testing strong types with cwl

cwl/GIS.yml

+cwlVersion: v1.2
+
+types:
+  - name: GeoTIFF
+    type: record  # Must be a record type
+    fields:
+      - name: file
+        type: File
+  - name: Shapefile
+    type: record
+    fields:
+      - name: shp
+        type: File
+        doc: "The main Shapefile (.shp)"
+      - name: shx
+        type: File
+        doc: "The shape index file (.shx)"
+      - name: dbf
+        type: File
+        doc: "The attribute data file (.dbf)"
+      - name: prj
+        type: File
+        doc: "The projection file (.prj)"
+      - name: cpg
+        type: File?
+        doc: "The character encoding file (.cpg) (optional)"
+      - name: qpj
+        type: File?
+        doc: "The additional projection file (.qpj) (optional)"
+

cwl/africapolis/test-job.json

 {
     "vector_input":{
         "class": "File",
-        "path": "/home/lolo/Documents/fishnet/data/samples/Corvara_IT.tiff",
+        "path": "/home/lolo/Documents/fishnet/data/samples/Corvara_IT.tiff"
     },
     "config":{
         "class":"File",

cwl/fishnet/2788f2d4bc612df66c3f8b81bec53ca805ed197c

+{
+    "config": {
+        "analysis-output-stem": "Analysis",
+        "binary-filters": [
+            {
+                "name": "InsidePolygonFilter"
+            }
+        ],
+        "centrality-measures": [
+            {
+                "name": "DegreeCentrality"
+            },
+            {
+                "name": "MeanLocalSignificance"
+            },
+            {
+                "name": "SmallerNeighboursRatio"
+            }
+        ],
+        "cleanup": true,
+        "concurrent-runs": true,
+        "contraction-output-stem": "Contraction",
+        "contraction-predicates": [
+            {
+                "distance": 500.0,
+                "name": "DistanceBiPredicate"
+            }
+        ],
+        "executor": {
+            "cwl-directory": "/home/lolo/Documents/fishnet/cwl/sda",
+            "flags": "--quiet --no-container",
+            "name": "CWLTOOL"
+        },
+        "hardware-concurrency": 0,
+        "last-job-type": "MERGE",
+        "maxDistanceMeters": 3000.0,
+        "maxNeighbours": 5,
+        "memgraph-host": "localhost",
+        "memgraph-port": 7687,
+        "merge-workers": 2,
+        "neighbouring-files-predicate": "WSF",
+        "neighbouring-predicates": [],
+        "splits": 0,
+        "unary-filters": [
+            {
+                "name": "ApproxAreaFilter",
+                "requiredArea": 5000.0
+            }
+        ],
+        "visualize-edges": true
+    },
+    "duration[s]": 0.032306679,
+    "input": "Corvara_IT.shp",
+    "output": "Corvara_IT_filtered.shp",
+    "polygon count": 26,
+    "type": "FILTER"
+}

cwl/fishnet/Corvara_IT_filtered.prj

+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
\ No newline at end of file

cwl/fishnet/filter.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand: [SettlementDelineationFilter]
+requirements: 
+  InlineJavascriptRequirement: {}
+inputs:
+  gisFile:
+    type: 
+      - $import: ../GIS.yml#GeoTIFF
+      - $import: ../GIS.yml#Shapefile
+    inputBinding:
+      position: 1
+      prefix: --input
+      valueFrom: $(self.file)  # Correctly reference the GeoTIFF file
+
+  config:
+    type: File
+    doc: "Configuration file for filter process"
+    inputBinding:
+      prefix: --config
+      position: 2
+
+outputs:
+  standardOut:
+    type: stdout
+  errorOut:
+    type: stderr
+  outFile:
+    type: ../GIS.yml#Shapefile
+    outputBinding:
+      glob: "*_filtered.shp"  # Ensure we find the shapefile output
+      outputEval: |
+        ${  
+          if (self.length === 0) {
+            throw new Error("No filtered shapefile found.");
+          }
+          
+          var shpFile = self[0];  // The matched .shp file
+          var baseName = shpFile.nameroot;  // Remove .shp extension
+
+          return {
+            "shp": shpFile,
+            "shx": self.find(function(f) { return f.basename === baseName + ".shx"; }) || null,
+            "dbf": self.find(function(f) { return f.basename === baseName + ".dbf"; }) || null,
+            "prj": self.find(function(f) { return f.basename === baseName + ".prj"; }) || null,
+            "cpg": self.find(function(f) { return f.basename === baseName + ".cpg"; }) || null,
+            "qpj": self.find(function(f) { return f.basename === baseName + ".qpj"; }) || null
+          };
+        }
+
+
+stderr: Filter_stderr.log

cwl/fishnet/test-filter.json

+{
+    "gisFile":{
+        "class": "GeoTIFF",
+        "file":{
+            "class": "File",
+            "path": "/home/lolo/Documents/fishnet/data/samples/Corvara_IT.tiff"
+        }
+    },
+    "config":{
+        "class":"File",
+        "path": "/home/lolo/Documents/fishnet/prod/local/sda-workflow-local.json"
+    }
+}
\ No newline at end of file

cwl/types/Shapefile.cwl

-cwlVersion: v1.2
-name: Shapefile
-type: record
-fields:
-  - name: shp
-    type: File
-    doc: "The main Shapefile (.shp)"
-  - name: shx
-    type: File
-    doc: "The shape index file (.shx)"
-  - name: dbf
-    type: File
-    doc: "The attribute data file (.dbf)"
-  - name: prj
-    type: File
-    doc: "The projection file (.prj)"
-  - name: cpg
-    type: File?
-    doc: "The character encoding file (.cpg) (optional)"
-  - name: qpj
-    type: File?
-    doc: "The additional projection file (.qpj) (optional)"