Add support for knitting in alternate directories

NEWS.md

@@ -7,4 +7,5 @@
 ### Miscellaneous
 
 * Implement support for changing editor tabs with the mouse wheel
+* Add option to knit in current working directory or project directory
 

src/cpp/session/SessionMain.cpp

@@ -686,6 +686,9 @@ void handleClientInit(const boost::function<void()>& initFunction,
    sessionInfo["knit_params_available"] =
          modules::rmarkdown::knitParamsAvailable();
 
+   sessionInfo["knit_working_dir_available"] = 
+         modules::rmarkdown::knitWorkingDirAvailable();
+
    sessionInfo["clang_available"] = modules::clang::isAvailable();
 
    // don't show help home until we figure out a sensible heuristic

src/cpp/session/modules/rmarkdown/NotebookDocQueue.cpp

@@ -31,6 +31,7 @@ using namespace rstudio::core;
 #define kDocQueueMaxUnits       "max_units"
 #define kDocQueueCommitMode     "commit_mode"
 #define kDocQueueCompletedUnits "completed_units"
+#define kDocQueueWorkingDir     "working_dir"
 
 namespace rstudio {
 namespace session {
@@ -39,8 +40,8 @@ namespace rmarkdown {
 namespace notebook {
 
 NotebookDocQueue::NotebookDocQueue(const std::string& docId, 
-      const std::string& jobDesc, CommitMode commitMode,
-      int pixelWidth, int charWidth, int maxUnits) :
+      const std::string& jobDesc, const std::string& workingDir, 
+      CommitMode commitMode, int pixelWidth, int charWidth, int maxUnits) :
       docId_(docId),
       jobDesc_(jobDesc),
       commitMode_(commitMode),
@@ -61,10 +62,19 @@ NotebookDocQueue::NotebookDocQueue(const std::string& docId,
 
    // read the default working dir; if it specifies a valid directory, use it
    // as the working directory for executing chunks in this document
-   std::string workingDir;
-   json::readObject(vals, kChunkWorkingDir, &workingDir);
-   if (!workingDir.empty())
+   std::string docWorkingDir;
+   json::readObject(vals, kChunkWorkingDir, &docWorkingDir);
+   if (!docWorkingDir.empty())
+   {
+      // working directory set in setup chunk (i.e. knitr root.dir) takes
+      // precedence
+      setWorkingDir(docWorkingDir);
+   }
+   else if (!workingDir.empty())
+   {
+      // working directory given by IDE (current dir or project dir)
       setWorkingDir(workingDir);
+   }
 
    // read external code chunk contents
    json::readObject(vals, kChunkExternals, &externalChunks_);
@@ -90,6 +100,7 @@ json::Object NotebookDocQueue::toJson() const
    json::Object queue;
    queue[kDocQueueId]             = docId_;
    queue[kDocQueueJobDesc]        = jobDesc_;
+   queue[kDocQueueWorkingDir]     = workingDir_.absolutePath();
    queue[kDocQueueCommitMode]     = commitMode_;
    queue[kDocQueuePixelWidth]     = pixelWidth_;
    queue[kDocQueueCharWidth]      = charWidth_;
@@ -106,10 +117,11 @@ core::Error NotebookDocQueue::fromJson(const core::json::Object& source,
    // extract contained unit for manipulation
    json::Array units; 
    int commitMode = 0, pixelWidth = 0, charWidth = 0, maxUnits = 0;
-   std::string docId, jobDesc;
+   std::string docId, jobDesc, workingDir;
    Error error = json::readObject(source, 
          kDocQueueId,         &docId,
          kDocQueueJobDesc,    &jobDesc,
+         kDocQueueWorkingDir, &workingDir,
          kDocQueueCommitMode, &commitMode,
          kDocQueuePixelWidth, &pixelWidth,
          kDocQueueCharWidth,  &charWidth,
@@ -118,7 +130,7 @@ core::Error NotebookDocQueue::fromJson(const core::json::Object& source,
    if (error)
       return error;
 
-   *pQueue = boost::make_shared<NotebookDocQueue>(docId, jobDesc,
+   *pQueue = boost::make_shared<NotebookDocQueue>(docId, jobDesc, workingDir,
          static_cast<CommitMode>(commitMode), pixelWidth, charWidth,
          maxUnits);
 

src/cpp/session/modules/rmarkdown/NotebookDocQueue.hpp

@@ -40,7 +40,8 @@ class NotebookDocQueue : boost::noncopyable
 {
 public:
    NotebookDocQueue(const std::string& docId, const std::string& jobDesc,
-         CommitMode commitMode, int pixelWith, int charWidth, int maxUnits);
+         const std::string& workingDir, CommitMode commitMode, int pixelWith, 
+         int charWidth, int maxUnits);
 
    static core::Error fromJson(const core::json::Object& source,
       boost::shared_ptr<NotebookDocQueue>* pQueue);

src/cpp/session/modules/rmarkdown/SessionRMarkdown.cpp

@@ -234,13 +234,15 @@ class RenderRmd : public async_r::AsyncRProcess
                                               bool sourceNavigation,
                                               bool asTempfile,
                                               bool asShiny,
-                                              std::string existingOutputFile)
+                                              const std::string& existingOutputFile,
+                                              const std::string& workingDir)
    {
       boost::shared_ptr<RenderRmd> pRender(new RenderRmd(targetFile,
                                                          sourceLine,
                                                          sourceNavigation,
                                                          asShiny));
-      pRender->start(format, encoding, paramsFile, asTempfile, existingOutputFile);
+      pRender->start(format, encoding, paramsFile, asTempfile, 
+                     existingOutputFile, workingDir);
       return pRender;
    }
 
@@ -301,7 +303,8 @@ class RenderRmd : public async_r::AsyncRProcess
               const std::string& encoding,
               const std::string& paramsFile,
               bool asTempfile,
-              std::string existingOutputFile)
+              const std::string& existingOutputFile,
+              const std::string& workingDir)
    {
       Error error;
       json::Object dataJson;
@@ -355,6 +358,13 @@ class RenderRmd : public async_r::AsyncRProcess
          renderOptions += ", params = readRDS('" + paramsFile + "')";
       }
 
+      // use the stated working directory if specified
+      if (!workingDir.empty())
+      {
+         renderOptions += ", knit_root_dir = '" + 
+                          string_utils::utf8ToSystem(workingDir) + "'";
+      }
+
       // output to a temporary directory if specified (no need to do this
       // for Shiny since it already renders to a temporary dir)
       if (asTempfile && !isShiny_)
@@ -897,7 +907,8 @@ void doRenderRmd(const std::string& file,
                  bool sourceNavigation,
                  bool asTempfile,
                  bool asShiny,
-                 std::string existingOutputFile,
+                 const std::string& existingOutputFile,
+                 const std::string& workingDir,
                  json::JsonRpcResponse* pResponse)
 {
    if (s_pCurrentRender_ &&
@@ -916,7 +927,8 @@ void doRenderRmd(const std::string& file,
                sourceNavigation,
                asTempfile,
                asShiny,
-               existingOutputFile);
+               existingOutputFile,
+               workingDir);
       pResponse->setResult(true);
    }
 }
@@ -925,7 +937,8 @@ Error renderRmd(const json::JsonRpcRequest& request,
                 json::JsonRpcResponse* pResponse)
 {
    int line = -1, type = kRenderTypeStatic;
-   std::string file, format, encoding, paramsFile, existingOutputFile;
+   std::string file, format, encoding, paramsFile, existingOutputFile,
+               workingDir;
    bool asTempfile = false;
    Error error = json::readParams(request.params,
                                   &file,
@@ -935,7 +948,8 @@ Error renderRmd(const json::JsonRpcRequest& request,
                                   &paramsFile,
                                   &asTempfile,
                                   &type,
-                                  &existingOutputFile);
+                                  &existingOutputFile,
+                                  &workingDir);
    if (error)
       return error;
 
@@ -978,7 +992,7 @@ Error renderRmd(const json::JsonRpcRequest& request,
       // not a notebook, do render work
       doRenderRmd(file, line, format, encoding, paramsFile,
                   true, asTempfile, type == kRenderTypeShiny, existingOutputFile, 
-                  pResponse);
+                  workingDir, pResponse);
    }
 
    return Success();
@@ -999,7 +1013,7 @@ Error renderRmdSource(const json::JsonRpcRequest& request,
       return error;
 
    doRenderRmd(rmdTempFile.absolutePath(), -1, "", "UTF-8", "",
-               false, false, false, "", pResponse);
+               false, false, false, "", "", pResponse);
 
    return Success();
 }
@@ -1356,6 +1370,10 @@ bool knitParamsAvailable()
           module_context::isPackageVersionInstalled("knitr", "1.10.18");
 }
 
+bool knitWorkingDirAvailable()
+{
+   return module_context::isPackageVersionInstalled("rmarkdown", "1.1.9017");
+}
 
 bool rmarkdownPackageAvailable()
 {

src/cpp/session/modules/rmarkdown/SessionRMarkdown.hpp

@@ -37,6 +37,8 @@ bool rmarkdownPackageAvailable();
 
 bool knitParamsAvailable();
 
+bool knitWorkingDirAvailable();
+
 core::Error evaluateRmdParams(const std::string& docId);
 
 core::Error initialize();

src/gwt/src/org/rstudio/core/client/widget/DocShadowPropMenuItem.java

@@ -0,0 +1,79 @@
+/*
+ * DocShadowPropMenuItem.java
+ *
+ * Copyright (C) 2009-16 by RStudio, Inc.
+ *
+ * Unless you have received this program directly from RStudio pursuant
+ * to the terms of a commercial license agreement with RStudio, then
+ * this program is licensed to you under the terms of version 3 of the
+ * GNU Affero General Public License. This program is distributed WITHOUT
+ * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
+ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
+ * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
+ *
+ */
+package org.rstudio.core.client.widget;
+
+import org.rstudio.studio.client.workbench.prefs.model.Prefs.PrefValue;
+import org.rstudio.studio.client.workbench.views.source.model.DocUpdateSentinel;
+
+import com.google.gwt.event.logical.shared.ValueChangeEvent;
+import com.google.gwt.event.logical.shared.ValueChangeHandler;
+
+/**
+ * DocShadowPropMenuItem is a menu item representing a local document property
+ * that shadows (overrides) a global property. 
+ */
+public class DocShadowPropMenuItem extends DocPropMenuItem
+{
+   /**
+    * Creates a new shadowed document property menu item.
+    * 
+    * @param label The label for the menu item
+    * @param docUpdate The update sentinel 
+    * @param pref The global preference to track
+    * @param propName The name of the document property to track
+    * @param targetValue The value of the document property when the menu item
+    *   is checked.
+    */
+   public DocShadowPropMenuItem(String label, DocUpdateSentinel docUpdate,
+         PrefValue<String> pref, String propName, String targetValue)
+   {
+      super(label, 
+            docUpdate, 
+            docUpdate.getProperty(propName, pref.getValue()) == targetValue,
+            propName,
+            targetValue);
+
+      propName_ = propName;
+      sentinel_ = docUpdate;
+      pref_ = pref;
+      target_ = targetValue;
+
+      pref_.addValueChangeHandler(new ValueChangeHandler<String>()
+      {
+         @Override
+         public void onValueChange(ValueChangeEvent<String> event)
+         {
+            onStateChanged();
+         }
+      });
+      onStateChanged();
+   }
+
+   @Override
+   public boolean isChecked()
+   {
+      if (sentinel_ == null)
+         return false;
+      else if (sentinel_.hasProperty(propName_))
+         return super.isChecked();
+      else
+         return pref_.getValue() == target_;
+   }
+
+   private final String propName_;
+   private final String target_;
+   private final DocUpdateSentinel sentinel_;
+   private final PrefValue<String> pref_;
+}

src/gwt/src/org/rstudio/core/client/widget/ToolbarPopupMenu.java

@@ -1,7 +1,7 @@
 /*
  * ToolbarPopupMenu.java
  *
- * Copyright (C) 2009-12 by RStudio, Inc.
+ * Copyright (C) 2009-16 by RStudio, Inc.
  *
  * Unless you have received this program directly from RStudio pursuant
  * to the terms of a commercial license agreement with RStudio, then
@@ -22,9 +22,11 @@
 import com.google.gwt.dom.client.NativeEvent;
 import com.google.gwt.event.dom.client.KeyCodes;
 import com.google.gwt.event.shared.HandlerRegistration;
+import com.google.gwt.safehtml.shared.SafeHtml;
 import com.google.gwt.user.client.Event;
 import com.google.gwt.user.client.Event.NativePreviewEvent;
 import com.google.gwt.user.client.Event.NativePreviewHandler;
+import com.google.gwt.user.client.ui.MenuBar;
 import com.google.gwt.user.client.ui.MenuItem;
 import com.google.gwt.user.client.ui.MenuItemSeparator;
 import com.google.gwt.user.client.ui.Widget;
@@ -81,6 +83,11 @@ public void addItem(MenuItem menuItem)
       menuBar_.addItem(menuItem);
    }
 
+   public void addItem(SafeHtml html, MenuBar popup)
+   {
+      menuBar_.addItem(html, popup);
+   }
+
    public void insertItem(MenuItem menuItem, int beforeIndex)
    {
      ScheduledCommand command = menuItem.getScheduledCommand() ;

src/gwt/src/org/rstudio/core/client/widget/ToolbarPopupMenuButton.java

@@ -1,7 +1,7 @@
 /*
  * ToolbarPopupMenuButton.java
  *
- * Copyright (C) 2009-12 by RStudio, Inc.
+ * Copyright (C) 2009-16 by RStudio, Inc.
  *
  * Unless you have received this program directly from RStudio pursuant
  * to the terms of a commercial license agreement with RStudio, then
@@ -21,7 +21,9 @@
 import com.google.gwt.event.logical.shared.ValueChangeEvent;
 import com.google.gwt.event.logical.shared.ValueChangeHandler;
 import com.google.gwt.event.shared.HandlerRegistration;
+import com.google.gwt.safehtml.shared.SafeHtmlBuilder;
 import com.google.gwt.user.client.Command;
+import com.google.gwt.user.client.ui.MenuBar;
 import com.google.gwt.user.client.ui.MenuItem;
 
 public class ToolbarPopupMenuButton extends ToolbarButton
@@ -74,6 +76,15 @@ public void execute()
       getMenu().addItem(item);
    }
 
+   public void addMenuItem(MenuBar subMenu, String label)
+   {
+      SafeHtmlBuilder html = new SafeHtmlBuilder();
+      html.appendHtmlConstant("<span style=\"margin-left: 25px;\">");
+      html.appendEscaped(label);
+      html.appendHtmlConstant("</span>");
+      getMenu().addItem(html.toSafeHtml(), subMenu);
+   }
+
    public void addSeparator()
    {
       getMenu().addSeparator();