Merge pull request #35 from Multiomics-Analytics-Group/st-autorun

St autorun argument and updated README

Author: sayalaruano

README.md

@@ -44,9 +44,9 @@ pip install -e path/to/vuegen # specify location
 pip install -e . # in case you pwd is in the vuegen directory
 ```
 
-### Quatro installation
+### Quarto installation
 
-Install quatro with vueguen if you don't have it globally installed.
+Install quarto with vueguen if you don't have it globally installed.
 
 ```bash
 pip install -e ".[quarto]" # specify location
@@ -65,12 +65,20 @@ Test your quarto installation by running the following command:
 quarto check
 ```
 
-
 ## Execution
 
+Run VueGen using a configuration file with the following command:
+
+```bash
+python vuegen/main.py --config docs/example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
+```
+
+By default, the `streamlit_autorun` argument is set to False, but you can use it in case you want to automatically run the streamlit app.
+
+It's also possible to provide a directory instead of a configuration file:
+
 ```bash
-cd docs
-python vuegen/main.py --config example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
+python vuegen/main.py --directory docs/example_data/MicW2Graph/ --report_type streamlit
 ```
 
 The current report types are streamlit, html, pdf, docx, odt, revealjs, pptx, and jupyter.

docs/example_data/MicW2Graph/MicW2Graph_config.yaml

@@ -13,59 +13,59 @@ sections:
     - 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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      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: ''
   - 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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/1_Exploratory_Data_Analysis/3_Extra_info/1_test_md.md
       description: ''
 - title: Microbial Association Networks
   description: ''
@@ -76,7 +76,7 @@ sections:
     - 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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/1_man_example.graphml
       description: ''
   - title: Network Visualization2
     description: ''
@@ -85,21 +85,21 @@ sections:
       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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/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
+      file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/example_data/MicW2Graph/2_Microbial_Association_Networks/4_Network_visualization4/1_ckg_network.html
       description: ''

docs/images/vuegen_logo.png

@@ -211,7 +211,6 @@ def _create_sect_config_fromdir(self, section_dir_path: Path) -> Dict[str, Union
 
         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.
@@ -234,11 +233,10 @@ def _resolve_base_dir(self, base_dir: str) -> Path:
 
         # 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.")
+            raise ValueError(f"Base directory '{base_dir}' does not exist or is not a directory. {project_dir} {base_dir_path}")
 
         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.

docs/images/vuegen_logo.svg

@@ -7,12 +7,11 @@
     # Parse command-line arguments
     args = get_args(prog_name="VueGen")
 
-    # Determine the configuration file path or directory
+    # Determine the vuegen arguments
     config_path = args.config
     dir_path = args.directory
-
-    # Report type
     report_type = args.report_type
+    streamlit_autorun = args.streamlit_autorun
 
     # Determine the report name for logger suffix
     if config_path:
@@ -21,14 +20,14 @@
         report_name = Path(dir_path).name
 
     # Define logger suffix based on report type and name
-    logger_suffix = f"{report_type}_report_{report_name}"
+    logger_suffix = f"{report_type}_report_{str(report_name)}"
 
     # Initialize logger
     logger = get_logger(f"{logger_suffix}")
 
     # Generate the report
-    report_generator.get_report(config_path = config_path,
+    report_generator.get_report(report_type = report_type, 
+                                logger = logger,
+                                config_path = config_path,
                                 dir_path = dir_path,
-                                report_type = report_type, 
-                                logger = logger)
-
+                                streamlit_autorun = streamlit_autorun)

vuegen/config_manager.py

@@ -1,6 +1,7 @@
 import os
 import subprocess
 from typing import List
+from pathlib import Path
 
 import networkx as nx
 import pandas as pd
@@ -498,18 +499,15 @@ def _generate_image_content(self, image_path: str, alt_text: str = "", width: in
         Returns
         -------
         str
-            The formatted HTML image content.
+            The formatted image content.
         """
         if is_url(image_path):
             src = image_path
         else:
-            src = os.path.abspath(image_path)
+            src = Path(image_path).resolve()
 
-        # Return the HTML content
-        return f"""
-<div style="text-align: center;">
-<img src="{src}" alt="{alt_text}" width="{width}" height="{height}" />
-</div>\n"""
+        # Return the image content
+        return f"""![](/{src}){{fig-alt={alt_text} width={width} height={height}}}\n"""
 
     def _show_dataframe(self, dataframe, is_report_static, static_dir: str = STATIC_FILES_DIR) -> List[str]:
         """

vuegen/main.py

@@ -7,7 +7,7 @@
 from .utils import assert_enum_value, load_yaml_config, write_yaml_config
 
 
-def get_report(report_type: str, logger: logging.Logger, config_path: str = None, dir_path: str = None) -> None:
+def get_report(report_type: str, logger: logging.Logger, config_path: str = None, dir_path: str = None, streamlit_autorun: bool = False) -> None:
     """
     Generate and run a report based on the specified engine.
 
@@ -21,6 +21,8 @@ def get_report(report_type: str, logger: logging.Logger, config_path: str = None
         Path to the YAML configuration file.
     dir_path : str, optional
         Path to the directory from which to generate the configuration file.
+    streamlit_autorun : bool, optional
+        Whether to automatically run the Streamlit report after generation (default is False).
 
     Raises
     ------
@@ -47,16 +49,17 @@ def get_report(report_type: str, logger: logging.Logger, config_path: str = None
     # Create and run ReportView object based on its type
     if report_type == ReportType.STREAMLIT:
         st_report = StreamlitReportView(
-            report=report,
-            report_type=report_type
+            report = report,
+            report_type = report_type,
+            streamlit_autorun = streamlit_autorun
         )
         st_report.generate_report()
         st_report.run_report()
 
     else:
         quarto_report = QuartoReportView(
-            report=report,
-            report_type=report_type
+            report = report,
+            report_type = report_type
         )
         quarto_report.generate_report()
         quarto_report.run_report()

vuegen/quarto_reportview.py

@@ -18,8 +18,9 @@ class StreamlitReportView(r.WebAppReportView):
     STATIC_FILES_DIR = os.path.join(BASE_DIR, 'static')
     REPORT_MANAG_SCRIPT = 'report_manager.py'
 
-    def __init__(self, report: r.Report, report_type: r.ReportType):
+    def __init__(self, report: r.Report, report_type: r.ReportType, streamlit_autorun: bool = False):
         super().__init__(report = report, report_type = report_type)
+        self.streamlit_autorun = streamlit_autorun
 
     def generate_report(self, output_dir: str = SECTIONS_DIR, static_dir: str = STATIC_FILES_DIR) -> None:
         """
@@ -113,14 +114,20 @@ def run_report(self, output_dir: str = SECTIONS_DIR) -> None:
         output_dir : str, optional
             The folder where the report was generated (default is SECTIONS_DIR).
         """
-        self.report.logger.info(f"Running '{self.report.title}' {self.report_type} report.")
-        try:
-            subprocess.run(["streamlit", "run", os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)], check=True)
-        except KeyboardInterrupt:
-            print("Streamlit process interrupted.")
-        except subprocess.CalledProcessError as e:
-            self.report.logger.error(f"Error running Streamlit report: {str(e)}")
-            raise
+        if self.streamlit_autorun:
+            self.report.logger.info(f"Running '{self.report.title}' {self.report_type} report.")
+            try:
+                subprocess.run(["streamlit", "run", os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)], check=True)
+            except KeyboardInterrupt:
+                print("Streamlit process interrupted.")
+            except subprocess.CalledProcessError as e:
+                self.report.logger.error(f"Error running Streamlit report: {str(e)}")
+                raise
+        else:
+            # If autorun is False, print instructions for manual execution
+            self.report.logger.info(f"All the scripts to build the Streamlit app are available at {output_dir}")
+            self.report.logger.info(f"To run the Streamlit app, use the following command:")
+            self.report.logger.info(f"streamlit run {os.path.join(output_dir, self.REPORT_MANAG_SCRIPT)}")             
 
     def _format_text(self, text: str, type: str, level: int = 1, color: str = '#000000', text_align: str = 'center') -> str:
         """

vuegen/report_generator.py

@@ -185,16 +185,23 @@ def get_args(prog_name: str, others: dict = {}) -> argparse.Namespace:
     parser.add_argument(
         "-dir",
         "--directory",
-        type=str,
-        default=None,
-        help="Path to the directory from which the YAML config will be inferred."
+        type = str,
+        default = None,
+        help = "Path to the directory from which the YAML config will be inferred."
     )
     parser.add_argument(
         "-rt",
         "--report_type",
-        type=str,
-        default='streamlit', # this is not a valid default
-        help="Type of the report to generate (streamlit, html, pdf, docx, odt, revealjs, pptx, or jupyter)."
+        type = str,
+        default = None, 
+        help = "Type of the report to generate (streamlit, html, pdf, docx, odt, revealjs, pptx, or jupyter)."
+    )
+    parser.add_argument(
+        "-st_autorun", 
+        "--streamlit_autorun",
+        action = "store_true",  # Automatically sets True if the flag is passed
+        default = False,
+        help = "Automatically run the Streamlit app after report generation."
     )
 
     # Parse arguments