Fix: Wrong pfam format

packages/df-wiki-cli/df_wiki_cli/content/main.py

@@ -178,7 +178,7 @@ def systems(
     with open(pfam, "r") as pf:
         pfam_df = pd.read_csv(pf, index_col="AC", keep_default_na=False)
         systems = []
-        if (output.exists()):
+        if output.exists():
             output.unlink()
         with open(output, "a") as ty:
             for file in dir.iterdir():
@@ -188,8 +188,8 @@ def systems(
                         metadata, _ = frontmatter.parse(f.read())
                         del metadata["layout"]
                         sanitizedMetadata = {**metadata}
-                        if "tableColumns" in metadata:
-                            table_data = metadata["tableColumns"]
+                        if "tableColumns" in sanitizedMetadata:
+                            table_data = sanitizedMetadata["tableColumns"]
                             if "PFAM" in table_data:
                                 pfams_list = [
                                     pfam.strip()
@@ -204,7 +204,6 @@ def systems(
                                         pfam_to_dict[pfam]["AC"] = pfam
                                         flatten_value = pfam_to_dict[pfam]
                                         pfam_metadata.append(flatten_value)
-
                                     except KeyError as err:
                                         console.print(f"[bold red]{err}", style="red")
                                         console.print(
@@ -215,14 +214,16 @@ def systems(
                                 sanitizedMetadata["PFAM"] = pfam_metadata
 
                             if "article" in table_data:
-                                metadata["doi"] = table_data["article"]["doi"]
+                                sanitizedMetadata["doi"] = table_data["article"]["doi"]
                                 if "abstract" in table_data["article"]:
-                                    metadata["abstract"] = table_data["article"][
+                                    sanitizedMetadata["abstract"] = table_data["article"][
                                         "abstract"
                                     ]
                                 del table_data["article"]
-                            del metadata["tableColumns"]
-                            sanitizedMetadata = {**metadata, **table_data}
+                            if "PFAM" in table_data:
+                                del table_data["PFAM"]
+                            del sanitizedMetadata["tableColumns"]
+                            sanitizedMetadata = {**sanitizedMetadata, **table_data}
                             systems.append(sanitizedMetadata)
 
             json_object = json.dumps(systems, indent=2)