Merge pull request #99 from FredHutch/44-same-json-use-by-multiple-tasks

44 same json use by multiple tasks

jsonTaskOrderTest/README.md

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+# Unit Test for JSON Input Handling & Task Order (jsonTaskOrderTest)
+
+## Overview
+
+The `jsonTaskOrderTest` workflow is a unit test designed to validate the behavior of JSON input handling in WDL (Workflow Description Language). It ensures that a JSON input string is correctly passed and utilized by multiple tasks while maintaining the correct execution order due to the second task's dependency on the output of the first task.
+
+## Purpose
+
+This workflow serves as a test case for:
+- Ensuring that the same JSON input is correctly used by multiple tasks.
+- Verifying that task execution order is strictly maintained.
+- Ensuring that Task 2 does not execute before Task 1 completes.
+- Validating proper dependency resolution between tasks.
+
+## Workflow Components
+
+### Workflow: `JsonOrderTest`
+
+This workflow consists of two tasks designed to test JSON input sharing and execution order.
+
+#### Inputs:
+- `input_json`: A JSON string used as input by both tasks.
+
+#### Outputs:
+- `task1_output`: Metadata file output from the `Task1` task.
+- `task2_output`: Metadata file output from the `Task2` task.
+
+### Tasks
+
+#### Task: `Task1`
+- **Purpose**: Reads and processes the JSON input.
+- **Operation**:
+  - Writes the JSON input to an output file.
+  - Confirms Task 1 execution by appending a success message.
+
+#### Task: `Task2`
+- **Purpose**: Uses the same JSON input but depends on `Task1`.
+- **Operation**:
+  - Waits for `Task1` to complete.
+  - Reads the same JSON input and appends `Task1`'s output to its own result file.
+
+### Expected Output Files
+
+- **Task1 Output (`task1_output.txt`)**
+  ```
+  Processing JSON in Task1: {"I am the text that from input.json"}
+  Task1 completed
+  ```
+
+- **Task2 Output (`task2_output.txt`)**
+  ```
+  Processing JSON in Task2: {"I am the text that from input.json"}
+  Task2 completed after Task1
+  Processing JSON in Task1: {"I am the text that from input.json"}
+  Task1 completed
+  ```
+
+## Version
+- **WDL Version**: 1.0
+
+## Additional Notes
+- This workflow demonstrates how multiple tasks can share the same JSON input while maintaining execution order.
+- The `Task2` execution is dependent on `Task1` completing successfully.
+- The unit test confirms that JSON input is processed consistently across tasks.
+- Any deviation in execution order or missing outputs indicates a failure in dependency resolution.
+

jsonTaskOrderTest/inputs.json

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+{
+  "jsonTaskOrderTest.input_json": "I am the text that from input.json"
+}

jsonTaskOrderTest/jsonTaskOrderTest.wdl

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+version 1.0
+
+workflow jsonTaskOrderTest {
+  input {
+    String input_json  # JSON string used as input for both tasks
+  }
+
+  call Task1 { input: input_json = input_json }
+  call Task2 { input: input_json = input_json, previous_output = Task1.output_file }
+
+  output {
+    File task1_output = Task1.output_file
+    File task2_output = Task2.output_file
+  }
+}
+
+task Task1 {
+  input {
+    String input_json
+  }
+
+  command <<<
+    echo "Processing JSON in Task1: ~{input_json}" > task1_output.txt
+    echo "Task1 completed" >> task1_output.txt
+  >>>
+
+  output {
+    File output_file = "task1_output.txt"
+  }
+
+  runtime {
+    cpu: 1
+    memory: "2G"
+  }
+}
+
+task Task2 {
+  input {
+    String input_json
+    File previous_output
+  }
+
+  command <<<
+    echo "Processing JSON in Task2: ~{input_json}" > task2_output.txt
+    echo "Task2 completed after Task1" >> task2_output.txt
+    cat ~{previous_output} >> task2_output.txt
+  >>>
+
+  output {
+    File output_file = "task2_output.txt"
+  }
+
+  runtime {
+    cpu: 1
+    memory: "2G"
+  }
+}

jsonTaskOrderTest/options.json

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+{
+    "workflow_failure_mode": "ContinueWhilePossible",
+    "write_to_cache": false,
+    "read_from_cache": false
+}