From cb2655b833e001e993be30d7e0419b428455345f Mon Sep 17 00:00:00 2001
From: Fabrice Brito <fabrice.brito@terradue.com>
Date: Thu, 2 Nov 2023 08:38:27 +0100
Subject: [PATCH] ls9 exec

---
 docs/cwl-workflow/exec-stage-in.md | 68 +++++++++++++++++++++++++++++-
 docs/cwl-workflow/stage-in.md      |  2 +-
 scripts/exec-app-water-body.sh     | 11 +++++
 3 files changed, 78 insertions(+), 3 deletions(-)
 create mode 100644 scripts/exec-app-water-body.sh

diff --git a/docs/cwl-workflow/exec-stage-in.md b/docs/cwl-workflow/exec-stage-in.md
index 3ddd01b..f994250 100644
--- a/docs/cwl-workflow/exec-stage-in.md
+++ b/docs/cwl-workflow/exec-stage-in.md
@@ -43,18 +43,82 @@ scripts/cwl-cli-stage-in-released.sh
 sh ${WORKSPACE}/scripts/cwl-cli-stage-in-released.sh
 ```
 
+The expected content after this step is:
+
+```bash
+(base) jovyan@coder-fbrito:~/runs$ tree
+.
+├── app-water-body.1.0.0.cwl
+├── lwft9j0o
+│   ├── LC09_L2SP_042033_20231015_02_T1
+│   │   ├── LC09_L2SP_042033_20231015_02_T1.json
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ANG.txt
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_MTL.json
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_MTL.txt
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_MTL.xml
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_QA_PIXEL.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_QA_RADSAT.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B1.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B2.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B3.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B4.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B5.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B6.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_B7.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_SR_QA_AEROSOL.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_ATRAN.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_B10.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_CDIST.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_DRAD.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_EMIS.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_EMSD.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_QA.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_TRAD.TIF
+│   │   ├── LC09_L2SP_042033_20231015_20231016_02_T1_ST_URAD.TIF
+│   │   ├── preview.png
+│   │   └── tilejson.json
+│   ├── catalog.json
+│   └── stage.py
+└── staged.json
+
+2 directories, 30 files
+```
+
 The result is redirected to a file named `staged.json` as we use `jq` to get the path of the staged product:
 
 ```bash title="terminal"
-cat staged.json | jq -r .staged
+cat staged.json | jq -r .staged.path
 ```
 
 This returns a path like `/workspace/runs/921x91vw`
 
 ### Step 4 - Execute the Application Package
 
+Use `cwltool` to run the application package using the staged Landsat-9 acquisition:
+
 ```bash linenums="1" hl_lines="5"
 --8<--
-scripts/cwl-workflow-staged.sh
+scripts/exec-app-water-body.sh
 --8<--
+```
+
+```
+sh ${WORKSPACE}/scripts/exec-app-water-body.sh
+```
+
+### Expected outcome
+
+The folder `/workspace/runs` contains: 
+
+``` hl_lines="3"
+(base) jovyan@coder-fbrito:~/runs$ tree .
+/workspace/runs/
+├── app-water-body-cloud-native.1.0.0.cwl
+└── cmtriamc
+    ├── S2B_10TFK_20210713_0_L2A
+    │   ├── S2B_10TFK_20210713_0_L2A.json
+    │   └── otsu.tif
+    └── catalog.json
+
+2 directories, 4 files
 ```
\ No newline at end of file
diff --git a/docs/cwl-workflow/stage-in.md b/docs/cwl-workflow/stage-in.md
index 1d45ac5..b064327 100644
--- a/docs/cwl-workflow/stage-in.md
+++ b/docs/cwl-workflow/stage-in.md
@@ -58,7 +58,7 @@ scripts/cwl-cli-stage-in.sh
 The result is redirected to a file named `staged.json` as we use `jq` to get the path of the staged product:
 
 ```bash title="terminal"
-cat staged.json | jq -r .staged
+cat staged.json | jq -r .staged.path
 ```
 
 This returns a path like `/workspace/runs/921x91vw`
\ No newline at end of file
diff --git a/scripts/exec-app-water-body.sh b/scripts/exec-app-water-body.sh
new file mode 100644
index 0000000..caae5c7
--- /dev/null
+++ b/scripts/exec-app-water-body.sh
@@ -0,0 +1,11 @@
+version="1.0.0"
+
+cwltool \
+    --podman \
+    --outdir /workspace/runs \
+    /workspace/runs/app-water-body.${version}.cwl \
+    --item $( cat staged.json | jq -r .staged.path ) \
+    --aoi="-118.985,38.432,-118.183,38.938" \
+    --epsg "EPSG:4326" \
+    --bands green \
+    --bands nir08
\ No newline at end of file