adds local paths

docs/cwl-cli/crop.md

@@ -1,6 +1,6 @@
 
 
-```yaml linenums="1" hl_lines="9-12 49-53" title="file: crop.cwl"
+```yaml linenums="1" hl_lines="9-12 49-53" title="cwl-cli/crop.cwl"
 --8<--
 cwl-cli/crop.cwl
 --8<--
@@ -16,7 +16,7 @@ Or
 
 ```yaml title="crop-params.yaml"
 --8<--
-docs/cwl-cli/crop-params.yaml
+cwl-cli/crop-params.yaml
 --8<--
 ```
 

docs/cwl-cli/norm-diff.md

@@ -1,6 +1,6 @@
 
 
-```yaml linenums="1" hl_lines="9-12 49-53"
+```yaml linenums="1" hl_lines="9-12 49-53" title="cwl-cli/norm-diff.cwl"
 --8<--
 cwl-cli/norm-diff.cwl
 --8<--

scripts/build-stage-container.sh

@@ -1,5 +1,7 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+
 podman \
     build \
     --format docker \
     -t localhost/stage:latest \
-    ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/stage-in
+    ${WORKSPACE}/water-bodies/command-line-tools/stage-in

scripts/build_containers.sh

@@ -1,4 +1,9 @@
-podman build --format docker -t localhost/crop:latest ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop
-podman build --format docker -t localhost/norm-diff:latest ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/norm_diff
-podman build --format docker -t localhost/otsu:latest ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/otsu
-podman build --format docker -t localhost/stac:latest ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/stac
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
+podman build --format docker -t localhost/crop:latest ${WORKSPACE}/water-bodies/command-line-tools/crop
+podman build --format docker -t localhost/norm-diff:latest ${WORKSPACE}/water-bodies/command-line-tools/norm_diff
+podman build --format docker -t localhost/otsu:latest ${WORKSPACE}/water-bodies/command-line-tools/otsu
+podman build --format docker -t localhost/stac:latest ${WORKSPACE}/water-bodies/command-line-tools/stac

scripts/build_containers_gh.sh

@@ -1,27 +1,13 @@
-podman build --format docker -t ghcr.io/terradue/ogc-eo-application-package-hands-on/crop:bids23 ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/crop
-podman push ghcr.io/terradue/ogc-eo-application-package-hands-on/crop:bids23
-
-podman build --format docker -t ghcr.io/terradue/ogc-eo-application-package-hands-on/norm-diff:bids23 ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/norm_diff
-podman push ghcr.io/terradue/ogc-eo-application-package-hands-on/norm:bids23
-
-podman build --format docker -t ghcr.io/terradue/ogc-eo-application-package-hands-on/otsu:bids23 ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/otsu
-podman push ghcr.io/terradue/ogc-eo-application-package-hands-on/otsu:bids23
-
-podman build --format docker -t ghcr.io/terradue/ogc-eo-application-package-hands-on/stac:bids23 ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/stac
-podman push ghcr.io/terradue/ogc-eo-application-package-hands-on/stac:bids23
-
-
-yq eval '(.$graph[] | select (.id == "crop") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/crop:aaa"' /workspace/mastering-app-package-/cwl-workflow/app-water-bodies-cloud-native.cwl
-
-WORKSPACE=/workspace
+WORKSPACE=/workspace/app-package-training-bids23
 
 version="bids23"
-repo="ghcr.io/terradue/ogc-eo-application-package-hands-on"
+repo="ghcr.io/terradue/${REPO}"
+
 for step in crop norm_diff otsu stac
 do
     tag=${repo}/${step}:${version}
-    podman build --format docker -t ${tag} ${WORKSPACE}/mastering-app-package-/water-bodies/command-line-tools/crop
+    podman build --format docker -t ${tag} ${WORKSPACE}/water-bodies/command-line-tools/crop
     podman push ${tag}
 
-    t="$tag" s="$step" yq eval -i '(.$graph[] | select (.id == env(s)) ).hints.DockerRequirement.dockerPull = env(t)' /workspace/mastering-app-package-/cwl-workflow/app-water-bodies-cloud-native.cwl
+    t="$tag" s="$step" yq eval -i '(.$graph[] | select (.id == env(s)) ).hints.DockerRequirement.dockerPull = env(t)' ${WORKSPACE}/cwl-workflow/app-water-bodies-cloud-native.cwl
 done

scripts/crop_green.sh

@@ -1,5 +1,10 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
 python \
-    ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop/app.py \
+    ${WORKSPACE}/water-bodies/command-line-tools/crop/app.py \
     --input-item "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --aoi "-121.399,39.834,-120.74,40.472" \
     --epsg "EPSG:4326" \

scripts/crop_nir.sh

@@ -1,5 +1,10 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
 python \
-    ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop/app.py \
+    ${WORKSPACE}/water-bodies/command-line-tools/crop/app.py \
     --input-item "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --aoi "-121.399,39.834,-120.74,40.472" \
     --epsg "EPSG:4326" \

scripts/cwl-cli-crop-green.sh

@@ -1,7 +1,9 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    crop.cwl \
+    ${WORKSPACE}/cwl-cli/crop.cwl \
     --item "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --aoi="-121.399,39.834,-120.74,40.472" \
     --epsg "EPSG:4326" \

scripts/cwl-cli-norm-diff.sh

@@ -1,7 +1,9 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    norm_diff.cwl \
+    ${WORKSPACE}/cwl-cli/norm_diff.cwl \
     --rasters \
     /workspace/runs/crop_green.tif \
     --rasters \

scripts/cwl-cli-otsu.sh

@@ -1,6 +1,6 @@
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    otsu.cwl \
+    ${WORKSPACE}/cwl-cli/otsu.cwl \
     --raster \
     /workspace/runs/norm_diff.tif

scripts/cwl-cli-stac.sh

@@ -1,7 +1,7 @@
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    stac.cwl \
+    ${WORKSPACE}/cwl-cli/stac.cwl \
     --item \
     "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --rasters \

scripts/cwl-cli-stage-in.sh

@@ -3,6 +3,6 @@ ls9_ref="https://planetarycomputer.microsoft.com/api/stac/v1/collections/landsat
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    stage-in.cwl \
+    ${WORKSPACE}/cwl-cli/stage-in.cwl \
     --reference \
     ${ls9_ref} > staged.json

scripts/cwl-cli-stage-out.sh

@@ -1,6 +1,6 @@
 cwltool \
     --podman \
-    stage-out.cwl \
+    ${WORKSPACE}/cwl-cli/stage-out.cwl \
     --aws_access_key_id $( cat ~/.aws/credentials | grep aws_access_key_id | cut -d "=" -f 2 ) \
     --aws_secret_access_key $( cat ~/.aws/credentials | grep aws_secret_access_key | cut -d "=" -f 2 ) \
     --endpoint_url $( cat ~/.aws/config | grep endpoint_url | head -n 1 | cut -d "=" -f 2 ) \

scripts/cwl-workflow-cloud-native-scatter.sh

@@ -1,8 +1,10 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+
 cwltool \
     --podman \
     --parallel \
     --outdir /workspace/runs \
-    app-water-bodies-cloud-native.cwl \
+    ${WORKSPACE}/cwl-workflow/app-water-bodies-cloud-native.cwl \
     --stac_items "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --stac_items "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2A_10TFK_20220524_0_L2A" \
     --aoi="-121.399,39.834,-120.74,40.472" \

scripts/cwl-workflow-cloud-native.sh

@@ -1,7 +1,7 @@
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    app-water-body-cloud-native.cwl \
+    ${WORKSPACE}/cwl-workflow/app-water-body-cloud-native.cwl \
     --item "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --aoi="-121.399,39.834,-120.74,40.472" \
     --epsg "EPSG:4326"

scripts/cwl-workflow-staged.sh

@@ -1,7 +1,7 @@
 cwltool \
     --podman \
     --outdir /workspace/runs \
-    cwl-workflow/app-water-body.cwl \
+    ${WORKSPACE}/cwl-workflow/cwl-workflow/app-water-body.cwl \
     --item $( cat staged.json | jq -r .staged.path ) \
     --aoi="-118.985,38.432,-118.183,38.938" \
     --epsg "EPSG:4326" \

scripts/cwltool-scripted-execution.py

@@ -32,7 +32,7 @@ def get_job_order():
     podman=True,
     parallel=True,
     outdir="/workspace/runs",
-    workflow=f"/workspace/mastering-app-package-/app-water-bodies-cloud-native.{version}.cwl#water_bodies",
+    workflow=f"/workspace/app-package-training-bids23/app-water-bodies-cloud-native.{version}.cwl#water_bodies",
     job_order=get_job_order(),
 )
 

scripts/download-cwl.sh

@@ -1,3 +1,3 @@
 version="1.4.1"
 
-wget https://github.com/Terradue/ogc-eo-application-package-hands-on/releases/download/$version/app-water-bodies-cloud-native.$version.cwl
+wget https://github.com/Terradue/app-package-training-bids23/releases/download/$version/app-water-bodies-cloud-native.$version.cwl

scripts/norm_diff.sh

@@ -1,4 +1,9 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
 python \
-    ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/norm_diff/app.py \
+    ${WORKSPACE}/water-bodies/command-line-tools/norm_diff/app.py \
     crop_green.tif \
     crop_nir.tif

scripts/otsu.sh

@@ -1,3 +1,8 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
 python \
-    ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/otsu/app.py \
+    ${WORKSPACE}/water-bodies/command-line-tools/otsu/app.py \
     norm_diff.tif

scripts/setup.sh

@@ -1,4 +1,4 @@
-export WORKSPACE=/workspace
+export WORKSPACE=/workspace/app-package-training-bids23
 export RUNTIME=/workspace/runs
 mkdir -p ${RUNTIME}
 cd ${RUNTIME}

scripts/stac.sh

@@ -1,4 +1,9 @@
+export WORKSPACE=/workspace/app-package-training-bids23
+export RUNTIME=/workspace/runs
+mkdir -p ${RUNTIME}
+cd ${RUNTIME}
+
 python \
-    ${WORKSPACE}/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/stac/app.py \
+    ${WORKSPACE}/water-bodies/command-line-tools/stac/app.py \
     --input-item "https://earth-search.aws.element84.com/v0/collections/sentinel-s2-l2a-cogs/items/S2B_10TFK_20210713_0_L2A" \
     --water-body otsu.tif