Merge pull request #104 from refgenie/staging

v0.6.0

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

.github/workflows/deploy_release_software.yml

@@ -2,7 +2,9 @@ on:
   release:
     types:
       - created
-
+  workflow_dispatch:
+    inputs: null
+
 name: Deploy to Dockerhub on release
 
 jobs:

.github/workflows/deploy_staging_software.yml

@@ -26,8 +26,8 @@
 
 
 # 1. push the base refgenieserver image to dockerhub
-# 2. check out the demo repo, then run the aws deploy
-  # 2a. build aws package with demo config file, push, deploy to cluster
+# 2. check out the rg.databio.org repo, then run the aws deploy
+  # 2a. build aws package with rg.databio.org config file, push, deploy to cluster
 
 on:
   push:
@@ -36,13 +36,16 @@ on:
   pull_request:
     branches:
       - staging
+  workflow_dispatch:
+    inputs: null
 
 name: Deploy to Amazon ECS - software-staging
 
 jobs:
   deploy:
     env:
-      server: software-staging
+      service: dev1
+      data-repo: rg.databio.org
     name: Deploy
     runs-on: ubuntu-latest
     steps:
@@ -56,14 +59,15 @@ jobs:
         password: ${{ secrets.DOCKER_PASSWORD }}
         repository: databio/refgenieserver
         tags: staging
+        dockerfile: staging.Dockerfile
 
 
     - name: Checkout demo repo
       uses: actions/checkout@v2   
       with:
-        repository: refgenie/refgenomes.databio.org
+        repository: refgenie/${{ env.data-repo }}
         refs: refs/heads/master
-        path: server_data
+        path: ${{ env.data-repo }}
 
     - name: Configure AWS credentials
       uses: aws-actions/configure-aws-credentials@v1
@@ -86,23 +90,34 @@ jobs:
         # Build a docker container and
         # push it to ECR so that it can
         # be deployed to ECS.
-        cd server_data
-        docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG -f Dockerfiles/staging.Dockerfile .
+        cd ${{ env.data-repo }}
+        docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG -f Dockerfiles/${{ env.data-repo }}.Dockerfile .
         docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
         echo "::set-output name=image::$ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG"
 
     - name: Fill in the new image ID in the Amazon ECS task definition
       id: task-def
       uses: aws-actions/amazon-ecs-render-task-definition@v1
       with:
-        task-definition: task_defs/${{ env.server }}.json
+        task-definition: task_defs/${{ env.service }}.json
         container-name: rgs-container
         image: ${{ steps.build-image.outputs.image }}
 
     - name: Deploy Amazon ECS task definition
       uses: aws-actions/amazon-ecs-deploy-task-definition@v1
       with:
         task-definition: ${{ steps.task-def.outputs.task-definition }}
-        service: rgs-service-${{ env.server }}
-        cluster: hydra
+        service: rgs-service-${{ env.service }}
+        cluster: yeti
         wait-for-service-stability: true
+  test:
+    needs: deploy
+    runs-on: ubuntu-latest
+    name: test REST API
+    steps:
+      - uses: actions/checkout@master
+      - uses: matt-ball/newman-action@master
+        name: Newman Action
+        with:
+          collection: refgenieserver.postman_collection.json
+          environment: refgenieserver.postman_environment.json

changelog.md

@@ -2,6 +2,19 @@
 
 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. 
 
+## [0.6.0] -- 2021-03-11
+### Added
+- API v3, which is a complete redesign and extension of the previous version
+- in `refgenieserver archive`, when a `archive_checksum` is missing for a previously archived asset it will be recalculated.
+- response models to API endpoints
+- API version tags in the openAPI specification
+- a `legacy_archive_digest` to the tag attributes
+
+### Changed
+- split the user interface into: index, genome and asset pages
+- grouped endpoints by API version in the swagger docs
+- the archives created with `refgenieserver archive` are now named after digests
+
 ## [0.5.1] -- 2020-07-10
 ### Changed
 - in `refgenieserver archive`:

dir2cfg_template.py

@@ -4,13 +4,21 @@
 import sys
 import yaml
 import argparse
-from refgenconf import CFG_GENOMES_KEY, CFG_SERVER_KEY, CFG_FOLDER_KEY, CFG_ARCHIVE_KEY, CFG_ASSET_PATH_KEY
+from refgenconf import (
+    CFG_GENOMES_KEY,
+    CFG_SERVER_KEY,
+    CFG_FOLDER_KEY,
+    CFG_ARCHIVE_KEY,
+    CFG_ASSET_PATH_KEY,
+)
 
 
 class _VersionInHelpParser(argparse.ArgumentParser):
     def format_help(self):
         """ Add version information to help text. """
-        return "version: {}\n".format(V) + super(_VersionInHelpParser, self).format_help()
+        return (
+            "version: {}\n".format(V) + super(_VersionInHelpParser, self).format_help()
+        )
 
 
 def build_dir2yaml_parser():
@@ -19,24 +27,25 @@ def build_dir2yaml_parser():
 
     :return argparse.ArgumentParser
     """
-    banner = "%(prog)s builds a refgenieserver config template for the directory structure." \
-             " Keep in mind that the produced config will require some adjustments."
+    banner = (
+        "%(prog)s builds a refgenieserver config template for the directory structure."
+        " Keep in mind that the produced config will require some adjustments."
+    )
     additional_description = "\nhttps://github.com/databio/refgenieserver"
 
-    parser = _VersionInHelpParser(
-        description=banner,
-        epilog=additional_description)
+    parser = _VersionInHelpParser(description=banner, epilog=additional_description)
 
     parser.add_argument(
-        "-V", "--version",
-        action="version",
-        version="%(prog)s {v}".format(v=V))
+        "-V", "--version", action="version", version="%(prog)s {v}".format(v=V)
+    )
     parser.add_argument(
-        "-p", "--path",
+        "-p",
+        "--path",
         dest="path",
         help="A path to the directory that the YAML should be build for. If not provided, current working directory "
-             "will be used ({})".format(os.getcwd()),
-        default=None)
+        "will be used ({})".format(os.getcwd()),
+        default=None,
+    )
     return parser
 
 
@@ -72,7 +81,7 @@ def main():
                     CFG_FOLDER_KEY: None,
                     CFG_SERVER_KEY: "http://www.refgenomes.databio.org",
                     CFG_ARCHIVE_KEY: None,
-                    CFG_GENOMES_KEY: None
+                    CFG_GENOMES_KEY: None,
                 }
                 rgc[CFG_GENOMES_KEY] = dir_as_dict(p)[os.path.basename(p)]
                 yaml.dump(rgc, f)