Include Trait Synonyms in Trial Downloads

[dwaring87]

Description

This adds an option to the CXGN::Phenotypes::PhenotypeMatrix and CXGN::Trial::Download classes to include trait synonyms in the names / column headers of traits. For example, when enabled it will change the column header from "Plant height - cm|CO_350:0000232" to "PH = Plant height - cm|CO_350:0000232".

The sgn.conf file has been updated to include configuration variables that change the default phenotype download options (displayed trial detail page, search wizard, stock detail page, manage trials page).

# these are the default initial values for the phenotype download dialog
# the user can change the behavior for each individual download
pheno_download_default_repeat_measurements              average   # repeat measurements - one of: first, last, average, sum, all_values_single_line, all_values_multiple_line
pheno_download_default_include_timestamps               0         # include timestamps - boolean
pheno_download_default_include_intercrop_accessions     0         # include intercrop accessions columns - boolean
pheno_download_default_include_entry_numbers            0         # include entry numbers column - boolean
pheno_download_default_include_trait_synonyms           0         # include trait synonyms - boolean
exclude_phenotype_outliers                              0         # supress user-defined outliers - boolean (used in downloads and some analysis tools)

It also adds options for to intercrop accessions, entry numbers, and repetitive measurements type to missing download dialogs.

If there is more than one synonym for a particular trait, it will just use the first (alphabetically) one.

Fixes #5878

Checklist

• Refactoring only
• Documentation only
• Fixture update only
• Bug fix
  • The relevant issue has been closed.
  • Further work is required.
• New feature
  • Relevant tests have been created and run.
  • Data was added to the fixture
    • Data was added via a patch in /t/data/fixture/patches/.
  • User-Facing Change
    • The user manual in /docs has been updated.
  • Any new Perl has been documented using perldoc.
  • Any new JavaScript has been documented using JSDoc.
  • Any new legacy JavaScript has been moved from /js to /js/source/legacy.