From 970f4bf2335ffc05d1b8e841da88f4fb14fa08db Mon Sep 17 00:00:00 2001
From: Daniel Loos <dloos@bgc-jena.mpg.de>
Date: Wed, 11 Dec 2024 16:47:18 +0100
Subject: [PATCH] Update cwl directory output

---
 ogc-app-cwl/fairsendd.cwl | 18 ++++++++++++++----
 ogc-app-cwl/run.jl        | 36 ++++++++++++++++++++++++++++--------
 ogc-app-cwl/run.sh        |  7 ++-----
 3 files changed, 44 insertions(+), 17 deletions(-)
 mode change 100644 => 100755 ogc-app-cwl/fairsendd.cwl

diff --git a/ogc-app-cwl/fairsendd.cwl b/ogc-app-cwl/fairsendd.cwl
old mode 100644
new mode 100755
index 76784f3..48ad287
--- a/ogc-app-cwl/fairsendd.cwl
+++ b/ogc-app-cwl/fairsendd.cwl
@@ -10,6 +10,10 @@ $graph:
       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
@@ -18,13 +22,14 @@ $graph:
   outputs:
     out_cube:
       doc: Path to output zarr data cube
-      type: File
+      type: Directory
       outputSource: rqa/out_cube
 
   steps:
     rqa:
       in:
         continent: continent
+        in-dir: in-dir
         tile: tile
       run: '#cmd-rqa'
       out:
@@ -35,21 +40,26 @@ $graph:
   requirements:
     DockerRequirement:
       dockerPull: danlooo/fairsendd:latest
-    InlineJavascriptRequirement: {}
 
   inputs:
     continent:
       type: string
+      inputBinding:
+        position: 2
+    in-dir:
+      type: Directory
       inputBinding:
         position: 1
     tile:
       type: string
       inputBinding:
-        position: 2
+        position: 3
 
   outputs:
     out_cube:
-      type: stdout
+      type: Directory
+      outputBinding:
+        glob: out.zarr
   id: cmd-rqa
 $namespaces:
   edam: http://edamontology.org/
diff --git a/ogc-app-cwl/run.jl b/ogc-app-cwl/run.jl
index 8233792..5281dc1 100755
--- a/ogc-app-cwl/run.jl
+++ b/ogc-app-cwl/run.jl
@@ -5,7 +5,7 @@ using Glob: glob
 using YAXArrays: YAXDefaults
 using ArgParse
 using RQADeforestation: gdalcube, rqatrend
-using DimensionalData: (..)
+using DimensionalData
 using Dates: Date
 using Distributed: addprocs, @everywhere
 
@@ -35,6 +35,10 @@ function parse_commandline()
         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
@@ -54,18 +58,33 @@ function main()
     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
-    println(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"]
@@ -74,7 +93,8 @@ function main()
         filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
 
         cube = gdalcube(filenames)
-        path = joinpath(outdir, "$(tilefolder)_rqatrend_$(pol)_$(relorbit)_thresh_$(thresh)_year_$(y)")
+        path = joinpath(outdir, "$(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)]
 
diff --git a/ogc-app-cwl/run.sh b/ogc-app-cwl/run.sh
index 6ce25e5..99feaab 100755
--- a/ogc-app-cwl/run.sh
+++ b/ogc-app-cwl/run.sh
@@ -1,8 +1,5 @@
 #! /usr/bin/env sh
 
 docker build . -t danlooo/fairsendd
-docker push danlooo/fairsendd
-
-cwltool fairsendd.cwl#rqa --continent AF --tile E036N075T3
-docker run danlooo/fairsendd AF E036N075T3
-docker run --env=HOME=/tmp/YgEokx --user 1234:1234 danlooo/fairsendd AF E036N075T3
\ No newline at end of file
+# docker push danlooo/fairsendd
+cwltool fairsendd.cwl#rqa --continent NA --tile E036N075T3 --in-dir ../etc/data/eodc/products/eodc.eu/S1_CSAR_IWGRDH/SIG0/ 
\ No newline at end of file