chore: more file tests for task evaluation.

These test cases come directly from the 1.2 WDL specification.

wdl-engine/tests/tasks/change-extension-task/files/foo.data

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+data

wdl-engine/tests/tasks/change-extension-task/files/foo.index

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+index

wdl-engine/tests/tasks/change-extension-task/inputs.json

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+{
+    "change_extension.prefix": "foo"
+}

wdl-engine/tests/tasks/change-extension-task/outputs.json

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+{
+  "change_extension.data_file": "work/foo.data",
+  "change_extension.data": "data",
+  "change_extension.index": "index"
+}

wdl-engine/tests/tasks/change-extension-task/source.wdl

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+version 1.2
+
+task change_extension {
+  input {
+    String prefix
+  }
+
+  command <<<
+    printf "data" > '~{prefix}.data'
+    printf "index" > '~{prefix}.index'
+  >>>
+
+  output {
+    File data_file = "~{prefix}.data"
+    String data = read_string(data_file)
+    String index = read_string(sub(data_file, "\\.data$", ".index"))
+  }
+
+  requirements {
+    container: "ubuntu:latest"
+  }
+}

wdl-engine/tests/tasks/file-sizes-task/error.txt

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+error: type mismatch: argument to function `size` expects type `None`, `File?`, `String?`, `Directory?`, or `X` where `X`: any compound type that recursively contains a `File` or `Directory`, but found type `Map[String, Pair[Int, String?]]`
+   ┌─ tests/tasks/file-sizes-task/source.wdl:14:31
+   │  
+14 │       Float nested_bytes = size({
+   │ ╭───────────────────────────────^
+15 │ │       "a": (10, "created_file"),
+16 │ │       "b": (50, missing_file)
+17 │ │     })
+   │ ╰─────^ this is type `Map[String, Pair[Int, String?]]`
+

wdl-engine/tests/tasks/file-sizes-task/files/created_file

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+this file is 22 bytes

wdl-engine/tests/tasks/file-sizes-task/inputs.json

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+{}

wdl-engine/tests/tasks/file-sizes-task/outputs.json

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+{
+  "file_sizes.created_file": "work/created_file",
+  "file_sizes.missing_file_bytes": 0.0,
+  "file_sizes.created_file_bytes": 22.0,
+  "file_sizes.multi_file_kb": 0.022,
+  "file_sizes.nested_bytes": 22.0
+}

wdl-engine/tests/tasks/file-sizes-task/source.wdl

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+version 1.2
+
+task file_sizes {
+  command <<<
+    printf "this file is 22 bytes\n" > created_file
+  >>>
+
+  File? missing_file = None
+
+  output {
+    File created_file = "created_file"
+    Float missing_file_bytes = size(missing_file)
+    Float created_file_bytes = size(created_file, "B")
+    Float multi_file_kb = size([created_file, missing_file], "K")
+    Float nested_bytes = size({
+      "a": (10, created_file),
+      "b": (50, missing_file)
+    })
+  }
+
+  requirements {
+    container: "ubuntu:latest"
+  }
+}

wdl-engine/tests/tasks/test-basename/inputs.json

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+{}

wdl-engine/tests/tasks/test-basename/outputs.json

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+{
+  "test_basename.is_true1": true,
+  "test_basename.is_true2": true,
+  "test_basename.is_true3": true
+}

wdl-engine/tests/tasks/test-basename/source.wdl

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+version 1.2
+
+task test_basename {
+  command <<<>>>
+
+  output {
+    Boolean is_true1 = basename("/path/to/file.txt") == "file.txt"
+    Boolean is_true2 = basename("/path/to/file.txt", ".txt") == "file"
+    Boolean is_true3 = basename("/path/to/dir") == "dir" 
+  }
+}

wdl-engine/tests/tasks/test-ceil/inputs.json

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+{
+    "test_ceil.i1": 2
+}

wdl-engine/tests/tasks/test-ceil/outputs.json

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+{
+  "test_ceil.all_true": [
+    true,
+    true
+  ]
+}

wdl-engine/tests/tasks/test-ceil/source.wdl

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+version 1.2
+
+task test_ceil {
+  input {
+    Int i1
+  }
+
+  Int i2 = i1 + 1
+  Float f1 = i1
+  Float f2 = i1 + 0.1
+
+  command <<<>>>
+
+  output {
+    Array[Boolean] all_true = [ceil(f1) == i1, ceil(f2) == i2]
+  }
+}

wdl-engine/tests/tasks/test-find/inputs.json

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+{}

wdl-engine/tests/tasks/test-find/outputs.json

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+{
+  "find_string.match1": "ello",
+  "find_string.match2": null
+}

wdl-engine/tests/tasks/test-find/source.wdl

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+version 1.2
+
+task find_string {
+  input {
+    String in = "hello world"
+    String pattern1 = "e..o"
+    String pattern2 = "goodbye"
+  }
+
+  command <<<>>>
+
+  output {
+    String? match1 = find(in, pattern1)  # "ello"
+    String? match2 = find(in, pattern2)  # None
+  }
+}

wdl-engine/tests/tasks/test-floor/inputs.json

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+{
+    "test_floor.i1": 2
+}

wdl-engine/tests/tasks/test-floor/outputs.json

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+{
+  "test_floor.all_true": [
+    true,
+    true
+  ]
+}

wdl-engine/tests/tasks/test-floor/source.wdl

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+version 1.2
+
+task test_floor {
+  input {
+    Int i1
+  }
+
+  Int i2 = i1 - 1
+  Float f1 = i1
+  Float f2 = i1 - 0.1
+
+  command <<<>>>
+
+  output {
+    Array[Boolean] all_true = [floor(f1) == i1, floor(f2) == i2]
+  }
+}

wdl-engine/tests/tasks/test-join-paths/files/mydir/mydata.txt

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+hello

wdl-engine/tests/tasks/test-join-paths/inputs.json

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+{}

wdl-engine/tests/tasks/test-join-paths/outputs.json

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+{
+  "resolve_paths_task.bins_equal": true,
+  "resolve_paths_task.result": "hello",
+  "resolve_paths_task.missing_file": null
+}

wdl-engine/tests/tasks/test-join-paths/source.wdl

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+version 1.2
+
+task resolve_paths_task {
+  input {
+    File abs_file = "/usr"
+    String abs_str = "/usr"
+    String rel_dir_str = "bin"
+    File rel_file = "echo"
+    File rel_dir_file = "mydir"
+    String rel_str = "mydata.txt"
+  }
+
+  # these are all equivalent to '/usr/bin/echo'
+  File bin1 = join_paths(abs_file, [rel_dir_str, rel_file])
+  File bin2 = join_paths(abs_str, [rel_dir_str, rel_file])
+  File bin3 = join_paths([abs_str, rel_dir_str, rel_file])
+
+  # the default behavior is that this resolves to 
+  # '<working dir>/mydir/mydata.txt'
+  File data = join_paths(rel_dir_file, rel_str)
+
+  # this resolves to '<working dir>/bin/echo', which is non-existent
+  File doesnt_exist = join_paths([rel_dir_str, rel_file])
+  command <<<
+    mkdir ~{rel_dir_file}
+    echo -n "hello" > ~{data}
+  >>>
+
+  output {
+    Boolean bins_equal = (bin1 == bin2) && (bin1 == bin3)
+    String result = read_string(data)
+    File? missing_file = doesnt_exist
+  }
+
+  runtime {
+    container: "ubuntu:latest"
+  }
+}

wdl-engine/tests/tasks/test-matches/inputs.json

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+{
+    "contains_string.fastq": "sample1234_R1.fastq"
+}

wdl-engine/tests/tasks/test-matches/outputs.json

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+{
+  "contains_string.is_compressed": false,
+  "contains_string.is_read1": true
+}

wdl-engine/tests/tasks/test-matches/source.wdl

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+version 1.2
+
+task contains_string {
+  input {
+    File fastq
+  }
+
+  command <<<>>>
+
+  output {
+    Boolean is_compressed = matches(basename(fastq), "\\.(gz|zip|zstd)")
+    Boolean is_read1 = matches(basename(fastq), "_R1")
+  }
+}

wdl-engine/tests/tasks/test-max/inputs.json

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+{
+    "test_max.value1": 1,
+    "test_max.value2": 2.0
+}

wdl-engine/tests/tasks/test-max/outputs.json

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+{
+  "test_max.max1": 2.0,
+  "test_max.max2": 2.0
+}

wdl-engine/tests/tasks/test-max/source.wdl

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+version 1.2
+
+task test_max {
+  input {
+    Int value1
+    Float value2
+  }
+
+  command <<<>>>
+
+  output {
+    # these two expressions are equivalent
+    Float max1 = if value1 > value2 then value1 else value2
+    Float max2 = max(value1, value2)
+  }
+}

wdl-engine/tests/tasks/test-min/inputs.json

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+{
+    "test_min.value1": 1,
+    "test_min.value2": 2.0
+}

wdl-engine/tests/tasks/test-min/outputs.json

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+{
+  "test_min.min1": 1.0,
+  "test_min.min2": 1.0
+}

wdl-engine/tests/tasks/test-min/source.wdl

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+version 1.2
+
+task test_min {
+  input {
+    Int value1
+    Float value2
+  }
+
+  command <<<>>>
+
+  output {
+    # these two expressions are equivalent
+    Float min1 = if value1 < value2 then value1 else value2
+    Float min2 = min(value1, value2)
+  }
+}

wdl-engine/tests/tasks/test-round/inputs.json

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+{
+    "test_round.i1": 2
+}

wdl-engine/tests/tasks/test-round/outputs.json

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+{
+  "test_round.all_true": [
+    true,
+    true
+  ]
+}

wdl-engine/tests/tasks/test-round/source.wdl

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+version 1.2
+
+task test_round {
+  input {
+    Int i1
+  }
+
+  Int i2 = i1 + 1
+  Float f1 = i1 + 0.49
+  Float f2 = i1 + 0.50
+
+  command <<<>>>
+
+  output {
+    Array[Boolean] all_true = [round(f1) == i1, round(f2) == i2]
+  }
+}

wdl-engine/tests/tasks/test-stderr/inputs.json

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+{}

wdl-engine/tests/tasks/test-stderr/outputs.json

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+{
+  "echo_stderr.message": "hello world"
+}

wdl-engine/tests/tasks/test-stderr/source.wdl

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+version 1.2
+
+task echo_stderr {
+  command <<< >&2 printf "hello world" >>>
+
+  output {
+    String message = read_string(stderr())
+  }
+}

wdl-engine/tests/tasks/test-stderr/stderr

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+hello world

wdl-engine/tests/tasks/test-stdout/inputs.json

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+{}

wdl-engine/tests/tasks/test-stdout/outputs.json

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+{
+  "echo_stdout.message": "hello world"
+}