Adapt ogc app cwl 2

ogc-app-cwl/Dockerfile

@@ -1,12 +1,14 @@
 FROM julia:1.11.2-bookworm
 WORKDIR /work
 
-ENV JULIA_PROJECT=/work
 ENV JULIA_NUM_THREADS=auto
 
-COPY Project.toml .
-COPY Manifest.toml .
-RUN julia -e 'using Pkg; Pkg.instantiate()'
+ENV JULIA_DEPOT_PATH=/.julia
+RUN julia -e 'using Pkg; Pkg.activate("/.julia/environments/v1.11"); Pkg.instantiate(); Pkg.status()'
+COPY Project.toml /.julia/environments/v1.11/
+COPY Manifest.toml /.julia/environments/v1.11/
+RUN julia -e 'using Pkg; Pkg.activate("/.julia/environments/v1.11"); Pkg.instantiate(); Pkg.status()'
+ENV JULIA_DEPOT_PATH=~/.julia:/.julia
 
 ADD run.jl ./
-ENTRYPOINT ["/work/run.jl"]
+ENTRYPOINT ["/work/run.jl"]

ogc-app-cwl/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.2"
 manifest_format = "2.0"
-project_hash = "fcba262f40e7f619c7dd24e2647b2795d595bca9"
+project_hash = "c5fb35d827c7d4456361ae4b4a9d46d5b535215a"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f"
@@ -975,9 +975,9 @@ version = "1.14.3+3"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "6c22309e9a356ac1ebc5c8a217045f9bae6f8d9a"
+git-tree-sha1 = "627fcacdb7cb51dc67f557e1598cdffe4dda386d"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.13"
+version = "1.10.14"
 
 [[deps.HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
@@ -1146,9 +1146,9 @@ weakdeps = ["Dates", "Test"]
     InverseFunctionsTestExt = "Test"
 
 [[deps.InvertedIndices]]
-git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
+git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe"
 uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
-version = "1.3.0"
+version = "1.3.1"
 
 [[deps.Ipopt]]
 deps = ["Ipopt_jll", "LinearAlgebra", "MathOptInterface", "OpenBLAS32_jll", "PrecompileTools"]
@@ -1427,9 +1427,9 @@ version = "2.16.0+0"
 
 [[deps.LogExpFunctions]]
 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea"
+git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.28"
+version = "0.3.29"
 
     [deps.LogExpFunctions.extensions]
     LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -1566,10 +1566,10 @@ version = "0.9.20"
     Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.ManifoldsBase]]
-deps = ["LinearAlgebra", "Markdown", "Printf", "Random", "Requires"]
-git-tree-sha1 = "2bddabebe8f7ec16cdd693ce8615fb5d3625af87"
+deps = ["LinearAlgebra", "Markdown", "Printf", "Random"]
+git-tree-sha1 = "57df0b7daa74bf82d3367702e133d936c28882ff"
 uuid = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb"
-version = "0.15.22"
+version = "0.15.23"
 
     [deps.ManifoldsBase.extensions]
     ManifoldsBasePlotsExt = "Plots"
@@ -1820,9 +1820,9 @@ version = "3.2.4+0"
 
 [[deps.OpenJpeg_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "libpng_jll"]
-git-tree-sha1 = "f4cb457ffac5f5cf695699f82c537073958a6a6c"
+git-tree-sha1 = "0a41c2d8e204a3ad713242139628e01a29556967"
 uuid = "643b3616-a352-519d-856d-80112ee9badc"
-version = "2.5.2+0"
+version = "2.5.3+0"
 
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -2116,8 +2116,8 @@ version = "1.11.0"
 [[deps.RQADeforestation]]
 deps = ["ArchGDAL", "ArgParse", "CairoMakie", "ConstructionBase", "Dates", "DimensionalData", "DiskArrayEngine", "DiskArrayTools", "DiskArrays", "Distances", "Distributed", "Distributions", "Extents", "FillArrays", "GDAL", "GeoFormatTypes", "Glob", "KML", "LoggingExtras", "Missings", "NetCDF", "Proj", "Rasters", "RecurrenceAnalysis", "Statistics", "StatsBase", "TimeseriesSurrogates", "UnicodePlots", "YAXArrayBase", "YAXArrays", "Zarr"]
 git-tree-sha1 = "797418ea1c3f97e67364d6bd61d2f48cb6b81c39"
-repo-rev = "main"
-repo-url = "https://github.com/EarthyScience/RQADeforestation.jl#a611912"
+repo-rev = "a611912"
+repo-url = "https://github.com/EarthyScience/RQADeforestation.jl"
 uuid = "3f1d9318-18cc-4ffd-9937-04025ce33b74"
 version = "1.0.0-DEV"
 
@@ -2415,9 +2415,9 @@ version = "1.11.0"
 
 [[deps.SpecialFunctions]]
 deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14"
+git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.4.0"
+version = "2.5.0"
 weakdeps = ["ChainRulesCore"]
 
     [deps.SpecialFunctions.extensions]

ogc-app-cwl/Project.toml

@@ -1,2 +1,6 @@
 [deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 RQADeforestation = "3f1d9318-18cc-4ffd-9937-04025ce33b74"
+YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"

ogc-app-cwl/fairsendd.cwl

@@ -0,0 +1,79 @@
+#!/usr/bin/env cwl-runner
+
+$graph:
+- class: Workflow
+  label: rqa
+  doc: FAIRSenDD Recurrence Analysis for Sentinel-1 based Deforestation Detection
+
+  inputs:
+    continent:
+      label: continent
+      doc: Continent ID within Equi7Grid. One of AF, AN, AS, EU, NA, OC, SA
+      type: string
+    in-dir:
+      label: in-dir
+      doc: Path to input directory containing Sentinel-1 Sigma0 tile data
+      type: Directory
+    tile:
+      label: tile
+      doc: tile ID of the area to be analyzed within Equi7Grid, e.g. E036N075T3
+      type: string
+
+  outputs:
+    out_cube:
+      doc: Path to output zarr data cube
+      type: Directory
+      outputSource: rqa/out_cube
+
+  steps:
+    rqa:
+      in:
+        continent: continent
+        in-dir: in-dir
+        tile: tile
+      run: '#cmd-rqa'
+      out:
+      - out_cube
+  id: rqa
+- class: CommandLineTool
+
+  requirements:
+    DockerRequirement:
+      dockerPull: danlooo/fairsendd:latest
+
+  inputs:
+    continent:
+      type: string
+      inputBinding:
+        position: 2
+    in-dir:
+      type: Directory
+      inputBinding:
+        position: 1
+    tile:
+      type: string
+      inputBinding:
+        position: 3
+
+  outputs:
+    out_cube:
+      type: Directory
+      outputBinding:
+        glob: out.zarr
+  id: cmd-rqa
+$namespaces:
+  edam: http://edamontology.org/
+  s: https://schema.org/
+$schemas:
+- https://schema.org/version/latest/schemaorg-current-https.rdf
+- http://edamontology.org/EDAM_1.18.owl
+cwlVersion: v1.2
+s:author:
+- class: s:Person
+  s:email: [email protected]
+  s:identifier: https://orcid.org/0000-0002-4024-4443
+  s:name: Daniel Loos
+s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
+s:codeRepository: https://github.com/EarthyScience/FAIRSenDD/
+s:dateCreated: '2024-10-28'
+s:license: https://spdx.org/licenses/Apache-2.0

ogc-app-cwl/run.jl

@@ -1,19 +1,14 @@
-#!/usr/bin/env -S julia --color=yes --startup-file=no --project=. --threads=auto
+#!/usr/bin/env -S julia --color=yes --startup-file=no --threads=auto
 
-using YAXArrays: YAXDefaults
+using Pkg
 using Glob: glob
+using YAXArrays: YAXDefaults
 using ArgParse
 using RQADeforestation: gdalcube, rqatrend
-using DimensionalData: (..)
+using DimensionalData
 using Dates: Date
 using Distributed: addprocs, @everywhere
 
-YAXDefaults.workdir[] = "/mnt/felix1/worldmap/data"
-exeflags = `--threads=10 --heap-size-hint=8G`
-#addprocs(4;exeflags)
-#@everywhere using YAXArrays, RQADeforestation
-
-
 function parse_commandline()
     s = ArgParseSettings()
 
@@ -36,6 +31,14 @@ function parse_commandline()
         help = "One of: Orbit number, 'A' for ascending, 'D' for descending, '*' for all orbits"
         default = "*"
 
+        "--out-dir", "-d"
+        help = "Path to output zarr dataset"
+        default = "out.zarr"
+
+        "in-dir"
+        help = "Path to input"
+        required = true
+
         "continent"
         help = "continent code for the tile to be processed"
         required = true
@@ -50,32 +53,52 @@ end
 
 function main()
     parsed_args = parse_commandline()
-    @info parsed_args
 
     pol = parsed_args["polarisation"]
     orbit = parsed_args["orbit"]
     thresh = parsed_args["threshold"]
 
-    indir = "/eodc/products/eodc.eu/S1_CSAR_IWGRDH/SIG0/"
+    indir = parsed_args["in-dir"]
+    readdir(indir) # check if inputdir is available
+
+    if isdir(indir) && isempty(indir)
+        @error "Input directory $indir must not be empty"
+    end
+
+    outdir = parsed_args["out-dir"]
+
+    if isdir(outdir)
+        @warn "Resume from existing output directory"
+    else
+        mkdir(outdir)
+        @info "Write output to $outdir"
+    end
+
+    YAXDefaults.workdir[] = outdir
+
     continent = parsed_args["continent"]
-    tilefolder = parsed_args["tile"]
-    folders = ["V01R01", "V0M2R4", "V1M0R1", "V1M1R1", "V1M1R2"]
+    tile = parsed_args["tile"]
 
-    filenamelist = [glob("$(sub)/*$(continent)*20M/$(tilefolder)/*$(pol)_$(orbit)*.tif", indir) for sub in folders]
-    allfilenames = collect(Iterators.flatten(filenamelist))
+    pattern = "V*R*/EQUI7_$continent*20M/$tile/*"
+    allfilenames = glob(pattern, indir) |> collect
+
+    if length(allfilenames) == 0
+        error("No input files found for given tile $tile")
+    end
 
     relorbits = unique([split(basename(x), "_")[5][2:end] for x in allfilenames])
     y = parsed_args["year"]
 
     for relorbit in relorbits
         filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
-        @time cube = gdalcube(filenames)
-        path = joinpath(YAXDefaults.workdir[], "$(tilefolder)_rqatrend_$(pol)_$(relorbit)_thresh_$(thresh)_year_$(y)")
+
+        cube = gdalcube(filenames)
+        path = joinpath(outdir, "$(tile)_rqatrend_$(pol)_$(relorbit)_thresh_$(thresh)_year_$(y)")
+
         ispath(path * ".done") && continue
         tcube = cube[Time=Date(y - 1, 7, 1) .. Date(y + 1, 7, 1)]
 
-        @time rqatrend(tcube; thresh, outpath=path * ".zarr", overwrite=true)
-        touch(path * ".done")
+        rqatrend(tcube; thresh, outpath=path * ".zarr", overwrite=true)
     end
 end
 

ogc-app-cwl/run.sh

@@ -1,5 +1,5 @@
 #! /usr/bin/env sh
 
-docker build . -t danlooo/cwl-example
-docker push danlooo/cwl-example
-cwltool example.cwl#add-numbers -a 1.2 -b 3.4
+docker build . -t danlooo/fairsendd
+# docker push danlooo/fairsendd
+cwltool fairsendd.cwl#rqa --continent NA --tile E036N075T3 --in-dir ../etc/data/eodc/products/eodc.eu/S1_CSAR_IWGRDH/SIG0/