Config generator from a directory

.gitignore

@@ -126,6 +126,4 @@ quarto_report/
 UML_diagrams/
 Graphical_abstract/
 docs/presentations/
-test.py
-vuegen/yaml_generator.py
-MicW2Graph_config.yaml
+test.py

example_data/MicW2Graph/MicW2Graph_config.yaml

@@ -0,0 +1,105 @@
+report:
+  title: Micw2Graph
+  description: ''
+  graphical_abstract: ''
+  logo: ''
+sections:
+- title: Exploratory Data Analysis
+  description: ''
+  subsections:
+  - title: Abundance Data
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: plotly
+      title: Top Species Plot Biome Plotly
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/1_top_species_plot_biome_plotly.json
+      description: ''
+    - component_type: plot
+      plot_type: altair
+      title: Multilineplot Altair
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/2_multilineplot_altair.json
+      description: ''
+    - component_type: dataframe
+      file_format: csv
+      delimiter: ','
+      title: Abundance Data Allbiomes
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/3_abundance_data_allbiomes.csv
+      description: ''
+    - component_type: dataframe
+      file_format: xls
+      title: Abundance Data Allbiomes
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/4_abundance_data_allbiomes.xls
+      description: ''
+  - title: Sample Data
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: plotly
+      title: Pie Plot Countries Plotly
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/1_pie_plot_countries_plotly.json
+      description: ''
+    - component_type: plot
+      plot_type: plotly
+      title: Pie Plots Biomes Plotly
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/2_pie_plots_biomes_plotly.json
+      description: ''
+    - component_type: plot
+      plot_type: static
+      title: Number Samples Per Study
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/3_number_samples_per_study.png
+      description: ''
+    - component_type: dataframe
+      file_format: parquet
+      title: Sample Info Allbiomes
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/4_sample_info_allbiomes.parquet
+      description: ''
+    - component_type: dataframe
+      file_format: txt
+      delimiter: \t
+      title: Sample Info Allbiomes
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/5_sample_info_allbiomes.txt
+      description: ''
+  - title: Extra Info
+    description: ''
+    components:
+    - component_type: markdown
+      title: Test Md
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/3_Extra_info/1_test_md.md
+      description: ''
+- title: Microbial Association Networks
+  description: ''
+  subsections:
+  - title: Network Visualization1
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: interactive_network
+      title: Man Example
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/1_man_example.graphml
+      description: ''
+  - title: Network Visualization2
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: interactive_network
+      csv_network_format: edgelist
+      title: Man Example Edgelist
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example_edgelist.csv
+      description: ''
+  - title: Network Visualization3
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: interactive_network
+      title: Man Example
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/3_Network_visualization3/1_man_example.cyjs
+      description: ''
+  - title: Network Visualization4
+    description: ''
+    components:
+    - component_type: plot
+      plot_type: interactive_network
+      title: Ckg Network
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/4_Network_visualization4/1_ckg_network.html
+      description: ''

vuegen/config_manager.py

@@ -1,3 +1,7 @@
+import os
+from pathlib import Path
+from typing import Dict, List, Union, Tuple
+
 from . import report as r
 from .utils import assert_enum_value, get_logger
 
@@ -17,6 +21,261 @@ def __init__(self, logger=None):
         """
         self.logger = logger or get_logger("report")
 
+    def _create_title_fromdir(self, file_dirname: str) -> str:
+        """
+        Infers title from a file or directory, removing leading numeric prefixes.
+
+        Parameters
+        ----------
+        file_dirname : str
+            The file or directory name to infer the title from.
+
+        Returns
+        -------
+        str
+            A title generated from the file or directory name.
+        """
+        # Remove leading numbers and underscores if they exist
+        name = os.path.splitext(file_dirname)[0]
+        parts = name.split("_", 1)
+        title = parts[1] if parts[0].isdigit() and len(parts) > 1 else name
+        return title.replace("_", " ").title()
+
+    def _create_component_config_fromfile(self, file_path: Path) -> Dict[str, str]:
+        """
+        Infers a component config from a file, including component type, plot type, and additional fields.
+
+        Parameters
+        ----------
+        file_path : Path
+            The file path to analyze.
+
+        Returns
+        -------
+        component_config : Dict[str, str]
+            A dictionary containing inferred component configuration.
+        """
+        file_ext = file_path.suffix.lower()
+        component_config = {}
+
+        # Infer component config
+        if file_ext in [r.DataFrameFormat.CSV.value_with_dot, r.DataFrameFormat.TXT.value_with_dot]:
+            # Check for CSVNetworkFormat keywords
+            if "edgelist" in file_path.stem.lower():
+                component_config["component_type"] = r.ComponentType.PLOT.value
+                component_config["plot_type"] = r.PlotType.INTERACTIVE_NETWORK.value
+                component_config ["csv_network_format"] = r.CSVNetworkFormat.EDGELIST.value
+            elif "adjlist" in file_path.stem.lower():
+                component_config ["component_type"] = r.ComponentType.PLOT.value
+                component_config ["plot_type"] = r.PlotType.INTERACTIVE_NETWORK.value
+                component_config ["csv_network_format"] = r.CSVNetworkFormat.ADJLIST.value
+            # Fill the config with dataframe content
+            else:
+                component_config ["component_type"] = r.ComponentType.DATAFRAME.value
+                component_config ["file_format"] = r.DataFrameFormat.CSV.value if file_ext == r.DataFrameFormat.CSV.value_with_dot else r.DataFrameFormat.TXT.value
+                component_config ["delimiter"] = "," if file_ext == r.DataFrameFormat.CSV.value_with_dot else "\\t"
+        # Check other DataframeFormats than csv and txt
+        elif file_ext in [fmt.value_with_dot for fmt in r.DataFrameFormat if fmt not in [r.DataFrameFormat.CSV, r.DataFrameFormat.TXT]]:
+            component_config ["component_type"] = r.ComponentType.DATAFRAME.value
+            component_config ["file_format"] = next(fmt.value for fmt in r.DataFrameFormat if fmt.value_with_dot == file_ext)
+        # Check for network formats
+        elif file_ext in [fmt.value_with_dot for fmt in r.NetworkFormat]:
+            component_config ["component_type"] = r.ComponentType.PLOT.value
+            if file_ext in [
+                r.NetworkFormat.PNG.value_with_dot,
+                r.NetworkFormat.JPG.value_with_dot,
+                r.NetworkFormat.JPEG.value_with_dot,
+                r.NetworkFormat.SVG.value_with_dot,
+            ]:
+                component_config ["plot_type"] = r.PlotType.STATIC.value
+            else:
+                component_config ["plot_type"] = r.PlotType.INTERACTIVE_NETWORK.value
+        # Check for interactive plots 
+        elif file_ext == ".json":
+            component_config ["component_type"] = r.ComponentType.PLOT.value
+            if "plotly" in file_path.stem.lower():
+                component_config ["plot_type"] = r.PlotType.PLOTLY.value
+            elif "altair" in file_path.stem.lower():
+                component_config ["plot_type"] = r.PlotType.ALTAIR.value
+            else:
+                component_config ["plot_type"] = "unknown"
+        elif file_ext == ".md":
+            component_config ["component_type"] = r.ComponentType.MARKDOWN.value
+        else:
+            error_msg = (
+                f"Unsupported file extension: {file_ext}. "
+                f"Supported extensions include:\n"
+                f"  - Network formats: {', '.join(fmt.value_with_dot for fmt in r.NetworkFormat)}\n"
+                f"  - DataFrame formats: {', '.join(fmt.value_with_dot for fmt in r.DataFrameFormat)}"
+            )
+            #self.logger.error(error_msg)
+            raise ValueError(error_msg)
+
+        return component_config 
+
+    def _sort_paths_by_numprefix(self, paths: List[Path]) -> List[Path]:
+        """
+        Sorts a list of Paths by numeric prefixes in their names, placing non-numeric items at the end.
+
+        Parameters
+        ----------
+        paths : List[Path]
+            The list of Path objects to sort.
+
+        Returns
+        -------
+        List[Path]
+            The sorted list of Path objects.
+        """
+        def get_sort_key(path: Path) -> tuple:
+            parts = path.name.split("_", 1)
+            if parts[0].isdigit():
+                numeric_prefix = int(parts[0])
+            else:
+                # Non-numeric prefixes go to the end
+                numeric_prefix = float('inf')  
+            return numeric_prefix, path.name.lower()  
+
+        return sorted(paths, key=get_sort_key)
+
+    def _create_subsect_config_fromdir(self, subsection_dir_path: Path) -> Dict[str, Union[str, List[Dict]]]:
+        """
+        Creates subsection config from a directory.
+
+        Parameters
+        ----------
+        subsection_dir_path : Path
+            Path to the subsection directory.
+
+        Returns
+        -------
+        Dict[str, Union[str, List[Dict]]]
+            The subsection config.
+        """
+        subsection_config = {
+            "title": self._create_title_fromdir(subsection_dir_path.name),
+            "description": "",
+            "components": [],
+        }
+
+        # Sort files by number prefix
+        sorted_files = self._sort_paths_by_numprefix(list(subsection_dir_path.iterdir()))
+
+        for file in sorted_files:
+            if file.is_file():
+                component_config = self._create_component_config_fromfile(file)
+
+                # Ensure the file path is absolute
+                file_path = file.resolve()  
+
+                component_config_updt = {
+                    "title": self._create_title_fromdir(file.name),
+                    "file_path": str(file_path), 
+                    "description": "",
+                }
+
+                # Update inferred config information
+                component_config.update(component_config_updt)
+
+                subsection_config["components"].append(component_config)
+
+        return subsection_config
+
+    def _create_sect_config_fromdir(self, section_dir_path: Path) -> Dict[str, Union[str, List[Dict]]]:
+        """
+        Creates section config from a directory.
+
+        Parameters
+        ----------
+        section_dir_path : Path
+            Path to the section directory.
+
+        Returns
+        -------
+        Dict[str, Union[str, List[Dict]]]
+            The section config.
+        """
+        section_config = {
+            "title": self._create_title_fromdir(section_dir_path.name),
+            "description": "",
+            "subsections": [],
+        }
+
+        # Sort subsections by number prefix 
+        sorted_subsections = self._sort_paths_by_numprefix(list(section_dir_path.iterdir()))
+
+        for subsection_dir in sorted_subsections:
+            if subsection_dir.is_dir():
+                section_config["subsections"].append(self._create_subsect_config_fromdir(subsection_dir))
+
+        return section_config
+
+
+    def _resolve_base_dir(self, base_dir: str) -> Path:
+        """
+        Resolves the provided base directory to an absolute path from the root, accounting for relative paths.
+
+        Parameters
+        ----------
+        base_dir : str
+            The relative or absolute path to the base directory.
+
+        Returns
+        -------
+        Path
+            The absolute path to the base directory.
+        """
+        # Check if we are in a subdirectory and need to go up one level
+        project_dir = Path(__file__).resolve().parents[1]
+
+        # If the base_dir is a relative path, resolve it from the project root
+        base_dir_path = project_dir / base_dir
+
+        # Make sure the resolved base directory exists
+        if not base_dir_path.is_dir():
+            raise ValueError(f"Base directory '{base_dir}' does not exist or is not a directory.")
+
+        return base_dir_path
+
+
+    def create_yamlconfig_fromdir(self, base_dir: str) -> Tuple[Dict[str, Union[str, List[Dict]]], Path]:
+        """
+        Generates a YAML-compatible config file from a directory. It also returns the resolved folder path.
+
+        Parameters
+        ----------
+        base_dir : str
+            The base directory containing section and subsection folders.
+
+        Returns
+        -------
+        Tuple[Dict[str, Union[str, List[Dict]]], Path]
+            The YAML config and the resolved directory path.
+        """
+        # Get absolute path from base directory
+        base_dir_path = self._resolve_base_dir(base_dir)
+
+        # Generate the YAML config
+        yaml_config = {
+            "report": {
+                "title": self._create_title_fromdir(base_dir_path.name),
+                "description": "",
+                "graphical_abstract": "",
+                "logo": "",
+            },
+            "sections": [],
+        }
+
+        # Sort sections by their number prefix
+        sorted_sections = self._sort_paths_by_numprefix(list(base_dir_path.iterdir()))
+
+        # Generate sections and subsections config 
+        for section_dir in sorted_sections:
+            if section_dir.is_dir():
+                yaml_config["sections"].append(self._create_sect_config_fromdir(section_dir))
+
+        return yaml_config, base_dir_path
+
     def initialize_report(self, config: dict) -> tuple[r.Report, dict]:
         """
         Extracts report metadata from a YAML config file and returns a Report object and the raw metadata.