Add README

Add README

Author: HadleyKing

README.md

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+BioCompute Editor
+=================
+
+The BioCompute Editor is a web application that can be used to create and edit BioCompute objects based on BioCompute schema described in the BCO specification document. This editor uses <a href="https://github.com/jdorn/json-editor">JSON Editor</a> developed by Jeremy Dorn.
+
+
+Software requirement
+====================
+* Any linux operating system
+* MongoDB Community or Enterprise version
+
+
+### MongoDB Installation Example
+If you do not have MongoDB installed on your server, here is an example of [MongoDB installation instruction steps](mongodb_installation.md) steps for CentOs server. 
+
+
+### Downloading BioCompute Editor
+Use git clone to clone the bco_editor repository
+
+```
+git clone https://github.com/biocompute-objects/bco_editor.git
+
+```
+
+### BioCompute Editor Setup
+Assuming you have followed [MongoDB installation instructions steps](mongodb_installation.md), edit the config.json file under cgi-bin/conf/ subdirectory to customize it to your server. In the example given below, the name of the mongodb database is "bcodb_1_tst", and requires an authenticated mongodb user who has a "readWrite" role to write to it. In the example config file given below, the mongodb username and password are "bcodbadmin" and "pass123!" respectively.
+
+
+```
+  "dbinfo":{
+        "mongodbname":"bcodb_1_tst"
+        ,"mongodbuser":"bcodbadmin"
+        ,"mongodbpassword":"bcodbpass"
+        ,"sessionlife":3600
+        ,"collections":{
+            "bco":"c_bco"
+            ,"counters":"c_counters"
+            ,"users":"c_users"
+        }
+    }    
+    ,"pathinfo":{
+        "htmlroot":"http://example.com/bco_editor/"
+        ,"htmlpath":"/myrepositories/bco_editor/html/"
+    }
+
+```
+
+As for html and cgi-bin directories, the easiest way (assuming your apache is set to allow following symbolic links) is to make symbolic links from your server html and cgi-bin roots.
+
+```
+  $ sudo ln -s  /myrepositories/bco_editor/cgi-bin /var/www/cgi-bin/bco_editor
+  $ sudo ln -s  /myrepositories/bco_editor/html /var/www/html/bco_editor
+```
+
+Or you can copy the folders physically.
+
+```
+  $ sudo cp -r /myrepositories/bco_editor/cgi-bin /var/www/cgi-bin/bco_editor
+  $ sudo cp -r /myrepositories/bco_editor/html /var/www/html/bco_editor
+```
+
+You also need to make sure that apache has write access to /var/www/html/bco_editor/log/.
+
+```
+  $ sudo chown -R apache:apache /var/www/html/bco_editor/log/
+```
+
+Finally, you need to make sure the htmlRoot and cgiRoot javascript variables in bco_editor/html/index.html are assigned right values
+
+```
+  <script>
+    var htmlRoot = '/bco_editor/';
+    var cgiRoot = '/cgi-bin/bco_editor/';
+  </script>
+```
+
+### Admin Utility
+The script admin_util under cgi-bin/ subdirectory is used to manage the BioCompute Editor portal. Given below are commands (issued from the cgi-bin subdirectory) that can be used to perform various tasks.
+ 
+```
+Listing registered users 
+  $ python admin_util -a list_users
+
+Registration is public but users cannot login before they are activated using this admin_util tool (read below on how to activate pending registerations).
+
+Adding new user
+  $ python admin_util -a upsert_user -e jim.jones@gmail.com -f James -l Jones -p pass123 -s 1
+
+Activating or updating user
+ $ python admin_util -a upsert_user -e jim.jones@gmail.com -s 1
+
+Removing user
+  $ python admin_util -a delete_user -e jim.jones@gmail.com
+
+Listing BioCompute objects
+  $ python admin_util -a list_bco
+
+Deleting BioCompute object
+  $ python admin_util -a delete_bco -o 2
+
+```
+
+
+
+### Other Links
+BioCompute Partnership: http://biocomputeobject.org
+
+GitHub repository for BioCompute Objects:
+https://github.com/biocompute-objects/bco_editor
+
+
+

mongodb_installation.md

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+
+### MongoDB Installation Example
+
+If you do not have MongoDB installed on your server, here is an example installation steps for CentOs server (taken from
+https://docs.mongodb.com/manual/tutorial/install-mongodb-on-red-hat/)
+
+```
+
+1) Create a /etc/yum.repos.d/mongodb-org-4.0.repo file so that you can install MongoDB directly using yum:
+
+[mongodb-org-4.0]
+name=MongoDB Repository
+baseurl=https://repo.mongodb.org/yum/redhat/$releasever/mongodb-org/4.0/x86_64/
+gpgcheck=1
+enabled=1
+gpgkey=https://www.mongodb.org/static/pgp/server-4.0.asc
+
+2) sudo yum install -y mongodb-org
+
+3) Start mongod
+        $ sudo service mongod start
+
+4) Start MongoDB without authentication
+        $ mongo
+        
+5) Create the user administrator
+        > use admin
+        > db.createUser({ 
+                user: "superadmin", 
+                pwd: "superpass", 
+                roles: ["userAdminAnyDatabase", "dbAdminAnyDatabase","readWriteAnyDatabase"]
+        })
+        
+Then disconnect from the mongo shell (Ctrl+D).
+
+6. Disconnect from mongo shell and enable authentication in mongod configuration file and change "disabled" to "enabled"
+        $ sudo vi /etc/mongod.conf
+      
+        #security:
+        #        authorization: "disabled"
+
+7) Restart mongod
+        $ sudo service mongod restart
+  
+    From now on, all clients connecting to this server must authenticate themselves as a valid users, and they will be only able to perform actions as determined by their assigned roles.
+
+
+8) Connect and authenticate as the user administrator, and create additional users
+
+        $ mongo 
+        > use admin
+        > db.auth("superadmin", "superpass")
+        1
+        > use bcodb_1_tst
+        > db.createUser({user: "bcodbadmin", pwd: "bcodbpass", roles: [ { role: "readWrite", db: "bcodb_1_tst" } ]})
+        
+```