felixakk / synthbio Goto Github PK

Some minimum widths should be defined for the layout elements in the CSS so the modelling field doesn't collapse. As a side effect this will probably also make the app more compatible with mobile devices. Low priority though.

Chrome won't load the main webpage (index.html), because a JavaScript framework violates the security policy (Cross origin requests are only supported for HTTP). This is due to less.js (The framework that parses the .less stylesheet) trying execute AJAX communication. I heard an alternative exists (something called PAJAX or something), which can be included and easily fixes this.

Raw error:

XMLHttpRequest cannot load file:///D:/TUDelft/TI2800/synthbio/program/css/style.less. Cross origin requests are only supported for HTTP.
less-1.3.0.min.js:8Uncaught Error: NETWORK_ERR: XMLHttpRequest Exception 101

And sending it in.

Time estimate: 2

Server/client: create and display connection state by ping/pong heartbeat. Write a JavaScript action listener to display this in the status bar of the GUI.

Assigned to:

• atennapel
• NielsAD

Things to worry about:

• Lots of meaningful Javadoc comments for every class, property, method; use tags wisely.
• Check consistency of indentation.

Hey allemaal. Ik zal even te kijken naar Jieters mooie nieuwe code en bedacht me het volgende:

Hoe gaan we groupings aangeven?
Misschien iets van nested gates ofzo? { "type": "not", "position": {"x": 2,"y": 2}, {"type": "and", "position": {"x": 2,"y": 2} } }
Of berekenen we gewoon de gates en hoe ze gelinkt zijn op basis van de position (en waarom hebben we dan grouping?)
En als we het doen op position, hoe zit dat dan met compound gates later inladen en die bij een bestaande gate group toevoegen? Dan moeten de y-waarden misschien veranderd worden anders plak je misschien gates over elkaar heen...
Denk dat we hier even een goed idee van moeten hebben voordat we dingen verder gaan implementeren...

Could have:

Assign mnemonics and shortcut key combinations to the menu. This greatly accelerates the workflow of the application for experienced users.

Make it pretty. And also easier to use.

Includes stuff like:

• Polish circuit styles.
• Fix position of gates below mouse while dragging.
• Style of gate while dragging.
• Size and drop area of endpoints so they are easier to connect/disconnect.
• Implement deleting of wires and gates using delete.
• Highlighting/selecting gates to move multiple or delete multiple.
• Making input and output fields resize and display open connections that still need to be defined.
• Also stylize the input/output areas.

Design the JavaScript object structure on the client side. Also document this in the GitHub Wiki.

Create function to converting of Circuit ⇔ JSON.

Time estimate: 7 hours.

Thomas and I both couldn't get the server working with the Windows instructions. The service would start but we'd still get a 404 on the address. We would probably check that with someone who did got it working.

We both had XAMPP installed, and luckily we could easily get it to work on that (see new section in the Wiki).

Create GUI element(s) to draw/specify input signals for each "wire" by specifying whether a protein concentration is high or low (absolute numbers to be specified by Albert in issue #48 ), which is represented by 0 or 1 in the GUI. Also write the JavaScript to convert this to JSON.

Time estimate: huge ... I mean; 16 hours

Convert circuit JSON to SBML XML (simulator input).

Time estimate: 14 hours.

Hey allen,

Ik zie jullie morgen niet denk ik, dus ik zet maar even een issue uit voor mijn probleem. Leek me wel de geschikte plaats.
Over de requests, waar moet alles heen verwijzen? Hebben we al enig idee waar we files op gaan slaan?
Komt er een java file die alle requests afvangt of moet ik voor elke request een aparte servlet file maken?
Ik zag al CircuitServlet staan. Is het de bedoeling dat die alles af gaat vangen en dat dus alles daar ook naar verwijst?

Verder, Jieter, jij had callbacks ingebouwd binnen die request functies. Ik nam aan dat die dienen als functie objecten om resultaten in mee te geven, maar moeten die perse als parameter meegeven worden? Als ik het compleet mis heb, corrigeer me dan aub. Ik zal morgen ochtend verder kijken naar de code.

Vanaf morgen middag ben ik naar het congres maar ik probeer elke avond gewoon hieraan door te werken (en andere dingen zoals code checken).

Could have:

Compile the .less stylesheets into .css server side so this doesn't have to be done client side by the less.js. This already takes up 150ms last time I checked.

Document workings/protocols of calling simulator, conversion of circuit, etc.

Time estimate: 1 hour.

Niels moet zijn peer review nog invullen.
(Test van het issue systeem)

-How does the conversion to SBML work?
-What is valid input for simulation?

Gates should be removable.

When using Firefox 12.

When I drag an AND gate to the working area, one input connector is not on the gate but somewhere else.
https://github.com/FelixAkk/synthbio/raw/6c006d9ddd5cf0454476b05b3fe7c619e9d62376/screenshots/2012-05-05-Firefox-AND-gate.png

When I hover over the connector, it jumps to the place it should be.

Create several classes that make up the scaffolding holding up the HTTP server. Implement the HTTP server by setting up the Apache Tomcat server, and making it serve a very simple HTML page displaying Hello World, when a HTTP request is made from localhost (and possibly outside).

Assigned to:

• NielsAD
• atennapel

Convert to JavaScript object, convert to JSON, send circuit to server and give confirmation/feedback in the GUI.

Time estimate: 5 hours

For the sake of completeness an issue for an already finished task:

Display a list of Proteins in the client.

Alexey suggested the function to sort the list of proteins. I'm used to DataTables, they even have a guide how to use it with bootstrap: http://datatables.net/blog/Twitter_Bootstrap_2

Hey gasten,

Ik heb een probleem dat mijn tests het niet doen... dat kan aan mij liggen.. maar wat in ieder geval ook niet klopt is dat de ping het niet meer doet. Dus of ik doe iets verkeerd of iemand heeft iets aan de server veranderd waardoor er geen connection meer is. Kan dit kloppen, ervaart iemand anders dit ook?

Create the basic GUI structure in the index.html webpage. This includes menus, status bar, the primary content blocks and the modelling grid. Write the JavaScript action listeners scaffolding that will handle the interactions between these elements.

Research the best approach to implementing the modelling grid and content blocks that will do display complex graphics.

Optional task: make a drop-down when you click on the protein selection. This should be in the grid and not as a modal (which it is now). Make it so that used proteins don't show up in the menu.

So implementing the drag-drop proved to be more troublesome than expected. I've been wrestling with some bugs for hours, but when I understood this one I realized it's for another time.

So when you drag-drop a gate you'll notice the new gate appears but sort of loses focus (it's actually that it's not responding to an even). This is because the newly visible element is not the one that received the mouse down event, so it won't start dragging. This should be do-able by manually triggering the "mouse.draggable" event on the new element when example gate was clicked, but this doesn't seem to work.

Fixing this should be possible. This post lines out how it could be fixed, but the implications are rather big on the implementation. It would cost some time.

Request list of circuit from server, process reply by presenting user with a list in the GUI. Process selection event by sending to the server and load the returned circuit by the server in the modeller.

Time estimate: 10 hours

Forward call to the solver (includes converting circuit JSON to SBML XML, see issue #48) and reply result back to the client.

Time estimate: 2 hours.

Can everyone add @author "Name" to their code?
And we need to figure out a cool new name instead of BioBrick modeller...

** After list is supplied by Alexey

• Create parsers for the csv file.
• Define Java objects
• Convert to Java Objects
• Define JSON converters
• Define servlet

When a Gate is connected to another node, and the connection is removed, the output disappears.

Could have: Write meaningful and nice contents in the about dialog on the webpage.

Client: Show available basic gates (AND, NOT) in the basic gates content block. Create graphics for these gates.

Design the JSON format for circuits (.syn files). Also design how the protein list should be set in JSON. Both of these standards should be documented in the GitHub wiki.