Add javascript code snippet validation (#662)

* Add validation for javascript expressions.

Fixes #594. To do this, it is needed to add jshint and refractor
js_sandbox to so that it can be useful for this.

Author: ThomasHickman

MANIFEST.in

@@ -19,6 +19,9 @@ include cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/*.yml
 include cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/*.md
 include cwltool/cwlNodeEngine.js
 include cwltool/cwlNodeEngineJSConsole.js
+include cwltool/cwlNodeEngineWithContext.js
 include cwltool/extensions.yml
+include cwltool/jshint/jshint_wrapper.js
+include cwltool/jshint/jshint.js
 global-exclude *~
 global-exclude *.pyc

appveyor.yml

@@ -1,6 +1,8 @@
 version: .{build}-{branch}
 
 environment:
+  nodejs_version: "8"
+
   SYSTEMROOT: "C:\\WINDOWS"
 
   matrix:
@@ -22,18 +24,18 @@ environment:
 
 
 install:
+  # Get the latest stable version of Node.js or io.js
+  - ps: Install-Product node $env:nodejs_version
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-  - "python --version"
-  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
 
 build_script:
-  - "%CMD_IN_ENV% python -m pip install -U setuptools"
+  - "%CMD_IN_ENV% python -m pip install -U setuptools pip"
+  - "%CMD_IN_ENV% pip install pytest mock"
   - "%CMD_IN_ENV% pip install ."
 
 
 test_script:
-
-  - "%CMD_IN_ENV% python setup.py test"
+  - "%CMD_IN_ENV% py.test --verbose -p no:cacheprovider"
 
 branches:
   only:

cwltool/argparser.py

@@ -152,6 +152,11 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         "timestamps to the errors, warnings, and "
                         "notifications.")
     parser.add_argument("--js-console", action="store_true", help="Enable javascript console output")
+    parser.add_argument("--disable-js-validation", action="store_true", help="Disable javascript validation.")
+    parser.add_argument("--js-hint-options-file",
+                        type=Text,
+                        help="File of options to pass to jshint."
+                        "This includes the added option \"includewarnings\". ")
     dockergroup = parser.add_mutually_exclusive_group()
     dockergroup.add_argument("--user-space-docker-cmd", metavar="CMD",
                         help="(Linux/OS X only) Specify a user space docker "

cwltool/cwlNodeEngineWithContext.js

@@ -0,0 +1,37 @@
+"use strict";
+process.stdin.setEncoding("utf8");
+var incoming = "";
+var firstInput = true;
+var context = {};
+
+process.stdin.on("data", function(chunk) {
+  incoming += chunk;
+  var i = incoming.indexOf("\n");
+  while (i > -1) {
+    try{
+      var input = incoming.substr(0, i);
+      incoming = incoming.substr(i+1);
+      var fn = JSON.parse(input);
+      if(firstInput){
+        context = require("vm").runInNewContext(fn, {});
+      }
+      else{
+        process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, context)) + "\n");
+      }
+    }
+    catch(e){
+      console.error(e);
+    }
+    if(firstInput){
+      firstInput = false;
+    }
+    else{
+      /*strings to indicate the process has finished*/
+      console.log("r1cepzbhUTxtykz5XTC4");
+      console.error("r1cepzbhUTxtykz5XTC4");
+    }
+
+    i = incoming.indexOf("\n");
+  }
+});
+process.stdin.on("end", process.exit);

cwltool/jshint/jshint.js

@@ -0,0 +1,47 @@
+"use strict";
+// set a global object, in order for jshint to work
+var global = this;
+
+function validateJS(input) {
+  var jshintGlobalsObj = {};
+  input.globals.forEach(function (global) {
+    jshintGlobalsObj[global] = true;
+  })
+  var includewarnings;
+
+  if (input.options.includewarnings !== undefined) {
+    includewarnings = input.options.includewarnings;
+    delete input.options.includewarnings;
+  }
+
+  JSHINT(
+    input.code,
+    input.options,
+    jshintGlobalsObj
+  )
+
+  var jshintData = JSHINT.data();
+  if (jshintData.errors !== undefined) {
+    if (includewarnings !== undefined) {
+      jshintData.errors = jshintData.errors.filter(function (error) {
+        return includewarnings.indexOf(error.code) !== -1 || error.code[0] == "E";
+      })
+    }
+
+    jshintData.errors.forEach(function (error) {
+      if (error.code == "W104" || error.code == "W119") {
+        if (error.code == "W104"){
+          var jslint_suffix = " (use 'esversion: 6') or Mozilla JS extensions (use moz)."
+        }
+        else{
+          var jslint_suffix = " (use 'esversion: 6')"
+        }
+
+        error.reason = error.reason.slice(0, -jslint_suffix.length - 1) +
+          ". CWL only supports ES5.1";
+      }
+    })
+  }
+
+  return jshintData;
+}

cwltool/jshint/jshint_wrapper.js

@@ -187,7 +187,7 @@ def validate_document(document_loader,  # type: Loader
                       fetcher_constructor=None,  # type: FetcherConstructorType
                       skip_schemas=None,  # type: bool
                       overrides=None,  # type: List[Dict]
-                      metadata=None,  # type: Optional[Dict]
+                      metadata=None  # type: Optional[Dict]
                       ):
     # type: (...) -> Tuple[Loader, Names, Union[Dict[Text, Any], List[Dict[Text, Any]]], Dict[Text, Any], Text]
     """Validate a CWL document."""

cwltool/load_tool.py

@@ -30,6 +30,7 @@
 from schema_salad.sourceline import SourceLine
 from six.moves import urllib
 
+from .validate_js import validate_js_expressions
 from .utils import cmp_like_py2
 from .builder import Builder
 from .errors import UnsupportedRequirement, WorkflowException
@@ -548,6 +549,19 @@ def __init__(self, toolpath_object, **kwargs):
                                                (Text(e), self.tool["id"],
                                                 json.dumps(self.outputs_record_schema, indent=4)))
 
+        if toolpath_object.get("class") is not None and not kwargs.get("disable_js_validation", False):
+            if kwargs.get("js_hint_options_file") is not None:
+                try:
+                    with open(kwargs["js_hint_options_file"]) as options_file:
+                        validate_js_options = json.load(options_file)
+                except (OSError, ValueError) as e:
+                    _logger.error("Failed to read options file %s" % kwargs["js_hint_options_file"])
+                    raise e
+            else:
+                validate_js_options = None
+
+            validate_js_expressions(cast(CommentedMap, toolpath_object), self.doc_schema.names[toolpath_object["class"]], validate_js_options)
+
     def _init_job(self, joborder, **kwargs):
         # type: (Dict[Text, Text], **Any) -> Builder
         """