MeLuDI v.1.4.0 bug fixes and improvements

[olle]

This ticket covers bug fixes and improvements to MeLuDI v.1.4.0.

[olle]

Ticket accepted.

[olle]

Traceability note:

• MeLuDi v.1.0 was introduced in Ticket #690 (MeLuDi - Registration wizard for melanoma-lung cancer projects).
• MeLuDi v.1.1 was introduced in Ticket #718 (MeLuDi v.1.0 bug fixes and improvements).
• MeLuDi v.1.2 was introduced in Ticket #725 (MeLuDi v.1.1 bug fixes and improvements).
• MeLuDI v.1.2.1 was introduced in Ticket #759 (MeLuDi v.1.2 bug fixes and improvements).
• MeLuDI v.1.2.2 was introduced in Ticket #767 (MeLuDI v.1.2.1 bug fixes and improvements).
• MeLuDI v.1.2.3 was introduced in Ticket #768 (MeLuDI v.1.2.2 bug fixes and improvements).
• MeLuDI v.1.2.4 was introduced in Ticket #777 (MeLuDI v.1.2.3 bug fixes and improvements).
• MeLuDI v.1.2.5 was introduced in Ticket #786 (MeLuDI v.1.2.4 bug fixes and improvements).
• MeLuDI v.1.3.1 was introduced in Ticket #792 (MeLuDI v.1.2.5 bug fixes and improvements).
• First version of library preparation wizards was introduced in Ticket #801 (MeLuDI library preparation wizards first version).
• MeLuDI v.1.3.2 was introduced in Ticket #802 (MeLuDI v.1.3.1 bug fixes and improvements).
• MeLuDI v.1.3.3 was introduced in Ticket #815 (MeLuDI v.1.3.2 bug fixes and improvements).
• MeLuDI v.1.4.0 was introduced in Ticket #816 (MeLuDI v.1.3.3 bug fixes and improvements).

[olle]

(In [3708]) Refs #836. Updates due to version number change to "1.4.1-dev".

1. Version number changed to "1.4.1-dev":
   a. Outermost Ant XML build file build.xml in / updated.
   b. Extensions XML configuration file extensions.xml in META-INF/ updated.
   c. Javascript file meludi-2.js in resources/ updated.
   d. Javascript file samplereportgenerator.js in resources/reports/ updated.
   e. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.

[olle]

Functional specification update:

• Wizard "Create new start DNA plate" in sub-section "Start DNA plate wizards" in section "Library preparation wizards" should be updated in step 4 showing plate view by adding "Switch" functionality for switching exactly two selected wells in the left FPA part of the plate view (only wells in this part can be selected):
  
  a. A "Switch" button should be added to a tool bar directly above the plate view.
  b. A "Switch" menu item should be added to the pop-up menu shown when right-clicking on a selected well.
  c. When the contents of two wells in the FPA part of the plate are switched, the corresponding wells in the FPB part of the plate view should also be switched.
  d. The index primers for a well will not be moved when well contents are switched, but will still be determined entirely by the well position on the plate.

Design update:

1. JSP file select_dna_for_start_plate.jsp in resources/libprep/ updated:
   a. Well pop-up menu item with id "mnuSwitch" made active by uncommenting code section.
   b. Tool bar with button with id "btnSwich" added by uncommenting code sections.
2. Javascript file select_dna_for_start_plate.js in resources/libprep/ updated:
   a. Click handler for tool bar button with id "btnSwitch" coupled to function switchSelected(event) added by uncommenting code.
   b. Event handler for pop-up menu item with id "mnuSwitch" coupled to function switchSelected(event) added by uncommenting code.
   c. Function switchSelected(event) already exists and has previously been updated to switch corresponding wells in the FPB part of the plate view, when two wells in the FPA part are switched.

[olle]

(In [3709]) Refs #836. Wizard "Create new start DNA plate" in sub-section "Start DNA plate wizards" in section "Library preparation wizards" updated in step 4 showing plate view by adding "Switch" functionality for switching exactly two selected wells in the left FPA part of the plate view (only wells in this part can be selected):

a. A "Switch" button has been added to a tool bar directly above the plate view.
b. A "Switch" menu item has been added to the pop-up menu shown when right-clicking on a selected well.
c. When the contents of two wells in the FPA part of the plate are switched, the corresponding wells in the FPB part of the plate view are also switched.
d. The index primers for a well will not be moved when well contents are switched, but will still be determined entirely by the well position on the plate.

Design update:

1. JSP file select_dna_for_start_plate.jsp in resources/libprep/ updated:
   a. Well pop-up menu item with id "mnuSwitch" made active by uncommenting code section.
   b. Tool bar with button with id "btnSwich" added by uncommenting code sections.
2. Javascript file select_dna_for_start_plate.js in resources/libprep/ updated:
   a. Click handler for tool bar button with id "btnSwitch" coupled to function switchSelected(event) added by uncommenting code.
   b. Event handler for pop-up menu item with id "mnuSwitch" coupled to function switchSelected(event) added by uncommenting code.
   c. Function switchSelected(event) already exists and has previously been updated to switch corresponding wells in the FPB part of the plate view, when two wells in the FPA part are switched.

[olle]

It was decided to make a fast release of MeLuDI v1.4.1, since the new well "Switch" functionality was desired, in order to fix older plate data, where alternative well placing rules were used.

[olle]

(In [3710]) Refs #836. Updates due to version number change to "1.4.1".

1. Version number changed to "1.4.1":
   a. Outermost Ant XML build file build.xml in / updated.
   b. Extensions XML configuration file extensions.xml in META-INF/ updated.
   c. Javascript file meludi-2.js in resources/ updated.
   d. Javascript file samplereportgenerator.js in resources/reports/ updated.
   e. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.

[olle]

Ticket closed as MeLuDI version 1.4.1 has been created.