Merge branch 'dev'

pom.xml

@@ -9,7 +9,7 @@
   <groupId>org.broadinstitute.compositetask</groupId>
   <artifactId>Wdl</artifactId>
   <packaging>jar</packaging>
-  <version>0.0.2</version>
+  <version>0.0.3</version>
   <name>Wdl</name>
   <url>http://github.com/broadinstitute/wdl</url>
 

src/main/java/org/broadinstitute/compositetask/CompositeTask.java

@@ -9,6 +9,8 @@
 import java.util.LinkedHashSet;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.broadinstitute.parser.Ast;
 import org.broadinstitute.parser.AstNode;
@@ -75,6 +77,20 @@ public Ast verify(AstNode wdl_ast) throws SyntaxError {
 
             set_parents(CompositeTask.this);
 
+            Pattern expressionPattern = Pattern.compile("\\$\\{([^}]+)\\}");
+            for ( Map.Entry<String, Terminal> output_file : this.output_files.entrySet() ) {
+              Matcher matcher = expressionPattern.matcher(output_file.getValue().getSourceString());
+              while ( matcher.find() ) {
+                String filename_var = matcher.group(1);
+                for ( Map.Entry<CompositeTaskVariable, Terminal> step_output : this.output_variables.entrySet() ) {
+                  String output_var = step_output.getKey().getName();
+                  if ( output_var.equals(filename_var) ) {
+                    throw new SyntaxError(this.syntaxErrorFormatter.variable_used_as_filename_and_step_output(output_file.getValue(), matcher.start(), step_output.getValue()));
+                  }
+                }
+              }
+            }
+
             return composite_task;
         }
 

src/main/java/org/broadinstitute/compositetask/WdlSyntaxErrorFormatter.java

@@ -99,4 +99,14 @@ public String step_doesnt_use_loop_iterator(Terminal loop_iterator, Terminal ste
            this.code.getLine(loop_iterator.getLine()) + "\n" + Utility.getIndentString(loop_iterator.getColumn()-1) + "^\n";
   }
 
+  public String variable_used_as_filename_and_step_output(Terminal filename_var, int filename_var_offset, Terminal output_var) {
+    return String.format("Variable %s used to construct an output filename and also as an output variable.  One of these variable names must change.\n\n", output_var.getSourceString()) +
+           String.format("Line %d, Column %d:\n", filename_var.getLine(), filename_var.getColumn()) +
+           this.code.getLine(filename_var.getLine()) + "\n" +
+           Utility.getIndentString(filename_var.getColumn() + filename_var_offset - 1) + "^\n" +
+           String.format("Line %d, Column %d:\n", output_var.getLine(), output_var.getColumn()) +
+           this.code.getLine(output_var.getLine()) + "\n" +
+           Utility.getIndentString(output_var.getColumn()-1) + "^\n";
+  }
+
 }

test-files/syntax-error/6/errors

@@ -0,0 +1,8 @@
+org.broadinstitute.parser.SyntaxError: Variable filtered_bam_name used to construct an output filename and also as an output variable.  One of these variable names must change.
+
+Line 3, Column 18:
+    output: File("${filtered_bam_name}.bam") as filtered_bam_name;
+                  ^
+Line 3, Column 49:
+    output: File("${filtered_bam_name}.bam") as filtered_bam_name;
+                                                ^

test-files/syntax-error/6/source.wdl

@@ -0,0 +1,8 @@
+composite_task CufflinksPipeline {
+  step FilterBamForAlignedReads[version=8] {
+    output: File("${filtered_bam_name}.bam") as filtered_bam_name;
+  }
+  step Cufflinks[version=29] {
+    input: input.bam=filtered_bam_name;
+  }
+}

test-files/syntax-error/7/errors

@@ -0,0 +1,8 @@
+org.broadinstitute.parser.SyntaxError: Variable filtered_bam_name used to construct an output filename and also as an output variable.  One of these variable names must change.
+
+Line 3, Column 18:
+    output: File("${abc}.${filtered_bam_name}.bam") as filtered_bam_name;
+                         ^
+Line 3, Column 56:
+    output: File("${abc}.${filtered_bam_name}.bam") as filtered_bam_name;
+                                                       ^

test-files/syntax-error/7/source.wdl

@@ -0,0 +1,8 @@
+composite_task CufflinksPipeline {
+  step FilterBamForAlignedReads[version=8] {
+    output: File("${abc}.${filtered_bam_name}.bam") as filtered_bam_name;
+  }
+  step Cufflinks[version=29] {
+    input: input.bam=filtered_bam_name;
+  }
+}

test-files/syntax-error/8/errors

@@ -0,0 +1,8 @@
+org.broadinstitute.parser.SyntaxError: Variable xyz used to construct an output filename and also as an output variable.  One of these variable names must change.
+
+Line 3, Column 18:
+    output: File("${abc}.${xyz}.bam") as filtered_bam_name,
+                         ^
+Line 4, Column 35:
+            File("${abc}.bam") as xyz;
+                                  ^

test-files/syntax-error/8/source.wdl

@@ -0,0 +1,9 @@
+composite_task CufflinksPipeline {
+  step FilterBamForAlignedReads[version=8] {
+    output: File("${abc}.${xyz}.bam") as filtered_bam_name,
+            File("${abc}.bam") as xyz;
+  }
+  step Cufflinks[version=29] {
+    input: input.bam=xyz;
+  }
+}