adds cloud native vs staged

.github/workflows/build.yaml

@@ -4,6 +4,7 @@ on:
     branches:
       - master
       - main
+      - bids23
 
     paths:
       # Only rebuild website when apps have changed
@@ -127,9 +128,14 @@ jobs:
       - run: yq -i eval '(.$graph[] | select (.id == "crop") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/crop:${{needs.version.outputs.app-version}}"' water-bodies/app-package.cwl 
       - run: yq -i eval '(.$graph[] | select (.id == "norm_diff") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/norm_diff:${{needs.version.outputs.app-version}}"' water-bodies/app-package.cwl 
       - run: yq -i eval '(.$graph[] | select (.id == "otsu") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/otsu:${{needs.version.outputs.app-version}}"' water-bodies/app-package.cwl 
-      - run: yq -i eval '(.$graph[] | select (.id == "stac") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/stac:${{needs.version.outputs.app-version}}"' water-bodies/app-package.cwl    
+      - run: yq -i eval '(.$graph[] | select (.id == "stac") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/stac:${{needs.version.outputs.app-version}}"' water-bodies/app-package.cwl 
+      - run: yq -i eval '(.$graph[] | select (.id == "crop") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/crop:${{needs.version.outputs.app-version}}"' water-bodies/app-package-cloud-native.cwl 
+      - run: yq -i eval '(.$graph[] | select (.id == "norm_diff") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/norm_diff:${{needs.version.outputs.app-version}}"' water-bodies/app-package-cloud-native.cwl
+      - run: yq -i eval '(.$graph[] | select (.id == "otsu") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/otsu:${{needs.version.outputs.app-version}}"' water-bodies/app-package-cloud-native.cwl
+      - run: yq -i eval '(.$graph[] | select (.id == "stac") ).hints.DockerRequirement.dockerPull = "ghcr.io/terradue/ogc-eo-application-package-hands-on/stac:${{needs.version.outputs.app-version}}"' water-bodies/app-package-cloud-native.cwl
       - run: mkdir downloads
       - run: cp water-bodies/app-package.cwl downloads/app-water-bodies.${{needs.version.outputs.app-version}}.cwl
+      - run: cp water-bodies/app-package-cloud-native.cwl downloads/app-water-bodies-cloud-native.${{needs.version.outputs.app-version}}.cwl
       - run: ls downloads/app-water-bodies.${{needs.version.outputs.app-version}}.cwl
       - uses: actions/upload-artifact@v2
         with: 
@@ -154,4 +160,13 @@ jobs:
           upload_url: ${{ steps.create_release.outputs.upload_url }}
           asset_path: downloads/app-water-bodies.${{needs.version.outputs.app-version}}.cwl
           asset_name: app-water-bodies.${{needs.version.outputs.app-version}}.cwl
+          asset_content_type: text/yaml
+      - name: upload linux artifact cloud native
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: downloads/app-water-bodies-cloud-native.${{needs.version.outputs.app-version}}.cwl
+          asset_name: app-water-bodies-cloud-native.${{needs.version.outputs.app-version}}.cwl
           asset_content_type: text/yaml

water-bodies/app-package-cloud-native.cwl

@@ -0,0 +1,264 @@
+cwlVersion: v1.0
+
+$namespaces:
+  s: https://schema.org/
+s:softwareVersion: 1.1.9
+schemas:
+- http://schema.org/version/9.0/schemaorg-current-http.rdf
+
+$graph:
+- class: Workflow
+
+  id: water_bodies
+  label: Water bodies detection based on NDWI and otsu threshold
+  doc: Water bodies detection based on NDWI and otsu threshold
+
+  requirements:
+  - class: ScatterFeatureRequirement
+  - class: SubworkflowFeatureRequirement
+
+  inputs:
+    aoi: 
+      label: area of interest
+      doc: area of interest as a bounding box
+      type: string
+    epsg:
+      label: EPSG code
+      doc: EPSG code 
+      type: string
+      default: "EPSG:4326"
+    stac_items:
+      label: Sentinel-2 STAC items
+      doc: list of Sentinel-2 COG STAC items
+      type: string[]
+
+  outputs:
+  - id: stac_catalog
+    outputSource:
+    - node_stac/stac_catalog
+    type: Directory
+
+  steps:
+    node_water_bodies:
+      run: "#detect_water_body"
+      in:
+        item: stac_items
+        aoi: aoi
+        epsg: epsg
+      out:
+      - detected_water_body
+      scatter: item
+      scatterMethod: dotproduct
+    node_stac:
+      run: "#stac"
+      in: 
+        item: stac_items
+        rasters:
+          source: node_water_bodies/detected_water_body
+      out:
+      - stac_catalog
+
+- class: Workflow
+
+  id: detect_water_body
+  label: Water body detection based on NDWI and otsu threshold
+  doc: Water body detection based on NDWI and otsu threshold
+
+  requirements:
+  - class: ScatterFeatureRequirement
+
+  inputs:
+    aoi: 
+      doc: area of interest as a bounding box
+      type: string
+    epsg:
+      doc: EPSG code 
+      type: string
+      default: "EPSG:4326"
+    bands: 
+      doc: bands used for the NDWI
+      type: string[]
+      default: ["green", "nir"]
+    item:
+      doc: STAC item
+      type: string
+
+  outputs:
+    - id: detected_water_body
+      outputSource: 
+      - node_otsu/binary_mask_item
+      type: File
+
+  steps:
+    node_crop:
+      run: "#crop"
+      in:
+        item: item
+        aoi: aoi
+        epsg: epsg
+        band: 
+          default: ["green", "nir"]
+      out:
+        - cropped
+      scatter: band
+      scatterMethod: dotproduct
+    node_normalized_difference:
+      run: "#norm_diff"
+      in: 
+        rasters: 
+          source: node_crop/cropped
+      out:
+      - ndwi
+    node_otsu:
+      run: "#otsu"
+      in:
+        raster:
+          source: node_normalized_difference/ndwi
+      out:
+        - binary_mask_item
+
+- class: CommandLineTool
+  id: crop
+
+  requirements:
+    InlineJavascriptRequirement: {}
+    EnvVarRequirement:
+      envDef: 
+        PATH: /srv/conda/envs/env_crop/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+        PYTHONPATH: /workspaces/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop:/home/jovyan/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop:/home/jovyan/water-bodies/command-line-tools/crop:/workspaces/vscode-binder/command-line-tools/crop
+        PROJ_LIB: /srv/conda/envs/env_crop/share/proj/
+    ResourceRequirement:
+      coresMax: 2
+      ramMax: 2028
+
+  hints:
+    DockerRequirement:
+      dockerPull: crop
+
+  baseCommand: ["python", "-m", "app"]
+  arguments: []
+  inputs:
+    item:
+      type: string
+      inputBinding:
+        prefix: --input-item
+    aoi:
+      type: string
+      inputBinding:
+        prefix: --aoi
+    epsg:
+      type: string  
+      inputBinding:
+        prefix: --epsg
+    band:
+      type: string  
+      inputBinding:
+        prefix: --band
+  outputs: 
+    cropped:
+      outputBinding:
+        glob: '*.tif'
+      type: File
+
+- class: CommandLineTool
+  id: norm_diff
+
+  requirements:
+    InlineJavascriptRequirement: {}
+    EnvVarRequirement:
+      envDef: 
+        PATH: /srv/conda/envs/env_norm_diff/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+        PYTHONPATH: /workspaces/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/norm_diff:/home/jovyan/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/norm_diff:/workspaces/vscode-binder/command-line-tools/norm_diff
+        PROJ_LIB: /srv/conda/envs/env_norm_diff/share/proj/
+    ResourceRequirement:
+      coresMax: 2
+      ramMax: 2028
+
+  hints:
+    DockerRequirement:
+      dockerPull: norm_diff
+
+  baseCommand: ["python", "-m", "app"]
+  arguments: []
+  inputs:
+    rasters:
+      type: File[]
+      inputBinding:
+        position: 1
+  outputs: 
+    ndwi:
+      outputBinding:
+        glob: '*.tif'
+      type: File
+
+- class: CommandLineTool
+  id: otsu
+
+  requirements:
+    InlineJavascriptRequirement: {}
+    EnvVarRequirement:
+      envDef: 
+        PATH: /srv/conda/envs/env_otsu/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+        PYTHONPATH: /workspaces/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/otsu:/home/jovyan/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/otsu:/workspaces/vscode-binder/command-line-tools/otsu
+        PROJ_LIB: /srv/conda/envs/env_otsu/share/proj/
+    ResourceRequirement:
+      coresMax: 2
+      ramMax: 2028
+
+  hints:
+    DockerRequirement:
+      dockerPull: otsu
+
+  baseCommand: ["python", "-m", "app"]
+  arguments: []
+  inputs:
+    raster:
+      type: File
+      inputBinding:
+        position: 1
+  outputs: 
+    binary_mask_item:
+      outputBinding:
+        glob: '*.tif'
+      type: File
+
+- class: CommandLineTool
+  id: stac
+
+  requirements:
+    InlineJavascriptRequirement: {}
+    EnvVarRequirement:
+      envDef: 
+        PATH: /srv/conda/envs/env_stac/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+        PYTHONPATH: /workspaces/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/stac:/home/jovyan/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/stac:/workspaces/vscode-binder/command-line-tools/stac
+        PROJ_LIB: /srv/conda/envs/env_stac/lib/python3.9/site-packages/rasterio/proj_data
+    ResourceRequirement:
+      coresMax: 2
+      ramMax: 2028
+
+  hints:
+    DockerRequirement:
+      dockerPull: stac
+
+  baseCommand: ["python", "-m", "app"]
+  arguments: []
+  inputs:
+    item:
+      type:
+        type: array
+        items: string
+        inputBinding:
+          prefix: --input-item
+
+    rasters:
+      type:
+        type: array
+        items: File
+        inputBinding:
+          prefix: --water-body
+
+  outputs: 
+    stac_catalog:
+      outputBinding:
+        glob: .
+      type: Directory

water-bodies/app-package.cwl

@@ -2,7 +2,7 @@ cwlVersion: v1.0
 
 $namespaces:
   s: https://schema.org/
-s:softwareVersion: 1.1.8
+s:softwareVersion: 1.1.9
 schemas:
 - http://schema.org/version/9.0/schemaorg-current-http.rdf
 
@@ -30,7 +30,7 @@ $graph:
     stac_items:
       label: Sentinel-2 STAC items
       doc: list of Sentinel-2 COG STAC items
-      type: string[]
+      type: Directory[]
 
   outputs:
   - id: stac_catalog
@@ -81,7 +81,7 @@ $graph:
       default: ["green", "nir"]
     item:
       doc: STAC item
-      type: string
+      type: Directory
 
   outputs:
     - id: detected_water_body
@@ -139,7 +139,7 @@ $graph:
   arguments: []
   inputs:
     item:
-      type: string
+      type: Directory
       inputBinding:
         prefix: --input-item
     aoi:

water-bodies/command-line-tools/crop/app.py

@@ -1,3 +1,4 @@
+import os
 import click
 from urllib.parse import urlparse
 from osgeo import gdal
@@ -42,6 +43,7 @@ def get_asset(item, common_name):
 def vsi_href(uri):
 
     parsed = urlparse(uri)
+
     if parsed.scheme.startswith("http"):
         return "/vsicurl/{}".format(uri)
     elif parsed.scheme.startswith("file"):
@@ -62,7 +64,7 @@ def vsi_href(uri):
 @click.option(
     "--input-item",
     "item_url",
-    help="STAC Item URL",
+    help="STAC Item URL or staged STAC catalog",
     required=True,
 )
 @click.option(
@@ -85,14 +87,18 @@ def vsi_href(uri):
 )
 def crop(item_url, aoi, band, epsg):
 
-    item = pystac.read_file(item_url)
+    if os.path.isdir(item_url):
+        catalog = pystac.read_file(os.path.join(item_url, "catalog.json"))
+        item = next(catalog.get_items())
+    else:
+        item = pystac.read_file(item_url)
 
     asset = get_asset(item, band)
 
     if not asset:
         raise ValueError(f"Common band name {band} not found in the assets")
 
-    asset_href = vsi_href(asset.href)
+    asset_href = vsi_href(asset.get_absolute_href())
 
     bbox = aoi2box(aoi)