Remove unnecesary parameters like name and id from all the report components to simplify the config file. Also, description and caption were set as opational params and id is generated internally. All class constructors updated with these changes

Author: sayalaruano

report_metadata_micw2graph.yaml

@@ -1,6 +1,4 @@
 report:
-  id: 1213412
-  name: "MicW2Graph"
   title: "MicW2Graph"
   description: >
     Wastewater treatment (WWT) is the process of removing contaminants from used water before it is discharged back 
@@ -13,154 +11,88 @@ report:
     and potential ecological functions.
   graphical_abstract: "example_data/MicW2Graph/Methods_MicW2Graph.png"
   logo: "example_data/mona_logo.png"
-  report_type: "streamlit"
-  report_format: ""
+  report_type: "document"
+  report_format: "html"
 sections:
-  - id: 21324
-    name: "Exploratory Data analysis"
-    title: "Exploratory Data analysis"
-    description: ""
+  - title: "Exploratory Data Analysis"
     subsections:
-      - id: 5001
-        name: "Abundance data"
-        title: "Abundance data"
-        description: ""
+      - title: "Abundance data"
+        description: "Optional description"
         components:
-          - id: 3423
-            name: "plotly_plot1"
+          - title: "Top 5 species by biome (plotly)"
             component_type: "plot"
             plot_type: "interactive"
             file_path: "example_data/MicW2Graph/top_species_plot_biome.json"
             int_visualization_tool: "plotly"
-            title: "Top 5 species by biome (plotly)"
-            caption: ""
-          - id: 3350
-            name: "altair_plot1"
+            caption: "Optional caption"
+          - title: "Multiline plot (altair)"
             component_type: "plot"
             plot_type: "interactive"
             file_path: "example_data/altair_multilineplot.json"
             int_visualization_tool: "altair"
-            title: "Multiline plot (altair)"
-            caption: ""
-          - id: 3358
-            name: "df1"
+          - title: "Abundance data for all studies (csv)"
             component_type: "dataframe"
             file_path: "example_data/MicW2Graph/abundance_data_allbiomes.csv"
             file_format: "csv"
             delimiter: ","
-            title: "Abundance data for all studies (csv)"
-            caption: ""
-          - id: 3358
-            name: "df2"
+          - title: "Abundance data for all studies (excel)"
             component_type: "dataframe"
             file_path: "example_data/MicW2Graph/abundance_data_allbiomes.xls"
             file_format: "excel"
             delimiter: ","
-            title: "Abundance data for all studies (excel)"
-            caption: ""
-      - id: 5002
-        name: "Sample data"
-        title: "Sample data"
-        description: ""
+      - title: "Sample data"
         components:
-          - id: 3324
-            name: "png_plot1"
+          - title: "Number of samples per study (png)"
             component_type: "plot"
             plot_type: "static"
             file_path: "example_data/MicW2Graph/number_samples_per_study.png"
-            title: "Number of samples per study (png)"
-            caption: ""
-          - id: 3323
-            name: "plotly_plot2"
+          - title: "Sampling countries for all studies (plotly)"
             component_type: "plot"
             plot_type: "interactive"
             file_path: "example_data/MicW2Graph/pie_plot_countries.json"
             int_visualization_tool: "plotly"
-            title: "Sampling countries for all studies (plotly)"
-            caption: ""
-          - id: 24324
-            name: "df3"
+          - title: "Sample data for all studies (txt)"
             component_type: "dataframe"
             file_path: "example_data/MicW2Graph/sample_info_allbiomes.txt"
             file_format: "txt"
-            title: "Sample data for all studies (txt)"
-            caption: ""
-          - id: 24324
-            name: "df4"
+          - title: "Sample data for all studies (parquet)"
             component_type: "dataframe"
             file_path: "example_data/MicW2Graph/sample_info_allbiomes.parquet"
             file_format: "parquet"
-            title: "Sample data for all studies (parquet)"
-            caption: ""
-      - id: 5003
-        name: "Extra information"
-        title: "Extra information"
-        description: ""
+      - title: "Extra information"
         components:
-          - id: 3358
-            name: "md1"
+          - title: "Markdown example"
             component_type: "markdown"
             file_path: "example_data/test_md.md"
-            title: "Markdown example"
-            caption: "This is a markdown example"
-  - id: 24324
-    name: "Microbial Association Networks"
-    title: "Microbial Association Networks"
-    description: ""
+  - title: "Microbial Association Networks"
     subsections:
-      - id: 5003
-        name: "Network Visualization1"
-        title: "Network Visualization1"
-        description: ""
+      - title: "Network Visualization1"
         components:
-          - id: 2247
-            name: "network1"
+          - title: "Network1 (graphml)"
             component_type: "plot"
             plot_type: "interactive"
             int_visualization_tool: "pyvis"
             file_path: "example_data/MicW2Graph/man_example.graphml"
-            title: "Network1 (graphml)"
-            caption: ""
-      - id: 5003
-        name: "Network Visualization2"
-        title: "Network Visualization2"
-        description: ""
+      - title: "Network Visualization2"
         components:
-          - id: 2240
-            name: "network2"
+          - title: "Network2 (edge list csv)"
             component_type: "plot"
             plot_type: "interactive"
             int_visualization_tool: "pyvis"
             csv_network_format: "edgelist"
             file_path: "example_data/MicW2Graph/man_example.csv"
-            title: "Network2 (edge list csv)"
-            caption: ""
-      - id: 5004
-        name: "Edge list"
-        title: "Edge list"
-        description: ""
+      - title: "Edge list"
         components:
-          - id: 3358
-            name: "df5"
+          - title: "Edge list (csv)"
             component_type: "dataframe"
             file_path: "example_data/MicW2Graph/man_example.csv"
             file_format: "csv"
             delimiter: ","
-            title: "Edge list (csv)"
             caption: "This is the edge list of the network"
-  - id: 2436
-    name: "APICall test"
-    title: "APICall test"
-    description: ""
+  - title: "APICall test"
     subsections:
-      - id: 5031
-        name: "Simple test"
-        title: "Simple test"
-        description: ""
+      - title: "Simple test"
         components:
-          - id: 2987
-            name: "APIcall_test"
+          - title: "APICall test"
             component_type: "apicall"
             api_url: "https://jsonplaceholder.typicode.com/todos/1"
-            title: "APICall test"
-            caption: ""

vuegen/main.py

@@ -4,13 +4,13 @@
 if __name__ == '__main__':
     # Load the YAML configuration file with the report metadata
     config_path = "report_metadata_micw2graph.yaml"
-    report_metadata = load_yaml_config(config_path)
+    report_config = load_yaml_config(config_path)
 
     # Define logger suffix based on report engine, type and name
-    report_engine = "streamlit" 
-    report_type = report_metadata['report'].get('report_type')
-    report_format = report_metadata['report'].get('report_format')
-    report_name = report_metadata['report'].get('name')
+    report_engine = "quarto" 
+    report_type = report_config['report'].get('report_type')
+    report_format = report_config['report'].get('report_format')
+    report_name = report_config['report'].get('name')
     if report_engine == "streamlit": 
         logger_suffix = f"{report_engine}_report_{report_name}"
     else:
@@ -20,5 +20,5 @@
     logger = get_logger(f"{logger_suffix}")
 
     # Generate the report
-    report_generator.get_report(metadata=report_metadata, report_engine=report_engine, logger=logger)
+    report_generator.get_report(config = report_config, report_engine = report_engine, logger = logger)