From 173fc6b14bcb4f8c82879b03ba99a4415c855905 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Tue, 25 Jun 2024 11:17:51 +0200
Subject: [PATCH] Move tests from bash to GitHub Action

---
 .github/workflows/run_tests.yaml     | 68 +++++++++++++++++++++++-----
 bin/extract_all_tools_test.sh        | 15 ------
 bin/extract_filter_tutorials_test.sh | 32 -------------
 3 files changed, 56 insertions(+), 59 deletions(-)
 delete mode 100755 bin/extract_all_tools_test.sh
 delete mode 100644 bin/extract_filter_tutorials_test.sh

diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml
index 8929bd6f..1fb837a0 100644
--- a/.github/workflows/run_tests.yaml
+++ b/.github/workflows/run_tests.yaml
@@ -2,29 +2,73 @@ name: Run tests
 on: [push, pull_request]
 
 jobs:
-  test:
+  test-tools:
     runs-on: ubuntu-20.04
     environment: fetch-tools
-    strategy:
-      matrix:
-        python-version: [3.8]
-        subset:
-         - test.list
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: '3.11'
       - name: Install requirement
         run: python -m pip install -r requirements.txt
-      - name: Test tool extraction
+      - name: Tool extraction
         # run: bash bin/extract_all_tools.sh
         run: | 
-          bash ./bin/extract_all_tools_test.sh "${{ matrix.subset }}"
+          python bin/extract_galaxy_tools.py \
+            extractools \
+            --api $GITHUB_API_KEY \
+            --all-tools "results/test_tools.tsv" \
+            --all-tools-json "results/test_tools.json" \
+            --planemo-repository-list "test.list" \
+            --test
         env: 
           GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }}
-      - name: Test tutorial extraction and filtering
+      - name: Tool filter
         run: | 
-          bash ./bin/extract_filter_tutorials_test.sh
+          python bin/extract_galaxy_tools.py \
+            filtertools \
+            --tools "results/all_tools.json" \
+            --ts-filtered-tools "results/microgalaxy/tools_filtered_by_ts_categories.tsv" \
+            --filtered-tools "results/microgalaxy/tools.tsv" \
+            --categories "data/communities/microgalaxy/categories" \
+            --status "data/communities/microgalaxy/tool_status.tsv"
+      - name: Create interactive table
+        run: | 
+          python bin/create_interactive_table.py \
+            --table "results/$community/tools.tsv" \
+            --template "data/interactive_table_template.html" \
+            --output "results/$community/index.html"
+      - name: Create wordcloud
+        run: | 
+          python bin/create_wordcloud.py \
+            --table  "results/$community/tools.tsv" \
+            --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
+            --output "results/$community/tools_wordcloud.png" \
+            --stats_column "No. of tool users (2022-2023) (usegalaxy.eu)"
+  test-tutorials:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install requirement
+        run: python -m pip install -r requirements.txt
+      - name: Tutorial extraction
+        run: | 
+          python bin/extract_gtn_tutorials.py \
+            extracttutorials \
+            --all_tutorials "results/test_tutorials.json" \
+            --tools "results/all_tools.json" \
+            --api $PLAUSIBLE_API_KEY \
+            --test
         env: 
-          PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
\ No newline at end of file
+          PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
+      - name: Tutorial filtering
+        run: | 
+          python bin/extract_gtn_tutorials.py \
+            filtertutorials \
+            --all_tutorials "results/test_tutorials.json" \
+            --filtered_tutorials "results/microgalaxy/test_tutorials.tsv" \
+            --tags "data/communities/microgalaxy/tutorial_tags"
\ No newline at end of file
diff --git a/bin/extract_all_tools_test.sh b/bin/extract_all_tools_test.sh
deleted file mode 100755
index 2ba40be5..00000000
--- a/bin/extract_all_tools_test.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env bash
-
-mkdir -p 'results/'
-
-tsv_output="results/${1}_tools.tsv"
-json_output="results/${1}_tools.json"
-
-python bin/extract_galaxy_tools.py \
-        extractools \
-        --api $GITHUB_API_KEY \
-        --all-tools $tsv_output \
-        --all-tools-json $json_output \
-        --planemo-repository-list $1 \
-        --test
-
diff --git a/bin/extract_filter_tutorials_test.sh b/bin/extract_filter_tutorials_test.sh
deleted file mode 100644
index b4d066c3..00000000
--- a/bin/extract_filter_tutorials_test.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env bash
-
-mkdir -p 'results/'
-
-tsv_output="results/${1}_tools.tsv"
-json_output="results/${1}_tools.json"
-
-python bin/extract_gtn_tutorials.py \
-        extracttutorials \
-        --all_tutorials "results/test_tutorials.json" \
-        --tools "results/all_tools.json" \
-        --api $PLAUSIBLE_API_KEY \
-        --test
-
-if [[ ! -f "results/test_tutorials.json" ]] ; then
-    echo 'File "results/test_tutorials.json" is not there, aborting.'
-    exit
-fi
-
-python bin/extract_gtn_tutorials.py \
-        filtertutorials \
-        --all_tutorials "results/test_tutorials.json" \
-        --filtered_tutorials "results/microgalaxy/test_tutorials.tsv" \
-        --tags "data/communities/microgalaxy/tutorial_tags"
-
-if [[ ! -f "results/microgalaxy/test_tutorials.tsv" ]] ; then
-    echo 'File "results/microgalaxy/test_tutorials.tsv" is not there, aborting.'
-    exit
-fi
-
-rm "results/test_tutorials.json"
-rm "results/microgalaxy/test_tutorials.tsv"