From 32aa420818e2bce608a0c206b563686f9856d091 Mon Sep 17 00:00:00 2001
From: Miller <millerd15@email.chop.edu>
Date: Mon, 19 Feb 2024 16:39:44 -0500
Subject: [PATCH] :robot: add docker table builder

---
 .github/scripts/workflow_to_docker_table.py | 73 +++++++++++++++++++++
 .github/workflows/update_docker_tables.yml  | 39 +++++++++++
 2 files changed, 112 insertions(+)
 create mode 100644 .github/scripts/workflow_to_docker_table.py
 create mode 100644 .github/workflows/update_docker_tables.yml

diff --git a/.github/scripts/workflow_to_docker_table.py b/.github/scripts/workflow_to_docker_table.py
new file mode 100644
index 0000000..8ce7075
--- /dev/null
+++ b/.github/scripts/workflow_to_docker_table.py
@@ -0,0 +1,73 @@
+#!/usr/bin/env python3
+
+import argparse
+import pathlib
+
+def parse_command():
+    """Function to parse the command line input
+    Args:
+        None
+    Return:
+        Namespace: returns the args as a standard Namespace object
+    """
+    parser = argparse.ArgumentParser(description='Generate Table of Tools and Their Dockers from a CWL Workflow')
+    parser.add_argument('input_file')
+    parser.add_argument('--output_file',
+        default='TABLE.md',
+        help='Path to output file.')
+    args = parser.parse_args()
+    if not args.output_file.endswith('.md'): args.output_file = args.output_file + ".md"
+    return args
+
+def parse_workflow(filepath: str, pathdict: dict | None = None) -> dict:
+    """Function to recursively build dict of unique subworkflows and tools from a file.
+    Args:
+        filepath: Path to the input cwl
+        pathdict: Dict to store the unique subworkflows and tools
+    Return:
+        pathdict: Dict containing two lists. One of unique subworkflows; one of unique tools
+    """ 
+    if not pathdict: pathdict = {}
+    if "workflows" not in pathdict: pathdict["workflows"] = set()
+    if "tools" not in pathdict: pathdict["tools"] = set()
+    inpath = pathlib.Path(filepath).resolve()
+    with open(inpath) as fh:
+        for line in fh:
+            if not line.strip().startswith('run:'): continue
+            if not line.strip().endswith('.cwl'): continue
+            relpath = inpath.parent / line.strip().split(' ')[-1]
+            respath = relpath.resolve()
+            if respath in pathdict["workflows"] or respath in pathdict["tools"]: continue
+            if not respath.match('*/tools/*'):
+                pathdict["workflows"].add(respath)
+                pathdict = parse_workflow(respath, pathdict)
+            else:
+                pathdict["tools"].add(respath)
+    return pathdict
+
+def get_docker(filepath: str) -> str:
+    """
+    Args:
+        filepath: Path to the input cwl
+    Return:
+        string: Name of item in dockerPull field or None
+    """
+    inpath = pathlib.Path(filepath)
+    with open(inpath) as toolfile:
+        for line in toolfile:
+            if "dockerPull" in line:
+                return line.strip().split(' ')[-1].strip("\"'")
+    return "None"
+
+def main():
+    args = parse_command()
+    appdict: dict = parse_workflow(args.input_file)
+    payload: list[tuple[str]] = sorted([(cwltool.name, get_docker(cwltool)) for cwltool in appdict['tools']])
+    with open(args.output_file, 'w') as outfile:
+        print(f"# Dockers of {pathlib.Path(args.input_file).name}\n", file=outfile)
+        print("TOOL|DOCKER\n-|-", file=outfile)
+        for item in payload:
+            print('|'.join(item), file=outfile)
+
+if __name__ == '__main__':
+    main()
diff --git a/.github/workflows/update_docker_tables.yml b/.github/workflows/update_docker_tables.yml
new file mode 100644
index 0000000..d734b37
--- /dev/null
+++ b/.github/workflows/update_docker_tables.yml
@@ -0,0 +1,39 @@
+name: Update Docker Tables
+
+on: [pull_request]
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-tables:
+    name: Update Docker Tables
+    runs-on: ubuntu-22.04
+    steps:
+      - id: checkout
+        uses: actions/checkout@v3
+        name: Checkout Repo
+        with:
+          ref: ${{ github.head_ref }}
+      - id: make-germline-table
+        name: Make Docker Table for Germline Workflow
+        run: |
+          python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_consensus.md workflows/kfdrc-germline-snv-annot-workflow.cwl
+      - id: make-somatic-table
+        name: Make Docker Table for Somatic Workflow
+        run: |
+          python .github/scripts/workflow_to_docker_table.py --output_file docs/dockers_somatic.md workflows/kfdrc-somatic-snv-annot-workflow.cwl
+      - id: cpr
+        name: Create Pull Request
+        uses: peter-evans/create-pull-request@v5
+        with:
+          commit-message: update docker table
+          title: Update Production WF Docker Tables
+          body: |
+            Automated changes by [create-pull-request](https://github.com/peter-evans/create-pull-request) GitHub action.
+
+            Docker tables for production workflows now have most up-to-date and complete list of Dockers.
+          delete-branch: true
+          branch: ${{ github.head_ref }}-adjust-dockers
+          labels: bix-dev