Testing of object, map, and array literals

.gitignore

@@ -1,7 +1,13 @@
 __pycache__
+.DS_Store
 
-# cromwell jar files
+# cromwell jar files, etc.
+cromwell-executions
+cromwell-workflow-logs
 *.jar
+pytest-wdl-tests/tests/literals/run.sh
+pytest-wdl-tests/tests/literals/validate.sh
+pytest-wdl-tests/tests/literals/json.sh
 
 # python virtual environment
-env/
+env/

pytest-wdl-tests/tests/literals/data/array_literals_out

@@ -0,0 +1,7 @@
+INTS
+0
+1
+2
+STRINGS
+array
+literal

pytest-wdl-tests/tests/literals/data/map_literals_out

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+INTS
+1	10
+2	11
+MIXED
+a	1
+b	2

pytest-wdl-tests/tests/literals/data/object_literals_out

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+a	b
+10	11

pytest-wdl-tests/tests/literals/data/object_map_coercion_out

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+OBJECT_SYNTAX
+key1	key2	key3
+7	8	9
+MAP_COERCION
+key1name	key2name	key3name
+10	11	12

pytest-wdl-tests/tests/literals/data/pair_literals_out

@@ -0,0 +1 @@
+23 twenty-three

pytest-wdl-tests/tests/literals/literals.wdl

@@ -0,0 +1,157 @@
+# This workflow tests the the literals sections of the WDL 1.0 Spec
+# It also requires the use of some functions such as write_lines(), write_object(), write_map(), and stdout()
+# write_map() is slightly broken as it does not print a \n after writing like the related functions do.
+
+version 1.0
+
+workflow literals {
+	input {
+		### Array Literals
+		Array[String] array_literal_strings = ["array", "literal"]
+		Array[Int] array_literal_ints = [0, 1, 2]
+
+		### Map Literals
+		Map[Int, Int] map_literal_ints = {1: 10, 2: 11}
+		Map[String, Int] map_literal_mixed = {"a": 1, "b": 2}
+
+		### Object Literals
+		Object object_literal = object {
+			a: 10,
+			b: 11
+		}
+
+		### Object Coercion from Map
+		# "object" keyword before {} indicates Object, absence of indicates Map.
+		String key1 = "key1name"
+		String key2 = "key2name"
+		String key3 = "key3name"
+
+		Object object_syntax = object {
+			key1: 7,
+			key2: 8,
+			key3: 9
+		}
+
+		Object map_coercion = {
+			key1: 10,
+			key2: 11,
+			key3: 12
+		}
+
+		### Pair Literals
+		Pair[Int, String] pair_literal_mixed = (23, "twenty-three")
+	}
+	call array_literals {
+		input:
+			array_literal_strings=write_lines(array_literal_strings),
+			array_literal_ints=write_lines(array_literal_ints)
+	}
+	call map_literals {
+		input:
+			map_literal_ints=write_map(map_literal_ints),
+			map_literal_mixed=write_map(map_literal_mixed)
+	}
+	call object_literals {
+		input:
+			object_literal = write_object(object_literal)
+	}
+	call object_map_coercion {
+		input:
+			object_syntax=write_object(object_syntax),
+			map_coercion=write_object(map_coercion)
+	}
+	call pair_literals {
+		input:
+			pair_literal_mixed_left=pair_literal_mixed.left,
+			pair_literal_mixed_right=pair_literal_mixed.right
+	}
+	output {
+		File array_literals_out = array_literals.array_literals_out
+		File map_literals_out = map_literals.map_literals_out
+		File object_literals_out = object_literals.object_literals_out
+		File object_map_coercion_out = object_map_coercion.object_map_coercion_out
+		File pair_literals_out = pair_literals.pair_literals_out
+	}
+}
+
+task array_literals {
+	input {
+		File array_literal_ints
+		File array_literal_strings
+	}
+	command {
+		set -e
+		echo INTS
+		cat ~{array_literal_ints}
+		printf "STRINGS\n"
+		cat ~{array_literal_strings}
+	}
+	output {
+		File array_literals_out = stdout()
+	}
+}
+
+task map_literals {
+	input {
+		File map_literal_ints
+		File map_literal_mixed
+	}
+	command {
+		set -e
+
+		echo INTS
+		cat ~{map_literal_ints}
+		printf "\nMIXED\n"
+		cat ~{map_literal_mixed}
+	}
+	output {
+		File map_literals_out = stdout()
+	}
+}
+
+task object_literals {
+	input {
+		File object_literal
+	}
+	command {
+		set -e
+
+		cat ~{object_literal}
+	}
+	output {
+		File object_literals_out = stdout()
+	}
+}
+
+task object_map_coercion {
+	input {
+		File object_syntax
+		File map_coercion
+	}
+	command {
+		set -e
+
+		echo OBJECT_SYNTAX
+		cat ~{object_syntax}
+		printf "MAP_COERCION\n"
+		cat ~{map_coercion}
+	}
+	output {
+		File object_map_coercion_out = stdout()
+	}
+}
+
+task pair_literals {
+	input {
+		Int pair_literal_mixed_left
+		String pair_literal_mixed_right
+	}
+	command {
+		set -e
+
+		echo ~{pair_literal_mixed_left} ~{pair_literal_mixed_right}
+	}
+	output {
+		File pair_literals_out = stdout()
+	}
+}

pytest-wdl-tests/tests/literals/test_data.json

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+{
+}
+

pytest-wdl-tests/tests/literals/test_literals.py

@@ -0,0 +1,4 @@
+def test_literals(workflow_data, workflow_runner):
+	inputs = {}
+	expected = workflow_data.get_dict("array_literals_out", "map_literals_out", "object_literals_out", "object_map_coercion_out", "pair_literals_out")
+	workflow_runner("literals.wdl", inputs, expected, workflow_name="literals")

pytest-wdl-tests/tests/whitespace/data/spaces_out

@@ -0,0 +1,2 @@
+I am a document. I am all spaces. Let me pass!
+Look now I'm in this python heredoc! I am a document. I am all spaces. Let me pass!

pytest-wdl-tests/tests/whitespace/data/tabs_out

@@ -0,0 +1,2 @@
+I am a document. I am all tabs. Let me pass!
+Look now I'm in this python heredoc! I am a document. I am all tabs. Let me pass!

pytest-wdl-tests/tests/whitespace/indented_heredoc.wdl

@@ -0,0 +1,31 @@
+# This workflow has tab indents and one extra indent at the heredoc! It is intended to fail miserably.
+
+version 1.0
+
+workflow indented_heredoc {
+	input {
+		String message = "I am a document. I am indented incorrectly at the heredoc. Let me fail!"
+	}
+	call t {
+		input: message=message
+	}
+	output {
+		File indented_heredoc_out = t.out
+	}
+}
+
+task t {
+	input {
+		String message
+	}
+	command {
+		echo ~{message}
+		python <<CODE
+			for i in range(0,1):
+				print("Look now I'm in this python heredoc! ~{message}")
+		CODE
+	}
+	output {
+		File out = stdout()
+	}
+}

pytest-wdl-tests/tests/whitespace/mixed.wdl

@@ -0,0 +1,31 @@
+# This workflow has 2-space indents and one tab at the heredoc! It is intended to fail miserably.
+
+version 1.0
+
+workflow mixed {
+  input {
+    String message = "I am a document. I am mixed. Let me fail!"
+  }
+  call t {
+    input: message=message
+  }
+  output {
+    File mixed_out = t.out
+  }
+}
+
+task t {
+  input {
+    String message
+  }
+  command {
+    echo ~{message}
+    python <<CODE
+    for i in range(0,1):
+    	print("Look now I'm in this python heredoc! ~{message}")
+    CODE
+  }
+  output {
+    File out = stdout()
+  }
+}

pytest-wdl-tests/tests/whitespace/proper_whitespace.wdl

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+# This main workflow is all tab-indented, but it calls both a tab-indented and a 2-space indented subworkflow. 
+# It is intended to run successfully.
+
+version 1.0
+
+import "tabs.wdl" as t
+import "spaces.wdl" as s
+
+workflow proper_whitespace {
+	call t.tabs as tabs
+	call s.spaces as spaces
+	output {
+		File tabs_out = tabs.tabs_out
+		File spaces_out = spaces.spaces_out
+	}
+}

pytest-wdl-tests/tests/whitespace/spaces.wdl

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+# This workflow is all 2-space-indented, it is intended to run successfully.
+
+version 1.0
+
+workflow spaces {
+  input {
+    String message = "I am a document. I am all spaces. Let me pass!"
+  }
+  call t {
+    input: message=message
+  }
+  output {
+    File spaces_out = t.out
+  }
+}
+
+task t {
+  input {
+    String message
+  }
+  command {
+    echo ~{message}
+    python <<CODE
+    for i in range(0,1):
+      print("Look now I'm in this python heredoc! ~{message}")
+    CODE
+  }
+  output {
+    File out = stdout()
+  }
+}

pytest-wdl-tests/tests/whitespace/tabs.wdl

@@ -0,0 +1,31 @@
+# This workflow is all tab-indented, it is intended to run successfully.
+
+version 1.0
+
+workflow tabs {
+	input {
+		String message = "I am a document. I am all tabs. Let me pass!"
+	}
+	call t {
+		input: message=message
+	}
+	output {
+		File tabs_out = t.out
+	}
+}
+
+task t {
+	input {
+		String message
+	}
+	command {
+		echo ~{message}
+		python <<CODE
+		for i in range(0,1):
+			print("Look now I'm in this python heredoc! ~{message}")
+		CODE
+	}
+	output {
+		File out = stdout()
+	}
+}

pytest-wdl-tests/tests/whitespace/test_data.json

@@ -0,0 +1,2 @@
+{
+}