Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.3.0/bin/create_mqc_data_table.py @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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kkonganti@92 1 #!/usr/bin/env python
kkonganti@92 2
kkonganti@92 3 import sys
kkonganti@92 4 import yaml
kkonganti@92 5 from textwrap import dedent
kkonganti@92 6
kkonganti@92 7 def main() :
kkonganti@92 8 """
kkonganti@92 9 Takes a tab-delimited text file with a mandatory header
kkonganti@92 10 column and generates an HTML table.
kkonganti@92 11 """
kkonganti@92 12
kkonganti@92 13 args = sys.argv
kkonganti@92 14 if (len(args) < 2 or len(args) > 3):
kkonganti@92 15 print(f"\nTwo CL arguments are required!\n")
kkonganti@92 16 exit(1)
kkonganti@92 17
kkonganti@92 18 table_sum_on = args[1].lower()
kkonganti@92 19 workflow_name = args[2].lower()
kkonganti@92 20
kkonganti@92 21 with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
kkonganti@92 22 header = tbl.readline()
kkonganti@92 23 header_cols = header.strip().split('\t')
kkonganti@92 24
kkonganti@92 25 html = [
kkonganti@92 26 dedent(
kkonganti@92 27 f"""<script type="text/javascript">
kkonganti@92 28 $(document).ready(function () {{
kkonganti@92 29 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@92 30 scrollX: true,
kkonganti@92 31 fixedColumns: true, dom: 'Bfrtip',
kkonganti@92 32 buttons: [
kkonganti@92 33 'copy',
kkonganti@92 34 {{
kkonganti@92 35 extend: 'print',
kkonganti@92 36 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@92 37 }},
kkonganti@92 38 {{
kkonganti@92 39 extend: 'excel',
kkonganti@92 40 filename: '{table_sum_on}_results',
kkonganti@92 41 }},
kkonganti@92 42 {{
kkonganti@92 43 extend: 'csv',
kkonganti@92 44 filename: '{table_sum_on}_results',
kkonganti@92 45 }}
kkonganti@92 46 ]
kkonganti@92 47 }});
kkonganti@92 48 }});
kkonganti@92 49 </script>
kkonganti@92 50 <div class="table-responsive">
kkonganti@92 51 <style>
kkonganti@92 52 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@92 53 background-color: #f2f2f2;
kkonganti@92 54 }}
kkonganti@92 55 </style>
kkonganti@92 56 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@92 57 <thead>
kkonganti@92 58 <tr>"""
kkonganti@92 59 )
kkonganti@92 60 ]
kkonganti@92 61
kkonganti@92 62 for header_col in header_cols:
kkonganti@92 63 html.append(
kkonganti@92 64 dedent(
kkonganti@92 65 f"""
kkonganti@92 66 <th> {header_col} </th>"""
kkonganti@92 67 )
kkonganti@92 68 )
kkonganti@92 69
kkonganti@92 70 html.append(
kkonganti@92 71 dedent(
kkonganti@92 72 """
kkonganti@92 73 </tr>
kkonganti@92 74 </thead>
kkonganti@92 75 <tbody>"""
kkonganti@92 76 )
kkonganti@92 77 )
kkonganti@92 78
kkonganti@92 79 for row in tbl:
kkonganti@92 80 html.append("<tr>\n")
kkonganti@92 81 data_cols = row.strip().split('\t')
kkonganti@92 82 if ( len(header_cols) != len(data_cols) ):
kkonganti@92 83 print(f"\nWARN: Number of header columns ({len(header_cols)}) and data " +
kkonganti@92 84 f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n")
kkonganti@92 85 if ( len(header_cols) > len(data_cols) ):
kkonganti@92 86 data_cols += (( len(header_cols) - len(data_cols) ) * ' ' )
kkonganti@92 87 print(len(data_cols))
kkonganti@92 88 else:
kkonganti@92 89 header_cols += (( len(data_cols) - len(header_cols) ) * ' ')
kkonganti@92 90
kkonganti@92 91 html.append(
kkonganti@92 92 dedent(
kkonganti@92 93 f"""
kkonganti@92 94 <td><samp>{data_cols[0]}</samp></td>
kkonganti@92 95 """
kkonganti@92 96 )
kkonganti@92 97 )
kkonganti@92 98
kkonganti@92 99 for data_col in data_cols[1:]:
kkonganti@92 100 html.append(
kkonganti@92 101 dedent(
kkonganti@92 102 f"""<td>{data_col}</td>
kkonganti@92 103 """
kkonganti@92 104 )
kkonganti@92 105 )
kkonganti@92 106 html.append("</tr>\n")
kkonganti@92 107 html.append("</tbody>\n")
kkonganti@92 108 html.append("</table>\n")
kkonganti@92 109 html.append("</div>\n")
kkonganti@92 110
kkonganti@92 111 mqc_yaml = {
kkonganti@92 112 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@92 113 "section_name": f"{table_sum_on.upper()}",
kkonganti@92 114 "section_href": f"https://cfsan-git.fda.gov/Kranti.Konganti/{workflow_name}",
kkonganti@92 115 "plot_type": "html",
kkonganti@92 116 "description": "The results table shown here is a collection from all samples.",
kkonganti@92 117 "data": ('').join(html),
kkonganti@92 118 }
kkonganti@92 119
kkonganti@92 120 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@92 121 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@92 122
kkonganti@92 123 if __name__ == "__main__":
kkonganti@92 124 main()