From b42d0716a230e0f358f6d4080cedcbc79473e0d1 Mon Sep 17 00:00:00 2001
From: paulzierep <paul.zierep@googlemail.com>
Date: Thu, 7 Nov 2024 16:38:59 +0100
Subject: [PATCH] test

---
 communities/microgalaxy/lab/base.yml          |  2 +-
 .../microgalaxy/lab/sections/5_tools.yml      |  9 +--
 .../resources/.~lock.curated_tools.tsv#       |  1 +
 sources/bin/populate_labs.py                  | 70 +++++++++++++++++++
 4 files changed, 74 insertions(+), 8 deletions(-)
 create mode 100644 communities/microgalaxy/resources/.~lock.curated_tools.tsv#
 create mode 100644 sources/bin/populate_labs.py

diff --git a/communities/microgalaxy/lab/base.yml b/communities/microgalaxy/lab/base.yml
index 5a1f1be7..f48401be 100644
--- a/communities/microgalaxy/lab/base.yml
+++ b/communities/microgalaxy/lab/base.yml
@@ -64,6 +64,6 @@ sections:
   - sections/1_beginner.yml
   - sections/3_advanced.yml
   - sections/4_community.yml
-  # - sections/5_tools.yml
+  - sections/5_tools.yml
 
 # -----------------------------------------------------------------------------
diff --git a/communities/microgalaxy/lab/sections/5_tools.yml b/communities/microgalaxy/lab/sections/5_tools.yml
index 11a75ac8..323d36c2 100644
--- a/communities/microgalaxy/lab/sections/5_tools.yml
+++ b/communities/microgalaxy/lab/sections/5_tools.yml
@@ -5,10 +5,5 @@ tabs:
   title: List of community curated tools available for microGalaxy
   content:
   - title_md: PAMPA
-    description_md: Tools to compute and analyse biodiversity metrics
-  - title_md: TreeBest
-    description_md: TreeBeST best
-  - title_md: abacas
-    description_md: Order and Orientate Contigs
-  - title_md: abricate
-    description_md: Mass screening of contigs for antiobiotic resistance genes
+    description_md: >
+      Tools to compute and analyse biodiversity metrics
diff --git a/communities/microgalaxy/resources/.~lock.curated_tools.tsv# b/communities/microgalaxy/resources/.~lock.curated_tools.tsv#
new file mode 100644
index 00000000..b540fde2
--- /dev/null
+++ b/communities/microgalaxy/resources/.~lock.curated_tools.tsv#
@@ -0,0 +1 @@
+,paul,paul-LIFEBOOK-U7410,07.11.2024 12:25,file:///home/paul/.config/libreoffice/4;
\ No newline at end of file
diff --git a/sources/bin/populate_labs.py b/sources/bin/populate_labs.py
new file mode 100644
index 00000000..6e28ce12
--- /dev/null
+++ b/sources/bin/populate_labs.py
@@ -0,0 +1,70 @@
+import argparse
+import os
+from typing import List
+
+import oyaml as yaml
+import pandas as pd
+
+# import yaml
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Create community tools.yml from tool.tsv.")
+
+    # Adding positional arguments with short options
+    parser.add_argument(
+        "-c", "--tool_tsv", type=str, required=True, help="Path to the TSV file (e.g., curated_tools.tsv)"
+    )
+    parser.add_argument(
+        "-y", "--tool_yml", type=str, required=True, help="Path to the output YAML file (e.g., tools.yml)"
+    )
+
+    args = parser.parse_args()
+
+    # Check if the tool TSV file exists
+    if not os.path.exists(args.tool_tsv):
+        print(f"Error: The file '{args.tool_tsv}' does not exist.")
+        return
+
+    try:
+        # Read the TSV file with pandas (use tab delimiter)
+        data = pd.read_csv(args.tool_tsv, sep="\t")
+
+        # Construct the YAML data structure
+        yaml_data = {
+            "id": "tools",
+            "title": "Community Tools",
+            "tabs": [
+                {"id": "tool_list", "title": "List of community curated tools available for microGalaxy", "content": []}
+            ],
+        }
+
+        # Populate the content section with each row from the TSV
+        for _, row in data.iterrows():
+            # Use the first column (assumed to be the tool title) as the title_md
+            title_md = row[data.columns[0]]  # Get the first column's value as title_md
+
+            # Start the unordered list <ul> and construct each <li> for every other column in the row
+            description = row["Description"]
+            # for column in data.columns[1:]:  # Skip the first column (since it's title_md)
+            #     description += f"  <li>{column}: {row[column]}</li>\n"
+            # description += "</ul>"
+
+            # Create the tool entry with the formatted HTML list
+            tool_entry = {
+                "title_md": title_md,
+                "description_md": description,  # Directly insert the HTML string without escape sequences
+            }
+            yaml_data["tabs"][0]["content"].append(tool_entry)
+
+        # Write the YAML data to the output file
+        with open(args.tool_yml, "w") as yaml_file:
+            yaml.dump(yaml_data, yaml_file, default_flow_style=False, allow_unicode=True, indent=2)
+        print(f"Data successfully written to '{args.tool_yml}'")
+
+    except Exception as e:
+        print(f"An error occurred: {e}")
+
+
+if __name__ == "__main__":
+    main()