Avocado

In an effort to make the contributing to Avocado more transparent and safer for all, a Developer Certificate of Origin (DCO) has been added to the [CONTRIBUTING.md](https://github.com/cbmi/avocado/blob/master/CONTRIBUTING.md). As a contributor, this certifies that you are legally allowed to contribute the code submitted as patches (in pull requests or otherwise).

This requires that all contributors to the repository now sign off their commits using the `git commit --signoff` (or `-s` for short). A script has been added to the Travis-CI config to check for the presence of the `Signed-off-by:` line. If any commit does not contain this, the build will error which will prevent core contributors from merging your code.

**Features**

PR 181 introduces four new optional fields on the `DataField` model. These are names of fields on the instance's model that are supplementary to the _base field_ denoted by`field_name`:
- `label_field_name`
- `order_field_name`
- `search_field_name`
- `code_field_name`

The model field object can be accessed through the corresponding datafield property (without the `_name` suffix). This feature supersedes the need for direct integration of the Lexicon and ObjectSet classes in the `DataField` API since the supplementary fields can now be set explicitly. Detection of these types will be removed in 2.4, however the detection in the `avocado init` will remain for now.
- The `DataConcept.type` and `DataField.type` fields have been added to lay the foundation for refactoring how fields and concepts behave. Read more here 88
- The `DataField` API now supports making use of pre-defined choices on the field instance (157)

**Enhancements**
- Parent categories are now included in the search index for fields and concepts (142)
- Categories can be auto-created during an `avocado init` call when the `--categories` flag is passed
- Fields and concepts that are created will be associated with the category which is named after the associated model.
- The `Registry.register` function can now be used as a decorator when registering classes or instances (95)
- The parent category of field and concepts are now included in the free-text search index (142)
- Categories can now be optionally created during an `avocado init` call by passing the `--categories` flag

**Bugs**
- Fixed hard-coded label field name for objectset-based models
- Fixed condition where revision data is null and causes an error during creating a diff
- The `published` field is now correctly exposed and editable from the `DataCategory` admin list view (196)
- Query sharing now use a case-insensitive lookup on email addresses (197)
- Fixed an issue when metadata migrations would fail due to a schema dependency (185)
- This now includes a `depends_on` attribute with the latest Avocado migration

**Enhancements**
- The built-in support for object sets have been replaced with the more optimal third-party [django-objectset](http://cbmi.github.io/django-objectset/) library
- This requires 'django-objectset` to be installed for you project
- The free-text search support has been updated to use Haystack 2.0.0
- Note, this requires a minor configuration change in the Django project settings file - see below.
- The `force_distinct` option for the exporter `read()` method now ensures rows are distinct for the whole iterable
- The exporter `read()` method now takes optional `offset` and `limit` arguments to control the window and number of formatted rows to return

**Bugs**
- Concepts without associated fields are now properly excluded in the `published` manager method
- The data cache API no longer caches data from methods that had arguments supplied
- This may be supported in the future
- Fix the `--no-fake` option in the metadata migration command

**Required Changes**

In your project's configuration file, replace the following settings:

python
HAYSTACK_SITECONF = 'avocado.search_sites'
HAYSTACK_SEARCH_ENGINE = 'whoosh'
HAYSTACK_WHOOSH_PATH = os.path.join(os.path.dirname(__file__), 'whoosh.index')


with the dict-based setting:

python
HAYSTACK_CONNECTIONS = {
'default': {
'ENGINE': 'haystack.backends.whoosh_backend.WhooshEngine',
'PATH': os.path.join(os.path.dirname(__file__), 'whoosh.index'),
}
}

Fixes an issue where arguments were being ignored when the data cache API was being used. The fix prevents the data cache from being used when arguments are supplied. This may be refactored in a future release to handle differentiating cache based relative to the arguments.

**Features**
- Support for flagging `DataQuery` instances as _public_. This can be used by clients to differentiate public vs private queries.

**Enhancements**
- Changed internal structure of `DataView` to be more robust for error handling
- This is backwards compatible with the previous structure
- Checks if `METADATA_MIGRATION_APP` is defined prior to attempting a safe backup

**Changes**
- The `avocado init` command now immediately publishes fields and auto-creates concepts for each field to more quickly get up and running on new instances.
- The previous behavior can be retained by passing the `--no-publish` and `--no-concepts` flags

**Bugs**
- Fixed 136 which prevented using the data cache feature

DATA_CACHE_ENABLED` is now disabled by default until 136 is fixed.

**Features**
- Support for saving and sharing queries*\* (see 119)
- Automatic versioning of `DataContext`, `DataView`, and `DataQuery` objects (see 115)

**Enhancements**
- Add `accessed` field on `DataContext`, `DataView`, and `DataQuery` for tracking purposes
- Add `DataConcept.viewable` boolean field for toggling whether concepts are visible as output (see 69)
- `DataContext`, `DataView`, and `DataQuery` are now registered with the admin

**Changes**
- Introduced `avocado.query.validators.Validator` and `FieldValidator` for an improved foundation for query processing
- `avocado.core.loader.Registry` has been simplified
- Rename `OPERATOR_MAP` and `SIMPLE_TYPE_MAP` settings to `OPERATORS` and `SIMPLE_TYPES`, respectively
- Replace `DataConcept.queryview` for `DataConcept.querable` boolean (see 68)
- Removed `cached_property` method for various DataField properties (see 231264)
- Replace `DataField.data_modified` with `data_version` field
- Removed `archived` and `published` fields from `DataContext`, `DataView`, and `DataQuery`
- Remove `DataView.count` since it was not being used, nor made sense

**Bugs**
- Add support for exclusive ranges on date, time, datetime and number fields
- Use `os.makedirs` in migration subcommand to ensure the full path to migration fixtures is created