From c41856376141e5f0d5949915f36a9fbaf814af76 Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Wed, 3 Apr 2024 15:03:06 +0200
Subject: [PATCH] update markdown function to modify articles
---
.../df-wiki-cli/df_wiki_cli/content/main.py | 46 +++++++++++++++----
1 file changed, 38 insertions(+), 8 deletions(-)
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 19e39629..086f6db1 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -506,16 +506,46 @@ def markdown(
# with open(dst, "w") as tmp_f:
dst = Path(tmp_path)
dst.write_bytes(file.read_bytes())
+ # check if article has ## Structure, ## Experimental Validation, ## Distribution of the system among prokaryotes
with open(dst, "r+") as f:
- new_f = re.sub(
- r"##\s+Structure\n.*##\s+Experimental\s+validation",
- "## Structure\n\n::article-structure\n::\n\n## Experimental validation",
- f.read(),
- flags=re.DOTALL,
- )
- with open(file, "w") as f_out:
- f_out.write(new_f)
+
+ all_file = f.read()
+
+ if (
+ re.search(
+ r"#{2}\s+Structure",
+ all_file,
+ flags=re.IGNORECASE | re.MULTILINE,
+ )
+ and re.search(
+ r"#{2}\s+Experimental\s+validation",
+ all_file,
+ flags=re.IGNORECASE | re.MULTILINE,
+ )
+ and re.search(
+ r"#{2}\s+Distribution\s+of\s+the\s+system\s+among\s+prokaryotes",
+ all_file,
+ flags=re.IGNORECASE | re.MULTILINE,
+ )
+ ):
+
+ new_f_str = re.sub(
+ r"#{2}\s+Structure.*?#{2}\s+Experimental\s+validation",
+ "## Structure\n\n### pDockQ matrix\n\n::pdockq-matrix\n::\n\n### List predicted structures\n\n::article-structure\n::\n\n## Experimental validation",
+ all_file,
+ flags=re.DOTALL | re.IGNORECASE,
+ )
+ new_f = re.sub(
+ r"#{2}\s+Distribution\s+of\s+the\s+system\s+among\s+prokaryotes.*?#{2}\s+Structure",
+ "## Distribution of the system among prokaryotes\n\n::article-system-distribution-plot\n::\n\n## Structure",
+ new_f_str,
+ flags=re.DOTALL | re.IGNORECASE,
+ )
+ with open(file, "w") as f_out:
+ f_out.write(new_f)
+ else:
+ console.log(f"[bold red]check it manually")
def remove_version(assembly):
--
GitLab