Candig-server

This is the v1.1.0 of the candig-server.

This release introduces:

- the ability to add and retrieve DUO info of a dataset.
- the addition of `variants/gene/search` endpoint.
- the updated `variants` component for `/search` and `/count`, which now accepts a `gene`.
- the initial release of a public-facing doc available at https://candig-server.readthedocs.io.
- two updated API specs, one for regular endpoints, one for `/search` and `/count` endpoints.
- additional unit tests to the new `variants` components.

Fixes:
- the bug where the `nextPageToken` may not work correctly for `variants/search` endpoint.
- the bug where the `nextPageToken` may not work correctly for `/search` endpoint when you specify `fields`.
- the bug where the `/variantsbygenesearch` endpoint sometimes returns `variantsByGene` as the key under `/search` endpoint, while it should have been `variants`.
- the flaky firefox selenium test.

Deprecates:
- the endpoint, `/variantsbygenesearch`, you should use `variants/gene/search` instead. Everything else stays the same.
- the component key `variantsByGene`, you should now specify `variants` instead. Everything else stays the same.

---

Component | Changes were made | Backward compatibility
------------ | ------------- | -------------
API | Yes | Yes
Server Side Configs | No | N/A

This release mainly focuses on performance improvement, with minor improvement on error message handling.

This release introduces:
- Ingest commands add-variantset, add-readgroupset and add-featureset can now be completed faster.
- A larger default cache size for pysam file handles caching. We recommend users who set up the server in production environment manually overwrite this value should they feel the need, and adjust the file handles cache limit of their OS correspondingly.
- Improved error handling for ingesting duplicated pysam-related datasets.
- Use `<form`> element so users can click 'Enter' to initiate a search.

This is an intermediate release before the release v1.1.0, whose progress is available from https://github.com/CanDIG/candig-server/projects/2

This is a security and bug fix release.

This release introduces:

- Updated WerkZeug to 0.15.5 to resolve its security vulnerabilities.
- Updated Dockerfile.
- Updated server_info page.
- Updated gff3_db generate script to include a `CREATE INDEX` command.
- Renamed default db path for `Development config` to `candig-example-data`, this change is not backward compatible. Local test servers that are using this config should rename their db path as soon as possble. Such config should not be used for production environment.

This is an intermediate release before the release v1.1.0, whose progress is available from https://github.com/CanDIG/candig-server/projects/2

This is a bug fix release.

This release introduces:

- the removal of access_token, it is of no use in the current infrastructure, and may cause some issues.
- the improved handling of an exception that occurs when the files get removed after they have been ingested.

This release introduces:

- upgraded codebase (3.6).

Note:
- 3.7 is not currently supported since the particular version of pysam we use is not compatible with it.

This release introduces:

- An updated access list control mechanism

This is the last Pypi release of Python 2.7 codebase, and possibly the last release here. All changes, if deemed necessary, will be made to the `python2_archive` branch.

The `python2_archive` branch still accepts bug fix and security fixes.