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roocs · Dec 4, 2023 · 314f060 · 314f060
1 parent 1cc0b62
commit 314f060
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Showing 2 changed files with 35 additions and 9 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -96,8 +96,9 @@ RUN    cd $tmp_install_dir                                 && \
 
 #RUN source activate $MINICONDA_PREFIX/bin/conda                          && \
 #    conda activate daops                                                 && \
-RUN  $MINICONDA_PREFIX/envs/daops/bin/pip uninstall roocs_utils -y                                         && \
-    $MINICONDA_PREFIX/envs/daops/bin/pip install roocs-utils@git+https://github.com/roocs/roocs-utils.git@i106-enable-read-kerchunk#egg=roocs_utils
+RUN $MINICONDA_PREFIX/envs/daops/bin/pip uninstall roocs_utils -y         && \
+    $MINICONDA_PREFIX/envs/daops/bin/pip install \
+    roocs-utils@git+https://github.com/roocs/roocs-utils.git@master#egg=roocs_utils
 
 # ==== Create a directory that we can bind-mount ====
 RUN mkdir /outputs
@@ -110,7 +111,7 @@ RUN rm -fr /var/lib/{apt,dpkg,cache,log}
 #COPY ./kc-script.py /tmp/kc-script.py
 #RUN $MINICONDA_PREFIX/envs/daops/bin/python /tmp/kc-script.py
 
-# ==== Run daops at the command-line ====
+# ==== Test run daops at the command-line ====
 RUN ROOCS_CONFIG=$config_file $MINICONDA_PREFIX/envs/daops/bin/daops subset --area 0,-10,120,40 \
   --time 2085-01-16/2120-12-16 --levels / --time-components year:2090,2091,2092 \
   --output-dir /tmp --file-namer simple cmip5.output1.MOHC.HadGEM2-ES.rcp85.mon.atmos.Amon.r1i1p1.latest.tas

diff --git a/app-package.cwl b/app-package.cwl
@@ -15,9 +15,18 @@ $graph:
       - class: ScatterFeatureRequirement
 
     inputs:
+      area:
+          doc: area
+          type: string
       time:
           doc: time
           type: string
+      time_components:
+          doc: time_components
+          type: string
+      levels:
+          doc: levels
+          type: string
       collection:
           doc: collection
           type: string
@@ -38,7 +47,10 @@ $graph:
       subset:
         run: "#clt"
         in:
+            area: area
             time: time
+            time_components: time_components
+            levels: levels
             collection: collection
             file_namer: file_namer
             output_dir: output_dir
@@ -53,8 +65,6 @@ $graph:
         envDef:  
            ROOCS_CONFIG: /root/roocs.ini
 #          PATH: /srv/conda/envs/env_crop/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-#          PYTHONPATH: /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: 1
 #        ramMax: 500Mb
@@ -65,25 +75,40 @@ $graph:
 
     arguments: []
     inputs:
+      area:
+        type: string
+        inputBinding:
+          prefix: --area
+          position: 1
       time:
         type: string
         inputBinding:
           prefix: --time
-          position: 1
+          position: 2
+      time_components:
+        type: string
+        inputBinding:
+          prefix: --time-components
+          position: 3
+      levels:
+        type: string
+        inputBinding:
+          prefix: --levels
+          position: 4
       file_namer:
         type: string
         inputBinding:
           prefix: --file-namer
-          position: 2
+          position: 5
       output_dir:
         type: string
         inputBinding:
           prefix: --output-dir
-          position: 3
+          position: 6
       collection:
         type: string
         inputBinding:
-          position: 4
+          position: 7
     outputs:
       results:
         outputBinding: