✨ Feat: Allow to read project, section, and subsection descriptions from a md file when creating streamlit and quarto reports from a directory

Author: sayalaruano

docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/description.md

@@ -0,0 +1 @@
+Optional description for section.

docs/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/description.md

@@ -0,0 +1 @@
+Optional description for subsection.

docs/example_data/MicW2Graph/MicW2Graph_config.yaml

@@ -1,14 +1,28 @@
 report:
   title: Micw2Graph
-  description: ''
+  description: 'Wastewater treatment (WWT) is the process of removing contaminants
+    from used water before it is discharged back into the environment, which contributes
+    to address water scarcity and to protect aquatic ecosystems. In this project,
+    we investigated the microbiome of WWT to build MicW2Graph, an open-source knowledge
+    graph (KG) that integrates metagenomic and metatranscriptomic information with
+    their biological context, including biological processes, environmental and phenotypic
+    features, chemical compounds, and additional metadata. We developed a workflow
+    to collect meta-omics datasets from MGnify and infer potential interactions among
+    microorganisms through microbial association networks (MANs). MicW2Graph enables
+    the investigation of research questions related to WWT, focusing on aspects such
+    as microbial connections, community memberships, and potential ecological functions.
+
+    '
   graphical_abstract: ''
   logo: ''
 sections:
 - title: Exploratory Data Analysis
   description: ''
   subsections:
   - title: Abundance Data
-    description: ''
+    description: 'Optional description for section.
+
+      '
     components:
     - component_type: plot
       plot_type: plotly
@@ -31,6 +45,10 @@ sections:
       title: Abundance Data Allbiomes
       file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/4_abundance_data_allbiomes.xls
       description: ''
+    - component_type: markdown
+      title: Description
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/description.md
+      description: ''
   - title: Sample Data
     description: ''
     components:
@@ -75,13 +93,19 @@ sections:
   description: ''
   subsections:
   - title: Network Visualization1
-    description: ''
+    description: 'Optional description for subsection.
+
+      '
     components:
     - component_type: plot
       plot_type: interactive_network
       title: Man Example
       file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/1_man_example.graphml
       description: ''
+    - component_type: markdown
+      title: Description
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/description.md
+      description: ''
   - title: Network Visualization2
     description: ''
     components:

docs/example_data/MicW2Graph/description.md

@@ -0,0 +1 @@
+Wastewater treatment (WWT) is the process of removing contaminants from used water before it is discharged back into the environment, which contributes to address water scarcity and to protect aquatic ecosystems. In this project, we investigated the microbiome of WWT to build MicW2Graph, an open-source knowledge graph (KG) that integrates metagenomic and metatranscriptomic information with their biological context, including biological processes, environmental and phenotypic features, chemical compounds, and additional metadata. We developed a workflow to collect meta-omics datasets from MGnify and infer potential interactions among microorganisms through microbial association networks (MANs). MicW2Graph enables the investigation of research questions related to WWT, focusing on aspects such as microbial connections, community memberships, and potential ecological functions.

vuegen/config_manager.py

@@ -143,6 +143,25 @@ def get_sort_key(path: Path) -> tuple:
             return numeric_prefix, path.name.lower()  
 
         return sorted(paths, key=get_sort_key)
+    
+    def _read_description_file(self, folder_path: Path) -> str:
+        """
+        Reads the content of a description.md file if it exists in the given folder.
+        
+        Parameters
+        ----------
+        folder_path : Path
+            Path to the folder where description.md might be located.
+        
+        Returns
+        -------
+        str
+            Content of the description.md file if found, otherwise an empty string.
+        """
+        description_file = folder_path / "description.md"
+        if description_file.exists():
+            return f"{description_file.read_text().strip().replace('\n', '\n  ')}\n"
+        return ""
 
     def _create_subsect_config_fromdir(self, subsection_dir_path: Path) -> Dict[str, Union[str, List[Dict]]]:
         """
@@ -160,7 +179,7 @@ def _create_subsect_config_fromdir(self, subsection_dir_path: Path) -> Dict[str,
         """
         subsection_config = {
             "title": self._create_title_fromdir(subsection_dir_path.name),
-            "description": "",
+            "description": self._read_description_file(subsection_dir_path),
             "components": [],
         }
 
@@ -206,7 +225,7 @@ def _create_sect_config_fromdir(self, section_dir_path: Path) -> Dict[str, Union
         """
         section_config = {
             "title": self._create_title_fromdir(section_dir_path.name),
-            "description": "",
+            "description": self._read_description_file(section_dir_path),
             "subsections": [],
         }
 
@@ -240,7 +259,7 @@ def create_yamlconfig_fromdir(self, base_dir: str) -> Tuple[Dict[str, Union[str,
         yaml_config = {
             "report": {
                 "title": self._create_title_fromdir(base_dir_path.name),
-                "description": "",
+                "description": self._read_description_file(base_dir_path),
                 "graphical_abstract": "",
                 "logo": "",
             },

vuegen/quarto_reportview.py

@@ -239,7 +239,7 @@ def _generate_subsection(self, subsection, is_report_static, is_report_revealjs)
                 subsection_content.extend(self._generate_plot_content(component, is_report_static))
             elif component.component_type == r.ComponentType.DATAFRAME:
                 subsection_content.extend(self._generate_dataframe_content(component, is_report_static))
-            elif component.component_type == r.ComponentType.MARKDOWN:
+            elif component.component_type == r.ComponentType.MARKDOWN and component.title.lower() != "description":
                 subsection_content.extend(self._generate_markdown_content(component))
             elif component.component_type == r.ComponentType.HTML and not is_report_static:
                 subsection_content.extend(self._generate_html_content(component))

vuegen/streamlit_reportview.py

@@ -296,7 +296,8 @@ def _generate_subsection(self, subsection) -> tuple[List[str], List[str]]:
                 subsection_content.extend(self._generate_plot_content(component))
             elif component.component_type == r.ComponentType.DATAFRAME:
                 subsection_content.extend(self._generate_dataframe_content(component))
-            elif component.component_type == r.ComponentType.MARKDOWN:
+            # If md files is called "description.md", do not include it in the report
+            elif component.component_type == r.ComponentType.MARKDOWN and component.title.lower() != "description":
                 subsection_content.extend(self._generate_markdown_content(component))
             elif component.component_type == r.ComponentType.HTML:
                 subsection_content.extend(self._generate_html_content(component))