Fix merge

compose.yml

@@ -50,7 +50,7 @@ services:
   runner-julia:
     container_name: biab-runner-julia
     image: geobon/bon-in-a-box:runner-julia
-    # build:
+    #build:
     #   context: ./runners
     #   dockerfile: julia-dockerfile
     command: sh # Avoids launching julia session that will not be used.

pipelines/SDM/BRT_julia_viewer.json

@@ -297,8 +297,8 @@
       "id": "33",
       "type": "output",
       "position": {
-        "x": 2396.121814241836,
-        "y": 98.93945151650797
+        "x": 2379.6499938964844,
+        "y": 122
       },
       "data": {
         "label": "Output"
@@ -353,11 +353,11 @@
       }
     },
     {
-      "id": "39",
+      "id": "38",
       "type": "output",
       "position": {
-        "x": 2687.4770663161003,
-        "y": 233.61776005508665
+        "x": 1504.2802457138919,
+        "y": 294.44054742414664
       },
       "data": {
         "label": "Output"
@@ -604,11 +604,11 @@
       "id": "reactflow__edge-30-37"
     },
     {
-      "source": "21",
-      "sourceHandle": "n_clean",
-      "target": "39",
+      "source": "1",
+      "sourceHandle": "total_records",
+      "target": "38",
       "targetHandle": null,
-      "id": "reactflow__edge-21n_clean-39"
+      "id": "reactflow__edge-1total_records-38"
     }
   ],
   "inputs": {
@@ -718,7 +718,7 @@
         "identifier": "https://orcid.org/0000-0002-6506-6487"
       },
       {
-        "name": "Thimothée Poisot",
+        "name": "Timothée Poisot",
         "identifier": "https://orcid.org/0000-0002-0735-5184"
       }
     ],

runners/julia-dockerfile

@@ -3,4 +3,7 @@ FROM julia:1.9.3
 # Pre-compiling Julia dependencies
 RUN  julia -e 'pwd(); using Pkg; Pkg.add.(["SpeciesDistributionToolkit", "JSON", "CSV", "DataFrames", "StatsBase", "EvoTrees", "MultivariateStats" ]); Pkg.instantiate();'
 
+#COPY Project.toml /root/Project.toml
+#COPY instantiate.jl /root/instantiate.jl
+#RUN julia --project=. /root/instantiate.jl
 RUN date +"%Y-%m-%d %R" > /version.txt

scripts/SDM/julia_sdms/fitBRT.jl

@@ -109,7 +109,6 @@ function main()
 
     pseudoabsences = CSV.read(pseudoabs_path, DataFrame, delim="\t")
     pseudoabs_layer = create_occurrence_layer(similar(predictors[1]), pseudoabsences)
-    #pseudoabs_layer = create_occurrence_layer(similar(predictors[1]), pseudoabs_df)
 
     X, y, p_and_a_coords = get_features_and_labels(occurrence_layer, pseudoabs_layer, predictors)
 

scripts/SDM/julia_sdms/fitBRT.yml

@@ -19,17 +19,21 @@ inputs:
     label: predictors
     description: layer names (predictors) as a list
     type: image/tiff;application=geotiff[]
-    example: ["/output/data/loadFromStac/ea82148a2926d97acf85cea61a110194/bio1_242b2b01561981-01-01.tif","/output/data/loadFromStac/ea82148a2926d97acf85cea61a110194/bio2_243a4e7f541981-01-01.tif"]
+    example:
+      [
+        "/output/data/loadFromStac/ea82148a2926d97acf85cea61a110194/bio1_242b2b01561981-01-01.tif",
+        "/output/data/loadFromStac/ea82148a2926d97acf85cea61a110194/bio2_243a4e7f541981-01-01.tif",
+      ]
 outputs:
   sdm:
     label: sdm
     description: map of predicted occurrence probability
     type: image/tiff;application=geotiff
   sdm_uncertainty:
-    label: sdm uncertainty
-    description: map of relative uncertainty 
+    label: sdm_uncertainty
+    description: map of relative uncertainty
     type: image/tiff;application=geotiff
   fit_stats:
     label: fit_stats
-    description: JSON of model fit stats and threshold 
+    description: JSON of model fit stats and threshold
     type: text/json

scripts/SDM/julia_sdms/pcaLayers.jl

@@ -40,12 +40,13 @@ function make_pca_layers(layers, land_idx)
 end
 
 function write_outputs(runtime_dir, layers)
+
     predictor_paths = []
 
     for (i,l) in enumerate(layers)
         outpath = joinpath(runtime_dir, "predictor$i.tif")
         push!(predictor_paths, outpath)
-        SpeciesDistributionToolkit.save(outpath, l)
+        SpeciesDistributionToolkit._write_geotiff(outpath, l; compress="COG")
     end
 
     output_json_path = joinpath(runtime_dir, "output.json")