Coverage for tasks/basdai.py: 44%

1""" 

2camcops_server/tasks/basdai.py 

3 

4=============================================================================== 

5 

6 Copyright (C) 2012, University of Cambridge, Department of Psychiatry. 

7 Created by Rudolf Cardinal (rnc1001@cam.ac.uk). 

8 

9 This file is part of CamCOPS. 

10 

11 CamCOPS is free software: you can redistribute it and/or modify 

12 it under the terms of the GNU General Public License as published by 

13 the Free Software Foundation, either version 3 of the License, or 

14 (at your option) any later version. 

15 

16 CamCOPS is distributed in the hope that it will be useful, 

17 but WITHOUT ANY WARRANTY; without even the implied warranty of 

18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

19 GNU General Public License for more details. 

20 

21 You should have received a copy of the GNU General Public License 

22 along with CamCOPS. If not, see <https://www.gnu.org/licenses/>. 

23 

24=============================================================================== 

25 

26**Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) task.** 

27 

28""" 

29 

30import statistics 

31from typing import Any, List, Optional, Type 

32 

33import cardinal_pythonlib.rnc_web as ws 

34from cardinal_pythonlib.stringfunc import strseq 

35from sqlalchemy.sql.sqltypes import Float 

36 

37from camcops_server.cc_modules.cc_constants import CssClass 

38from camcops_server.cc_modules.cc_db import add_multiple_columns 

39from camcops_server.cc_modules.cc_html import tr_qa, tr, answer 

40from camcops_server.cc_modules.cc_request import CamcopsRequest 

41from camcops_server.cc_modules.cc_summaryelement import SummaryElement 

42from camcops_server.cc_modules.cc_task import TaskHasPatientMixin, Task 

43from camcops_server.cc_modules.cc_trackerhelpers import ( 

44 TrackerAxisTick, 

45 TrackerInfo, 

46 TrackerLabel, 

47) 

48 

49 

50# ============================================================================= 

51# BASDAI 

52# ============================================================================= 

53 

54 

55class Basdai( # type: ignore[misc] 

56 TaskHasPatientMixin, 

57 Task, 

58): 

59 __tablename__ = "basdai" 

60 shortname = "BASDAI" 

61 provides_trackers = True 

62 

63 N_QUESTIONS = 6 

64 

65 @classmethod 

66 def extend_columns(cls: Type["Basdai"], **kwargs: Any) -> None: 

67 

68 add_multiple_columns( 

69 cls, 

70 "q", 

71 1, 

72 cls.N_QUESTIONS, 

73 coltype=Float, 

74 minimum=0, 

75 maximum=10, 

76 comment_fmt="Q{n} - {s}", 

77 comment_strings=[ 

78 "fatigue/tiredness 0-10 (none - very severe)", 

79 "AS neck, back, hip pain 0-10 (none - very severe)", 

80 "other joint pain/swelling 0-10 (none - very severe)", 

81 "discomfort from tender areas 0-10 (none - very severe)", 

82 "morning stiffness level 0-10 (none - very severe)", 

83 "morning stiffness duration 0-10 (none - 2 or more hours)", 

84 ], 

85 ) 

86 

87 FIELD_NAMES = strseq("q", 1, N_QUESTIONS) 

88 

89 MINIMUM = 0.0 

90 ACTIVE_CUTOFF = 4.0 

91 MAXIMUM = 10.0 

92 

93 @staticmethod 

94 def longname(req: "CamcopsRequest") -> str: 

95 _ = req.gettext 

96 return _("Bath Ankylosing Spondylitis Disease Activity Index") 

97 

98 def get_summaries(self, req: CamcopsRequest) -> List[SummaryElement]: 

99 return self.standard_task_summary_fields() + [ 

100 SummaryElement( 

101 name="basdai", 

102 coltype=Float(), 

103 value=self.basdai(), 

104 comment="BASDAI", 

105 ) 

106 ] 

107 

108 def is_complete(self) -> bool: 

109 if self.any_fields_none(self.FIELD_NAMES): 

110 return False 

111 

112 if not self.field_contents_valid(): 

113 return False 

114 

115 return True 

116 

117 def get_trackers(self, req: CamcopsRequest) -> List[TrackerInfo]: 

118 axis_min = self.MINIMUM - 0.5 

119 axis_max = self.MAXIMUM + 0.5 

120 axis_ticks = [ 

121 TrackerAxisTick(n, str(n)) for n in range(0, int(axis_max) + 1) 

122 ] 

123 

124 horizontal_lines = [self.MAXIMUM, self.ACTIVE_CUTOFF, self.MINIMUM] 

125 

126 horizontal_labels = [ 

127 TrackerLabel( 

128 self.ACTIVE_CUTOFF + 0.5, self.wxstring(req, "active") 

129 ), 

130 TrackerLabel( 

131 self.ACTIVE_CUTOFF - 0.5, self.wxstring(req, "inactive") 

132 ), 

133 ] 

134 

135 return [ 

136 TrackerInfo( 

137 value=self.basdai(), 

138 plot_label="BASDAI", 

139 axis_label="BASDAI", 

140 axis_min=axis_min, 

141 axis_max=axis_max, 

142 axis_ticks=axis_ticks, 

143 horizontal_lines=horizontal_lines, 

144 horizontal_labels=horizontal_labels, 

145 ) 

146 ] 

147 

148 def basdai(self) -> Optional[float]: 

149 """ 

150 Calculating the BASDAI 

151 A. Add scores for questions 1 – 4 

152 B. Calculate the mean for questions 5 and 6 

153 C. Add A and B and divide by 5 

154 

155 The higher the BASDAI score, the more severe the patient’s disability 

156 due to their AS. 

157 """ 

158 if not self.is_complete(): 

159 return None 

160 

161 score_a_field_names = strseq("q", 1, 4) 

162 score_b_field_names = strseq("q", 5, 6) 

163 

164 a = sum([getattr(self, q) for q in score_a_field_names]) 

165 b = statistics.mean([getattr(self, q) for q in score_b_field_names]) 

166 

167 return (a + b) / 5 

168 

169 def activity_state(self, req: CamcopsRequest) -> str: 

170 basdai = self.basdai() 

171 

172 if basdai is None: 

173 return "?" 

174 

175 if basdai < self.ACTIVE_CUTOFF: 

176 return self.wxstring(req, "inactive") 

177 

178 return self.wxstring(req, "active") 

179 

180 def get_task_html(self, req: CamcopsRequest) -> str: 

181 rows = "" 

182 for q_num in range(1, self.N_QUESTIONS + 1): 

183 q_field = "q" + str(q_num) 

184 qtext = self.xstring(req, q_field) # includes HTML 

185 min_text = self.wxstring(req, q_field + "_min") 

186 max_text = self.wxstring(req, q_field + "_max") 

187 qtext += f" <i>(0 = {min_text}, 10 = {max_text})</i>" 

188 question_cell = f"{q_num}. {qtext}" 

189 score = getattr(self, q_field) 

190 

191 rows += tr_qa(question_cell, score) 

192 

193 basdai = ws.number_to_dp(self.basdai(), 1, default="?") 

194 

195 html = """ 

196 <div class="{CssClass.SUMMARY}"> 

197 <table class="{CssClass.SUMMARY}"> 

198 {tr_is_complete} 

199 {basdai} 

200 </table> 

201 </div> 

202 <table class="{CssClass.TASKDETAIL}"> 

203 <tr> 

204 <th width="60%">Question</th> 

205 <th width="40%">Answer</th> 

206 </tr> 

207 {rows} 

208 </table> 

209 <div class="{CssClass.FOOTNOTES}"> 

210 [1] (A) Add scores for questions 1–4. 

211 (B) Calculate the mean for questions 5 and 6. 

212 (C) Add A and B and divide by 5, giving a total in the 

213 range 0–10. 

214 &lt;4.0 suggests inactive disease, 

215 &ge;4.0 suggests active disease. 

216 </div> 

217 """.format( 

218 CssClass=CssClass, 

219 tr_is_complete=self.get_is_complete_tr(req), 

220 basdai=tr( 

221 self.wxstring(req, "basdai") + " ^[1]", 

222 "{} ({})".format(answer(basdai), self.activity_state(req)), 

223 ), 

224 rows=rows, 

225 ) 

226 return html