Merge branch 'master' of https://github.com/Lazy-poet/sequenceserver into issue/551

Author: Lazy-poet

.github/workflows/codesee-arch-diagram.yml

@@ -0,0 +1,22 @@
+# This workflow was added by CodeSee. Learn more at https://codesee.io/
+# This is v2.0 of this workflow file
+on:
+  push:
+    branches:
+      - master
+  pull_request_target:
+    types: [opened, synchronize, reopened]
+
+name: CodeSee
+
+permissions: read-all
+
+jobs:
+  codesee:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    name: Analyze the repo with CodeSee
+    steps:
+      - uses: Codesee-io/codesee-action@v2
+        with:
+          codesee-token: ${{ secrets.CODESEE_ARCH_DIAG_API_TOKEN }}

.github/workflows/tests.yml

@@ -0,0 +1,71 @@
+# Run the old Travis tests within GitHub Actions, and upload the CodeClimate Report
+#
+# If nektos/act is installed as a GitHub CLI extension...
+# https://github.com/nektos/act#installation-as-github-cli-extension
+# ...then run this locally with:
+# gh act -j test
+# Appending to $PATH: https://www.scivision.dev/github-actions-path-append/
+# Conditionals predicated on status-codes:
+# https://github.com/orgs/community/discussions/25809
+#
+# One can *try* action-validator, but there are false-negatives:
+# (https://github.com/mpalmer/action-validator 
+#
+# State does *not* persist between jobs...
+# https://github.com/actions/checkout/issues/19
+# ...so all this needs to happen in a single job.
+#
+  name: Tests
+  on:
+    push:
+      branches:
+       - 1.0.x
+       - master
+    pull_request:
+      branches:
+       - 1.0.x
+       - master
+  env:
+    CC_TEST_REPORTER_ID: ec48bb03c72db6b43ce71fd488110b4707abfde4386c144d886d711378d8db64
+  jobs:
+    test:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v3
+        - name: Get BLAST
+          working-directory: /opt
+          run: wget -c "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
+        - name: BLAST PATH
+          run: mkdir /opt/bin && echo "/opt/bin:/opt/ncbi-blast-2.12.0+/bin" >> $GITHUB_PATH
+        - name: Get Chromium
+          run: sudo apt-get update && sudo apt-get install -y chromium-bsu chromium-driver
+        - name: Get CodeClimate
+          working-directory: /opt
+          run: wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter
+        - name: Set up Ruby
+          uses: ruby/setup-ruby@v1
+          with:
+            ruby-version: '3.2'
+            bundler-cache: true
+        - name: Install dependencies
+          run: bundle install
+        - name: Create SequenceServer config file
+          run: bundle exec bin/sequenceserver -s -d spec/database/v5/sample
+        - name: CodeClimate before-build hook
+          run: cc-test-reporter before-build
+        - name: Run main specs and import spec for BLAST 2.9.0+
+          id: rspec
+          continue-on-error: true
+          run: bundle exec rspec spec/*_spec.rb spec/blast_versions/blast_2.9.0/*
+        - name: CodeClimate after-build (success)
+          if: steps.rspec.outcome == 'success'
+          run: cc-test-reporter after-build --exit-code 0
+        - name: CodeClimate after-build (failure)
+          if: steps.rspec.outcome != 'success'
+          run: cc-test-reporter after-build --exit-code 1
+        - name: upload code coverage results
+          uses: actions/upload-artifact@v3
+          if: success() || failure()
+          with:
+            name: code-coverage-report
+            path: coverage

.gitignore

@@ -15,7 +15,7 @@ doc
 # jeweler generated
 pkg
 
-# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore:
 #
 # * Create a file at ~/.gitignore
 # * Include files you want ignored
@@ -28,7 +28,7 @@ pkg
 #
 # For MacOS:
 #
-#.DS_Store
+.DS_Store
 
 # For TextMate
 #*.tmproj
@@ -54,3 +54,6 @@ pkg
 .gems/*
 Gemfile.lock
 node_modules
+
+spec/dotdir/*
+spec/downloads/*

.rubocop.yml

@@ -1,5 +1,5 @@
 AllCops:
-  TargetRubyVersion: 2.6
+  TargetRubyVersion: 3.0
   Exclude:
     # Because these are vendor files.
     - 'node_modules/**/*'
@@ -8,6 +8,7 @@ Metrics/AbcSize:
   Exclude:
     # TODO
     - 'lib/sequenceserver.rb'
+    - 'spec/**/*'
 Metrics/MethodLength:
   # Because 15 lines in a method is just about as good as 10 (default). And we
   # have a couple that can't be helped.
@@ -30,6 +31,7 @@ Metrics/BlockLength:
   Exclude:
     - 'bin/sequenceserver'
     - 'sequenceserver.gemspec'
+    - 'spec/**/*'
 
 Style/UnlessElse:
   # TODO:

.travis.yml

@@ -1,8 +1,8 @@
 language: ruby
 
 rvm:
-  - 2.3
-  # - 2.5
+  - 3.0
+  - 3.2
 
 branches:
   only:

Dockerfile

@@ -1,9 +1,9 @@
 # Build variables. These need to be declared befored the first FROM
 # for the variables to be accessible in FROM instruction.
-ARG BLAST_VERSION=2.12.0
+ARG BLAST_VERSION=2.14.0
 
 ## Stage 1: gem dependencies.
-FROM ruby:2.7-slim-buster AS builder
+FROM ruby:3.2.0-slim-buster AS builder
 
 # Copy over files required for installing gem dependencies.
 WORKDIR /sequenceserver
@@ -17,13 +17,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 # Install gem dependencies using bundler.
 RUN bundle install --without=development
 
-
 ## Stage 2: BLAST+ binaries.
 # We will copy them from NCBI's docker image.
 FROM ncbi/blast:${BLAST_VERSION} AS ncbi-blast
 
 ## Stage 3: Puting it together.
-FROM ruby:2.7-slim-buster AS final
+FROM ruby:3.2.0-slim-buster AS final
 
 LABEL Description="Intuitive local web frontend for the BLAST bioinformatics tool"
 LABEL MailingList="https://groups.google.com/forum/#!forum/sequenceserver"
@@ -51,7 +50,7 @@ ENV PATH=/blast/bin:${PATH}
 # Setup working directory, volume for databases, port, and copy the code.
 # SequenceServer code.
 WORKDIR /sequenceserver
-VOLUME ["/db"]
+RUN mkdir /db
 EXPOSE 4567
 COPY . .
 
@@ -88,4 +87,20 @@ FROM final AS minify
 COPY --from=node /usr/src/app/public/sequenceserver-*.min.js public/
 COPY --from=node /usr/src/app/public/css/sequenceserver.min.css public/css/
 
+## Stage 6 (optional) Pull the example database from the debian package.
+FROM ruby:3.2.0-slim-buster AS example_db
+
+WORKDIR /tmp
+RUN apt-get update && apt-get download ncbi-blast+ && dpkg-deb -xv ncbi-blast+*.deb .
+
+FROM final AS dev
+
+RUN bundle install
+
+COPY --from=example_db /tmp/usr/share/doc/ncbi-blast+/examples /db/
+
+VOLUME ["/db"]
+
 FROM final
+
+VOLUME ["/db"]