Validate WDLs using miniwdl (#385)

* Implement WDL validation using miniwdl.

* Update scripts/test/miniwdl_validation.py

Co-authored-by: Mark Walker <[email protected]>

* Remove filtering the input for non-wdl files.

Co-authored-by: Mark Walker <[email protected]>

scripts/test/miniwdl_validation.py

@@ -0,0 +1,56 @@
+"""
+This Script checks the provided WDL files with miniwdl for
+syntax, validation, and import errors. See the following
+page on the checks. Note that this script does not
+check for "warning" or "suggestions"; you may use
+`$ miniwdl check WDL_FILENAME` to get warnings and suggestions.
+
+https://miniwdl.readthedocs.io/en/latest/WDL.html#module-WDL.Error
+"""
+
+import argparse
+import sys
+import WDL
+
+
+def format_error_message(error_type, message, pos):
+    return f"{error_type}: '{message}' at {pos.abspath}, Line: {pos.line}, Col: {pos.column}"
+
+
+def check(wdl_filename):
+    try:
+        WDL.load(wdl_filename)
+        return True
+    except WDL.Error.SyntaxError as e:
+        print(format_error_message("Syntax Error", e, e.pos))
+    except WDL.Error.ValidationError as e:
+        print(format_error_message("Validation Error", e, e.node.pos))
+    except WDL.Error.MultipleValidationErrors as e:
+        for ex in e.exceptions:
+            print(format_error_message("Validation Error", ex, ex.node.pos))
+    except WDL.Error.ImportError as e:
+        print(e)
+        print(format_error_message("Import Error", e, e.pos))
+    finally:
+        return False
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("files", nargs="+", help="The WDL files to be checked.")
+    args = parser.parse_args()
+
+    wdl_filenames = args.files
+
+    exit_code = 0
+    counter = 0
+    for wdl_filename in wdl_filenames:
+        if not check(wdl_filename):
+            exit_code = 1
+            counter += 1
+    print(f"{counter} of {len(wdl_filenames)} checked WDL files failed the miniwdl validation.")
+    sys.exit(exit_code)
+
+
+if __name__ == "__main__":
+    main()