Merge pull request #266 from Murali-group/master

Updating develop branch up-to-date.

.bowerrc

@@ -0,0 +1,3 @@
+{
+  "directory": "static/components/"
+}

.gitignore

@@ -11,7 +11,10 @@ production.py
 # Ignore updates to IDE specific configurations
 .idea
 
-GraphSpace.egg-info
+static/components/*
+
+GraphSpace_Server.egg-info
 dist
 build
-venv
+venv
+debug*

CONTRIBUTING.md

@@ -0,0 +1,77 @@
+Contributing to the Project
+=========================
+
+All contributions to the project should follow the following procedure:
+
+1. Create an issue. See the [guidelines for issues](#create-an-issue) given below for more information.
+2. Create a pull request. See the [guidelines for pull request](#create-pull-request) given below for more information.
+
+*Note:* Only the administrators of project are allowed to make changes without a pull request.
+
+Create an Issue
+---------------
+
+If you find a bug in a project you’re using, have trouble following the documentation or have a question about the project – create an issue! 
+
+For more information on how issues work, check out our [Issues guide](http://guides.github.com/features/issues).
+
+#### Guidelines for Issues
+
+
+ - Before creating an issue, check existing issues to see if it already
+   exists. Try to avoid duplication of issues.
+
+ - Be clear about what your problem is: what was the expected outcome,
+   what happened instead? Detail how someone else can recreate the
+   problem. Link to demos recreating the problem on things like JSFiddle
+   or CodePen. Include system details like what the browser, library or
+   operating system you’re using and its version.
+
+ - Paste error output or logs in your issue or in a Gist. If pasting
+   them in the issue, wrap it in three backticks: " ``` "  so that it
+   renders nicely.
+
+- Tag the issues with a proper label. 
+	- feature: If you are requesting for a new feature.
+	- bug: If the issue reports a bug in the current functionality.
+	- question: If you have a doubt/question regarding the project.
+	- enhancement: If you are requesting for an enhancement in an existing feature.
+	- duplicate: If you find that your issue is duplicate of an existing issue.
+
+
+Create Pull Request
+------------
+
+If you’re able to patch a bug or add a feature, make a pull request with the code! Once you’ve submitted a pull request the maintainer(s) can compare your branch to the existing one and decide whether or not to incorporate (pull in) your changes.
+
+Once you’ve opened a pull request a discussion will start around your proposed changes. Other contributors and users may comment on the pull request, but ultimately the decision is made by the maintainer(s). You may be asked to make some changes to your pull request, if so, add more commits to your branch and push them – they’ll automatically go into the existing pull request.
+
+#### Guidelines for Pull Request
+
+- **[Fork](http://guides.github.com/activities/forking/)** the repository and clone it locally. 
+- Connect your local to the original ‘upstream’ repository by adding it as a remote. 
+- **Pull in changes** from ‘upstream’ often so that you stay up to date so that when you submit your pull request, merge conflicts will be less likely. See more [detailed instructions here](https://help.github.com/articles/syncing-a-fork).
+- **Create a branch** for your edits. See [guidelines for naming branches](#create-a-branch) for naming conventions.
+- **[Create a pull request](https://help.github.com/articles/creating-a-pull-request/)** to `develop` branch in the original 'upstream' repository i.e. `https://github.com/Murali-group/GraphSpace/`.
+- Add `fixes #<issue_number>` phrase in the pull request description to add a reference to the corresponding issue. See [information here](https://github.com/blog/957-introducing-issue-mentions) for referencing issues in the pull request.
+- Explain in your pull request what steps you have taken to ensure that the code change doesnt break the existing project's functionality.
+- **Include screenshots** of the before and after if your changes include differences in HTML/CSS. Drag and drop the images into the body of your pull request.
+- **Add comments in code** to help the maintainer to merge/understand the code change.
+
+Create a branch
+-----------------
+
+**Use short branch names.**  
+
+This is important, because branch names show up in the merge commits that result from accepting pull requests and should be as expressive and concise as possible.
+
+#### Naming Conventions
+
+- Branches used when submitting pull requests should preferably be named according to GitHub issues, e.g. 'b#1234' or 'f#1234'.
+  - If the branch resolves an issue with a `bug` label then name the branch as `b#<issue_number>` e.g.: 'b#123'
+  - If the branch resolves an issue with a `feature` label then name the branch as `f#<issue_number>` e.g.: 'f#123'
+  - If the branch resolves an issue with a `enhancement` label then name the branch as `e#<issue_number>` e.g.: 'e#123'
+
+- Otherwise, use succinct, lower-case, dash (-) delimited names, such as 'fix-warnings', 'fix-typo', etc. 
+
+

README.md

@@ -12,8 +12,10 @@ GraphSpace has three dummy users:
 Requirements
 ===================================
 1. Python v2.7.10
-2. sqlite3 v3.8.10
+2. [postgreSQL](https://github.com/Murali-group/GraphSpace/wiki/PostgreSQL-Installation)
 3. virtualenv
+4. [bower](https://bower.io/)
+5. [ElasticSearch](https://github.com/Murali-group/GraphSpace/wiki/Steps-for-setting-up-ElasticSearch-on-AWS)
 
 Running GraphSpace locally
 ===================================
@@ -33,9 +35,11 @@ Running GraphSpace on Apache
 
 This section describes the steps required to launch GraphSpace on a server that has `apache2` running on it.  First, please follow the steps in **Running GraphSpace locally**.  Next, execute the instructions below. 
 
-1. Follow instructions 1-5 in `Running GraphSpace locally` 
-2. Set `URL_PATH` to the URL where your server will be running.  *Note: Please add the ending '/' character at the end of this value: For example: http://graphspace.org/*
-3. Modify the `PATH` to point to where GraphSpace directory exists.  *Note: Please add the ending '/' character at the end of this value: For example: /home/ubuntu/GraphSpace/*
+1. Follow instructions 1-5 in `Running GraphSpace locally`
+2. Add settings file `production.py` by copying local settings file. `cp graphspace/settings/local.py graphspace/settings/`
+3. Update your `production.py` settings file.
+  1. InSet `URL_PATH` to the URL where your server will be running.  *Note: Please add the ending '/' character at the end of this value: For example: http://graphspace.org/*
+  2. Modify the `PATH` to point to where GraphSpace directory exists.  *Note: Please add the ending '/' character at the end of this value: For example: /home/ubuntu/GraphSpace/*
 4. Visit the `apache2` directory: `cd /path_to/apache2`. An example of the full path to this directory is `/etc/apache2`.
 5. Navigate to the `sites-enabled` directory: `cd sites-enabled`
 6. Create a file called `graphspace.conf` and access this file using admin privileges: `sudo vim graphspace.conf'
@@ -46,7 +50,7 @@ WSGIDaemonProcess GraphSpace python-path=/path_to_GraphSpace:/path_to_GraphSpace
 WSGIProcessGroup GraphSpace
 WSGIScriptAlias / /path_to_GraphSpace/graphspace/wsgi.py
 
-  <Directory /path_to_GraphSpace/graphspace>
+  <Directory /path_to_GraphSpace/graphspace/>
      <Files wsgi.py>
          Order deny,allow
          Require all granted
@@ -55,7 +59,7 @@ WSGIScriptAlias / /path_to_GraphSpace/graphspace/wsgi.py
   
   Alias /static/ /path_to_GraphSpace/graphs/static/
   
-  <Directory /path_to_GraphSpace/graphs/static>
+  <Directory /path_to_GraphSpace/graphs/static/>
       Require all granted
   </Directory>
   
@@ -82,3 +86,8 @@ Testing the GraphSpace REST API
 2. Enter python command to run test cases: `python restapi_test.py`
 
 This script will test all the REST API commands supported by the GraphSpace server.  If something fails, it will display the error.
+
+Contributing
+=================
+
+Feel free to fork and send us pull requests. Here are the [guidelines for contribution](https://github.com/Murali-group/GraphSpace/blob/master/CONTRIBUTING.md) in GraphSpace.

alembic.ini

@@ -0,0 +1,68 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = migration
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# max length of characters to apply to the
+# "slug" field
+#truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; this defaults
+# to migration/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path
+# version_locations = %(here)s/bar %(here)s/bat migration/versions
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+sqlalchemy.url = postgresql://localhost:5432/test_database
+
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S