Added dummy example process get_species_data.

README.md

@@ -7,3 +7,67 @@
 [pygeoapi](https://pygeoapi.io) is a Python server implementation of the [OGC API](https://ogcapi.ogc.org) suite of standards. The project emerged as part of the next generation OGC API efforts in 2018 and provides the capability for organizations to deploy a RESTful OGC API endpoint using OpenAPI, GeoJSON, and HTML. pygeoapi is [open source](https://opensource.org/) and released under an [MIT license](https://github.com/geopython/pygeoapi/blob/master/LICENSE.md).
 
 Please read the docs at [https://docs.pygeoapi.io](https://docs.pygeoapi.io) for more information.
+
+
+
+## AquaInfra case
+
+Please add these steps when installing pygeoapi for the AquaInfra case, as they are needed to run the `get_species_data` process!
+
+* Please install the python module `geojson` in the virtual environment that runs the service (most likely running `cd /home/.../pygeoapi/pygeoapi && . ../bin/activate && pip install geojson` will do the job).
+* Please create a directory for the input data, e.g. `/home/.../work/pygeo/data`
+* Into that directory, add a directory `basin_481051` and into that, put the input vector file `basin_481051.gpkg`. The same for any other river basin you want to support (`481051` being the drainage basin id).
+* Then, tell pygeoapi where to find the data, by executing: `export PYGEOAPI_DATA_DIR='/home/.../work/pygeo/data'`.
+* Please install the R library `rgbif`.
+
+(Merret, 2023-10-18)
+
+
+### Creating basin_481051.gpkg
+
+You can create this file using R and the package [hydrographr](https://github.com/glowabio/hydrographr/) with the following steps. The source of the data is [hydrography90m](https://hydrography.org/).
+
+```
+library(hydrographr)
+
+### Merret, 2023-10-17
+### To allow downloading and creating the vector layer needed for the pygeoapi
+### test service "get_species_data": basin_481051.gpkg
+### Instructions are a subset of:
+### https://glowabio.github.io/hydrographr/articles/case_study_brazil.html
+
+### Download three tiles that comprise basin 481051
+wdir = "/home/.../work/"
+tile_id = c("h12v08", "h12v10", "h14v08")
+vars_gpkg <- c("basin", "order_vect_segment")
+download_tiles(variable = vars_gpkg, tile_id = tile_id, file_format = "gpkg", download_dir =   paste0(wdir, "/data"))
+
+### Filter basin 481051
+# Define a directory for the São Francisco drainage basin
+saofra_dir <-  paste0(wdir, "/data/basin_481051")
+if(!dir.exists(saofra_dir)) dir.create(saofra_dir)
+# Get the full paths of the basin  GeoPackage tiles
+basin_dir <- list.files(wdir, pattern = "basin_h[v0-8]+.gpkg$", full.names = TRUE, recursive = TRUE)
+
+# Filter basin ID from the GeoPackages of the basin tiles
+# Save the filtered tiles
+for(itile in basin_dir) {
+  filtered_tile <- read_geopackage(itile, import_as = "sf", subc_id = 481051, name = "ID")
+  write_sf(filtered_tile, paste(saofra_dir, paste0(str_remove(basename(itile), ".gpkg"),"_tmp.gpkg"), sep="/"))
+}
+
+### Merge basin 481051
+# Merge filtered GeoPackage tiles
+merge_tiles(tile_dir = saofra_dir, tile_names = list.files(saofra_dir, full.names = FALSE, pattern = "basin_.+_tmp.gpkg$"),
+            out_dir = saofra_dir,
+            file_name = "basin_481051.gpkg",
+            name = "ID",
+            read = FALSE)
+
+
+```
+
+
+(Merret, 2023-10-18)
+
+

pygeoapi-config.yml

@@ -38,7 +38,6 @@ server:
     languages:
         # First language is the default language
         - en-US
-        - fr-CA
     # cors: true
     pretty_print: true
     limit: 10
@@ -55,250 +54,44 @@ server:
     # ogc_schemas_location: /opt/schemas.opengis.net
 
 logging:
-    level: ERROR
+    level: DEBUG
     #logfile: /tmp/pygeoapi.log
 
 metadata:
     identification:
         title:
-            en: pygeoapi default instance
-            fr: instance par défaut de pygeoapi
+            en: AquaInfra processing services
         description:
-            en: pygeoapi provides an API to geospatial data
-            fr: pygeoapi fournit une API aux données géospatiales
+            en: An OGC conformant API to AquaInfra processing services
         keywords:
             en:
                 - geospatial
                 - data
                 - api
-            fr:
-                - géospatiale
-                - données
-                - api
         keywords_type: theme
         terms_of_service: https://creativecommons.org/licenses/by/4.0/
         url: https://example.org
     license:
-        name: CC-BY 4.0 license
+        name: CC-BY 4.0 license (TODO check)
         url: https://creativecommons.org/licenses/by/4.0/
     provider:
-        name: Organization Name
-        url: https://pygeoapi.io
+        name: Leibniz Institute for Freshwater Ecology and Inland Fisheries (FVB-IGB), Berlin
+        url: https://igb-berlin.de
     contact:
-        name: Lastname, Firstname
-        position: Position Title
-        address: Mailing Address
-        city: City
-        stateorprovince: Administrative Area
-        postalcode: Zip or Postal Code
-        country: Country
-        phone: +xx-xxx-xxx-xxxx
-        fax: +xx-xxx-xxx-xxxx
-        email: [email protected]
-        url: Contact URL
-        hours: Mo-Fr 08:00-17:00
-        instructions: During hours of service. Off on weekends.
+        name: Buurman, Merret
+        position: Scientific Staff
+        address: Müggelseedamm 310
+        city: Berlin
+        stateorprovince: Berlin
+        postalcode: 12587
+        country: Germany
+        email: [email protected]
+        url: https://glowabio.org/
         role: pointOfContact
 
 resources:
-    obs:
-        type: collection
-        title: Observations
-        description: My cool observations
-        keywords:
-            - observations
-            - monitoring
-        linked-data:
-            context:
-                - datetime: https://schema.org/DateTime
-                - vocab: https://example.com/vocab#
-                  stn_id: "vocab:stn_id"
-                  value: "vocab:value"
-        links:
-            - type: text/csv
-              rel: canonical
-              title: data
-              href: https://github.com/mapserver/mapserver/blob/branch-7-0/msautotest/wxs/data/obs.csv
-              hreflang: en-US
-            - type: text/csv
-              rel: alternate
-              title: data
-              href: https://raw.githubusercontent.com/mapserver/mapserver/branch-7-0/msautotest/wxs/data/obs.csv
-              hreflang: en-US
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-            temporal:
-                begin: 2000-10-30T18:24:39Z
-                end: 2007-10-30T08:57:29Z
-        providers:
-            - type: feature
-              name: CSV
-              data: tests/data/obs.csv
-              id_field: id
-              geometry:
-                  x_field: long
-                  y_field: lat
-
-    lakes:
-        type: collection
-        title:
-            en: Large Lakes
-            fr: Grands Lacs
-        description:
-            en: lakes of the world, public domain
-            fr: lacs du monde, domaine public
-        keywords:
-            en:
-                - lakes
-                - water bodies
-            fr:
-                - lacs
-                - plans d'eau
-        links:
-            - type: text/html
-              rel: canonical
-              title: information
-              href: http://www.naturalearthdata.com/
-              hreflang: en-US
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-            temporal:
-                begin: 2011-11-11T11:11:11Z
-                end: null  # or empty (either means open ended)
-        providers:
-            - type: feature
-              name: GeoJSON
-              data: tests/data/ne_110m_lakes.geojson
-              id_field: id
-              title_field: name
-
-    mapserver_world_map:
-        type: collection
-        title: MapServer demo WMS world map
-        description: MapServer demo WMS world map
-        keywords:
-            - MapServer
-            - world map
-        links:
-            - type: text/html
-              rel: canonical
-              title: information
-              href: https://demo.mapserver.org
-              hreflang: en-US
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-        providers:
-            - type: map
-              name: WMSFacade
-              data: https://demo.mapserver.org/cgi-bin/msautotest
-              options:
-                  layer: world_latlong
-                  style: default
-              format:
-                    name: png
-                    mimetype: image/png
-
-    gdps-temperature:
-        type: collection
-        title: Global Deterministic Prediction System sample
-        description: Global Deterministic Prediction System sample
-        keywords:
-            - gdps
-            - global
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-        links:
-            - type: text/html
-              rel: canonical
-              title: information
-              href: https://eccc-msc.github.io/open-data/msc-data/nwp_gdps/readme_gdps_en
-              hreflang: en-CA
-        providers:
-            - type: coverage
-              name: rasterio
-              data: tests/data/CMC_glb_TMP_TGL_2_latlon.15x.15_2020081000_P000.grib2
-              options:
-                  DATA_ENCODING: COMPLEX_PACKING
-              format:
-                  name: GRIB
-                  mimetype: application/x-grib2
-
-    test-data:
-        type: stac-collection
-        title: pygeoapi test data
-        description: pygeoapi test data
-        keywords:
-            - poi
-            - portugal
-        links:
-            - type: text/html
-              rel: canonical
-              title: information
-              href: https://github.com/geopython/pygeoapi/tree/master/tests/data
-              hreflang: en-US
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-        providers:
-            - type: stac
-              name: FileSystem
-              data: tests/data
-              file_types:
-                  - .gpkg
-                  - .sqlite
-                  - .csv
-                  - .grib2
-                  - .tif
-                  - .shp
-
-    canada-metadata:
-        type: collection
-        title:
-            en: Open Canada sample data
-            fr: Exemple de donn\u00e9es Canada Ouvert
-        description:
-            en: Sample metadata records from open.canada.ca
-            fr: Exemples d'enregistrements de m\u00e9tadonn\u00e9es sur ouvert.canada.ca
-        keywords:
-            en:
-                - canada
-                - open data
-            fr:
-                - canada
-                - donn\u00e9es ouvertes
-        links:
-            - type: text/html
-              rel: canonical
-              title: information
-              href: https://open.canada.ca/en/open-data
-              hreflang: en-CA
-            - type: text/html
-              rel: alternate
-              title: informations
-              href: https://ouvert.canada.ca/fr/donnees-ouvertes
-              hreflang: fr-CA
-        extents:
-            spatial:
-                bbox: [-180,-90,180,90]
-                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
-        providers:
-            - type: record
-              name: TinyDBCatalogue
-              data: tests/data/open.canada.ca/sample-records.tinydb
-              id_field: externalId
-              time_field: recordCreated
-              title_field: title
 
-    hello-world:
+    get-species-data:
         type: process
         processor:
-            name: HelloWorld
+            name: GetSpeciesData

pygeoapi/plugin.py

@@ -66,7 +66,8 @@
         'CSV': 'pygeoapi.formatter.csv_.CSVFormatter'
     },
     'process': {
-        'HelloWorld': 'pygeoapi.process.hello_world.HelloWorldProcessor'
+        'HelloWorld': 'pygeoapi.process.hello_world.HelloWorldProcessor',
+        'GetSpeciesData': 'pygeoapi.process.get_species_data_pygeo.GetSpeciesData'
     },
     'process_manager': {
         'Dummy': 'pygeoapi.process.manager.dummy.DummyManager',