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cbio-cancer-genomics-portal's Issues

Lower case gene name error 

What steps will reproduce the problem?
1. Go to home page
2. Select OVA, Mutations
3. Input tp53 (in lower case)
4. submit

Original issue reported on code.google.com by [email protected] on 23 Aug 2011 at 4:26

Show progress icon during JSON load on home page 

There is a slight delay on the home page while the JSON document is loaded.

We should not show any of the form input elements during the loading process, 
and should show an AJAX progress icon instead.  Once JSON is loaded, we can 
toggle the whole form.

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:45

Network loading suggestion: use AJAX GIF, instead of text 

For the network loading AJAX, I think we should include an AJAX loading icon, 
instead of the current text that says network is loading.

We have two AJAX icons checked in under images:

ajax-loader.gif 
ajax-loader2.gif 

Or, you can pick a new one from here:  http://www.ajaxload.info/

Original issue reported on code.google.com by [email protected] on 22 Jul 2011 at 1:40

Tabs lose state upon return via back button 

I think we have had this issue before, but I think there is now a better 
solution.

Please check out:

http://www.asual.com/jquery/address/

and, this demo w/ tabs:

http://www.asual.com/jquery/address/samples/tabs/#Overview

Discuss more in person...

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:56

Duplicated nodes in network 

Nodes retrieved from cPath2 with different UniProt Acc may have the same gene 
symbol, and therefore duplicated in the network. How to deal with that.

See the following link at localhost. Look for MYB
http://tinyurl.com/3mgaba5

Original issue reported on code.google.com by [email protected] on 9 Aug 2011 at 3:48

Secure web site with HTTPS 

I am just putting this here, so we don't forget it.

Need to secure web site and web service with HTTPS.

Original issue reported on code.google.com by [email protected] on 23 Aug 2011 at 7:13

Mutation details gone missing 

Mutation details are no longer showing up.

I know you already are working on this, but thought we would log it here...

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 8:59

Clicking Sign out should result in message to the user 

After I click "Sign out", I get taken to the main login page.

Which is good.

However, at the top of the page, there should be a message that says:

You are now signed out.

If Ben can add the basic functionality, Caitlin can add the UI.  I suggest we 
use the built-in JQuery style shown at:  Hey! Sample ui-state-highlight style. 
http://jqueryui.com/themeroller/

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 8:53

Code review Request 

Please review the following two classes:

http://code.google.com/p/cbio-cancer-genomics-portal/source/browse/portal/src/or
g/mskcc/portal/remote/GetCancerTypes.java?spec=svnb98b44a63631b70a5cc3ba078e92f0
79c93efd17&r=b98b44a63631b70a5cc3ba078e92f079c93efd17

http://code.google.com/p/cbio-cancer-genomics-portal/source/browse/portal/src/or
g/mskcc/portal/remote/GetCaseSets.java?spec=svnb98b44a63631b70a5cc3ba078e92f079c
93efd17&r=b98b44a63631b70a5cc3ba078e92f079c93efd17

Original issue reported on code.google.com by [email protected] on 17 Aug 2011 at 7:16

mRNA Expression Threshold is Lost in Modify Query Section 

To reproduce:

1.  Go to home page.
2.  Select GBM, mRNA Expression, w/ threshold 3.0
3.  Click submit.
4.  On results page, click Modify Query.
5.  Note that mRNA Expression is checked.  But, expression threshold is not 
shown.  It should be shown and set to 3.0.

Original issue reported on code.google.com by [email protected] on 16 Aug 2011 at 4:52

Add back genomic profiles subgroup checkbox 

Add back genomic profiles subgroup checkbox.

This should be identical to what we had before.

For example, if a user selects a radio button for an individual mRNA profile, 
the checkbox next to mRNA Expression data should be auto-selected.  If a user 
then un-selects this checkbox, all radio buttons should be cleared.

Note that this could should now be generic enough to handle the case of copy 
number and mutation groups as well.

This code should go in:  js/dynamicQuery.js .

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:43

Video tutorial will be out of date 

The video tutorial will soon be very out of date.

I vote to drop the tutorial for this release.  And, discuss the Open Helix 
option for future releases.

We will need to drop from tab and right nav bar.

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 10:39

Code review Request 

http://code.google.com/p/cbio-cancer-genomics-portal/source/detail?r=3d6e6f33159
5857605bc58d5dcd1bc9f8b93fd41

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 6:44

Code review request 

Purpose of code changes on this branch:
Refactor GetProteinArrayData using CGDS dao and model

When reviewing my code changes, please focus on:
GetProteinArrayData.java

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 2:39

Form validation forgets what CNA profile I picked 

To reproduce...

1.  Go to home page.
2.  Select GBM
3.  Select Copy Number, RAE
4.  Leave genes blank.
5.  Click submit.
6.  On results page, not the error, but not that Copy Number, RAE is no longer 
selected.

Original issue reported on code.google.com by [email protected] on 16 Aug 2011 at 5:13

Add support for cross-cancer study queries to home page 

On the main query page:

1.  Change "Select Cancer Type:" to "Select Cancer Study".

2.  Modify Javascript to automatically add new option to cancer study pull down 
menu:  "All Cancer Studies" (should appear first).

3.  By default, "All Cancer Studies" will be selected, and the following panels 
will be hidden:

a.  Select Genomic Profiles
b.  Select Patient/Case Set
c.  Optional Arguments.

4.  If a user selects a cancer study other than "All Cancer Studies", the 
panels a-c are dynamically shown.

5.  If a user subsequently selects "All Cancer Studies", a-c are dynamically 
hidden.

6.  When a user clicks submit, Javascript intercepts the event:

a.  If user has selected "All Cancer Studies", submit to:  cross_cancer.do

b.  Otherwise, submit to:  index.do

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:36

Wrong grouping of radio boxes 

What steps will reproduce the problem?
1. Select OVA as cancer type
2. Click radio box of GISTIC under CNA
3. Click radio box of AllGenes under mRNA

Original issue reported on code.google.com by [email protected] on 29 Jul 2011 at 4:09

Network redraws when network tab is clicked again 

Summary:

I do a query, and click the network tab.

I then see the network fine.

I then click Mutation details.

I then click network tab again.

Network redraws itself, and the layout is redone.

I posted this issue some time ago to the Cytoscape web mailing list:  

http://groups.google.com/group/cytoscapeweb-discuss/search?group=cytoscapeweb-di
scuss&q=cerami&qt_g=Search+this+group

This may have some ideas on how to fix it.

Original issue reported on code.google.com by [email protected] on 22 Jul 2011 at 1:37

Download Tab Not working 

Using the very latest code, the download tab is not working.

In the Javascript console, I get this message:

Error: console is not defined
Source File: http://localhost:8080/cgx/js/dynamicQuery.js
Line: 118

Original issue reported on code.google.com by [email protected] on 16 Aug 2011 at 4:42

After signing in, cannot click on any tabs 

I have successfully logged in.

However, after that, I cannot click on any of the tabs.

For example, clicking on FAQ, I get:

message Access is denied

description Access to the specified resource (Access is denied) has been 
forbidden.

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 8:58

Add Tooltips to all Tabs on Results Page 

Add tooltips via TipTips to all Tabs on Results Page.

Suggested text:

Summary = "Summary of Genomic Alteration"
Network = "Network Visualization and Analysis"
Plots = "Multiple Plots, including CNA v. mRNA Expression"
Survival = "Survival Analysis and Kaplan Meier curves"
Event Map = "Detailed Event Map of all Genomic Alterations"
Data Download = "Download all alterations or copy and paste into Excel"
Bookmark/Email = "Bookmark or Generate a URL for Email"

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:54

Need to update the News Page 

We need to update the news page for the next release.

The last news item was for:  March 2, 2011

I think this is done in Markdown.

Original issue reported on code.google.com by [email protected] on 22 Aug 2011 at 7:16

Modify query section shows AJAX progress button 

To recreate:

1.  To go home page.

2.  Enter a query, e.g. GBM, TP53, BRCA1.

3.  Submit.

4.  On the results page, click Modify Query.  Scroll down the page.

You will see the loading icon spinning.

Original issue reported on code.google.com by [email protected] on 16 Aug 2011 at 4:48

Add back help icons and tooltips for genomic profiles 

Add back help icons and tooltips for all genomic profiles in the main query 
page under section:  "Select Genomic Profiles."

Please use TipTip library, and display to right by default.

Code for this should go in:  js/dynamicQuery.js.

Original issue reported on code.google.com by [email protected] on 26 Jul 2011 at 1:39

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