From f88c04d76f64b775daaf05315e0b5b10788e0a7d Mon Sep 17 00:00:00 2001 From: Floris Calkoen <44444001+FlorisCalkoen@users.noreply.github.com> Date: Fri, 1 Sep 2023 01:07:27 +0200 Subject: [PATCH] Refactor to python package and restructure project directory (#16) * rename generate.py to example.py and mv to directory with STAC generation scripts * mkdir tests and mv validation.py to test_validation.py * make dir for ci scripts; add convert.py to this dir. * etl and coclico stac configs into src/coclicodata directory that can be packaged * refactor * add poetry for package management * add azure vars to env * mv keys function to cloud utils * snakecase convention * mv scripts to subdirs * setup deltares drive configs * refactor to python package * usage instructions and integrated readme in package dirs here * usage instructions and integrated readme in package dirs here * mv readme to proj root * coastal mask with coclicodata and coastmonitor package * do not require deltares fields * change id to raw gh path * test schema * change path * deltares props no longer as required * fp to href * description for all files in repo * bash script to upload stacs to azure cloud * change schema uri to update json schema * make stacs without deltares properties as required * test to avoid collection id duplication * mv root inside test as convention * black formatting * pre commit config * pre commit cleanup * add pre commit instructions to readme * change href extension to main branch * coastal mask stacs without redundant frontend properties * added coastal mask to stac catalog * sync instead of uploading * load catalog outside function for CI tests * fix href to root in tests * reset hrefs to feature branch --------- Co-authored-by: floriscalkoen --- .env.example | 3 + .github/workflows/release.yml | 2 +- .pre-commit-config.yaml | 23 + README.md | 133 +- convert.py => ci/convert.py | 0 current/catalog.json | 250 +- current/cbca/collection.json | 860 +- 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create_stacs}/02_wef_stacs.py | 2 - scripts/{ => create_stacs}/03_eesl_stacs.py | 2 - scripts/{ => create_stacs}/04_smd_stacs.py | 2 - scripts/{ => create_stacs}/05_sc_stacs.py | 2 - scripts/{ => create_stacs}/06_cbca_stacs.py | 2 - scripts/{ => create_stacs}/07_cfr_stacs.py | 2 - scripts/{ => create_stacs}/17_slp6_stacs.py | 0 scripts/{ => create_stacs}/18_slp_stacs.py | 0 scripts/{ => create_stacs}/19_cm_stacs.py | 1 - scripts/{ => create_stacs}/20_cisi_stacs.py | 0 .../create_stacs/example.py | 7 +- .../coclico_common_vocab_from_stac.py | 3 - .../correction_to_zarr_store_example.py | 1 - scripts/{ => utils}/stac_to_cloud.py | 0 .../upload_and_generate_geojson.py | 0 src/coclicodata/__init__.py | 6 + src/coclicodata/coclico_stac/__init__.py | 0 .../coclicodata/coclico_stac}/datacube.py | 10 - .../coclicodata/coclico_stac/extension.py | 52 +- src/coclicodata/coclico_stac/io.py | 48 + src/coclicodata/coclico_stac/layouts.py | 87 + .../coclicodata/coclico_stac/templates.py | 84 +- .../coclicodata/coclico_stac}/utils.py | 9 +- .../coclicodata/drive_config.py | 9 +- src/coclicodata/etl/__init__.py | 0 .../coclicodata/etl/cf_compliancy_checker.py | 0 .../coclicodata/etl/cloud_utils.py | 75 +- {etl => src/coclicodata/etl}/extract.py | 5 +- stac/README.md | 97 - tests/test_all_collections_unique.py | 15 + validate.py => tests/test_validation.py | 1 - 358 files changed, 73076 insertions(+), 72805 deletions(-) create mode 100644 .pre-commit-config.yaml rename convert.py => ci/convert.py (100%) delete mode 100644 current/template/collection.json delete mode 100644 current/template/template-mapbox/item.json delete mode 100644 etl/README.md delete mode 100644 etl/keys.py delete mode 100644 notebooks/README.md rename scripts/{ => bash}/build-stacs.sh (100%) create mode 100644 scripts/bash/sync-stac-with-azure-container.sh rename scripts/{ => create_stacs}/01_ssl_stacs.py (100%) rename scripts/{ => create_stacs}/02_wef_stacs.py (99%) rename scripts/{ => create_stacs}/03_eesl_stacs.py (99%) rename scripts/{ => create_stacs}/04_smd_stacs.py (99%) rename scripts/{ => create_stacs}/05_sc_stacs.py (99%) rename scripts/{ => create_stacs}/06_cbca_stacs.py (99%) rename scripts/{ => create_stacs}/07_cfr_stacs.py (99%) rename scripts/{ => create_stacs}/17_slp6_stacs.py (100%) rename scripts/{ => create_stacs}/18_slp_stacs.py (100%) rename scripts/{ => create_stacs}/19_cm_stacs.py (99%) rename scripts/{ => create_stacs}/20_cisi_stacs.py (100%) rename generate.py => scripts/create_stacs/example.py (98%) rename scripts/{ => utils}/coclico_common_vocab_from_stac.py (99%) rename scripts/{ => utils}/correction_to_zarr_store_example.py (99%) rename scripts/{ => utils}/stac_to_cloud.py (100%) rename scripts/{ => utils}/upload_and_generate_geojson.py (100%) create mode 100644 src/coclicodata/__init__.py create mode 100644 src/coclicodata/coclico_stac/__init__.py rename {stac => src/coclicodata/coclico_stac}/datacube.py (96%) rename stac/coclico_extension.py => src/coclicodata/coclico_stac/extension.py (81%) create mode 100644 src/coclicodata/coclico_stac/io.py create mode 100644 src/coclicodata/coclico_stac/layouts.py rename stac/blueprint.py => src/coclicodata/coclico_stac/templates.py (68%) rename {stac => src/coclicodata/coclico_stac}/utils.py (93%) rename etl/__init__.py => src/coclicodata/drive_config.py (63%) create mode 100644 src/coclicodata/etl/__init__.py rename etl/CF_compliancy_checker.py => src/coclicodata/etl/cf_compliancy_checker.py (100%) rename etl/cloud_services.py => src/coclicodata/etl/cloud_utils.py (63%) rename {etl => src/coclicodata/etl}/extract.py (96%) delete mode 100644 stac/README.md create mode 100644 tests/test_all_collections_unique.py rename validate.py => tests/test_validation.py (96%) diff --git a/.env.example b/.env.example index 6f0fb9d9e7..7d98ed0693 100644 --- a/.env.example +++ b/.env.example @@ -1 +1,4 @@ MAPBOX_ACCESS_TOKEN="" +AZURE_STORAGE_ACCOUNT="" +AZURE_STORAGE_SAS_TOKEN="" +GH_COASTMONITOR_TOKEN="" diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5e2ac07ac3..de4b92ff51 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -36,7 +36,7 @@ jobs: path: live - name: Release run: | - python convert.py + python ci/convert.py rm -rf ../live/current cp -rp live ../live/current cd ../live diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000000..f73fe0d0ef --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,23 @@ +ci: + autofix_prs: false + autoupdate_schedule: weekly + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: trailing-whitespace + - id: debug-statements + - id: check-yaml + - id: check-added-large-files + + - repo: https://github.com/psf/black + rev: 23.7.0 + hooks: + - id: black + language_version: python3.11 + + - repo: https://github.com/kynan/nbstripout + rev: 0.6.1 + hooks: + - id: nbstripout diff --git a/README.md b/README.md index bfa0e77337..8fbe1552c5 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,127 @@ # coclicodata -STAC catalog for CoCliCo -This is a **relative** STAC catalog for development purposes. +This repository contains code to maintain the CoCliCo STAC catalog. Please note that +this is a **relative** STAC catalog for development purposes. + +## Usage + +Given that `coclicodata` is under active development, it's recommended to clone the repository and then install it in 'editable' mode. This way, any changes made to the package are immediately available without needing a reinstall. + +Follow these steps for installation: + +1. **Clone the repository**: + + ``` bash + git clone https://github.com/openearth/coclicodata.git + ``` + +2. **Install the environment**: + + ``` bash + mamba install -f /path/to/coclicodata/environment.yaml + ``` + +3. **Activate the environment**: + + ``` bash + mamba activate coclico + ``` + +4. **Install the package in editable mode**: + + ``` bash + pip install -e /path/to/coclicodata + ``` + +After installation, you can easily import and use any module or function from the +`coclicodata` package in your Python scripts or interactive sessions: + +```python +from coclicodata.coclico_stac import utils +# Further code utilizing the utils module... +``` + +## Use pre-commit locally + +Ensure consistent code formatting and avoid big repositories by removing output with pre-commit. + +In the root of the repository run: + +```bash +pre-commit install +``` + +If the hooks catch issues when you commit your changes, they will fix them automatically.: + +```bash +git commit -m "Your message" +``` +Once hooks pass, push your changes. ## Test -You can run pytest to check whether you current STAC collection is valid + +You can run `pytest` to check whether you current STAC collection is valid. The command +will automatically run the test scripts that are maintained in `tests/test_*.py` ## Release -On succesfull validation of STAC catalog in the main branch, an **absolute** version + +On successful validation of STAC catalog in the main branch, an **absolute** version of the catalog will be published in the `live` branch that can be used externally. +## CoCliCoData repository structure + +- **ci** + - `convert.py`: CI script to convert current to live stacs. + +- **current**: STAC catalog that is used for web portal development. + +- **docs**: Various documentation images like flowcharts and diagrams representing data formats and workflows. + +- **json-schema** + - `schema.json`: JSON schema definition for the frontend Deltares STAC extension. + +- **live**: STAC catalog that is used by the web-portal to serve end users. + +- **notebooks**: Jupyter notebooks used to load, explore and transform the data; + typically one per dataset, to make it CF compliant. + +- **scripts** + - **bash**: Shell scripts, like `build-stacs.sh` and `upload-stacs-to-azure.sh`, for various automation tasks. + - **create_stacs**: Python scripts for creating STACs, each typically corresponding to a specific dataset or processing step. + - **utils**: Utility scripts, like `coclico_common_vocab_from_stac.py` and `upload_and_generate_geojson.py`, for various data operations. + +- **src/coclicodata** + - `__init__.py`: Main package initialization. + - `drive_config.py`: Configuration settings for the drive or storage medium. + - **etl** + - `__init__.py`: Subpackage initialization. + - `cf_compliancy_checker.py`: Checks for compliancy with the Climate and Forecast (CF) conventions. + - `cloud_utils.py`: Utilities for cloud-based operations and data processing. + - `extract.py`: Data extraction and transform functionalities. + + - **coclico_stac** + - `__init__.py`: Subpackage initialization. + - `datacube.py`: Functions for extracting dimension shapes and metadata from zarr stores. + - `extension.py`: CoCliCo STAC extension that is used for frontend visualization. + - `io.py`: Defines the CoCLiCo JSON I/O strategy for STAC catalogs. + - `layouts.py`: Provides CoCliCo layout strategies for STAC for the data formats used. + - `templates.py`: Defines CoCliCo templates for generating STAC items, assets and collections. + - `utils.py`: Utility functions for data migration and other STAC-related operations. + +- **stories**: Contains narrative data and associated images. + +- **tests**: Contains test scripts to ensure code quality and functionality. + +- `.pre-commit-config.yaml`: Hooks that will be run when making a commit. +- `metadata_template.json`: Template file for a STAC collection from a dataset. + ## Metadata The following attributes are required at dataset level: -- title - -- title abbreviation - -- description - description that will be used to as dataset explanation in the web portal. +- title - +- title abbreviation - +- description - description that will be used to as dataset explanation in the web portal. - short description - description which is convenient when loading the data into a programming environment - institution - data producer @@ -24,13 +129,13 @@ The following attributes are required at dataset level: - name - url - roles - e.g., providers, licensor - - description - -- history - list of institutions and people who have processed the data + - description - +- history - list of institutions and people who have processed the data - media_type - [also known as mime type](https://www.iana.org/assignments/media-types/media-types.xhtml) - spatial extent - bbox [minx, miny, maxx, maxy] - temporal extent - time interval in [iso 8601](https://en.wikipedia.org/wiki/ISO_8601), i.e., YYYY-MM-DDTHH:mm:ssZ -- license - -- author - +- license - +- author - The following attributes are optional at dataset level: - keywords - these can be used to search using the STAC API @@ -39,13 +144,13 @@ The following attributes are optional at dataset level: Publisher. (resourceTypeGeneral). Identifier format (Zenodo specification) - doi - following [Zenodo specification](https://about.zenodo.org/principles/) - thumbnail asset image - image that will be shown to represent the dataset -- columns - when data is tabular and has column names +- columns - when data is tabular and has column names The following attributes are required at variable level - long_name - descriptive name - standard_name - iff available in [CF convention standard table](https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html) -- units - follow CF conventions where possible; leave blank when no units. +- units - follow CF conventions where possible; leave blank when no units. - cell_bnds The following attributes are optional at variable level: @@ -54,7 +159,7 @@ The following attributes are optional at variable level: The following coordinate labels are required: - crs or spatial_ref -- time +- time ### Controlled vocabulary | **name** | **long_name** | **standard_name** | **data_structure_type** | **dtype** | diff --git a/convert.py b/ci/convert.py similarity index 100% rename from convert.py rename to ci/convert.py diff --git a/current/catalog.json b/current/catalog.json index b000f6cc2a..8a4c7e0157 100644 --- a/current/catalog.json +++ b/current/catalog.json @@ -1,130 +1,130 @@ { - "type": "Catalog", - "id": "coclico-catalog", - "stac_version": "1.0.0", - "description": "CoCliCo Catalog", - "links": [ - { - "rel": "root", - "href": "./catalog.json", - "type": "application/json", - "title": "CoCliCo STAC Catalog" + "type": "Catalog", + "id": "coclico-catalog", + "stac_version": "1.0.0", + "description": "CoCliCo Catalog", + "links": [ + { + "rel": "root", + "href": "./catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + }, + { + "rel": "child", + "href": "./ssl/collection.json", + "type": "application/json", + "title": "Extreme surge level" + }, + { + "rel": "child", + "href": "./wef/collection.json", + "type": "application/json", + "title": "Wave energy flux" + }, + { + "rel": "child", + "href": "./eesl/collection.json", + "type": "application/json", + "title": "Extreme sea level" + }, + { + "rel": "child", + "href": "./floodmaps/collection.json", + "type": "application/json", + "title": "Floodmaps" + }, + { + "rel": "child", + "href": "./sc/collection.json", + "type": "application/json", + "title": "Shoreline change" + }, + { + "rel": "child", + "href": "./cbca/collection.json", + "type": "application/json", + "title": "Cost benefit coastal adaptation" + }, + { + "rel": "child", + "href": "./cfr/collection.json", + "type": "application/json", + "title": "Coastal flood risk" + }, + { + "rel": "child", + "href": "./cm/collection.json", + "type": "application/json", + "title": "Coastal mask" + }, + { + "rel": "child", + "href": "./smd/collection.json", + "type": "application/json", + "title": "Global shoreline morphodynamics" + }, + { + "rel": "child", + "href": "./cisi/collection.json", + "type": "application/json", + "title": "Critical Infrastructure Spatial Index" + }, + { + "rel": "child", + "href": "./slp5/collection.json", + "type": "application/json", + "title": "AR5 sea level rise projections" + }, + { + "rel": "child", + "href": "./slp6/collection.json", + "type": "application/json", + "title": "AR6 sea level rise projections" + }, + { + "rel": "child", + "href": "./coastal-mask/collection.json", + "type": "application/json", + "title": "Coastal Mask" + } + ], + "assets": { + "metadata": { + "href": "https://www.deltares.nl/en/news/development-of-a-new-european-platform-on-climate-services-for-coastal-risks-and-adaptation/", + "type": "application/html", + "title": "Deltares Website", + "description": "Deltares Website about CoCliCo", + "roles": [ + "metadata" + ] + } }, - { - "rel": "child", - "href": "./ssl/collection.json", - "type": "application/json", - "title": "Extreme surge level" - }, - { - "rel": "child", - "href": "./wef/collection.json", - "type": "application/json", - "title": "Wave energy flux" - }, - { - "rel": "child", - "href": "./eesl/collection.json", - "type": "application/json", - "title": "Extreme sea level" - }, - { - "rel": "child", - "href": "./floodmaps/collection.json", - "type": "application/json", - "title": "Floodmaps" - }, - { - "rel": "child", - "href": "./sc/collection.json", - "type": "application/json", - "title": "Shoreline change" - }, - { - "rel": "child", - "href": "./cbca/collection.json", - "type": "application/json", - "title": "Cost benefit coastal adaptation" - }, - { - "rel": "child", - "href": "./cfr/collection.json", - "type": "application/json", - "title": "Coastal flood risk" - }, - { - "rel": "child", - "href": "./cm/collection.json", - "type": "application/json", - "title": "Coastal mask" - }, - { - "rel": "child", - "href": "./smd/collection.json", - "type": "application/json", - "title": "Global shoreline morphodynamics" - }, - { - "rel": "child", - "href": "./cisi/collection.json", - "type": "application/json", - "title": "Critical Infrastructure Spatial Index" - }, - { - "rel": "child", - "href": "./slp5/collection.json", - "type": "application/json", - "title": "AR5 sea level rise projections" - }, - { - "rel": "child", - "href": "./slp6/collection.json", - "type": "application/json", - "title": "AR6 sea level rise projections" - }, - { - "rel": "child", - "href": "./coastal-mask/collection.json", - "type": "application/json", - "title": "Coastal Mask" - } - ], - "assets": { - "metadata": { - "href": "https://www.deltares.nl/en/news/development-of-a-new-european-platform-on-climate-services-for-coastal-risks-and-adaptation/", - "type": "application/html", - "title": "Deltares Website", - "description": "Deltares Website about CoCliCo", - "roles": [ - "metadata" - ] - } - }, - "summaries": { - "keywords": [ - "CoCliCo" - ] - }, - "extent": { - "spatial": { - "bbox": [ - [ - -180, - -90, - 180, - 90 + "summaries": { + "keywords": [ + "CoCliCo" ] - ] }, - "temporal": { - "interval": [ - [ - "2015-10-22T00:00:00Z", - null - ] - ] - } - }, - "license": "various", - "title": "CoCliCo STAC Catalog" + "extent": { + "spatial": { + "bbox": [ + [ + -180, + -90, + 180, + 90 + ] + ] + }, + "temporal": { + "interval": [ + [ + "2015-10-22T00:00:00Z", + null + ] + ] + } + }, + "license": "various", + "title": "CoCliCo STAC Catalog" } \ No newline at end of file diff --git a/current/cbca/collection.json b/current/cbca/collection.json index 2ff448ab06..6740b6a201 100644 --- a/current/cbca/collection.json +++ b/current/cbca/collection.json @@ -1,452 +1,452 @@ { - "type": "Collection", - "id": "cbca", - "stac_version": "1.0.0", - "description": "Dataset describing the costs and benefits of raising coastal defenses along the European coastline aggregated per coastal NUTS2 region (provinces), in view of climate change. Variables are cost (\u20ac), benefit (\u20ac), cost-benefit ratio (cbr, -) and extra benefit of raising coastal protection (eb, m) for two different climate scenarios (RCP4.5 and RCP8.5) coupled to two types of socio-economic growth (SSP1 \u2013 sustainability and SSP5 \u2013 fossil fuel development). This dataset is part of the [LISCOAST](https://data.jrc.ec.europa.eu/collection/LISCOAST) project. See this [article](https://doi.org/10.1038/s41467-020-15665-3) for more dataset-specific information.", - "links": [ - { - "rel": "item", - "href": "./nuts2-regions/nuts2-regions.json", - "type": "application/json", - "properties": { - "scenarios": "RCP45-SSP1" - } - }, - { - "rel": "root", - "href": "../catalog.json", - "type": "application/json", - "title": "CoCliCo STAC Catalog" - }, - { - "rel": "parent", - "href": "../catalog.json", - "type": "application/json", - "title": "CoCliCo STAC Catalog" - } - ], - "stac_extensions": [ - "https://stac-extensions.github.io/datacube/v2.0.0/schema.json" - ], - "deltares:units": "m", - "deltares:plotSeries": "scenario", - "deltares:plotType": "bar", - "deltares:min": 0, - "deltares:max": 3, - "deltares:linearGradient": [ - { - "color": "hsl(0,90%,80%)", - "offset": "0.000%", - "opacity": 100 - }, - { - "color": "hsla(55,88%,53%,0.5)", - "offset": "50.000%", - "opacity": 100 - }, - { - "color": "hsl(110,90%,70%)", - "offset": "100.000%", - "opacity": 100 - } - ], - "units": "m", - "cube:dimensions": { - "lon": { - "axis": "x", - "extent": [ - -9.039207141, - 33.22610589 - ], - "description": "Longitude of the centroid of the NUTS2 region (2010 version).", - "reference_system": { - "$schema": "https://proj.org/schemas/v0.4/projjson.schema.json", - "type": "GeographicCRS", - "name": "WGS 84", - "datum_ensemble": { - "name": "World Geodetic System 1984 ensemble", - "members": [ - { - "name": "World Geodetic System 1984 (Transit)", - "id": { - "authority": "EPSG", - "code": 1166 - } - }, - { - "name": "World Geodetic System 1984 (G730)", - "id": { - "authority": "EPSG", - "code": 1152 - } - }, - { - "name": "World Geodetic System 1984 (G873)", - "id": { - "authority": "EPSG", - "code": 1153 - } - }, - { - "name": "World Geodetic System 1984 (G1150)", - "id": { - "authority": "EPSG", - "code": 1154 - } - }, - { - "name": "World Geodetic System 1984 (G1674)", - "id": { - "authority": "EPSG", - "code": 1155 - } - }, - { - "name": "World Geodetic System 1984 (G1762)", - "id": { - "authority": "EPSG", - "code": 1156 - } - }, - { - "name": "World Geodetic System 1984 (G2139)", - "id": { - "authority": "EPSG", - "code": 1309 - } + "type": "Collection", + "id": "cbca", + "stac_version": "1.0.0", + "description": "Dataset describing the costs and benefits of raising coastal defenses along the European coastline aggregated per coastal NUTS2 region (provinces), in view of climate change. Variables are cost (\u20ac), benefit (\u20ac), cost-benefit ratio (cbr, -) and extra benefit of raising coastal protection (eb, m) for two different climate scenarios (RCP4.5 and RCP8.5) coupled to two types of socio-economic growth (SSP1 \u2013 sustainability and SSP5 \u2013 fossil fuel development). This dataset is part of the [LISCOAST](https://data.jrc.ec.europa.eu/collection/LISCOAST) project. See this [article](https://doi.org/10.1038/s41467-020-15665-3) for more dataset-specific information.", + "links": [ + { + "rel": "item", + "href": "./nuts2-regions/nuts2-regions.json", + "type": "application/json", + "properties": { + "scenarios": "RCP45-SSP1" } - ], - "ellipsoid": { - "name": "WGS 84", - "semi_major_axis": 6378137, - "inverse_flattening": 298.257223563 - }, - "accuracy": "2.0", - "id": { - "authority": "EPSG", - "code": 6326 - } }, - "coordinate_system": { - "subtype": "ellipsoidal", - "axis": [ - { - "name": "Geodetic latitude", - "abbreviation": "Lat", - "direction": "north", - "unit": "degree" - }, - { - "name": "Geodetic longitude", - "abbreviation": "Lon", - "direction": "east", - "unit": "degree" - } - ] + { + "rel": "root", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + }, + { + "rel": "parent", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + } + ], + "stac_extensions": [ + "https://stac-extensions.github.io/datacube/v2.0.0/schema.json" + ], + "deltares:units": "m", + "deltares:plotSeries": "scenario", + "deltares:plotType": "bar", + "deltares:min": 0, + "deltares:max": 3, + "deltares:linearGradient": [ + { + "color": "hsl(0,90%,80%)", + "offset": "0.000%", + "opacity": 100 }, - 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See this [article](https://doi.org/10.1038/s41558-018-0260-4) for more dataset-specific information.", - "links": [ - { - "rel": "item", - "href": "./nuts0-regions/nuts0-regions.json", - "type": "application/json", - "title": "nuts0-regions", - "properties": { - "scenarios": "RCP4.5-SSP1", - "time": 2000 - } - }, - { - "rel": "root", - "href": "../catalog.json", - "type": "application/json", - "title": "CoCliCo STAC Catalog" - }, - { - "rel": "parent", - "href": "../catalog.json", - "type": "application/json", - "title": "CoCliCo STAC Catalog" - } - ], - "stac_extensions": [ - "https://raw.githubusercontent.com/openearth/coclicodata/feat/update-deltares-stac-properties/json-schema/schema.json", - "https://stac-extensions.github.io/datacube/v2.0.0/schema.json" - ], - "deltares:units": "m", - "deltares:plotSeries": "scenarios", - "deltares:plotxAxis": "time", - "deltares:plotType": "line", - "deltares:min": 0, - "deltares:max": 3, - "deltares:linearGradient": [ - { - "color": "hsl(0,90%,80%)", - "offset": "0.000%", - "opacity": 100 - }, - { - "color": "hsla(55,88%,53%,0.5)", - "offset": "50.000%", - "opacity": 100 - }, - { - "color": "hsl(110,90%,70%)", - "offset": "100.000%", - "opacity": 100 - } - ], - "units": "m", - "cube:dimensions": { - "time": { - "extent": [ - "2000", - "2100" - ], - "description": "time", - "type": "temporal" - }, - "lon": { - "axis": "x", - "extent": [ - -8.516135879, - 33.22610589 - ], - "description": "longitude of the centroid of NUTS0", - "reference_system": { - "$schema": "https://proj.org/schemas/v0.4/projjson.schema.json", - "type": "GeographicCRS", - "name": "WGS 84", - "datum_ensemble": { - "name": "World Geodetic System 1984 ensemble", - "members": [ - { - "name": "World Geodetic System 1984 (Transit)", - "id": { - "authority": "EPSG", - "code": 1166 - } - }, - { - "name": "World Geodetic System 1984 (G730)", - "id": { - "authority": "EPSG", - "code": 1152 - } - }, - { - "name": "World Geodetic System 1984 (G873)", - "id": { - "authority": "EPSG", - "code": 1153 - } - }, - { - "name": "World Geodetic System 1984 (G1150)", - "id": { - "authority": "EPSG", - "code": 1154 - } - }, - { - "name": "World Geodetic System 1984 (G1674)", - "id": { - "authority": "EPSG", - "code": 1155 - } - }, - { - "name": "World Geodetic System 1984 (G1762)", - "id": { - "authority": "EPSG", - "code": 1156 - } - }, - { - "name": "World Geodetic System 1984 (G2139)", - "id": { - "authority": "EPSG", - "code": 1309 - } + "type": "Collection", + "id": "cfr", + "stac_version": "1.0.0", + "description": "Dataset presenting the results of a European coastal flood risk assessment (present till 2100), incorporating impacts of climate change scenarios (RCP4.5 and RCP8.5) and different socio-economic pathways (SSP1, SSP3 and SSP5). 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See this [article](https://doi.org/10.1038/s41558-018-0260-4) for more dataset-specific information.", + "links": [ + { + "rel": "item", + "href": "./nuts0-regions/nuts0-regions.json", + "type": "application/json", + "title": "nuts0-regions", + "properties": { + "scenarios": "RCP4.5-SSP1", + "time": 2000 } - ], - "ellipsoid": { - "name": "WGS 84", - "semi_major_axis": 6378137, - "inverse_flattening": 298.257223563 - }, - "accuracy": "2.0", - "id": { - "authority": "EPSG", - "code": 6326 - } }, - "coordinate_system": { - "subtype": "ellipsoidal", - "axis": [ - { - "name": "Geodetic latitude", - "abbreviation": "Lat", - "direction": "north", - "unit": "degree" - }, - { - "name": "Geodetic longitude", - "abbreviation": "Lon", - "direction": "east", - "unit": "degree" - } - ] + { + "rel": "root", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + }, + { + "rel": "parent", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + } + ], + "stac_extensions": [ + "https://raw.githubusercontent.com/openearth/coclicodata/feat/update-deltares-stac-properties/json-schema/schema.json", + "https://stac-extensions.github.io/datacube/v2.0.0/schema.json" + ], + "deltares:units": "m", + "deltares:plotSeries": "scenarios", + "deltares:plotxAxis": "time", + "deltares:plotType": "line", + "deltares:min": 0, + "deltares:max": 3, + "deltares:linearGradient": [ + { + "color": "hsl(0,90%,80%)", + "offset": "0.000%", + "opacity": 100 }, - 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This dataset is hosted through WMS servers from [BRGM](https://sealevelrise.brgm.fr/slr). See this [article](https://doi.org/10.1007/978-3-319-74669-2_12) for more dataset-specific information.", + "links": [ + { + "rel": "root", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + }, + { + "rel": "item", + "href": "./floodmaps_wms-0.0/floodmaps_wms-0.0.json", + "type": "application/json", + "title": "floodmaps_wms-0.0", + "properties": { + "slr": "0.0" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-0.5/floodmaps_wms-0.5.json", + "type": "application/json", + "title": "floodmaps_wms-0.5", + "properties": { + "slr": "0.5" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-1.0/floodmaps_wms-1.0.json", + "type": "application/json", + "title": "floodmaps_wms-1.0", + "properties": { + "slr": "1.0" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-1.5/floodmaps_wms-1.5.json", + "type": "application/json", + "title": "floodmaps_wms-1.5", + "properties": { + "slr": "1.5" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-2.0/floodmaps_wms-2.0.json", + "type": "application/json", + "title": "floodmaps_wms-2.0", + "properties": { + "slr": "2.0" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-2.5/floodmaps_wms-2.5.json", + "type": "application/json", + "title": "floodmaps_wms-2.5", + "properties": { + "slr": "2.5" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-3.0/floodmaps_wms-3.0.json", + "type": "application/json", + "title": "floodmaps_wms-3.0", + "properties": { + "slr": "3.0" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-3.5/floodmaps_wms-3.5.json", + "type": "application/json", + "title": "floodmaps_wms-3.5", + "properties": { + "slr": "3.5" + } + }, + { + "rel": "item", + "href": "./floodmaps_wms-4.0/floodmaps_wms-4.0.json", + "type": "application/json", + "title": "floodmaps_wms-4.0", + "properties": { + "slr": "4.0" + } + }, + { + "rel": "parent", + "href": "../catalog.json", + "type": "application/json", + "title": "CoCliCo STAC Catalog" + } + ], + "deltares:mapService": "WMS", + "title": "Floodmaps", + "extent": { + "spatial": { + "bbox": [ + [ + -180.0, + -90.0, + 180.0, + 90.0 + ] + ] + }, + "temporal": { + "interval": [ + [ + "2015-10-22T00:00:00Z", + null + ] + ] + } }, - { - "rel": "item", - "href": "./floodmaps_wms-0.0/floodmaps_wms-0.0.json", - "type": "application/json", - "title": "floodmaps_wms-0.0", - "properties": { - "slr": "0.0" - } - }, - { - "rel": "item", - "href": "./floodmaps_wms-0.5/floodmaps_wms-0.5.json", - "type": "application/json", - "title": "floodmaps_wms-0.5", - "properties": { - "slr": "0.5" - } - }, - { - "rel": "item", - "href": "./floodmaps_wms-1.0/floodmaps_wms-1.0.json", - "type": "application/json", - "title": "floodmaps_wms-1.0", - "properties": { - "slr": "1.0" - } - }, - { - "rel": "item", - "href": "./floodmaps_wms-1.5/floodmaps_wms-1.5.json", - "type": "application/json", - "title": "floodmaps_wms-1.5", - "properties": { - "slr": "1.5" - } - }, - { - "rel": "item", - "href": "./floodmaps_wms-2.0/floodmaps_wms-2.0.json", - "type": "application/json", - "title": "floodmaps_wms-2.0", - "properties": { - "slr": "2.0" - } - }, - { - "rel": "item", - "href": "./floodmaps_wms-2.5/floodmaps_wms-2.5.json", - "type": "application/json", - 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projections for the year 2050 under RCP4.5 zarr dataset on public Google Cloud Storage.", - "roles": [ - "data", - "zarr-root", - "gcs" - ] + "assets": { + "data": { + "href": "https://storage.googleapis.com/dgds-data-public/coclico/shoreline_change_projections.zarr", + "title": "Global shoreline change projections for the year 2050 under RCP4.5 zarr root", + "description": "The root of the Global shoreline change projections for the year 2050 under RCP4.5 zarr dataset on public Google Cloud Storage.", + "roles": [ + "data", + "zarr-root", + "gcs" + ] + } } - } } \ No newline at end of file diff --git a/current/slp5/collection.json b/current/slp5/collection.json index 28f62eaf53..dda0f6cfa2 100644 --- a/current/slp5/collection.json +++ b/current/slp5/collection.json @@ -1,4315 +1,4315 @@ { - "type": "Collection", - "id": "slp5", - "stac_version": "1.0.0", - "description": "Regional sea level data from IPCC AR5 distributed in netCDF format by the Integrated Climate Data Center ICDC, 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"direction": "north", - "unit": "degree" + "first_land_lon": { + "type": "auxiliary", + "description": "transect longitude first persistent permanent land", + "dimensions": [ + "nstations" + ], + "unit": "degrees_east", + "attrs": { + "description": "transect longitude first persistent permanent land", + "long_name": "transect longitude first persistent permanent land", + "units": "degrees_east" }, - { - "name": "Geodetic longitude", - "abbreviation": "Lon", - "direction": "east", - "unit": "degree" - } - ] + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] }, - "scope": "Horizontal component of 3D system.", - "area": "World.", - "bbox": { - "south_latitude": -90, - "west_longitude": -180, - "north_latitude": 90, - "east_longitude": 180 + "first_year": { + "type": "auxiliary", + "description": "first year of observations", + "dimensions": [ + "nstations" + ], + "unit": "yr", + "attrs": { + "description": "first year of observations", + "long_name": "first year of observations", + "units": "yr" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] }, - "id": { - "authority": "EPSG", - "code": 4326 - } - }, - "type": "spatial" - }, - "lat": { - "axis": "y", - "extent": [ - -62.9936453412, - 62.9965817763 - ], - "description": "latitude", - "reference_system": { - "$schema": "https://proj.org/schemas/v0.4/projjson.schema.json", - "type": "GeographicCRS", - "name": "WGS 84", - "datum_ensemble": { - "name": "World Geodetic System 1984 ensemble", - "members": [ - { - "name": "World Geodetic System 1984 (Transit)", - "id": { - "authority": "EPSG", - "code": 1166 - } + "land_found": { + "type": "auxiliary", + "description": "1 if persistent permanent land was found, 0 if not. Transects without persistent permanent land should be discarded", + "dimensions": [ + "nstations" + ], + "unit": "1", + "attrs": { + "description": "1 if persistent permanent land was found, 0 if not. Transects without persistent permanent land should be discarded", + "long_name": "persistent permanent land found", + "units": "1" }, - { - "name": "World Geodetic System 1984 (G730)", - "id": { - "authority": "EPSG", - "code": 1152 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "land_to_active_zone": { + "type": "data", + "description": "transition length land to active zone", + "dimensions": [ + "nstations" + ], + "unit": "m", + "attrs": { + "description": "transition length land to active zone", + "long_name": "land to active zone", + "units": "m" }, - { - "name": "World Geodetic System 1984 (G873)", - "id": { - "authority": "EPSG", - "code": 1153 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "land_to_sea": { + "type": "data", + "description": "transition length land to sea", + "dimensions": [ + "nstations" + ], + "unit": "m", + "attrs": { + "description": "transition length land to sea", + "long_name": "land to sea", + "units": "m" }, - { - "name": "World Geodetic System 1984 (G1150)", - "id": { - "authority": "EPSG", - "code": 1154 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "last_year": { + "type": "auxiliary", + "description": "last year of observations", + "dimensions": [ + "nstations" + ], + "unit": "yr", + "attrs": { + "description": "last year of observations", + "long_name": "last year of observations", + "units": "yr" }, - { - "name": "World Geodetic System 1984 (G1674)", - "id": { - "authority": "EPSG", - "code": 1155 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "lat": { + "type": "auxiliary", + "description": "transect id latitude", + "dimensions": [ + "nstations" + ], + "unit": "degrees_north", + "attrs": { + "description": "transect id latitude", + "long_name": "latitude", + "units": "degrees_north" }, - { - "name": "World Geodetic System 1984 (G1762)", - "id": { - "authority": "EPSG", - "code": 1156 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "lat_land": { + "type": "auxiliary", + "description": "transect latitude land side", + "dimensions": [ + "nstations" + ], + "unit": "degrees_north", + "attrs": { + "description": "transect latitude land side", + "long_name": "transect latitude land side", + "units": "degrees_north" }, - { - "name": "World Geodetic System 1984 (G2139)", - "id": { - "authority": "EPSG", - "code": 1309 - } - } - ], - "ellipsoid": { - "name": "WGS 84", - "semi_major_axis": 6378137, - "inverse_flattening": 298.257223563 - }, - "accuracy": "2.0", - "id": { - "authority": "EPSG", - "code": 6326 - } + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] }, - "coordinate_system": { - "subtype": "ellipsoidal", - "axis": [ - { - "name": "Geodetic latitude", - "abbreviation": "Lat", - "direction": "north", - "unit": "degree" + "lat_sea": { + "type": "auxiliary", + "description": "transect latitude sea side", + "dimensions": [ + "nstations" + ], + "unit": "degrees_north", + "attrs": { + "description": "transect latitude sea side", + "long_name": "transect latitude sea side", + "units": "degrees_north" }, - { - "name": "Geodetic longitude", - "abbreviation": "Lon", - "direction": "east", - "unit": "degree" - } - ] + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] }, - "scope": "Horizontal component of 3D system.", - "area": "World.", - "bbox": { - "south_latitude": -90, - "west_longitude": -180, - "north_latitude": 90, - "east_longitude": 180 + "lon": { + "type": "auxiliary", + "description": "transect id longitude", + "dimensions": [ + "nstations" + ], + "unit": "degrees_east", + "attrs": { + "description": "transect id longitude", + "long_name": "longitude", + "units": "degrees_east" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "lon_land": { + "type": "auxiliary", + "description": "transect longitude land side", + "dimensions": [ + "nstations" + ], + "unit": "degrees_east", + "attrs": { + "description": "transect longitude land side", + "long_name": "transect longitude land side", + "units": "degrees_east" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "lon_sea": { + "type": "auxiliary", + "description": "transect longitude sea side", + "dimensions": [ + "nstations" + ], + "unit": "degrees_east", + "attrs": { + "description": "transect longitude sea side", + "long_name": "transect longitude sea side", + "units": "degrees_east" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "quality_flag": { + "type": "auxiliary", + "description": "1 if the transect is acceptable if (landfound and errorid == 0 and spuriousratio <= 0.3)", + "dimensions": [ + "nstations" + ], + "unit": "1", + "attrs": { + "description": "1 if the transect is acceptable if (landfound and errorid == 0 and spuriousratio <= 0.3)", + "long_name": "quality flag", + "units": "1" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "sea_to_active_zone": { + "type": "data", + "description": "transition length sea to active zone", + "dimensions": [ + "nstations" + ], + "unit": "m", + "attrs": { + "description": "transition length sea to active zone", + "long_name": "transition length sea to active zone", + "units": "m" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] }, - "id": { - "authority": "EPSG", - "code": 4326 + "sea_to_land": { + "type": "data", + "description": "transition length sea to land", + "dimensions": [ + "nstations" + ], + "unit": "m", + "attrs": { + "description": "transition length sea to land", + "long_name": "transition length sea to land", + "units": "m" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "spurious_ratio": { + "type": "auxiliary", + "description": "erroneous transition ratio, good if <= 0.3", + "dimensions": [ + "nstations" + ], + "unit": "1", + "attrs": { + "description": "erroneous transition ratio, good if <= 0.3", + "long_name": "spurious transition ratio", + "units": "1" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] + }, + "stations": { + "type": "auxiliary", + "description": "id transect", + "dimensions": [ + "nstations" + ], + "unit": "1", + "attrs": { + "description": "id transect", + "long_name": "stations", + "units": "1" + }, + "shape": [ + 2142679 + ], + "chunks": [ + 66959 + ] } - }, - "type": "spatial" - } - }, - "cube:variables": { - "active_zone_to_land": { - "type": "data", - "description": "transition length active zone to land", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length active zone to land", - "long_name": "active zone to land", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "active_zone_to_sea": { - "type": "data", - "description": "transition length active zone to sea", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length active zone to sea", - "long_name": "active zone to sea", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "coastal_segment": { - "type": "auxiliary", - "description": "id coastal segment", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "id coastal segment", - "long_name": "id coastal segment", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "country": { - "type": "auxiliary", - "description": "id land body, different for different continents/islands", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "id land body, different for different continents/islands", - "long_name": "country", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "error_id": { - "type": "auxiliary", - "description": "0: no error; 100: transect starting on transition; 101: transect ending on transition; 102: transect starting on land; 110: no persistent permanent land found; 200: other failures", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "0: no error; 100: transect starting on transition; 101: transect ending on transition; 102: transect starting on land; 110: no persistent permanent land found; 200: other failures", - "long_name": "error id", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "first_land_lat": { - "type": "auxiliary", - "description": "transect latitude first persistent permanent land", - "dimensions": [ - "nstations" - ], - "unit": "degrees_north", - "attrs": { - "description": "transect latitude first persistent permanent land", - "long_name": "transect latitude first persistent permanent land", - "units": "degrees_north" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "first_land_lon": { - "type": "auxiliary", - "description": "transect longitude first persistent permanent land", - "dimensions": [ - "nstations" - ], - "unit": "degrees_east", - "attrs": { - "description": "transect longitude first persistent permanent land", - "long_name": "transect longitude first persistent permanent land", - "units": "degrees_east" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "first_year": { - "type": "auxiliary", - "description": "first year of observations", - "dimensions": [ - "nstations" - ], - "unit": "yr", - "attrs": { - "description": "first year of observations", - "long_name": "first year of observations", - "units": "yr" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "land_found": { - "type": "auxiliary", - "description": "1 if persistent permanent land was found, 0 if not. Transects without persistent permanent land should be discarded", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "1 if persistent permanent land was found, 0 if not. Transects without persistent permanent land should be discarded", - "long_name": "persistent permanent land found", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "land_to_active_zone": { - "type": "data", - "description": "transition length land to active zone", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length land to active zone", - "long_name": "land to active zone", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "land_to_sea": { - "type": "data", - "description": "transition length land to sea", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length land to sea", - "long_name": "land to sea", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "last_year": { - "type": "auxiliary", - "description": "last year of observations", - "dimensions": [ - "nstations" - ], - "unit": "yr", - "attrs": { - "description": "last year of observations", - "long_name": "last year of observations", - "units": "yr" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] }, - "lat": { - "type": "auxiliary", - "description": "transect id latitude", - "dimensions": [ - "nstations" - ], - "unit": "degrees_north", - "attrs": { - "description": "transect id latitude", - "long_name": "latitude", - "units": "degrees_north" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "lat_land": { - "type": "auxiliary", - "description": "transect latitude land side", - "dimensions": [ - "nstations" - ], - "unit": "degrees_north", - "attrs": { - "description": "transect latitude land side", - "long_name": "transect latitude land side", - "units": "degrees_north" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "lat_sea": { - "type": "auxiliary", - "description": "transect latitude sea side", - "dimensions": [ - "nstations" - ], - "unit": "degrees_north", - "attrs": { - "description": "transect latitude sea side", - "long_name": "transect latitude sea side", - "units": "degrees_north" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "lon": { - "type": "auxiliary", - "description": "transect id longitude", - "dimensions": [ - "nstations" - ], - "unit": "degrees_east", - "attrs": { - "description": "transect id longitude", - "long_name": "longitude", - "units": "degrees_east" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "lon_land": { - "type": "auxiliary", - "description": "transect longitude land side", - "dimensions": [ - "nstations" - ], - "unit": "degrees_east", - "attrs": { - "description": "transect longitude land side", - "long_name": "transect longitude land side", - "units": "degrees_east" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "lon_sea": { - "type": "auxiliary", - "description": "transect longitude sea side", - "dimensions": [ - "nstations" - ], - "unit": "degrees_east", - "attrs": { - "description": "transect longitude sea side", - "long_name": "transect longitude sea side", - "units": "degrees_east" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "quality_flag": { - "type": "auxiliary", - "description": "1 if the transect is acceptable if (landfound and errorid == 0 and spuriousratio <= 0.3)", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "1 if the transect is acceptable if (landfound and errorid == 0 and spuriousratio <= 0.3)", - "long_name": "quality flag", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "sea_to_active_zone": { - "type": "data", - "description": "transition length sea to active zone", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length sea to active zone", - "long_name": "transition length sea to active zone", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "sea_to_land": { - "type": "data", - "description": "transition length sea to land", - "dimensions": [ - "nstations" - ], - "unit": "m", - "attrs": { - "description": "transition length sea to land", - "long_name": "transition length sea to land", - "units": "m" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "spurious_ratio": { - "type": "auxiliary", - "description": "erroneous transition ratio, good if <= 0.3", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "erroneous transition ratio, good if <= 0.3", - "long_name": "spurious transition ratio", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - }, - "stations": { - "type": "auxiliary", - "description": "id transect", - "dimensions": [ - "nstations" - ], - "unit": "1", - "attrs": { - "description": "id transect", - "long_name": "stations", - "units": "1" - }, - "shape": [ - 2142679 - ], - "chunks": [ - 66959 - ] - } - }, - "title": "Global shoreline morphodynamics", - "extent": { - "spatial": { - "bbox": [ - [ - -180.0, - -90.0, - 180.0, - 90.0 - ] - ] + "title": "Global shoreline morphodynamics", + "extent": { + "spatial": { + "bbox": [ + [ + -180.0, + -90.0, + 180.0, + 90.0 + ] + ] + }, + "temporal": { + "interval": [ + [ + null, + null + ] + ] + } }, - "temporal": { - "interval": [ - [ - null, - null - ] - ] - } - }, - "license": "proprietary", - "keywords": [ - "CoCliCo" - ], - "providers": [ - { - "name": "Deltares", - "description": "Deltares is an independent institute for applied research in the field of water and subsurface.", - "roles": [ - "producer", - "processor" - ], - "url": "https://www.deltares.nl" - } - ], - "assets": { - "data": { - "href": "https://storage.googleapis.com/dgds-data-public/coclico/global_shoreline_morphodynamics.zarr", - "title": "smd zarr root", - "description": "The root of the smd zarr dataset on public Google Cloud Storage.", - "roles": [ - "data", - "zarr-root", - "gcs" - ] + "license": "proprietary", + "keywords": [ + "CoCliCo" + ], + "providers": [ + { + "name": "Deltares", + "description": "Deltares is an independent institute for applied research in the field of water and subsurface.", + "roles": [ + "producer", + "processor" + ], + "url": "https://www.deltares.nl" + } + ], + "assets": { + "data": { + "href": "https://storage.googleapis.com/dgds-data-public/coclico/global_shoreline_morphodynamics.zarr", + "title": "smd zarr root", + "description": "The root of the smd zarr dataset on public Google Cloud Storage.", + "roles": [ + "data", + "zarr-root", + "gcs" + ] + } } - } } \ No newline at end of file diff --git a/current/ssl/collection.json b/current/ssl/collection.json index cc70f3105e..e806a8afd4 100644 --- a/current/ssl/collection.json +++ b/current/ssl/collection.json @@ -1,630 +1,630 @@ { - "type": "Collection", - "id": "ssl", - "stac_version": "1.0.0", - "description": "Dataset with extreme Storm Surge Levels (SSL) at the European scale. SSL are estimated for three climate scenarios (Historical, RCP4.5 and RCP8.5) for eight return periods (5, 10, 20, 50, 100, 200, 500 and 1000) according to the Peak Over Threshold method. This dataset is part of the [LISCOAST](https://data.jrc.ec.europa.eu/collection/LISCOAST) project. 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and subsurface.", - "roles": [ - "producer", - "processor" - ], - "url": "https://www.deltares.nl" - } - ], - "summaries": { - "rp": [ - 5.0, - 10.0, - 20.0, - 50.0, - 100.0, - 200.0, - 500.0, - 1000.0 - ], - "time": [ - 1995.0, - 2010.0, - 2020.0, - 2030.0, - 2040.0, - 2050.0, - 2060.0, - 2070.0, - 2080.0, - 2090.0, - 2100.0 - ] - }, - "assets": { - "data": { - "href": "https://storage.googleapis.com/dgds-data-public/coclico/global_wave_energy_flux.zarr", - "title": "Global Wave Energy Flux zarr root", - "description": "The root of the Global Wave Energy Flux zarr dataset on public Google Cloud Storage.", - "roles": [ - "data", - "zarr-root", - "gcs" - ] + "assets": { + "data": { + "href": "https://storage.googleapis.com/dgds-data-public/coclico/global_wave_energy_flux.zarr", + "title": "Global Wave Energy Flux zarr root", + "description": "The root of the Global Wave Energy Flux zarr dataset on public Google Cloud Storage.", + "roles": [ + "data", + "zarr-root", + "gcs" + ] + } } - } } \ No newline at end of file diff --git a/etl/README.md b/etl/README.md deleted file mode 100644 index 9eb6c184a8..0000000000 --- a/etl/README.md +++ /dev/null @@ -1,19 +0,0 @@ -# Automate data processing for the CoCliCo web portal - -This document describes how the scripts in [the etl module](../etl) directory can be -used to transform, format and process coclico data and store the results in the cloud. - -## Table of contents - -- [Cloud Services](#cloud-services) -- [Keys](#keys) - -## Cloud Services - -[cloud_services.py](./cloud_services.py) contains functions to interact with cloud -services including Google Cloud and Mapbox. - -[extract.py](./extract.py) contains functions to extract geospatial features from xarray -datasets. - -[keys.py](./keys.py) contains functions to manage access keys to cloud services. diff --git a/etl/keys.py b/etl/keys.py deleted file mode 100644 index 35bab3d26e..0000000000 --- a/etl/keys.py +++ /dev/null @@ -1,66 +0,0 @@ -import os -import pathlib -import warnings -from typing import Optional, Union - -from dotenv import load_dotenv -from google.cloud import storage - -from etl import p_drive, rel_root - - -class CredentialLeakageWarning(Warning): - pass - - -def load_env_variables(env_var_keys: list = list()) -> None: - env_fpath = rel_root.joinpath(".env") - if not env_fpath.exists(): - raise FileNotFoundError( - "Processing data requires access keys for cloud services, which should be" - f" stored as environment variables in .../{rel_root.joinpath('.env')}" - ) - - load_dotenv(env_fpath) - for env_var in env_var_keys: - if not env_var in os.environ: - raise KeyError(f"{env_var} not in environmental variables.") - print("Environmental variables loaded.") - - -def load_google_credentials(google_token_fp: Union[pathlib.Path, None] = None) -> None: - - if google_token_fp: - # TODO: Manage keys at user level, not with shared drive. The code block below - # should tested by Windows users to see if gcloud credentials behave similar on - # that os. If so, the code block below can be used instead. - warnings.warn( - "Keys loaded from shared network drive.", CredentialLeakageWarning - ) - if not google_token_fp.exists(): - if not p_drive.exists(): - raise FileNotFoundError( - "Deltares drive not found, mount drive to access Google keys." - ) - raise FileNotFoundError("Credential file does not exist.") - os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = str(google_token_fp) - print("Google Application Credentials load into environment.") - - else: - # TODO: Migrate to token=None in gcsfs when bug that no credentials can be found is fixed. - gmail_pattern = "*@gmail.com" - p = pathlib.Path.home().joinpath( - ".config", "gcloud", "legacy_credentials", gmail_pattern, "adc.json" - ) - p = list(p.parent.parent.expanduser().glob(p.parent.name))[0].joinpath(p.name) - if not p.exists(): - raise FileNotFoundError("Google credentials not found.") - os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = str(p) - print("Google Application Credentials load into environment.") - - -if __name__ == "__main__": - - coclico_data_dir = pathlib.Path(p_drive, "11205479-coclico", "data") - load_env_variables(env_var_keys=["MAPBOX_TOKEN"]) - load_google_credentials(coclico_data_dir.joinpath("google_credentials.json")) diff --git a/json-schema/schema.json b/json-schema/schema.json index 71a5796221..3d34ae61c3 100644 --- a/json-schema/schema.json +++ b/json-schema/schema.json @@ -1,6 +1,6 @@ { "$schema": "http://json-schema.org/draft-07/schema#", - "$id": "https://storage.googleapis.com/dgds-data-public/coclico/json-schema/schema.json#", + "$id": "https://raw.githubusercontent.com/openearth/coclicodata/refactor-to-python-package/json-schema/schema.json", "title": "Deltares Extension", "description": "STAC Deltares Extension for STAC Items and STAC Collections.", "oneOf": [ @@ -23,16 +23,6 @@ }, "properties": { "allOf": [ - { - "$comment": "Require fields here for Item Properties.", - "required": [ - "deltares:item_key", - "deltares:paint", - "deltares:type", - "deltares:stations", - "deltares:onclick" - ] - }, { "$ref": "#/definitions/fields" } @@ -71,18 +61,6 @@ { "$comment": "This is the schema for the top-level fields in a Collection.", "allOf": [ - { - "$comment": "Require fields here for Collections (top-level).", - "required": [ - "deltares:units", - "deltares:plotSeries", - "deltares:plotxAxis", - "deltares:plotType", - "deltares:min", - "deltares:max", - "deltares:linearGradient" - ] - }, { "$ref": "#/definitions/fields" } @@ -162,78 +140,13 @@ "stac_extensions": { "type": "array", "contains": { - "const": "https://raw.githubusercontent.com/openearth/coclicodata/feat/update-deltares-stac-properties/json-schema/schema.json" + "const": "https://raw.githubusercontent.com/openearth/coclicodata/refactor-to-python-package/json-schema/schema.json" } } } }, - "require_any_field": { - "$comment": "Please list all fields here so that we can force the existence of one of them in other parts of the schemas.", - "anyOf": [ - { - "required": [ - "deltares:item_id" - ] - }, - { - "required": [ - "deltares:paint" - ] - }, - { - "required": [ - "deltares:type" - ] - }, - { - "required": [ - "deltares:stations" - ] - }, - { - "required": [ - "deltares:onclick" - ] - }, - { - "required": [ - "deltares:units" - ] - }, - { - "required": [ - "deltares:plotSeries" - ] - }, - { - "required": [ - "deltares:plotType" - ] - }, - { - "required": [ - "deltares:plotxAxis" - ] - }, - { - "required": [ - "deltares:min" - ] - }, - { - "required": [ - "deltares:max" - ] - }, - { - "required": [ - "deltares:linearGradient" - ] - } - ] - }, "fields": { - "$comment": "Add your new fields here. Don't require them here, do that above in the corresponding schema.", + "$comment": "Deltares fields definitions", "type": "object", "properties": { "deltares:item_key": { diff --git a/notebooks/19_coastal_mask.ipynb b/notebooks/19_coastal_mask.ipynb index 96cf107311..dd062d1a4f 100644 --- a/notebooks/19_coastal_mask.ipynb +++ b/notebooks/19_coastal_mask.ipynb @@ -13,13 +13,6 @@ "execution_count": null, "id": "25ee6977-26e0-4b85-ac11-1fd7bf0a9ca7", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:26.538074Z", - "iopub.status.busy": "2023-08-25T17:08:26.537873Z", - "iopub.status.idle": "2023-08-25T17:08:27.527166Z", - "shell.execute_reply": "2023-08-25T17:08:27.526872Z", - "shell.execute_reply.started": "2023-08-25T17:08:26.538053Z" - }, "tags": [] }, "outputs": [], @@ -54,6 +47,39 @@ "from tqdm import tqdm" ] }, + { + "cell_type": "markdown", + "id": "8f70eabd-05f2-412b-bedd-60ac5a34dbd0", + "metadata": {}, + "source": [ + "## Install CoCliCodata package" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "50914feb-f1e3-4653-b757-5ebe707da3dc", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "# uncomment these lines if you do not have coclicodata in development mode installed\n", + "# dev_dir = pathlib.Path.home() / \"dev\" # set the path to the location where you would like to clone the package\n", + "# dev_dir.mkdir(parents=True, exist_ok=True)\n", + "\n", + "# # Clone the repository\n", + "# os.system(f\"git clone https://github.com/openearth/coclicodata.git {dev_dir / 'coclicodata'}\")\n", + "\n", + "# # Install the package in development mode\n", + "# os.system(f\"pip install -e {dev_dir / 'coclicodata'}\")\n", + "\n", + "from coclicodata.coclico_stac.io import CoCliCoStacIO\n", + "from coclicodata.coclico_stac.layouts import CoCliCoCOGLayout\n", + "from coclicodata.drive_config import p_drive\n", + "from coclicodata.coclico_stac.extension import CoclicoExtension" + ] + }, { "cell_type": "markdown", "id": "d113838a-51f1-4dca-b069-acf9bbf58870", @@ -67,13 +93,6 @@ "execution_count": null, "id": "49605712-ffcf-4272-8177-17fe6b37d5a1", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:27.528091Z", - "iopub.status.busy": "2023-08-25T17:08:27.528016Z", - "iopub.status.idle": "2023-08-25T17:08:27.607669Z", - "shell.execute_reply": "2023-08-25T17:08:27.607359Z", - "shell.execute_reply.started": "2023-08-25T17:08:27.528083Z" - }, "tags": [] }, "outputs": [], @@ -87,14 +106,13 @@ "# f\"pip install git+https://{gh_coastmonitor_token}@github.com/floriscalkoen/coastmonitor.git \"\n", "# )\n", "\n", - "from coastmonitor import p_drive\n", "from coastmonitor.cloud_utils import (\n", " to_https_url,\n", " to_storage_location,\n", " to_uri_protocol,\n", " write_block,\n", ")\n", - "from coastmonitor.stac_utils import ListItemLayout, name_block" + "from coastmonitor.stac_utils import name_block" ] }, { @@ -110,13 +128,6 @@ "execution_count": null, "id": "918f4e0d-1ea6-4f03-8d9f-aa0dc1a9e9d8", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:27.608107Z", - "iopub.status.busy": "2023-08-25T17:08:27.608027Z", - "iopub.status.idle": "2023-08-25T17:08:27.610695Z", - "shell.execute_reply": "2023-08-25T17:08:27.610454Z", - "shell.execute_reply.started": "2023-08-25T17:08:27.608099Z" - }, "tags": [] }, "outputs": [], @@ -127,19 +138,23 @@ "PRC_DIR = DATA_DIR / \"prc\"\n", "LIVE_DIR = DATA_DIR / \"live\"\n", "\n", - "STAC_DIR = pathlib.Path.home() / \"stac\" / \"calkoen\"\n", "STAC_DIR = pathlib.Path.cwd().parent / \"current\"\n", + "\n", "COASTAL_MASK_DIR = SRC_DIR / \"19_coastal_mask\"\n", "# COASTAL_MASK_DIR = p_drive / \"11205479-coclico\" / \"data\" / \"19_coastal_mask\" # read data from p drive\n", + "\n", "CM_FP = COASTAL_MASK_DIR / \"Global_merit_coastal_mask_landwards.tif\"\n", "# CM_FP = COASTAL_MASK_DIR / \"Europe_merit_coastplain_elecz_H100+2m_partioned.tif\" # not sure which one to use\n", - "OUTDIR = TMP_DIR / \"19_cm_test\"\n", + "\n", + "# OUTDIR = TMP_DIR / \"19_cm_test\"\n", "\n", "GCS_PROTOCOL = \"https://storage.googleapis.com\"\n", "GCS_PROJECT = \"DGDS - I1000482-002\"\n", "BUCKET_NAME = \"dgds-data-public\"\n", "BUCKET_PROJ = \"coclico\"\n", - "HREF_PREFIX = \"https://storage.googleapis.com/dgds-data-public/coclico/coastal_mask\"" + "HREF_PREFIX = (\n", + " \"https://storage.googleapis.com/dgds-data-public/coclico/coastal_mask\"\n", + ")" ] }, { @@ -147,13 +162,6 @@ "execution_count": null, "id": "e5c233e9-d570-422c-a44f-3b27284d645d", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:31.478927Z", - "iopub.status.busy": "2023-08-25T17:08:31.478488Z", - "iopub.status.idle": "2023-08-25T17:08:31.495172Z", - "shell.execute_reply": "2023-08-25T17:08:31.494377Z", - "shell.execute_reply.started": "2023-08-25T17:08:31.478895Z" - }, "tags": [] }, "outputs": [], @@ -254,6 +262,14 @@ "\n", " pystac.extensions.scientific.ScientificExtension.add_to(collection)\n", " collection.extra_fields[\"sci:citation\"] = \"Lincke et al., 2023, in progress\"\n", + "\n", + " # add coclico frontend properties to collection\n", + " coclico_ext = CoclicoExtension.ext(collection, add_if_missing=True)\n", + " coclico_ext.units = \"bool\"\n", + " coclico_ext.plot_type = \"raster\"\n", + " coclico_ext.min = 0\n", + " coclico_ext.max = 1\n", + "\n", " return collection" ] }, @@ -262,13 +278,6 @@ "execution_count": null, "id": "374ceb9f-d897-4617-b44f-ca849cef4e1b", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:32.491508Z", - "iopub.status.busy": "2023-08-25T17:08:32.490443Z", - "iopub.status.idle": "2023-08-25T17:08:32.509074Z", - "shell.execute_reply": "2023-08-25T17:08:32.508553Z", - "shell.execute_reply.started": "2023-08-25T17:08:32.491446Z" - }, "tags": [] }, "outputs": [], @@ -314,6 +323,12 @@ " ext.transform = list(block.rio.transform())[:6]\n", " ext.add_to(item)\n", "\n", + " # add CoCliCo frontend properties to visualize it in the web portal\n", + " # TODO: This is just example. We first need to decide which properties frontend needs for COG visualization\n", + " coclico_ext = CoclicoExtension.ext(item, add_if_missing=True)\n", + " coclico_ext.item_key = item_id\n", + " coclico_ext.add_to(item)\n", + "\n", " # add more functions to describe the data at item level, for example the frontend properties to visualize it\n", " ...\n", "\n", @@ -369,13 +384,6 @@ "execution_count": null, "id": "03aad3fa-b7aa-4931-8e37-fbe7e5512c87", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:33.617192Z", - "iopub.status.busy": "2023-08-25T17:08:33.616291Z", - "iopub.status.idle": "2023-08-25T17:08:33.635122Z", - "shell.execute_reply": "2023-08-25T17:08:33.633445Z", - "shell.execute_reply.started": "2023-08-25T17:08:33.617136Z" - }, "tags": [] }, "outputs": [], @@ -412,7 +420,7 @@ " block,\n", " storage_prefix=\"\",\n", " name_prefix=name_prefix,\n", - " include_band=False,\n", + " include_band=None,\n", " time_dim=time_dim,\n", " x_dim=x_dim,\n", " y_dim=y_dim,\n", @@ -444,7 +452,7 @@ "\n", " # TODO: include this file checking\n", " # if not file_exists(file, str(storage_destination), existing_blobs):\n", - " nbytes = write_block(da, uri, storage_options, profile_options)\n", + " nbytes = write_block(da, uri, storage_options, profile_options, overwrite=True)\n", "\n", " item = create_asset(\n", " item,\n", @@ -472,13 +480,6 @@ "execution_count": null, "id": "fd4c81ef-dc0e-436d-9c38-5539d19fb21e", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:08:35.029626Z", - "iopub.status.busy": "2023-08-25T17:08:35.028713Z", - "iopub.status.idle": "2023-08-25T17:08:36.097360Z", - "shell.execute_reply": "2023-08-25T17:08:36.097007Z", - "shell.execute_reply.started": "2023-08-25T17:08:35.029572Z" - }, "tags": [] }, "outputs": [], @@ -497,13 +498,6 @@ "execution_count": null, "id": "bc5c5801-f79d-495b-bc86-5c755037b1ce", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:09:06.306853Z", - "iopub.status.busy": "2023-08-25T17:09:06.306488Z", - "iopub.status.idle": "2023-08-25T17:17:48.815001Z", - "shell.execute_reply": "2023-08-25T17:17:48.814532Z", - "shell.execute_reply.started": "2023-08-25T17:09:06.306821Z" - }, "tags": [] }, "outputs": [], @@ -569,19 +563,12 @@ "execution_count": null, "id": "cafbbb2d-57b3-4387-8292-bdd3d52127d4", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:17:48.816404Z", - "iopub.status.busy": "2023-08-25T17:17:48.816245Z", - "iopub.status.idle": "2023-08-25T17:17:49.081159Z", - "shell.execute_reply": "2023-08-25T17:17:49.080797Z", - "shell.execute_reply.started": "2023-08-25T17:17:48.816381Z" - }, "tags": [] }, "outputs": [], "source": [ - "stac_io = StacIO.default()\n", - "layout = ListItemLayout()\n", + "stac_io = CoCliCoStacIO()\n", + "layout = CoCliCoCOGLayout()\n", "\n", "collection = create_collection()\n", "\n", @@ -591,7 +578,7 @@ "collection.update_extent_from_items()\n", "\n", "\n", - "catalog = pystac.Catalog.from_file(STAC_DIR / \"catalog.json\")\n", + "catalog = pystac.Catalog.from_file(str(STAC_DIR / \"catalog.json\"))\n", "\n", "if catalog.get_child(collection.id):\n", " catalog.remove_child(collection.id)\n", @@ -611,29 +598,26 @@ { "cell_type": "code", "execution_count": null, - "id": "4b869572-f148-4f37-9fcf-bf1134ca1757", + "id": "18c43b86-5aa2-4347-9197-998874642121", "metadata": { - "execution": { - "iopub.execute_input": "2023-08-25T17:21:49.937584Z", - "iopub.status.busy": "2023-08-25T17:21:49.936720Z", - "iopub.status.idle": "2023-08-25T17:22:56.096900Z", - "shell.execute_reply": "2023-08-25T17:22:56.096486Z", - "shell.execute_reply.started": "2023-08-25T17:21:49.937533Z" - }, "tags": [] }, "outputs": [], "source": [ - "catalog.validate_all()" + "collection.validate_all()" ] }, { "cell_type": "code", "execution_count": null, "id": "16c06c18-7330-42bc-b4b9-c1d6dd5e5614", - "metadata": {}, + "metadata": { + "tags": [] + }, "outputs": [], - "source": [] + "source": [ + "catalog.validate_all()" + ] } ], "metadata": { diff --git a/notebooks/README.md b/notebooks/README.md deleted file mode 100644 index a0ad015cc1..0000000000 --- a/notebooks/README.md +++ /dev/null @@ -1,87 +0,0 @@ -# Notebooks used for CoCliCo fast-track preprocessing - -## CF conventions - -Datasets should follow CF conventions where possible. These conventions are described -[here](https://cfconventions.org/). - -## TODO: Description dimension, coordinates, variables - - -### Controlled vocabulary - -#### TODO: Description use controlled vocabulary - -| src_name | dst_name | long_name | standard_name | cf_type | dtype | -|------------------|---------------------|---------------------|---------------|---------|-----------------------| -| RP | rp | return period | | dim | int | -| decades | time | time | time | dim | cftime | -| id | nstations | number of stations | | dim | int | -| lat | lat | latitude | latitude | dim | float | -| latitude | lat | latitude | latitude | dim | float | -| lon | lon | longitude | longitude | dim | float | -| longitude | lon | longitude | longitude | dim | float | -| nens | nensemble | number of ensembles | | dim | int | -| nlayers | nlayers | number of layers | | dim | int | -| npoints | nstations | number of stations | | dim | int | -| nrp | rp | return period | | dim | int | -| nscenarios | nscenarios | number of scenarios | | dim | int | -| nsdec | time | time | | dim | cftime | -| ntransect | nstations | number of stations | | dim | int | -| ptid | nstations | number of stations | | dim | int | -| rp | rp | return period | | dim | int | -| ensmbl | ensemble | ensemble | | coord | zero-terminated bytes | -| id | stations | stations | | coord | zero-terminated bytes | -| ptid | stations | stations | | coord | zero-terminated bytes | -| layers | layers | layers | | coord | zero-terminated bytes | -| scenario | scenario | scenario | | coord | zero-terminated bytes | -| transect | stations | stations | | coord | zero-terminated bytes | -| activezonetoland | active_zone_to_land | active zone to land | | var | float | -| activezonetosea | active_zone_to_sea | active zone to sea | | var | float | -| eewl | eewl | | | var | float | -| errorid | error_id | error id | | var | str | -| esl | esl | extreme sea level | | var | float | -| landid | country | country | | var | str | -| landtoactivezone | land_to_active_zone | land to active zone | | var | float | -| landtosea | land_to_sea | land to sea | | var | float | -| ssl | ssl | sea surface level | | var | float | -| sustain | sustain | sustainability | | var | float | -| wef | wef | wave energy flux | | var | float | -| base2000 | | | | | | -| cfpi | | | | | | -| col | | | | | | -| copula | | | | | | -| cor | | | | | | -| dd10 | | | | | | -| ffbd2050 | scenario? | | | | | -| ffbd2100 | scenario? | | | | | -| ffd | ffd | | | | | -| firstYear | first_year | | | | | -| firstlandlat | first_land_lat | | | | | -| firstlandlon | first_land_lot | | | | | -| frag2050 | scenario? | | | | | -| frag2100 | scenario? | | | | | -| landfound | land_found | | | | | -| lastYear | last_year | | | | | -| latland | lat_land | | | | | -| latsea | lat_sea | | | | | -| lonland | lon_land | | | | | -| lonsea | lon_sea | | | | | -| perc1 | | | | | | -| perc17 | | | | | | -| perc5 | | | | | | -| perc50 | | | | | | -| perc83 | | | | | | -| perc95 | | | | | | -| perc99 | | | | | | -| pp10 | | | | | | -| qualityflag | quality_flag | | | | | -| ret_per | ret_per | | | | | -| row | stations? | | | | | -| seatoactivezone | sea_to_active_zone | | | | | -| seatoland | sea_to_land | | | | | -| segmentid | instance? | | | | | -| spuriousratio | spurious_ratio | | | | | -| ss10 | | | | | | -| sust2050 | scenario? | | | | | -| sust2100 | scenario? | | | | | diff --git a/pyproject.toml b/pyproject.toml index 2eb6efecc1..a69a04f2df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,31 @@ +[tool.poetry] +name = "coclicodata" +version = "0.1.0" +description = "Python tools for the CoCliCo project" +authors = ["Etienne Kras", "Floris Calkoen", "Luis Rodriguez Galvez", "Maarten Pronk"] +license = "MIT" +readme = "README.md" +repository = "https://github.com/openearth/coclicodata" + +[tool.poetry.dependencies] +python = "^3.10" +pystac = "^1.8.0" + +[tool.poetry.dev-dependencies] +pytest = "^7.4.0" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + [tool.pytest.ini_options] minversion = "7.0" +# compact view of the test results with a summary at the end. addopts = "-ra -q" testpaths = [ - ".", + "tests", ] -python_files = "validate.py" +python_files = "test_*.py" + + + diff --git a/scripts/build-stacs.sh b/scripts/bash/build-stacs.sh similarity index 100% rename from scripts/build-stacs.sh rename to scripts/bash/build-stacs.sh diff --git a/scripts/bash/sync-stac-with-azure-container.sh b/scripts/bash/sync-stac-with-azure-container.sh new file mode 100644 index 0000000000..3ba549c997 --- /dev/null +++ b/scripts/bash/sync-stac-with-azure-container.sh @@ -0,0 +1,2 @@ +#!/bin/bash +az storage blob sync --account-name coclico --source ./current --container stac/v1 diff --git a/scripts/01_ssl_stacs.py b/scripts/create_stacs/01_ssl_stacs.py similarity index 100% rename from scripts/01_ssl_stacs.py rename to scripts/create_stacs/01_ssl_stacs.py diff --git a/scripts/02_wef_stacs.py b/scripts/create_stacs/02_wef_stacs.py similarity index 99% rename from scripts/02_wef_stacs.py rename to scripts/create_stacs/02_wef_stacs.py index 7d3e646e7e..37f4748475 100644 --- a/scripts/02_wef_stacs.py +++ b/scripts/create_stacs/02_wef_stacs.py @@ -174,13 +174,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(title, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/03_eesl_stacs.py b/scripts/create_stacs/03_eesl_stacs.py similarity index 99% rename from scripts/03_eesl_stacs.py rename to scripts/create_stacs/03_eesl_stacs.py index cb2ecc909d..0fc4163d57 100644 --- a/scripts/03_eesl_stacs.py +++ b/scripts/create_stacs/03_eesl_stacs.py @@ -172,13 +172,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(title, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/04_smd_stacs.py b/scripts/create_stacs/04_smd_stacs.py similarity index 99% rename from scripts/04_smd_stacs.py rename to scripts/create_stacs/04_smd_stacs.py index fd05f15f0b..739c3775c4 100644 --- a/scripts/04_smd_stacs.py +++ b/scripts/create_stacs/04_smd_stacs.py @@ -157,13 +157,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(var, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/05_sc_stacs.py b/scripts/create_stacs/05_sc_stacs.py similarity index 99% rename from scripts/05_sc_stacs.py rename to scripts/create_stacs/05_sc_stacs.py index f91023c4f8..4e0bcad1a6 100644 --- a/scripts/05_sc_stacs.py +++ b/scripts/create_stacs/05_sc_stacs.py @@ -186,13 +186,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(title, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/06_cbca_stacs.py b/scripts/create_stacs/06_cbca_stacs.py similarity index 99% rename from scripts/06_cbca_stacs.py rename to scripts/create_stacs/06_cbca_stacs.py index d9994b1e3b..fab3da43fc 100644 --- a/scripts/06_cbca_stacs.py +++ b/scripts/create_stacs/06_cbca_stacs.py @@ -170,13 +170,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(title, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/07_cfr_stacs.py b/scripts/create_stacs/07_cfr_stacs.py similarity index 99% rename from scripts/07_cfr_stacs.py rename to scripts/create_stacs/07_cfr_stacs.py index 56fcbe0627..aa44dcafab 100644 --- a/scripts/07_cfr_stacs.py +++ b/scripts/create_stacs/07_cfr_stacs.py @@ -170,13 +170,11 @@ def get_paint_props(item_key: str): # create stac collection per variable and add to dataset collection for var in VARIABLES: - # add zarr store as asset to stac_obj collection.add_asset("data", gen_zarr_asset(title, gcs_api_zarr_store)) # stac items are generated per AdditionalDimension (non spatial) for dimcomb in dimcombs: - mapbox_url = get_mapbox_url(MAPBOX_PROJ, DATASET_FILENAME, var) # generate stac item key and add link to asset to the stac item diff --git a/scripts/17_slp6_stacs.py b/scripts/create_stacs/17_slp6_stacs.py similarity index 100% rename from scripts/17_slp6_stacs.py rename to scripts/create_stacs/17_slp6_stacs.py diff --git a/scripts/18_slp_stacs.py b/scripts/create_stacs/18_slp_stacs.py similarity index 100% rename from scripts/18_slp_stacs.py rename to scripts/create_stacs/18_slp_stacs.py diff --git a/scripts/19_cm_stacs.py b/scripts/create_stacs/19_cm_stacs.py similarity index 99% rename from scripts/19_cm_stacs.py rename to scripts/create_stacs/19_cm_stacs.py index 4f774717e6..fe753fee53 100644 --- a/scripts/19_cm_stacs.py +++ b/scripts/create_stacs/19_cm_stacs.py @@ -330,7 +330,6 @@ def collate(items: xr.DataArray) -> List[pystac.Item]: # rename or swap dimension names, the latter in case the name already exists as coordinate if __name__ == "__main__": - # hard-coded input params at project level GCS_PROTOCOL = "https://storage.googleapis.com" GCS_PROJECT = "DGDS - I1000482-002" diff --git a/scripts/20_cisi_stacs.py b/scripts/create_stacs/20_cisi_stacs.py similarity index 100% rename from scripts/20_cisi_stacs.py rename to scripts/create_stacs/20_cisi_stacs.py diff --git a/generate.py b/scripts/create_stacs/example.py similarity index 98% rename from generate.py rename to scripts/create_stacs/example.py index 9a693f1f37..1838c91087 100644 --- a/generate.py +++ b/scripts/create_stacs/example.py @@ -44,7 +44,9 @@ def list_replace_value(l, old, new): return x def json_dumps(self, json_dict: Dict[str, Any], *args: Any, **kwargs: Any) -> str: - return json.dumps(IO.dict_replace_value(json_dict, "\\", "/"), *args, indent=4, **kwargs) + return json.dumps( + IO.dict_replace_value(json_dict, "\\", "/"), *args, indent=4, **kwargs + ) class Layout(BestPracticesLayoutStrategy): @@ -109,7 +111,6 @@ def gen_default_props( key="rp_5", **kwargs, ): - return { **kwargs, "deltares:stations": "locationId", @@ -257,7 +258,7 @@ def extend_links(collection, dimension_names): feature = gen_default_item(f"{variable}-mapbox-{key}") feature.add_asset("mapbox", gen_mapbox_asset(mapbox_url, mapbox_source)) feature.properties = gen_default_props(key=key) - for (k, v) in zip(dimvals.keys(), values): + for k, v in zip(dimvals.keys(), values): feature.properties[k] = v dataset.add_item(feature, strategy=layout) diff --git a/scripts/coclico_common_vocab_from_stac.py b/scripts/utils/coclico_common_vocab_from_stac.py similarity index 99% rename from scripts/coclico_common_vocab_from_stac.py rename to scripts/utils/coclico_common_vocab_from_stac.py index 3e92cb5cba..8778868e2b 100644 --- a/scripts/coclico_common_vocab_from_stac.py +++ b/scripts/utils/coclico_common_vocab_from_stac.py @@ -27,7 +27,6 @@ # rename or swap dimension names, the latter in case the name already exists as coordinate if __name__ == "__main__": - # hard-coded input params at project level catalog = pystac_client.Client.open( @@ -45,7 +44,6 @@ if "cube:variables" in dict_: for k, v in dict_["cube:variables"].items(): if "attrs" in v: - # if "long_name" in v["attrs"]: # d = {k: v["attrs"]["long_name"]} # result.append(d) @@ -70,7 +68,6 @@ d = dict() d["name"] = k if "long_name" in v["attrs"]: - d["long_name"] = v["attrs"]["long_name"] # d = {k: v["attrs"]["long_name"]} if "standard_name" in v["attrs"]: diff --git a/scripts/correction_to_zarr_store_example.py b/scripts/utils/correction_to_zarr_store_example.py similarity index 99% rename from scripts/correction_to_zarr_store_example.py rename to scripts/utils/correction_to_zarr_store_example.py index 5ad85f6a75..67f8fc9459 100644 --- a/scripts/correction_to_zarr_store_example.py +++ b/scripts/utils/correction_to_zarr_store_example.py @@ -9,7 +9,6 @@ from etl.extract import clear_zarr_information if __name__ == "__main__": - BUCKET_NAME = "dgds-data-public" BUCKET_PROJ = "coclico" DATASET_FILENAME = "global_wave_energy_flux.zarr" diff --git a/scripts/stac_to_cloud.py b/scripts/utils/stac_to_cloud.py similarity index 100% rename from scripts/stac_to_cloud.py rename to scripts/utils/stac_to_cloud.py diff --git a/scripts/upload_and_generate_geojson.py b/scripts/utils/upload_and_generate_geojson.py similarity index 100% rename from scripts/upload_and_generate_geojson.py rename to scripts/utils/upload_and_generate_geojson.py diff --git a/src/coclicodata/__init__.py b/src/coclicodata/__init__.py new file mode 100644 index 0000000000..bb5687f54c --- /dev/null +++ b/src/coclicodata/__init__.py @@ -0,0 +1,6 @@ +""" +coclicodata: Python tools for the CoCliCo project. +""" + +__version__ = "0.1.0" +__author__ = "Etienne Kras, Floris Calkoen, Luis Rodriguez Galvez, Maarten Pronk" diff --git a/src/coclicodata/coclico_stac/__init__.py b/src/coclicodata/coclico_stac/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/stac/datacube.py b/src/coclicodata/coclico_stac/datacube.py similarity index 96% rename from stac/datacube.py rename to src/coclicodata/coclico_stac/datacube.py index a5a15b3de7..7dacf35f55 100644 --- a/stac/datacube.py +++ b/src/coclicodata/coclico_stac/datacube.py @@ -1,5 +1,3 @@ -from typing import Dict, Union - import numpy as np import pandas as pd import pystac @@ -8,17 +6,12 @@ from pystac.extensions.datacube import ( AdditionalDimension, DatacubeExtension, - Dimension, DimensionType, - HorizontalSpatialDimension, - TemporalDimension, - Variable, ) from xstac._xstac import ( build_horizontal_dimension, build_temporal_dimension, build_variables, - maybe_infer_reference_system, maybe_infer_step, ) @@ -97,7 +90,6 @@ def add_datacube( dimensions = {} if temporal_dimension is not False: - # convert time formatted year ([%Y]) to datetime. Without this conversion build_temporal_dimension # from xstac will interpret the time integer as 1970-01-01 00:00:00.000002015 if ds[temporal_dimension].dtype.kind in np.typecodes["AllInteger"]: @@ -117,7 +109,6 @@ def add_datacube( ) if x_dimension: - dimensions[x_dimension] = build_horizontal_dimension( ds, x_dimension, @@ -140,7 +131,6 @@ def add_datacube( ) for additional_dimension in additional_dimensions: - dimensions[additional_dimension] = build_additional_dimension( ds, additional_dimension, diff --git a/stac/coclico_extension.py b/src/coclicodata/coclico_stac/extension.py similarity index 81% rename from stac/coclico_extension.py rename to src/coclicodata/coclico_stac/extension.py index f988a6cafa..b3fc2d5e9a 100644 --- a/stac/coclico_extension.py +++ b/src/coclicodata/coclico_stac/extension.py @@ -1,27 +1,21 @@ -import json -from datetime import datetime, timedelta -from pprint import pprint +""" +Module implementing the Coclico Extension for STAC items and collections. + +The Coclico Extension is a custom extension to the STAC specification that provides +additional properties tailored to specific use-cases. This module offers utility +methods and classes to apply and retrieve these properties. + +""" + from typing import Any, Dict, Generic, List, Optional, TypeVar, Union, cast -from uuid import uuid4 import pystac from pystac.extensions.base import ExtensionManagementMixin, PropertiesExtension -from pystac.utils import ( - StringEnum, - datetime_to_str, - get_required, - map_opt, - str_to_datetime, -) T = TypeVar("T", pystac.Collection, pystac.Item, pystac.Asset) -# TODO: make schema for frontend coclico properties -# host schema at a server, for example: -SCHEMA_URI = "https://raw.githubusercontent.com/openearth/coclicodata/feat/update-deltares-stac-properties/json-schema/schema.json" - +SCHEMA_URI = "https://raw.githubusercontent.com/openearth/coclicodata/refactor-to-python-package/json-schema/schema.json" -# TODO: property getters/setters per property. Props below are not used yet. PREFIX: str = "deltares:" # list of properties that are added at item level @@ -46,12 +40,8 @@ class CoclicoExtension( PropertiesExtension, ExtensionManagementMixin[Union[pystac.Collection, pystac.Item]], ): - """An abstract class that can be used to extend the properties of a - :class:`~pystac.Collection`, :class:`~pystac.Item`, or :class:`~pystac.Asset` with - properties from the :stac-ext:`CoCliCo Extension `. - - """ + """A class extending the properties of STAC Collection, Item, or Asset with Coclico properties.""" def apply( self, @@ -68,7 +58,7 @@ def apply( max_: Optional[int] = None, linear_gradient: Optional[List[Dict[str, Any]]] = None, ) -> None: - + """Apply Coclico properties to the STAC item or collection.""" # these are added at item level self.item_key = item_key self.paint = paint @@ -183,13 +173,12 @@ def linear_gradient(self, v: Optional[List[Dict[str, Any]]]) -> None: @classmethod def get_schema_uri(cls) -> str: + """Retrieve the schema URI for the Coclico properties.""" return SCHEMA_URI @classmethod def ext(cls, obj: T, add_if_missing: bool = False) -> "CoclicoExtension[T]": - """Extends the given STAC Object with properties from the :stac-ext:`Coclico Extension - `. This extension can be applied to instances of :class:`~pystac.Collection`, - :class:`~pystac.Item`. + """Extend the given STAC Object with the Coclico Extension properties. Adopted from both: - https://github.com/stac-utils/pystac/blob/3c5176f178a4345cb50d5dab83f1dab504ed2682/pystac/extensions/datacube.py @@ -211,11 +200,7 @@ def ext(cls, obj: T, add_if_missing: bool = False) -> "CoclicoExtension[T]": class CollectionCoclicoExtension(CoclicoExtension[pystac.Collection]): - """A concrete implementation of :class:`CoclicoExtension` on an - :class:`~pystac.Collection` that extends the properties of the Item to include - properties defined in the :stac-ext:`Coclico Extension `. - This class should generally not be instantiated directly. Instead, call - :meth:`CoclicoExtension.ext` on an :class:`~pystac.Collection` to extend it. + """A class extending the properties of a STAC Collection with Coclico properties. Adopted from both: - https://github.com/stac-utils/pystac/blob/3c5176f178a4345cb50d5dab83f1dab504ed2682/pystac/extensions/datacube.py @@ -228,6 +213,7 @@ class CollectionCoclicoExtension(CoclicoExtension[pystac.Collection]): properties: Dict[str, Any] def __init__(self, collection: pystac.Collection): + """Initialize the extension for a STAC collection.""" self.collection = collection self.properties = collection.extra_fields @@ -238,11 +224,7 @@ def __repr__(self) -> str: class ItemCoCliCoExtension(CoclicoExtension[pystac.Item]): - """A concrete implementation of :class:`DatacubeExtension` on an - :class:`~pystac.Item` that extends the properties of the Item to include properties - defined in the :stac-ext:`Datacube Extension `. - This class should generally not be instantiated directly. Instead, call - :meth:`DatacubeExtension.ext` on an :class:`~pystac.Item` to extend it. + """A class extending the properties of a STAC Item with Coclico properties. Adopted from both: - https://github.com/stac-utils/pystac/blob/3c5176f178a4345cb50d5dab83f1dab504ed2682/pystac/extensions/datacube.py diff --git a/src/coclicodata/coclico_stac/io.py b/src/coclicodata/coclico_stac/io.py new file mode 100644 index 0000000000..5d68f62b81 --- /dev/null +++ b/src/coclicodata/coclico_stac/io.py @@ -0,0 +1,48 @@ +import json +from typing import Any, Dict + +from pystac.stac_io import DefaultStacIO + + +class CoCliCoStacIO(DefaultStacIO): + "Custom IO to format our CoCliCo STAC json with an indentation of 4 spaces." + + def __init__(self) -> None: + super().__init__() + import warnings + + warnings.warn( + "CoCliCoStacIO will be deprecated in future versions. " + "Newer versions of pystac (1.8+) should natively handle Windows paths.", + FutureWarning, + ) + + # enabling a GitHub Actions compatible Windows created STAC --> i.e. replacing '\\' by '/' + def _dict_replace_value(self, d, old, new): + x = {} + for k, v in d.items(): + if isinstance(v, dict): + v = self._dict_replace_value(v, old, new) + elif isinstance(v, list): + v = self._list_replace_value(v, old, new) + elif isinstance(v, str): + v = v.replace(old, new) + x[k] = v + return x + + def _list_replace_value(self, l, old, new): + x = [] + for e in l: + if isinstance(e, list): + e = self._list_replace_value(e, old, new) + elif isinstance(e, dict): + e = self._dict_replace_value(e, old, new) + elif isinstance(e, str): + e = e.replace(old, new) + x.append(e) + return x + + def json_dumps(self, json_dict: Dict[str, Any], *args: Any, **kwargs: Any) -> str: + return json.dumps( + self._dict_replace_value(json_dict, "\\", "/"), *args, indent=4, **kwargs + ) diff --git a/src/coclicodata/coclico_stac/layouts.py b/src/coclicodata/coclico_stac/layouts.py new file mode 100644 index 0000000000..86c46fb9e8 --- /dev/null +++ b/src/coclicodata/coclico_stac/layouts.py @@ -0,0 +1,87 @@ +import pathlib + +from pystac import Item +from pystac.layout import BestPracticesLayoutStrategy +from pystac.utils import JoinType, join_path_or_url, safe_urlparse + + +class CoCliCoZarrLayout(BestPracticesLayoutStrategy): + """ + Custom layout for Zarrs within CoCliCo STAC collections. + + Modifies the item path to: + variable-mapbox/variable-mapbox-dim-value-dim-value.json + Instead of the default: + /variable-mapbox-dim-value-dim-value/variable-mapbox-dim-value-dim-value.json + """ + + def get_item_href(self, item: Item, parent_dir: str) -> str: + """ + Determines the item href based on the custom layout for Zarrs. + + Args: + item (Item): The STAC item. + parent_dir (str): The parent directory path. + + Returns: + str: The constructed item href. + """ + parsed_parent_dir = safe_urlparse(parent_dir) + join_type = JoinType.from_parsed_uri(parsed_parent_dir) + custom_id = "-".join(item.id.split("-")[0:2]) + item_root = join_path_or_url(join_type, parent_dir, "{}".format(custom_id)) + return join_path_or_url(join_type, item_root, "{}.json".format(item.id)) + + +class CoCliCoCOGLayout(BestPracticesLayoutStrategy): + """ + Custom layout for CoGs within CoCliCo STAC collections. + + Modifies the item path to: + items/variable-mapbox-dim-value-dim-value.json + Instead of the default: + /variable-mapbox-dim-value-dim-value/variable-mapbox-dim-value-dim-value.json + """ + + def get_item_href(self, item: Item, parent_dir: str) -> str: + """ + Determines the item href based on the custom layout for CoGs. + + Args: + item (Item): The STAC item. + parent_dir (str): The parent directory path. + + Returns: + str: The constructed item href. + """ + parsed_parent_dir = safe_urlparse(parent_dir) + join_type = JoinType.from_parsed_uri(parsed_parent_dir) + items_dir = "items" + custom_id = pathlib.Path(item.id).with_suffix(".json") + return join_path_or_url(join_type, parent_dir, items_dir, str(custom_id)) + + +class CoCliCoParquetLayout(BestPracticesLayoutStrategy): + """ + Custom layout for Parquets within CoCliCo STAC collections. + + Items will be stored in a directory named "items", listing different Parquet partitions. + """ + + def get_item_href(self, item: Item, parent_dir: str) -> str: + """ + Determines the item href based on the custom layout for Parquet. + + Args: + item (Item): The STAC item. + parent_dir (str): The parent directory path. + + Returns: + str: The constructed item href. + """ + parsed_parent_dir = safe_urlparse(parent_dir) + join_type = JoinType.from_parsed_uri(parsed_parent_dir) + items_dir = "items" + # Assuming the parquet file's ID will be the partition name + custom_id = pathlib.Path(item.id).with_suffix(".json") + return join_path_or_url(join_type, parent_dir, items_dir, str(custom_id)) diff --git a/stac/blueprint.py b/src/coclicodata/coclico_stac/templates.py similarity index 68% rename from stac/blueprint.py rename to src/coclicodata/coclico_stac/templates.py index f1d3544ae6..181060717d 100644 --- a/stac/blueprint.py +++ b/src/coclicodata/coclico_stac/templates.py @@ -1,90 +1,8 @@ -import json from copy import deepcopy from datetime import datetime -from itertools import product -from sre_constants import GROUPREF_EXISTS -from typing import Any, Dict, Optional, Union -import pathlib import pystac -import zarr -from pystac import Asset, CatalogType, Collection, Item, RelType, Summaries -from pystac.extensions.datacube import DatacubeExtension, Dimension, Variable -from pystac.layout import BestPracticesLayoutStrategy -from pystac.stac_io import DefaultStacIO -from pystac.utils import JoinType, join_path_or_url, safe_urlparse - - -class IO(DefaultStacIO): - """Custom IO to ident our STAC json with 4.""" - - # enabling a GitHub Actions compatible Windows created STAC --> i.e. replacing '\\' by '/' - def _dict_replace_value(self, d, old, new): - x = {} - for k, v in d.items(): - if isinstance(v, dict): - v = self._dict_replace_value(v, old, new) - elif isinstance(v, list): - v = self._list_replace_value(v, old, new) - elif isinstance(v, str): - v = v.replace(old, new) - x[k] = v - return x - - def _list_replace_value(self, l, old, new): - x = [] - for e in l: - if isinstance(e, list): - e = self._list_replace_value(e, old, new) - elif isinstance(e, dict): - e = self._dict_replace_value(e, old, new) - elif isinstance(e, str): - e = e.replace(old, new) - x.append(e) - return x - - def json_dumps(self, json_dict: Dict[str, Any], *args: Any, **kwargs: Any) -> str: - return json.dumps( - self._dict_replace_value(json_dict, "\\", "/"), *args, indent=4, **kwargs - ) - - -class LayoutZarr(BestPracticesLayoutStrategy): - """Custom layout for Zarrs within CoCliCo STAC collections. - - Set the item path to - variable-mapbox/variable-mapbox-dim-value-dim-value.json - instead of - /variable-mapbox-dim-value-dim-value/variable-mapbox-dim-value-dim-value.json - - """ - - def get_item_href(self, item, parent_dir) -> str: - parsed_parent_dir = safe_urlparse(parent_dir) - join_type = JoinType.from_parsed_uri(parsed_parent_dir) - - custom_id = "-".join(item.id.split("-")[0:2]) - item_root = join_path_or_url(join_type, parent_dir, "{}".format(custom_id)) - return join_path_or_url(join_type, item_root, "{}.json".format(item.id)) - - -class LayoutCoG(BestPracticesLayoutStrategy): - """Custom layout for CoGs within CoCliCo STAC collections. - - Set the item path to - items/variable-mapbox-dim-value-dim-value.json - instead of - /variable-mapbox-dim-value-dim-value/variable-mapbox-dim-value-dim-value.json - - """ - - def get_item_href(self, item, parent_dir) -> str: - parsed_parent_dir = safe_urlparse(parent_dir) - join_type = JoinType.from_parsed_uri(parsed_parent_dir) - items_dir = "items" - custom_id = pathlib.Path(item.id).with_suffix(".json") - # item_root = join_path_or_url(join_type, parent_dir, items_dir) - return join_path_or_url(join_type, parent_dir, items_dir, str(custom_id)) +from pystac import Asset, Collection, RelType def gen_default_item(name="unique"): diff --git a/stac/utils.py b/src/coclicodata/coclico_stac/utils.py similarity index 93% rename from stac/utils.py rename to src/coclicodata/coclico_stac/utils.py index 4419ab2a25..339b6cdd3c 100644 --- a/stac/utils.py +++ b/src/coclicodata/coclico_stac/utils.py @@ -1,15 +1,10 @@ -import os -import pathlib import re -from copy import deepcopy from itertools import product -from typing import Any, Dict, List, Union +from typing import Any, Dict, List import numpy as np -import pystac +import rioxarray import xarray as xr -from pystac import Collection -from pystac.extensions.datacube import DatacubeExtension, Dimension, Variable def rm_special_characters( diff --git a/etl/__init__.py b/src/coclicodata/drive_config.py similarity index 63% rename from etl/__init__.py rename to src/coclicodata/drive_config.py index 9dbc4afd80..732e9759de 100644 --- a/etl/__init__.py +++ b/src/coclicodata/drive_config.py @@ -1,7 +1,10 @@ +import os import pathlib import platform -from importlib.resources import path +import sys +# read version from installed packag# Hacky solution for vscode debugger in modular mode. +sys.path.append(os.path.dirname(os.path.dirname(__file__))) # Deltares drive configurations. operating_system = platform.system() @@ -12,7 +15,7 @@ p_drive = pathlib.Path("/Volumes/p/") elif operating_system == "Linux": p_drive = pathlib.Path("/p/") -else: # linux or other +else: raise ValueError(f"Cannot set p drive path for {operating_system}") -rel_root = pathlib.Path(__file__).parent.parent +proj_dir = pathlib.Path(__file__).parent.parent diff --git a/src/coclicodata/etl/__init__.py b/src/coclicodata/etl/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/etl/CF_compliancy_checker.py b/src/coclicodata/etl/cf_compliancy_checker.py similarity index 100% rename from etl/CF_compliancy_checker.py rename to src/coclicodata/etl/cf_compliancy_checker.py diff --git a/etl/cloud_services.py b/src/coclicodata/etl/cloud_utils.py similarity index 63% rename from etl/cloud_services.py rename to src/coclicodata/etl/cloud_utils.py index 38a2002783..2eca4537b4 100644 --- a/etl/cloud_services.py +++ b/src/coclicodata/etl/cloud_utils.py @@ -2,21 +2,18 @@ import pathlib import subprocess import tempfile +import warnings from itertools import product from posixpath import join as urljoin +from typing import Optional, Union import gcsfs import geojson import xarray as xr -from stac.utils import ( - get_dimension_dot_product, - get_dimension_values, - get_mapbox_item_id, -) +from dotenv import load_dotenv +from google.cloud import storage -from etl import p_drive -from etl.extract import clear_zarr_information, get_geojson -from etl.keys import load_env_variables, load_google_credentials +from coclicodata.drive_config import p_drive, proj_dir def _validate_fpath(*args: pathlib.Path) -> None: @@ -126,6 +123,67 @@ def geojson_to_mapbox(source_fpath: pathlib.Path, mapbox_url: str) -> None: subprocess.run(mapbox_cmd, shell=True) +class CredentialLeakageWarning(Warning): + pass + + +def load_env_variables(env_var_keys: list = list()) -> None: + warnings.warn( + "This function will be deprecated in the future, please the pacakge" + " python_dotenv to load environment variables.", + FutureWarning, + ) + env_fpath = proj_dir.joinpath(".env") + if not env_fpath.exists(): + raise FileNotFoundError( + "Processing data requires access keys for cloud services, which should be" + f" stored as environment variables in .../{proj_dir.joinpath('.env')}" + ) + + load_dotenv(env_fpath) + for env_var in env_var_keys: + if not env_var in os.environ: + raise KeyError(f"{env_var} not in environmental variables.") + print("Environmental variables loaded.") + + +def load_google_credentials(google_token_fp: Union[pathlib.Path, None] = None) -> None: + warnings.warn( + "This function will be deprecated in the future, please use environment" + " variables instead. When Google cloud is installed on your computer" + " credentials can set using 'GOOGLE_DEFAULT' in the storage_kwargs argument", + FutureWarning, + ) + + if google_token_fp: + # TODO: Manage keys at user level, not with shared drive. The code block below + # should tested by Windows users to see if gcloud credentials behave similar on + # that os. If so, the code block below can be used instead. + warnings.warn( + "Keys loaded from shared network drive.", CredentialLeakageWarning + ) + if not google_token_fp.exists(): + if not p_drive.exists(): + raise FileNotFoundError( + "Deltares drive not found, mount drive to access Google keys." + ) + raise FileNotFoundError("Credential file does not exist.") + os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = str(google_token_fp) + print("Google Application Credentials load into environment.") + + else: + # TODO: Migrate to token=None in gcsfs when bug that no credentials can be found is fixed. + gmail_pattern = "*@gmail.com" + p = pathlib.Path.home().joinpath( + ".config", "gcloud", "legacy_credentials", gmail_pattern, "adc.json" + ) + p = list(p.parent.parent.expanduser().glob(p.parent.name))[0].joinpath(p.name) + if not p.exists(): + raise FileNotFoundError("Google credentials not found.") + os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = str(p) + print("Google Application Credentials load into environment.") + + if __name__ == "__main__": # hard-coded input params DATASET_FILENAME = "CoastAlRisk_Europe_EESSL.zarr" @@ -162,3 +220,4 @@ def geojson_to_mapbox(source_fpath: pathlib.Path, mapbox_url: str) -> None: # ds = dataset_from_google_cloud( # bucket_name=BUCKET_NAME, bucket_proj=BUCKET_PROJ, zarr_filename=DATASET_FILENAME # ) + # ) diff --git a/etl/extract.py b/src/coclicodata/etl/extract.py similarity index 96% rename from etl/extract.py rename to src/coclicodata/etl/extract.py index db45b226bf..a0062ad250 100644 --- a/etl/extract.py +++ b/src/coclicodata/etl/extract.py @@ -9,11 +9,8 @@ import xarray as xr from shapely import wkb from shapely.geometry import mapping -from stac.utils import get_mapbox_item_id -# def get_mapbox_url(mapbox_proj: str, filename: str, var: str) -> str: -# """Generate tileset name""" -# return f"{mapbox_proj}.{pathlib.Path(filename).stem}_{var}" +from coclicodata.coclico_stac.utils import get_mapbox_item_id def get_mapbox_url( diff --git a/stac/README.md b/stac/README.md deleted file mode 100644 index 4c7e815cb5..0000000000 --- a/stac/README.md +++ /dev/null @@ -1,97 +0,0 @@ -# CoCliCo STAC tools - -This directory contains python files with functions to define and generate a STAC -catalogue based upon datasets available in zarr format. - -[generate_stac.py](../scripts/generate_stac.py) provides an example of how the functions -in this directory can be used to build a stac catalogue from a zarr store. - -## Table of contents - -[blueprint.py](./blueprint.py) contains the STAC layout class and functions to generate -the default CoCliCo STAC collections and items. - -[datacube.py](./datacube.py) contains functions to extract dimension shapes and metadata -from zarr stores. The methods rely and are inspired on -[xstac](https://github.com/TomAugspurger/xstac). - -[utils.py](./utils.py) contains a few custom functins useful for migrating xarray data to -a stac catalogue. - - -## Metadata - -The following attributes are required at dataset level: - -- title - -- description - description that will be used to as dataset explanation in the web portal. -- short description - description which is convenient when loading the data into a - programming environment -- institution - data producer -- providers - data host (Deltares / CoCliCo) - - name - - url - - roles - e.g., providers, licensor - - description - the -- source - -- history - list of institutions and people who have processed the data -- media_type - [also known as mime type](https://en.wikipedia.org/wiki/Media_type) -- spatial extent - bbox [minx, miny, maxx, maxy] -- temporal extent - time interval in [iso 8601](https://en.wikipedia.org/wiki/ISO_8601), i.e., YYYY-MM-DDTHH:mm:ssZ -- license - -- author - - -The following attributes are optional at dataset level: -- keywords - these can be used to search using the STAC API -- tags - these can be used to search using the STAC API -- citation - if available, preferably following Creator (PublicationYear): Title. - Publisher. (resourceTypeGeneral). Identifier format (Zenodo specification) -- doi - following [Zenodo specification](https://about.zenodo.org/principles/) -- thumbnail asset image - image that will be shown to represent the dataset -- columns - when data is tabular and has column names - -The following attributes are required at variable level - -- long_name - descriptive name -- standard_name - iff available in [CF convention standard table](https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html) -- units - follow CF conventions where possible; leave blank when no units. - -The following attributes are optional at variable level: -- comment - provide extra information about variable - -The following coordinate labels are required: - -- crs or spatial_ref -- time - -### Controlled vocabulary -| **name** | **long_name** | **standard_name** | **data_structure_type** | **dtype** | -|-------------|---------------------------------------------------------------------------------------------|-------------------|-------------------------|-----------------------| -| lat | Latitude | latitude | dim | float | -| lon | Longitude | longitude | dim | float | -| nensemble | Number of ensembles | | dim | int | -| nscenario | Number of scenarios | | dim | int | -| nstation | Number of station | | dim | int | -| rp | Return period | | dim | int | -| time | Time | time | dim | cftime | -| ensemble | Ensemble | | coord | zero-terminated bytes | -| scenario | Scenario | | coord | zero-terminated bytes | -| stations | Stations | | coord | zero-terminated bytes | -| geometry | Geometry | | coord | well-known binary | -| spatial_ref | Coordinate system and its properties | | coord | zero-terminated bytes | -| country | Country | | var | zero-terminated bytes | -| esl | Extreme sea level | | var | float | -| ssl | Sea surface level | | var | float | -| sustain | Sustainability | | var | float | -| wef | Wave energy flux | | var | float | -| benefit | Benefits of raising coastal defences along the European coastline in view of climate change | | var | float | -| cbr | Benefits of raising coastal defences along the European coastline in view of climate change | | var | float | -| cost | Cost of raising coastal defences along the European coastline in view of climate change | | var | float | -| ead | Expected annual damage | | var | float | -| ead_gdp | Expected annual damage per GDP | | var | float | -| eapa | Expected annual people affected | | var | float | -| eb | Expected benefit to cost ratios of raising coastal protection per NUTS2 region | | var | float | -| eewl | Episodic extreme water level | | var | float | -| sc | Shoreline change | | var | float | -| ssl | Storm surge level | | var | float | -| wef | Wave energy flux | | var | float | diff --git a/tests/test_all_collections_unique.py b/tests/test_all_collections_unique.py new file mode 100644 index 0000000000..ffba0e04b7 --- /dev/null +++ b/tests/test_all_collections_unique.py @@ -0,0 +1,15 @@ +from pystac import Catalog + +href = "./current/catalog.json" +root = Catalog.from_file(href) + + +def test_all_collections_unique(): + collections = root.get_all_collections() + collection_ids = [collection.id for collection in collections] + + unique_ids = set(collection_ids) + + assert len(collection_ids) == len( + unique_ids + ), "Some collections have duplicate IDs!" diff --git a/validate.py b/tests/test_validation.py similarity index 96% rename from validate.py rename to tests/test_validation.py index 5abf31af32..66089226e1 100644 --- a/validate.py +++ b/tests/test_validation.py @@ -2,7 +2,6 @@ href = "./current/catalog.json" root = Catalog.from_file(href) -root.describe() def test_catalog_is_valid():