kkonganti@92: #!/usr/bin/env python
kkonganti@92: 
kkonganti@92: import sys
kkonganti@92: import yaml
kkonganti@92: from textwrap import dedent
kkonganti@92: 
kkonganti@92: def main() :
kkonganti@92:     """
kkonganti@92:     Takes a tab-delimited text file with a mandatory header
kkonganti@92:     column and generates an HTML table.
kkonganti@92:     """
kkonganti@92: 
kkonganti@92:     args = sys.argv
kkonganti@92:     if (len(args) < 2 or len(args) > 3):
kkonganti@92:         print(f"\nTwo CL arguments are required!\n")
kkonganti@92:         exit(1)
kkonganti@92: 
kkonganti@92:     table_sum_on = args[1].lower()
kkonganti@92:     workflow_name = args[2].lower()
kkonganti@92: 
kkonganti@92:     with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
kkonganti@92:         header = tbl.readline()
kkonganti@92:         header_cols = header.strip().split('\t')
kkonganti@92: 
kkonganti@92:         html = [
kkonganti@92:             dedent(
kkonganti@92:                 f"""<script type="text/javascript">
kkonganti@92:                     $(document).ready(function () {{
kkonganti@92:                         $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@92:                             scrollX: true,
kkonganti@92:                             fixedColumns: true, dom: 'Bfrtip',
kkonganti@92:                             buttons: [
kkonganti@92:                                 'copy',
kkonganti@92:                                 {{
kkonganti@92:                                     extend: 'print',
kkonganti@92:                                     title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@92:                                 }},
kkonganti@92:                                 {{
kkonganti@92:                                     extend: 'excel',
kkonganti@92:                                     filename: '{table_sum_on}_results',
kkonganti@92:                                 }},
kkonganti@92:                                 {{
kkonganti@92:                                     extend: 'csv',
kkonganti@92:                                     filename: '{table_sum_on}_results',
kkonganti@92:                                 }}
kkonganti@92:                             ]
kkonganti@92:                         }});
kkonganti@92:                     }});
kkonganti@92:                 </script>
kkonganti@92:                 <div class="table-responsive">
kkonganti@92:                 <style>
kkonganti@92:                 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@92:                     background-color: #f2f2f2;
kkonganti@92:                 }}
kkonganti@92:                 </style>
kkonganti@92:                 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@92:                 <thead>
kkonganti@92:                 <tr>"""
kkonganti@92:             )
kkonganti@92:         ]
kkonganti@92: 
kkonganti@92:         for header_col in header_cols:
kkonganti@92:             html.append(
kkonganti@92:                 dedent(
kkonganti@92:                     f"""
kkonganti@92:                         <th> {header_col} </th>"""
kkonganti@92:                 )
kkonganti@92:             )
kkonganti@92:         
kkonganti@92:         html.append(
kkonganti@92:             dedent(
kkonganti@92:                 """
kkonganti@92:                 </tr>
kkonganti@92:                 </thead>
kkonganti@92:                 <tbody>"""
kkonganti@92:             )
kkonganti@92:         )
kkonganti@92: 
kkonganti@92:         for row in tbl:
kkonganti@92:             html.append("<tr>\n")
kkonganti@92:             data_cols = row.strip().split('\t')
kkonganti@92:             if ( len(header_cols) != len(data_cols) ):
kkonganti@92:                 print(f"\nWARN: Number of header columns ({len(header_cols)}) and data " +
kkonganti@92:                     f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n")
kkonganti@92:                 if ( len(header_cols) > len(data_cols) ):
kkonganti@92:                     data_cols += (( len(header_cols) - len(data_cols) ) * ' ' )
kkonganti@92:                     print(len(data_cols))
kkonganti@92:                 else:
kkonganti@92:                     header_cols += (( len(data_cols) - len(header_cols) ) * ' ') 
kkonganti@92: 
kkonganti@92:             html.append(
kkonganti@92:                 dedent(
kkonganti@92:                     f"""
kkonganti@92:                         <td><samp>{data_cols[0]}</samp></td>
kkonganti@92:                     """
kkonganti@92:                 )
kkonganti@92:             )
kkonganti@92: 
kkonganti@92:             for data_col in data_cols[1:]:
kkonganti@92:                 html.append(
kkonganti@92:                     dedent(
kkonganti@92:                         f"""<td>{data_col}</td>
kkonganti@92:                         """
kkonganti@92:                     )
kkonganti@92:                 )
kkonganti@92:             html.append("</tr>\n")
kkonganti@92:         html.append("</tbody>\n")
kkonganti@92:         html.append("</table>\n")
kkonganti@92:         html.append("</div>\n")
kkonganti@92: 
kkonganti@92:         mqc_yaml = {
kkonganti@92:             "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@92:             "section_name": f"{table_sum_on.upper()}",
kkonganti@92:             "section_href": f"https://cfsan-git.fda.gov/Kranti.Konganti/{workflow_name}",
kkonganti@92:             "plot_type": "html",
kkonganti@92:             "description": "The results table shown here is a collection from all samples.",
kkonganti@92:             "data": ('').join(html),
kkonganti@92:         }
kkonganti@92: 
kkonganti@92:         with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@92:             yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@92: 
kkonganti@92: if __name__ == "__main__":
kkonganti@92:     main()