Fix may issues with examples

CHANGELOG.md

@@ -42,6 +42,12 @@ version development
   consist of multiple files.
   [PR 241](https://github.com/openwdl/wdl/pull/241) by @cjllanwarne.
 
+version 1.1.3
+---------------------------
+
+* Fix issues with examples (#653, #654, #661, #662, #663, #664, #665, #666, #668). Thanks to @stxue1!
+* Clarify that a file is not required to exist or be accessible until and unless it is accessed.
+
 version 1.1.2
 ---------------------------
 

README.md

@@ -14,7 +14,7 @@ The WDL *language* has a two-number version (e.g., `1.1`).
 An increase in the minor (second) version number (e.g., `1.0` to `1.1`) indicates the addition of, or non-breaking changes to, the language or standard library functions.
 An increase in the major (first) version number (e.g., `1.0` to `2.0`) indicates that breaking changes have been made.
 
-The WDL *specification* has a three-number version (e.g., `1.1.2`).
+The WDL *specification* has a three-number version (e.g., `1.1.3`).
 The specification version tracks the language version, but there may also be patch releases (indicated by a change to the patch, or third, version number) that include fixes for typos, additional examples, or non-breaking clarifications of ambiguous language.
 
 ## Language Specifications

SPEC.md

@@ -1,11 +1,12 @@
 # Workflow Description Language (WDL)
 
-This is version 1.1.2 of the Workflow Description Language (WDL) specification. It describes WDL `version 1.1`. It introduces a number of new features (denoted by the ✨ symbol) and clarifications to the [1.0](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md) version of the specification. It also deprecates several aspects of the 1.0 specification that will be removed in the [next major WDL version](https://github.com/openwdl/wdl/blob/wdl-2.0/SPEC.md) (denoted by the 🗑 symbol).
+This is version 1.1.3 of the Workflow Description Language (WDL) specification. It describes WDL `version 1.1`. It introduces a number of new features (denoted by the ✨ symbol) and clarifications to the [1.0](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md) version of the specification. It also deprecates several aspects of the 1.0 specification that will be removed in the [next major WDL version](https://github.com/openwdl/wdl/blob/wdl-2.0/SPEC.md) (denoted by the 🗑 symbol).
 
 ## Revisions
 
 Revisions to this specification are made periodically in order to correct errors, clarify language, or add additional examples. Revisions are released as "patches" to the specification, i.e., the third number in the specification version is incremented. No functionality is added or removed after the initial revision of the specification is ratified.
 
+* [1.1.3]():
 * [1.1.2](https://github.com/openwdl/wdl/tree/release-1.1.2/SPEC.md): 2024-04-12
 * [1.1.1](https://github.com/openwdl/wdl/tree/release-1.1.1/SPEC.md): 2023-10-04
 * [1.1.0](https://github.com/openwdl/wdl/tree/release-1.1.0/SPEC.md): 2021-01-29
@@ -419,7 +420,7 @@ There is no special syntax for multi-line comments - simply use a `#` at the sta
     # This comment will not be included within the command
     command <<<
       # This comment WILL be included within the command after it has been parsed
-      cat ~{number * 2}
+      echo ~{number * 2}
     >>>
 
     output {
@@ -534,7 +535,12 @@ The following primitive types exist in WDL:
 * A `File` represents a file (or file-like object).
     * A `File` declaration can have a string value indicating a relative or absolute path on the local file system.
     * Within a WDL file, literal values for files may only be local (relative or absolute) paths.
+    * The path assigned to a `File` is not required to be valid unless and until it is accessed.
+      * To read from a file, it must exist and be assigned appropriate permissions.
+      * To write to a file, the parent directory must be assigned appropriate permissions.
     * An execution engine may support other ways to specify [`File` inputs (e.g. as URIs)](#input-and-output-formats), but prior to task execution it must [localize inputs](#task-input-localization) so that the runtime value of a `File` variable is a local path.
+      * Remote files must be treated as read-only.
+      * A remote file is only required to be vaild at the time that the execution engine needs to localize it.
 
 <details>
   <summary>
@@ -1148,7 +1154,7 @@ Example output:
 
 ```json
 {
-  "test_struct.person": {
+  "test_struct.john": {
     "name": "John",
     "account": {
       "account_number": "123456",
@@ -1424,18 +1430,20 @@ workflow map_to_struct {
   String b = "key"
   String c = "lookup"
 
-  # What are the keys to this Struct?
-  Words literal_syntax = Words {
-    a: 10,
-    b: 11,
-    c: 12
-  }
+  output {
+    # What are the keys to this Struct?
+    Words literal_syntax = Words {
+      a: 10,
+      b: 11,
+      c: 12
+    }
 
-  # What are the keys to this Struct?
-  Words map_coercion = {
-    a: 10,
-    b: 11,
-    c: 12
+    # What are the keys to this Struct?
+    Words map_coercion = {
+      a: 10,
+      b: 11,
+      c: 12
+    }
   }
 }
 ```
@@ -3606,12 +3614,12 @@ task python_strip {
   }
 
   command<<<
-  python <<CODE
+    python <<CODE
     with open("~{infile}") as fp:
       for line in fp:
         if not line.startswith('#'):
           print(line.strip())
-  CODE
+    CODE
   >>>
 
   output {
@@ -3637,7 +3645,7 @@ Example output:
 
 ```json
 {
-  "python_strip": ["A", "B", "C"]
+  "python_strip.lines": ["A", "B", "C"]
 }
 ```
 </p>
@@ -3647,10 +3655,10 @@ Given an `infile` value of `/path/to/file`, the execution engine will produce th
 
 ```sh
 python <<CODE
-  with open("/path/to/file") as fp:
-    for line in fp:
-      if not line.startswith('#'):
-        print(line.strip())
+with open("/path/to/file") as fp:
+  for line in fp:
+    if not line.startswith('#'):
+      print(line.strip())
 CODE
 ```
 
@@ -4238,6 +4246,7 @@ task test_gpu {
   }
 
   runtime {
+    container: "archlinux:latest"
     gpu: true
   }
 }
@@ -5680,7 +5689,8 @@ Example input:
   "allow_nested.msg1": "hello",
   "allow_nested.msg2": "goodbye",
   "allow_nested.my_ints": [1, 2, 3],
-  "allow_nested.ref_file": "hello.txt"
+  "allow_nested.ref_file": "hello.txt",
+  "allow_nested.repeat2.i": 2
 }
 ```
 
@@ -5690,7 +5700,6 @@ Example output:
 {
   "allow_nested.lines1": ["hello", "hello", "hello"],
   "allow_nested.lines2": ["goodbye", "goodbye"],
-  "allow_nested.repeat2.i": 2,
   "allow_nested.incrs": [2, 3, 4]
 }
 ```
@@ -6054,12 +6063,12 @@ workflow if_else {
 
   # the body *is not* evaluated since 'b' is false
   if (is_morning) {
-    call greet as morning { time = "morning" }
+    call greet as morning { input: time = "morning" }
   }
 
   # the body *is* evaluated since !b is true
   if (!is_morning) {
-    call greet as afternoon { time = "afternoon" }
+    call greet as afternoon { input: time = "afternoon" }
   }
 
   output {
@@ -6104,7 +6113,7 @@ workflow nested_if {
 
   if (morning) {
     if (friendly) {
-      call if_else.greet { time = "morning" }
+      call if_else.greet { input: time = "morning" }
     }
   }
 
@@ -8090,7 +8099,7 @@ workflow test_prefix {
   Array[Int] env2 = [1, 2, 3]
 
   output {
-    Array[String] env_prefixed = prefix("-e ", env1)
+    Array[String] env1_prefixed = prefix("-e ", env1)
     Array[String] env2_prefixed = prefix("-f ", env2)
   }
 }
@@ -9864,7 +9873,7 @@ Example output:
 
 ```json
 {
-  "serialize_array_delim.strings": [
+  "serialize_array_delim.heads": [
     "hello world",
     "hello world",
     "hi_world"