implement read_lines() with a functional test (#181)

fix read_tsv() and add functional test
common-workflow-lab · Feb 16, 2022 · 63d60b5 · 63d60b5
1 parent 48a1569
commit 63d60b5
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Showing 10 changed files with 845 additions and 24 deletions.
diff --git a/wdl2cwl/main.py b/wdl2cwl/main.py
@@ -236,16 +236,20 @@ def get_literal_value(expr: WDL.Expr.Base) -> Optional[Any]:
   if (contents == 'true') { return true;}
   if (contents == 'false') { return false;}
   throw "'read_boolean' received neither 'true' nor 'false': " + self[0].contents;
+}""",
+    "read_lines": r"""${
+  var contents = self[0].contents.replace(/\r\n$/, "").replace(/\n$/, "").replace(/\r$/, "");
+  // ^ remove any trailing newline to prevent a null being returned
+  return contents.split(/\r\n|\r|\n/);
 }""",
     "read_tsv": r"""${
-  var result;
-  self.contents.split(/\n|(\n\r)/).forEach(function(line) {
-    var line_array;
-    line.split('\t').forEach(function(field) {
-      line_array.push(field)
-    })
-    result.push(line_array);
-  })
+  var result = Array();
+  var contents = self[0].contents.replace(/\r\n$/, "").replace(/\n$/, "").replace(/\r$/, "");
+  // ^ remove any trailing newline to prevent a null being returned
+  contents.split(/\r\n|\r|\n/).forEach(function(line) {
+    result.push(line.split('\t'));
+  });
+  return result;
 }""",
 }
 
@@ -763,6 +767,7 @@ def get_expr_apply(self, wdl_apply_expr: WDL.Expr.Apply) -> str:
             "read_int",
             "read_boolean",
             "read_tsv",
+            "read_lines",
         }
         function_name = wdl_apply_expr.function_name
         arguments = wdl_apply_expr.arguments

diff --git a/wdl2cwl/tests/cwl_files/FunctionalEquivalence.cwl b/wdl2cwl/tests/cwl_files/FunctionalEquivalence.cwl
@@ -264,14 +264,13 @@ $graph:
             glob: sequence_grouping.txt
             outputEval: |-
                 ${
-                  var result;
-                  self.contents.split(/\n|(\n\r)/).forEach(function(line) {
-                    var line_array;
-                    line.split('\t').forEach(function(field) {
-                      line_array.push(field)
-                    })
-                    result.push(line_array);
-                  })
+                  var result = Array();
+                  var contents = self[0].contents.replace(/\r\n$/, "").replace(/\n$/, "").replace(/\r$/, "");
+                  // ^ remove any trailing newline to prevent a null being returned
+                  contents.split(/\r\n|\r|\n/).forEach(function(line) {
+                    result.push(line.split('\t'));
+                  });
+                  return result;
                 }
       - id: sequence_grouping_with_unmapped
         type:
@@ -284,14 +283,13 @@ $graph:
             glob: sequence_grouping_with_unmapped.txt
             outputEval: |-
                 ${
-                  var result;
-                  self.contents.split(/\n|(\n\r)/).forEach(function(line) {
-                    var line_array;
-                    line.split('\t').forEach(function(field) {
-                      line_array.push(field)
-                    })
-                    result.push(line_array);
-                  })
+                  var result = Array();
+                  var contents = self[0].contents.replace(/\r\n$/, "").replace(/\n$/, "").replace(/\r$/, "");
+                  // ^ remove any trailing newline to prevent a null being returned
+                  contents.split(/\r\n|\r|\n/).forEach(function(line) {
+                    result.push(line.split('\t'));
+                  });
+                  return result;
                 }
   - cwlVersion: v1.2
     id: BaseRecalibrator