Merge branch 'develop' of github.com:parklab/refinery-platform into d…

…evelop

.gitignore

@@ -62,10 +62,10 @@ deployment/Puppetfile.lock
 /refinery/ui/bower_components/
 /refinery/ui/node_modules/
 /refinery/ui/.tmp/
-/media/
-/static/
 /isa-tab/
 /import/
+/static/
+/transfer/
 *.conflict
 *.sublime-*
 .editorconfig

.travis.yml

@@ -0,0 +1,28 @@
+language: python
+python:
+  - 2.7
+services:
+  - postgresql
+install:
+  - pip install -r requirements.txt
+env:
+  - DJANGO_SETTINGS_MODULE=settings.dev
+before_script:
+  - createuser --createdb --no-superuser --no-createrole vagrant
+  - createdb -O vagrant refinery
+  - cd refinery
+  - cp config.json.sample config.json
+  - python manage.py syncdb --migrate --noinput
+script:
+  - python manage.py test analysis_manager
+  - python manage.py test annotation_server
+  - python manage.py test core
+  - python manage.py test data_set_manager
+  - python manage.py test file_server
+  - python manage.py test file_store
+  - python manage.py test galaxy_connector
+  - python manage.py test visualization_manager
+  - python manage.py test workflow_manager
+notifications:
+  slack:
+    secure: nDs9Oj08nRizuD0edl6WcrSgaTPMyITQjZc4qPZpt+yOxUehWbrAmVhqYypfyvdj4qSi1E72rPTXftuBB1E1IZBgX4CCkrCkWGLgIxHaaValTd64oOX66eC3BbSehQxuJB7w1DWw54xBUkTy6+ufjAqiwhLpoEUeE296urAWYHU=

README.md

@@ -0,0 +1,91 @@
+# Refinery Platform [![Build Status](https://travis-ci.org/parklab/refinery-platform.svg?branch=develop)](https://travis-ci.org/parklab/refinery-platform)
+
+## Installing and Launching for Development
+
+### Prerequisites
+
+Install [Git][gi], [Vagrant][va] (1.7.2) and [Virtualbox][vb] (4.3.26).
+
+### Configure and Load Virtual Machine
+
+```bash
+$ git clone [email protected]:parklab/refinery-platform.git
+$ cd refinery-platform
+$ vagrant up
+```
+
+The above step should take about 15 minutes depending on the speed of
+your machine and Internet connection. If you get an error, simply retry
+by:
+
+```bash
+$ vagrant provision
+```
+
+Open <http://192.168.50.50:8000/> in your web browser.
+
+### Configure Deployment Environment on the Host
+
+Create a Python 2.7 virtual environment (optional but recommended,
+assumes virtualenvwrapper is installed, for example in Ubuntu: apt-get
+install virtualenvwrapper):
+
+```bash
+$ mkvirtualenv -a $(pwd) refinery-deployment
+```
+
+Install Fabric (assumes header files for Python are installed, for
+example in Ubuntu: apt-get install python-dev):
+
+```bash
+$ pip install -r deployment/requirements.txt
+```
+
+Use fabricrc.sample to update or initialize Fabric configuration, for
+example:
+
+```bash
+$ cp fabricrc.sample ~/.fabricrc
+```
+
+To pull the latest code and update Refinery installation:
+
+```bash
+$ fab vm update
+```
+
+### Refinery Operations on the VM
+
+Connect to the initialized VM:
+
+```bash
+$ vagrant ssh
+$ workon refinery-platform
+$ ./manage.py [command]
+```
+
+Log in to Refinery (<http://192.168.50.50:8000/>) with the default guest
+user account (username: guest, password: guest).
+
+Log in to Django admin UI (<http://192.168.50.50:8000/admin/>) with the
+default superuser account (username: admin, password: refinery).
+
+Please see [installation notes] for more details, including information
+on how to configure Galaxy for this setup.
+
+## Troubleshooting
+
+- Refinery deployment requires a lot of external dependencies. You
+  might have to run `vagrant provision` repeatedly to install all
+  dependencies successfully. *Any errors* in the output of
+  `vagrant provision` indicate that you have to re-run the command.
+- If you run into a build error in OS X when trying to install Fabric:
+  `export C_INCLUDE_PATH=/usr/local/include`
+- If you have a VPN connection running, you may need to disconnect and
+  reconnect before you can access the VM. In some cases you may have
+  to reboot the host machine.
+
+[gi]: http://git-scm.com/
+[va]: http://www.vagrantup.com/
+[vb]: https://www.virtualbox.org/
+[in]: https://refinery-platform.readthedocs.org/en/latest/administrator/setup.html

deployment/manifests/default.pp

@@ -97,10 +97,7 @@
   group => $appgroup,
 }
 
-file { ["/vagrant/media",
-        "/vagrant/static",
-        "/vagrant/isa-tab",
-        "/vagrant/import" ]:
+file { ["/vagrant/isa-tab", "/vagrant/import", "/vagrant/static"]:
   ensure => directory,
   owner => $appuser,
   group => $appgroup,
@@ -125,7 +122,6 @@
   user => $appuser,
   group => $appgroup,
   require => [
-               File["/vagrant/media"],
                Python::Requirements[$requirements],
                Postgresql::Server::Db["refinery"]
              ],
@@ -282,6 +278,7 @@
 ->
 exec { "supervisord":
   command => "${virtualenv}/bin/supervisord",
+  environment => ["DJANGO_SETTINGS_MODULE=settings.dev"],
   cwd => $project_root,
   creates => "/tmp/supervisord.pid",
   user => $appuser,

docs/_themes/flask_theme_support.py

@@ -10,77 +10,89 @@ class FlaskyStyle(Style):
 
     styles = {
         # No corresponding class for the following:
-        #Text:                     "", # class:  ''
-        Whitespace:                "underline #f8f8f8",      # class: 'w'
-        Error:                     "#a40000 border:#ef2929", # class: 'err'
-        Other:                     "#000000",                # class 'x'
+        # Text:                     "", # class:  ''
+        Whitespace:                "underline #f8f8f8",       # class: 'w'
+        Error:                     "#a40000 border:#ef2929",  # class: 'err'
+        Other:                     "#000000",                 # class 'x'
 
-        Comment:                   "italic #8f5902", # class: 'c'
-        Comment.Preproc:           "noitalic",       # class: 'cp'
+        Comment:                   "italic #8f5902",  # class: 'c'
+        Comment.Preproc:           "noitalic",        # class: 'cp'
 
-        Keyword:                   "bold #004461",   # class: 'k'
-        Keyword.Constant:          "bold #004461",   # class: 'kc'
-        Keyword.Declaration:       "bold #004461",   # class: 'kd'
-        Keyword.Namespace:         "bold #004461",   # class: 'kn'
-        Keyword.Pseudo:            "bold #004461",   # class: 'kp'
-        Keyword.Reserved:          "bold #004461",   # class: 'kr'
-        Keyword.Type:              "bold #004461",   # class: 'kt'
+        Keyword:                   "bold #004461",    # class: 'k'
+        Keyword.Constant:          "bold #004461",    # class: 'kc'
+        Keyword.Declaration:       "bold #004461",    # class: 'kd'
+        Keyword.Namespace:         "bold #004461",    # class: 'kn'
+        Keyword.Pseudo:            "bold #004461",    # class: 'kp'
+        Keyword.Reserved:          "bold #004461",    # class: 'kr'
+        Keyword.Type:              "bold #004461",    # class: 'kt'
 
-        Operator:                  "#582800",   # class: 'o'
-        Operator.Word:             "bold #004461",   # class: 'ow' - like keywords
+        Operator:                  "#582800",         # class: 'o'
+        # class: 'ow' - like keywords
+        Operator.Word:             "bold #004461",
 
-        Punctuation:               "bold #000000",   # class: 'p'
+        Punctuation:               "bold #000000",    # class: 'p'
 
         # because special names such as Name.Class, Name.Function, etc.
         # are not recognized as such later in the parsing, we choose them
         # to look the same as ordinary variables.
-        Name:                      "#000000",        # class: 'n'
-        Name.Attribute:            "#c4a000",        # class: 'na' - to be revised
-        Name.Builtin:              "#004461",        # class: 'nb'
-        Name.Builtin.Pseudo:       "#3465a4",        # class: 'bp'
-        Name.Class:                "#000000",        # class: 'nc' - to be revised
-        Name.Constant:             "#000000",        # class: 'no' - to be revised
-        Name.Decorator:            "#888",           # class: 'nd' - to be revised
-        Name.Entity:               "#ce5c00",        # class: 'ni'
-        Name.Exception:            "bold #cc0000",   # class: 'ne'
-        Name.Function:             "#000000",        # class: 'nf'
-        Name.Property:             "#000000",        # class: 'py'
-        Name.Label:                "#f57900",        # class: 'nl'
-        Name.Namespace:            "#000000",        # class: 'nn' - to be revised
-        Name.Other:                "#000000",        # class: 'nx'
-        Name.Tag:                  "bold #004461",   # class: 'nt' - like a keyword
-        Name.Variable:             "#000000",        # class: 'nv' - to be revised
-        Name.Variable.Class:       "#000000",        # class: 'vc' - to be revised
-        Name.Variable.Global:      "#000000",        # class: 'vg' - to be revised
-        Name.Variable.Instance:    "#000000",        # class: 'vi' - to be revised
+        Name:                      "#000000",         # class: 'n'
+        # class: 'na' - to be revised
+        Name.Attribute:            "#c4a000",
+        Name.Builtin:              "#004461",         # class: 'nb'
+        Name.Builtin.Pseudo:       "#3465a4",         # class: 'bp'
+        # class: 'nc' - to be revised
+        Name.Class:                "#000000",
+        # class: 'no' - to be revised
+        Name.Constant:             "#000000",
+        # class: 'nd' - to be revised
+        Name.Decorator:            "#888",
+        Name.Entity:               "#ce5c00",         # class: 'ni'
+        Name.Exception:            "bold #cc0000",    # class: 'ne'
+        Name.Function:             "#000000",         # class: 'nf'
+        Name.Property:             "#000000",         # class: 'py'
+        Name.Label:                "#f57900",         # class: 'nl'
+        # class: 'nn' - to be revised
+        Name.Namespace:            "#000000",
+        Name.Other:                "#000000",         # class: 'nx'
+        # class: 'nt' - like a keyword
+        Name.Tag:                  "bold #004461",
+        # class: 'nv' - to be revised
+        Name.Variable:             "#000000",
+        # class: 'vc' - to be revised
+        Name.Variable.Class:       "#000000",
+        # class: 'vg' - to be revised
+        Name.Variable.Global:      "#000000",
+        # class: 'vi' - to be revised
+        Name.Variable.Instance:    "#000000",
 
-        Number:                    "#990000",        # class: 'm'
+        Number:                    "#990000",         # class: 'm'
 
-        Literal:                   "#000000",        # class: 'l'
-        Literal.Date:              "#000000",        # class: 'ld'
+        Literal:                   "#000000",         # class: 'l'
+        Literal.Date:              "#000000",         # class: 'ld'
 
-        String:                    "#4e9a06",        # class: 's'
-        String.Backtick:           "#4e9a06",        # class: 'sb'
-        String.Char:               "#4e9a06",        # class: 'sc'
-        String.Doc:                "italic #8f5902", # class: 'sd' - like a comment
-        String.Double:             "#4e9a06",        # class: 's2'
-        String.Escape:             "#4e9a06",        # class: 'se'
-        String.Heredoc:            "#4e9a06",        # class: 'sh'
-        String.Interpol:           "#4e9a06",        # class: 'si'
-        String.Other:              "#4e9a06",        # class: 'sx'
-        String.Regex:              "#4e9a06",        # class: 'sr'
-        String.Single:             "#4e9a06",        # class: 's1'
-        String.Symbol:             "#4e9a06",        # class: 'ss'
+        String:                    "#4e9a06",         # class: 's'
+        String.Backtick:           "#4e9a06",         # class: 'sb'
+        String.Char:               "#4e9a06",         # class: 'sc'
+        # class: 'sd' - like a comment
+        String.Doc:                "italic #8f5902",
+        String.Double:             "#4e9a06",         # class: 's2'
+        String.Escape:             "#4e9a06",         # class: 'se'
+        String.Heredoc:            "#4e9a06",         # class: 'sh'
+        String.Interpol:           "#4e9a06",         # class: 'si'
+        String.Other:              "#4e9a06",         # class: 'sx'
+        String.Regex:              "#4e9a06",         # class: 'sr'
+        String.Single:             "#4e9a06",         # class: 's1'
+        String.Symbol:             "#4e9a06",         # class: 'ss'
 
-        Generic:                   "#000000",        # class: 'g'
-        Generic.Deleted:           "#a40000",        # class: 'gd'
-        Generic.Emph:              "italic #000000", # class: 'ge'
-        Generic.Error:             "#ef2929",        # class: 'gr'
-        Generic.Heading:           "bold #000080",   # class: 'gh'
-        Generic.Inserted:          "#00A000",        # class: 'gi'
-        Generic.Output:            "#888",           # class: 'go'
-        Generic.Prompt:            "#745334",        # class: 'gp'
-        Generic.Strong:            "bold #000000",   # class: 'gs'
-        Generic.Subheading:        "bold #800080",   # class: 'gu'
-        Generic.Traceback:         "bold #a40000",   # class: 'gt'
+        Generic:                   "#000000",         # class: 'g'
+        Generic.Deleted:           "#a40000",         # class: 'gd'
+        Generic.Emph:              "italic #000000",  # class: 'ge'
+        Generic.Error:             "#ef2929",         # class: 'gr'
+        Generic.Heading:           "bold #000080",    # class: 'gh'
+        Generic.Inserted:          "#00A000",         # class: 'gi'
+        Generic.Output:            "#888",            # class: 'go'
+        Generic.Prompt:            "#745334",         # class: 'gp'
+        Generic.Strong:            "bold #000000",    # class: 'gs'
+        Generic.Subheading:        "bold #800080",    # class: 'gu'
+        Generic.Traceback:         "bold #a40000",    # class: 'gt'
     }