Removed error handling, added climate pipelines

GEO-BON · Dec 18, 2024 · c045fcd · c045fcd
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diff --git a/pipelines/GenesFromSpace/Tool/Climate_niche_v_GBIF_bbox.json b/pipelines/GenesFromSpace/Tool/Climate_niche_v_GBIF_bbox.json
@@ -0,0 +1,291 @@
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+        "descriptionFile": "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json"
+      }
+    },
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+      "data": {
+        "descriptionFile": "GFS_IndicatorsTool>getClimateNicheLand.yml"
+      }
+    }
+  ],
+  "edges": [
+    {
+      "source": "178",
+      "sourceHandle": "GFS_IndicatorsTool>get_pop_poly.yml@5|population_polygons",
+      "target": "177",
+      "targetHandle": "pipeline@161",
+      "id": "reactflow__edge-178GFS_IndicatorsTool>get_pop_poly.yml@5|population_polygons-177pipeline@161"
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+    {
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+      "sourceHandle": "GFS_IndicatorsTool>get_Indicators.yml@162|pm",
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+      "source": "177",
+      "sourceHandle": "GFS_IndicatorsTool>get_Indicators.yml@162|ne500",
+      "target": "180",
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+      "id": "reactflow__edge-177GFS_IndicatorsTool>get_Indicators.yml@162|ne500-180"
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+      "sourceHandle": "GFS_IndicatorsTool>get_Indicators.yml@162|ne_table",
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+      "sourceHandle": "GFS_IndicatorsTool>get_pop_poly.yml@5|population_polygons",
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+      "targetHandle": "pop_poly",
+      "id": "reactflow__edge-178GFS_IndicatorsTool>get_pop_poly.yml@5|population_polygons-183pop_poly"
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+    {
+      "source": "183",
+      "sourceHandle": "yearly_cover",
+      "target": "177",
+      "targetHandle": "GFS_IndicatorsTool>get_Indicators.yml@162|cover_maps",
+      "id": "reactflow__edge-183yearly_cover-177GFS_IndicatorsTool>get_Indicators.yml@162|cover_maps"
+    },
+    {
+      "source": "183",
+      "sourceHandle": "climate_map",
+      "target": "177",
+      "targetHandle": "pipeline@160",
+      "id": "reactflow__edge-183climate_map-177pipeline@160"
+    }
+  ],
+  "inputs": {
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|ne_nc": {
+      "description": "Estimated Ne:Nc ratio for the studied species. Multiple values can be provided, separated by a comma.",
+      "label": "Ne:Nc ratio estimate",
+      "weight": 0,
+      "type": "float[]",
+      "example": [
+        0.1,
+        0.2
+      ]
+    },
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|runtitle": {
+      "description": "Set a name for the pipeline run.",
+      "label": "Title of the run",
+      "weight": 1,
+      "type": "text",
+      "example": "Quercus sartorii, Mexico, Habitat decline by tree cover loss, 2000-2023"
+    },
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|pop_density": {
+      "description": "Estimated density of the population [number of individuals per km2]. Multiple values can be provided, separated by a comma.",
+      "label": "Population density",
+      "weight": 2,
+      "type": "float[]",
+      "example": [
+        50,
+        100,
+        1000
+      ]
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|pipeline@12": {
+      "description": "Scientific name of the species, used to look for occurrences in GBIF. ",
+      "label": "Species names",
+      "weight": 3,
+      "type": "text",
+      "example": "Quercus sartorii"
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|pipeline@21": {
+      "description": "Vector of float, bbox coordinates of the bbox in the order xmin, ymin, xmax, ymax",
+      "label": "Bounding box ",
+      "weight": 4,
+      "type": "float[]",
+      "example": [
+        "-99",
+        "22",
+        "-92",
+        "29"
+      ]
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|GFS_IndicatorsTool>get_pop_poly.yml@5|buffer_size": {
+      "description": "Radius size [in km] to determine population presence around the coordinates of species observations.",
+      "label": "Size of buffer",
+      "weight": 5,
+      "type": "float",
+      "example": 10
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|GFS_IndicatorsTool>get_pop_poly.yml@5|pop_distance": {
+      "description": "Distance [in km] to separate species observations in different populations.",
+      "label": "Distance between populations",
+      "weight": 6,
+      "type": "float",
+      "example": 50
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|pipeline@15": {
+      "description": "Integer, 4 digit year, end date to retrieve occurrences",
+      "label": "End year",
+      "weight": 7,
+      "type": "int",
+      "example": 2000
+    },
+    "GenesFromSpace>ToolComponents>GetPopulationPolygons>GFS_Population_polygons_from_GBIF_occurences_bbox.json@178|pipeline@14": {
+      "description": "Integer, 4 digit year, start date to retrieve occurrences",
+      "label": "Start year",
+      "weight": 8,
+      "type": "int",
+      "example": 1980
+    },
+    "GFS_IndicatorsTool>getClimateNicheLand.yml@183|start_year": {
+      "description": "Starting year of species observation extracted from the input JSON file.",
+      "label": "Starting year of species observation",
+      "type": "int",
+      "example": 1990,
+      "weight": 9
+    },
+    "GFS_IndicatorsTool>getClimateNicheLand.yml@183|end_year": {
+      "description": "Ending year of species observation extracted from the input JSON file.",
+      "label": "Ending year of species observation",
+      "type": "int",
+      "example": 2000,
+      "weight": 10
+    },
+    "GFS_IndicatorsTool>getClimateNicheLand.yml@183|yoi": {
+      "description": "Years of interest extracted from the input JSON file.",
+      "label": "Years of interest",
+      "type": "int[]",
+      "example": [
+        2000,
+        2005,
+        2010,
+        2015,
+        2020
+      ],
+      "weight": 11
+    }
+  },
+  "outputs": {
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|pm": {
+      "description": "Estimated proportion of mantained populations, comparing earliest and latest time point. A value of 1 means that no populations went extinct over the time frame.",
+      "label": "Population maintained indicator",
+      "weight": 0,
+      "type": "float"
+    },
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|ne500": {
+      "description": "Estimated proportion of populations with Ne>500 at latest time point.",
+      "label": "Ne>500 indicator",
+      "weight": 1,
+      "type": "float"
+    },
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|ne_table": {
+      "description": "Estimated effective size of every population, based on the latest time point of the habitat cover map.",
+      "label": "Effective population size",
+      "weight": 2,
+      "type": "text/tab-separated-values"
+    },
+    "GenesFromSpace>ToolComponents>GetIndicators>GFS_Indicators.json@177|GFS_IndicatorsTool>get_Indicators.yml@162|interactive_plot": {
+      "description": "An interactive interface to explore indicators trends across geographical space and time.",
+      "label": "Interactive plot",
+      "weight": 3,
+      "type": "text/html"
+    }
+  },
+  "metadata": {
+    "name": "Climate niche by populations from GBIF occurrences (bbox)",
+    "description": "Genes from Space tool. The tool retrieves species occurrence from GBIF, then used to define polygons of population distribution based on geographic proximity.  The tool then draws a habitat suitability map over time, based on the presence of land cover classes of interest.  Finally, the tool estimates the size of suitable habitat over time for every population, and computes indicators of genetic diversity monitoring accordingly (Ne500 and Populations Maintained indicators). Population maps and genetic diversity indicators are displayed through an interactive interface. ",
+    "author": [
+      {
+        "name": "Oliver Selmoni",
+        "email": "[email protected]"
+      }
+    ],
+    "license": "MIT",
+    "external_link": "https://teams.issibern.ch/genesfromspace/",
+    "references": [
+      {
+        "text": "Schuman et al., EcoEvoRxiv.",
+        "doi": "https://doi.org/10.32942/X2RS58"
+      },
+      {
+        "text": "ESA. Land Cover CCI Product User Guide Version 2. Tech. Rep. (2017)",
+        "doi": "https://maps.elie.ucl.ac.be/CCI/viewer/download/ESACCI-LC-Ph2-PUGv2_2.0.pdf"
+      }
+    ]
+  }
+}
diff --git a/runners/r-environment.yml b/runners/r-environment.yml
@@ -42,4 +42,5 @@ dependencies:
   - r-tidyselect  ssh -i ~/.ssh/id_rsa [email protected]
   - r-tidyverse
   - r-stringr
-  - r-ecmwfr
+  - r-ecmwfr
+  - r-dismo
diff --git a/scripts/GFS_IndicatorsTool/getClimateNicheLand.R b/scripts/GFS_IndicatorsTool/getClimateNicheLand.R
@@ -1,16 +1,13 @@
 #### Load packages
 
-packages <- c("dismo", "ecmwfr", "elevatr", "terra", "raster", "foreach", "doParallel", "sf")
+packages <- c("ecmwfr")
 new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
 if(length(new.packages)) install.packages(new.packages)
-
+ 
 library(dismo) # for maxent
 library(ecmwfr) # to get climate data
-library(elevatr) # to get altitude data
 library(terra)
 library(raster)
-library(foreach)
-library(doParallel)
 library(sf)
 
 
@@ -54,8 +51,7 @@ maxY = max(yoi)
 ############
 ############  Get climate data 
 ############
-print(packageVersion('ecmwfr') )
-options(keyring_backend = "file")
+options(keyring_backend = "env")
 wf_set_key(user = APIuserID, key = APIkey)
 
 ### set name of temporary variables

diff --git a/scripts/GFS_IndicatorsTool/getClimateNicheLand.yml b/scripts/GFS_IndicatorsTool/getClimateNicheLand.yml
@@ -10,30 +10,33 @@ inputs:
   pop_poly:
     label: Population polygons
     description: Population polygons extracted from the input JSON file.
-    type: text
-    example: 'Extracted from input JSON'
+    type: application/geo+json
+    example: /userdata/population_polygons_switzerland.geojson
 
   start_year:
     label: Starting year of species observation
     description: Starting year of species observation extracted from the input JSON file.
     type: int
-    example: 'Extracted from input JSON'
+    example: 1990
 
   end_year:
     label: Ending year of species observation
     description: Ending year of species observation extracted from the input JSON file.
     type: int
-    example: 'Extracted from input JSON'
+    example: 2000
 
   yoi:
     label: Years of interest
     description: Years of interest extracted from the input JSON file.
     type: int[]
-    example: 'Extracted from input JSON'
+    example: [2000, 2005, 2010, 2015, 2020]
 
 outputs:
   climate_map:
-    label: Climate map
-    description: Climate map of the species habitat
-    type: text/tab-separated-values
-
+    label: pop_map
+    description: Population map of the species habitat
+    type: text
+  yearly_cover:
+    label: Yearly cover
+    description: Yearly cover of the species habitat
+    type: text