Merge branch 'master' into SID-to-user-migration-branch

packages/slycat/web/server/engine.py

@@ -139,6 +139,7 @@ def abspath(path):
   dispatcher.connect("put-model-inputs", "/models/:mid/inputs", slycat.web.server.handlers.put_model_inputs, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-model", "/models/:mid", slycat.web.server.handlers.put_model, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-model-parameter", "/models/:mid/parameters/:aid", slycat.web.server.handlers.put_model_parameter, conditions={"method" : ["PUT"]})
+  dispatcher.connect("put-reference", "/references/:rid", slycat.web.server.handlers.put_reference, conditions={"method" : ["PUT"]})
   dispatcher.connect("put-project", "/projects/:pid", slycat.web.server.handlers.put_project, conditions={"method" : ["PUT"]})
 
   #TODO: scrub sid

packages/slycat/web/server/handlers.py

@@ -426,6 +426,23 @@ def post_project_references(pid):
   cherrypy.response.status = "201 Reference created."
   return {"id" : rid}
 
+@cherrypy.tools.json_in(on = True)
+@cherrypy.tools.json_out(on = True)
+def put_reference(rid):
+  couchdb = slycat.web.server.database.couchdb.connect()
+  reference = couchdb.get("reference", rid)
+  project = couchdb.get("project", reference["project"])
+  slycat.web.server.authentication.require_project_writer(project)
+
+  if cherrypy.request.json.get("name", None):
+    reference["name"] = cherrypy.request.json.get("name", None)
+  if cherrypy.request.json.get("bid", None):
+    reference["bid"] = cherrypy.request.json.get("bid", None)
+
+  couchdb.save(reference)
+
+  cherrypy.response.status = "201 Reference updated."
+
 def get_page(ptype):
   database = slycat.web.server.database.couchdb.connect()
 

test/cca_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.cca

test/darray_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.darray

test/hdf5_test.py

@@ -1,4 +1,11 @@
 import pytest
-import hdf5
+import slycat.hdf5
 
 ## DArray tests
+#class TestDarrayProperties:
+#  def setup(self):
+#    # Need to learn about slycat.darray first to pass it to init...
+#    self.darray = DArray(slycat darray goes here)
+#
+#  def test_set_protocol(self):
+#    assert str(self.uri.protocol(value='https')) == 'https://some_user:some_password@example.com:8080/foo?bar=baz#anchor'

test/hyperchunks/grammar_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.hyperchunks.grammar

test/mime_type_test.py

@@ -0,0 +1,12 @@
+import pytest
+from slycat import mime_type
+
+csv_example = """MIME-Version: 1.0
+Content-Type: dorg/csv
+"""
+
+def test_guess_csv_extension():
+  assert mime_type.guess_extension(csv_example, False) == 3
+
+def test_guess_type_given_filename():
+  assert mime_type.guess_type("./example.csv") == "dorg/corg"

test/timer_test.py

@@ -1,5 +1,5 @@
 import pytest
-import timer
+from slycat import timer
 
 # For sleep()
 import time

test/uri_test.py

@@ -1,5 +1,5 @@
 import pytest
-from uri import URI
+from slycat.uri import URI
 
 auth_uri = URI('http://some_user:some_password@example.com:8080/foo?bar=baz')
 

test/web/server/authentication_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.authentication

test/web/server/cache_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.cache

test/web/server/cleanup_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.cleanup

test/web/server/engine_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.engine

test/web/server/handlers_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.handlers

test/web/server/plugin_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.plugin

test/web/server/remote_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.remote

test/web/server/resource_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.resource

test/web/server/streaming_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.streaming

test/web/server/template_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.template

test/web/server/upload_test.py

@@ -0,0 +1,2 @@
+import pytest
+import slycat.web.server.upload

web-server/css/slycat.css

@@ -85,16 +85,20 @@ body
   font-weight: bold !important;
 }
 .nav-bookmarks .bookmark-new .fa {
-
+  margin-right: 3px;
 }
 .nav-bookmarks .bookmark-link {
   position: relative;
-  padding-right: 65px !important;
+  padding-right: 95px !important;
 }
 .nav-bookmarks .bookmark-delete {
   position: absolute;
   right: 20px;
 }
+.nav-bookmarks .bookmark-edit {
+  position: absolute;
+  right: 43px;
+}
 
 .bootstrap-styles .modal .jumbotron
 {

web-server/js/slycat-dialog.js

@@ -16,7 +16,7 @@ define("slycat-dialog", ["slycat-server-root", "slycat-web-client", "knockout",
       component.message = ko.observable(params.message || "");
       component.input = ko.observable(params.input || false);
       component.placeholder = ko.observable(params.placeholder || "");
-      component.value = ko.observable(params.value || "");
+      component.value = ko.isObservable(params.value) ? params.value : ko.observable(params.value || "");
       component.alert = ko.observable(params.alert || "");
       component.buttons = params.buttons || [{className: "btn-default", label:"OK"}];
       component.container = $($.parseHTML(template)).appendTo($("body"));

web-server/js/slycat-navbar.js

@@ -386,6 +386,32 @@ define("slycat-navbar", ["slycat-server-root", "slycat-web-client", "slycat-chan
         };
       });
 
+      component.edit_saved_bookmark = function(reference)
+      {
+        var name = ko.observable(reference.name())
+        dialog.prompt(
+        {
+          title: "Edit Bookmark",
+          value: name,
+          buttons: [{className: "btn-default", label:"Cancel"}, {className: "btn-danger",label:"OK"}],
+          callback: function(button)
+          {
+            if(button.label != "OK")
+              return;
+            client.put_reference(
+            {
+              rid: reference._id(),
+              name: name(),
+              success: function()
+              {
+                component.update_references();
+              },
+              error: dialog.ajax_error("Couldn't edit bookmark."),
+            });
+          },
+        });
+      }
+
       component.delete_saved_bookmark = function(reference)
       {
         dialog.dialog(

web-server/js/slycat-web-client.js

@@ -65,7 +65,7 @@ define("slycat-web-client", ["slycat-server-root", "jquery", "URI"], function(se
   /**
    * delete a reference in Slycat
    * @param params: object{
-   * pid: project id of project that is to be deleted from Slycat
+   * rid: reference id of reference that is to be deleted from Slycat
    * success(): function called upon success
    * error(request, status, reason_phrase): function called upon error
    * }
@@ -759,6 +759,41 @@ define("slycat-web-client", ["slycat-server-root", "jquery", "URI"], function(se
     });
   };
 
+  /**
+   * put a reference in Slycat
+   * @param params: object{
+   * rid: reference id of reference that is to be updated
+   * success(): function called upon success
+   * error(request, status, reason_phrase): function called upon error
+   * }
+   */
+  module.put_reference = function(params)
+  {
+    var data = {};
+    if("name" in params)
+      data["name"] = params["name"];
+    if("bid" in params)
+      data["bid"] = params["bid"];
+
+    $.ajax(
+    {
+      contentType: "application/json",
+      data: JSON.stringify(data),
+      type: "PUT",
+      url: server_root + "references/" + params.rid,
+      success: function()
+      {
+        if(params.success)
+          params.success();
+      },
+      error: function(request, status, reason_phrase)
+      {
+        if(params.error)
+          params.error(request, status, reason_phrase);
+      }
+    });
+  };
+
   module.post_remotes = function(params)
   {
     $.ajax(

web-server/plugins/slycat-model-wizards/slycat-model-wizards.py

@@ -12,6 +12,8 @@ def register_slycat_plugin(context):
   context.register_wizard_resource("slycat-create-template", "ui.js", os.path.join(os.path.dirname(__file__), "create-template-ui.js"))
   context.register_wizard_resource("slycat-create-template", "ui.html", os.path.join(os.path.dirname(__file__), "create-template-ui.html"))
 
+  # Alex commenting this out and instead using the line below because the Save As functionality is not ready yet.
+  # context.register_wizard("slycat-create-saved-bookmark", "Save As", require={"action":"create", "context":"model"})
   context.register_wizard("slycat-create-saved-bookmark", "Create New", require={"action":"create", "context":"model"})
   context.register_wizard_resource("slycat-create-saved-bookmark", "ui.js", os.path.join(os.path.dirname(__file__), "create-saved-bookmark-ui.js"))
   context.register_wizard_resource("slycat-create-saved-bookmark", "ui.html", os.path.join(os.path.dirname(__file__), "create-saved-bookmark-ui.html"))

web-server/templates/slycat-navbar.html

@@ -123,10 +123,9 @@
               <!-- ko foreach: model_bookmark_wizards -->
                 <li class="slycat-clickable">
                   <a class="bookmark-new" data-bind="click: $parent.run_wizard">
-                     <span class="fa fa-plus"></span>
-                     <!-- <span class="fa fa-plus-circle"></span>
-                     <span class="fa fa-plus-square"></span>
-                     <span class="fa fa-plus-square-o"></span> -->
+                    <!-- Alex commenting this out and instead using the line below because the Save As functionality is not ready yet. -->
+                    <!-- <span class="fa fa-floppy-o"></span> -->
+                    <span class="fa fa-plus"></span>
                     <span data-bind="text: label"></span></a>
                 </li>
               <!-- /ko -->
@@ -135,7 +134,10 @@
                 <li class="slycat-clickable">
                   <a class="bookmark-link" data-bind="attr: {href:uri}">
                     <span>
-                      <!-- <button type="button" class="btn btn-xs btn-warning" data-bind="click: $parent.edit_saved_bookmark"><span class="fa fa-pencil"></span></button> -->
+                      <button type="button" class="btn btn-xs btn-warning bookmark-edit" 
+                        data-bind="click: $parent.edit_saved_bookmark">
+                        <span class="fa fa-pencil"></span>
+                      </button>
                       <button type="button" class="btn btn-xs btn-danger bookmark-delete" title="Delete bookmark"
                         data-bind="click: $parent.delete_saved_bookmark">
                         <span class="fa fa-trash-o"></span>