Merge branch '2.x' of https://github.com/tripal/tripal_blast into 2.x

.github/workflows/ALL-PHPUnit.yml

@@ -0,0 +1,43 @@
+
+name: PHPUnit
+on: [push]
+
+env:
+  PKG_NAME: tripal_blast
+  MODULES: "tripal_blast"
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        php-version:
+          - "8.0"
+          - "8.1"
+        pgsql-version:
+          - "13"
+        drupal-version:
+          - "9.3.x-dev"
+          - "9.4.x-dev"
+          - "9.5.x-dev"
+          # - "10.0.x-dev"
+#        exclude:
+#          - php-version: "8.0"
+#            pgsql-version: "13"
+#            drupal-version: "10.0.x-dev"
+
+    steps:
+      # Check out the repo
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      # Here we pull the development tripaldocker image for this combo in our matrix
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: $PKG_NAME
+          modules: $MODULES
+          php-version: ${{ matrix.php-version }}
+          pgsql-version: ${{ matrix.pgsql-version }}
+          drupal-version: ${{ matrix.drupal-version }}

.github/workflows/ALL-testCoverage-codeclimate.yml

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+# Run some PHPUnit tests
+name: Test Coverage
+on: [push]
+
+env:
+  PKG_NAME: tripal_blast
+  MODULES: "tripal_blast"
+  IMAGE_TAG: drupal9.5.x-dev-php8.1-pgsql13
+  SIMPLETEST_BASE_URL: "http://localhost"
+  SIMPLETEST_DB: "pgsql://drupaladmin:drupal9developmentonlylocal@localhost/sitedb"
+  BROWSER_OUTPUT_DIRECTORY: "/var/www/drupal9/web/sites/default/files/simpletest"
+
+jobs:
+  # Job 1: 'build'
+  run-tests:
+    # Runner type
+    runs-on: ubuntu-latest
+    name: Test Coverage
+
+    steps:
+      # Check out the repo
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      # Here we pull the development tripaldocker image for this combo in our matrix
+      - name: Pull TripalDocker Image
+        run: |
+          docker pull tripalproject/tripaldocker:$IMAGE_TAG
+      # Just spin up docker the good ol' fashion way
+      # mounting our currently checked out package inside the docker container.
+      - name: Spin up Docker locally
+        run: |
+          docker run --publish=80:80 --name=tripaldocker -tid \
+            --volume=`pwd`:/var/www/drupal9/web/modules/contrib/$PKG_NAME tripalproject/tripaldocker:$IMAGE_TAG
+      # Install the modules
+      - name: Install our package in Docker
+        run: |
+          docker exec tripaldocker service postgresql restart
+          docker exec tripaldocker drush en $MODULES --yes
+      # Ensure we have the variables we need.
+      - name: Inject slug/short variables
+        uses: rlespinasse/[email protected]
+      # Prepare for code coverage.
+      - name: Prepare for Code Coverage
+        run: |
+          curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
+          docker cp cc-test-reporter tripaldocker:/var/www/drupal9/web/modules/contrib/$PKG_NAME
+          docker exec tripaldocker chmod a+x /var/www/drupal9/web/modules/contrib/$PKG_NAME/cc-test-reporter
+          docker exec --workdir=/var/www/drupal9/web/modules/contrib/$PKG_NAME tripaldocker ./cc-test-reporter before-build --debug
+      # Runs the PHPUnit tests.
+      # https://github.com/mheap/phpunit-github-actions-printer is used
+      # to report PHPUnit fails in a meaningful way to github in PRs.
+      # Stopped using mheap due to warning w/ phpunit8->9
+      - name: Run Tests for Coverage
+        env:
+          SIMPLETEST_BASE_URL: "http://localhost"
+          SIMPLETEST_DB: "pgsql://drupaladmin:drupal9developmentonlylocal@localhost/sitedb"
+          BROWSER_OUTPUT_DIRECTORY: "/var/www/drupal9/web/sites/default/files/simpletest"
+        run: |
+          docker exec tripaldocker service postgresql restart
+          docker exec -e SIMPLETEST_BASE_URL=$SIMPLETEST_BASE_URL \
+            -e SIMPLETEST_DB=$SIMPLETEST_DB \
+            -e BROWSER_OUTPUT_DIRECTORY=$BROWSER_OUTPUT_DIRECTORY \
+            --workdir=/var/www/drupal9/web/modules/contrib/$PKG_NAME \
+            tripaldocker phpunit --coverage-text \
+              --coverage-clover /var/www/drupal9/web/modules/contrib/$PKG_NAME/clover.xml
+          docker exec tripaldocker ls /var/www/drupal9/web/modules/contrib/$PKG_NAME
+      - name: Publish code coverage to Code Climate
+        run: |
+          docker exec --workdir=/var/www/drupal9/web/modules/contrib/$PKG_NAME tripaldocker \
+            git config --global --add safe.directory /var/www/drupal9/web/modules/contrib/$PKG_NAME
+          docker exec --workdir=/var/www/drupal9/web/modules/contrib/$PKG_NAME \
+            tripaldocker ./cc-test-reporter after-build clover.xml \
+            --id ${{ secrets.CODECLIMATE_TEST_REPORTER_ID }} \
+            --debug -t clover -p /var/www/drupal9/web/modules/contrib/$PKG_NAME

.github/workflows/MAIN-phpunit-Grid1A.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.0'
+          pgsql-version: '13'
+          drupal-version: '9.3.x-dev'

.github/workflows/MAIN-phpunit-Grid1B.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.0'
+          pgsql-version: '13'
+          drupal-version: '9.4.x-dev'

.github/workflows/MAIN-phpunit-Grid1C.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.0'
+          pgsql-version: '13'
+          drupal-version: '9.5.x-dev'

.github/workflows/MAIN-phpunit-Grid2A.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.1'
+          pgsql-version: '13'
+          drupal-version: '9.3.x-dev'

.github/workflows/MAIN-phpunit-Grid2B.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.1'
+          pgsql-version: '13'
+          drupal-version: '9.4.x-dev'

.github/workflows/MAIN-phpunit-Grid2C.yml

@@ -0,0 +1,19 @@
+name: PHPUnit
+on:
+  push:
+    branches:
+      - 2.x
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+      - name: Run Automated testing
+        uses: tripal/[email protected]
+        with:
+          directory-name: 'tripal_blast'
+          modules: 'tripal_blast'
+          php-version: '8.1'
+          pgsql-version: '13'
+          drupal-version: '9.5.x-dev'

.github/workflows/README.md

@@ -0,0 +1,19 @@
+
+GitHub Actions
+=================
+
+This directory contains automated workflows executed by GitHub Actions.
+
+Naming Conventions
+--------------------
+
+### File Name: [scope]-[purpose]-[extra_info].yml
+
+	- [scope] should be one of the following:
+		- MAIN for only against the master branch
+		- ALL for against all branches
+		- PR if specific to pull requests
+	- [purpose] should be a one word description of the purpose (e.g. phpunit, coverage)
+		- use snake-case if you must use more then one word (e.g. buildDocker)
+	- [extra_info] should be any additional information needed to make the file
+		name unique. For multiple words, separate words using an underscore.

.gitignore

@@ -1 +1,2 @@
-supervisord*
+supervisord*
+.phpunit.*

README.md

@@ -0,0 +1,69 @@
+![Tripal Dependency](https://img.shields.io/badge/Tripal-4.0--alpha1-brightgreen)
+![Development Status](https://img.shields.io/badge/Status-Active%20Development-orange)
+
+**Developed by the University of Saskatchewan, Pulse Crop Bioinformatics team.**
+
+## Introduction
+
+This module provides a basic interface to allow your users to utilize your
+server's NCBI BLAST+.
+
+Specifically it provides blast program-specific forms (blastn, blastp, tblastn,
+blastx are supported). In the future, there will be a single form where you
+will be able to select either a nucleotide or a protein database to BLAST
+against regardless of the type of query and it will decide which BLAST
+program to use based on the combination of query/database type (ie: if you
+selected a protein database on the nucleotide BLAST form then blastx would
+be used).
+
+BLAST submissions result in the creation of Tripal jobs which then need to run
+from the command-line. This ensures that long running BLASTs will not cause
+page time-outs but does add some management overhead and might result in longer
+waits for users depending on how often you have cron set to run Tripal jobs.
+
+The BLAST results page is an expandable summary table with each hit being
+listed as a row in the table with query/hit/e-value information. The row can
+then be expanded to include additional information including the alignment.
+Download formats are allow users to download these results in the familiar
+tabular, GFF3 or HTML NCBI formats.
+
+## Automated Testing
+
+This package is dedicated to a high standard of automated testing. We use
+PHPUnit for testing and CodeClimate to ensure good test coverage and maintainability.
+There are more details on [our CodeClimate project page] describing our specific
+maintainability issues and test coverage.
+
+![MaintainabilityBadge]
+![TestCoverageBadge]
+
+The following compatibility is proven via automated testing workflows.
+
+![Tripal Version for following tests](https://img.shields.io/badge/Tripal-4.x--dev-green)
+
+| Drupal | 9.3.x | 9.4.x | 9.5.x | 10.0.x |
+|--------|-------|-------|-------|--------|
+| **PHP 8.0** | ![Grid1A-Badge] | ![Grid1B-Badge] | ![Grid1C-Badge] |  |
+| **PHP 8.1** | ![Grid2A-Badge] | ![Grid2B-Badge] | ![Grid2C-Badge] |  |
+
+[our CodeClimate project page]: https://codeclimate.com/github/tripal/tripal_blast
+[MaintainabilityBadge]: https://api.codeclimate.com/v1/badges/5071f91a02a3fcafc275/maintainability
+[TestCoverageBadge]: https://api.codeclimate.com/v1/badges/5071f91a02a3fcafc275/test_coverage
+
+[Grid1A-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid1A.yml/badge.svg
+[Grid1B-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid1B.yml/badge.svg
+[Grid1C-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid1C.yml/badge.svg
+
+[Grid2A-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid2A.yml/badge.svg
+[Grid2B-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid2B.yml/badge.svg
+[Grid2C-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid2C.yml/badge.svg
+[Grid2D-Badge]: https://github.com/tripal/tripal_blast/actions/workflows/MAIN-phpunit-Grid2D.yml/badge.svg
+
+## Docker
+
+```
+git clone https://github.com/tripal/tripal_blast.git
+cd tripal_blast
+docker build --tag=tripal/tripal_blast:latest .
+docker run --publish=80:80 -tid --volume=`pwd`:/var/www/drupal9/web/modules/contrib/tripal_blast tripal/tripal_blast:latest
+```

config/schema/tripal_blast.settings.schema.yml

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+# @file
+# Tripal Blast module variables/configuration.
+
+tripal_blast.settings:
+  type: config_object
+  mapping:
+
+    # GENERAL CONFIGURATIONS:
+    tripal_blast_config_general:
+      type: mapping
+      mapping:
+        path:
+          type: string
+          label: 'Path to BLAST executables'
+        threads:
+          type: integer
+          label: 'Processor Threads for Blast'
+        eval:
+          type: float
+          label: 'E-value Threshold'
+        qrange:
+          type: integer
+          label: 'Max Matches in a Query Range'
+
+    # UPLOAD CONFIGURATIONS:
+    tripal_blast_config_upload:
+      type: mapping
+      mapping:
+        allow_query:
+          type: boolean
+          label: 'Allow Query Sequence Upload'
+        allow_target:
+          type: boolean
+          label: 'Allow Target Database Upload'
+
+    # SEQUENCE CONFIGURATIONS:
+    tripal_blast_config_sequence:
+      type: mapping
+      mapping:
+        nucleotide:
+          type: text
+          label: 'Nucleotide Example Fasta Record'
+        protein:
+          type: text
+          label: 'Protein Example Fasta Record'
+
+    # LARGE JOBS CONFIGURATIONS:
+    tripal_blast_config_jobs:
+      type: mapping
+      mapping:
+        max_result:
+          type: integer
+          label: 'Max Results to Display'
+
+    # NOTIFICATION CONFIGURATIONS
+    tripal_blast_config_notification:
+      type: mapping
+      mapping:
+        warning_text:
+          type: text
+          label: 'Warning Text on Blast Page'