|
0
|
1 #!/usr/bin/env python
|
|
|
2 """
|
|
|
3 Validate the metadata file associated with Affymetrix 96 well plate data.
|
|
|
4 """
|
|
|
5 import argparse
|
|
|
6 import datetime
|
|
|
7 import decimal
|
|
|
8 import re
|
|
|
9 import shutil
|
|
|
10 import sys
|
|
|
11
|
|
|
12 parser = argparse.ArgumentParser()
|
|
|
13 parser.add_argument('--input', dest='input', help='Metadata file for Affymetrix 96 well plate data')
|
|
|
14 parser.add_argument('--output', dest='output', help='Output dataset'),
|
|
|
15 args = parser.parse_args()
|
|
|
16
|
|
|
17 EMAIL_MAX_LEN = 255
|
|
|
18 VALID_EMAIL_RE = re.compile("[^@]+@[^@]+\.[^@]+")
|
|
|
19
|
|
|
20
|
|
|
21 def add_error_msg(accumulated_msgs, msg):
|
|
|
22 return "%s\n%s" % (accumulated_msgs, msg)
|
|
|
23
|
|
|
24
|
|
|
25 def empty_value(line_no, label, accumulated_msgs):
|
|
|
26 return add_error_msg(accumulated_msgs, "The required %s value is missing on line %d." % (label, line_no))
|
|
|
27
|
|
|
28
|
|
|
29 def stop_error(msg):
|
|
|
30 sys.exit(msg)
|
|
|
31
|
|
|
32
|
|
|
33 def string_as_boolean_string(string):
|
|
|
34 if str(string).lower() in ['true', 'yes', 'on', '1']:
|
|
|
35 return 'True'
|
|
|
36 else:
|
|
|
37 return 'False'
|
|
|
38
|
|
|
39
|
|
|
40 def validate_date_string(line_no, date_string, column, accumulated_msgs):
|
|
|
41 if len(date_string) == 0:
|
|
|
42 return accumulated_msgs
|
|
|
43 try:
|
|
|
44 datetime.datetime.strptime(date_string, '%Y-%m-%d')
|
|
|
45 return accumulated_msgs
|
|
|
46 except ValueError:
|
|
|
47 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (%s must be YYYY-MM-DD) for column %s." % (line_no, date_string, column))
|
|
|
48
|
|
|
49
|
|
|
50 def validate_decimal(line_no, decimal_string, column, accumulated_msgs):
|
|
|
51 try:
|
|
|
52 decimal.Decimal(decimal_string)
|
|
|
53 return accumulated_msgs
|
|
|
54 except Exception:
|
|
|
55 return add_error_msg(accumulated_msgs, "Line %d contains an incorrect decimal value (%s) for column %s." % (line_no, decimal_string, column))
|
|
|
56
|
|
|
57
|
|
|
58 def validate_email(line_no, email, accumulated_msgs):
|
|
|
59 if not (VALID_EMAIL_RE.match(email)):
|
|
|
60 return add_error_msg(accumulated_msgs, "Line %d contains an invalid email address (%s). " % (line_no, email))
|
|
|
61 elif len(email) > EMAIL_MAX_LEN:
|
|
|
62 return add_error_msg(accumulated_msgs, "Line %d contains an email address (%) that is longer than the maximum length, %d characters." % (line_no, email))
|
|
|
63 return accumulated_msgs
|
|
|
64
|
|
|
65
|
|
|
66 accumulated_msgs = ""
|
|
|
67 # Parse the input file, skipping the header, and validating
|
|
|
68 # that each data line consists of 31 comma-separated items.
|
|
|
69 with open(args.input, "r") as ih:
|
|
|
70 for i, line in enumerate(ih):
|
|
|
71 if i == 0:
|
|
|
72 # Skip the header.
|
|
|
73 continue
|
|
|
74 # Keep 1-based line value for error messages.
|
|
|
75 line_no = i + 1
|
|
|
76 line = line.rstrip("\r\n")
|
|
|
77 items = line.split("\t")
|
|
|
78 if len(items) != 32:
|
|
|
79 accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 32)." % (line_no, len(items)))
|
|
|
80 stop_error(accumulated_msgs)
|
|
|
81 # Required and validated.
|
|
|
82 # Required.
|
|
|
83 user_specimen_id = items[0]
|
|
|
84 if len(user_specimen_id) == 0:
|
|
|
85 accumulated_msgs = empty_value(line_no, "user_specimen_id", accumulated_msgs)
|
|
|
86 # Optional.
|
|
|
87 field_call = items[1]
|
|
|
88 # Optional.
|
|
|
89 bcoral_genet_id = items[2]
|
|
|
90 # Optional.
|
|
|
91 bsym_genet_id = items[3]
|
|
|
92 # Required.
|
|
|
93 reef = items[4]
|
|
|
94 if len(reef) == 0:
|
|
|
95 accumulated_msgs = empty_value(line_no, "reef", accumulated_msgs)
|
|
|
96 # Required.
|
|
|
97 region = items[5]
|
|
|
98 if len(region) == 0:
|
|
|
99 accumulated_msgs = empty_value(line_no, "region", accumulated_msgs)
|
|
|
100 # Required and validated.
|
|
|
101 latitude = items[6]
|
|
|
102 accumulated_msgs = validate_decimal(line_no, latitude, "latitude", accumulated_msgs)
|
|
|
103 # Required and validated.
|
|
|
104 longitude = items[7]
|
|
|
105 accumulated_msgs = validate_decimal(line_no, longitude, "longitude", accumulated_msgs)
|
|
|
106 # Optional.
|
|
|
107 geographic_origin = items[8]
|
|
|
108 # Optional.
|
|
|
109 colony_location = items[9]
|
|
|
110 depth = items[10]
|
|
3
|
111 # If depth has a value, then it must be a decimal.
|
|
2
|
112 if len(depth) > 0:
|
|
3
|
113 accumulated_msgs = validate_decimal(line_no, depth, "depth", accumulated_msgs)
|
|
0
|
114 # Optional.
|
|
|
115 disease_resist = items[11]
|
|
|
116 # Optional.
|
|
|
117 bleach_resist = items[12]
|
|
|
118 # Optional.
|
|
|
119 mortality = items[13]
|
|
|
120 # Optional.
|
|
|
121 tle = items[14]
|
|
|
122 # Optional.
|
|
|
123 spawning = string_as_boolean_string(items[15])
|
|
|
124 # Required.
|
|
|
125 collector_last_name = items[16]
|
|
|
126 if len(collector_last_name) == 0:
|
|
|
127 accumulated_msgs = empty_value(line_no, "collector_last_name", accumulated_msgs)
|
|
|
128 # Required.
|
|
|
129 collector_first_name = items[17]
|
|
|
130 if len(collector_first_name) == 0:
|
|
|
131 accumulated_msgs = empty_value(line_no, "collector_first_name", accumulated_msgs)
|
|
|
132 # Required.
|
|
|
133 org = items[18]
|
|
|
134 if len(org) == 0:
|
|
|
135 accumulated_msgs = empty_value(line_no, "org", accumulated_msgs)
|
|
|
136 # Required and validated.
|
|
|
137 collection_date = items[19]
|
|
|
138 accumulated_msgs = validate_date_string(line_no, collection_date, "collection_date", accumulated_msgs)
|
|
|
139 # Required and validated.
|
|
|
140 contact_email = items[20]
|
|
|
141 accumulated_msgs = validate_email(line_no, contact_email, accumulated_msgs)
|
|
|
142 # Required.
|
|
|
143 seq_facility = items[21]
|
|
|
144 if len(seq_facility) == 0:
|
|
|
145 accumulated_msgs = empty_value(line_no, "seq_facility", accumulated_msgs)
|
|
|
146 # Optional.
|
|
|
147 array_version = items[22]
|
|
|
148 # Optional.
|
|
|
149 public = string_as_boolean_string(items[23])
|
|
|
150 # Optional.
|
|
|
151 public_after_date = items[24]
|
|
|
152 accumulated_msga = validate_date_string(line_no, public_after_date, "public_after_date", accumulated_msgs)
|
|
|
153 # Required and validated.
|
|
|
154 sperm_motility = items[25]
|
|
|
155 accumulated_msgs = validate_decimal(line_no, sperm_motility, "sperm_motility", accumulated_msgs)
|
|
|
156 # Required and validated.
|
|
|
157 healing_time = items[26]
|
|
|
158 accumulated_msgs = validate_decimal(line_no, healing_time, "healing_time", accumulated_msgs)
|
|
|
159 # Optional.
|
|
|
160 dna_extraction_method = items[27]
|
|
|
161 # Optional.
|
|
|
162 dna_concentration = items[28]
|
|
|
163 # If dna_concentration has a value, then it must be decimal.
|
|
|
164 if len(dna_concentration) > 0:
|
|
|
165 accumulated_msgs = validate_decimal(line_no, dna_concentration, "dna_concentration", accumulated_msgs)
|
|
|
166 # Optional.
|
|
|
167 registry_id = items[29]
|
|
|
168 # Optional.
|
|
|
169 result_folder_name = items[30]
|
|
|
170 # Optional.
|
|
|
171 plate_barcode = items[31]
|
|
|
172
|
|
|
173
|
|
|
174 if len(accumulated_msgs) > 0:
|
|
|
175 stop_error(accumulated_msgs)
|
|
|
176
|
|
|
177 shutil.copyfile(args.input, args.output)
|
