{abst}
\")\n", - "\n", - " folium.GeoJson(\n", - " data=layers[layer],\n", - " name=\"BioEco: {}\".format(name),\n", - " tooltip=tooltip,\n", - " popup=popup, show=False,\n", - " ).add_to(m)\n", - "\n", - "folium.LayerControl(collapsed=True).add_to(m)\n", - "\n", - "m.fit_bounds(m.get_bounds()) \n", - "\n", - "m" - ] - }, - { - "cell_type": "markdown", - "id": "9b8d1409", - "metadata": {}, - "source": [ - "## Save the map as a webpage for gh-pages" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "5b1e50df", - "metadata": {}, - "outputs": [], - "source": [ - "m.save(\"docs/index.html\")" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.6" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/map-of-activities.py b/map-of-activities.py new file mode 100644 index 0000000..8340bcf --- /dev/null +++ b/map-of-activities.py @@ -0,0 +1,176 @@ +""" +Creating US MBON Map of Activities portal + +This notebook creates the US MBON Map of Activities portal. +It harvests information from the [GOOS Bio-Eco portal](https://bioeco.goosocean.org/) and [OBIS](https://obis.org/). +GOOS BioEco collection - https://geonode.goosocean.org/maps/1043 +OBIS US MBON collection - https://obis.org/institute/23070 + +Grab the GOOS BioEco portal US MBON collection + +https://geonode.goosocean.org/maps/1043 + +""" + + +import folium +import geopandas +import numpy as np +import pandas as pd +import pyobis +import requests + +pk = 1043 # Matt's map +url = f"https://geonode.goosocean.org/api/v2/maps/{1043}/local_layers" + +data = requests.get(url).json() + + +def get_original_data(layer): + # we can use WFS GeoJSON response when https://github.com/iobis/bioeco-geonode/issues/166 is solved. + url = f"https://geonode.goosocean.org/download/{layer['pk']}" + + fmat = "json" + url2 = f"https://geonode.goosocean.org/geoserver/ows?service=WFS&version=1.0.0&request=GetFeature&typename=geonode%3A{layer['name']}&outputFormat={fmat}&srs=EPSG%3A4326&format_options=charset%3AUTF-8" + + try: + gdf = geopandas.read_file(url) + except Exception as err: + print(f"Could not read {url=}.\nGot {err}.\nTrying\n{url2}\n") + gdf = geopandas.read_file(url2) + + return gdf + + +layers = {layer["name"]: get_original_data(layer) for layer in data} + + +# Grab OBIS US MBON bounding boxes +# https://obis.org/institute/23070 + +# Grab OBIS US MBON geohash precision 8 points + + +combined = pd.DataFrame() + +query = pyobis.dataset.search(instituteid="23070") + +df = pd.DataFrame(query.execute()) + +df_meta = pd.DataFrame.from_records(df["results"]) + +for datasetid in df_meta["id"]: + dset = pyobis.occurrences.getpoints(datasetid=datasetid).execute() + + meta = pyobis.dataset.get(id=datasetid).execute()["results"][0] + short_name = meta["url"].split("=")[-1] + + df = pd.DataFrame(dset) + + df["dataset_id"] = datasetid + df["short_name"] = meta["url"].split("=")[-1] + df["short_name_group"] = ( + df["short_name"].replace(r"\d", "", regex=True).str.rstrip("_") + ) + df["url"] = meta["url"].replace( + "https://www1.usgs.gov/obis-usa/ipt", "https://ipt-obis.gbif.us" + ) + df["metadata"] = str(meta) + df["title"] = meta["title"] + df["abstract"] = meta["abstract"] + + df[["decimalLongitude", "decimalLatitude"]] = pd.DataFrame( + df["coordinates"].tolist() + ) + + combined = pd.concat([combined, df], ignore_index=True) + + +# Write OBIS records to a GeoDataFrame. +# To save space only keep a few columns. If we include `abstract` and `metadata` the resultant map/html file is crazy big. + +cols = ["title", "url", "short_name", "short_name_group"] + +gdf = geopandas.GeoDataFrame( + combined[cols], + geometry=geopandas.points_from_xy( + combined.decimalLongitude, combined.decimalLatitude + ), + crs="epsg:4326", +) + + +# Now make a map with those layers +m = folium.Map( + tiles=None, + zoom_start=13, +) + + +# Base Layers +tiles = "https://server.arcgisonline.com/ArcGIS/rest/services/Ocean/World_Ocean_Base/MapServer/tile/{z}/{y}/{x}" +gh_repo = "https://github.com/marinebon/map-of-activities" +attr = f'Tiles © Esri — Sources: GEBCO, NOAA, CHS, OSU, UNH, CSUMB, National Geographic, DeLorme, NAVTEQ, and Esri | {gh_repo}' +folium.raster_layers.TileLayer( + name="Ocean", + tiles=tiles, + attr=attr, +).add_to(m) + +folium.raster_layers.TileLayer( + name="CartoDB", + tiles="cartodbdark_matter", +).add_to(m) + +tiles = "https://server.arcgisonline.com/ArcGIS/rest/services/Ocean/World_Ocean_Reference/MapServer/tile/{z}/{y}/{x}" +folium.raster_layers.TileLayer( + tiles=tiles, + name="OceanRef", + attr=attr, + overlay=True, + control=False, +).add_to(m) + +# OBIS - layer per dataset "group" (as defined above - from url) +for name, group in gdf.groupby(by="short_name_group"): + group["ref"] = [ + f'{url}' for url in group["url"] + ] + + folium.GeoJson( + data=group, + name="OBIS: {}".format(name), + marker=folium.CircleMarker(radius=1, color="green"), + tooltip=folium.features.GeoJsonTooltip( + fields=["title"], + aliases=[""], + ), + popup=folium.features.GeoJsonPopup( + fields=["ref"], + aliases=[""], + ), + show=False, + ).add_to(m) + + +# GOOS Bio-Eco layers +for layer in layers.keys(): + name = next(item for item in data if item["name"] == layer)["name"] + tooltip = next(item for item in data if item["name"] == layer)["title"] + url = next(item for item in data if item["name"] == layer)["detail_url"] + # abst = next(item for item in data if item["name"] == layer)['abstract'] + popup = folium.map.Popup( + f'{url}' + ) # "{abst}
") + + folium.GeoJson( + data=layers[layer], + name="BioEco: {}".format(name), + tooltip=tooltip, + popup=popup, + show=False, + ).add_to(m) + +folium.LayerControl(collapsed=True).add_to(m) +m.fit_bounds(m.get_bounds()) +m.save("docs/index.html")