Fixes and improvements:

* Validation errors are now aggregated into an output list. Resolves #4
* Output directory is now optional.  The tool will only perform validations in this case. Resolves #1
* Path trim error fixed. Resolves #2
* Exception stack traces are now ommitted for validation errors. Resolves #3

.gitignore

@@ -15,3 +15,4 @@ jss-deref-test-*
 *.o
 *.obj
 *.lst
+js-deref

readme.adoc

@@ -5,12 +5,15 @@
 image:https://img.shields.io/github/release/EuPathDB-Infra/js-deref.svg?style=flat-square[GitHub tag,link=https://github.com/EuPathDB-Infra/js-deref/releases/latest]
 image:https://img.shields.io/travis/EuPathDB-Infra/js-deref/master.svg?style=flat-square[Travis (.org) branch,link=https://travis-ci.org/EuPathDB-Infra/js-deref]
 
-
 Recursively resolves `"$ref"` properties and appends the
 external schema content to the root `"definitions"` object.
 
-Reads entire directory trees and copies the input files to
-the output location.
+If an output directory is provided, the tool writes the
+dereferenced json files to the output directory, mirroring
+the structure of the input directory.
+
+If no output directory is provided, the tool simply performs
+the validation checks.
 
 WARNING: This utility is not presently suited for general
 use as a json schema ref resolver.  It is tailored to the
@@ -21,7 +24,7 @@ root of a java project's resource directory.
 
 [source, bash session]
 ----
-$ js-deref <input_dir> <output_dir>
+$ js-deref <input_dir> [output_dir]
 ----
 
 == Rule checks

source/app.d

@@ -1,20 +1,46 @@
-import std.file: getcwd;
+import std.file: getcwd, exists;
 import std.path: buildPath;
-import std.stdio: writeln;
+import std.stdio: writefln, writeln, stderr;
 
 import lib.deref;
+import lib.err.valid: ValidationException;
 
 int main(string[] args)
 {
   if (args.length < 2) {
     writeln(`js-deref
     usage:
-      js-deref <input-dir> <output-dir>`);
+      js-deref <input-dir> [output-dir]`);
     return 1;
   }
 
   const string cwd = getcwd();
-  new Dereferencer(cwd.buildPath(args[1]), cwd.buildPath(args[2])).run();
 
-  return 0;
+  Dereferencer deref;
+  const string inPath = cwd.buildPath(args[1]).trailingSlash();
+
+  if (!inPath.exists()) {
+    writefln("Input path does not exist: %s", inPath);
+    return 1;
+  }
+
+  if (args.length == 2) {
+    deref = new Dereferencer(inPath);
+  } else {
+    const string outPath = cwd.buildPath(args[2]).trailingSlash();
+    deref = new Dereferencer(inPath, outPath);
+  }
+
+  try {
+    return deref.run();
+  } catch (ValidationException e) {
+    stderr.writeln(e.msg);
+    return 1;
+  }
+}
+
+//TODO: Rehome us
+
+private string trailingSlash(const string path) {
+  return path[$-1] == '/' ? path : path ~ '/';
 }

source/lib/deref.d

@@ -1,29 +1,20 @@
 module lib.deref;
 
-import std.stdio: writefln, toFile;
+import std.stdio: writefln, writeln, toFile;
 import std.file: dirEntries, SpanMode, readText, mkdirRecurse;
 import std.path: buildNormalizedPath, dirName, baseName, buildPath;
 import std.json: JSONValue, parseJSON, JSONException, JSONType;
 import std.string: indexOf, split, format;
 
 import lib.schema;
 import lib.json_schema;
+import lib.err;
 debug(deref) import lib.bug.pdb: printDebug;
 
 private const string INCLUDES_DIR = "includes";
 
 private const string SCHEMA_FILTER = "*.json";
 
-private const string ERR_ILLEGAL_REF = "References must be absolute paths to "
-  ~ `the root of the resource directory.  Example '/schema/wdk/...'.
-    Invalid Ref: %s
-    Schema File: %s`;
-
-private const string ERR_OUT_OF_SCOPE = "References not found in the resource "
-  ~ `directory.
-    Invalid Ref: %s
-    Schema File: %s`;
-
 private const string ERR_JSON_PARSE = `Failed to parse JSON file contents.
     Schema File: %s`;
 
@@ -33,6 +24,8 @@ class Dereferencer {
 
   private const string inDir;
 
+  private const bool writeOutput;
+
   private const string outDir;
 
   /**
@@ -43,32 +36,70 @@ class Dereferencer {
     debug(deref) printDebug(["inDir": inDir, "outDir": outDir]);
     this.inDir  = inDir;
     this.outDir = outDir;
+    this.writeOutput = true;
+  }
+
+  /**
+   * @param inDir  input schema home
+   * @param outDir schema output directory
+   */
+  this(const string inDir) {
+    debug(deref) printDebug(["inDir": inDir]);
+    this.inDir  = inDir;
+    this.outDir = "";
+    this.writeOutput = false;
   }
 
   /**
    *
    */
-  public void run() {
+  public int run() {
     debug(deref) printDebug([]);
 
-    scanDir();
+    if (!scanDir())
+      return 1;
 
-    foreach(const string path, Schema s; all) {
-      if (!s.hasRef())
-        continue;
+    if (!seekAll(this.all))
+      return 1;
 
-      seek(s, s.getValue());
-    }
+    if(!writeOutput)
+      return 0;
 
     foreach(Schema s; all) {
       s.resolveDefs();
       writeOut(s);
     }
+
+    return 0;
+  }
+
+  private bool seekAll(ref Schema[string] all) {
+    string[] errors;
+
+    foreach(const string path, Schema s; all) {
+      if (!s.hasRef())
+        continue;
+
+      try {
+        seek(s, s.getValue());
+      } catch (ValidationException e) {
+        errors ~= e.msg;
+      }
+    }
+
+    if (errors.length == 0)
+      return true;
+
+    writefln("Error: validation failed for %d schema files.\n", errors.length);
+    foreach(const string e; errors)
+      writefln("%s\n", e);
+
+    return false;
   }
 
   private void writeOut(Schema s) {
     debug(deref) printDebug(["s": &s]);
-    
+
     const string outPath = buildPath(outDir, s.getLocalDir());
 
     if (baseName(outPath) == INCLUDES_DIR)
@@ -127,7 +158,7 @@ class Dereferencer {
    */
   void seekArray(Schema s, JSONValue* value) {
     debug(deref) printDebug(["s": &s, "value": value]);
-    
+
     foreach(ref JSONValue cur; value.array)
       seek(s, &cur);
   }
@@ -140,7 +171,7 @@ class Dereferencer {
     debug(deref) printDebug(["path": &path, "s": &s]);
 
     if(path[0] != '/')
-      throw new Exception(format(ERR_ILLEGAL_REF, path, s.getPath()));
+      throw new InvalidRefException(path, s.getPath());
 
     return localResolve(path, s);
   }
@@ -155,7 +186,7 @@ class Dereferencer {
     Schema* found = (normal in all);
 
     if (found is null) {
-      throw new Exception(format(ERR_OUT_OF_SCOPE, path, s.getPath()));
+      throw new NotFoundException(path, s.getPath());
     }
 
     return *found;
@@ -165,11 +196,26 @@ class Dereferencer {
    * Scan given directory for entries matching SCHEMA_FILTER
    * and pass them to processFile
    */
-  private void scanDir() {
+  private bool scanDir() {
     debug(deref) printDebug([]);
+    string[] errors;
+
+    foreach (string file; dirEntries(inDir, SCHEMA_FILTER, SpanMode.breadth)) {
+      try {
+        processFile(file);
+      } catch (ValidationException e) {
+        errors ~= e.msg;
+      }
+    }
 
-    foreach (string file; dirEntries(inDir, SCHEMA_FILTER, SpanMode.breadth))
-      processFile(file);
+    if (errors.length > 0) {
+      writefln("Error: %d files could not be read due to JSON syntax errors", errors.length);
+      foreach (const string e; errors) {
+        writeln(e);
+      }
+      return false;
+    }
+    return true;
   }
 
   /**
@@ -180,15 +226,18 @@ class Dereferencer {
     debug(deref) printDebug(["path": &path]);
 
     const string body = readText(path);
+    const string shortPath = dirName(path[inDir.length..$]);
 
     try {
-      all[path] = new Schema(baseName(path), dirName(path[inDir.length + 1..$]), checkRefs(body), parseJSON(body));
+      all[path] = new Schema(baseName(path), shortPath, checkRefs(body), parseJSON(body));
     } catch(JSONException e) {
-      throw new Exception(format(ERR_JSON_PARSE, path), e);
+      throw new BadJsonException(shortPath, e);
     }
   }
 }
 
+
+
 private string defPath(const string next) {
   debug(deref) printDebug(["next": &next]);
 

source/lib/err/BadJsonException.d

@@ -0,0 +1,13 @@
+module lib.err.json;
+
+import std.json: JSONException;
+import std.string: format;
+
+import lib.err.valid : ValidationException;
+
+public class BadJsonException: ValidationException {
+  public this(const string file, const JSONException e) {
+    super(format(`%s:
+    %s`, file, e.msg));
+  }
+}

source/lib/err/InvalidRefException.d

@@ -0,0 +1,14 @@
+module lib.err.iref;
+
+import std.string: format;
+
+import lib.err.valid: ValidationException;
+
+public class InvalidRefException : ValidationException {
+  this(const string path, const string schema) {
+    super(format("References must be absolute paths to "
+    ~ `the root of the resource directory.  Example '/schema/wdk/...'.
+    Invalid Ref: %s
+    Schema File: %s`, path, schema));
+  }
+}

source/lib/err/NotFoundException.d

@@ -0,0 +1,13 @@
+module lib.err.nf;
+
+import std.string: format;
+
+import lib.err.valid: ValidationException;
+
+public class NotFoundException : ValidationException {
+  this(const string path, const string schema) {
+    super(format(`References not found in the resource directory.
+    Invalid Ref: %s
+    Schema File: %s`, path, schema));
+  }
+}

source/lib/err/ValidationException.d

@@ -0,0 +1,9 @@
+module lib.err.valid;
+
+import std.exception;
+
+public class ValidationException : Exception {
+  public this(const string message) {
+    super(message);
+  }
+}

source/lib/err/package.d

@@ -0,0 +1,6 @@
+module lib.err;
+
+public import lib.err.nf;
+public import lib.err.iref;
+public import lib.err.valid;
+public import lib.err.json;