--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/popoto_dev/js/app-ismi.js	Fri Oct 02 01:08:46 2015 -0400
@@ -0,0 +1,401 @@
+/**
+ * URL used to access Neo4j REST API to execute queries.
+ * Update this parameter to your running server instance.
+ *
+ * For more information on Neo4J REST API the documentation is available here: http://neo4j.com/docs/stable/rest-api-cypher.html
+ */
+popoto.rest.CYPHER_URL = "https://ismi-dev.mpiwg-berlin.mpg.de/neo4j-ismi/db/data/transaction/commit";
+//popoto.rest.CYPHER_URL = "http://localhost:7474/db/data/transaction/commit";
+
+/**
+ * Add this authorization property if your Neo4j server uses basic HTTP authentication.
+ * The value of this property must be "Basic <payload>", where "payload" is a base64 encoded string of "username:password".
+ *
+ * "btoa" is a JavaScript function that can be used to encode the user and password value in base64 but it is recommended to directly use the Base64 value.
+ *
+ *  For example Base64 encoding value of "neo4j:password" is "bmVvNGo6cGFzc3dvcmQ="
+ */
+popoto.rest.AUTHORIZATION = "Basic " + btoa("neo4j:neo5j");
+//popoto.rest.AUTHORIZATION = "Basic " + btoa("neo4j:eagrussell");
+
+/**
+ * These functions fill the predefinedConstraints array for "PERSON"
+ * Called when the filter button is hit
+ *
+ * Uses the text box implementation currently
+ */
+    // TODO: finish textbox implementation as backup
+    // have single filter button which on click sets constraints equal to d3.select("#constraintNUMBS)[0][0].value
+    // for a bunch of spots in the array
+    // will have to create only 1 d3.select
+    // the d3.select will need to know what constraints to pull from input boxes based on ids related to whether they
+    // are person/codex/witness/etc attributes and put them into the corresponding arrays
+    // personPredefinedConstraints codexPreDef
+var personPredefinedConstraints = [];
+var codexPredefinedConstraints = [];
+var witnessPredefinedConstraints = [];
+d3.select("#filter-button").on("click", function (d) {
+    personPredefinedConstraints = [];
+    codexPredefinedConstraints = [];
+    witnessPredefinedConstraints = [];
+
+    var person1 = d3.select("#person-constraint")[0][0].value;
+    var person2 = d3.select("#person-constraint2")[0][0].value;
+
+    var codex1 = d3.select("#codex-constraint")[0][0].value;
+    var codex2 = d3.select("#codex-constraint2")[0][0].value;
+
+    var witness1 = d3.select("#witness-constraint")[0][0].value;
+    var witness2 = d3.select("#witness-constraint2")[0][0].value;
+
+    if (person1.substring(person1.indexOf('"')+1,person1.lastIndexOf('"'))) personPredefinedConstraints.push(person1);
+    if (person2.substring(person2.indexOf('"')+1,person2.lastIndexOf('"'))) personPredefinedConstraints.push(person2);
+
+    if (codex1.substring(codex1.indexOf('"')+1,codex1.lastIndexOf('"'))) codexPredefinedConstraints.push(codex1);
+    if (codex2.substring(codex2.indexOf('"')+1,codex2.lastIndexOf('"'))) codexPredefinedConstraints.push(codex2);
+
+    if (witness1.substring(witness1.indexOf('"')+1,witness1.lastIndexOf('"'))) witnessPredefinedConstraints.push(witness1);
+    if (witness2.substring(witness2.indexOf('"')+1,witness2.lastIndexOf('"'))) witnessPredefinedConstraints.push(witness2);
+
+    // Recreate taxonomies panel
+    d3.select("#" + popoto.taxonomy.containerId).selectAll("ul").data([]).exit().remove();
+    popoto.taxonomy.createTaxonomyPanel();
+
+    popoto.tools.reset();
+});
+
+d3.select("#clear-button").on("click", function (d) {
+    personPredefinedConstraints = [];
+    codexPredefinedConstraints = [];
+    witnessPredefinedConstraints = [];
+
+    // Recreate taxonomies panel
+    d3.select("#" + popoto.taxonomy.containerId).selectAll("ul").data([]).exit().remove();
+    popoto.taxonomy.createTaxonomyPanel();
+
+    popoto.tools.reset();
+});
+
+
+/**
+ * Define the Label provider you need for your application.
+ * This configuration is mandatory and should contain at least all the labels you could find in your graph model.
+ *
+ * In this alpha version only nodes with a label are supported.
+ *
+ * By default If no attributes are specified Neo4j internal ID will be used.
+ * These label provider configuration can be used to customize the node display in the graph.
+ * See www.popotojs.com or example for more details on available configuration options.
+ */
+// TODO: add in predefined constraint functions for other nodeProviders
+popoto.provider.nodeProviders = {
+    "CODEX": {
+        "returnAttributes": ["label", "ismi_id", "identifier"],
+        "displayAttribute": "label",
+        "getPredefinedConstraints": function (node) {
+            return codexPredefinedConstraints;
+        },
+    },
+    "WITNESS": {
+        "returnAttributes": ["label", "ismi_id", "folios"],
+        "displayAttribute": "label",
+        "getPredefinedConstraints": function (node) {
+            return witnessPredefinedConstraints;
+        },
+    },
+    "TEXT": {
+        "returnAttributes": ["label", "full_title", "ismi_id"],
+        "displayAttribute": "label",
+        //"getPredefinedConstraints": function (node) {
+        //    return textPredefinedConstraints;
+        //},
+    },
+    "PERSON": {
+        "returnAttributes": ["label", "ismi_id", "death_date_text", "url"],
+        "displayAttribute": "label",
+        "getPredefinedConstraints": function (node) {
+            return personPredefinedConstraints;
+        },
+    },
+    "REPOSITORY": {
+        "returnAttributes": ["label", "ismi_id"],
+        "displayAttribute": "label",
+        //"getPredefinedConstraints": function (node) {
+        //    return repositoryPredefinedConstraints;
+        //},
+    },
+    "FLORUIT_DATE": {
+    	"isSearchable": false,
+        //"getPredefinedConstraints": function (node) {
+        //    return floruitPredefinedConstraints;
+        //},
+    }
+};
+
+/**
+ * Popoto label provider
+ * Define the label provider used to customize the link displayed text:
+ */
+// TODO: ensure these cover all the different relations. Commented out for now.
+/*
+popoto.provider.linkProvider = {
+
+    // Customize the text displayed on links:
+    "getLinkTextValue": function (link) {
+
+        // The links labels are just changed in lower case in this example.
+        // But it is possible to use a localization mechanism here to replace values.
+        if (link.type === popoto.graph.link.LinkTypes.RELATION) {
+
+            if (link.source.label == "PERSON") {
+                switch (link.label) {
+                    case "was_student_of":
+                        return "was student of";
+                    case "is_prime_alias_name_of":
+                        return "is prime alias name of";
+                    case "was_born_in":
+                        return "was born in";
+                    case "lived_in":
+                        return "lived in";
+                    case "has_role":
+                        return "has role";
+                    case "has_floruit_date":
+                        return "has floruit date";
+                    case "died_in":
+                        return "died in";
+                    default :
+                        return ""
+                }
+            }
+            if (link.source.label == "CODEX") {
+                switch (link.label) {
+                    case "owned_by":
+                        return "owned by";
+                    case "is_alias_of":
+                        return "is alias of";
+                    case "is_part_of":
+                        return "is part of";
+                }
+            }
+            if (link.source.label == "WITNESS") {
+                switch (link.label) {
+                    case "was_copied_in":
+                        return "was copied in";
+                    case "was_studied_by":
+                        return "was studied by";
+                    case "had_patron":
+                        return "had patron";
+                    case "is_part_of":
+                        return "is part of";
+                    case "is_exemplar_of":
+                        return "is exemplar of";
+                    case "has_title_written_as":
+                        return "has title written as";
+                    case "has_author_written_as":
+                        return "as author written as";
+                    case "was_copied_by":
+                        return "was copied by";
+                }
+            }
+            if (link.source.label == "PLACE") {
+                switch (link.label) {
+                    case "is_part_of":
+                        return "is part of";
+                    case "is_in":
+                        return "is in";
+                }
+            }
+        } else {
+            return popoto.provider.getSemanticValue(link.target);
+        }
+    }
+
+};
+*/
+
+
+
+
+
+
+
+//d3.select("#clear-button").on("click", function (d) {
+//    popoto.graph.node.expandNode()
+//});
+
+//take d3.select of any click that calls popoto.graph.node.expandNode()
+// make sure to search in popoto.js what kind of events trigger the expandNode fn
+//
+// on these events, instead of executing the normal expandNode function, call a modified function that will generate an
+//   html table with the required results. Still maintaining the info being sent to results but ensuring that what is
+//   displayed is thrown into a table.
+
+// to override the popoto.graph.node.expandNode() fn just use:
+
+// Expand Override
+var tableArray = [];
+(function() {
+    var oldVersionExpand = popoto.graph.node.expandNode;
+    popoto.graph.node.expandNode = function(clickedNode) {
+        console.log("NODES OPEN");
+        //var result = oldVersionExpand.apply(this, arguments);
+        // do some more stuff
+        //return result;
+
+        var dataToAdd = clickedNode.data;
+        // Then each node is created
+        var i = 1;
+        dataToAdd.forEach(function (d) {
+            // for each of these bits of data make sure to add the id and the attributes into the html list
+            var nx = clickedNode.x;
+            var ny = clickedNode.y;
+
+            var node = {
+                "id": (++popoto.graph.node.idgen),
+                "parent": clickedNode,
+                "attributes": d,
+                "type": popoto.graph.node.NodeTypes.VALUE,
+                "label": clickedNode.label,
+                "count": d.count,
+                "x": nx,
+                "y": ny,
+                "internalID": d[popoto.query.NEO4J_INTERNAL_ID.queryInternalName]
+            };
+
+            popoto.graph.force.nodes().push(node);
+            // add this node to an array of node values
+            // popoto.graph.force.nodes().push(node);
+            tableArray.push(node);
+
+            var dd = document.getElementById("dropdown");
+            var newListOption = document.createElement("option");
+
+            // TODO: Haven't been able to
+            newListOption.text = node.internalID;
+            console.log(node.internalID);
+            dd.add(newListOption);
+
+            i++;
+        });
+
+        $('#dropdown').attr('style','visibility: visible; overflow: scroll; position: fixed; left: '+clickedNode.x+'px; bottom: '+clickedNode.y+'px; z-index: 10;');
+        //$('#dropdown').attr('style','visibility: visible; overflow: scroll; position: fixed;');
+
+        // Pin clicked node and its parent to avoid the graph to move for selection, only new value nodes will blossom around the clicked node.
+        clickedNode.fixed = true;
+
+        if (clickedNode.parent && clickedNode.parent.type !== popoto.graph.node.NodeTypes.ROOT) {
+            clickedNode.parent.fixed = true;
+        }
+        // Change node state
+        clickedNode.valueExpanded = true;
+        popoto.update();
+
+    };
+})();
+
+// Collapse Override
+(function() {
+    popoto.graph.node.collapseNode = function(clickedNode) {
+
+        if (clickedNode.valueExpanded) { // node is collapsed only if it has been expanded first
+            console.log("NODES CLOSED");
+
+            popoto.logger.debug("collapseNode (" + clickedNode.label + ")");
+
+            // Node has been fixed when expanded so we unfix it back here.
+            if (clickedNode.type !== popoto.graph.node.NodeTypes.ROOT) {
+                clickedNode.fixed = false;
+            }
+
+            // Parent node too if not root
+            if (clickedNode.parent && clickedNode.parent.type !== popoto.graph.node.NodeTypes.ROOT) {
+                clickedNode.parent.fixed = false;
+            }
+
+            clickedNode.valueExpanded = false;
+            popoto.update();
+
+            $('#dropdown').attr('style','visibility: hidden; overflow: scroll; position: fixed;');
+            //TODO: need to delete existing options
+            var x = document.getElementById("dropdown");
+            for (i=x.length; i > 0; i--) {
+                if (x.length > 1) {
+                    x.remove(x.length-1);
+                }
+            }
+
+        } else {
+            popoto.logger.debug("collapseNode called on an unexpanded node");
+        }
+    };
+})();
+
+
+d3.select("#dropdown").on("change", function (d) {
+    if (document.getElementById('dropdown').value != '- Select -') {
+        console.log(document.getElementById('dropdown').value);
+        popoto.graph.node.valueNodeClick(document.getElementById('dropdown').value);
+    }
+});
+// Value click override
+(function() {
+    popoto.graph.node.valueNodeClick = function(selectValue) {
+        console.log("NODE SELECTED");
+
+        popoto.logger.debug("valueNodeClick (" + selectValue.label + ")");
+        // change this next line to take the node id from the table and pull it from the nodes list
+
+        var clickedNode;
+        for (i in tableArray) {
+            if (i.label == selectValue) {
+                clickedNode = i;
+            }
+        }
+
+        clickedNode.parent.value = clickedNode;
+        popoto.result.hasChanged = true;
+        popoto.graph.hasGraphChanged = true;
+
+        popoto.graph.node.collapseNode(clickedNode.parent);
+    };
+})();
+
+
+/**
+ * Here a listener is used to retrieve the total results count and update the page accordingly.
+ * This listener will be called on every graph modification.
+ */
+popoto.result.onTotalResultCount(function (count) {
+    document.getElementById("result-total-count").innerHTML = "(" + count + ")";
+});
+
+/**
+ * The number of results returned can be changed with the following parameter.
+ * Default value is 100.
+ *
+ * Note that in this current alpha version no pagination mechanism is available in displayed results
+ */
+popoto.query.RESULTS_PAGE_SIZE = 1000;
+
+
+/**
+ * For the alpha version, popoto.js has been generated with debug traces you can activate with the following properties:
+ * The value can be one in DEBUG, INFO, WARN, ERROR, NONE.
+ *
+ * With INFO level all the executed cypher query can be seen in the navigator console.
+ * Default is NONE
+ */
+popoto.logger.LEVEL = popoto.logger.LogLevels.INFO;
+
+/**
+ * Start popoto.js generation.
+ * The function requires the label to use as root element in the graph.
+ */
+popoto.start("PERSON");
+
+/* do not zoom with scroll wheel */
+popoto.graph.WHEEL_ZOOM_ENABLED = false;
+
+/* show source and target relations */
+popoto.query.USE_RELATION_DIRECTION = true;