Mercurial > repos > iuc > ena_upload

annotate process_xlsx.py @ 4:26ccb678abc8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
author iuc
date Tue, 19 Oct 2021 15:57:14 +0000
parents 59bb6d34fca6
children 4aab5ae907b6
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diff changeset
1 import argparse
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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2 import pathlib
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3 import sys
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4
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5 import xlrd
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6 import yaml
4
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7 from check_remote import check_remote_entry
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8 from mappings import optional_samples_cols_mapping
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10 FILE_FORMAT = 'fastq'
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12
4
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13 def identify_action(entry_type, alias):
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14 ''' define action ['add' | 'modify'] that needs to be perfomed for this entry '''
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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15 query = {entry_type + '_alias': alias}
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16 remote_accessions = check_remote_entry(entry_type, query)
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17 if len(remote_accessions) > 0:
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18 print(f'Found: {entry_type} entry with alias {alias}')
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19 return 'modify'
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20 else:
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21 print(f'No {entry_type} entry found with alias {alias}')
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22 return 'add'
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23
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24
2
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25 def extract_data(xl_sheet, expected_columns, optional_cols=None):
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26 """
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27 1. Check that the columns I expect are present in the sheet
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28 (any order and mixed with others, it's just a verification that
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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29 the user filled the correct template)
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30 2. Fill a dictionary with the rows data indexed by first column in list"""
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31 sheet_columns = {}
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32 if optional_cols is None:
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33 optional_cols = []
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34 optional_cols_loaded = []
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35 for sh_col in range(xl_sheet.ncols):
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36 if (xl_sheet.cell(0, sh_col).value in expected_columns) \
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37 or (xl_sheet.cell(0, sh_col).value in optional_cols):
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38 if xl_sheet.cell(0, sh_col).value in sheet_columns.keys():
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39 sys.exit("Duplicated columns found")
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40 else:
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41 sheet_columns[xl_sheet.cell(0, sh_col).value] = sh_col
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42 if xl_sheet.cell(0, sh_col).value in optional_cols:
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43 # store the list of optional cols available
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44 optional_cols_loaded.append(xl_sheet.cell(0, sh_col).value)
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45 provided_cols = expected_columns + optional_cols_loaded
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46
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47 # check that the required columns are all present
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48 # TODO: revise this for optional columns
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49 for col in range(len(expected_columns)):
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50 assert expected_columns[col] in sheet_columns.keys(), \
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51 "Expected column %s not found" % expected_columns[col]
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52
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53 # fetch rows in a dict
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54 data_dict = {}
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55 # the first of the expected columns will be the index
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56 index_col = sheet_columns[expected_columns[0]]
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57 # skip first 2 rows: column names + comments rows
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58 for row_id in range(2, xl_sheet.nrows):
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59 row_dict = {}
2
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60 for col in range(1, len(provided_cols)):
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61 sheet_col_index = sheet_columns[provided_cols[col]]
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62 row_dict[provided_cols[col]] = xl_sheet.cell(row_id, sheet_col_index).value
0
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63 # should check for duplicate alias/ids?
1
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64 if xl_sheet.cell(row_id, index_col).value in data_dict.keys():
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65 tmp = data_dict[xl_sheet.cell(row_id, index_col).value]
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66 data_dict[xl_sheet.cell(row_id, index_col).value] = [tmp]
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67 data_dict[xl_sheet.cell(row_id, index_col).value].append(row_dict)
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68 else:
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69 data_dict[xl_sheet.cell(row_id, index_col).value] = row_dict
2
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70 return data_dict, optional_cols_loaded
0
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71
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72
1
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73 def paste_xls2yaml(xlsx_path):
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74 print('YAML -------------')
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75 xls = xlrd.open_workbook(xlsx_path)
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76 content_dict = {}
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77 for sheet_name in xls.sheet_names():
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78 if sheet_name == 'controlled_vocabulary':
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79 continue
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80 xls_sheet = xls.sheet_by_name(sheet_name)
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81 sheet_contents_dict = {}
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82 colnames = []
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83 for col in range(xls_sheet.ncols):
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84 colnames.append(xls_sheet.cell(0, col).value)
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85 # skip first 2 rows (column names and suggestions)
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parents: 0
diff changeset
86 for row_id in range(2, xls_sheet.nrows):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
87 row_dict = {}
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
88 for col_id in range(0, xls_sheet.ncols):
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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89 row_dict[colnames[col_id]] = xls_sheet.cell(row_id, col_id).value
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
90 # should check for duplicate alias/ids?
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
91 sheet_contents_dict[row_id] = row_dict
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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92 content_dict[sheet_name] = sheet_contents_dict
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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93 yaml.dump(content_dict, sys.stdout)
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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94 print('YAML -------------')
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parents: 0
diff changeset
95
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iuc
parents: 0
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96
0
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iuc
parents:
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97 parser = argparse.ArgumentParser()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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98 parser.add_argument('--form', dest='xlsx_path', required=True)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
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99 parser.add_argument('--out_dir', dest='out_path', required=True)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
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100 parser.add_argument('--action', dest='action', required=True)
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parents:
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101 parser.add_argument('--vir', dest='viral_submission', required=False, action='store_true')
4
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102 parser.add_argument('--dev', dest='dev_submission', required=False, action='store_true')
1
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103 parser.add_argument('--verbose', dest='verbose', required=False, action='store_true')
0
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iuc
parents:
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104 args = parser.parse_args()
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105
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iuc
parents:
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106 xl_workbook = xlrd.open_workbook(args.xlsx_path)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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107
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parents:
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108 # PARSE STUDIES
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parents:
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109 #################
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110 xl_sheet = xl_workbook.sheet_by_name('ENA_study')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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111 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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112 raise ValueError('No entries found in studies sheet')
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113 studies_dict = {}
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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114 studies_col = ['alias', 'title', 'study_type', 'study_abstract']
2
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115 studies_dict, _ = extract_data(xl_sheet, studies_col)
0
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116
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117 # PARSE SAMPLES
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118 #################
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119 xl_sheet = xl_workbook.sheet_by_name('ENA_sample')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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120 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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121 raise ValueError('No entries found in samples')
2
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122
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123 samples_cols_excel = ['alias', 'title', 'scientific_name', 'sample_description']
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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124 # optional_samples_cols_mapping = {}
0
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125 if args.viral_submission:
2
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126 # load columns names from the table
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127 samples_cols_excel = samples_cols_excel + ['geographic location (country and/or sea)',
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128 'host common name', 'host health state',
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129 'host sex', 'host scientific name', 'collector name',
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130 'collecting institution', 'isolate']
0
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131
2
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132 samples_dict, samples_optional_cols_loaded = extract_data(xl_sheet, samples_cols_excel,
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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133 optional_samples_cols_mapping.keys())
0
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134 # PARSE EXPERIMENTS
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135 #################
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136 xl_sheet = xl_workbook.sheet_by_name('ENA_experiment')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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parents:
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137 if xl_sheet.nrows < 3:
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138 raise ValueError('No experiments found in experiments sheet')
1
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parents: 0
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139 exp_columns = ['alias', 'title', 'study_alias', 'sample_alias', 'design_description',
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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140 'library_name', 'library_strategy', 'library_source', 'library_selection',
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141 'library_layout', 'insert_size', 'library_construction_protocol',
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iuc
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142 'platform', 'instrument_model']
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143
2
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144 experiments_dict, _ = extract_data(xl_sheet, exp_columns)
0
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145
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146 # PARSE RUNS SHEET
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147 #################
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148 xl_sheet = xl_workbook.sheet_by_name('ENA_run')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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149 if xl_sheet.nrows < 3:
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150 raise ValueError('No entries found in runs sheet')
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iuc
parents:
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151 run_cols = ['alias', 'experiment_alias', 'file_name', 'file_format']
2
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152 runs_dict, _ = extract_data(xl_sheet, run_cols)
0
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153
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parents:
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154 # WRITE HEADERS TO TABLES
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iuc
parents:
diff changeset
155 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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156 studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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157 'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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diff changeset
158 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
2
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159
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160 samples_cols = ['alias', 'title', 'scientific_name', 'sample_description']
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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161 # extend the samples_cols list to add the ones that are filled by the CLI
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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162 samples_cols = samples_cols + ['status', 'accession', 'taxon_id', 'submission_date']
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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163 if args.viral_submission:
2
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parents: 1
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164 # extend the samples columns with the viral specific data
4
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165 samples_cols = samples_cols + ['geographic location (country and/or sea)', 'host common name',
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166 'host subject id', 'host health state', 'host sex',
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parents: 3
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167 'host scientific name', 'collector name',
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168 'collecting institution', 'isolate']
2
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iuc
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169 if len(samples_optional_cols_loaded) > 0:
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170 for optional_cols_excel in samples_optional_cols_loaded:
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171 samples_cols.append(optional_samples_cols_mapping[optional_cols_excel])
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172 samples_table.write('\t'.join(samples_cols) + '\n')
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173
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174 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
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175 experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
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176 'sample_alias', 'design_description', 'library_name',
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177 'library_strategy', 'library_source', 'library_selection',
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178 'library_layout', 'insert_size', 'library_construction_protocol',
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179 'platform', 'instrument_model', 'submission_date']) + '\n')
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180
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181 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
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182 runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
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183 'file_format', 'file_checksum', 'submission_date']) + '\n')
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184 action = args.action
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185 # actionable_items
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186 # WRITE DICTIONARIES TO TABLE FILES
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187
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188 # ADD A TIMESTAMP TO THE ALIAS? SEEMS LIKE ENA REQUIRES ALL ENTRIES FOR A WEBIN TO HAVE UNIQUE IDS?
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189 # dt_oobj = datetime.now(tz=None)
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190 # timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
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191 runs_included = []
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192 exp_included = []
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193 for study_alias, study in studies_dict.items():
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194 # study_alias = study_alias + '_' + timestamp
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195 if args.dev_submission:
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196 entry_action = args.action
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197 else:
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198 entry_action = identify_action('study', study_alias)
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199 studies_table.write('\t'.join([study_alias, entry_action, 'ENA_accession', study['title'],
0
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200 study['study_type'], study['study_abstract'], '',
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iuc
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201 'ENA_submission_data']) + '\n') # assuming no pubmed_id
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202 for sample_alias, sample in samples_dict.items():
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203 # sample_alias = sample_alias + '_' + timestamp
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204 if args.dev_submission:
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205 entry_action = args.action
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206 else:
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207 entry_action = identify_action('sample', sample_alias)
2
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208 samples_row_values = [sample_alias, sample['title'], sample['scientific_name'],
4
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209 sample['sample_description'], entry_action, 'ena_accession',
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210 '', 'ENA_submission_date']
0
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211 if args.viral_submission:
2
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212 # add the values that are unique for the viral samples
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213 if sample['collector name'] == '':
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214 sample['collector name'] = 'unknown'
2
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215 samples_row_values = samples_row_values + \
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216 [sample['geographic location (country and/or sea)'], sample['host common name'],
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217 'host subject id', sample['host health state'], sample['host sex'],
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218 sample['host scientific name'], sample['collector name'],
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219 sample['collecting institution'], sample['isolate']]
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220 # add the (possible) optional columns values
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221 if len(samples_optional_cols_loaded) > 0:
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222 for optional_col in samples_optional_cols_loaded:
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223 # parse values stored as in excel date format (=float)
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224 if optional_col in ('collection date', 'receipt date'):
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225 # check if excel stored it as date
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226 if isinstance(sample[optional_col], float):
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227 year, month, day, hour, minute, second = xlrd.xldate_as_tuple(
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228 sample[optional_col], xl_workbook.datemode)
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229 month = "{:02d}".format(month)
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230 day = "{:02d}".format(day)
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231 hour = "{:02d}".format(hour)
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232 minute = "{:02d}".format(minute)
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233 second = "{:02d}".format(second)
3
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234 if optional_col in ('collection date'):
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235 # collection date uses the format 2008-01-23T19:23:10
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236 sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day) + \
59bb6d34fca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 28d2a0cfcbb04d88b6e19a7d898a2bada3bce149"
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237 'T' + str(hour) + ':' + str(minute) + ':' + str(second)
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238 if optional_col in ('receipt date'):
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239 # receipt date uses forma: 2008-01-23
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240 sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day)
2
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241 # excel stores everything as float so I need to check if
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242 # the value was actually an int and keep it as int
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243 if isinstance(sample[optional_col], float):
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244 if int(sample[optional_col]) == sample[optional_col]:
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245 # it is not really a float but an int
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246 sample[optional_col] = int(sample[optional_col])
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247 samples_row_values.append(str(sample[optional_col]))
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248 samples_table.write('\t'.join(samples_row_values) + '\n')
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249
0
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250 for exp_alias, exp in experiments_dict.items():
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251 # should I check here if any experiment has a study or sample alias that is incorrect?
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252 # (not listed in the samples or study dict)
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253 # process the experiments for this sample
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254 if exp['sample_alias'] == sample_alias:
4
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255 # check the remote status
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256 if args.dev_submission:
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257 entry_action = args.action
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258 else:
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259 entry_action = identify_action('experiment', exp_alias)
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260 experiments_table.write('\t'.join([exp_alias, entry_action, 'accession_ena', exp['title'],
0
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261 exp['study_alias'], sample_alias,
3
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262 exp['design_description'], exp['library_name'],
0
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263 exp['library_strategy'], exp['library_source'],
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264 exp['library_selection'],
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265 exp['library_layout'].lower(),
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iuc
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266 str(int(exp['insert_size'])),
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267 exp['library_construction_protocol'],
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268 exp['platform'], exp['instrument_model'],
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iuc
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269 'submission_date_ENA']) + '\n')
1
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270 exp_included.append(exp_alias)
0
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271 for run_alias, run in runs_dict.items():
1
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272 # check that the experiments library_layout is set to paired
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273 # when multiple entries are associated with the same run alias
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274 if not isinstance(run, list):
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275 runs_list = [run]
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276 else:
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277 runs_list = run
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iuc
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278 for run_entry in runs_list:
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279 if run_entry['experiment_alias'] == exp_alias:
4
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iuc
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280 if args.dev_submission:
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281 entry_action = args.action
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282 else:
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283 entry_action = identify_action('run', run_alias)
26ccb678abc8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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284 runs_table.write('\t'.join([run_alias, entry_action, 'ena_run_accession',
1
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iuc
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285 exp_alias, run_entry['file_name'],
4
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286 FILE_FORMAT, '',
1
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iuc
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287 'submission_date_ENA']) + '\n')
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288 runs_included.append(run_alias)
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289
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290 # check if any experiment or run was not associated with any sample
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291 for run in runs_dict.keys():
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292 if run not in runs_included:
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293 print(f'The run {run} is listed in the runs section but not associated with any \
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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294 used experiment')
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295
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296 for exp in experiments_dict.keys():
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297 if exp not in exp_included:
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298 print(f'The experiment {exp} is listed in the experiments section but not associated \
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299 with any used sample')
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300
0
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301 studies_table.close()
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302 samples_table.close()
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parents:
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303 experiments_table.close()
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parents:
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304 runs_table.close()
1
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iuc
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305
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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diff changeset
306 if args.verbose:
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diff changeset
307 paste_xls2yaml(args.xlsx_path)