Documentation cleanup

[Nicklas Nordborg]

We should go through the documentation and at least fix things that are incorrect. Some parts may be missing information due to functionality that has been added. It would be good if we could fill in missing parts of incomplete sections. Then, there are several sections that hasn't been written yet, but that is not part of this ticket.

[Nicklas Nordborg]

(In [5633]) References #1590: Documentation cleanup

Checked and changed the following chapters in Part IV: Developer documentation:

• Developer overview of BASE
• Plug-in developer (sections 1-5)

[Nicklas Nordborg]

(In [5640]) References #1590: Documentation cleanup

Checked and changed the following chapters in Part IV: Developer documentation:

• Plug-in developer sections 7-9. (section 6 is not yet done since there are tickets that will affect lots of information in this section)
• Extensions developer + added a new section with more information about extension points shipped with BASE.

[Nicklas Nordborg]

(In [5654]) References #1590: Documentation cleanup

Checked and changed the following chapters in Part IV: Developer documentation:

• Plug-in developer sections 6. Removed documentation about file validators since that is now an extensions.
• Extensions developer section 8. Added documentation about file set validators.

Made a modification in the docbook templates so that the full package+class name is shown in the link leading to the javadoc.

[Nicklas Nordborg]

(In [5655]) References #1590: Documentation cleanup

Fixed some minor issues in the Web services section.

[Nicklas Nordborg]

(In [5656]) References #1590: Documentation cleanup

Fixed "Core developer reference: Building BASE". The old documentation has now been moved to the wiki instead.

[Nicklas Nordborg]

(In [5673]) References #1590: Documentation cleanup

Fixed "Core developer reference: Coding rules and guidelines". First 4 sub-sections.

[Nicklas Nordborg]

(In [5676]) References #1590: Documentation cleanup

• Fixed link to syntax highlighter
• Changed color of left border used on code examples and <hr> tags
• Changed date format to "yyyy-MM-dd" for last modified footer
• Added last modified information to title page
• Decreased vertical white space around some headers
• Added more links/title information to navigation header and footer

[Nicklas Nordborg]

(In [5677]) References #1590: Documentation cleanup

• Removed migration-related information from the appendix
• Removed "Appendix: Menu guide".
• Removed BASE 2.x-related information from the appendix (API changes that may affect backwards compatibility and Things to consider when updating an existing BASE installation).

[Nicklas Nordborg]

(In [5678]) References #1590: Documentation cleanup

• Checked jobagent, raw data types, extended properties and web.xml reference in the appendix.

[Nicklas Nordborg]

(In [5680]) References #1590: Documentation cleanup

• base.config reference.
• Removed support for "export.max.items" since it was only needed with older MySQL versions and only the table exporter used it anyway.

[Nicklas Nordborg]

(In [5682]) References #1590: Documentation cleanup

FAQ section and removed information related to the Tab2Mage exporter.

[Nicklas Nordborg]

(In [5683]) References #1590: Documentation cleanup

Account administration.

[Nicklas Nordborg]

(In [5684]) References #1590: Documentation cleanup

User documentation chapter 5 and 6 but not screenshots and still some incorrect information about validating labeled extracts in the "Item overview" section.

[Nicklas Nordborg]

(In [5705]) References #1590: Documentation cleanup

User documentation chapters 7, 8 and 9 except for screenshots.

Re-ordered some properties in the View job dialog.

[Nicklas Nordborg]

(In [5706]) References #1590: Documentation cleanup

User documentation chapter 10 to 15. Added new chapter about "Item subtypes". Removed sections about protocol types, hardware types and software types. Merged "Hardware" and "Software" into a single chapter.

Added some menu separators in the New annotation type menu.

As usual, screen shots have not yet been updated.

[Nicklas Nordborg]

(In [5708]) References #1590: Documentation cleanup

Biomaterials section. Added empty sections for biomaterial lists and bioplate events that hopefully will be written some day. All screen shots must be updated.

Fixed spelling of "bioplate" in a lot of jsp scripts.

Display well coordinates without brackets. A1 instead of [A,1].

Fixed an issue with the regular expression used to link different help texts in the web client.

Reorganized the biomaterial lims menu so that it is consistent with the documentation.

[Nicklas Nordborg]

(In [5724]) References #1590: Documentation cleanup

Added section about bioplate events in the biomaterials chapter. No screenshots yet.

[Nicklas Nordborg]

(In [5725]) References #1590: Documentation cleanup

Updated UML diagrams. I hope that most of them now reflect the implemented code. I'll create new images for each section later.

[Nicklas Nordborg]

(In [5726]) References #1590: Documentation cleanup

Images from [5725]

[Nicklas Nordborg]

(In [5737]) References #1590: Documentation cleanup

Updated Admin documentation:

• Installation and updgrade instructions
• Plug-ins and extensions

A lot of information has been moved around/merged with other parts. Screen shots are the old ones, which can be a bit confusing since the differences are big.

[Nicklas Nordborg]

(In [5738]) References #1590: Documentation cleanup

Re-orgarnized file/directory structure of documentation to make the paths a little bit shorter.

[Nicklas Nordborg]

(In [5780]) References #1590: Documentation cleanup

Updated developer documentation "API overview". The chapter has been renamed to "The BASE API" and I intend to merge some information from the "Core developer reference" with this chapter.

[Nicklas Nordborg]

(In [5781]) References #1590: Documentation cleanup

Moved "Internals of the Core API" to "The BASE API" section.

[Nicklas Nordborg]

(In [5782]) References #1590: Documentation cleanup

Restructured documentation to generate shorter filenames.

[Nicklas Nordborg]

(In [5783]) References #1590: Documentation cleanup

Experiments and analysis chapter.

[Nicklas Nordborg]

(In [5784]) References #1590: Documentation cleanup

Import and export of data.

[Nicklas Nordborg]

(In [5789]) References #1590: Documentation cleanup

New screenshots for chapter 4 and 5 in User documentation (except for "Item overview" since it is not yet fully working). Minor changes in the texts.

[Nicklas Nordborg]

(In [5791]) References #1590: Documentation cleanup

• New icons for tip, note, warning, etc.
• Use rounder corners for notes, etc.
• Create HTML files with DOCTYPE
• Fixed white background around numbered lables in some screenshots

[Nicklas Nordborg]

(In [5792]) References #1590: Documentation cleanup

New and updated screenshots for chapter 6 "Projects and the permission system".

[Nicklas Nordborg]

(In [5794]) References #1590: Documentation cleanup

New and updated screenshots for chapter 7 "File management".

[Nicklas Nordborg]

(In [5795]) References #1590: Documentation cleanup

New and updated screenshots for chapter 8-14.

[Nicklas Nordborg]

(In [5796]) References #1590: Documentation cleanup

New and updated screenshots for chapter 15 - Array LIMS.

[Nicklas Nordborg]

(In [5797]) References #1590: Documentation cleanup

New and updated screenshots for chapter 16 - Biomaterial LIMS.

[Nicklas Nordborg]

(In [5798]) References #1590: Documentation cleanup

New and updated screenshots for chapter 18+19 - Import/export.

[Nicklas Nordborg]

(In [5799]) References #1590: Documentation cleanup

• Homepage screenshot was missing top and left line of pixels.
• Made a smalled "Select import plug-in" screen shot.
• Fixed incorrect help text ids in "Edit extract" dialog.
• Help text dialog follows window resizing.
• Zoom edit dialog follows window resizing.
• Notes, warnings, etc. in help text use rounded corners.

[Nicklas Nordborg]

(In [5800]) References #1590: Documentation cleanup

New and updated screenshots for chapter 17 - Experiment and analysis

[Nicklas Nordborg]

(In [5801]) References #1590: Documentation cleanup

New and updated screenshots for chapters 20-22 - Admin documentation.

[Nicklas Nordborg]

(In [5815]) References #1590: Documentation cleanup

New screenshots and some minor text changes in the "Item overview" section.

[Nicklas Nordborg]

(In [5816]) References #1590: Documentation cleanup

3 chapters in the Developer documentation should now be up-to-date:

• Overview
• Plug-in developer
• Extensions developer

[Nicklas Nordborg]

(In [5818]) References #1590: Documentation cleanup

Some more sections in the developer documentation should now be up-to-date:

• Web services
• Parts of "The BASE API"
  • section 1: The public api of BASE.
  • section 2: The data layer api
  • section 3.9: Using files to store data
  • section 3.10: Sending signals to plug-ins

Sections 3.1 -- 3.8 are in the old format and will not be updated now.

"The Query API" and "The Dynamic API" are in the old format and will not be updated now.

"The Extensions API" need a big re-write.

Also fixed a lot of javadoc links leading to the developer documentation.

[Nicklas Nordborg]

(In [5819]) References #1590: Documentation cleanup

The chapter about writing docbook documentation has been updated.

[Nicklas Nordborg]

(In [5820]) References #1590: Documentation cleanup

Last part of the "Write documentation" chapter and FAQ and Apecix sections.

[Nicklas Nordborg]

(In [5823]) References #1590: Documentation cleanup

Fixed javadoc warnings.

[Nicklas Nordborg]

(In [5826]) References #1590: Documentation cleanup

Updated diagram and text about how the Extensions API is designed.

[Nicklas Nordborg]

(In [5830]) References #1590: Documentation cleanup

Some final updates to the upgrade and migration instructions. Removed screenshots that are no longer used in the documentation. Some minor fixes in UML diagrams.