From 07329bc2c6891fd582ebdb72b04075eb91883479 Mon Sep 17 00:00:00 2001
From: Mihail Anton <mihail.anton@chalmers.se>
Date: Fri, 7 Jul 2023 16:20:45 +0800
Subject: [PATCH 1/3] feat: gene essentiality workflow with pr comment

---
 .github/workflows/commentsFromTests.md  |  7 ++++++
 .github/workflows/gene-essentiality.yml | 32 +++++++++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100644 .github/workflows/commentsFromTests.md
 create mode 100644 .github/workflows/gene-essentiality.yml

diff --git a/.github/workflows/commentsFromTests.md b/.github/workflows/commentsFromTests.md
new file mode 100644
index 00000000..dd2ba900
--- /dev/null
+++ b/.github/workflows/commentsFromTests.md
@@ -0,0 +1,7 @@
+This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/Human-GEM/actions/runs/{GH_ACTION_RUN}). Here is the output of the gene essentiality test:
+
+<pre>
+{TEST_RESULTS}
+</pre>
+
+> _Note: In the case of multiple test runs, this post will be edited._
diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml
new file mode 100644
index 00000000..687954c3
--- /dev/null
+++ b/.github/workflows/gene-essentiality.yml
@@ -0,0 +1,32 @@
+name: Check gene essentiality with Hart 2015
+
+on:
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+  check-metabolictasks:
+    runs-on: self-hosted
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Run gene essentiality
+        id: essentiality
+        run: |
+          TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "ihuman = importYaml('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/')
+          PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}"
+          PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}"
+          echo "results=$PARSED_RESULTS" >> $GITHUB_OUTPUT
+
+      - name: Post comment
+        uses: NejcZdovc/comment-pr@v2
+        with:
+          file: "commentsFromTests.md"
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+          TEST_RESULTS: ${{steps.essentiality.outputs.results}}
+          GH_ACTION_RUN: ${{github.run_id}}

From 1bba24db9adab892ba89153a35322cd127456319 Mon Sep 17 00:00:00 2001
From: Mihail Anton <mihail.anton@chalmers.se>
Date: Fri, 6 Oct 2023 10:04:17 +0300
Subject: [PATCH 2/3] chore: expand workflow targets

---
 .github/workflows/gene-essentiality.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml
index 687954c3..371743a3 100644
--- a/.github/workflows/gene-essentiality.yml
+++ b/.github/workflows/gene-essentiality.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - "main"
+      - "develop"
 
 jobs:
   check-metabolictasks:

From aff8211e1ec5ce2006397675445c07d2109f3083 Mon Sep 17 00:00:00 2001
From: Mihail Anton <mihail.anton@chalmers.se>
Date: Fri, 6 Oct 2023 12:37:24 +0300
Subject: [PATCH 3/3] fix: add to matlab path

---
 .github/workflows/gene-essentiality.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gene-essentiality.yml b/.github/workflows/gene-essentiality.yml
index 371743a3..169efc71 100644
--- a/.github/workflows/gene-essentiality.yml
+++ b/.github/workflows/gene-essentiality.yml
@@ -17,7 +17,7 @@ jobs:
       - name: Run gene essentiality
         id: essentiality
         run: |
-          TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "ihuman = importYaml('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/')
+          TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); ihuman = importYaml('Human-GEM.yml'); taskStruct = parseTaskList('data/metabolicTasks/metabolicTasks_Essential.txt'); eGenes = estimateEssentialGenes(ihuman, 'Hart2015_RNAseq.txt', taskStruct); disp(evaluateHart2015Essentiality(eGenes));" | awk 'NR>9 && !/^\.+/')
           PARSED_RESULTS="${TEST_RESULTS//'%'/'%25'}"
           PARSED_RESULTS="${PARSED_RESULTS//$'\n'/'<br>'}"
           PARSED_RESULTS="${PARSED_RESULTS//$'\r'/'<br>'}"