306 lines
15 KiB
Python
306 lines
15 KiB
Python
#!/usr/bin/env python3
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"""Expand HerbAPI species database with common permaculture/garden species."""
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import json
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import time
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import urllib.request
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import urllib.parse
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import urllib.error
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import ssl
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BASE_URL = "http://herbapi01.corp.sub-net.at:8080/api/v1"
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AUTH = "Bearer km2WjhgyMTHlltwgch5TZADHQ-4uIg0NxBeowD-DHGk"
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DELAY = 0.15
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# SSL context for GBIF (https)
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ssl_ctx = ssl.create_default_context()
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def api_get(path):
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req = urllib.request.Request(f"{BASE_URL}{path}", headers={"Authorization": AUTH})
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with urllib.request.urlopen(req) as resp:
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return json.loads(resp.read())
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def api_post(path, data):
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body = json.dumps(data).encode()
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req = urllib.request.Request(
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f"{BASE_URL}{path}",
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data=body,
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headers={"Authorization": AUTH, "Content-Type": "application/json"},
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method="POST",
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)
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try:
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with urllib.request.urlopen(req) as resp:
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return json.loads(resp.read()), resp.status
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except urllib.error.HTTPError as e:
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err_body = e.read().decode()
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print(f" ERROR {e.code}: {err_body}")
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return None, e.code
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def gbif_get_german_name(scientific_name):
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"""Query GBIF for the German vernacular name."""
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try:
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url = f"https://api.gbif.org/v1/species/match?name={urllib.parse.quote(scientific_name)}"
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req = urllib.request.Request(url)
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with urllib.request.urlopen(req, context=ssl_ctx, timeout=10) as resp:
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match = json.loads(resp.read())
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usage_key = match.get("usageKey")
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if not usage_key:
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return None
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url2 = f"https://api.gbif.org/v1/species/{usage_key}/vernacularNames?limit=100"
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req2 = urllib.request.Request(url2)
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with urllib.request.urlopen(req2, context=ssl_ctx, timeout=10) as resp:
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vn = json.loads(resp.read())
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for r in vn.get("results", []):
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if r.get("language") == "deu":
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return r["vernacularName"]
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return None
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except Exception as e:
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print(f" GBIF lookup failed for {scientific_name}: {e}")
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return None
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# ── Families to ensure exist ─────────────────────────────────────────
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FAMILIES_NEEDED = {
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"Fabaceae": {"name_en": "Legumes", "name_de": "Hülsenfrüchtler"},
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"Solanaceae": {"name_en": "Nightshade family", "name_de": "Nachtschattengewächse"},
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"Cucurbitaceae": {"name_en": "Gourd family", "name_de": "Kürbisgewächse"},
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"Asteraceae": {"name_en": "Daisy family", "name_de": "Korbblütler"},
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"Chenopodiaceae": {"name_en": "Goosefoot family", "name_de": "Gänsefußgewächse"},
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"Brassicaceae": {"name_en": "Cabbage family", "name_de": "Kreuzblütler"},
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"Amaryllidaceae": {"name_en": "Amaryllis family", "name_de": "Amaryllisgewächse"},
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"Apiaceae": {"name_en": "Carrot family", "name_de": "Doldenblütler"},
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"Poaceae": {"name_en": "Grass family", "name_de": "Süßgräser"},
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"Lamiaceae": {"name_en": "Mint family", "name_de": "Lippenblütler"},
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"Caprifoliaceae": {"name_en": "Honeysuckle family", "name_de": "Geißblattgewächse"},
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"Rosaceae": {"name_en": "Rose family", "name_de": "Rosengewächse"},
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"Grossulariaceae": {"name_en": "Gooseberry family", "name_de": "Stachelbeergewächse"},
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"Ericaceae": {"name_en": "Heath family", "name_de": "Heidekrautgewächse"},
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"Moraceae": {"name_en": "Mulberry family", "name_de": "Maulbeergewächse"},
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# New families not yet in the DB:
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"Hypericaceae": {"name_en": "St John's wort family", "name_de": "Johanniskrautgewächse"},
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"Tropaeolaceae": {"name_en": "Nasturtium family", "name_de": "Kapuzinerkressengewächse"},
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"Elaeagnaceae": {"name_en": "Oleaster family", "name_de": "Ölweidengewächse"},
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}
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# ── Species to add ───────────────────────────────────────────────────
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# Format: (scientific_name, family, name_en, name_de, plant_layer, extra_fields)
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SPECIES = [
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# Vegetables
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("Phaseolus vulgaris", "Fabaceae", "common bean", "Gartenbohne", "herbaceous",
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{"nitrogen_fixer": True, "food_uses": "Beans (pods, seeds)"}),
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("Phaseolus coccineus", "Fabaceae", "runner bean", "Feuerbohne", "herbaceous",
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{"nitrogen_fixer": True, "food_uses": "Beans (pods, seeds), flowers", "attracts_pollinators": True}),
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("Pisum sativum", "Fabaceae", "pea", "Erbse", "herbaceous",
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{"nitrogen_fixer": True, "food_uses": "Peas, shoots"}),
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("Capsicum annuum", "Solanaceae", "pepper", "Paprika", "herbaceous",
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{"food_uses": "Fruit"}),
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("Cucumis sativus", "Cucurbitaceae", "cucumber", "Gurke", "ground_cover",
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{"food_uses": "Fruit"}),
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("Cucurbita maxima", "Cucurbitaceae", "winter squash", "Riesenkürbis", "ground_cover",
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{"food_uses": "Fruit, seeds, flowers"}),
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("Cucurbita moschata", "Cucurbitaceae", "butternut squash", "Moschuskürbis", "ground_cover",
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{"food_uses": "Fruit, seeds"}),
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("Lactuca sativa", "Asteraceae", "lettuce", "Salat", "herbaceous",
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{"food_uses": "Leaves"}),
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("Spinacia oleracea", "Chenopodiaceae", "spinach", "Spinat", "herbaceous",
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{"food_uses": "Leaves"}),
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("Brassica oleracea", "Brassicaceae", "cabbage / kale", "Kohl", "herbaceous",
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{"food_uses": "Leaves, flower buds, stems"}),
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("Brassica rapa", "Brassicaceae", "turnip", "Rübe", "herbaceous",
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{"food_uses": "Root, leaves"}),
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("Raphanus sativus", "Brassicaceae", "radish", "Rettich", "herbaceous",
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{"food_uses": "Root, leaves, seed pods"}),
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("Allium cepa", "Amaryllidaceae", "onion", "Zwiebel", "herbaceous",
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{"food_uses": "Bulb, leaves"}),
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("Allium sativum", "Amaryllidaceae", "garlic", "Knoblauch", "herbaceous",
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{"food_uses": "Bulb, scapes", "medicinal_uses": "Antimicrobial, cardiovascular"}),
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("Allium schoenoprasum", "Amaryllidaceae", "chives", "Schnittlauch", "herbaceous",
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{"food_uses": "Leaves, flowers", "attracts_pollinators": True}),
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("Petroselinum crispum", "Apiaceae", "parsley", "Petersilie", "herbaceous",
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{"food_uses": "Leaves, root"}),
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("Apium graveolens", "Apiaceae", "celery", "Sellerie", "herbaceous",
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{"food_uses": "Stalks, root, leaves"}),
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("Foeniculum vulgare", "Apiaceae", "fennel", "Fenchel", "herbaceous",
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{"food_uses": "Bulb, fronds, seeds", "attracts_beneficial_insects": True}),
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("Pastinaca sativa", "Apiaceae", "parsnip", "Pastinake", "herbaceous",
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{"food_uses": "Root"}),
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("Zea mays", "Poaceae", "corn", "Mais", "herbaceous",
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{"food_uses": "Kernels, cobs"}),
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("Solanum melongena", "Solanaceae", "eggplant", "Melanzani", "herbaceous",
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{"food_uses": "Fruit"}),
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# Herbs
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("Ocimum basilicum", "Lamiaceae", "basil", "Basilikum", "herbaceous",
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{"food_uses": "Leaves", "attracts_pollinators": True}),
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("Origanum vulgare", "Lamiaceae", "oregano", "Oregano", "herbaceous",
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{"food_uses": "Leaves", "attracts_pollinators": True, "attracts_beneficial_insects": True}),
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("Mentha x piperita", "Lamiaceae", "peppermint", "Pfefferminze", "herbaceous",
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{"food_uses": "Leaves (tea, culinary)", "medicinal_uses": "Digestive, headache relief", "invasiveness": "spreading"}),
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("Rosmarinus officinalis", "Lamiaceae", "rosemary", "Rosmarin", "herbaceous",
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{"food_uses": "Leaves", "attracts_pollinators": True}),
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("Anethum graveolens", "Apiaceae", "dill", "Dill", "herbaceous",
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{"food_uses": "Leaves, seeds", "attracts_beneficial_insects": True}),
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("Coriandrum sativum", "Apiaceae", "coriander", "Koriander", "herbaceous",
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{"food_uses": "Leaves, seeds", "attracts_beneficial_insects": True}),
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("Artemisia absinthium", "Asteraceae", "wormwood", "Wermut", "herbaceous",
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{"medicinal_uses": "Digestive, anti-parasitic", "other_uses": "Companion plant pest deterrent", "allelopathic": True}),
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("Achillea millefolium", "Asteraceae", "yarrow", "Schafgarbe", "herbaceous",
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{"food_uses": "Young leaves (salad)", "medicinal_uses": "Wound healing, anti-inflammatory",
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"dynamic_accumulator": True, "dynamic_accumulator_nutrients": "K, P, Cu",
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"attracts_beneficial_insects": True, "attracts_pollinators": True}),
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("Hypericum perforatum", "Hypericaceae", "St John's wort", "Johanniskraut", "herbaceous",
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{"medicinal_uses": "Antidepressant, wound healing", "attracts_pollinators": True}),
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("Echinacea purpurea", "Asteraceae", "echinacea", "Sonnenhut", "herbaceous",
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{"medicinal_uses": "Immune stimulant", "attracts_pollinators": True, "wildlife_value": "Seeds for birds"}),
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("Valeriana officinalis", "Caprifoliaceae", "valerian", "Baldrian", "herbaceous",
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{"medicinal_uses": "Sedative, sleep aid", "attracts_pollinators": True,
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"other_uses": "Earthworm attractant (biodynamic)"}),
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# Flowers & cover crops
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("Tagetes patula", "Asteraceae", "French marigold", "Studentenblume", "herbaceous",
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{"other_uses": "Nematode suppression, companion plant", "attracts_pollinators": True}),
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("Helianthus annuus", "Asteraceae", "sunflower", "Sonnenblume", "herbaceous",
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{"food_uses": "Seeds, oil", "attracts_pollinators": True, "wildlife_value": "Seeds for birds"}),
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("Tropaeolum majus", "Tropaeolaceae", "nasturtium", "Kapuzinerkresse", "ground_cover",
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{"food_uses": "Leaves, flowers, seeds (capers)", "other_uses": "Trap crop for aphids"}),
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("Centaurea cyanus", "Asteraceae", "cornflower", "Kornblume", "herbaceous",
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{"food_uses": "Flowers (edible garnish)", "attracts_pollinators": True, "attracts_beneficial_insects": True}),
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("Sinapis alba", "Brassicaceae", "white mustard", "Weißer Senf", "herbaceous",
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{"food_uses": "Seeds, young leaves", "other_uses": "Green manure, biofumigant"}),
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("Trifolium repens", "Fabaceae", "white clover", "Weißklee", "ground_cover",
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{"nitrogen_fixer": True, "food_uses": "Flowers (tea), young leaves",
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"ground_cover_quality": "excellent", "attracts_pollinators": True}),
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("Medicago sativa", "Fabaceae", "alfalfa", "Luzerne", "herbaceous",
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{"nitrogen_fixer": True, "food_uses": "Sprouts",
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"dynamic_accumulator": True, "dynamic_accumulator_nutrients": "N, K, Ca, Mg, Fe",
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"other_uses": "Green manure, deep-rooting soil improver"}),
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# Fruit / Trees
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("Prunus avium", "Rosaceae", "sweet cherry", "Süßkirsche", "canopy",
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{"food_uses": "Fruit", "attracts_pollinators": True, "wildlife_value": "Fruit for birds"}),
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("Prunus cerasus", "Rosaceae", "sour cherry", "Sauerkirsche", "understory",
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{"food_uses": "Fruit (cooking, preserves)", "attracts_pollinators": True}),
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("Pyrus communis", "Rosaceae", "pear", "Birne", "canopy",
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{"food_uses": "Fruit", "attracts_pollinators": True}),
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("Ribes uva-crispa", "Grossulariaceae", "gooseberry", "Stachelbeere", "shrub",
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{"food_uses": "Berries"}),
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("Rubus fruticosus", "Rosaceae", "blackberry", "Brombeere", "shrub",
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{"food_uses": "Berries, leaves (tea)", "attracts_pollinators": True,
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"wildlife_value": "Berries for birds, nesting habitat", "invasiveness": "spreading"}),
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("Vaccinium myrtillus", "Ericaceae", "bilberry", "Heidelbeere", "shrub",
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{"food_uses": "Berries", "medicinal_uses": "Antioxidant, eye health"}),
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("Hippophae rhamnoides", "Elaeagnaceae", "sea buckthorn", "Sanddorn", "shrub",
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{"nitrogen_fixer": True, "food_uses": "Berries (juice, oil)",
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"medicinal_uses": "High vitamin C, skin care",
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"other_uses": "Erosion control, windbreak"}),
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("Morus alba", "Moraceae", "white mulberry", "Weiße Maulbeere", "canopy",
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{"food_uses": "Fruit, young leaves", "wildlife_value": "Fruit for birds"}),
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]
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def main():
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# 1. Load existing families
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print("=== Loading existing families ===")
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fam_resp = api_get("/families?per_page=100")
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family_map = {} # name_scientific -> id
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for f in fam_resp["data"]:
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family_map[f["name_scientific"]] = f["id"]
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print(f" Found {len(family_map)} existing families")
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# 2. Create missing families
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print("\n=== Creating missing families ===")
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families_created = 0
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for fam_name, fam_info in FAMILIES_NEEDED.items():
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if fam_name in family_map:
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print(f" SKIP (exists): {fam_name}")
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continue
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payload = {
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"name_scientific": fam_name,
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"name_en": fam_info["name_en"],
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"name_de": fam_info["name_de"],
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}
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print(f" CREATE: {fam_name} ...", end=" ")
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result, status = api_post("/families", payload)
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if result and "id" in result:
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family_map[fam_name] = result["id"]
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print(f"OK ({result['id']})")
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families_created += 1
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else:
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print(f"FAILED (status={status})")
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time.sleep(DELAY)
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print(f"\n Families created: {families_created}")
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# 3. Load existing species
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print("\n=== Loading existing species ===")
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sp_resp = api_get("/species?per_page=200")
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existing_species = set()
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for s in sp_resp["data"]:
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existing_species.add(s["name_scientific"])
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print(f" Found {len(existing_species)} existing species")
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# 4. Add new species
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print("\n=== Adding new species ===")
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created = 0
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skipped = 0
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failed = 0
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for sci_name, family, name_en, name_de, plant_layer, extras in SPECIES:
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if sci_name in existing_species:
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print(f" SKIP (exists): {sci_name}")
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skipped += 1
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continue
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# Look up family ID
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fam_id = family_map.get(family)
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if not fam_id:
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print(f" SKIP (no family '{family}'): {sci_name}")
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failed += 1
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continue
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# Try GBIF for German name
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gbif_de = gbif_get_german_name(sci_name)
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if gbif_de:
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print(f" GBIF name for {sci_name}: {gbif_de}")
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# Use GBIF name if it differs (prefer catalog name as primary, GBIF as validation)
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# Keep our curated name_de but log the GBIF one
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payload = {
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"name_scientific": sci_name,
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"family_id": fam_id,
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"name_en": name_en,
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"name_de": name_de,
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"plant_layer": plant_layer,
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}
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# Add extra fields
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for k, v in extras.items():
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payload[k] = v
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print(f" CREATE: {sci_name} ({name_de}) ...", end=" ")
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result, status = api_post("/species", payload)
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if result and "id" in result:
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print(f"OK ({result['id']})")
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created += 1
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else:
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print(f"FAILED (status={status})")
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failed += 1
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time.sleep(DELAY)
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print(f"\n{'='*50}")
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print(f"SUMMARY")
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print(f" Families created: {families_created}")
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print(f" Species created: {created}")
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print(f" Species skipped: {skipped}")
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print(f" Species failed: {failed}")
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print(f" Total species now: {len(existing_species) + created}")
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if __name__ == "__main__":
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main()
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