First pass at SpecimenProcessing class

examples/combined/akc_cat.sh

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+#!/bin/bash
+
+# Check if the correct number of arguments is provided
+# This processes all of the JSON file in input_directory
+# and generates a single combined file. Lists at the top
+# level of the objects are merged across the files to 
+# create a single long list. There is an expected top level
+# object called AIRRKnowledgeCommons that contains the lists.
+# E.g. All AKC "investigations" across all of the AKC files
+# will be merged into a single "investigations" list.
+if [ "$#" -ne 2 ]; then
+  echo "Usage: $0 <input_directory> <output_file>"
+  exit 1
+fi
+
+# Read arguments
+JSON_DIR="$1"
+OUTPUT_FILE="$2"
+
+# Check if the input directory exists
+if [ ! -d "$JSON_DIR" ]; then
+  echo "Error: Directory $JSON_DIR does not exist."
+  exit 1
+fi
+
+# Check if the directory exists
+if [ ! -d "$JSON_DIR" ]; then
+  echo "Directory $JSON_DIR does not exist."
+  exit 1
+fi
+
+# Use jq to dynamically merge all top-level lists from AIRRKnowledgeCommons
+# Thanks to ChatGPT for the jq magic...
+jq -s '
+  reduce .[] as $item ({};
+    if $item.AIRRKnowledgeCommons then
+      reduce ($item.AIRRKnowledgeCommons | keys_unsorted)[] as $key (.;
+        if $item.AIRRKnowledgeCommons[$key] | type == "object" then
+          .[$key] += $item.AIRRKnowledgeCommons[$key]
+        elif $item.AIRRKnowledgeCommons[$key] | type == "array" then
+          .[$key] += ($item.AIRRKnowledgeCommons[$key] | map(.))
+        else
+          .
+        end
+      )
+    else
+      .
+    end
+  )' "$JSON_DIR"/*.json > "$OUTPUT_FILE"
+
+# Check if the operation succeeded
+if [ $? -eq 0 ]; then
+  echo "Combined lists written to $OUTPUT_FILE"
+else
+  echo "An error occurred while combining the files."
+fi
+