Implement wizards for RNA->cDNA processing

[Nicklas Nordborg]

This ticket is the master ticket for the multiple wizards that are needed to process RNA into cDNA which is about half-way in the library preparation process. We have identified about five sub-steps/wizards that are needed (subtickets will be created later):

1. (#424) Select RNA items and place on a plate. Sub-items and sub-plates are created without creation date to indicate that the laboratory process has not yet been completed.
2. (#425) Generate a lab protocol with necessary information such as storage location, etc.
3. (#440) Generate files that are needed by laboratory instruments so that users don't have to type or copy information manually.
4. (#436) Import quality control measurements.
5. (#441) Register the cDNA process as completed, including information about dates, operators, protocols, etc.

[Nicklas Nordborg]

Overview of items and information to be registered

[Nicklas Nordborg]

(In [1734]) References #422: Implement wizards for RNA->cDNA processing

Added subtypes and bioplate types to the installation servlet. Added some more RNA items to the test data file which can be used to test the new wizards. Added a new section on the index page (links not working).

[Nicklas Nordborg]

(In [1746]) References #422: Implement wizards for RNA->cDNA processing

Installing 'Stratagene' as a pre-defined extract so that we can use it in the wizards.

Also updated the Rna.findRnaWithoutQc() method so that it ignores all extracts that doesn't have a creation date.

[Nicklas Nordborg]

(In [1789]) References #422, #424 and #425. Renamed 'Stratagene' to 'Stratagene.r' to follow the general naming convention for RNA items.

[Nicklas Nordborg]

(In [1815]) References #422 and #423. Rearranged the Reggie main page since it was becoming a bit unbalanced. Moved all lab-related wizards to the left column and all administrative wizards to the right column. Added a new section for pooling and flow-cell related wizards and changed the icon for the barcoding and library preparation wizards.

[Nicklas Nordborg]

(In [1867]) References #422, #423 and other related tickets. Updated @since javadoc annotations to @since 2.12 for new methods and classes.

[Nicklas Nordborg]

(In [1892]) References #422: Implement wizards for RNA->cDNA processing

Remove debug flag. The four RNA->cDNA wizards should more or less be fully working now.

[Nicklas Nordborg]

(In [1899]) References #422 and #423. New name pattern for mRNA, cDNA and Library plates: MRnaPlateNNNN, CDnaPlateNNNN and LibPlateNNNN.

[Nicklas Nordborg]

(In [1920]) References #422, #423 and #478. Disabled links to non-working wizards in preparation for beta-release.

[Nicklas Nordborg]

(In [1924]) References #422, #423 and #478. Re-enabled links to wizards in development.

[Nicklas Nordborg]

(In [1977]) References #422, #423, #478 and more... Added Operator annotation and use it for all steps in the library preparation and pooling.

[Nicklas Nordborg]

(In [2004]) References #422, #423 and #478. Added several bioplate annotation types into categories so that they will be easier to find those that are useful for bioplates of a given bioplate type in the regular BASE interface (assuming that BASE 3.2.3 has been installed; see ​http://base.thep.lu.se/ticket/1761).

[Nicklas Nordborg]

Closing this now since the wizards seems to be working well.