From 6b344aa3d6d3a3c1560853f7c162d077e75a2b00 Mon Sep 17 00:00:00 2001
From: Avnish Pratap Singh <as74@sanger.ac.uk>
Date: Fri, 19 Jul 2024 22:23:50 +0100
Subject: [PATCH] Automatic confluence update

---
 .gitlab-ci.yml                    | 34 +++++++++++++++++++++++++++++++
 Changes                           |  3 +++
 docs/CtoA_substitution_metrics.md | 17 ++++++++++++++++
 docs/includes/repo-metadata.md    |  1 +
 docs/qc_outcomes_change_howto.md  | 17 ++++++++++++++++
 5 files changed, 72 insertions(+)
 create mode 100644 .gitlab-ci.yml
 create mode 100644 docs/includes/repo-metadata.md

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 00000000..8049f5f0
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,34 @@
+stages:
+  - generate
+  - publish
+
+generate-job:
+  stage: generate
+  tags:
+    - autoscale
+  rules:
+    - if: $CI_COMMIT_BRANCH == "devel" || $CI_COMMIT_BRANCH == "master"
+        changes:
+          - docs/**/*
+  variables:
+    REPO_METADATA_FILE: docs/includes/repo-metadata.md
+  script: >
+    echo "Created from: [$CI_PROJECT_NAMESPACE / $CI_PROJECT_TITLE]($CI_PROJECT_URL) Version: $(git describe --always)" > "$REPO_METADATA_FILE"
+  artifacts:
+    paths:
+      - "$REPO_METADATA_FILE"
+
+mark-job:
+  stage: publish
+  rules:
+    - if: $CI_COMMIT_BRANCH == "devel" || $CI_COMMIT_BRANCH == "master"
+      changes:
+        - docs/**/*
+  image: wsinpg/mark:latest
+  tags:
+    - autoscale
+  script: >
+    for f in $(find . -name includes -type d -prune -o -name 'README*.md' -prune -o -name '*.md' -print0 | xargs -0); do
+      sed -i 's/<!--CONFLUENCE_INFO \| CONFLUENCE_INFO-->//g' "$f";
+      echo 'username = ""' && echo "password = '$CONFLUENCE_PERSONAL_ACCESS_TOKEN'" | mark -c /dev/stdin -b https://ssg-confluence.internal.sanger.ac.uk -f "$f" --trace;
+    done
diff --git a/Changes b/Changes
index dee2ed80..ddf991ec 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,8 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - docs
+  - automated creation/update of confluence pages for docs
+
 release 72.1.2 (2024-07-25)
  - handle cases where the same tag sequence is seen in both index reads
 
diff --git a/docs/CtoA_substitution_metrics.md b/docs/CtoA_substitution_metrics.md
index e9f0ede0..de8e6a1f 100644
--- a/docs/CtoA_substitution_metrics.md
+++ b/docs/CtoA_substitution_metrics.md
@@ -1,3 +1,20 @@
+<!-- Space: NPG -->
+<!-- Parent: Illumina Sequencing -->
+<!-- Title: C->A short read sequencing substitution metrics -->
+
+<!-- Macro: :box:([^:]+):([^:]*):(.+):
+     Template: ac:box
+     Icon: true
+     Name: ${1}
+     Title: ${2}
+     Body: ${3} -->
+
+<!--CONFLUENCE_INFO :box:info:Note:This page is automatically generated; any edits will be overwritten: CONFLUENCE_INFO-->
+
+<!--CONFLUENCE_INFO ###### Repository information CONFLUENCE_INFO-->
+
+<!-- Include: includes/repo-metadata.md -->
+
 # C->A short read sequencing substitution metrics
 
 - Author - Irina Abnizova
diff --git a/docs/includes/repo-metadata.md b/docs/includes/repo-metadata.md
new file mode 100644
index 00000000..e8cc8a76
--- /dev/null
+++ b/docs/includes/repo-metadata.md
@@ -0,0 +1 @@
+Created from: -  Version: -
\ No newline at end of file
diff --git a/docs/qc_outcomes_change_howto.md b/docs/qc_outcomes_change_howto.md
index b7a8b245..64666c80 100644
--- a/docs/qc_outcomes_change_howto.md
+++ b/docs/qc_outcomes_change_howto.md
@@ -1,3 +1,20 @@
+<!-- Space: NPG -->
+<!-- Parent: Illumina Sequencing -->
+<!-- Title: Guidance for Changing QC Outcomes -->
+
+<!-- Macro: :box:([^:]+):([^:]*):(.+):
+     Template: ac:box
+     Icon: true
+     Name: ${1}
+     Title: ${2}
+     Body: ${3} -->
+
+<!--CONFLUENCE_INFO :box:info:Note:This page is automatically generated; any edits will be overwritten: CONFLUENCE_INFO-->
+
+<!--CONFLUENCE_INFO ###### Repository information CONFLUENCE_INFO-->
+
+<!-- Include: includes/repo-metadata.md -->
+
 # Guidance for Changing QC Outcomes
 
 - Use the correct RT ticket number.