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Merged
labkey-klum merged 8 commits into from
Sep 22, 2025
Merged

Signal data improvements #927

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fbef3d3
do a better job of showing errors that might occur during run import
labkey-klum Sep 9, 2025
913c2f0
refactor getSignalDataResourcesAction to handle multiple file paths a…
labkey-klum Sep 10, 2025
090f2e1
update comment
labkey-klum Sep 11, 2025
c18b8b8
code review feedback
labkey-klum Sep 11, 2025
f854a91
Merge branch 'develop' into fb_issue_53786
labkey-klum Sep 16, 2025
03cf08a
code review feedback
labkey-klum Sep 16, 2025
bca56c1
Add error tests for Signal Data tests. Cover Issue 53786
labkey-danield Sep 19, 2025
e36c4f0
Add some comments.
labkey-danield Sep 19, 2025
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57 changes: 24 additions & 33 deletions signalData/resources/views/mockSignalDataWatch.html
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Original file line number Diff line number Diff line change
Expand Up @@ -61,23 +61,23 @@
}
});

var dataRows = [],
dataInputs = [];
var dataRows = [], dataInputs = [];

Ext4.each(fileSet, function(file) {
var fileName = file['FileName'];
dataRows.push({
Name: file.text,
DataFile: SIGNAL_DATA_FILE_ROOT + file.text,
Name: fileName,
DataFile: SIGNAL_DATA_FILE_ROOT + fileName,
TestType: 'SMP'
});
dataInputs.push({
name: file.text,
dataFileURL: file.dataFileURL
name: fileName,
dataFileURL: file['DataFileUrl']
});
});

run.dataRows = dataRows;
run.dataInputs = dataInputs;

return run;
}

Expand Down Expand Up @@ -197,33 +197,24 @@
{
if (Ext4.isFunction(callback)) {

var received = 0;
var newFiles = [];

function done(file, results)
{
Ext4.each(files, function(f) {
if (f.text === file.text) {
f['dataFileURL'] = results['DataFileUrl'];
newFiles.push(f);
}
});
received++;

if (received == files.length) {
callback.call(scope || this, newFiles);
}
}
var paths = [];
var fileNames = [];
files.forEach(function (file) {
paths.push(decodeURIComponent(file.id));
fileNames.push(file.text);
}, this);

Ext4.each(files, function(file) {
LABKEY.Ajax.request({
url: LABKEY.ActionURL.buildURL('signaldata', 'getSignalDataResource.api'),
method: 'POST',
params: { path: decodeURIComponent(file.id), test: true },
success: function(response) {
done(file, Ext4.decode(response.responseText));
}
});
LABKEY.Ajax.request({
url: LABKEY.ActionURL.buildURL('SignalData', 'getSignalDataResource.api'),
method: 'POST',
jsonData: {
paths : paths,
files : fileNames
},
success: LABKEY.Utils.getCallbackWrapper(function(response) {
callback.call(scope || this, response.files);
}, this),
scope: this
});
}
}
Expand Down
18 changes: 11 additions & 7 deletions signalData/resources/web/signaldata/ResultUpdate/resultupdate.js
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ var getResultData = function(assay) {
requiredVersion: 13.2,
filterArray: [LABKEY.Filter.create('RowId', LABKEY.ActionURL.getParameter('rowId'))],
success: function(results){
if (results.length > 0) {
init(assay, results.getRow(0));
if (results.rowCount > 0) {
init(assay, results.rows[0]);
}
else {
// Use an ExtJS alert instead of a raw browser alert to avoid alarming the crawler
Expand Down Expand Up @@ -64,12 +64,16 @@ var init = function(assay, row){
LABKEY.Ajax.request({
url: LABKEY.ActionURL.buildURL('SignalData', 'getSignalDataResource.api'),
method: 'POST',
params: {path: decodeURIComponent(file.internalId), test: true},
success: function (response) {
var fileResource = Ext4.decode(response.responseText);
var updatedRow = setRunFields(form, fileResource);
updateRunResult(updatedRow, fileResource);
params: {
paths: [decodeURIComponent(file.internalId)],
files: [file.name]
},
success: LABKEY.Utils.getCallbackWrapper(function(response) {
Ext4.each(response.files, function(file) {
var updatedRow = setRunFields(form, file);
updateRunResult(updatedRow, file);
}, this);
}, this),
scope: this
});
}
Expand Down
119 changes: 80 additions & 39 deletions signalData/resources/web/signaldata/UploadView/UploadLog.js
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Original file line number Diff line number Diff line change
Expand Up @@ -244,17 +244,56 @@ Ext4.define('LABKEY.SignalData.UploadLog', {
if (Ext4.isFunction(callback)) {
var me = this;
var destination = this.fileSystem.concatPaths(this.fileSystem.getBaseURL(), targetDirectory);
this.fileSystem.renamePath({
source: this.getWorkingPath(),
destination: destination,
isFile: false,
success: function () {
me.resolveFileResources(targetDirectory, callback, scope, runProperties);

const getResourcesCallback = function(files) {
if (files && files.length > 0) {
// files currently exist, validate and resolve before creating the run
me.resolveDataFileURL(files, callback, scope, runProperties);
}
});
else {
// files need to be moved to the target directory
this.fileSystem.renamePath({
source: this.getWorkingPath(),
destination: destination,
isFile: false,
success: function () {
me.resolveFileResources(targetDirectory, callback, scope, runProperties);
}
});
}
};

// get the list of files in the target directory (if any)
this.getTargetDirResources(targetDirectory, getResourcesCallback, this);
}
},

/**
* Returns the list of data files in the target directory. Uploaded run data files are moved from
* a temporary location to the target directory before the run is created.
*/
getTargetDirResources : function (targetDirectory, callback, callbackScope) {
var fileUri = this.fileSystem.concatPaths(this.fileSystem.getAbsoluteURL(), targetDirectory);
LABKEY.Ajax.request({
url: fileUri,
method: 'GET',
params: {method: 'JSON'},
success: function (response) {
var json = Ext4.decode(response.responseText);
var files = [];
if (Ext4.isDefined(json) && Ext4.isArray(json.files))
files = json.files;

callback.call(callbackScope, files);
},
failure: function() {
// this is normal in the case where the target directory does not yet exist or
// the files have not yet been moved there
callback.call(callbackScope, []);
}
});
},

resolveFileResources: function (targetDirectory, callback, callbackScope, runProperties) {
var fileUri = this.fileSystem.concatPaths(this.fileSystem.getAbsoluteURL(), targetDirectory);
LABKEY.Ajax.request({
Expand All @@ -269,9 +308,10 @@ Ext4.define('LABKEY.SignalData.UploadLog', {
}
}
},
failure: function () {
}
, scope: this
failure: LABKEY.Utils.getCallbackWrapper(function(json, response, opts) {
LABKEY.Utils.alert('Error', 'Unable to resolve file resources : ' + response.exception);
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Copilot AI Sep 17, 2025

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Similar to the previous error message, this could display 'undefined' if response.exception is not set. Consider adding a fallback: 'Unable to resolve file resources: ' + (response.exception || 'Unknown error').

Suggested change
LABKEY.Utils.alert('Error', 'Unable to resolve file resources : ' + response.exception);
LABKEY.Utils.alert('Error', 'Unable to resolve file resources : ' + (response.exception || 'Unknown error'));

Copilot uses AI. Check for mistakes.
}, this, true),
scope: this
}, this);
},

Expand All @@ -281,41 +321,42 @@ Ext4.define('LABKEY.SignalData.UploadLog', {
resolveDataFileURL: function (files, callback, scope, runProperties) {
if (Ext4.isFunction(callback)) {

var received = 0;
var newFiles = [];

var me = this;
var paths = [];
var fileNames = [];
files.forEach(function (file) {
paths.push(decodeURIComponent(file.id));
fileNames.push(file.text);
}, this);

function done(file, results) {
LABKEY.Ajax.request({
url: LABKEY.ActionURL.buildURL('SignalData', 'getSignalDataResource.api'),
method: 'POST',
jsonData: {
paths : paths,
files : fileNames
},
success: function (response) {
let result = Ext4.decode(response.responseText);
let store = this.getStore();

var store = me.getStore();
var idx = store.find(me.DATA_FILE, file.text);
var process = store.getAt(idx);
Ext4.each(result.files, function(file) {

//Set upload time
process.set(me.FILENAME, results[me.DATA_FILE]);
process.set(me.FILE_URL, results['DataFileUrl']);
process.set('file', file);
newFiles.push(file);
received++;
var idx = store.find(this.DATA_FILE, file["FileName"]);
var rec = store.getAt(idx);

if (received == files.length) {
callback.call(scope || me, newFiles, runProperties);
}
}
if (rec) {
//Set upload time in the store record
rec.set(me.FILENAME, file[this.DATA_FILE]);
rec.set(me.FILE_URL, file['DataFileUrl']);
rec.set('file', true);
}
}, this);

//TODO: This should be refactored to use a single ajax call for the array
files.forEach(function (file) {
LABKEY.Ajax.request({
url: LABKEY.ActionURL.buildURL('SignalData', 'getSignalDataResource.api'),
method: 'POST',
params: {path: decodeURIComponent(file.id), test: true},
success: function (response) {
done(file, Ext4.decode(response.responseText));
},
scope: this
});
}, this);
callback.call(scope || me, runProperties);
},
scope: this
});
}
},

Expand Down
8 changes: 4 additions & 4 deletions signalData/resources/web/signaldata/UploadView/uploadResultFiles.js
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Original file line number Diff line number Diff line change
Expand Up @@ -366,13 +366,13 @@ LABKEY.SignalData.initializeDataFileUploadForm = function (metadataFormId, eleme
window.location = returnUrl;
},this);
},
failure: function(response){
//TODO: Should probably do something here...
}
failure: LABKEY.Utils.getCallbackWrapper(function(json, response, opts) {
LABKEY.Utils.alert('Error', 'Unable to save run : ' + response.exception);
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Copilot AI Sep 17, 2025

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The error message concatenation could result in 'Unable to save run : undefined' if response.exception is undefined. Consider using optional chaining or a fallback message like 'Unable to save run: ' + (response.exception || 'Unknown error').

Suggested change
LABKEY.Utils.alert('Error', 'Unable to save run : ' + response.exception);
LABKEY.Utils.alert('Error', 'Unable to save run : ' + (response.exception || 'Unknown error'));

Copilot uses AI. Check for mistakes.
}, this, true)
}, this);
}

var generateAndSaveRun = function(files, fieldValues) {
var generateAndSaveRun = function(fieldValues) {

var dataRows = [];
var dataInputs = [];
Expand Down
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