update markdown function to modify articles

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):