ecological-agent-skills 3.1.0

package/skills/ecological-data-foundation/scripts/download_from_iucn.py

@@ -0,0 +1,344 @@
+# ecological-agent-skills / Copyright (C) 2026 Francisco Diego Barros Barata
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""Download species assessment data from the IUCN Red List API v3.
+
+Usage: python download_from_iucn.py <species_name_or_list_csv> <output_dir> [include_range_maps]
+
+Arguments:
+    species_name_or_list_csv : Species name (e.g., "Panthera onca") or path to CSV
+                               with column 'scientificName'
+    output_dir               : Directory for outputs (created if absent)
+    include_range_maps       : 'true' or 'false' — download range data if available (default: false)
+
+Requires:
+    IUCN_REDLIST_KEY environment variable — obtain at: https://apiv3.iucnredlist.org/
+
+Outputs (per species):
+    iucn_status_{species}.csv           — Red List category, criteria, country occurrences
+    iucn_habitats_{species}.csv         — suitable habitats
+    download_metadata_IUCN_{species}.txt — provenance and citation
+
+Standard output schema (iucn_status CSV):
+    species, decimalLatitude, decimalLongitude, eventDate, countryCode,
+    basisOfRecord, coordinateUncertaintyInMeters, datasetName, occurrenceID,
+    source, download_doi
+Extra IUCN columns:
+    rl_category, rl_criteria, population_trend, assessment_year
+"""
+
+import logging
+import os
+import sys
+from datetime import datetime
+from pathlib import Path
+
+SKILL_NAME = "ecological-data-foundation"
+_LOG_DIR   = Path("logs")
+_LOG_DIR.mkdir(parents=True, exist_ok=True)
+_log_file  = _LOG_DIR / f"skill_{SKILL_NAME}_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
+logging.basicConfig(
+    level=logging.INFO,
+    format="[%(asctime)s] [%(levelname)s] [" + SKILL_NAME + "] %(message)s",
+    datefmt="%Y-%m-%d %H:%M:%S",
+    handlers=[
+        logging.StreamHandler(sys.stdout),
+        logging.FileHandler(_log_file, encoding="utf-8"),
+    ],
+)
+logger = logging.getLogger(SKILL_NAME)
+
+def log_step(n: int, desc: str) -> None:
+    logger.info("-- STEP %d: %s", n, desc)
+
+def log_decision(var: str, val, why: str) -> None:
+    logger.info("DECISION | %s = %s | %s", var, val, why)
+
+
+from datetime import date
+
+try:
+    import requests
+    import pandas as pd
+except ImportError as e:
+    logger.error(
+        "Dependencia ausente: %s\n  Instale com: pip install requests pandas\n  Skill anterior: ecological-data-foundation",
+        e,
+    )
+    sys.exit(1)
+
+
+# ── Constants ─────────────────────────────────────────────────────────────────
+IUCN_API_BASE = "https://apiv3.iucnredlist.org/api/v3"
+
+
+# ── Helper functions ──────────────────────────────────────────────────────────
+
+def iucn_get(endpoint: str, api_key: str) -> dict:
+    """Make an authenticated GET request to the IUCN API."""
+    url = f"{IUCN_API_BASE}/{endpoint}?token={api_key}"
+    try:
+        resp = requests.get(url, timeout=30)
+        resp.raise_for_status()
+        return resp.json()
+    except requests.RequestException as e:
+        logger.error(
+            "Falha na requisicao IUCN API '%s': %s\n  Causa provavel: chave invalida ou API indisponivel.\n  Verifique: https://apiv3.iucnredlist.org/\n  Skill anterior: ecological-data-foundation",
+            endpoint, e,
+        )
+        raise
+
+
+def fetch_assessment(species_name: str, api_key: str) -> dict:
+    """Fetch the most recent IUCN assessment for a species."""
+    sp_encoded = species_name.replace(" ", "%20")
+    return iucn_get(f"species/{sp_encoded}", api_key)
+
+
+def fetch_country_occurrences(species_name: str, api_key: str) -> list[dict]:
+    """Fetch country-level occurrences from IUCN."""
+    sp_encoded = species_name.replace(" ", "%20")
+    try:
+        data = iucn_get(f"species/countries/name/{sp_encoded}", api_key)
+        return data.get("result", [])
+    except Exception as e:
+        logger.warning("Falha ao buscar paises de ocorrencia para '%s': %s", species_name, e)
+        return []
+
+
+def fetch_habitats(species_name: str, api_key: str) -> list[dict]:
+    """Fetch suitable habitats for a species."""
+    sp_encoded = species_name.replace(" ", "%20")
+    try:
+        data = iucn_get(f"habitats/species/name/{sp_encoded}", api_key)
+        return data.get("result", [])
+    except Exception as e:
+        logger.warning("Falha ao buscar habitats para '%s': %s", species_name, e)
+        return []
+
+
+def standardise_records(assessment: dict, countries: list[dict],
+                         species_name: str) -> "pd.DataFrame":
+    """Convert IUCN assessment data to the standard occurrence schema."""
+    results = assessment.get("result", [])
+    if not results:
+        return pd.DataFrame()
+
+    res         = results[0]
+    taxon_id    = res.get("taxonid", "")
+    category    = res.get("category", "")
+    criteria    = res.get("criteria", "")
+    pop_trend   = res.get("population_trend", "")
+    assess_year = res.get("assessment_date", "")[:4] if res.get("assessment_date") else ""
+
+    if not countries:
+        rows = [{
+            "species":                       species_name,
+            "decimalLatitude":               None,
+            "decimalLongitude":              None,
+            "eventDate":                     None,
+            "countryCode":                   None,
+            "basisOfRecord":                 "LITERATURE",
+            "coordinateUncertaintyInMeters": None,
+            "datasetName":                   "IUCN Red List",
+            "occurrenceID":                  f"IUCN:{taxon_id}",
+            "source":                        "IUCN",
+            "download_doi":                  None,
+            "rl_category":                   category,
+            "rl_criteria":                   criteria,
+            "population_trend":              pop_trend,
+            "assessment_year":               assess_year,
+        }]
+    else:
+        rows = []
+        for ctry in countries:
+            rows.append({
+                "species":                       species_name,
+                "decimalLatitude":               None,
+                "decimalLongitude":              None,
+                "eventDate":                     None,
+                "countryCode":                   ctry.get("code", ""),
+                "basisOfRecord":                 "LITERATURE",
+                "coordinateUncertaintyInMeters": None,
+                "datasetName":                   "IUCN Red List",
+                "occurrenceID":                  f"IUCN:{taxon_id}:{ctry.get('code', '')}",
+                "source":                        "IUCN",
+                "download_doi":                  None,
+                "rl_category":                   category,
+                "rl_criteria":                   criteria,
+                "population_trend":              pop_trend,
+                "assessment_year":               assess_year,
+            })
+
+    return pd.DataFrame(rows)
+
+
+def save_metadata(output_dir: Path, species_name: str, taxon_id,
+                  category: str, assess_year: str) -> None:
+    safe_name = species_name.replace(" ", "_")
+    today = date.today().isoformat()
+    year  = date.today().year
+    month = f"{date.today().month:02d}"
+    lines = [
+        f"Species: {species_name}",
+        f"IUCN Taxon ID: {taxon_id}",
+        f"Source: IUCN Red List (https://www.iucnredlist.org)",
+        f"API version: v3 (https://apiv3.iucnredlist.org)",
+        f"Red List category: {category}",
+        f"Assessment year: {assess_year}",
+        f"Download date: {today}",
+        (f"Citation: IUCN {year}. The IUCN Red List of Threatened Species. "
+         f"Version {year}-{month}. https://www.iucnredlist.org Accessed on {today}."),
+        "License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/)",
+    ]
+    meta_path = output_dir / f"download_metadata_IUCN_{safe_name}.txt"
+    try:
+        meta_path.write_text("\n".join(lines), encoding="utf-8")
+        logger.info("Metadados gravados: %s", meta_path)
+    except OSError as e:
+        logger.error(
+            "Falha ao gravar metadados: %s\n  Skill anterior: ecological-data-foundation", e,
+        )
+        raise
+
+
+# ── Main download logic ────────────────────────────────────────────────────────
+
+def download_species(species_name: str, output_dir: Path, api_key: str) -> None:
+    logger.info("--- Iniciando download IUCN: %s ---", species_name)
+    safe_name = species_name.replace(" ", "_")
+
+    log_step(1, f"Buscar avaliacao IUCN para '{species_name}'")
+    assessment = fetch_assessment(species_name, api_key)
+
+    results = assessment.get("result", [])
+    if not results:
+        logger.warning("Nenhum resultado IUCN para '%s'. Especie pode nao estar avaliada.", species_name)
+        return
+
+    res         = results[0]
+    taxon_id    = res.get("taxonid", "")
+    category    = res.get("category", "")
+    criteria    = res.get("criteria", "")
+    pop_trend   = res.get("population_trend", "")
+    assess_date = res.get("assessment_date", "")
+    assess_year = assess_date[:4] if assess_date else ""
+
+    logger.info("Categoria IUCN: %s | Criterios: %s | Tendencia: %s | Ano: %s",
+                category, criteria, pop_trend, assess_year)
+
+    if category in ("CR", "EN"):
+        logger.warning(
+            "Especie '%s' e %s — dados de distribuicao podem ser restritos por razoes de seguranca.",
+            species_name, category,
+        )
+
+    log_step(2, f"Buscar ocorrencias por pais para '{species_name}'")
+    countries = fetch_country_occurrences(species_name, api_key)
+    logger.info("Paises de ocorrencia: %d", len(countries))
+
+    log_step(3, f"Buscar habitats adequados para '{species_name}'")
+    habitats = fetch_habitats(species_name, api_key)
+    logger.info("Habitats identificados: %d", len(habitats))
+
+    log_step(4, "Padronizar registros para schema de saida")
+    df = standardise_records(assessment, countries, species_name)
+    logger.info("Registros no schema padrao: %d", len(df))
+
+    log_step(5, "Gravar CSV de status IUCN")
+    csv_path = output_dir / f"iucn_status_{safe_name}.csv"
+    try:
+        df.to_csv(csv_path, index=False)
+        logger.info("Gravado: %s", csv_path)
+    except OSError as e:
+        logger.error(
+            "Falha ao gravar CSV IUCN: %s\n  Skill anterior: ecological-data-foundation", e,
+        )
+        raise
+
+    if habitats:
+        hab_df       = pd.DataFrame(habitats)
+        hab_df["species"] = species_name
+        hab_path     = output_dir / f"iucn_habitats_{safe_name}.csv"
+        try:
+            hab_df.to_csv(hab_path, index=False)
+            logger.info("Habitats gravados: %s", hab_path)
+        except OSError as e:
+            logger.warning("Falha ao gravar habitats: %s", e)
+
+    log_step(6, "Gravar metadados")
+    save_metadata(output_dir, species_name, taxon_id, category, assess_year)
+
+
+# ── Entry point ────────────────────────────────────────────────────────────────
+
+def main():
+    logger.info("Script: download_from_iucn.py | Skill: %s", SKILL_NAME)
+
+    # Check API key
+    api_key = os.environ.get("IUCN_REDLIST_KEY", "")
+    if not api_key:
+        logger.error(
+            "Variavel IUCN_REDLIST_KEY nao definida.\n  Causa provavel: chave nao configurada no ambiente.\n  Verifique: export IUCN_REDLIST_KEY=your_key (Linux/Mac) ou setx IUCN_REDLIST_KEY your_key (Windows)\n  Skill anterior: ecological-data-foundation",
+        )
+        sys.exit(1)
+    logger.info("Chave IUCN detectada (primeiros 4 chars): %s...", api_key[:4])
+    log_decision("api_key", "***", "lida de IUCN_REDLIST_KEY; nunca exibida em logs")
+
+    argv = sys.argv[1:]
+
+    if len(argv) < 2:
+        species_input = "Panthera onca"
+        output_dir    = Path("output/iucn")
+        logger.warning("Menos de 2 argumentos fornecidos. Usando valores padrao para teste.")
+    else:
+        species_input = argv[0]
+        output_dir    = Path(argv[1])
+
+    logger.info("Species input  : %s", species_input)
+    logger.info("Output dir     : %s", output_dir)
+
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # Build species list
+    log_step(0, "Construir lista de especies")
+    if species_input.endswith(".csv") and Path(species_input).exists():
+        try:
+            df_sp = pd.read_csv(species_input)
+            if "scientificName" not in df_sp.columns:
+                logger.error(
+                    "Coluna 'scientificName' nao encontrada em: %s\n  Skill anterior: ecological-data-foundation",
+                    species_input,
+                )
+                sys.exit(1)
+            species_list = df_sp["scientificName"].dropna().unique().tolist()
+            logger.info("Modo batch: %d especies carregadas", len(species_list))
+            log_decision("mode", "batch", "CSV valido com coluna scientificName")
+        except Exception as e:
+            logger.error(
+                "Falha ao ler lista de especies: %s\n  Skill anterior: ecological-data-foundation", e,
+            )
+            sys.exit(1)
+    else:
+        species_list = [species_input.strip()]
+        logger.info("Modo especie unica: %s", species_list[0])
+        log_decision("mode", "single_species", "argumento nao e arquivo CSV")
+
+    for sp in species_list:
+        try:
+            download_species(sp, output_dir, api_key)
+        except FileNotFoundError as e:
+            logger.error(
+                "Arquivo de entrada nao encontrado: %s\n  Skill anterior: ecological-data-foundation", e,
+            )
+        except Exception as e:
+            logger.error(
+                "Falha ao baixar '%s' do IUCN: %s\n  Causa provavel: chave invalida, especie nao avaliada ou API indisponivel.\n  Skill anterior: ecological-data-foundation",
+                sp, e,
+            )
+
+    logger.info("Todos os downloads IUCN concluidos. Verifique: %s", output_dir)
+
+
+if __name__ == "__main__":
+    main()

package/skills/ecological-data-foundation/scripts/download_from_obis.R

@@ -0,0 +1,248 @@
+# ecological-agent-skills / Copyright (C) 2026 Francisco Diego Barros Barata
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+# Usage: Rscript download_from_obis.R <species_name_or_list_csv> <output_dir> [year_from] [year_to] [wkt_geometry]
+
+# ── Inline logger ─────────────────────────────────────────────────────────────
+SKILL_NAME <- "ecological-data-foundation"
+.log_ts  <- function() format(Sys.time(), "[%Y-%m-%d %H:%M:%S]")
+log_info <- function(...) message(.log_ts(), " [INFO]  ", sprintf(...))
+log_warn <- function(...) message(.log_ts(), " [WARN]  ", sprintf(...))
+log_error<- function(...) message(.log_ts(), " [ERROR] ", sprintf(...))
+log_step <- function(n, d) log_info("-- STEP %d: %s", n, d)
+log_decision <- function(v, val, why) log_info("DECISION | %s = %s | %s", v, val, why)
+dir.create("logs", recursive=TRUE, showWarnings=FALSE)
+
+#
+# Arguments:
+#   species_name_or_list_csv : Species name (e.g., "Chelonia mydas") or path to CSV
+#                              with column "scientificName"
+#   output_dir               : Directory to write outputs (created if absent)
+#   year_from                : Minimum year of observation (optional, default: 1950)
+#   year_to                  : Maximum year of observation (optional, default: current year)
+#   wkt_geometry             : WKT polygon to restrict query (optional, e.g., "POLYGON((-80 -30,-80 10,-30 10,-30 -30,-80 -30))")
+#
+# Outputs (per species):
+#   occurrences_raw_OBIS_{species}_{date}.csv  — standardised occurrence records
+#   download_metadata_OBIS_{species}.txt        — download provenance and citation
+#
+# Standard output schema:
+#   species, decimalLatitude, decimalLongitude, eventDate, countryCode,
+#   basisOfRecord, coordinateUncertaintyInMeters, datasetName, occurrenceID,
+#   source, download_doi
+# Extra OBIS columns:
+#   depth, marine
+
+suppressPackageStartupMessages(library(robis))
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(readr))
+
+# ── 1. Parse arguments ───────────────────────────────────────────────────────
+log_step(1, "Analisar argumentos da linha de comando")
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) < 2) {
+  species_input <- "Chelonia mydas"
+  output_dir    <- "output/obis"
+  year_from     <- 1950
+  year_to       <- as.integer(format(Sys.Date(), "%Y"))
+  wkt_geometry  <- NULL
+  log_warn("Menos de 2 argumentos fornecidos. Usando valores padrao para teste.")
+} else {
+  species_input <- args[1]
+  output_dir    <- args[2]
+  year_from     <- if (length(args) >= 3) as.integer(args[3]) else 1950
+  year_to       <- if (length(args) >= 4) as.integer(args[4]) else as.integer(format(Sys.Date(), "%Y"))
+  wkt_geometry  <- if (length(args) >= 5 && args[5] != "") args[5] else NULL
+}
+
+log_info("Script: download_from_obis.R | Skill: %s", SKILL_NAME)
+log_info("Species input  : %s", species_input)
+log_info("Output dir     : %s", output_dir)
+log_info("Year range     : %d - %d", year_from, year_to)
+log_info("WKT geometry   : %s", ifelse(is.null(wkt_geometry), "nenhum (global)", wkt_geometry))
+
+log_decision("absence", "FALSE",
+             "apenas registros de presenca confirmada; OBIS inclui dados de ausencia em alguns datasets")
+log_decision("year_from", year_from, "filtro temporal; 1950 cobre era moderna de registros marinhos")
+
+# ── 2. Create output directory ───────────────────────────────────────────────
+log_step(2, "Criar diretorio de saida")
+dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
+
+# ── 3. Build species list ────────────────────────────────────────────────────
+log_step(3, "Construir lista de especies")
+if (grepl("\\.csv$", species_input, ignore.case = TRUE) && file.exists(species_input)) {
+  tryCatch({
+    species_df <- read_csv(species_input, show_col_types = FALSE)
+    if (!"scientificName" %in% names(species_df)) {
+      log_error(
+        "Coluna 'scientificName' nao encontrada em: %s\nCausa provavel: CSV mal formatado.\nSkill anterior: ecological-data-foundation",
+        species_input
+      )
+      stop("Missing column 'scientificName'")
+    }
+    species_list <- unique(trimws(species_df$scientificName))
+    log_info("Modo batch: %d especies carregadas", length(species_list))
+    log_decision("mode", "batch", "CSV valido com coluna scientificName")
+  }, error = function(e) {
+    log_error(
+      "Falha ao ler lista de especies: %s\nSkill anterior: ecological-data-foundation",
+      conditionMessage(e)
+    )
+    stop(e)
+  })
+} else {
+  species_list <- trimws(species_input)
+  log_info("Modo especie unica: %s", species_list)
+  log_decision("mode", "single_species", "argumento nao e arquivo CSV")
+}
+
+# ── 4. Download function ─────────────────────────────────────────────────────
+download_obis_species <- function(sp_name) {
+  log_info("--- Iniciando download OBIS: %s ---", sp_name)
+  today_str <- format(Sys.Date(), "%Y%m%d")
+  safe_name <- gsub(" ", "_", sp_name)
+
+  # Build query
+  query_args <- list(
+    scientificname = sp_name,
+    absence        = FALSE,
+    startdate      = paste0(year_from, "-01-01"),
+    enddate        = paste0(year_to,   "-12-31")
+  )
+  if (!is.null(wkt_geometry)) {
+    query_args$geometry <- wkt_geometry
+  }
+
+  occ_raw <- tryCatch({
+    do.call(robis::occurrence, query_args)
+  }, error = function(e) {
+    log_error(
+      "Falha em robis::occurrence para '%s': %s\nCausa provavel: sem conexao com a internet ou API OBIS indisponivel.\nVerifique: https://api.obis.org/\nSkill anterior: ecological-data-foundation",
+      sp_name, conditionMessage(e)
+    )
+    stop(e)
+  })
+
+  if (is.null(occ_raw) || nrow(occ_raw) == 0) {
+    log_warn("Nenhum registro OBIS encontrado para '%s'.", sp_name)
+    return(invisible(NULL))
+  }
+
+  n_raw <- nrow(occ_raw)
+  log_info("Registros brutos recuperados: %d", n_raw)
+
+  # ── Apply OBIS quality flags ───────────────────────────────────────────────
+  # Remove records flagged as having coordinate issues
+  qc_cols <- c("flags")
+  if ("flags" %in% names(occ_raw)) {
+    bad_flags <- c("NO_COORD", "ZERO_COORD", "ON_LAND", "DEPTH_EXCEEDS_BATH")
+    occ_raw <- occ_raw[!grepl(paste(bad_flags, collapse = "|"),
+                               occ_raw$flags, ignore.case = TRUE), ]
+    log_info("Registros apos filtro de flags OBIS: %d", nrow(occ_raw))
+  }
+
+  # ── Standardise to output schema ──────────────────────────────────────────
+  get_col <- function(df, ...) {
+    cols <- c(...)
+    for (col in cols) {
+      if (col %in% names(df)) return(df[[col]])
+    }
+    return(rep(NA, nrow(df)))
+  }
+
+  std <- data.frame(
+    species                       = sp_name,
+    decimalLatitude               = as.numeric(get_col(occ_raw, "decimalLatitude", "latitude")),
+    decimalLongitude              = as.numeric(get_col(occ_raw, "decimalLongitude", "longitude")),
+    eventDate                     = as.character(get_col(occ_raw, "eventDate", "date_start")),
+    countryCode                   = as.character(get_col(occ_raw, "countryCode", "country")),
+    basisOfRecord                 = as.character(get_col(occ_raw, "basisOfRecord")),
+    coordinateUncertaintyInMeters = as.numeric(get_col(occ_raw, "coordinateUncertaintyInMeters")),
+    datasetName                   = as.character(get_col(occ_raw, "datasetName", "dataset_name")),
+    occurrenceID                  = as.character(get_col(occ_raw, "occurrenceID", "id")),
+    source                        = "OBIS",
+    download_doi                  = NA_character_,
+    depth                         = as.numeric(get_col(occ_raw, "depth")),
+    marine                        = TRUE,
+    stringsAsFactors              = FALSE
+  )
+
+  # Replace empty basisOfRecord
+  std$basisOfRecord[is.na(std$basisOfRecord) | std$basisOfRecord == ""] <- "OCCURRENCE"
+
+  # Remove records with missing coordinates
+  n_before <- nrow(std)
+  std <- std[!is.na(std$decimalLatitude) & !is.na(std$decimalLongitude), ]
+  n_removed <- n_before - nrow(std)
+  if (n_removed > 0) {
+    log_warn("%d registros removidos por coordenadas ausentes.", n_removed)
+  }
+
+  n_final <- nrow(std)
+  log_info("Registros com coordenadas validas: %d", n_final)
+
+  if (n_final < 30) {
+    log_warn(
+      "Registros insuficientes para analise confiavel (n = %d). Considere relaxar filtros de datas ou area.",
+      n_final
+    )
+  }
+
+  # ── Save CSV ───────────────────────────────────────────────────────────────
+  csv_path <- file.path(output_dir, paste0("occurrences_raw_OBIS_", safe_name, "_", today_str, ".csv"))
+  tryCatch({
+    write_csv(std, csv_path)
+    log_info("Gravado: %s (%d registros)", csv_path, n_final)
+  }, error = function(e) {
+    log_error(
+      "Falha ao gravar CSV para '%s': %s\nSkill anterior: ecological-data-foundation",
+      sp_name, conditionMessage(e)
+    )
+    stop(e)
+  })
+
+  # ── Save metadata ──────────────────────────────────────────────────────────
+  meta_lines <- c(
+    paste("Species:", sp_name),
+    paste("Source: Ocean Biodiversity Information System (OBIS) — https://obis.org"),
+    paste("API endpoint: https://api.obis.org/v3/occurrence"),
+    paste("Absence records excluded: TRUE"),
+    paste("OBIS quality flags applied: TRUE (NO_COORD, ZERO_COORD, ON_LAND, DEPTH_EXCEEDS_BATH removed)"),
+    paste("Year range:", year_from, "-", year_to),
+    paste("WKT geometry:", ifelse(is.null(wkt_geometry), "none (global)", wkt_geometry)),
+    paste("n_records:", n_final),
+    paste("Download date:", Sys.Date()),
+    paste("Citation: OBIS (", format(Sys.Date(), "%Y"), ") Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. www.obis.org. Accessed on", Sys.Date()),
+    paste("License: CC0 1.0 (https://creativecommons.org/publicdomain/zero/1.0/)")
+  )
+  meta_path <- file.path(output_dir, paste0("download_metadata_OBIS_", safe_name, ".txt"))
+  tryCatch({
+    writeLines(meta_lines, meta_path)
+    log_info("Gravado: %s", meta_path)
+  }, error = function(e) {
+    log_error(
+      "Falha ao gravar metadados para '%s': %s\nSkill anterior: ecological-data-foundation",
+      sp_name, conditionMessage(e)
+    )
+  })
+
+  return(invisible(csv_path))
+}
+
+# ── 5. Run for all species ───────────────────────────────────────────────────
+log_step(4, "Executar download OBIS para todas as especies")
+for (sp in species_list) {
+  tryCatch(
+    download_obis_species(sp),
+    error = function(e) {
+      log_error(
+        "Falha ao baixar '%s' do OBIS: %s\nCausa provavel: problema de rede ou especie nao encontrada.\nSkill anterior: ecological-data-foundation",
+        sp, conditionMessage(e)
+      )
+    }
+  )
+}
+
+log_info("Todos os downloads OBIS concluidos. Verifique: %s", output_dir)