- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 00:41:19+12:00
- Desc:
- Updating Noble 1962 model:
* Exposing the membrane potential to the top-level model;
* adding SED-ML for the paced and pacemaker variants of the model.
Using OpenCOR Snapshot release 2021-09-14.
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/f954e59183314cd37f86c8832dc81317d01c8ec5/dojo-presentation/js/dojo/dojox/data/CsvStore.js
dojo.provide("dojox.data.CsvStore");
dojo.require("dojo.data.util.filter");
dojo.require("dojo.data.util.simpleFetch");
dojo.declare("dojox.data.CsvStore", null, {
// summary:
// The CsvStore implements the dojo.data.api.Read API and reads
// data from files in CSV (Comma Separated Values) format.
// All values are simple string values. References to other items
// are not supported as attribute values in this datastore.
//
// Example data file:
// name, color, age, tagline
// Kermit, green, 12, "Hi, I'm Kermit the Frog."
// Fozzie Bear, orange, 10, "Wakka Wakka Wakka!"
// Miss Piggy, pink, 11, "Kermie!"
//
// Note that values containing a comma must be enclosed with quotes ("")
// Also note that values containing quotes must be escaped with two consecutive quotes (""quoted"")
/* examples:
* var csvStore = new dojox.data.CsvStore({url:"movies.csv");
* var csvStore = new dojox.data.CsvStore({url:"http://example.com/movies.csv");
*/
constructor: function(/* Object */ keywordParameters){
// summary: initializer
// keywordParameters: {url: String}
// keywordParameters: {data: String}
// keywordParameters: {label: String} The column label for the column to use for the label returned by getLabel.
this._attributes = []; // e.g. ["Title", "Year", "Producer"]
this._attributeIndexes = {}; // e.g. {Title: 0, Year: 1, Producer: 2}
this._dataArray = []; // e.g. [[<Item0>],[<Item1>],[<Item2>]]
this._arrayOfAllItems = []; // e.g. [{_csvId:0,_csvStore:store},...]
this._loadFinished = false;
if(keywordParameters.url){
this.url = keywordParameters.url;
}
this._csvData = keywordParameters.data;
if(keywordParameters.label){
this.label = keywordParameters.label;
}else if(this.label === ""){
this.label = undefined;
}
this._storeProp = "_csvStore"; // Property name for the store reference on every item.
this._idProp = "_csvId"; // Property name for the Item Id on every item.
this._features = {
'dojo.data.api.Read': true,
'dojo.data.api.Identity': true
};
this._loadInProgress = false; //Got to track the initial load to prevent duelling loads of the dataset.
this._queuedFetches = [];
},
url: "", //Declarative hook for setting Csv source url.
label: "", //Declarative hook for setting the label attribute.
_assertIsItem: function(/* item */ item){
// summary:
// This function tests whether the item passed in is indeed an item in the store.
// item:
// The item to test for being contained by the store.
if(!this.isItem(item)){
throw new Error("dojox.data.CsvStore: a function was passed an item argument that was not an item");
}
},
_assertIsAttribute: function(/* item || String */ attribute){
// summary:
// This function tests whether the item passed in is indeed a valid 'attribute' like type for the store.
// attribute:
// The attribute to test for being contained by the store.
if(!dojo.isString(attribute)){
throw new Error("dojox.data.CsvStore: a function was passed an attribute argument that was not an attribute object nor an attribute name string");
}
},
/***************************************
dojo.data.api.Read API
***************************************/
getValue: function( /* item */ item,
/* attribute || attribute-name-string */ attribute,
/* value? */ defaultValue){
// summary:
// See dojo.data.api.Read.getValue()
// Note that for the CsvStore, an empty string value is the same as no value,
// so the defaultValue would be returned instead of an empty string.
this._assertIsItem(item);
this._assertIsAttribute(attribute);
var itemValue = defaultValue;
if(this.hasAttribute(item, attribute)){
var itemData = this._dataArray[this.getIdentity(item)];
itemValue = itemData[this._attributeIndexes[attribute]];
}
return itemValue; //String
},
getValues: function(/* item */ item,
/* attribute || attribute-name-string */ attribute){
// summary:
// See dojo.data.api.Read.getValues()
// CSV syntax does not support multi-valued attributes, so this is just a
// wrapper function for getValue().
var value = this.getValue(item, attribute);
return (value ? [value] : []); //Array
},
getAttributes: function(/* item */ item){
// summary:
// See dojo.data.api.Read.getAttributes()
this._assertIsItem(item);
var attributes = [];
var itemData = this._dataArray[this.getIdentity(item)];
for(var i=0; i<itemData.length; i++){
// Check for empty string values. CsvStore treats empty strings as no value.
if(itemData[i] !== ""){
attributes.push(this._attributes[i]);
}
}
return attributes; //Array
},
hasAttribute: function( /* item */ item,
/* attribute || attribute-name-string */ attribute){
// summary:
// See dojo.data.api.Read.hasAttribute()
// The hasAttribute test is true if attribute has an index number within the item's array length
// AND if the item has a value for that attribute. Note that for the CsvStore, an
// empty string value is the same as no value.
this._assertIsItem(item);
this._assertIsAttribute(attribute);
var attributeIndex = this._attributeIndexes[attribute];
var itemData = this._dataArray[this.getIdentity(item)];
return (typeof attributeIndex !== "undefined" && attributeIndex < itemData.length && itemData[attributeIndex] !== ""); //Boolean
},
containsValue: function(/* item */ item,
/* attribute || attribute-name-string */ attribute,
/* anything */ value){
// summary:
// See dojo.data.api.Read.containsValue()
var regexp = undefined;
if(typeof value === "string"){
regexp = dojo.data.util.filter.patternToRegExp(value, false);
}
return this._containsValue(item, attribute, value, regexp); //boolean.
},
_containsValue: function( /* item */ item,
/* attribute || attribute-name-string */ attribute,
/* anything */ value,
/* RegExp?*/ regexp){
// summary:
// Internal function for looking at the values contained by the item.
// description:
// Internal function for looking at the values contained by the item. This
// function allows for denoting if the comparison should be case sensitive for
// strings or not (for handling filtering cases where string case should not matter)
//
// item:
// The data item to examine for attribute values.
// attribute:
// The attribute to inspect.
// value:
// The value to match.
// regexp:
// Optional regular expression generated off value if value was of string type to handle wildcarding.
// If present and attribute values are string, then it can be used for comparison instead of 'value'
var values = this.getValues(item, attribute);
for(var i = 0; i < values.length; ++i){
var possibleValue = values[i];
if(typeof possibleValue === "string" && regexp){
return (possibleValue.match(regexp) !== null);
}else{
//Non-string matching.
if(value === possibleValue){
return true; // Boolean
}
}
}
return false; // Boolean
},
isItem: function(/* anything */ something){
// summary:
// See dojo.data.api.Read.isItem()
if(something && something[this._storeProp] === this){
var identity = something[this._idProp];
if(identity >= 0 && identity < this._dataArray.length){
return true; //Boolean
}
}
return false; //Boolean
},
isItemLoaded: function(/* anything */ something){
// summary:
// See dojo.data.api.Read.isItemLoaded()
// The CsvStore always loads all items, so if it's an item, then it's loaded.
return this.isItem(something); //Boolean
},
loadItem: function(/* item */ item){
// summary:
// See dojo.data.api.Read.loadItem()
// description:
// The CsvStore always loads all items, so if it's an item, then it's loaded.
// From the dojo.data.api.Read.loadItem docs:
// If a call to isItemLoaded() returns true before loadItem() is even called,
// then loadItem() need not do any work at all and will not even invoke
// the callback handlers.
},
getFeatures: function(){
// summary:
// See dojo.data.api.Read.getFeatures()
return this._features; //Object
},
getLabel: function(/* item */ item){
// summary:
// See dojo.data.api.Read.getLabel()
if(this.label && this.isItem(item)){
return this.getValue(item,this.label); //String
}
return undefined; //undefined
},
getLabelAttributes: function(/* item */ item){
// summary:
// See dojo.data.api.Read.getLabelAttributes()
if(this.label){
return [this.label]; //array
}
return null; //null
},
// The dojo.data.api.Read.fetch() function is implemented as
// a mixin from dojo.data.util.simpleFetch.
// That mixin requires us to define _fetchItems().
_fetchItems: function( /* Object */ keywordArgs,
/* Function */ findCallback,
/* Function */ errorCallback){
// summary:
// See dojo.data.util.simpleFetch.fetch()
var self = this;
var filter = function(requestArgs, arrayOfAllItems){
var items = null;
if(requestArgs.query){
items = [];
var ignoreCase = requestArgs.queryOptions ? requestArgs.queryOptions.ignoreCase : false;
//See if there are any string values that can be regexp parsed first to avoid multiple regexp gens on the
//same value for each item examined. Much more efficient.
var regexpList = {};
for(var key in requestArgs.query){
var value = requestArgs.query[key];
if(typeof value === "string"){
regexpList[key] = dojo.data.util.filter.patternToRegExp(value, ignoreCase);
}
}
for(var i = 0; i < arrayOfAllItems.length; ++i){
var match = true;
var candidateItem = arrayOfAllItems[i];
for(var key in requestArgs.query){
var value = requestArgs.query[key];
if(!self._containsValue(candidateItem, key, value, regexpList[key])){
match = false;
}
}
if(match){
items.push(candidateItem);
}
}
}else{
// We want a copy to pass back in case the parent wishes to sort the array. We shouldn't allow resort
// of the internal list so that multiple callers can get lists and sort without affecting each other.
if(arrayOfAllItems.length> 0){
items = arrayOfAllItems.slice(0,arrayOfAllItems.length);
}
}
findCallback(items, requestArgs);
};
if(this._loadFinished){
filter(keywordArgs, this._arrayOfAllItems);
}else{
if(this.url !== ""){
//If fetches come in before the loading has finished, but while
//a load is in progress, we have to defer the fetching to be
//invoked in the callback.
if(this._loadInProgress){
this._queuedFetches.push({args: keywordArgs, filter: filter});
}else{
this._loadInProgress = true;
var getArgs = {
url: self.url,
handleAs: "text"
};
var getHandler = dojo.xhrGet(getArgs);
getHandler.addCallback(function(data){
self._processData(data);
filter(keywordArgs, self._arrayOfAllItems);
self._handleQueuedFetches();
});
getHandler.addErrback(function(error){
self._loadInProgress = false;
if(errorCallback){
errorCallback(error, keywordArgs);
}else{
throw error;
}
});
}
}else if(this._csvData){
this._processData(this._csvData);
this._csvData = null;
filter(keywordArgs, this._arrayOfAllItems);
}else{
var error = new Error("dojox.data.CsvStore: No CSV source data was provided as either URL or String data input.");
if(errorCallback){
errorCallback(error, keywordArgs);
}else{
throw error;
}
}
}
},
close: function(/*dojo.data.api.Request || keywordArgs || null */ request){
// summary:
// See dojo.data.api.Read.close()
},
// -------------------------------------------------------------------
// Private methods
_getArrayOfArraysFromCsvFileContents: function(/* string */ csvFileContents){
/* summary:
* Parses a string of CSV records into a nested array structure.
* description:
* Given a string containing CSV records, this method parses
* the string and returns a data structure containing the parsed
* content. The data structure we return is an array of length
* R, where R is the number of rows (lines) in the CSV data. The
* return array contains one sub-array for each CSV line, and each
* sub-array contains C string values, where C is the number of
* columns in the CSV data.
*/
/* example:
* For example, given this CSV string as input:
* "Title, Year, Producer \n Alien, 1979, Ridley Scott \n Blade Runner, 1982, Ridley Scott"
* this._dataArray will be set to:
* [["Alien", "1979", "Ridley Scott"],
* ["Blade Runner", "1982", "Ridley Scott"]]
* And this._attributes will be set to:
* ["Title", "Year", "Producer"]
* And this._attributeIndexes will be set to:
* { "Title":0, "Year":1, "Producer":2 }
*/
if(dojo.isString(csvFileContents)){
var lineEndingCharacters = new RegExp("\r\n|\n|\r");
var leadingWhiteSpaceCharacters = new RegExp("^\\s+",'g');
var trailingWhiteSpaceCharacters = new RegExp("\\s+$",'g');
var doubleQuotes = new RegExp('""','g');
var arrayOfOutputRecords = [];
var arrayOfInputLines = this._splitLines(csvFileContents);
for(var i = 0; i < arrayOfInputLines.length; ++i){
var singleLine = arrayOfInputLines[i];
if(singleLine.length > 0){
var listOfFields = singleLine.split(',');
var j = 0;
while(j < listOfFields.length){
var space_field_space = listOfFields[j];
var field_space = space_field_space.replace(leadingWhiteSpaceCharacters, ''); // trim leading whitespace
var field = field_space.replace(trailingWhiteSpaceCharacters, ''); // trim trailing whitespace
var firstChar = field.charAt(0);
var lastChar = field.charAt(field.length - 1);
var secondToLastChar = field.charAt(field.length - 2);
var thirdToLastChar = field.charAt(field.length - 3);
if(field.length === 2 && field == "\"\""){
listOfFields[j] = ""; //Special case empty string field.
}else if((firstChar == '"') &&
((lastChar != '"') ||
((lastChar == '"') && (secondToLastChar == '"') && (thirdToLastChar != '"')))){
if(j+1 === listOfFields.length){
// alert("The last field in record " + i + " is corrupted:\n" + field);
return null; //null
}
var nextField = listOfFields[j+1];
listOfFields[j] = field_space + ',' + nextField;
listOfFields.splice(j+1, 1); // delete element [j+1] from the list
}else{
if((firstChar == '"') && (lastChar == '"')){
field = field.slice(1, (field.length - 1)); // trim the " characters off the ends
field = field.replace(doubleQuotes, '"'); // replace "" with "
}
listOfFields[j] = field;
j += 1;
}
}
arrayOfOutputRecords.push(listOfFields);
}
}
// The first item of the array must be the header row with attribute names.
this._attributes = arrayOfOutputRecords.shift();
for(var i=0; i<this._attributes.length; i++){
// Store the index of each attribute
this._attributeIndexes[this._attributes[i]] = i;
}
this._dataArray = arrayOfOutputRecords; //Array
}
},
_splitLines: function(csvContent){
// summary:
// Function to split the CSV file contents into separate lines.
// Since line breaks can occur inside quotes, a Regexp didn't
// work as well. A quick passover parse should be just as efficient.
var split = [];
var i;
var line = "";
var inQuotes = false;
for(i = 0; i < csvContent.length; i++){
var c = csvContent.charAt(i);
switch(c){
case '\"':
inQuotes = !inQuotes;
line += c;
break;
case '\r':
if(inQuotes){
line += c;
}else{
split.push(line);
line = "";
if (i < (csvContent.length - 1) && csvContent.charAt(i + 1) == '\n') {
i++; //Skip it, it's CRLF
}
}
break;
case '\n':
if(inQuotes){
line += c;
}else{
split.push(line);
line = "";
}
break;
default:
line +=c;
}
}
if(line !== ""){
split.push(line);
}
return split;
},
_processData: function(/* String */ data){
this._getArrayOfArraysFromCsvFileContents(data);
this._arrayOfAllItems = [];
for(var i=0; i<this._dataArray.length; i++){
this._arrayOfAllItems.push(this._createItemFromIdentity(i));
}
this._loadFinished = true;
this._loadInProgress = false;
},
_createItemFromIdentity: function(/* String */ identity){
var item = {};
item[this._storeProp] = this;
item[this._idProp] = identity;
return item; //Object
},
/***************************************
dojo.data.api.Identity API
***************************************/
getIdentity: function(/* item */ item){
// summary:
// See dojo.data.api.Identity.getIdentity()
if(this.isItem(item)){
return item[this._idProp]; //String
}
return null; //null
},
fetchItemByIdentity: function(/* Object */ keywordArgs){
// summary:
// See dojo.data.api.Identity.fetchItemByIdentity()
//Hasn't loaded yet, we have to trigger the load.
if(!this._loadFinished){
var self = this;
if(this.url !== ""){
//If fetches come in before the loading has finished, but while
//a load is in progress, we have to defer the fetching to be
//invoked in the callback.
if(this._loadInProgress){
this._queuedFetches.push({args: keywordArgs});
}else{
this._loadInProgress = true;
var getArgs = {
url: self.url,
handleAs: "text"
};
var getHandler = dojo.xhrGet(getArgs);
getHandler.addCallback(function(data){
var scope = keywordArgs.scope?keywordArgs.scope:dojo.global;
try{
self._processData(data);
var item = self._createItemFromIdentity(keywordArgs.identity);
if(!self.isItem(item)){
item = null;
}
if(keywordArgs.onItem){
keywordArgs.onItem.call(scope, item);
}
self._handleQueuedFetches();
}catch(error){
if(keywordArgs.onError){
keywordArgs.onError.call(scope, error);
}
}
});
getHandler.addErrback(function(error){
this._loadInProgress = false;
if(keywordArgs.onError){
var scope = keywordArgs.scope?keywordArgs.scope:dojo.global;
keywordArgs.onError.call(scope, error);
}
});
}
}else if(this._csvData){
self._processData(self._csvData);
self._csvData = null;
var item = self._createItemFromIdentity(keywordArgs.identity);
if(!self.isItem(item)){
item = null;
}
if(keywordArgs.onItem){
var scope = keywordArgs.scope?keywordArgs.scope:dojo.global;
keywordArgs.onItem.call(scope, item);
}
}
}else{
//Already loaded. We can just look it up and call back.
var item = this._createItemFromIdentity(keywordArgs.identity);
if(!this.isItem(item)){
item = null;
}
if(keywordArgs.onItem){
var scope = keywordArgs.scope?keywordArgs.scope:dojo.global;
keywordArgs.onItem.call(scope, item);
}
}
},
getIdentityAttributes: function(/* item */ item){
// summary:
// See dojo.data.api.Identity.getIdentifierAttributes()
//Identity isn't a public attribute in the item, it's the row position index.
//So, return null.
return null;
},
_handleQueuedFetches: function(){
// summary:
// Internal function to execute delayed request in the store.
//Execute any deferred fetches now.
if (this._queuedFetches.length > 0) {
for(var i = 0; i < this._queuedFetches.length; i++){
var fData = this._queuedFetches[i];
var delayedFilter = fData.filter;
var delayedQuery = fData.args;
if(delayedFilter){
delayedFilter(delayedQuery, this._arrayOfAllItems);
}else{
this.fetchItemByIdentity(fData.args);
}
}
this._queuedFetches = [];
}
}
});
//Mix in the simple fetch implementation to this class.
dojo.extend(dojox.data.CsvStore,dojo.data.util.simpleFetch);
