rename scripts/ -> src/

4 files changed, 0 insertions, 990 deletions

diff --git a/scripts/model/core.js b/scripts/model/core.js
deleted file mode 100644
index 43a87b5d..00000000
--- a/scripts/model/core.js
+++ /dev/null
@@ -1,80 +0,0 @@
-"use strict"
-
-/**
- * core model module - currently unused
- */
-define([], function() {
-
-    /**
-     * return a random id
-     */
-    var random_id = function() {
-        return Math.random().toString(36).substring(2);
-    }
-
-    function random_node_name() {
-        return Math.random().toString(36).substring(2, 10);
-    }
-
-    function Node() {
-    }
-
-    function create_node__set_random_id(node_spec) {
-        if (undefined == node_spec) {
-            node_spec = {};
-        }
-
-        var ret = new Node();
-        ret.id = random_id();
-
-        ret.name = node_spec.name;
-        ret.type = node_spec.type;
-        ret.state = node_spec.state;
-        ret.status = node_spec.status;
-        ret.url = node_spec.url;
-
-        ret.start = node_spec.start;
-        ret.end = node_spec.end;
-
-        return ret;
-    }
-
-    function create_link__set_random_id(link_spec) {
-        var ret = new Link();
-        ret.id = random_id();
-    }
-
-    /**
-     * determine if nodes are equal by ID
-     *
-     * @param other_node
-     * @returns {Boolean}
-     */
-    Node.prototype.equlas_by_id = function(other) {
-        ret = this.id.toLowerCase() == other.id.toLowerCase();
-        if (false == ret) {
-            console.debug(this.id + ' != ' + other.id);
-        }
-        return ret;
-    }
-
-    function Link() {
-
-    }
-
-    /**
-     * determine if links are equal by ID
-     *
-     * @param other_node
-     * @returns {Boolean}
-     */
-    Link.prototype.equlas_by_id = function(other) {
-        return this.id.toLowerCase() == other.id.toLowerCase();
-    }
-
-    return {
-        random_node_name : random_node_name,
-        create_node__set_random_id : create_node__set_random_id,
-        create_link__set_random_id : create_link__set_random_id,
-    };
-});
diff --git a/scripts/model/diff.js b/scripts/model/diff.js
deleted file mode 100644
index 1bcfc5a2..00000000
--- a/scripts/model/diff.js
+++ /dev/null
@@ -1,144 +0,0 @@
-"use strict"
-
-/**
- * Diff module
- */
-define([],
-       function() {
-
-            /**
-             * A set of diff objects
-             */
-            function Diff_Set(obj_spec) {
-                this.__diff_set_topo = [];
-                this.__diff_set_attr = [];
-                this.__diff_set_vis = [];
-            }
-            Diff_Set.prototype.add_diff_obj = function(diff_obj) {
-                if (diff_obj instanceof Topo_Diff) {
-                    this.__diff_set_topo.push(diff_obj);
-                }
-                if (diff_obj instanceof Attr_Diff) {
-                    this.__diff_set_attr.push(diff_obj);
-                }
-                if (diff_obj instanceof Vis_Diff) {
-                    this.__diff_set_vis.push(diff_obj);
-                }
-            }
-
-            /**
-             * Topological diff object
-             */
-            function Topo_Diff(obj_spec) {
-
-                this.link_set_rm = obj_spec.link_set_rm;
-                this.node_set_rm = obj_spec.node_set_rm;
-                this.node_set_add = obj_spec.node_set_add;
-                this.link_set_add = obj_spec.link_set_add;
-            }
-
-            /**
-             * Attribute diff object, organized by type, where currently
-             * node,link types are supported
-             */
-            function Attr_Diff(obj_spec) {
-                this.__type_node = {}
-                this.__type_link = {}
-            }
-
-            Attr_Diff.prototype.init_attr_diff = function(type, id) {
-
-                if ('node' != type && 'link' != type) {
-                    console
-                            .error('attempt to init attribute diff for unsupported type: '
-                                    + type);
-                    return;
-                }
-
-                var type_field = '__type_' + type;
-                this[type_field][id] = {
-                    '__attr_write' : {},
-                    '__attr_remove' : []
-                };
-
-                return this;
-            }
-
-            Attr_Diff.prototype.init_attr_diff_node = function(id) {
-                return this.init_attr_diff('node', id);
-            }
-
-            Attr_Diff.prototype.init_attr_diff_link = function(id) {
-                return this.init_attr_diff('link', id);
-            }
-
-            Attr_Diff.prototype.add_attr_write_node = function(n_id, attr_name,
-                    attr_val) {
-
-                if (undefined == this.__type_node[n_id]) {
-                    this.init_attr_diff_node(n_id);
-                }
-                this.__type_node[n_id].__attr_write[attr_name] = attr_val;
-                return this;
-            }
-
-            Attr_Diff.prototype.add_attr_rm_node = function(n_id, attr_name) {
-                if (undefined == this[n_id]) {
-                    this.init_attr_diff(n_id);
-                }
-                this.__type_node[n_id].__attr_remove.push(attr_name);
-                return this;
-            }
-
-            /**
-             * Visual diff object expressing any visual change to the state of a
-             * particular visualization type
-             */
-            function Vis_Diff(obj_spec) {
-            }
-
-            function new_topo_diff(obj_spec) {
-                /*
-                 * validate obj_spec
-                 */
-                // TODO
-                var ret = new Topo_Diff(obj_spec);
-                return ret;
-            }
-
-            function new_attr_diff(obj_spec) {
-                /*
-                 * validate obj_spec
-                 */
-                // TODO
-                var ret = new Attr_Diff(obj_spec);
-                ret.__type_node = {}; // id-to-obj map
-                ret.__type_link = {}; // id-to-obj map
-                return ret;
-            }
-
-            function new_vis_diff(obj_spec) {
-                /*
-                 * validate obj_spec
-                 */
-                // TODO
-                var ret = new Vis_Diff(obj_spec);
-                return ret;
-            }
-
-            function new_diff_set(obj_spec) {
-                /*
-                 * validate obj_spec
-                 */
-                // TODO
-                var ret = new Diff_Set(obj_spec);
-                return ret;
-            }
-
-            return {
-                new_topo_diff : new_topo_diff,
-                new_attr_diff : new_attr_diff,
-                new_vis_diff : new_vis_diff,
-                new_diff_set : new_diff_set,
-            }
-        });
\ No newline at end of file
diff --git a/scripts/model/graph.js b/scripts/model/graph.js
deleted file mode 100644
index 820daef0..00000000
--- a/scripts/model/graph.js
+++ /dev/null
@@ -1,649 +0,0 @@
-"use strict"
-
-define(['signal', 'consts', 'util', 'textanalysis', 'model/core', 'model/util', 'rz_api_backend', 'rz_api_mesh'],
-function (signal, consts, util, textanalysis, model_core, model_util, rz_api_backend, rz_api_mesh) {
-
-function Graph(el) {
-
-    var nodes = [],
-        links = [];
-
-    function id_generator_generator() {
-        var id = 0;
-        function get_next() {
-            var next = id;
-            id += 1;
-            return next;
-        }
-        return get_next;
-    }
-    var id_generator = id_generator_generator();
-
-    ///FUNCTIONS
-    this.addNode = function(name, type, state) {
-        if (type === undefined) {
-            console.log('bug: adding undefined type');
-        }
-        var new_node = this._addNodeNoHistory(
-            {name:name,
-             type:type,
-             state:state,
-             start:0,
-             end:0,
-             status:"unknown"});
-        if (new_node) {
-            signal.signal(consts.APPLIED_GRAPH_DIFF, [{
-                nodes: {add: [new_node]}}]);
-            return new_node;
-        }
-    }
-
-    this._addNodeNoHistory = function(spec) {
-        // No history recorded - this is a helper for loading from files / constant graphs
-        var node;
-        if (spec.id === undefined) {
-            node = findNodeByName(spec.name, null);
-        } else {
-            if (spec.id !== undefined) {
-                node = findNode(spec.id, null);
-            }
-        }
-        if (node === undefined) {
-            node = {
-                "id": spec.id || id_generator(),
-                "name": spec.name,
-                "type": spec.type,
-                "state": spec.state,
-                "start": spec.start,
-                "end": spec.end,
-                "status": spec.status,
-                'url': spec.url,
-                'x': spec.x,
-                'y': spec.y,
-            };
-            nodes.push(node);
-        }
-        return node;
-    }
-
-    this.removeNode = function(id, state) {
-        var i = 0;
-        var n = findNode(id, state);
-        while (i < links.length) {
-            if ((links[i]['source'] === n) || (links[i]['target'] == n)) links.splice(i, 1);
-            else i++;
-        }
-        var index = findNodeIndex(id, state);
-        if (index !== undefined) {
-            nodes.splice(index, 1);
-        }
-        signal.signal(consts.APPLIED_GRAPH_DIFF, [{nodes: {removed: [id]}}]);
-    }
-
-    this.removeNodes = function(state) {
-        var id = null;
-        var ns = findNodes(null, state);
-        for (var j = 0; j < ns.length; j++) {
-            var n = ns[j];
-            var i = 0;
-            while (i < links.length) {
-                if ((links[i]['source'] === n) || (links[i]['target'] == n)) links.splice(i, 1);
-                else i++;
-            }
-            var index = findNodeIndex(id, state);
-            if (index !== undefined) {
-                nodes.splice(index, 1);
-            }
-        }
-        if (ns.length > 0) {
-            signal.signal(consts.APPLIED_GRAPH_DIFF, [{nodes: {removed: ns.map(function(n) { return n.id; })}}]);
-        }
-    }
-
-    /**
-     *
-     * getConnectedNodesAndLinks
-     *
-     * @id
-     * @state - defines the starting node (must have id and state)
-     * @d - depth defining connected component. If -1 returns the entire connected component. (can be the whole graph)
-     * 
-     * NOTE: chainlinks are treated specially, they don't count for distance. So all their decendants will be added.
-     *
-     * NOTE: temp state nodes (n.state === 'temp') are ignored.
-     *
-     * @return - {
-     *  'node': [node]
-     *  'link': [link]
-     *  }
-     *
-     * TODO: rewrite using efficient data structure. Right now iterates over everything
-     * TODO: implement for d !== 1
-     *
-     */
-    this.getConnectedNodesAndLinks = function(n, d) {
-        var i = 0,
-            j = 0,
-            adjacentnode,
-            link,
-            link2,
-            ret = {'nodes':[], 'links':[]};
-
-        $(".debug").html(n.state);
-
-        if (n === undefined) {
-            console.log('getConnectedNodesAndLinks: bug: called with undefined node');
-            return;
-        }
-        if (d !== 1) {
-            console.log('getConnectedNodesAndLinks: bug: not implemented for d == ' + d);
-        }
-        d = d || 1;
-
-        while (i < links.length) {
-            link = links[i];
-            // XXX: using name comparison because n might be stale
-            if (compareNames(link.source.name, n.name)) {
-                adjacentnode = findNode(link.target.id, null);
-                if (adjacentnode.state !== "temp") {
-                    ret.nodes.push({type: 'exit', node: adjacentnode});
-                }
-                ret.links.push({type: 'exit', link: link});
-
-                if (link.target.type === "chainlink") {
-                    while (j < links.length) {
-                        link2 = links[j];
-                        if (link.target.id === link2.target.id &&
-                            link2.target.type === "chainlink" &&
-                            link2.target.state !== "temp") {
-                            adjacentnode = findNode(link2.source.id, null);
-                            if (adjacentnode.state !== "temp") {
-                                ret.nodes.push({type: 'enter', node: adjacentnode});
-                            }
-                            ret.links.push({type: 'enter', link: link2});
-                        }
-                        j++;
-                    }
-                }
-                j=0;
-            }
-            if (compareNames(links[i].target.name, n.name)) {
-                adjacentnode = findNode(links[i].source.id, null);
-                if (adjacentnode.state !== "temp") adjacentnode.state = "enter";
-                links[i].state = "enter";
-            }
-            i++;
-        }
-        return ret;
-    }
-
-    /* compareSubset:
-     *  state: one of the optional states that defines a subgraph
-     *  new_nodes: array of objects with name
-     *  new_links: array of length two arrays [source_name, target_name]
-     *  returns: true if current and new graph are homomorphic up to
-     *  a single node id change. false otherwise
-     */
-    this.compareSubset = function(state, new_nodes, new_links) {
-        // Note: the nodes include a state=='temp', type=='bubble' node
-        // but it's ok since it exists both in new_nodes and in state_nodes
-        var state_nodes = findNodes(null, state).filter(function (nd) {
-            return nd.type !== 'bubble';
-        });
-        var state_links = findLinks(state).map(function(link) {
-            return [link.source.name, link.target.name];
-        }).sort();
-        var k;
-        var state_source, state_target, new_source, new_target;
-        var changed_nodes;
-        var verbose = false; // XXX should be global.
-        var set_old_name, set_new_name;
-
-        new_nodes.map(function (f) {
-            if (!f.name) {
-                console.log('missing name on node. node follows');
-                console.log(f);
-            }
-        });
-        new_nodes.sort();
-        new_links.sort();
-        if (new_nodes.length != state_nodes.length || new_links.length != state_links.length) {
-            if (verbose) {
-                console.log('not same size: new/old ' + new_nodes.length + ' / ' + state_nodes.length + '; ' +
-                            new_links.length + ' / ' + state_links.length);
-            }
-            return {graph_same: false};
-        }
-        changed_nodes = util.set_diff(util.set_from_array(state_nodes.map(function(d) { return d.name; })),
-                                 util.set_from_array(new_nodes.map(function (f) { return f.name; })));
-        // we allow any number of changed nodes as long as we it is 1 or 2 :)
-        if (changed_nodes.a_b.length > 2) {
-            if (verbose) {
-                console.log('changed too many nodes');
-                console.log(changed_nodes);
-            }
-            return {graph_same: false};
-        }
-        set_old_name = util.set_from_array(changed_nodes.a_b);
-        set_new_name = util.set_from_array(changed_nodes.b_a);
-        for (k = 0 ; k < state_links.length ; ++k) {
-            state_source = state_links[k][0];
-            state_target = state_links[k][1];
-            new_source = new_links[k][0];
-            new_target = new_links[k][1];
-            if ((state_source !== new_source &&
-                 !(state_source in set_old_name && new_source in set_new_name))
-                ||
-               (state_target !== new_target &&
-                 !(state_target in set_old_name && new_target in set_new_name))) {
-                if (verbose) {
-                    console.log('not same link: ' +
-                                state_source + '->' + state_target + ' != ' +
-                                new_source + '->' + new_target);
-                    console.log('state_source === new_source: ' + String(state_source === new_source));
-                    console.log('state_target === new_target: ' + String(state_target === new_target));
-                    console.log(set_old_name);
-                    console.log(set_new_name);
-                }
-                return {graph_same: false};
-            }
-        }
-        return {graph_same: true, old_name: changed_nodes.a_b, new_name: changed_nodes.b_a};
-    }
-
-    this.addLinkByName = function(sourceName, targetName, name, state, drop_conjugator_links) {
-        var source = findNodeByName(sourceName, null),
-            target = findNodeByName(targetName, null),
-            sourceId = source ? source.id : null,
-            targetId = target ? target.id : null;
-
-        if (sourceId === null || targetId === null) {
-            console.log('error: link of missing nodes: ' + sourceName + ' (' + sourceId + ') -> '
-                        + targetName + ' (' + targetId + ')');
-            return;
-        }
-        this.addLink(sourceId, targetId, name, state, drop_conjugator_links);
-    }
-
-    this.addLink = function(sourceId, targetId, name, state, drop_conjugator_links) {
-        var sourceNode = findNode(sourceId, null);
-        var targetNode = findNode(targetId, null);
-        var found = findLink(sourceId,targetId,name);
-
-        if (drop_conjugator_links && name && (name.replace(/ /g,"") === "and")) {
-            state = "temp";
-        }
-        if (sourceNode === undefined || targetNode === undefined) {
-            return;
-        }
-        if (!found) {
-            var id = id_generator(),
-                link = {
-                source: sourceNode,
-                target: targetNode,
-                name: name,
-                state: state,
-                id: id,
-            };
-            links.push(link);
-            signal.signal(consts.APPLIED_GRAPH_DIFF, [{links: {add: [link]}}]);
-        } else {
-            found.name = name;
-            found.state = state;
-        }
-    }
-
-    this.editLink = function(sourceId, targetId, newname, newstate) {
-        var link = findLink(sourceId, targetId, newname);
-        if (link !== undefined) {
-            link.name = newname;
-            if (newstate !== undefined) {
-                link.state = newstate;
-            }
-        }
-    }
-
-    this.editLinkTarget = function(sourceId, targetId, newTarget) {
-        var link = findLink(sourceId, targetId, null);
-        if (link !== undefined) {
-            link.target = findNode(newTarget, null);
-
-        } else {
-
-        }
-    }
-
-    this.editNameByName = function(old_name, new_name) {
-        var node = findNodeByName(old_name, null);
-
-        if (node === undefined) {
-            console.log('editNameByName: error: cannot find node with name ' + old_name);
-            return;
-        }
-        return this.editName(node.id, new_name); // TODO: introduce Node class (yes Amir, I'm now down with that).
-    }
-
-    this.editName = function(id, new_name) {
-        var index2 = findNodeByName(new_name, null);
-        var index = findNode(id, null);
-        var acceptReplace=true;
-
-        if ((index !== undefined)) {
-            if (index2 !== undefined) {
-                acceptReplace = confirm('"' + index2.name + '" will replace "' + index.name + '", are you sure?');
-                if (acceptReplace){
-                    for (var i = 0; i < links.length; i++) {
-                        if (links[i].source === index) {
-                            links[i].source = index2;
-                        }
-                        if (links[i].target === index) {
-                            links[i].target = index2;
-                        }
-                    }
-                    this.removeNode(index.id,null);
-                }
-            } else {
-                index.name = new_name;
-            }
-        }
-    }
-
-    this.editDates = function(id, type, start, end) {
-        var index = findNode(id, type);
-        if ((index !== undefined)) {
-            index.start = start;
-            index.end = end;
-        }
-    }
-
-    /**
-     * editType:
-     * 
-     * @return true if type changed
-     */
-    this.editType = function(id, state, newtype) {
-        var index = findNode(id, state);
-        if ((index !== undefined)) {
-            index.type = newtype;
-        }
-    }
-
-    this.editURL = function(id, state, url) {
-        var index = findNode(id, state);
-        if ((index === undefined)) return;
-        index.url = url;
-    }
-
-    this.editState = function(id, state, newstate) {
-        var index = findNode(id, state);
-
-        if ((index !== undefined)) {
-            index.state = newstate;
-        }
-    }
-
-    this.findCoordinates = function(id, type) {
-        var index = findNode(id, type);
-        if ((index !== undefined)) {
-            $('.typeselection').css('top', index.y - 90);
-            $('.typeselection').css('left', index.x - 230);
-        }
-    }
-
-    this.removeLink = function(link) {
-        var link,
-            i;
-
-        for ( i = 0 ; i < links.length; ++i ) {
-            if (link.id !== undefined) {
-                if (link.id === links[i].id) {
-                    links.splice(i, 1);
-                    return;
-                }
-            } else {
-                if (link.sourceId === links[i].sourceId && link.targetId === links[i].targetId) {
-                    links.splice(i, 1);
-                    return;
-                }
-            }
-        }
-        console.log('bug: attempt to remove non existant link');
-    }
-
-    this.removeLinks = function(state) {
-        var id = null;
-        var ls = findLinks(state);
-        for (var j = 0; j < ls.length; j++) {
-            var l = ls[j];
-            var i = 0;
-            while (i < links.length) {
-                if (links[i] === l) links.splice(i, 1);
-                else i++;
-            }
-        }
-    }
-
-    var findLink = function(sourceId, targetId, name) {
-        for (var i = 0; i < links.length; i++) {
-            if (links[i].source.id === sourceId && links[i].target.id === targetId) {
-                return links[i];
-            }
-        }
-    }
-
-    var findLinks = function(state) {
-        var foundLinks = [];
-        for (var i = 0; i < links.length; i++) {
-            if (links[i].state == state) {
-                foundLinks.push(links[i]);
-            }
-        }
-        return foundLinks;
-    }
-
-    var compareNames = function(name1, name2) {
-        return name1.toLowerCase() === name2.toLowerCase();
-    };
-
-    var hasNodeByName = function(name, state) {
-        var i;
-
-        for (i = 0 ; i < nodes.length; ++i) {
-            if (compareNames(nodes[i].name, name) && nodes[i].state === state) {
-                return true;
-            }
-        }
-        return false;
-    }
-    this.hasNodeByName = hasNodeByName;
-
-    var hasNode = function(id, state) {
-        var i;
-
-        for (i = 0 ; i < nodes.length; ++i) {
-            if (nodes[i].id === id && nodes[i].state === state) {
-                return true;
-            }
-        }
-        return false;
-    }
-    this.hasNode = hasNode;
-
-    var findNode = function(id, state) {
-        for (var i = 0; i < nodes.length; i++) {
-            if (nodes[i].id === id || nodes[i].state === state)
-                return nodes[i];
-        };
-    }
-
-    var findNodeByName = function(name, state) {
-        for (var i = 0 ; i < nodes.length ; ++i) {
-            if (compareNames(nodes[i].name, name) || nodes[i].state === state) {
-                return nodes[i];
-            }
-        }
-    }
-
-    var findNodes = function(id, state) {
-        // id=id.toLowerCase();
-        var foundNodes = [];
-        for (var i = 0; i < nodes.length; i++) {
-            if ((id && nodes[i].id === id) || (state && nodes[i].state === state))
-                foundNodes.push(nodes[i]);
-        }
-        return foundNodes;
-    }
-
-    var findNodeIndex = function(id, state) {
-        for (var i = 0; i < nodes.length; i++) {
-            if ((id && nodes[i].id === id) || (state && nodes[i].state === state))
-                return i;
-        };
-    }
-
-    function clear() {
-        nodes.length = 0;
-        links.length = 0;
-    }
-    this.clear = clear;
-
-    function empty() {
-        return nodes.length == 0 && links.length == 0;
-    }
-    this.empty = empty;
-
-    // @ajax-trans
-    this.commit_diff_set = function (diff_set) {
-        
-        function on_success(data){
-            // TODO impl
-        }
-        
-        rz_api_mesh.broadcast_possible_next_diff_block(diff_set);
-    }
-
-    /**
-     * perform initial DB load from backend
-     */
-    // @ajax-trans
-    function load_from_backend() {
-
-        function on_success(data){
-            var n_set = [];
-            var l_set = [];
-            var len;
-
-            len = data['node_set'].length;
-            for (var i = 0; i < len; i++) {
-                var n_raw = data['node_set'][i];
-                var n = model_util.adapt_format_read_node(n_raw);
-                n_set.push(n);
-            }
-            
-            len = data['link_set'].length;
-            for (var i = 0; i < len; i++) {
-                var l_raw = data['link_set'][i];
-                var l = model_util.adapt_format_read_link(l_raw);
-                l_set.push(l);
-            }
-            
-            len = n_set.length
-            for (var i = 0; i < len; i++) {
-                var n = n_set[i];
-                graph.addNode(n.id, n.type, n.state)
-            }
-            
-            len = l_set.length
-            for (var i = 0; i < len; i++) {
-                var l = l_set[i];
-                graph.addLink_byIds(l.sourceId, l.targetId, l.name, "perm")
-            }
-        }
-        
-        rz_api_backend.clone(0, on_success);
-    }
-
-    this.load_from_json = function(json) {
-        var data = JSON.parse(json);
-        var i, node, link;
-
-        clear();
-        if (data == null) {
-            console.log('load callback: no data to load');
-            return;
-        }
-        for(i = 0; i < data["nodes"].length; i++){
-          node = data.nodes[i];
-          this._addNodeNoHistory({id:node.id, name:node.name ? node.name : node.id,
-                                 type:node.type,state:"perm",
-                                 start:new Date(node.start),
-                                 end:new Date(node.end),
-                                 status:node.status,
-                                 url:node.url,
-                                 x: node.x,
-                                 y: node.y,
-                                });
-          textanalysis.autoSuggestAddName(node.name.toLowerCase());
-        }
-        for(i = 0; i < data["links"].length; i++){
-          link = data.links[i];
-          this.addLink(link.source, link.target, link.name, "perm");
-        }
-        this.clear_history();
-    }
-
-    this.save_to_json = function() {
-        var d = {"nodes":[], "links":[]};
-        for(var i = 0 ; i < nodes.length ; i++){
-          var node = nodes[i];
-          d['nodes'].push({
-            "id": node.id,
-            "name": node.name,
-            "type":node.type,
-            "state":"perm",
-            "start":node.start,
-            "end":node.end,
-            "status": node.status,
-            "url": node.url,
-            "x": node.x,
-            "y": node.y,
-          });
-        }
-        for(var j=0 ; j < links.length ; j++){
-          var link = links[j];
-          d['links'].push({
-            "source":link.source.id,
-            "target":link.target.id,
-            "name":link.name
-          });
-        }
-        return JSON.stringify(d);
-    }
-
-    this.set_user = function(user) {
-        this.user = user;
-        this.history = new History(this.user, $('svg g.zoom')[0]);
-        console.log('new user: ' + user);
-    }
-
-    function clear_history() {
-        if (this.history !== undefined) {
-            this.history.clear();
-        }
-    }
-
-    this.clear_history = clear_history;
-
-    var get_nodes = function() { return nodes; };
-    this.nodes = get_nodes;
-
-    var get_links = function() { return links; };
-    this.links = get_links;
-
-}
-
-return {
-    Graph: Graph,
-};
-
-});
diff --git a/scripts/model/util.js b/scripts/model/util.js
deleted file mode 100644
index 43fa66db..00000000
--- a/scripts/model/util.js
+++ /dev/null
@@ -1,117 +0,0 @@
-"use strict"
-
-/**
- * model utility functions:
- *    - convert from/to client/backend data representations
- */
-define(['jquery', 'model/diff'], 
-function($, model_diff) {
-
-    /**
-     * read by adapting from backend format
-     */
-    function adapt_format_read_node(n_raw) {
-        var ret;
-
-        ret = $.extend({
-            'type' : n_raw['__type'].toLowerCase(), // discard all
-            // labels except
-            'state' : 'temp',
-        }, n_raw);
-
-        delete ret.__label_set;
-
-        return ret;
-    }
-
-    /**
-     * write by adapting to backend format
-     */
-    function adapt_format_write_node(n_raw) {
-        var ret = $.extend({
-            '__type' : n_raw.type,
-        }, n_raw);
-
-        delete ret.type;
-        delete ret.state;
-
-        return ret
-    }
-
-    /**
-     * read by adapting from backend format
-     */
-    function adapt_format_read_link(l_raw) {
-        var ret;
-
-        ret = $.extend({
-            'sourceId' : l_raw['__src'],
-            'targetId' : l_raw['__dst'],
-            'type' : l_raw['__type'].toLowerCase(), // discard all
-            // labels except
-            'state' : 'temp',
-        }, l_raw);
-
-        ret['name'] = ret['type'];
-
-        delete ret.__src;
-        delete ret.__dst;
-        delete ret.__type;
-
-        return ret;
-    }
-
-    /**
-     * write by adapting to backend format
-     */
-    function adapt_format_write_link(l_raw) {
-        var ret = $.extend({
-            '__src' : l_raw.sourceId,
-            '__dst' : l_raw.targetId,
-            '__type' : 'textual_link',
-        }, l_raw);
-
-        delete ret.source;
-        delete ret.target;
-        delete ret.state;
-
-        return ret;
-    }
-
-    /**
-     * write adapt diff from node set, link set. sets may be passed by reference
-     * as they are cloned
-     */
-    function adapt_format_write_topo_diff(n_set, l_set) {
-
-        var new_n_set = $.extend([], n_set);
-        var new_l_set = $.extend([], l_set);
-
-        // filter out 'bubble' nodes
-        new_n_set = new_n_set.filter(function(n) {
-            return 'bubble' != n.type;
-        });
-
-        new_n_set = $.map(new_n_set, function(n, _) {
-            return adapt_format_write_node(n);
-        })
-
-        new_l_set = $.map(new_l_set, function(l, _) {
-            return adapt_format_write_link(l);
-        })
-
-        var topo_diff = new model_diff.new_topo_diff({
-            node_set_add : new_n_set,
-            link_set_add : new_l_set
-        });
-        return topo_diff;
-    }
-
-    return {
-        adapt_format_read_node : adapt_format_read_node,
-        adapt_format_read_link : adapt_format_read_link,
-        adapt_format_write_node : adapt_format_write_node,
-        adapt_format_write_link : adapt_format_write_link,
-        adapt_format_write_topo_diff : adapt_format_write_topo_diff,
-    }
-});
\ No newline at end of file