-
Notifications
You must be signed in to change notification settings - Fork 20
/
aggregate.py
198 lines (176 loc) · 7.37 KB
/
aggregate.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
'''
Aggregates all the variables in the supplied metadata files
into a single csv output file for input in visualization.
It also generates the dictionary file with the type for each
variable
@copyright: Fathom Information Design 2014
'''
import sys, os, csv, math
import xml.etree.ElementTree as ET
def get_variables(xml, var_names, var_types, var_ranges, var_files, var_equiv):
vname = ""
vname_full = ""
vname_old = []
vtype = ""
vranges = []
for child in xml:
if child.tag == "short":
vname = child.text
if vname == 'SEQN':
return
if child.tag == "old":
vname_old = child.text.split(";")
if child.tag == "full":
vname_full = child.text
if child.tag == "type":
vtype = child.text
if child.tag == "datafile":
filenames = child.text.split(";")
for fn in filenames:
if not fn in var_files: var_files[fn] = set()
var_files[fn].add(vname)
if child.tag == "range":
rstr = child.text
if vtype == "float":
temp = rstr.split(";")
vranges = [float(x) for x in temp[0].split(",")]
if 1 < len(temp):
for x in temp[1:len(temp)]:
vranges.append(float(x.split(":")[0]))
elif vtype == "integer":
temp = rstr.split(";")
vranges = [int(x) for x in temp[0].split(",")]
if 1 < len(temp):
for x in temp[1:len(temp)]:
vranges.append(int(x.split(":")[0]))
elif vtype == "category":
vranges = [x.split(":")[0] for x in rstr.split(";")]
if vname != "":
var_names.append([vname, vname_full])
var_types[vname] = vtype
var_ranges[vname] = vranges
var_equiv[vname] = vname_old
argc = len(sys.argv)
out_folder = sys.argv[1]
in_metadata = sys.argv[2:argc - 1]
data_file = sys.argv[argc - 1]
out_data_filename = os.path.abspath(os.path.join(out_folder, data_file))
all_seqn = set([])
all_var_values = []
all_var_names = []
all_var_types = []
all_var_ranges = []
print("Getting variable values...")
for meta in in_metadata:
xml_filename = os.path.abspath(os.path.join(out_folder, meta))
tree = ET.parse(xml_filename)
root = tree.getroot()
for el in root:
if (el.tag == "data"):
group = el.attrib["name"]
if (el.tag == "table"):
if el.attrib["include"] != "yes": continue
var_names = []
var_types = {}
var_ranges = {}
var_files = {}
var_equiv = {}
for child in el:
if child.tag == "var":
if child.attrib["include"] == "yes":
get_variables(child, var_names, var_types, var_ranges, var_files, var_equiv)
if var_names != []:
for filename in var_files.keys():
if not os.path.exists(filename):
print(" Warning: File " + filename + " is missing, won't add values for variables " + ",".join(list(var_files[filename])))
continue
csv_file = open(filename, 'r', encoding='latin1')
csv_reader = csv.reader(csv_file, delimiter=',', quotechar='"')
# The replace is needed because the variable names in the source csv files
# use "." instead of "_" even though the variable name in the codebook has
# "_"
title_row = [x.upper().replace(".", "_") for x in next(csv_reader)]
data_rows = [row for row in csv_reader]
# Getting the values for each variable
var_set = var_files[filename]
for var in var_set:
typ = var_types[var]
rang = var_ranges[var]
if "SEQN" in title_row:
seqn_col = title_row.index("SEQN")
else:
print(" Warning: Not adding the values of variable " + var + " because SEQN is missing from its datafile " + filename)
continue
try:
if -1 < var.find("."): var0 = var.split(".")[0]
else: var0 = var
var_col = title_row.index(var0)
except ValueError:
for oname in var_equiv[var]:
if -1 < oname.find("."): oname = oname.split(".")[0]
try:
var_col = title_row.index(oname)
break
except ValueError:
idx = -1
if var_col == -1:
print(" Warning: Variable " + var + " is missing from " + filename)
continue
idx = 0
try:
idx = all_var_names.index(var)
except ValueError:
idx = -1
if idx == -1:
all_var_names.append(var)
all_var_types.append(typ)
all_var_ranges.append(rang)
values_dict = {}
all_var_values.append(values_dict)
else:
values_dict = all_var_values[idx]
for row in data_rows:
seqn = int(row[seqn_col])
all_seqn.add(seqn)
value = row[var_col]
values_dict[seqn] = value
csv_file.close()
print("Done.")
# Construct title line
name = "SEQN"
title_line = name
count = len(all_var_names)
for i in range(0, count):
nami = all_var_names[i]
typi = all_var_types[i]
if typi != "recorded":
name = nami
title_line = title_line + "\t" + name
print("Writing aggregated data file...")
data_file = open(out_data_filename, 'w')
data_file.write(title_line + "\n")
rowCount = 0
list_seqn = list(all_seqn)
list_seqn.sort()
for seqn in list_seqn:
colCount = 1
line = str(seqn)
for i in range(0, count):
typi = all_var_types[i]
if typi != "recorded":
colCount = colCount + 1
vali = all_var_values[i]
if seqn in vali:
if vali[seqn] == "NA" or vali[seqn] == "":
line = line + "\tNA"
else:
line = line + "\t" + vali[seqn]
else:
line = line + "\tNA"
if colCount != count + 1:
sys.stderr.write("Number of columns is inconsistent at row " + rowCount + ". It is " + colCount + "but should be " + count + "\n")
sys.exit(1)
rowCount = rowCount + 1
data_file.write(line + "\n")
data_file.close()
print("Done: written",rowCount,"rows and",count,"columns.")