comparison validate_affy_metadata.py @ 21:90688364136c draft

Uploaded
author greg
date Thu, 14 Feb 2019 13:13:33 -0500
parents 38166b76f47a
children 84478b80cc47
comparison
equal deleted inserted replaced
20:2df07ae9af2d 21:90688364136c
74 line = line.rstrip("\r\n") 74 line = line.rstrip("\r\n")
75 if i > 97: 75 if i > 97:
76 accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).") 76 accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).")
77 stop_error(accumulated_msgs) 77 stop_error(accumulated_msgs)
78 items = line.split("\t") 78 items = line.split("\t")
79 if len(items) != 28: 79 if len(items) != 30:
80 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 28)." % (i, len(items))) 80 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 30)." % (i, len(items)))
81 stop_error(accumulated_msgs) 81 stop_error(accumulated_msgs)
82 # Required and validated. 82 # Required and validated.
83 # Required. 83 # Required.
84 user_specimen_id = items[0] 84 user_specimen_id = items[0]
85 if len(user_specimen_id) == 0: 85 if len(user_specimen_id) == 0:
153 # Optional. 153 # Optional.
154 public = string_as_boolean_string(items[26]) 154 public = string_as_boolean_string(items[26])
155 # Optional. 155 # Optional.
156 public_after_date = items[27] 156 public_after_date = items[27]
157 accumulated_msga = validate_date_string(i, public_after_date, accumulated_msgs) 157 accumulated_msga = validate_date_string(i, public_after_date, accumulated_msgs)
158 # Required and validated.
159 sperm_motility = items[28]
160 accumulated_msgs = validate_decimal(i, sperm_motility, accumulated_msgs)
161 # Required and validated.
162 healing_time = items[29]
163 accumulated_msgs = validate_decimal(i, healing_time, accumulated_msgs)
158 164
159 if len(accumulated_msgs) > 0: 165 if len(accumulated_msgs) > 0:
160 stop_error(accumulated_msgs) 166 stop_error(accumulated_msgs)
161 167
162 shutil.copyfile(args.input, args.output) 168 shutil.copyfile(args.input, args.output)