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Add STAC catalog #297

Merged
merged 91 commits into from
Aug 8, 2023
Merged

Add STAC catalog #297

merged 91 commits into from
Aug 8, 2023

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matprov
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@matprov matprov commented Feb 24, 2023 •
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Overview

  • Adds STAC to the stack (optional) when ./components/stac is added to EXTRA_CONF_DIRS.

Changes

  • Service stac (API) gets added with endpoints /twitcher/ows/proxy/stac and /stac.

  • STAC catalog can be explored via the stac-browser component, available under /stac-browser.

  • Image crim-ca/stac-app is a STAC implementation based on stac-utils/stac-fastapi.

  • Image crim-ca/stac-browser is a fork of radiantearth/stac-browser.

  • Adds Magpie permissions and service for stac endpoints.

  • Uses stac-populator to populate STAC catalog with sample collection
    items via CEDA STAC Generator, employed in sample
    CMIP Dataset Ingestion Workflows.

Demo Instance

STAC API : https://stac-dev.crim.ca/stac/
STAC Browser : https://stac-dev.crim.ca/stac-browser/

Note that by default STAC API will return 10 items to reduce payload size. It is however possible to change this limitation by adding ?limit=200 to the URL in order to query 200 items. In the response payload you'll have a link referring to the next items, adding a token to the query params in order for STAC API to return next results.

Sample STAC API collection query using a CLI

Remove the -c flag for global query across any collection.

pip install pystac-client
stac-client search https://stac-dev.crim.ca/stac -c c604ffb6d610adbb9a6b4787db7b8fd7 --query "variable_id=txgt_32" "scenario=ssp585"

Sample STAC API global query using CQL via cURL call

Note that the operators are describe here : https://portal.ogc.org/files/96288

curl --location --globoff 'https://stac-dev.crim.ca/stac/search' \
--header 'Content-Type: application/json' \
--data '{
   "filter":{
      "and":[
         {
            "eq":[
               {
                  "property":"freq"
               },
               "MS"
            ]
         },
         {
            "like":[
               {
                  "property":"variable_id"
               },
               "tr_%"
            ]
         }
      ],
      "intersects":[
         {
            "property":"geometry"
         },
         {
            "type":"Polygon",
            "coordinates":[
               [
                  [
                     -140.99778,
                     41.6751050889
                  ],
                  [
                     -140.99778,
                     83.23324
                  ],
                  [
                     -52.6480987209,
                     83.23324
                  ],
                  [
                     -52.6480987209,
                     41.6751050889
                  ],
                  [
                     -140.99778,
                     41.6751050889
                  ]
               ]
            ]
         }
      ],
      "anyinteracts":[
         {
            "property":"datetime"
         },
         [
            "2010-05-03T13:21:30.040Z",
            "2022-05-03T13:21:30.040Z"
         ]
      ]
   }
}'

Get the queryables of the CMIP6 collection, statically created at collection creation

https://stac-dev.crim.ca/stac/collections/c604ffb6d610adbb9a6b4787db7b8fd7

Get the queryables of the CMIP6 collection, dynamically created at query time

https://stac-dev.crim.ca/stac/collections/c604ffb6d610adbb9a6b4787db7b8fd7/queryables

Get the queryables of the union of the CMIP5 and CMIP6 collections, dynamically created at query time

https://stac-dev.crim.ca/stac/queryables?collections=0798aa197d54eb4332767a5a4077fb0f,c604ffb6d610adbb9a6b4787db7b8fd7

daccs_configs_branch: stac_populator
daccs_skip_ci: true

fyi @huard @mishaschwartz

Mathieu Provencher added 30 commits December 6, 2022 23:14
add stac components to compose
24ee7bf
added pgstac container healthcheck
148501f
moved stac to components
e0c4231
stac configs
b182aa4
stac magpie config
0c024c5
remove stac extra_host
0aecb0f
added Forwarded nginx header to twitcher
a41fbea
Merge branch 'master' into add_stac
3cf6441
specify ROUTER_PREFIX
4671626
register stac-browser in nginx
fef2f1d
added comment
ad3cbd5
stac proxy redirect
3671d21
remove stac command
de276cd
ignore
dfbfcdd
proxy for stac-browser
5ae391f
added todo
3840abe
added stac populator
2964165
adding stac populator
1e34626
stac asset populator
74a05a3
wip
4d3c348
working asset generator timeout
394b36f
stac-populator env vars
dd07828
stac-populator env var
9dbf1c9
renamed pgstac
be2c29d
fix stac crawling
800f060
added wait-for-it for stac-populator
bc5e2a2
stac-browser catalogUrl
8466780
stac-browser env vars
079fcd2
use POSTGRES_PAVICS_* env vars
88ccb34
added comment
ac90cbf
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E2E Test Results

DACCS-iac Pipeline Results

Build URL : http://daccs-jenkins.crim.ca:80/job/DACCS-iac-birdhouse/1830/
Result : failure

BIRDHOUSE_DEPLOY_BRANCH : add_stac
DACCS_CONFIGS_BRANCH : stac_populator
PAVICS_E2E_WORKFLOW_TESTS_BRANCH : master
PAVICS_SDI_BRANCH : master

DESTROY_INFRA_ON_EXIT : true
PAVICS_HOST : https://host-140-133.rdext.crim.ca

Infrastructure deployment failed. Instance has not been destroyed. @matprov

fmigneault
fmigneault requested changes Jul 20, 2023
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Quick review pass.
Will review again once the platform works with those configs.

birdhouse/components/stac/config/canarie-api/_docker-compose-extra.yml Outdated Show resolved Hide resolved
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@fmigneault fmigneault mentioned this pull request Jul 21, 2023
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matprov commented Jul 27, 2023

Is there a way to change or remove these links so that they're not confusing to the end-user?

@mishaschwartz Now possible via

stac:
    environment:
         - OPENAPI_URL=/stac/api
         - DOCS_URL=/stac/api.html

fmigneault
fmigneault approved these changes Aug 7, 2023
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Just a minor edit left to fix.

Is there anything still blocking this PR?

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matprov commented Aug 8, 2023

Is there anything still blocking this PR?

Only approvals of @mishaschwartz and @tlvu

@matprov matprov merged commit bc3273c into master Aug 8, 2023
3 checks passed
@matprov matprov deleted the add_stac branch August 8, 2023 14:41
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@matprov
The bump versions were not applied. Are they planned in a follow-up PR?

tlvu
tlvu reviewed Aug 9, 2023
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First off, totally sorry for my late review. I had too much on my plate lately and I completely forgot about this PR given it has been opened for like 6 months and movement seems to only be picked up lately.

I found a few things to fix here but it's alright since all are in the new codes so no regression at all.

CHANGES.md
@@ -15,7 +15,32 @@
[Unreleased](https://github.com/bird-house/birdhouse-deploy/tree/master) (latest)
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@matprov No bumpversion? FYI the release procedure https://github.com/bird-house/birdhouse-deploy/blob/master/birdhouse/README.rst#release-procedure

Planning on a quick subsequent PR?

birdhouse/components/stac/docker-compose-extra.yml
services:
stac:
container_name: stac
image: ghcr.io/crim-ca/stac-app:main
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Not using exact version for reproductibility?

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@mishaschwartz mishaschwartz Aug 10, 2023 •
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I'm guessing this first? crim-ca/stac-app#1

birdhouse/components/stac/docker-compose-extra.yml
environment:
- POSTGRES_USER=${STAC_POSTGRES_USER}
- POSTGRES_PASS=${STAC_POSTGRES_PASSWORD}
- POSTGRES_DBNAME=postgis
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Just curious, is postgis hardcoded somewhere? Why not call the DB simply stac?

birdhouse/components/stac/docker-compose-extra.yml

stac-browser:
container_name: stac-browser
image: ghcr.io/crim-ca/stac-browser:docker_image_push
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Versionned image for reproductibility?

birdhouse/components/stac/docker-compose-extra.yml
- PGDATABASE=postgis
volumes:
- stac-db:/var/lib/postgresql/data
healthcheck:
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Nice to have a healthcheck here. The other 2 containers, would be nice to have some sort of healthcheck as well.

birdhouse/components/stac/docker-compose-extra.yml
retries: 5

# extend proxy with endpoint and config for STAC API access
proxy:
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Duplicate fragment with existing file birdhouse/components/stac/config/proxy/docker-compose-extra.yml !

birdhouse/config/twitcher/config/proxy/conf.extra-service.d/twitcher.conf.template
@@ -4,4 +4,5 @@
proxy_set_header X-Forwarded-Proto $real_scheme;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Host $host:$server_port;
proxy_set_header Forwarded "proto=https;host=${PAVICS_FQDN}"; # Helps the STAC component to craft URLs containing the full PAVICS_FQDN
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Better use PAVICS_FQDN_PUBLIC for anything public facing.

birdhouse/optional-components/stac-populator/docker-compose-extra.yml
# populates STAC catalog with sample collection items
stac-populator:
container_name: stac-populator
image: ghcr.io/crim-ca/stac-populator:master
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Versionned image for reproductibility?

birdhouse/optional-components/stac-populator/docker-compose-extra.yml
- STAC_ASSET_GENERATOR_TIMEOUT=${STAC_ASSET_GENERATOR_TIMEOUT}
- STAC_HOST=http://stac:8000/stac # STAC API internally accessed to avoid Twitcher authentication
command: >
bash -c "./wait-for-it.sh stac:8000 -t 30 && ./populate.sh"
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Noob question about the stac-populator: does this just populate once and exit or it stays in the background and listen for new data and repopulate?

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Another Noob question about the stac-populator: how does it knows which collection to crawl and populate the stac-db? Is the path https://pavics.ouranos.ca/twitcher/ows/proxy/thredds/catalog/datasets/catalog.html hardcoded? This should be configurable.

Or are we crawling directly on disk? But then I do not see any volume-mount.

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#297 (comment)

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@tlvu The pipeline for populating STAC is being handled in a separate repo (https://github.com/crim-ca/stac-populator). I think this is just for testing.

birdhouse/optional-components/stac-public-access/docker-compose-extra.yml
@@ -0,0 +1,6 @@
version: "3.4"
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This entire file should be in birdhouse/optional-components/stac-public-access/config/magpie/docker-compose-extra.yml to follow the new layout I think.

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@mishaschwartz Oh this one is a special case ! If this file move to birdhouse/optional-components/stac-public-access/config/magpie/docker-compose-extra.yml, then there is no file docker-compose-extra.yml at the root of this component birdhouse/optional-components/stac-public-access/ !

Would the "inner" docker-compose fragment file be discovered even if no file at the root of the component?

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This works... but if we want to follow the pattern we use elsewhere we should really add this to birdhouse/optional-components/stac-public-access/config/magpie/docker-compose-extra.yml so that it will only be set if magpie is enabled as well.

We're almost certainly going to make magpie a required component but it would be nicer to keep the pattern we've already established.

Thanks for finding that @tlvu

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Yes agreed. The new directory layout pattern is not only for looking nice and tidy, it's to allow 100% flexible deployment.

I think we need to document this pattern here https://github.com/bird-house/birdhouse-deploy/blob/master/birdhouse/README.rst and explain the proper reason behind it.

This was referenced Aug 10, 2023
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mishaschwartz added a commit that referenced this pull request Aug 10, 2023
@mishaschwartz
quick fixes as suggested in review in #297
2d27b1c
@mishaschwartz mishaschwartz mentioned this pull request Aug 10, 2023
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mishaschwartz added a commit that referenced this pull request Aug 15, 2023
@mishaschwartz
Small stac changes (#365)
93ed91b 
## Overview

This PR includes some changes that were suggested in a review for #297.
But because the PR was already merged they are included here:

- removes extra block to include in docker compose files (no longer
needed)
- moves docker compose file in `stac-public-access` component to the
correct location
- uses `PAVICS_FQDN_PUBLIC` for public facing URLs in all places

## Changes

**Non-breaking changes**
- code reorganization

**Breaking changes**
None

## Related Issue / Discussion

- Related to #297 

## Additional Information
@dchandan dchandan mentioned this pull request Aug 18, 2023
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@mishaschwartz mishaschwartz mishaschwartz approved these changes

@dchandan dchandan dchandan left review comments

@tlvu tlvu tlvu left review comments

@fmigneault fmigneault fmigneault approved these changes

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@matprov matprov

Labels
component/magpie Related to https://github.com/Ouranosinc/Magpie component/STAC Features or components related to STAC component/twitcher Related to https://github.com/bird-house/twitcher documentation Improvements or additions to documentation project/DACCS Related to DACCS project (https://github.com/orgs/DACCS-Climate)
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@matprov @crim-jenkins-bot @mishaschwartz @tlvu @fmigneault @dchandan