- 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/sql/_base.js
dojo.provide("dojox.sql._base");
dojo.require("dojox.sql._crypto");
dojo.mixin(dojox.sql, {
// summary:
// Executes a SQL expression.
// description:
// There are four ways to call this:
// 1) Straight SQL: dojox.sql("SELECT * FROM FOOBAR");
// 2) SQL with parameters: dojox.sql("INSERT INTO FOOBAR VALUES (?)", someParam)
// 3) Encrypting particular values:
// dojox.sql("INSERT INTO FOOBAR VALUES (ENCRYPT(?))", someParam, "somePassword", callback)
// 4) Decrypting particular values:
// dojox.sql("SELECT DECRYPT(SOMECOL1), DECRYPT(SOMECOL2) FROM
// FOOBAR WHERE SOMECOL3 = ?", someParam,
// "somePassword", callback)
//
// For encryption and decryption the last two values should be the the password for
// encryption/decryption, and the callback function that gets the result set.
//
// Note: We only support ENCRYPT(?) statements, and
// and DECRYPT(*) statements for now -- you can not have a literal string
// inside of these, such as ENCRYPT('foobar')
//
// Note: If you have multiple columns to encrypt and decrypt, you can use the following
// convenience form to not have to type ENCRYPT(?)/DECRYPT(*) many times:
//
// dojox.sql("INSERT INTO FOOBAR VALUES (ENCRYPT(?, ?, ?))",
// someParam1, someParam2, someParam3,
// "somePassword", callback)
//
// dojox.sql("SELECT DECRYPT(SOMECOL1, SOMECOL2) FROM
// FOOBAR WHERE SOMECOL3 = ?", someParam,
// "somePassword", callback)
dbName: null,
// summary:
// If true, then we print out any SQL that is executed
// to the debug window
debug: (dojo.exists("dojox.sql.debug") ? dojox.sql.debug:false),
open: function(dbName){
if(this._dbOpen && (!dbName || dbName == this.dbName)){
return;
}
if(!this.dbName){
this.dbName = "dot_store_"
+ window.location.href.replace(/[^0-9A-Za-z_]/g, "_");
// database names in Gears are limited to 64 characters long
if(this.dbName.length > 63){
this.dbName = this.dbName.substring(0, 63);
}
}
if(!dbName){
dbName = this.dbName;
}
try{
this._initDb();
this.db.open(dbName);
this._dbOpen = true;
}catch(exp){
throw exp.message||exp;
}
},
close: function(dbName){
// on Internet Explorer, Google Gears throws an exception
// "Object not a collection", when we try to close the
// database -- just don't close it on this platform
// since we are running into a Gears bug; the Gears team
// said it's ok to not close a database connection
if(dojo.isIE){ return; }
if(!this._dbOpen && (!dbName || dbName == this.dbName)){
return;
}
if(!dbName){
dbName = this.dbName;
}
try{
this.db.close(dbName);
this._dbOpen = false;
}catch(exp){
throw exp.message||exp;
}
},
_exec: function(params){
try{
// get the Gears Database object
this._initDb();
// see if we need to open the db; if programmer
// manually called dojox.sql.open() let them handle
// it; otherwise we open and close automatically on
// each SQL execution
if(!this._dbOpen){
this.open();
this._autoClose = true;
}
// determine our parameters
var sql = null;
var callback = null;
var password = null;
var args = dojo._toArray(params);
sql = args.splice(0, 1)[0];
// does this SQL statement use the ENCRYPT or DECRYPT
// keywords? if so, extract our callback and crypto
// password
if(this._needsEncrypt(sql) || this._needsDecrypt(sql)){
callback = args.splice(args.length - 1, 1)[0];
password = args.splice(args.length - 1, 1)[0];
}
// 'args' now just has the SQL parameters
// print out debug SQL output if the developer wants that
if(this.debug){
this._printDebugSQL(sql, args);
}
// handle SQL that needs encryption/decryption differently
// do we have an ENCRYPT SQL statement? if so, handle that first
if(this._needsEncrypt(sql)){
var crypto = new dojox.sql._SQLCrypto("encrypt", sql,
password, args,
callback);
return; // encrypted results will arrive asynchronously
}else if(this._needsDecrypt(sql)){ // otherwise we have a DECRYPT statement
var crypto = new dojox.sql._SQLCrypto("decrypt", sql,
password, args,
callback);
return; // decrypted results will arrive asynchronously
}
// execute the SQL and get the results
var rs = this.db.execute(sql, args);
// Gears ResultSet object's are ugly -- normalize
// these into something JavaScript programmers know
// how to work with, basically an array of
// JavaScript objects where each property name is
// simply the field name for a column of data
rs = this._normalizeResults(rs);
if(this._autoClose){
this.close();
}
return rs;
}catch(exp){
exp = exp.message||exp;
console.debug("SQL Exception: " + exp);
if(this._autoClose){
try{
this.close();
}catch(e){
console.debug("Error closing database: "
+ e.message||e);
}
}
throw exp;
}
},
_initDb: function(){
if(!this.db){
try{
this.db = google.gears.factory.create('beta.database', '1.0');
}catch(exp){
dojo.setObject("google.gears.denied", true);
dojox.off.onFrameworkEvent("coreOperationFailed");
throw "Google Gears must be allowed to run";
}
}
},
_printDebugSQL: function(sql, args){
var msg = "dojox.sql(\"" + sql + "\"";
for(var i = 0; i < args.length; i++){
if(typeof args[i] == "string"){
msg += ", \"" + args[i] + "\"";
}else{
msg += ", " + args[i];
}
}
msg += ")";
console.debug(msg);
},
_normalizeResults: function(rs){
var results = [];
if(!rs){ return []; }
while(rs.isValidRow()){
var row = {};
for(var i = 0; i < rs.fieldCount(); i++){
var fieldName = rs.fieldName(i);
var fieldValue = rs.field(i);
row[fieldName] = fieldValue;
}
results.push(row);
rs.next();
}
rs.close();
return results;
},
_needsEncrypt: function(sql){
return /encrypt\([^\)]*\)/i.test(sql);
},
_needsDecrypt: function(sql){
return /decrypt\([^\)]*\)/i.test(sql);
}
});
dojo.declare("dojox.sql._SQLCrypto", null, {
// summary:
// A private class encapsulating any cryptography that must be done
// on a SQL statement. We instantiate this class and have it hold
// it's state so that we can potentially have several encryption
// operations happening at the same time by different SQL statements.
constructor: function(action, sql, password, args, callback){
if(action == "encrypt"){
this._execEncryptSQL(sql, password, args, callback);
}else{
this._execDecryptSQL(sql, password, args, callback);
}
},
_execEncryptSQL: function(sql, password, args, callback){
// strip the ENCRYPT/DECRYPT keywords from the SQL
var strippedSQL = this._stripCryptoSQL(sql);
// determine what arguments need encryption
var encryptColumns = this._flagEncryptedArgs(sql, args);
// asynchronously encrypt each argument that needs it
var self = this;
this._encrypt(strippedSQL, password, args, encryptColumns, function(finalArgs){
// execute the SQL
var error = false;
var resultSet = [];
var exp = null;
try{
resultSet = dojox.sql.db.execute(strippedSQL, finalArgs);
}catch(execError){
error = true;
exp = execError.message||execError;
}
// was there an error during SQL execution?
if(exp != null){
if(dojox.sql._autoClose){
try{ dojox.sql.close(); }catch(e){}
}
callback(null, true, exp.toString());
return;
}
// normalize SQL results into a JavaScript object
// we can work with
resultSet = dojox.sql._normalizeResults(resultSet);
if(dojox.sql._autoClose){
dojox.sql.close();
}
// are any decryptions necessary on the result set?
if(dojox.sql._needsDecrypt(sql)){
// determine which of the result set columns needs decryption
var needsDecrypt = self._determineDecryptedColumns(sql);
// now decrypt columns asynchronously
// decrypt columns that need it
self._decrypt(resultSet, needsDecrypt, password, function(finalResultSet){
callback(finalResultSet, false, null);
});
}else{
callback(resultSet, false, null);
}
});
},
_execDecryptSQL: function(sql, password, args, callback){
// strip the ENCRYPT/DECRYPT keywords from the SQL
var strippedSQL = this._stripCryptoSQL(sql);
// determine which columns needs decryption; this either
// returns the value *, which means all result set columns will
// be decrypted, or it will return the column names that need
// decryption set on a hashtable so we can quickly test a given
// column name; the key is the column name that needs
// decryption and the value is 'true' (i.e. needsDecrypt["someColumn"]
// would return 'true' if it needs decryption, and would be 'undefined'
// or false otherwise)
var needsDecrypt = this._determineDecryptedColumns(sql);
// execute the SQL
var error = false;
var resultSet = [];
var exp = null;
try{
resultSet = dojox.sql.db.execute(strippedSQL, args);
}catch(execError){
error = true;
exp = execError.message||execError;
}
// was there an error during SQL execution?
if(exp != null){
if(dojox.sql._autoClose){
try{ dojox.sql.close(); }catch(e){}
}
callback(resultSet, true, exp.toString());
return;
}
// normalize SQL results into a JavaScript object
// we can work with
resultSet = dojox.sql._normalizeResults(resultSet);
if(dojox.sql._autoClose){
dojox.sql.close();
}
// decrypt columns that need it
this._decrypt(resultSet, needsDecrypt, password, function(finalResultSet){
callback(finalResultSet, false, null);
});
},
_encrypt: function(sql, password, args, encryptColumns, callback){
//console.debug("_encrypt, sql="+sql+", password="+password+", encryptColumns="+encryptColumns+", args="+args);
this._totalCrypto = 0;
this._finishedCrypto = 0;
this._finishedSpawningCrypto = false;
this._finalArgs = args;
for(var i = 0; i < args.length; i++){
if(encryptColumns[i]){
// we have an encrypt() keyword -- get just the value inside
// the encrypt() parantheses -- for now this must be a ?
var sqlParam = args[i];
var paramIndex = i;
// update the total number of encryptions we know must be done asynchronously
this._totalCrypto++;
// FIXME: This currently uses DES as a proof-of-concept since the
// DES code used is quite fast and was easy to work with. Modify dojox.sql
// to be able to specify a different encryption provider through a
// a SQL-like syntax, such as dojox.sql("SET ENCRYPTION BLOWFISH"),
// and modify the dojox.crypto.Blowfish code to be able to work using
// a Google Gears Worker Pool
// do the actual encryption now, asychronously on a Gears worker thread
dojox.sql._crypto.encrypt(sqlParam, password, dojo.hitch(this, function(results){
// set the new encrypted value
this._finalArgs[paramIndex] = results;
this._finishedCrypto++;
// are we done with all encryption?
if(this._finishedCrypto >= this._totalCrypto
&& this._finishedSpawningCrypto){
callback(this._finalArgs);
}
}));
}
}
this._finishedSpawningCrypto = true;
},
_decrypt: function(resultSet, needsDecrypt, password, callback){
//console.debug("decrypt, resultSet="+resultSet+", needsDecrypt="+needsDecrypt+", password="+password);
this._totalCrypto = 0;
this._finishedCrypto = 0;
this._finishedSpawningCrypto = false;
this._finalResultSet = resultSet;
for(var i = 0; i < resultSet.length; i++){
var row = resultSet[i];
// go through each of the column names in row,
// seeing if they need decryption
for(var columnName in row){
if(needsDecrypt == "*" || needsDecrypt[columnName]){
this._totalCrypto++;
var columnValue = row[columnName];
// forming a closure here can cause issues, with values not cleanly
// saved on Firefox/Mac OS X for some of the values above that
// are needed in the callback below; call a subroutine that will form
// a closure inside of itself instead
this._decryptSingleColumn(columnName, columnValue, password, i,
function(finalResultSet){
callback(finalResultSet);
});
}
}
}
this._finishedSpawningCrypto = true;
},
_stripCryptoSQL: function(sql){
// replace all DECRYPT(*) occurrences with a *
sql = sql.replace(/DECRYPT\(\*\)/ig, "*");
// match any ENCRYPT(?, ?, ?, etc) occurrences,
// then replace with just the question marks in the
// middle
var matches = sql.match(/ENCRYPT\([^\)]*\)/ig);
if(matches != null){
for(var i = 0; i < matches.length; i++){
var encryptStatement = matches[i];
var encryptValue = encryptStatement.match(/ENCRYPT\(([^\)]*)\)/i)[1];
sql = sql.replace(encryptStatement, encryptValue);
}
}
// match any DECRYPT(COL1, COL2, etc) occurrences,
// then replace with just the column names
// in the middle
matches = sql.match(/DECRYPT\([^\)]*\)/ig);
if(matches != null){
for(var i = 0; i < matches.length; i++){
var decryptStatement = matches[i];
var decryptValue = decryptStatement.match(/DECRYPT\(([^\)]*)\)/i)[1];
sql = sql.replace(decryptStatement, decryptValue);
}
}
return sql;
},
_flagEncryptedArgs: function(sql, args){
// capture literal strings that have question marks in them,
// and also capture question marks that stand alone
var tester = new RegExp(/([\"][^\"]*\?[^\"]*[\"])|([\'][^\']*\?[^\']*[\'])|(\?)/ig);
var matches;
var currentParam = 0;
var results = [];
while((matches = tester.exec(sql)) != null){
var currentMatch = RegExp.lastMatch+"";
// are we a literal string? then ignore it
if(/^[\"\']/.test(currentMatch)){
continue;
}
// do we have an encrypt keyword to our left?
var needsEncrypt = false;
if(/ENCRYPT\([^\)]*$/i.test(RegExp.leftContext)){
needsEncrypt = true;
}
// set the encrypted flag
results[currentParam] = needsEncrypt;
currentParam++;
}
return results;
},
_determineDecryptedColumns: function(sql){
var results = {};
if(/DECRYPT\(\*\)/i.test(sql)){
results = "*";
}else{
var tester = /DECRYPT\((?:\s*\w*\s*\,?)*\)/ig;
var matches;
while(matches = tester.exec(sql)){
var lastMatch = new String(RegExp.lastMatch);
var columnNames = lastMatch.replace(/DECRYPT\(/i, "");
columnNames = columnNames.replace(/\)/, "");
columnNames = columnNames.split(/\s*,\s*/);
dojo.forEach(columnNames, function(column){
if(/\s*\w* AS (\w*)/i.test(column)){
column = column.match(/\s*\w* AS (\w*)/i)[1];
}
results[column] = true;
});
}
}
return results;
},
_decryptSingleColumn: function(columnName, columnValue, password, currentRowIndex,
callback){
//console.debug("decryptSingleColumn, columnName="+columnName+", columnValue="+columnValue+", currentRowIndex="+currentRowIndex)
dojox.sql._crypto.decrypt(columnValue, password, dojo.hitch(this, function(results){
// set the new decrypted value
this._finalResultSet[currentRowIndex][columnName] = results;
this._finishedCrypto++;
// are we done with all encryption?
if(this._finishedCrypto >= this._totalCrypto
&& this._finishedSpawningCrypto){
//console.debug("done with all decrypts");
callback(this._finalResultSet);
}
}));
}
});
(function(){
var orig_sql = dojox.sql;
dojox.sql = new Function("return dojox.sql._exec(arguments);");
dojo.mixin(dojox.sql, orig_sql);
})();
