Mercurial > repos > kkonganti > cfsan_centriflaken

annotate 0.4.0/bin/create_mqc_data_table.py @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 #!/usr/bin/env python
kkonganti@101 2
kkonganti@101 3 import sys
kkonganti@101 4 import yaml
kkonganti@101 5 from textwrap import dedent
kkonganti@101 6
kkonganti@101 7 def main() :
kkonganti@101 8 """
kkonganti@101 9 Takes a tab-delimited text file with a mandatory header
kkonganti@101 10 column and generates an HTML table.
kkonganti@101 11 """
kkonganti@101 12
kkonganti@101 13 args = sys.argv
kkonganti@101 14 if (len(args) < 2 or len(args) > 3):
kkonganti@101 15 print(f"\nTwo CL arguments are required!\n")
kkonganti@101 16 exit(1)
kkonganti@101 17
kkonganti@101 18 table_sum_on = args[1].lower()
kkonganti@101 19 workflow_name = args[2].lower()
kkonganti@101 20
kkonganti@101 21 with open(f"{table_sum_on}.tblsum.txt", "r") as tbl:
kkonganti@101 22 header = tbl.readline()
kkonganti@101 23 header_cols = header.strip().split('\t')
kkonganti@101 24
kkonganti@101 25 html = [
kkonganti@101 26 dedent(
kkonganti@101 27 f"""<script type="text/javascript">
kkonganti@101 28 $(document).ready(function () {{
kkonganti@101 29 $('#cpipes-process-custom-res-{table_sum_on}').DataTable({{
kkonganti@101 30 scrollX: true,
kkonganti@101 31 fixedColumns: true, dom: 'Bfrtip',
kkonganti@101 32 buttons: [
kkonganti@101 33 'copy',
kkonganti@101 34 {{
kkonganti@101 35 extend: 'print',
kkonganti@101 36 title: 'CPIPES: MultiQC Report: {table_sum_on}'
kkonganti@101 37 }},
kkonganti@101 38 {{
kkonganti@101 39 extend: 'excel',
kkonganti@101 40 filename: '{table_sum_on}_results',
kkonganti@101 41 }},
kkonganti@101 42 {{
kkonganti@101 43 extend: 'csv',
kkonganti@101 44 filename: '{table_sum_on}_results',
kkonganti@101 45 }}
kkonganti@101 46 ]
kkonganti@101 47 }});
kkonganti@101 48 }});
kkonganti@101 49 </script>
kkonganti@101 50 <div class="table-responsive">
kkonganti@101 51 <style>
kkonganti@101 52 #cpipes-process-custom-res tr:nth-child(even) {{
kkonganti@101 53 background-color: #f2f2f2;
kkonganti@101 54 }}
kkonganti@101 55 </style>
kkonganti@101 56 <table class="table" style="width:100%" id="cpipes-process-custom-res-{table_sum_on}">
kkonganti@101 57 <thead>
kkonganti@101 58 <tr>"""
kkonganti@101 59 )
kkonganti@101 60 ]
kkonganti@101 61
kkonganti@101 62 for header_col in header_cols:
kkonganti@101 63 html.append(
kkonganti@101 64 dedent(
kkonganti@101 65 f"""
kkonganti@101 66 <th> {header_col} </th>"""
kkonganti@101 67 )
kkonganti@101 68 )
kkonganti@101 69
kkonganti@101 70 html.append(
kkonganti@101 71 dedent(
kkonganti@101 72 """
kkonganti@101 73 </tr>
kkonganti@101 74 </thead>
kkonganti@101 75 <tbody>"""
kkonganti@101 76 )
kkonganti@101 77 )
kkonganti@101 78
kkonganti@101 79 for row in tbl:
kkonganti@101 80 html.append("<tr>\n")
kkonganti@101 81 data_cols = row.strip().split('\t')
kkonganti@101 82 if ( len(header_cols) != len(data_cols) ):
kkonganti@101 83 print(f"\nWARN: Number of header columns ({len(header_cols)}) and data " +
kkonganti@101 84 f"columns ({len(data_cols)}) are not equal!\nWill append empty columns!\n")
kkonganti@101 85 if ( len(header_cols) > len(data_cols) ):
kkonganti@101 86 data_cols += (( len(header_cols) - len(data_cols) ) * ' ' )
kkonganti@101 87 print(len(data_cols))
kkonganti@101 88 else:
kkonganti@101 89 header_cols += (( len(data_cols) - len(header_cols) ) * ' ')
kkonganti@101 90
kkonganti@101 91 html.append(
kkonganti@101 92 dedent(
kkonganti@101 93 f"""
kkonganti@101 94 <td><samp>{data_cols[0]}</samp></td>
kkonganti@101 95 """
kkonganti@101 96 )
kkonganti@101 97 )
kkonganti@101 98
kkonganti@101 99 for data_col in data_cols[1:]:
kkonganti@101 100 html.append(
kkonganti@101 101 dedent(
kkonganti@101 102 f"""<td>{data_col}</td>
kkonganti@101 103 """
kkonganti@101 104 )
kkonganti@101 105 )
kkonganti@101 106 html.append("</tr>\n")
kkonganti@101 107 html.append("</tbody>\n")
kkonganti@101 108 html.append("</table>\n")
kkonganti@101 109 html.append("</div>\n")
kkonganti@101 110
kkonganti@101 111 mqc_yaml = {
kkonganti@101 112 "id": f"{table_sum_on.upper()}_collated_table",
kkonganti@101 113 "section_name": f"{table_sum_on.upper()}",
kkonganti@101 114 "section_href": f"https://cfsan-git.fda.gov/Kranti.Konganti/{workflow_name}",
kkonganti@101 115 "plot_type": "html",
kkonganti@101 116 "description": "The results table shown here is a collection from all samples.",
kkonganti@101 117 "data": ('').join(html),
kkonganti@101 118 }
kkonganti@101 119
kkonganti@101 120 with open(f"{table_sum_on.lower()}_mqc.yml", "w") as html_mqc:
kkonganti@101 121 yaml.dump(mqc_yaml, html_mqc, default_flow_style=False)
kkonganti@101 122
kkonganti@101 123 if __name__ == "__main__":
kkonganti@101 124 main()