aqua90m

Remote interaction with freshwater and related data, mainly via OGC processes deployed on pygeoapi instances.

List of processes

local subcatchment

• get_snapped_points
• get_snapped_points_plus
• get_local_subcids
• get_local_subcids_plural
• get_local_streamsegments
• get_local_streamsegments_subcatchments

upstream

• get_upstream_subcids
• get_upstream_streamsegments
• get_upstream_bbox
• get_upstream_subcatchments
• get_upstream_dissolved
• get_upstream_dissolved_aip (special version for usage by the AIP search interface, kept constant)

downstream

• get_shortest_path_two_points
• get_shortest_path_to_outlet

data access

• extract_point_stats
• subset_by_polygon (currently fails on aqua due to dependency issues with gdal)
• subset_by_bbox (currently fails on aqua due to dependency issues with gdal)

utils

• get_ddas_galaxy_link_textfile

Pygeoapi deployment

To deploy these processes, you first need a running pygeoapi instance (please see https://pygeoapi.io/ and follow their recommendations and best practices, e.g. about web servers, reverse-proxy usage and TLS certificates / HTTPS). We run pygeoapi via starlette behing an nginx webserver, via HTTPS.

To deploy the processes listed above on this pygeoapi instance, please modify the following existing files:

File pygeoapi/pygeoapi/plugin.py:

        # local subcatchment
        'SnappedPointsGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_snapped_points.SnappedPointsGetter',
        'SnappedPointsGetterPlus': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_snapped_points_plus.SnappedPointsGetterPlus',
        'LocalSubcidGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_local_subcids.LocalSubcidGetter',
        'LocalSubcidPluralGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_local_subcids_plural.LocalSubcidPluralGetter',
        'LocalStreamSegmentsGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_local_streamsegments.LocalStreamSegmentsGetter',
        'LocalStreamSegmentSubcatchmentGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_local_streamsegments_subcatchments.LocalStreamSegmentSubcatchmentGetter',
        # upstream
        'UpstreamSubcidGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_subcids.UpstreamSubcidGetter',
        'UpstreamStreamSegmentsGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_streamsegments.UpstreamStreamSegmentsGetter',
        'UpstreamBboxGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_bbox.UpstreamBboxGetter',
        'UpstreamSubcatchmentGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_subcatchments.UpstreamSubcatchmentGetter',
        'UpstreamDissolvedGetterCont': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_dissolved.UpstreamDissolvedGetter',
        'UpstreamDissolvedGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_upstream_dissolved_aip.UpstreamDissolvedGetter',
        # downstream
        'ShortestPathTwoPointsGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_shortest_path_two_points.ShortestPathTwoPointsGetter',
        'ShortestPathToOutletGetter': 'pygeoapi.process.aqua90m.pygeoapi_processes.rivernetwork.get_shortest_path_to_outlet.ShortestPathToOutletGetter',
        # data access
        'ExtractPointStatsProcessor': 'pygeoapi.process.aqua90m.pygeoapi_processes.data_access.extract_point_stats.ExtractPointStatsProcessor',
        #'SubsetterBbox': 'pygeoapi.process.aqua90m.pygeoapi_processes.data_access.subset_by_bbox.SubsetterBbox',
        #'SubsetterPolygon': 'pygeoapi.process.aqua90m.pygeoapi_processes.data_access.subset_by_polygon.SubsetterPolygon',
        # utils
        'HelferleinProcessor': 'pygeoapi.process.aqua90m.pygeoapi_processes.data_access.get_ddas_galaxy_link_textfile.HelferleinProcessor',

File pygeoapi/pygeoapi-config.yml:

   # local subcatchment

    get-snapped-points:
        type: process
        processor:
            name: SnappedPointsGetter

    get-snapped-point-plus:
        type: process
        processor:
            name: SnappedPointsGetterPlus

    get-local-subcids:
        type: process
        processor:
            name: LocalSubcidGetter

    get-local-subcids-plural:
        type: process
        processor:
            name: LocalSubcidPluralGetter

    get-local-streamsegments:
        type: process
        processor:
            name: LocalStreamSegmentsGetter

    get-local-streamsegments-subcatchments:
        type: process
        processor:
            name: LocalStreamSegmentSubcatchmentGetter



    # upstream

    get-upstream-subcids:
        type: process
        processor:
            name: UpstreamSubcidGetter

    get-upstream-streamsegments:
        type: process
        processor:
            name: UpstreamStreamSegmentsGetter

    get-upstream-bbox:
        type: process
        processor:
            name: UpstreamBboxGetter

    get-upstream-subcatchments:
        type: process
        processor:
            name: UpstreamSubcatchmentGetter

    get-upstream-dissolved:
        type: process
        processor:
            name: UpstreamDissolvedGetter

    get-upstream-dissolved-cont:
        type: process
        processor:
            name: UpstreamDissolvedGetterCont



    # downstream

    get-shortest-path-two-points:
        type: process
        processor:
            name: ShortestPathTwoPointsGetter

    get-shortest-path-to-outlet:
        type: process
        processor:
            name: ShortestPathToOutletGetter



    # data access

    extract-point-stats:
        type: process
        processor:
            name: ExtractPointStatsProcessor

    #FAILS (GDAL) get-subset-by-bbox:
        #type: process
        #processor:
              #name: SubsetterBbox

    # FAILS (GDAL) get-subset-by-polygon:
        #type: process
        #processor:
              #name: SubsetterPolygon



    # utils
    get-ddas-galaxy-link-textfile:
        type: process
        processor:
            name: HelferleinProcessor

Dependencies, to be added to dependencies.txt

TODO
# Also, how to install them?

In addition, you need to add a JSON config file for process-relevant config, located at any readable place, e.g. pygeoapi/config.json. The contents vary by processes (see process-specific details), but some entries are shared by all or many processes, such as:

• download_dir: The path to a directory from where users are able to download files, e.g. the static directory of the webserver that is running pygeoapi. In our case, it is /var/www/nginx/download/. It needs to be writeable by the Linux user who runs pygeoapi (in our case, pyguser), and readable by the Linux user who runs the webserver (in our case, www-data).
• download_url: The URL under which the contents of the above download_dir can be accessed by outside users. Here, the process results will be made available to the end users. (You can decide to make the directory password-protected by the web server if the results should not be public).

For many of the processes, you also need credentials to access to IGB's GeoFRESH database, which is restricted. For more information, please check https://geofresh.org/ or contact IGB Berlin.

For some other processes, R and the R package hydrographr need to be installed and runnable by the Linux user running pygeoapi.

Process-specific details

extract-point-stats

For this process, R and the R package hydrographr are needed.

For this process, the config file needs to contain these items:

• rasterlayer_lookup_table: Mapping between variable names and a local path or remote URL where the corresponding raster layer can be found, as GeoTIFF or VRT or any layer that gdallocationinfo can work with.
• hydrographr_bash_files: Path where the executable bash files of the hydrographr R package can be found.
• download_dir
• download_url

Example:

    "rasterlayer_lookup_table": {
        "basin": "https://2007367-nextcloud.a3s.fi/igb/vrt/basin.vrt",
        "sti": "/opt/aquainfra_inputs/Hydrography90m/sti_h18v02.tif"
    },
    "hydrographr_bash_files": "/opt/pyg_upstream_dev/pygeoapi/pygeoapi/process/hydrographr/inst/sh",
    "download_dir": "/var/www/nginx/download/",
    "download_url": "https://aqua.igb-berlin.de/download/",