Merge pull request #115 from refgenie/staging

v0.7.0

.github/workflows/black.yml

@@ -8,4 +8,4 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: psf/black@stable
+      - uses: psf/black@20.8b1

.pre-commit-config.yaml

@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.7.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black

README.md

@@ -1,8 +1,11 @@
-[![Build Status](https://travis-ci.org/databio/refgenieserver.svg?branch=master)](https://travis-ci.org/databio/refgenieserver)
+[![Deploy to Dockerhub on release](https://github.com/refgenie/refgenieserver/actions/workflows/deploy_release_software.yml/badge.svg)](https://github.com/refgenie/refgenieserver/actions/workflows/deploy_release_software.yml)
+[![Deploy to Amazon ECS - software-staging](https://github.com/refgenie/refgenieserver/actions/workflows/deploy_staging_software.yml/badge.svg)](https://github.com/refgenie/refgenieserver/actions/workflows/deploy_staging_software.yml)
+
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # refgenieserver
 
-This folder contains code for an API to provide reference genomes. `refgenieserver` can do 2 things: `archive` an existing refgenie folder, and then `serve` it. 
+This folder contains code for an API to provide reference genomes. `refgenieserver` can do 2 things: `archive` an existing refgenie folder, and then `serve` it.
 
 ## How to `serve`
 
@@ -27,7 +30,7 @@ Better, though, is to use the container. Mount a directory of files to serve at
 ```
 docker run --rm -p 80:80 --name refgenieservercon \
   -v $(pwd)/files:/genomes \
-  refgenieserverim refgenieserver serve -c refgenie.yaml 
+  refgenieserverim refgenieserver serve -c refgenie.yaml
 ```
 
 ### Running container for production:
@@ -37,7 +40,7 @@ Run the container from the image you just built:
 docker run --rm -d -p 80:80 \
   -v /path/to/genomes_archive:/genomes \
   --name refgenieservercon \
-  refgenieserverim refgenieserver serve -c /genomes/genome_config.yaml 
+  refgenieserverim refgenieserver serve -c /genomes/genome_config.yaml
 ```
 
 Make sure the `genome_config.yaml` filename matches what you've named your configuration file! We use `-d` to detach so it's in background. You shouldn't need to mount the app (`-v /path/to/refgenieserver:/app`) because in this case we're running it directly. Terminate container when finished:
@@ -88,15 +91,15 @@ First, make sure the config has a `genome_archive_folder` key that points to the
 
 Secondly, if you wish to store the refgenieserver configuration file separately from the `genome_archive_folder`, specify a `genome_archive_config` key. The path that this key points to will be considered relative to the refgenie configuration file, unless it's absolute.
 
-Then run: 
+Then run:
 ```
 refgenieserver archive -c CONFIG
 ````
 It just requires a `-c` argument or `$REFGENIE` environment variable.
 
 This command will:
 - create the `genome_archive` directory and structure that can be used to serve the assets
-- create a server config file in that directory, which includes a couple of extra asset attributes, like `archive_digest` and `archive_size`. 
+- create a server config file in that directory, which includes a couple of extra asset attributes, like `archive_digest` and `archive_size`.
 
 In case you already have some of the assets archived and just want to add a new one, use:
 

changelog.md

@@ -1,11 +1,22 @@
 # Changelog
 
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.6.1] -- 2021-03-18
+## [0.7.0] -- 2021-04-27
 ### Added
-- private endpoint serving genomes dict to openAPI schema; [#105](https://github.com/refgenie/refgenieserver/issues/105) 
+- `remotes` section in the refgenieserver config, which supersedes `remote_url_base`. It can be used to define multiple remote data providers.
+- new endpoints:
+  - `/remotes/dict` to get `remotes` dictionary
+  - `/assets/dir_contents/{genome}/{asset}` to get a JSON object (array of strings) listing all files in the asset directory
+  - `/assets/file_path/{genome}/{asset}/{seek_key}` to get a *remote* path to the specified file
+- direct *unarchived* asset file downloads from asset splash page, both for seek_keys and other asset files
+
+### Changed
+- endpoints that return digests return plain text instead of JSON objects for easier parsing; [#67](https://github.com/refgenie/refgenieserver/issues/67)
 
+## [0.6.1] -- 2021-03-18
+### Added
+- private endpoint serving genomes dict to openAPI schema; [#105](https://github.com/refgenie/refgenieserver/issues/105)
 
 ## [0.6.0] -- 2021-03-11
 ### Added
@@ -32,7 +43,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 - path specified in `genome_archive_config` is considered relative to the refgenie genome config file, unless absolute.
 - non-servable assets purging is now performed prior to serving rather than after each archive job completion
-- dropped Python 2 support 
+- dropped Python 2 support
 ### Removed
 - support for old `genome_archive` key; use `genome_archive_folder` and `genome_archive_config` from now on.
 
@@ -44,7 +55,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [0.4.3] -- 2020-01-16
 ### Added
 - a possibility to decouple genome archive directory and genome archive config file. `refgenieserver archive` uses new key (`genome_archive_config`) from `refgenconf`
-- a genome archive config file writability check 
+- a genome archive config file writability check
 
 ### Changed
 - key `genome_archive` to `genome_archive_folder`. Backwards compatiblity is preserved (both are currently supported)
@@ -55,10 +66,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [0.4.1] -- 2019-12-13
 ### Fixed
-- relationship info not being updated during specific asset archivization; [#70](https://github.com/refgenie/refgenieserver/issues/70) 
+- relationship info not being updated during specific asset archivization; [#70](https://github.com/refgenie/refgenieserver/issues/70)
 
 ### Changed
-- order of the assets adn tags in the table in the index page: sorted alphabetically instead of oldest to newest 
+- order of the assets adn tags in the table in the index page: sorted alphabetically instead of oldest to newest
 
 ## [0.4.0] -- 2019-12-06
 ### Added
@@ -113,7 +124,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - config manipulation support in multi-process contexts, it's racefree, uses file locks
 - archive removal support (added `-r` option in `refgenieserver archive`)
 - asset registry path support in `refgenieserver archive`
-    
+
 ### Changed
 - command order from `refgenieserver -c CONFIG -d archive/serve` to `refgenieserver archive/serve -c CONFIG -d`
 - the genome tarballs are not produced