB-459' of github.com:bcgov/biohubbc into SIMSB…
b280dca 
…IOHUB-459
@curtisupshall
SIMSBIOHUB-459: Remove wldtaxonomic_units_id in surveyspatialdata.tsx
d0e98b0
@curtisupshall
SIMSBIOHUB-459: Species observation saving works*
616aec9
@curtisupshall
SIMSBIOHUB-459: Replace BACKBONE_API_HOST with BACKBONE_INTERNAL_API_…
c1696a9 
…HOST
@curtisupshall
SIMSBIOHUB-459: Added BACKBONE_PUBLIC_API_HOST
f96264b
@KjartanE
fix/clean broken tests
cee537d
@codecov Codecov
Copy link

codecov bot commented Feb 8, 2024 •
edited
Loading

Codecov Report

Attention: 96 lines in your changes are missing coverage. Please review.

Comparison is base (cc7e913) 56.90% compared to head (086ab99) 56.63%.

Files Patch % Lines
api/src/services/observation-service.ts 10.00% 18 Missing ⚠️
api/src/services/survey-service.ts 57.89% 7 Missing and 1 partial ⚠️
...omponents/search-filter/ProjectAdvancedFilters.tsx 0.00% 8 Missing ⚠️
.../observations-table/ObservationsTableContainer.tsx 0.00% 7 Missing ⚠️
api/src/services/platform-service.ts 14.28% 5 Missing and 1 partial ⚠️
...c/components/species/AncillarySpeciesComponent.tsx 0.00% 6 Missing ⚠️
...p/src/components/species/FocalSpeciesComponent.tsx 0.00% 6 Missing ⚠️
app/src/contexts/observationsTableContext.tsx 0.00% 6 Missing ⚠️
...ts/species/components/SpeciesAutocompleteField.tsx 0.00% 5 Missing ⚠️
app/src/hooks/api/useTaxonomyApi.ts 71.42% 3 Missing and 1 partial ⚠️
... and 10 more
Additional details and impacted files 
@@            Coverage Diff             @@
##              dev    #1210      +/-   ##
==========================================
- Coverage   56.90%   56.63%   -0.28%     
==========================================
  Files         594      589       -5     
  Lines       18011    17903     -108     
  Branches     2774     2765       -9     
==========================================
- Hits        10249    10139     -110     
- Misses       7096     7105       +9     
+ Partials      666      659       -7

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@curtisupshall curtisupshall 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 Feb 9, 2024
@KjartanE KjartanE 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 12, 2024
KjartanE
KjartanE previously approved these changes Feb 13, 2024
View reviewed changes
Copy link
Contributor

@KjartanE KjartanE left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🐱

KjartanE
KjartanE approved these changes Feb 14, 2024
View reviewed changes
Copy link
Contributor

@KjartanE KjartanE left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🐈

@sonarqubecloud SonarQubeCloud
Copy link

Quality Gate Failed Quality Gate failed

Failed conditions
14.6% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

@curtisupshall curtisupshall merged commit d306ce3 into dev Feb 14, 2024
16 of 19 checks passed
@curtisupshall curtisupshall deleted the SIMSBIOHUB-459 branch February 14, 2024 03:44
curtisupshall added a commit that referenced this pull request Feb 20, 2024
@curtisupshall
SIMSBIOHUB-459 - Update SIMS To Use ITIS and BioHub Taxonomy (#1210)
1360732 
* `.env` and pipeline changed to reflect new environment variables: `BACKBONE_INTERNAL_API_HOST` and `BACKBONE_PUBLIC_API_HOST`.
* Removed code associated with elasticsearch.
* Replaced taxonomy-related API calls with BioHub taxonomy endpoint calls.
* Shows error dialog whenever observation import fails.
* Added new `Species` column alias support for observation importing.
* Minor edits to the ErrorDialog;
* Updates database seeds to use ITIS TSN instead of elasticsearch.
* Updates the `survey_observation` and `study_species` tables to support ITIS TSN/scientific name.

SIMSBIOHUB-483: Added new env vars for number of seed projects and surveys

SIMSBIOHUB-483: Removed code associated with project drafts. WIP.

SIMSBIOHUB-483: Removed code associated with project submitted status and project supplementary data.

SIMSBIOHUB-483: Removed code associated with project drafts from the Create Project page

SIMSBIOHUB-483: Renamed start and end date columns for project lists table

SIMSBIOHUB-483: Support project list server-side pagination (using common pagination API schema)

SIMSBIOHUB-483: Restructure projects list endpoint response schema and typing to accomodate pagination

SIMSBIOHUB-483: Render table counts using Number.toLocaleString

SIMSBIOHUB-483: Working frontend pagination

SIMSBIOHUB-483: Completed implementation of getProjectCount

SIMSBIOHUB-483: Lint and format fixes

SIMSBIOHUB-483: Support for column sorting

SIMSBIOHUB-483: Fix API tests

SIMSBIOHUB-483: Test coverage and added comments

SIMSBIOHUB-483: Minor tweaks to comments

SIMSBIOHUB-483: Lint/format fixes
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@KjartanE KjartanE KjartanE approved these changes

@NickPhura NickPhura NickPhura approved these changes

@al-rosenthal al-rosenthal Awaiting requested review from al-rosenthal

@MacQSL MacQSL Awaiting requested review from MacQSL

Assignees

@KjartanE KjartanE

Labels
Ready For Review PR is ready for review
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@curtisupshall @NickPhura @KjartanE