Update Reggie to new scripting pattern (first step)

[Nicklas Nordborg]

Similar to #564, but Reggie contains a lot more script than any of the other extensions.

First step is to make sure that Reggie code that appear in BASE (eg. the menu item and links to case summary) are fixed. When that is done Reggie should work with default BASE settings if released with <about safe-scripts="1" safe-resources="0">.

After that we can refactor each Reggie wizard one by one as we have time to spare.

[Nicklas Nordborg]

(In [2291]) References #571: Update Reggie to new scripting pattern

I think the most critical parts have been fixed now. Reggie 2.16 should now work properly on a BASE 3.3 server with the default configuration.

[Nicklas Nordborg]

(In [2369]) References #571: Update Reggie to new scripting pattern

Fixed on the index page.

[Nicklas Nordborg]

(In [2370]) References #571: Update Reggie to new scripting pattern

Fixed on the case summary page.

[Nicklas Nordborg]

(In [2374]) References #571: Update Reggie to new scripting pattern

Fixed for the INCA and monthly operation list exports.

[Nicklas Nordborg]

(In [2500]) References #571: Update Reggie to new scripting pattern

Fixed call to undefined function 'asWarning'.

[Nicklas Nordborg]

(In [2599]) References #571: Update Reggie to new scripting pattern

Started to work with this on two wizards:

• Consent form registration
• Start masking and alignment

reggie-2.js and reggie-2.css are replacing the reggie.js and reggie.csss.

[Nicklas Nordborg]

(In [2602]) References #571: Update Reggie to new scripting pattern

Updated the the two blood registration wizards.

[Nicklas Nordborg]

(In [2603]) References #571: Update Reggie to new scripting pattern

Updated the INCA and monthly export. They had more or less been fixed already but needed some minor changes to use the new script api and css.

[Nicklas Nordborg]

(In [2604]) References #571: Update Reggie to new scripting pattern

Updated the "missing data" and "missing consent" export wizards.

[Nicklas Nordborg]

(In [2608]) References #571: Update Reggie to new scripting pattern

Updated the Sample processing statistics wizard. Made some performance improvements by adding filters at the query level instead of the code level.

[Nicklas Nordborg]

(In [2609]) References #571: Update Reggie to new scripting pattern

New file part of [2608].

[Nicklas Nordborg]

(In [2610]) References #571: Update Reggie to new scripting pattern

Updated the case summary to use the new script and style sheet.

[Nicklas Nordborg]

(In [2611]) References #571: Update Reggie to new scripting pattern

Updated the Sample source report wizard. Parts of the javascript code was moved as-is to the samplereportgenerator.js file and can probably be cleaned up a lot more.

[Nicklas Nordborg]

(In [2612]) References #571: Update Reggie to new scripting pattern

Fixed the print template.

[Nicklas Nordborg]

(In [2615]) References #571: Update Reggie to new scripting pattern

Found some links being generated with 'onclick' attributes in the "Consent count report".

[Nicklas Nordborg]

(In [2616]) References #571: Update Reggie to new scripting pattern

Found a bug when formatting sampling date for no-specimen items.

[Nicklas Nordborg]

(In [2617]) References #571: Update Reggie to new scripting pattern

Updated the pathology referral form registration wizard.

[Nicklas Nordborg]

(In [2618]) References #571: Update Reggie to new scripting pattern

Updated the installation wizard to use the new script and style sheet.

[Nicklas Nordborg]

(In [2619]) References #571: Update Reggie to new scripting pattern

Updated the Open Grid Scheduler admin pages to use the new script and style sheet.

[Nicklas Nordborg]

(In [2620]) References #571: Update Reggie to new scripting pattern

Updated the index page to use the new script and style sheet. Implemented a check that disable all wizards unlessa a project is active.

[Nicklas Nordborg]

(In [2621]) References #571: Update Reggie to new scripting pattern

Updated the "Confirm masking and alignment" wizard.

[Nicklas Nordborg]

(In [2622]) References #571: Update Reggie to new scripting pattern

Updated the "Start demux and merge" wizard.

[Nicklas Nordborg]

(In [2623]) References #571: Update Reggie to new scripting pattern

Changes to the "Start masking and alignment" wizard to make it behave like the "Start demux and merge" wizard.

[Nicklas Nordborg]

(In [2624]) References #571: Update Reggie to new scripting pattern

Bad tag in INCA export.

[Nicklas Nordborg]

(In [2636]) References #571 and #547 and #548. The confirm demux wizard has been updated to the new script and style pattern.

Also added an option to delete items after a failed job and fixed the script so that it makes sure that the job, work and archive folders are empty before trying to use them.

[Nicklas Nordborg]

(In [2637]) References #571. Forgot to remove a few script lines.

[Nicklas Nordborg]

(In [2639]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Confirm sequencing run" wizard.

[Nicklas Nordborg]

(In [2646]) References #571: Update Reggie to new scripting pattern (first step)

Incorrect call to convert year to 4 digits.

[Nicklas Nordborg]

(In [2647]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Register sequencing started" wizard.

[Nicklas Nordborg]

(In [2648]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Register sequencing ended" wizard. Also fixed other wiards to display the flow cell type (HiSeq or NextSeq).

[Nicklas Nordborg]

(In [2649]) References #571: Update Reggie to new scripting pattern (first step)

Fixes a bug in case summary when invoked from the "Item overview" details frame (TypeError caseName is not defined).

[Nicklas Nordborg]

(In [2650]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Register clustering" wizard.

[Nicklas Nordborg]

(In [2651]) References #571: Update Reggie to new scripting pattern (first step)

Default widths for input fields are now set in the style sheet. Only need to override if an input field should be smaller.

[Nicklas Nordborg]

(In [2652]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Create flow cells" wizard.

[Nicklas Nordborg]

(In [2653]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Lab protocol for clustering and sequencing" wizard. Need to use BASE 3.3.1 due to favicon change.

[Nicklas Nordborg]

(In [2657]) References #571: Update Reggie to new scripting pattern (first step)

Use complete text from selection list (instead of only the name) in the following wizard step.

[Nicklas Nordborg]

(In [2658]) References #571: Update Reggie to new scripting pattern (first step)

Implemented a warning message that is displayed when trying to navigate away from a page before finalizing a wizard. Since most AJAX requests are now really asynchronus it was easy to by mistake click on something that aborted the final registration.

[Nicklas Nordborg]

(In [2659]) References #571: Update Reggie to new scripting pattern (first step)

Updated the pool registration wizard.

[Nicklas Nordborg]

(In [2662]) References #571: Update Reggie to new scripting pattern (first step)

Updated the pooling lab protocol wizard.

[Nicklas Nordborg]

(In [2663]) References #571: Update Reggie to new scripting pattern (first step)

Fixes error handling in the register sequencing started wizard.

[Nicklas Nordborg]

(In [2664]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "RNA dilution registration" wizard.

[Nicklas Nordborg]

(In [2666]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "mRNA registration" wizard.

[Nicklas Nordborg]

(In [2667]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "cDNA registration" wizard.

[Nicklas Nordborg]

(In [2668]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Lab protocols for mrna and cdna" wizard.

[Nicklas Nordborg]

(In [2669]) References #571: Update Reggie to new scripting pattern (first step)

Updated the quality control registration wizard for library preparation.

[Nicklas Nordborg]

(In [2670]) References #571: Update Reggie to new scripting pattern (first step)

toString() method may exists also on other objects than Error objects, so we need to check err.stack property separately.

[Nicklas Nordborg]

(In [2671]) References #571: Update Reggie to new scripting pattern (first step)

Check if a callback method has been specified before trying to call it.

[Nicklas Nordborg]

(In [2672]) References #571: Update Reggie to new scripting pattern (first step)

Forgot to remove old script from the "Lab protocols for mrna and cdna" wizard.

[Nicklas Nordborg]

(In [2673]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Lab protocols for library preparation" wizard.

[Nicklas Nordborg]

(In [2675]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Library registration" wizard. Required several changes to the Caliper plate importer for better error handling.

[Nicklas Nordborg]

(In [2676]) References #571: Update Reggie to new scripting pattern (first step)

Do not hide error messages if an async request is returned after a fatal error.

Do not ask for confirmation about leaving the page after a fatal error.

[Nicklas Nordborg]

(In [2677]) References #571: Update Reggie to new scripting pattern (first step)

Updated the specimen tube registration wizard.

[Nicklas Nordborg]

(In [2678]) References #571: Update Reggie to new scripting pattern (first step)

Some code was commented out during debugging.

[Nicklas Nordborg]

(In [2686]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "Lab tracking protocol for Allprep isolation" wizard

[Nicklas Nordborg]

(In [2688]) References #571: Update Reggie to new scripting pattern (first step)

Updated the "DNA/RNA/FlowThrough registration" wizard.

[Nicklas Nordborg]

(In [2691]) References #571: Update Reggie to new scripting pattern (first step)

Updated the 'keep session alive' functionality.

[Nicklas Nordborg]

(In [2692]) References #571: Update Reggie to new scripting pattern (first step)

Make sure "Restart" button works even if the wizard has been disabled.

[Nicklas Nordborg]

(In [2693]) References #571: Update Reggie to new scripting pattern (first step)

There is no 'Next' button in this wizard.

[Nicklas Nordborg]

(In [2694]) References #571: Update Reggie to new scripting pattern (first step)

Updated the RNA QC export wizard.

[Nicklas Nordborg]

(In [2695]) References #571: Update Reggie to new scripting pattern (first step)

Fixes an issue with not displaying a table correctly.

[Nicklas Nordborg]

(In [2698]) References #571: Update Reggie to new scripting pattern (first step)

Updated the RQS import wizard.

[Nicklas Nordborg]

(In [2705]) References #571: Update Reggie to new scripting pattern (first step)

Incorrect permission check prevented users from entering wizard which doesn't require any role membership.

[Nicklas Nordborg]

(In [2708]) References #571: Update Reggie to new scripting pattern (first step)

Fixes an issue with generated HTML being escaped and passed out to GUI as html markup and lots of other issues with user-generated input not being escaped at all.

[Nicklas Nordborg]

(In [2720]) References #571: Update Reggie to new scripting pattern (first step)

Added a step in the release procudure for checking that ALL debug flags in javascript files have been reset.