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Shit broken, but all DataReader function calls are looking good tonig…
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…ht mmm mmm mmm.
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@dns-mcdaid
dns-mcdaid committed Aug 4, 2016
1 parent e3e5f0e commit 58e492d
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Showing 5 changed files with 130 additions and 34 deletions.
18 changes: 18 additions & 0 deletions data/test_data_01.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
List1 | List2 | gene
1 | 0 | At1g01050
1 | 0 | At1g01450
1 | 0 | At1g01460
1 | 0 | At1g01510
1 | 0 | At1g01560
1 | 0 | At1g01740
1 | 0 | At1g02970
1 | 0 | At1g03030
1 | 0 | At1g03450
1 | 0 | At1g03590
0 | 1 | At1g77760
0 | 1 | At5g53460
0 | 1 | At1g05250
0 | 1 | At3g49960
0 | 1 | At5g17820
1 | 1 | At1g03740
1 | 1 | At1g03920
113 changes: 92 additions & 21 deletions public/javascripts/backend/visGeneServer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ const DataReader = require('../data/dataReader');
const DataSource = require('../data/dataSource');
const ExternalConnection = require('../data/externalConnection');
const VPConnection = require('../data/vpConnection');
const ParseException = require('../data/parseException');

/**
* @param u {URL}
Expand Down Expand Up @@ -71,17 +72,18 @@ VisGene.prototype = {
init : function(callback) {
var vpU = null;
try {
vpU = url.format("./index.html?sungearU=");
// TODO: Don't hardcode in production
vpU = url.parse("./index.html?data_url=test_data/test_data_01.txt");
this.extAttrib = VPConnection.makeAttributes(vpU);
} catch (e) {
console.error("old-style VP connection failed, trying generic external connection (exception follows)");
console.error(e.message);
console.log("old-style VP connection failed, trying generic external connection (exception follows)");
console.log(e.message);
if (vpU !== null) {
try {
this.extAttrib = ExternalConnection.makeExportAttributes(vpU);
} catch (e2) {
console.error("external connection failed, resorting to load menu (exception follows)");
console.error(e2.message);
console.log("external connection failed, resorting to load menu (exception follows)");
console.log(e2.message);
}
}
}
Expand All @@ -94,28 +96,97 @@ VisGene.prototype = {
this.dataDir += "/";
}
this.dataU = DataReader.makeURL(this.base, this.dataDir);
console.log(this.dataU);

var potato = function(callback) {
DataReader.testRequest(function() {
callback();
});
callback();
};

// prepare data source
//this.src = new DataSource(this.dataU);
this.src = new DataSource(this.dataU);
var exp = new ExperimentList(url.resolve(this.dataU, "exper.txt"), url.resolve(this.dataU, "species.txt"), this.dataU, function() {
this.exp = exp;
potato(callback);
this.run(callback);
}.bind(this));

},
run : function() {
run : function(callback) {
if (this.extAttrib !== null && this.extAttrib.get("sungearU") !== null) {
this.src.setAttributes(this.extAttrib, this.dataU);
this.openFile();
this.src.setAttributes(this.extAttrib, this.dataU, function() {
this.openFile(this.extAttrib, function() {
callback();
});
}.bind(this));

}
},

openFile : function(attrib, callback) {
console.log("data file: " + attrib.get("sungearU"));
// var status = new StatusDialog(f, this);
var t = new LoadThread(attrib);
t.run(this, function() {
if (t.getException() !== null) {
console.log(t.getException());
} else {
var iL = attrib.get("itemsLabel", "items");
var cL = attrib.get("categoriesLabel", "categories");
// Set titles for geneF, geneM, goF, and goM
var r = this.src.getReader();
if (this.showWarning && r.missingGenes.size() + r.dupGenes.size() > 0) {
var msg = "There are inconsistencies in this data file:";
if (r.missingGenes.size() > 0) {
msg += "\n" + r.missingGenes.size() + " input " + iL + " unkown to Sungear have been ignored.";
}
if (r.dupGenes.size() > 0) {
msg += "\n" + r.dupGenes.size() + " " + iL + " duplicated in the input file; only the first occurence of each has been used.";
}
msg += "\nThis will not prevent Sungear from running, but you may want to resolve these issues.";
msg += "\nSee Help | File Info for details about the " + iL + " involved.";
console.log(msg);
}
}
callback();
}.bind(this));
}
};

/**
* Experiment and master data load thread to separate the load
* operation from the main GUI thread.
* @author RajahBimmy
*/
/**
* Loads an experiment and, if necessary, master data, giving
* load status updates.
* @param u URL of the experiment file to load
* @param status dialog for status updates
*/
function LoadThread(attrib) {
this.attrib = attrib;
this.ex = null;
this.status = null;
}

LoadThread.prototype = {
constructor : LoadThread,
run : function(parent, callback) {
try {
console.log("Preparing Sungear Display");
parent.src.set(this.attrib, this.status, function() {
console.log("done!");
});
} catch (oo) {
if (typeof oo !== 'ParseException') {
console.log("Out of memory?");
// this.status.setModal(false);
//parent.src.getReader().clear();
this.ex = new ParseException("Out of memory");
} else {
this.ex = oo;
}
}
// this.status.setVisible(false);
// this.status.dispose();
return;
},
getException : function() {
return this.ex;
}
};

Expand All @@ -137,6 +208,7 @@ VisGene.usage = function(){
};
/**
* @param args {String[]}
* @callback {function}
*/
VisGene.main = function(args, callback) {
try {
Expand Down Expand Up @@ -172,9 +244,8 @@ VisGene.main = function(args, callback) {
for (var j = i; j < args.length; j++) {
plugin.push(args[j]);
}
var myUrl = url.format("./");
console.log(myUrl);
var vis = new VisGene(myUrl, warn, plugin, dataDir);
var localUrl = url.format("./");
var vis = new VisGene(localUrl, warn, plugin, dataDir);
vis.init(function() {
console.log("Made it back to vis init!");
callback(vis);
Expand Down
2 changes: 1 addition & 1 deletion public/javascripts/data/dataReader.js
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Original file line number Diff line number Diff line change
Expand Up @@ -431,7 +431,7 @@ DataReader.readURL = function(u, callback) {

// Print only read bytes to avoid junk.
if (bytes > 0) {
callback(buf.slice(0, bytes));
callback(buf.slice(0, bytes).toString());
}
});
});
Expand Down
28 changes: 17 additions & 11 deletions public/javascripts/data/dataSource.js
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Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,11 @@ DataSource.prototype = {
* @throws IOException on low-level file read and file not found errors
* @throws ParseException on Sungear-specific file format errors
*/
setAttributes : function(attrib, base) {
this.checkAttributes(attrib, base);
this.attrib = attrib;
setAttributes : function(attrib, base, callback) {
this.checkAttributes(attrib, base, function (response) {
this.attrib = response;
callback();
});
},
/**
* Get the attributes object.
Expand All @@ -79,7 +81,7 @@ DataSource.prototype = {
* @throws IOException if a file cannot be read, or a file with no default location cannot be read
* @throws ParseException if a file format issue is encountered
*/
checkAttributes : function(attrib, base) {
checkAttributes : function(attrib, base, callback) {
if (attrib.get("sungearU") === null) {
throw new ParseException("sungear file not specified");
}
Expand All @@ -95,6 +97,7 @@ DataSource.prototype = {
speciesFile = "species.txt";
}
var list = new SpeciesList(DataReader.makeURL(base, speciesFile), base);
console.log("List: " + list);
sp = list.getSpecies(sn);
// if there's a species file, assume we're dealing with gene data
if (attrib.get("itemsLabel") === null) {
Expand All @@ -106,17 +109,18 @@ DataSource.prototype = {
}
// the check basic attribs
if (attrib.get("geneU") == null) {
attrib.put("geneU", (sp !== null) ? sp.geneU : new URL(DataSource.GENE_DEFAULT, base));
attrib.put("geneU", (sp !== null) ? sp.geneU : DataReader.makeURL(base, DataSource.GENE_DEFAULT));
}
if (attrib.get("listU") == null) {
attrib.put("listU", (sp !== null) ? sp.listU : new URL(DataSource.LIST_DEFAULT, base));
attrib.put("listU", (sp !== null) ? sp.listU : DataReader.makeURL(base, DataSource.LIST_DEFAULT));
}
if (attrib.get("hierU") == null) {
attrib.put("hierU", (sp !== null) ? sp.hierU : new URL(DataSource.HIER_DEFAULT, base));
attrib.put("hierU", (sp !== null) ? sp.hierU : DataReader.makeURL(base, DataSource.HIER_DEFAULT));
}
if (attrib.get("assocU") == null) {
attrib.put("assocU", (sp !== null) ? sp.assocU : new URL(DataSource.ASSOC_DEFAULT, base));
attrib.put("assocU", (sp !== null) ? sp.assocU : DataReader.makeURL(base, DataSource.ASSOC_DEFAULT));
}
callback(attrib);
});
},

Expand All @@ -135,10 +139,11 @@ DataSource.prototype = {
* @throws IOException on low-level file errors
* @throws ParseException on Sungear-specific file format issues
*/
set : function(attrib, status) {
if (typeof status === 'undefined') {
this.set(attrib, null);
set : function(attrib, status, callback) {
if (typeof callback === 'undefined') {
this.set(attrib, null, status);
} else {
console.log("MADE IT TO SET: " + attrib);
var geneU = attrib.get("geneU");
var listU = attrib.get("listU");
var hierU = attrib.get("hierU");
Expand Down Expand Up @@ -179,6 +184,7 @@ DataSource.prototype = {
}
this.reader.readSungear(sungearU);
this.sunSrc = sungearU;
callback();
}
},
/**
Expand Down
3 changes: 2 additions & 1 deletion public/javascripts/data/vpConnection.js
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,12 @@ const ParseException = require('./parseException');

function makeAttributes(doc) {
var queryString = doc.query;
console.log(queryString);
if (queryString === null || typeof queryString === 'undefined') {
throw new ParseException("no query data");
}
var attrib = new Attributes(queryString);
if (attrib.get("session_id") === null) {
if (attrib.get("session_id") === null || typeof attrib.get("session_id") === 'undefined') {
throw new ParseException("missing required attribute: session_id");
}
attrib.put("export_session_id", attrib.get("session_id"));
Expand Down

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