Coverage for cc_modules/cc_snomed.py : 60%

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1#!/usr/bin/env python
3r"""
4camcops_server/cc_modules/cc_snomed.py
6===============================================================================
8 Copyright (C) 2012-2020 Rudolf Cardinal (rudolf@pobox.com).
10 This file is part of CamCOPS.
12 CamCOPS is free software: you can redistribute it and/or modify
13 it under the terms of the GNU General Public License as published by
14 the Free Software Foundation, either version 3 of the License, or
15 (at your option) any later version.
17 CamCOPS is distributed in the hope that it will be useful,
18 but WITHOUT ANY WARRANTY; without even the implied warranty of
19 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 GNU General Public License for more details.
22 You should have received a copy of the GNU General Public License
23 along with CamCOPS. If not, see <https://www.gnu.org/licenses/>.
25===============================================================================
27**CamCOPS code to support SNOMED-CT.**
29Note that the licensing arrangements for SNOMED-CT mean that the actual codes
30must be separate (and not part of the CamCOPS code). See the documentation.
32Some tests:
34.. code-block:: python
36 import logging
37 from cardinal_pythonlib.logs import main_only_quicksetup_rootlogger
38 from camcops_server.cc_modules.cc_request import get_command_line_request
39 from camcops_server.cc_modules.cc_snomed import *
40 from camcops_server.tasks.phq9 import Phq9
41 main_only_quicksetup_rootlogger(level=logging.DEBUG)
42 req = get_command_line_request()
44 # ---------------------------------------------------------------------
45 # Read the XML, etc.
46 # ---------------------------------------------------------------------
48 print(VALID_SNOMED_LOOKUPS)
49 concepts = get_all_snomed_concepts(req.config.snomed_xml_filename)
51 # ---------------------------------------------------------------------
52 # Test a task, and loading SNOMED data from XML via the CamCOPS config
53 # ---------------------------------------------------------------------
55 phq9 = Phq9()
56 print("\n".join(str(x) for x in phq9.get_snomed_codes(req)))
57 phq9.q1 = 2
58 phq9.q2 = 2
59 phq9.q3 = 2
60 phq9.q4 = 2
61 phq9.q5 = 2
62 phq9.q6 = 2
63 phq9.q7 = 2
64 phq9.q8 = 2
65 phq9.q9 = 2
66 phq9.q10 = 2
67 print("\n".join(repr(x) for x in phq9.get_snomed_codes(req)))
68 print("\n".join(str(x) for x in phq9.get_snomed_codes(req)))
70Note diagnostic coding maps:
72- https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html
73- https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html
75Other testing:
77.. code-block:: bash
79 camcops_server dev_cli --verbose
81.. code-block:: python
83 from camcops_server.cc_modules.cc_snomed import *
85 athena_concepts = get_athena_concepts(config.athena_concept_tsv_filename)
86 relationships = get_athena_concept_relationships(config.athena_concept_relationship_tsv_filename)
87 rel_ids = set(r.relationship_id for r in relationships)
88 icd9, icd10 = get_icd9cm_icd10_snomed_concepts(config.athena_concept_tsv_filename, config.athena_concept_relationship_tsv_filename)
90 ac = get_athena_concepts(config.athena_concept_tsv_filename, vocabulary_ids=[AthenaVocabularyId.SNOMED], concept_codes=["4303690"])
92Regarding temporal coding:
94- SNOMED CT has some concepts relating to time (e.g. "time aspect", "single
95 point in time", "date of birth", "date of event", "time (property)", "time
96 (attribute)"). HOWEVER, note that SNOMED-CT isn't intended for recording
97 event dates:
99 - https://confluence.ihtsdotools.org/display/DOCRSG/3.5.+Safely+representing+the+context+of+recorded+codes
101 "Contextual information that is not represented by SNOMED CT
103 Clinical statements that contain SNOMED CT Concept representations will
104 be associated with some information which is not intended to be
105 represented using SNOMED CT:
107 - Dates, times of an activity of recording and activity;
108 - Quantitative information including ranges and durations;
109 - Identifiers or names of authors, providers of information or other
110 parties involved in a recorded activity.
111 - SNOMED CT is not intended to represent this information. Appropriate
112 constructs in a standardized or proprietary record architecture
113 should be used to relate this information to SNOMED CT encoded
114 clinical statements."
116 - https://confluence.ihtsdotools.org/display/DOCRSG/3.4.+Record+architectures%2C+structures+and+semantics
118 "Using SNOMED CT in standard architectures
120 ...
122 Each health record component has the potential to include:
124 - Dates and times of actual and planned events.
125 - Associations with people, organizations, devices and other entities
126 that participate or are used in relations to a recorded event or
127 plan.
128 - Codes or other representations that name or provide the semantic
129 information container, link, or statement:
131 - SNOMED CT fulfills this role in a structured health record.
133 - Additional data including text, numeric values, images and other
134 digital data."
136- That explains why the grammar has no explanation of how to represent
137 dates/times, perhaps!
139""" # noqa
141from collections import OrderedDict
142import csv
143import logging
144from typing import Dict, List, Optional, Set, Tuple, Union
145import xml.etree.cElementTree as ElementTree
147from cardinal_pythonlib.athena_ohdsi import (
148 AthenaConceptRow,
149 AthenaRelationshipId,
150 AthenaVocabularyId,
151 get_athena_concept_relationships,
152 get_athena_concepts,
153)
154from cardinal_pythonlib.logs import BraceStyleAdapter
155from cardinal_pythonlib.reprfunc import simple_repr
156# noinspection PyUnresolvedReferences
157from cardinal_pythonlib.snomed import ( # noqa: F401
158 SnomedAttribute,
159 SnomedAttributeGroup,
160 SnomedAttributeSet,
161 SnomedConcept as SnomedConceptCardinalPythonlib,
162 SnomedExpression as SnomedExpressionCardinalPythonlib,
163 SnomedFocusConcept,
164 SnomedRefinement,
165 SnomedValue,
166)
168from camcops_server.cc_modules.cc_cache import cache_region_static, fkg
169from camcops_server.cc_modules.cc_xml import XmlDataTypes, XmlElement
171log = BraceStyleAdapter(logging.getLogger(__name__))
174# =============================================================================
175# Constants
176# =============================================================================
178# -----------------------------------------------------------------------------
179# Internal
180# -----------------------------------------------------------------------------
182SNOMED_XML_NAME = "snomed_ct_expression"
184# -----------------------------------------------------------------------------
185# ICD-9-CM; from the client: camcops --print_icd9_codes
186# -----------------------------------------------------------------------------
188CLIENT_ICD9CM_CODES = set("""
189290.0 290.1 290.10 290.11 290.12 290.13 290.2 290.20 290.21 290.3 290.4 290.40
190290.41 290.42 290.43 290.8 290.9 291.0 291.1 291.2 291.3 291.4 291.5 291.8
191291.81 291.82 291.89 291.9 292.0 292.1 292.11 292.12 292.2 292.8 292.81 292.82
192292.83 292.84 292.85 292.89 292.9 293.0 293.1 293.8 293.81 293.82 293.83 293.84
193293.89 293.9 294.0 294.1 294.10 294.11 294.2 294.20 294.21 294.8 294.9 295.0
194295.00 295.01 295.02 295.03 295.04 295.05 295.1 295.10 295.11 295.12 295.13
195295.14 295.15 295.2 295.20 295.21 295.22 295.23 295.24 295.25 295.3 295.30
196295.31 295.32 295.33 295.34 295.35 295.4 295.40 295.41 295.42 295.43 295.44
197295.45 295.5 295.50 295.51 295.52 295.53 295.54 295.55 295.6 295.60 295.61
198295.62 295.63 295.64 295.65 295.7 295.70 295.71 295.72 295.73 295.74 295.75
199295.8 295.80 295.81 295.82 295.83 295.84 295.85 295.9 295.90 295.91 295.92
200295.93 295.94 295.95 296.0 296.00 296.01 296.02 296.03 296.04 296.05 296.06
201296.1 296.10 296.11 296.12 296.13 296.14 296.15 296.16 296.2 296.20 296.21
202296.22 296.23 296.24 296.25 296.26 296.3 296.30 296.31 296.32 296.33 296.34
203296.35 296.36 296.4 296.40 296.41 296.42 296.43 296.44 296.45 296.46 296.5
204296.50 296.51 296.52 296.53 296.54 296.55 296.56 296.6 296.60 296.61 296.62
205296.63 296.64 296.65 296.66 296.7 296.8 296.80 296.81 296.82 296.89 296.9
206296.90 296.99 297.0 297.1 297.2 297.3 297.8 297.9 298.0 298.1 298.2 298.3 298.4
207298.8 298.9 299.0 299.00 299.01 299.1 299.10 299.11 299.8 299.80 299.81 299.9
208299.90 299.91 300.0 300.00 300.01 300.02 300.09 300.1 300.10 300.11 300.12
209300.13 300.14 300.15 300.16 300.19 300.2 300.20 300.21 300.22 300.23 300.29
210300.3 300.4 300.5 300.6 300.7 300.8 300.81 300.82 300.89 300.9 301.0 301.1
211301.10 301.11 301.12 301.13 301.2 301.20 301.21 301.22 301.3 301.4 301.5 301.50
212301.51 301.59 301.6 301.7 301.8 301.81 301.82 301.83 301.84 301.89 301.9 302.0
213302.1 302.2 302.3 302.4 302.5 302.50 302.51 302.52 302.53 302.6 302.7 302.70
214302.71 302.72 302.73 302.74 302.75 302.76 302.79 302.8 302.81 302.82 302.83
215302.84 302.85 302.89 302.9 303.0 303.00 303.01 303.02 303.03 303.0x 303.9
216303.90 303.91 303.92 303.93 304.0 304.00 304.01 304.02 304.03 304.1 304.10
217304.11 304.12 304.13 304.2 304.20 304.21 304.22 304.23 304.3 304.30 304.31
218304.32 304.33 304.4 304.40 304.41 304.42 304.43 304.5 304.50 304.51 304.52
219304.53 304.6 304.60 304.61 304.62 304.63 304.7 304.70 304.71 304.72 304.73
220304.8 304.80 304.81 304.82 304.83 304.9 304.90 304.91 304.92 304.93 305.0
221305.00 305.01 305.02 305.03 305.0x 305.1 305.10 305.11 305.12 305.13 305.2
222305.20 305.21 305.22 305.23 305.2x 305.3 305.30 305.31 305.32 305.33 305.3x
223305.4 305.40 305.41 305.42 305.43 305.4x 305.5 305.50 305.51 305.52 305.53
224305.5x 305.6 305.60 305.61 305.62 305.63 305.6x 305.7 305.70 305.71 305.72
225305.73 305.7x 305.8 305.80 305.81 305.82 305.83 305.8x 305.9 305.90 305.91
226305.92 305.93 305.9x 306.0 306.1 306.2 306.3 306.4 306.50 306.51 306.52 306.53
227306.59 306.6 306.7 306.8 306.9 307.0 307.1 307.2 307.20 307.21 307.22 307.23
228307.3 307.4 307.40 307.41 307.42 307.43 307.44 307.45 307.46 307.47 307.48
229307.49 307.5 307.50 307.51 307.52 307.53 307.54 307.59 307.6 307.7 307.8 307.80
230307.81 307.89 307.9 308.0 308.1 308.2 308.3 308.4 308.9 309.0 309.1 309.2
231309.21 309.22 309.23 309.24 309.28 309.29 309.3 309.4 309.8 309.81 309.82
232309.83 309.89 309.9 310.0 310.1 310.2 310.8 310.81 310.89 310.9 311 312.0
233312.00 312.01 312.02 312.03 312.1 312.10 312.11 312.12 312.13 312.2 312.20
234312.21 312.22 312.23 312.3 312.30 312.31 312.32 312.33 312.34 312.35 312.39
235312.4 312.8 312.81 312.82 312.89 312.9 313.0 313.1 313.2 313.21 313.22 313.23
236313.3 313.8 313.81 313.82 313.83 313.89 313.9 314.0 314.00 314.01 314.1 314.2
237314.8 314.9 315.0 315.00 315.01 315.02 315.09 315.1 315.2 315.3 315.31 315.32
238315.34 315.35 315.39 315.4 315.5 315.8 315.9 316 317 318.0 318.1 318.2 319
239V71.09
240""".split())
242# -----------------------------------------------------------------------------
243# ICD-10; from the client: camcops --print_icd10_codes
244# -----------------------------------------------------------------------------
246CLIENT_ICD10_CODES = set("""
247F00 F00.0 F00.00 F00.000 F00.001 F00.002 F00.01 F00.010 F00.011 F00.012 F00.02
248F00.020 F00.021 F00.022 F00.03 F00.030 F00.031 F00.032 F00.04 F00.040 F00.041
249F00.042 F00.1 F00.10 F00.100 F00.101 F00.102 F00.11 F00.110 F00.111 F00.112
250F00.12 F00.120 F00.121 F00.122 F00.13 F00.130 F00.131 F00.132 F00.14 F00.140
251F00.141 F00.142 F00.2 F00.20 F00.200 F00.201 F00.202 F00.21 F00.210 F00.211
252F00.212 F00.22 F00.220 F00.221 F00.222 F00.23 F00.230 F00.231 F00.232 F00.24
253F00.240 F00.241 F00.242 F00.9 F00.90 F00.900 F00.901 F00.902 F00.91 F00.910
254F00.911 F00.912 F00.92 F00.920 F00.921 F00.922 F00.93 F00.930 F00.931 F00.932
255F00.94 F00.940 F00.941 F00.942 F01 F01.0 F01.00 F01.000 F01.001 F01.002 F01.01
256F01.010 F01.011 F01.012 F01.02 F01.020 F01.021 F01.022 F01.03 F01.030 F01.031
257F01.032 F01.04 F01.040 F01.041 F01.042 F01.1 F01.10 F01.100 F01.101 F01.102
258F01.11 F01.110 F01.111 F01.112 F01.12 F01.120 F01.121 F01.122 F01.13 F01.130
259F01.131 F01.132 F01.14 F01.140 F01.141 F01.142 F01.2 F01.20 F01.200 F01.201
260F01.202 F01.21 F01.210 F01.211 F01.212 F01.22 F01.220 F01.221 F01.222 F01.23
261F01.230 F01.231 F01.232 F01.24 F01.240 F01.241 F01.242 F01.3 F01.30 F01.300
262F01.301 F01.302 F01.31 F01.310 F01.311 F01.312 F01.32 F01.320 F01.321 F01.322
263F01.33 F01.330 F01.331 F01.332 F01.34 F01.340 F01.341 F01.342 F01.8 F01.80
264F01.800 F01.801 F01.802 F01.81 F01.810 F01.811 F01.812 F01.82 F01.820 F01.821
265F01.822 F01.83 F01.830 F01.831 F01.832 F01.84 F01.840 F01.841 F01.842 F01.9
266F01.90 F01.900 F01.901 F01.902 F01.91 F01.910 F01.911 F01.912 F01.92 F01.920
267F01.921 F01.922 F01.93 F01.930 F01.931 F01.932 F01.94 F01.940 F01.941 F01.942
268F02 F02.0 F02.00 F02.000 F02.001 F02.002 F02.01 F02.010 F02.011 F02.012 F02.02
269F02.020 F02.021 F02.022 F02.03 F02.030 F02.031 F02.032 F02.04 F02.040 F02.041
270F02.042 F02.1 F02.10 F02.100 F02.101 F02.102 F02.11 F02.110 F02.111 F02.112
271F02.12 F02.120 F02.121 F02.122 F02.13 F02.130 F02.131 F02.132 F02.14 F02.140
272F02.141 F02.142 F02.2 F02.20 F02.200 F02.201 F02.202 F02.21 F02.210 F02.211
273F02.212 F02.22 F02.220 F02.221 F02.222 F02.23 F02.230 F02.231 F02.232 F02.24
274F02.240 F02.241 F02.242 F02.3 F02.30 F02.300 F02.301 F02.302 F02.31 F02.310
275F02.311 F02.312 F02.32 F02.320 F02.321 F02.322 F02.33 F02.330 F02.331 F02.332
276F02.34 F02.340 F02.341 F02.342 F02.4 F02.40 F02.400 F02.401 F02.402 F02.41
277F02.410 F02.411 F02.412 F02.42 F02.420 F02.421 F02.422 F02.43 F02.430 F02.431
278F02.432 F02.44 F02.440 F02.441 F02.442 F02.8 F02.80 F02.800 F02.801 F02.802
279F02.81 F02.810 F02.811 F02.812 F02.82 F02.820 F02.821 F02.822 F02.83 F02.830
280F02.831 F02.832 F02.84 F02.840 F02.841 F02.842 F03 F03.0 F03.00 F03.000 F03.001
281F03.002 F03.01 F03.010 F03.011 F03.012 F03.02 F03.020 F03.021 F03.022 F03.03
282F03.030 F03.031 F03.032 F03.04 F03.040 F03.041 F03.042 F04 F05 F05.0 F05.1
283F05.8 F05.9 F06 F06.0 F06.1 F06.2 F06.3 F06.4 F06.5 F06.6 F06.7 F06.8 F06.9 F07
284F07.0 F07.1 F07.2 F07.8 F07.9 F09 F10 F10.0 F10.00 F10.01 F10.02 F10.03 F10.04
285F10.05 F10.06 F10.07 F10.1 F10.2 F10.20 F10.200 F10.201 F10.202 F10.21 F10.22
286F10.23 F10.24 F10.241 F10.242 F10.25 F10.26 F10.3 F10.30 F10.31 F10.4 F10.40
287F10.41 F10.5 F10.50 F10.51 F10.52 F10.53 F10.54 F10.55 F10.56 F10.6 F10.7
288F10.70 F10.71 F10.72 F10.73 F10.74 F10.75 F10.8 F10.9 F11 F11.0 F11.00 F11.01
289F11.02 F11.03 F11.04 F11.05 F11.06 F11.1 F11.2 F11.20 F11.200 F11.201 F11.202
290F11.21 F11.22 F11.23 F11.24 F11.241 F11.242 F11.25 F11.26 F11.3 F11.30 F11.31
291F11.4 F11.40 F11.41 F11.5 F11.50 F11.51 F11.52 F11.53 F11.54 F11.55 F11.56
292F11.6 F11.7 F11.70 F11.71 F11.72 F11.73 F11.74 F11.75 F11.8 F11.9 F12 F12.0
293F12.00 F12.01 F12.02 F12.03 F12.04 F12.05 F12.06 F12.1 F12.2 F12.20 F12.200
294F12.201 F12.202 F12.21 F12.22 F12.23 F12.24 F12.241 F12.242 F12.25 F12.26 F12.3
295F12.30 F12.31 F12.4 F12.40 F12.41 F12.5 F12.50 F12.51 F12.52 F12.53 F12.54
296F12.55 F12.56 F12.6 F12.7 F12.70 F12.71 F12.72 F12.73 F12.74 F12.75 F12.8 F12.9
297F13 F13.0 F13.00 F13.01 F13.02 F13.03 F13.04 F13.05 F13.06 F13.1 F13.2 F13.20
298F13.200 F13.201 F13.202 F13.21 F13.22 F13.23 F13.24 F13.241 F13.242 F13.25
299F13.26 F13.3 F13.30 F13.31 F13.4 F13.40 F13.41 F13.5 F13.50 F13.51 F13.52
300F13.53 F13.54 F13.55 F13.56 F13.6 F13.7 F13.70 F13.71 F13.72 F13.73 F13.74
301F13.75 F13.8 F13.9 F14 F14.0 F14.00 F14.01 F14.02 F14.03 F14.04 F14.05 F14.06
302F14.1 F14.2 F14.20 F14.200 F14.201 F14.202 F14.21 F14.22 F14.23 F14.24 F14.241
303F14.242 F14.25 F14.26 F14.3 F14.30 F14.31 F14.4 F14.40 F14.41 F14.5 F14.50
304F14.51 F14.52 F14.53 F14.54 F14.55 F14.56 F14.6 F14.7 F14.70 F14.71 F14.72
305F14.73 F14.74 F14.75 F14.8 F14.9 F15 F15.0 F15.00 F15.01 F15.02 F15.03 F15.04
306F15.05 F15.06 F15.1 F15.2 F15.20 F15.200 F15.201 F15.202 F15.21 F15.22 F15.23
307F15.24 F15.241 F15.242 F15.25 F15.26 F15.3 F15.30 F15.31 F15.4 F15.40 F15.41
308F15.5 F15.50 F15.51 F15.52 F15.53 F15.54 F15.55 F15.56 F15.6 F15.7 F15.70
309F15.71 F15.72 F15.73 F15.74 F15.75 F15.8 F15.9 F16 F16.0 F16.00 F16.01 F16.02
310F16.03 F16.04 F16.05 F16.06 F16.1 F16.2 F16.20 F16.200 F16.201 F16.202 F16.21
311F16.22 F16.23 F16.24 F16.241 F16.242 F16.25 F16.26 F16.3 F16.30 F16.31 F16.4
312F16.40 F16.41 F16.5 F16.50 F16.51 F16.52 F16.53 F16.54 F16.55 F16.56 F16.6
313F16.7 F16.70 F16.71 F16.72 F16.73 F16.74 F16.75 F16.8 F16.9 F17 F17.0 F17.00
314F17.01 F17.02 F17.03 F17.04 F17.05 F17.06 F17.1 F17.2 F17.20 F17.200 F17.201
315F17.202 F17.21 F17.22 F17.23 F17.24 F17.241 F17.242 F17.25 F17.26 F17.3 F17.30
316F17.31 F17.4 F17.40 F17.41 F17.5 F17.50 F17.51 F17.52 F17.53 F17.54 F17.55
317F17.56 F17.6 F17.7 F17.70 F17.71 F17.72 F17.73 F17.74 F17.75 F17.8 F17.9 F18
318F18.0 F18.00 F18.01 F18.02 F18.03 F18.04 F18.05 F18.06 F18.1 F18.2 F18.20
319F18.200 F18.201 F18.202 F18.21 F18.22 F18.23 F18.24 F18.241 F18.242 F18.25
320F18.26 F18.3 F18.30 F18.31 F18.4 F18.40 F18.41 F18.5 F18.50 F18.51 F18.52
321F18.53 F18.54 F18.55 F18.56 F18.6 F18.7 F18.70 F18.71 F18.72 F18.73 F18.74
322F18.75 F18.8 F18.9 F19 F19.0 F19.00 F19.01 F19.02 F19.03 F19.04 F19.05 F19.06
323F19.1 F19.2 F19.20 F19.200 F19.201 F19.202 F19.21 F19.22 F19.23 F19.24 F19.241
324F19.242 F19.25 F19.26 F19.3 F19.30 F19.31 F19.4 F19.40 F19.41 F19.5 F19.50
325F19.51 F19.52 F19.53 F19.54 F19.55 F19.56 F19.6 F19.7 F19.70 F19.71 F19.72
326F19.73 F19.74 F19.75 F19.8 F19.9 F20 F20.0 F20.1 F20.2 F20.3 F20.4 F20.5 F20.6
327F20.8 F20.9 F21 F22 F22.0 F22.8 F22.9 F23 F23.0 F23.1 F23.2 F23.3 F23.8 F23.9
328F23.90 F23.91 F24 F25 F25.0 F25.00 F25.01 F25.1 F25.10 F25.11 F25.2 F25.20
329F25.21 F25.8 F25.80 F25.81 F25.9 F25.90 F25.91 F28 F29 F30 F30.0 F30.1 F30.2
330F30.20 F30.21 F30.8 F30.9 F31 F31.0 F31.1 F31.2 F31.20 F31.21 F31.3 F31.30
331F31.31 F31.4 F31.5 F31.50 F31.51 F31.6 F31.7 F31.8 F31.9 F32 F32.0 F32.00
332F32.01 F32.1 F32.10 F32.11 F32.2 F32.3 F32.30 F32.31 F32.8 F32.9 F33 F33.0
333F33.00 F33.01 F33.1 F33.10 F33.11 F33.2 F33.3 F33.30 F33.31 F33.4 F33.8 F33.9
334F34 F34.0 F34.1 F34.8 F34.9 F38 F38.0 F38.00 F38.1 F38.10 F38.8 F39 F40 F40.0
335F40.00 F40.01 F40.1 F40.2 F40.8 F40.9 F41 F41.0 F41.00 F41.01 F41.1 F41.2 F41.3
336F41.8 F41.9 F42 F42.0 F42.1 F42.2 F42.8 F42.9 F43 F43.0 F43.00 F43.01 F43.02
337F43.1 F43.2 F43.20 F43.21 F43.22 F43.23 F43.24 F43.25 F43.28 F43.8 F43.9 F44
338F44.0 F44.1 F44.2 F44.3 F44.4 F44.5 F44.6 F44.7 F44.8 F44.80 F44.81 F44.82
339F44.88 F44.9 F45 F45.0 F45.1 F45.2 F45.3 F45.30 F45.31 F45.32 F45.33 F45.34
340F45.38 F45.4 F45.8 F45.9 F48 F48.0 F48.1 F48.8 F48.9 F50 F50.0 F50.1 F50.2
341F50.3 F50.4 F50.5 F50.8 F50.9 F51 F51.0 F51.1 F51.2 F51.3 F51.4 F51.5 F51.8
342F51.9 F52 F52.0 F52.1 F52.10 F52.11 F52.2 F52.3 F52.4 F52.5 F52.6 F52.7 F52.8
343F52.9 F53 F53.0 F53.1 F53.8 F53.9 F54 F55 F59 F60 F60.0 F60.1 F60.2 F60.3
344F60.30 F60.31 F60.4 F60.5 F60.6 F60.7 F60.8 F60.9 F61 F62 F62.0 F62.1 F62.8
345F62.9 F63 F63.0 F63.1 F63.2 F63.3 F63.8 F63.9 F64 F64.0 F64.1 F64.2 F64.8 F64.9
346F65 F65.0 F65.1 F65.2 F65.3 F65.4 F65.5 F65.6 F65.8 F65.9 F66 F66.0 F66.1 F66.2
347F66.8 F66.9 F66.90 F66.91 F66.92 F66.98 F68 F68.0 F68.1 F68.8 F69 F70 F70.0
348F70.1 F70.8 F70.9 F71 F71.0 F71.1 F71.8 F71.9 F72 F72.0 F72.1 F72.8 F72.9 F73
349F73.0 F73.1 F73.8 F73.9 F78 F78.0 F78.1 F78.8 F78.9 F79 F79.0 F79.1 F79.8 F79.9
350F80 F80.0 F80.1 F80.2 F80.3 F80.8 F80.9 F81 F81.0 F81.1 F81.2 F81.3 F81.8 F81.9
351F82 F83 F84 F84.0 F84.1 F84.10 F84.11 F84.12 F84.2 F84.3 F84.4 F84.5 F84.8
352F84.9 F88 F89 F90 F90.0 F90.1 F90.8 F90.9 F91 F91.0 F91.1 F91.2 F91.3 F91.8
353F91.9 F92 F92.0 F92.8 F92.9 F93 F93.0 F93.1 F93.2 F93.3 F93.8 F93.80 F93.9 F94
354F94.0 F94.1 F94.2 F94.8 F94.9 F95 F95.0 F95.1 F95.2 F95.8 F95.9 F98 F98.0
355F98.00 F98.01 F98.02 F98.1 F98.10 F98.11 F98.12 F98.2 F98.3 F98.4 F98.40 F98.41
356F98.42 F98.5 F98.6 F98.8 F98.9 F99 R40 R40.0 R40.1 R40.2 R41 R41.0 R41.1 R41.2
357R41.3 R41.8 R42 R43 R43.0 R43.1 R43.2 R43.8 R44 R44.0 R44.1 R44.2 R44.3 R44.8
358R45 R45.0 R45.1 R45.2 R45.3 R45.4 R45.5 R45.6 R45.7 R45.8 R46 R46.0 R46.1 R46.2
359R46.3 R46.4 R46.5 R46.6 R46.7 R46.8 X60 X60.0 X60.00 X60.01 X60.02 X60.03
360X60.04 X60.08 X60.09 X60.1 X60.10 X60.11 X60.12 X60.13 X60.14 X60.18 X60.19
361X60.2 X60.20 X60.21 X60.22 X60.23 X60.24 X60.28 X60.29 X60.3 X60.30 X60.31
362X60.32 X60.33 X60.34 X60.38 X60.39 X60.4 X60.40 X60.41 X60.42 X60.43 X60.44
363X60.48 X60.49 X60.5 X60.50 X60.51 X60.52 X60.53 X60.54 X60.58 X60.59 X60.6
364X60.60 X60.61 X60.62 X60.63 X60.64 X60.68 X60.69 X60.7 X60.70 X60.71 X60.72
365X60.73 X60.74 X60.78 X60.79 X60.8 X60.80 X60.81 X60.82 X60.83 X60.84 X60.88
366X60.89 X60.9 X60.90 X60.91 X60.92 X60.93 X60.94 X60.98 X60.99 X61 X61.0 X61.00
367X61.01 X61.02 X61.03 X61.04 X61.08 X61.09 X61.1 X61.10 X61.11 X61.12 X61.13
368X61.14 X61.18 X61.19 X61.2 X61.20 X61.21 X61.22 X61.23 X61.24 X61.28 X61.29
369X61.3 X61.30 X61.31 X61.32 X61.33 X61.34 X61.38 X61.39 X61.4 X61.40 X61.41
370X61.42 X61.43 X61.44 X61.48 X61.49 X61.5 X61.50 X61.51 X61.52 X61.53 X61.54
371X61.58 X61.59 X61.6 X61.60 X61.61 X61.62 X61.63 X61.64 X61.68 X61.69 X61.7
372X61.70 X61.71 X61.72 X61.73 X61.74 X61.78 X61.79 X61.8 X61.80 X61.81 X61.82
373X61.83 X61.84 X61.88 X61.89 X61.9 X61.90 X61.91 X61.92 X61.93 X61.94 X61.98
374X61.99 X62 X62.0 X62.00 X62.01 X62.02 X62.03 X62.04 X62.08 X62.09 X62.1 X62.10
375X62.11 X62.12 X62.13 X62.14 X62.18 X62.19 X62.2 X62.20 X62.21 X62.22 X62.23
376X62.24 X62.28 X62.29 X62.3 X62.30 X62.31 X62.32 X62.33 X62.34 X62.38 X62.39
377X62.4 X62.40 X62.41 X62.42 X62.43 X62.44 X62.48 X62.49 X62.5 X62.50 X62.51
378X62.52 X62.53 X62.54 X62.58 X62.59 X62.6 X62.60 X62.61 X62.62 X62.63 X62.64
379X62.68 X62.69 X62.7 X62.70 X62.71 X62.72 X62.73 X62.74 X62.78 X62.79 X62.8
380X62.80 X62.81 X62.82 X62.83 X62.84 X62.88 X62.89 X62.9 X62.90 X62.91 X62.92
381X62.93 X62.94 X62.98 X62.99 X63 X63.0 X63.00 X63.01 X63.02 X63.03 X63.04 X63.08
382X63.09 X63.1 X63.10 X63.11 X63.12 X63.13 X63.14 X63.18 X63.19 X63.2 X63.20
383X63.21 X63.22 X63.23 X63.24 X63.28 X63.29 X63.3 X63.30 X63.31 X63.32 X63.33
384X63.34 X63.38 X63.39 X63.4 X63.40 X63.41 X63.42 X63.43 X63.44 X63.48 X63.49
385X63.5 X63.50 X63.51 X63.52 X63.53 X63.54 X63.58 X63.59 X63.6 X63.60 X63.61
386X63.62 X63.63 X63.64 X63.68 X63.69 X63.7 X63.70 X63.71 X63.72 X63.73 X63.74
387X63.78 X63.79 X63.8 X63.80 X63.81 X63.82 X63.83 X63.84 X63.88 X63.89 X63.9
388X63.90 X63.91 X63.92 X63.93 X63.94 X63.98 X63.99 X64 X64.0 X64.00 X64.01 X64.02
389X64.03 X64.04 X64.08 X64.09 X64.1 X64.10 X64.11 X64.12 X64.13 X64.14 X64.18
390X64.19 X64.2 X64.20 X64.21 X64.22 X64.23 X64.24 X64.28 X64.29 X64.3 X64.30
391X64.31 X64.32 X64.33 X64.34 X64.38 X64.39 X64.4 X64.40 X64.41 X64.42 X64.43
392X64.44 X64.48 X64.49 X64.5 X64.50 X64.51 X64.52 X64.53 X64.54 X64.58 X64.59
393X64.6 X64.60 X64.61 X64.62 X64.63 X64.64 X64.68 X64.69 X64.7 X64.70 X64.71
394X64.72 X64.73 X64.74 X64.78 X64.79 X64.8 X64.80 X64.81 X64.82 X64.83 X64.84
395X64.88 X64.89 X64.9 X64.90 X64.91 X64.92 X64.93 X64.94 X64.98 X64.99 X65 X65.0
396X65.00 X65.01 X65.02 X65.03 X65.04 X65.08 X65.09 X65.1 X65.10 X65.11 X65.12
397X65.13 X65.14 X65.18 X65.19 X65.2 X65.20 X65.21 X65.22 X65.23 X65.24 X65.28
398X65.29 X65.3 X65.30 X65.31 X65.32 X65.33 X65.34 X65.38 X65.39 X65.4 X65.40
399X65.41 X65.42 X65.43 X65.44 X65.48 X65.49 X65.5 X65.50 X65.51 X65.52 X65.53
400X65.54 X65.58 X65.59 X65.6 X65.60 X65.61 X65.62 X65.63 X65.64 X65.68 X65.69
401X65.7 X65.70 X65.71 X65.72 X65.73 X65.74 X65.78 X65.79 X65.8 X65.80 X65.81
402X65.82 X65.83 X65.84 X65.88 X65.89 X65.9 X65.90 X65.91 X65.92 X65.93 X65.94
403X65.98 X65.99 X66 X66.0 X66.00 X66.01 X66.02 X66.03 X66.04 X66.08 X66.09 X66.1
404X66.10 X66.11 X66.12 X66.13 X66.14 X66.18 X66.19 X66.2 X66.20 X66.21 X66.22
405X66.23 X66.24 X66.28 X66.29 X66.3 X66.30 X66.31 X66.32 X66.33 X66.34 X66.38
406X66.39 X66.4 X66.40 X66.41 X66.42 X66.43 X66.44 X66.48 X66.49 X66.5 X66.50
407X66.51 X66.52 X66.53 X66.54 X66.58 X66.59 X66.6 X66.60 X66.61 X66.62 X66.63
408X66.64 X66.68 X66.69 X66.7 X66.70 X66.71 X66.72 X66.73 X66.74 X66.78 X66.79
409X66.8 X66.80 X66.81 X66.82 X66.83 X66.84 X66.88 X66.89 X66.9 X66.90 X66.91
410X66.92 X66.93 X66.94 X66.98 X66.99 X67 X67.0 X67.00 X67.01 X67.02 X67.03 X67.04
411X67.08 X67.09 X67.1 X67.10 X67.11 X67.12 X67.13 X67.14 X67.18 X67.19 X67.2
412X67.20 X67.21 X67.22 X67.23 X67.24 X67.28 X67.29 X67.3 X67.30 X67.31 X67.32
413X67.33 X67.34 X67.38 X67.39 X67.4 X67.40 X67.41 X67.42 X67.43 X67.44 X67.48
414X67.49 X67.5 X67.50 X67.51 X67.52 X67.53 X67.54 X67.58 X67.59 X67.6 X67.60
415X67.61 X67.62 X67.63 X67.64 X67.68 X67.69 X67.7 X67.70 X67.71 X67.72 X67.73
416X67.74 X67.78 X67.79 X67.8 X67.80 X67.81 X67.82 X67.83 X67.84 X67.88 X67.89
417X67.9 X67.90 X67.91 X67.92 X67.93 X67.94 X67.98 X67.99 X68 X68.0 X68.00 X68.01
418X68.02 X68.03 X68.04 X68.08 X68.09 X68.1 X68.10 X68.11 X68.12 X68.13 X68.14
419X68.18 X68.19 X68.2 X68.20 X68.21 X68.22 X68.23 X68.24 X68.28 X68.29 X68.3
420X68.30 X68.31 X68.32 X68.33 X68.34 X68.38 X68.39 X68.4 X68.40 X68.41 X68.42
421X68.43 X68.44 X68.48 X68.49 X68.5 X68.50 X68.51 X68.52 X68.53 X68.54 X68.58
422X68.59 X68.6 X68.60 X68.61 X68.62 X68.63 X68.64 X68.68 X68.69 X68.7 X68.70
423X68.71 X68.72 X68.73 X68.74 X68.78 X68.79 X68.8 X68.80 X68.81 X68.82 X68.83
424X68.84 X68.88 X68.89 X68.9 X68.90 X68.91 X68.92 X68.93 X68.94 X68.98 X68.99 X69
425X69.0 X69.00 X69.01 X69.02 X69.03 X69.04 X69.08 X69.09 X69.1 X69.10 X69.11
426X69.12 X69.13 X69.14 X69.18 X69.19 X69.2 X69.20 X69.21 X69.22 X69.23 X69.24
427X69.28 X69.29 X69.3 X69.30 X69.31 X69.32 X69.33 X69.34 X69.38 X69.39 X69.4
428X69.40 X69.41 X69.42 X69.43 X69.44 X69.48 X69.49 X69.5 X69.50 X69.51 X69.52
429X69.53 X69.54 X69.58 X69.59 X69.6 X69.60 X69.61 X69.62 X69.63 X69.64 X69.68
430X69.69 X69.7 X69.70 X69.71 X69.72 X69.73 X69.74 X69.78 X69.79 X69.8 X69.80
431X69.81 X69.82 X69.83 X69.84 X69.88 X69.89 X69.9 X69.90 X69.91 X69.92 X69.93
432X69.94 X69.98 X69.99 X70 X70.0 X70.00 X70.01 X70.02 X70.03 X70.04 X70.08 X70.09
433X70.1 X70.10 X70.11 X70.12 X70.13 X70.14 X70.18 X70.19 X70.2 X70.20 X70.21
434X70.22 X70.23 X70.24 X70.28 X70.29 X70.3 X70.30 X70.31 X70.32 X70.33 X70.34
435X70.38 X70.39 X70.4 X70.40 X70.41 X70.42 X70.43 X70.44 X70.48 X70.49 X70.5
436X70.50 X70.51 X70.52 X70.53 X70.54 X70.58 X70.59 X70.6 X70.60 X70.61 X70.62
437X70.63 X70.64 X70.68 X70.69 X70.7 X70.70 X70.71 X70.72 X70.73 X70.74 X70.78
438X70.79 X70.8 X70.80 X70.81 X70.82 X70.83 X70.84 X70.88 X70.89 X70.9 X70.90
439X70.91 X70.92 X70.93 X70.94 X70.98 X70.99 X71 X71.0 X71.00 X71.01 X71.02 X71.03
440X71.04 X71.08 X71.09 X71.1 X71.10 X71.11 X71.12 X71.13 X71.14 X71.18 X71.19
441X71.2 X71.20 X71.21 X71.22 X71.23 X71.24 X71.28 X71.29 X71.3 X71.30 X71.31
442X71.32 X71.33 X71.34 X71.38 X71.39 X71.4 X71.40 X71.41 X71.42 X71.43 X71.44
443X71.48 X71.49 X71.5 X71.50 X71.51 X71.52 X71.53 X71.54 X71.58 X71.59 X71.6
444X71.60 X71.61 X71.62 X71.63 X71.64 X71.68 X71.69 X71.7 X71.70 X71.71 X71.72
445X71.73 X71.74 X71.78 X71.79 X71.8 X71.80 X71.81 X71.82 X71.83 X71.84 X71.88
446X71.89 X71.9 X71.90 X71.91 X71.92 X71.93 X71.94 X71.98 X71.99 X72 X72.0 X72.00
447X72.01 X72.02 X72.03 X72.04 X72.08 X72.09 X72.1 X72.10 X72.11 X72.12 X72.13
448X72.14 X72.18 X72.19 X72.2 X72.20 X72.21 X72.22 X72.23 X72.24 X72.28 X72.29
449X72.3 X72.30 X72.31 X72.32 X72.33 X72.34 X72.38 X72.39 X72.4 X72.40 X72.41
450X72.42 X72.43 X72.44 X72.48 X72.49 X72.5 X72.50 X72.51 X72.52 X72.53 X72.54
451X72.58 X72.59 X72.6 X72.60 X72.61 X72.62 X72.63 X72.64 X72.68 X72.69 X72.7
452X72.70 X72.71 X72.72 X72.73 X72.74 X72.78 X72.79 X72.8 X72.80 X72.81 X72.82
453X72.83 X72.84 X72.88 X72.89 X72.9 X72.90 X72.91 X72.92 X72.93 X72.94 X72.98
454X72.99 X73 X73.0 X73.00 X73.01 X73.02 X73.03 X73.04 X73.08 X73.09 X73.1 X73.10
455X73.11 X73.12 X73.13 X73.14 X73.18 X73.19 X73.2 X73.20 X73.21 X73.22 X73.23
456X73.24 X73.28 X73.29 X73.3 X73.30 X73.31 X73.32 X73.33 X73.34 X73.38 X73.39
457X73.4 X73.40 X73.41 X73.42 X73.43 X73.44 X73.48 X73.49 X73.5 X73.50 X73.51
458X73.52 X73.53 X73.54 X73.58 X73.59 X73.6 X73.60 X73.61 X73.62 X73.63 X73.64
459X73.68 X73.69 X73.7 X73.70 X73.71 X73.72 X73.73 X73.74 X73.78 X73.79 X73.8
460X73.80 X73.81 X73.82 X73.83 X73.84 X73.88 X73.89 X73.9 X73.90 X73.91 X73.92
461X73.93 X73.94 X73.98 X73.99 X74 X74.0 X74.00 X74.01 X74.02 X74.03 X74.04 X74.08
462X74.09 X74.1 X74.10 X74.11 X74.12 X74.13 X74.14 X74.18 X74.19 X74.2 X74.20
463X74.21 X74.22 X74.23 X74.24 X74.28 X74.29 X74.3 X74.30 X74.31 X74.32 X74.33
464X74.34 X74.38 X74.39 X74.4 X74.40 X74.41 X74.42 X74.43 X74.44 X74.48 X74.49
465X74.5 X74.50 X74.51 X74.52 X74.53 X74.54 X74.58 X74.59 X74.6 X74.60 X74.61
466X74.62 X74.63 X74.64 X74.68 X74.69 X74.7 X74.70 X74.71 X74.72 X74.73 X74.74
467X74.78 X74.79 X74.8 X74.80 X74.81 X74.82 X74.83 X74.84 X74.88 X74.89 X74.9
468X74.90 X74.91 X74.92 X74.93 X74.94 X74.98 X74.99 X75 X75.0 X75.00 X75.01 X75.02
469X75.03 X75.04 X75.08 X75.09 X75.1 X75.10 X75.11 X75.12 X75.13 X75.14 X75.18
470X75.19 X75.2 X75.20 X75.21 X75.22 X75.23 X75.24 X75.28 X75.29 X75.3 X75.30
471X75.31 X75.32 X75.33 X75.34 X75.38 X75.39 X75.4 X75.40 X75.41 X75.42 X75.43
472X75.44 X75.48 X75.49 X75.5 X75.50 X75.51 X75.52 X75.53 X75.54 X75.58 X75.59
473X75.6 X75.60 X75.61 X75.62 X75.63 X75.64 X75.68 X75.69 X75.7 X75.70 X75.71
474X75.72 X75.73 X75.74 X75.78 X75.79 X75.8 X75.80 X75.81 X75.82 X75.83 X75.84
475X75.88 X75.89 X75.9 X75.90 X75.91 X75.92 X75.93 X75.94 X75.98 X75.99 X76 X76.0
476X76.00 X76.01 X76.02 X76.03 X76.04 X76.08 X76.09 X76.1 X76.10 X76.11 X76.12
477X76.13 X76.14 X76.18 X76.19 X76.2 X76.20 X76.21 X76.22 X76.23 X76.24 X76.28
478X76.29 X76.3 X76.30 X76.31 X76.32 X76.33 X76.34 X76.38 X76.39 X76.4 X76.40
479X76.41 X76.42 X76.43 X76.44 X76.48 X76.49 X76.5 X76.50 X76.51 X76.52 X76.53
480X76.54 X76.58 X76.59 X76.6 X76.60 X76.61 X76.62 X76.63 X76.64 X76.68 X76.69
481X76.7 X76.70 X76.71 X76.72 X76.73 X76.74 X76.78 X76.79 X76.8 X76.80 X76.81
482X76.82 X76.83 X76.84 X76.88 X76.89 X76.9 X76.90 X76.91 X76.92 X76.93 X76.94
483X76.98 X76.99 X77 X77.0 X77.00 X77.01 X77.02 X77.03 X77.04 X77.08 X77.09 X77.1
484X77.10 X77.11 X77.12 X77.13 X77.14 X77.18 X77.19 X77.2 X77.20 X77.21 X77.22
485X77.23 X77.24 X77.28 X77.29 X77.3 X77.30 X77.31 X77.32 X77.33 X77.34 X77.38
486X77.39 X77.4 X77.40 X77.41 X77.42 X77.43 X77.44 X77.48 X77.49 X77.5 X77.50
487X77.51 X77.52 X77.53 X77.54 X77.58 X77.59 X77.6 X77.60 X77.61 X77.62 X77.63
488X77.64 X77.68 X77.69 X77.7 X77.70 X77.71 X77.72 X77.73 X77.74 X77.78 X77.79
489X77.8 X77.80 X77.81 X77.82 X77.83 X77.84 X77.88 X77.89 X77.9 X77.90 X77.91
490X77.92 X77.93 X77.94 X77.98 X77.99 X78 X78.0 X78.00 X78.01 X78.02 X78.03 X78.04
491X78.08 X78.09 X78.1 X78.10 X78.11 X78.12 X78.13 X78.14 X78.18 X78.19 X78.2
492X78.20 X78.21 X78.22 X78.23 X78.24 X78.28 X78.29 X78.3 X78.30 X78.31 X78.32
493X78.33 X78.34 X78.38 X78.39 X78.4 X78.40 X78.41 X78.42 X78.43 X78.44 X78.48
494X78.49 X78.5 X78.50 X78.51 X78.52 X78.53 X78.54 X78.58 X78.59 X78.6 X78.60
495X78.61 X78.62 X78.63 X78.64 X78.68 X78.69 X78.7 X78.70 X78.71 X78.72 X78.73
496X78.74 X78.78 X78.79 X78.8 X78.80 X78.81 X78.82 X78.83 X78.84 X78.88 X78.89
497X78.9 X78.90 X78.91 X78.92 X78.93 X78.94 X78.98 X78.99 X79 X79.0 X79.00 X79.01
498X79.02 X79.03 X79.04 X79.08 X79.09 X79.1 X79.10 X79.11 X79.12 X79.13 X79.14
499X79.18 X79.19 X79.2 X79.20 X79.21 X79.22 X79.23 X79.24 X79.28 X79.29 X79.3
500X79.30 X79.31 X79.32 X79.33 X79.34 X79.38 X79.39 X79.4 X79.40 X79.41 X79.42
501X79.43 X79.44 X79.48 X79.49 X79.5 X79.50 X79.51 X79.52 X79.53 X79.54 X79.58
502X79.59 X79.6 X79.60 X79.61 X79.62 X79.63 X79.64 X79.68 X79.69 X79.7 X79.70
503X79.71 X79.72 X79.73 X79.74 X79.78 X79.79 X79.8 X79.80 X79.81 X79.82 X79.83
504X79.84 X79.88 X79.89 X79.9 X79.90 X79.91 X79.92 X79.93 X79.94 X79.98 X79.99 X80
505X80.0 X80.00 X80.01 X80.02 X80.03 X80.04 X80.08 X80.09 X80.1 X80.10 X80.11
506X80.12 X80.13 X80.14 X80.18 X80.19 X80.2 X80.20 X80.21 X80.22 X80.23 X80.24
507X80.28 X80.29 X80.3 X80.30 X80.31 X80.32 X80.33 X80.34 X80.38 X80.39 X80.4
508X80.40 X80.41 X80.42 X80.43 X80.44 X80.48 X80.49 X80.5 X80.50 X80.51 X80.52
509X80.53 X80.54 X80.58 X80.59 X80.6 X80.60 X80.61 X80.62 X80.63 X80.64 X80.68
510X80.69 X80.7 X80.70 X80.71 X80.72 X80.73 X80.74 X80.78 X80.79 X80.8 X80.80
511X80.81 X80.82 X80.83 X80.84 X80.88 X80.89 X80.9 X80.90 X80.91 X80.92 X80.93
512X80.94 X80.98 X80.99 X81 X81.0 X81.00 X81.01 X81.02 X81.03 X81.04 X81.08 X81.09
513X81.1 X81.10 X81.11 X81.12 X81.13 X81.14 X81.18 X81.19 X81.2 X81.20 X81.21
514X81.22 X81.23 X81.24 X81.28 X81.29 X81.3 X81.30 X81.31 X81.32 X81.33 X81.34
515X81.38 X81.39 X81.4 X81.40 X81.41 X81.42 X81.43 X81.44 X81.48 X81.49 X81.5
516X81.50 X81.51 X81.52 X81.53 X81.54 X81.58 X81.59 X81.6 X81.60 X81.61 X81.62
517X81.63 X81.64 X81.68 X81.69 X81.7 X81.70 X81.71 X81.72 X81.73 X81.74 X81.78
518X81.79 X81.8 X81.80 X81.81 X81.82 X81.83 X81.84 X81.88 X81.89 X81.9 X81.90
519X81.91 X81.92 X81.93 X81.94 X81.98 X81.99 X82 X82.0 X82.00 X82.01 X82.02 X82.03
520X82.04 X82.08 X82.09 X82.1 X82.10 X82.11 X82.12 X82.13 X82.14 X82.18 X82.19
521X82.2 X82.20 X82.21 X82.22 X82.23 X82.24 X82.28 X82.29 X82.3 X82.30 X82.31
522X82.32 X82.33 X82.34 X82.38 X82.39 X82.4 X82.40 X82.41 X82.42 X82.43 X82.44
523X82.48 X82.49 X82.5 X82.50 X82.51 X82.52 X82.53 X82.54 X82.58 X82.59 X82.6
524X82.60 X82.61 X82.62 X82.63 X82.64 X82.68 X82.69 X82.7 X82.70 X82.71 X82.72
525X82.73 X82.74 X82.78 X82.79 X82.8 X82.80 X82.81 X82.82 X82.83 X82.84 X82.88
526X82.89 X82.9 X82.90 X82.91 X82.92 X82.93 X82.94 X82.98 X82.99 X83 X83.0 X83.00
527X83.01 X83.02 X83.03 X83.04 X83.08 X83.09 X83.1 X83.10 X83.11 X83.12 X83.13
528X83.14 X83.18 X83.19 X83.2 X83.20 X83.21 X83.22 X83.23 X83.24 X83.28 X83.29
529X83.3 X83.30 X83.31 X83.32 X83.33 X83.34 X83.38 X83.39 X83.4 X83.40 X83.41
530X83.42 X83.43 X83.44 X83.48 X83.49 X83.5 X83.50 X83.51 X83.52 X83.53 X83.54
531X83.58 X83.59 X83.6 X83.60 X83.61 X83.62 X83.63 X83.64 X83.68 X83.69 X83.7
532X83.70 X83.71 X83.72 X83.73 X83.74 X83.78 X83.79 X83.8 X83.80 X83.81 X83.82
533X83.83 X83.84 X83.88 X83.89 X83.9 X83.90 X83.91 X83.92 X83.93 X83.94 X83.98
534X83.99 X84 X84.0 X84.00 X84.01 X84.02 X84.03 X84.04 X84.08 X84.09 X84.1 X84.10
535X84.11 X84.12 X84.13 X84.14 X84.18 X84.19 X84.2 X84.20 X84.21 X84.22 X84.23
536X84.24 X84.28 X84.29 X84.3 X84.30 X84.31 X84.32 X84.33 X84.34 X84.38 X84.39
537X84.4 X84.40 X84.41 X84.42 X84.43 X84.44 X84.48 X84.49 X84.5 X84.50 X84.51
538X84.52 X84.53 X84.54 X84.58 X84.59 X84.6 X84.60 X84.61 X84.62 X84.63 X84.64
539X84.68 X84.69 X84.7 X84.70 X84.71 X84.72 X84.73 X84.74 X84.78 X84.79 X84.8
540X84.80 X84.81 X84.82 X84.83 X84.84 X84.88 X84.89 X84.9 X84.90 X84.91 X84.92
541X84.93 X84.94 X84.98 X84.99 Z00.4 Z03.2 Z71.1
542""".split())
545# =============================================================================
546# The SnomedConcept class, amended
547# =============================================================================
549class SnomedConcept(SnomedConceptCardinalPythonlib):
550 @classmethod
551 def create(cls, concept: SnomedConceptCardinalPythonlib) \
552 -> "SnomedConcept":
553 """
554 Creates a CamCOPS-friendly
555 :class:`camcops_server.cc_modules.cc_snomed.SnomedConcept` from a
556 :class:`cardinal_pythonlib.snomed.SnomedConcept`.
558 The result has extra methods.
559 """
560 return SnomedConcept(identifier=concept.identifier,
561 term=concept.term)
563 def xml_element(self, longform: bool = True) -> XmlElement:
564 """
565 Returns a :class:`camcops_server.cc_modules.cc_xml.XmlElement` for this
566 SNOMED-CT object.
568 Args:
569 longform: print SNOMED-CT concepts in long form?
570 """
571 return XmlElement(
572 name=SNOMED_XML_NAME,
573 value=self.as_string(longform),
574 datatype=XmlDataTypes.STRING
575 )
578# =============================================================================
579# The SnomedExpression class, amended
580# =============================================================================
582class SnomedExpression(SnomedExpressionCardinalPythonlib):
583 def xml_element(self, longform: bool = True) -> XmlElement:
584 """
585 Returns a :class:`camcops_server.cc_modules.cc_xml.XmlElement` for this
586 SNOMED-CT object.
588 Args:
589 longform: print SNOMED-CT expressions in long form?
590 """
591 return XmlElement(
592 name=SNOMED_XML_NAME,
593 value=self.as_string(longform),
594 datatype=XmlDataTypes.STRING
595 )
598# =============================================================================
599# The CamCOPS XML file format for SNOMED-CT
600# =============================================================================
602ROOT_TAG = "snomed_concepts"
603CONCEPT_TAG = "concept"
604LOOKUP_TAG = "lookup"
605LOOKUP_NAME_ATTR = "name"
606LOOKUP_ATTR = "lookup"
607ID_TAG = "id"
608TERM_TAG = "term"
609AUTOGEN_COMMENT = (
610 "Autogenerated XML (see camcops_server.cc_modules.cc_snomed.py); do not "
611 "edit"
612)
615def get_snomed_concepts_from_xml(xml_filename: str) \
616 -> Dict[str, Union[SnomedConcept, List[SnomedConcept]]]:
617 """
618 Reads in all SNOMED-CT concepts from an XML file according to the CamCOPS
619 format.
621 Args:
622 xml_filename: XML filename to read
624 Returns:
625 dict: mapping each lookup code found to a list of
626 :class:`SnomedConcept` objects
628 """
629 log.info("Reading SNOMED-CT XML file: {}", xml_filename)
630 parser = ElementTree.XMLParser(encoding="UTF-8")
631 tree = ElementTree.parse(xml_filename, parser=parser)
632 root = tree.getroot()
633 all_concepts = {} # type: Dict[str, List[SnomedConcept]]
634 find_lookup = "./{tag}[@{attr}]".format(tag=LOOKUP_TAG, attr=LOOKUP_NAME_ATTR) # noqa
635 find_concept = "./{tag}".format(tag=CONCEPT_TAG)
636 find_id_in_concept = "./{tag}".format(tag=ID_TAG)
637 find_name_in_concept = "./{tag}".format(tag=TERM_TAG)
638 for lookuproot in root.findall(find_lookup):
639 # Extract info from the XML
640 lookupname = lookuproot.attrib.get(LOOKUP_NAME_ATTR)
641 for conceptroot in lookuproot.findall(find_concept):
642 id_node = conceptroot.find(find_id_in_concept)
643 identifier = int(id_node.text)
644 name_node = conceptroot.find(find_name_in_concept)
645 name = name_node.text or ""
646 # Stash it
647 concept = SnomedConcept(identifier, name)
648 concepts_for_lookup = all_concepts.setdefault(lookupname, [])
649 concepts_for_lookup.append(concept)
650 # Done
651 return all_concepts
654def write_snomed_concepts_to_xml(
655 xml_filename: str,
656 concepts: Dict[str, List[SnomedConcept]],
657 comment: str = AUTOGEN_COMMENT) -> None:
658 """
659 Writes SNOMED-CT concepts to an XML file in the CamCOPS format.
661 Args:
662 xml_filename: XML filename to write
663 concepts: dictionary mapping lookup codes to a list of
664 :class:`SnomedConcept` objects
665 comment: comment for XML file
666 """
667 # https://stackoverflow.com/questions/3605680/creating-a-simple-xml-file-using-python
668 root = ElementTree.Element(ROOT_TAG)
669 comment_element = ElementTree.Comment(comment)
670 root.insert(0, comment_element)
671 for lookup, concepts_for_lookup in concepts.items():
672 l_el = ElementTree.SubElement(
673 root, LOOKUP_TAG, {LOOKUP_NAME_ATTR: lookup})
674 for concept in concepts_for_lookup:
675 c_el = ElementTree.SubElement(l_el, CONCEPT_TAG)
676 i_el = ElementTree.SubElement(c_el, ID_TAG)
677 i_el.text = str(concept.identifier)
678 n_el = ElementTree.SubElement(c_el, TERM_TAG)
679 n_el.text = concept.term
680 tree = ElementTree.ElementTree(root)
681 log.info("Writing to {!r}", xml_filename)
682 tree.write(xml_filename)
685# =============================================================================
686# SNOMED-CT concepts for CamCOPS tasks
687# =============================================================================
689# -----------------------------------------------------------------------------
690# CamCOPS lookup codes for SNOMED-CT concepts
691# -----------------------------------------------------------------------------
693class SnomedLookup(object):
694 """
695 We're not allowed to embed SNOMED-CT codes in the CamCOPS code. Therefore,
696 within CamCOPS, we use string constants represented in this class. If the
697 local institution is allowed (e.g. in the UK, as below), then it can
698 install additional data.
700 - UK license:
701 https://isd.digital.nhs.uk/trud3/user/guest/group/0/pack/26/subpack/101/licences
703 - To find codes: https://termbrowser.nhs.uk/
705 Abbreviations:
707 - "Finding" is not abbreviated
708 - "Obs" or "observable" is short for "observable entity"
709 - "Procedure" is not abbreviated
710 - "Scale" is short for "assessment scale"
711 - "Situation" is not abbreviated
713 Variable names are designed for clear code. Value strings are designed for
714 clear XML that matches SNOMED-CT, in the format TASK_CONCEPTTYPE_NAME.
716 """ # noqa
717 # https://snomedbrowser.com/Codes/Details/XXX # noqa
719 # -------------------------------------------------------------------------
720 # SNOMED-CT core concepts
721 # -------------------------------------------------------------------------
723 # Abstract physical quantities
724 MASS = "mass"
725 LENGTH = "length"
727 # Saying "units"
728 UNIT_OF_MEASURE = "unit_of_measure"
730 # Base physical units
731 KILOGRAM = "kilogram"
732 METRE = "metre"
733 CENTIMETRE = "centimetre"
735 # Compound physical units
736 KG_PER_SQ_M = "kilogram_per_square_metre"
738 # -------------------------------------------------------------------------
739 # Scales
740 # -------------------------------------------------------------------------
742 # ACE-R
743 ACE_R_SCALE = "ace_r_scale"
744 ACE_R_SUBSCALE_ATTENTION_ORIENTATION = "ace_r_subscale_attention_orientation" # noqa
745 ACE_R_SUBSCALE_FLUENCY = "ace_r_subscale_fluency"
746 ACE_R_SUBSCALE_LANGUAGE = "ace_r_subscale_language"
747 ACE_R_SUBSCALE_MEMORY = "ace_r_subscale_memory"
748 ACE_R_SUBSCALE_VISUOSPATIAL = "ace_r_subscale_visuospatial"
749 ACE_R_SCORE = "ace_r_observable_score"
750 ACE_R_SUBSCORE_ATTENTION_ORIENTATION = "ace_r_observable_subscore_attention_orientation" # noqa
751 ACE_R_SUBSCORE_FLUENCY = "ace_r_observable_subscore_fluency"
752 ACE_R_SUBSCORE_LANGUAGE = "ace_r_observable_subscore_language"
753 ACE_R_SUBSCORE_MEMORY = "ace_r_observable_subscore_memory"
754 ACE_R_SUBSCORE_VISUOSPATIAL = "ace_r_observable_subscore_visuospatial"
755 ACE_R_PROCEDURE_ASSESSMENT = "ace_r_procedure_assessment"
756 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_ATTENTION_ORIENTATION = "ace_r_procedure_assessment_subscale_attention_orientation" # noqa
757 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_FLUENCY = "ace_r_procedure_assessment_subscale_fluency" # noqa
758 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_LANGUAGE = "ace_r_procedure_assessment_subscale_language" # noqa
759 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_MEMORY = "ace_r_procedure_assessment_subscale_memory" # noqa
760 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_VISUOSPATIAL = "ace_r_procedure_assessment_subscale_visuospatial" # noqa
762 # AIMS
763 AIMS_SCALE = "aims_scale"
764 AIMS_TOTAL_SCORE = "aims_observable_total_score"
765 AIMS_PROCEDURE_ASSESSMENT = "aims_procedure_assessment"
767 # AUDIT, AUDIT-C
768 AUDIT_SCALE = "audit_scale"
769 AUDIT_SCORE = "audit_observable_score"
770 AUDIT_PROCEDURE_ASSESSMENT = "audit_procedure_assessment"
771 AUDITC_SCALE = "auditc_scale"
772 AUDITC_SCORE = "auditc_observable_score"
773 AUDITC_PROCEDURE_ASSESSMENT = "auditc_procedure_assessment"
775 # BADLS
776 BADLS_SCALE = "badls_scale"
777 BADLS_SCORE = "badls_observable_score"
778 BADLS_PROCEDURE_ASSESSMENT = "badls_procedure_assessment"
780 # BDI
781 BDI_SCALE = "bdi_scale"
782 BDI_SCORE = "bdi_observable_score"
783 BDI_PROCEDURE_ASSESSMENT = "bdi_procedure_assessment"
784 BDI_II_SCORE = "bdi_ii_observable_score"
785 BDI_II_PROCEDURE_ASSESSMENT = "bdi_ii_procedure_assessment"
787 # BMI
788 BMI_OBSERVABLE = "bmi_observable"
789 BMI_PROCEDURE_MEASUREMENT = "bmi_procedure_measurement"
790 BODY_HEIGHT_OBSERVABLE = "body_height_observable"
791 BODY_WEIGHT_OBSERVABLE = "body_weight_observable"
792 WAIST_CIRCUMFERENCE_PROCEDURE_MEASUREMENT = "waist_circumference_procedure_measurement" # noqa
793 WAIST_CIRCUMFERENCE_OBSERVABLE = "waist_circumference_observable"
795 # BPRS, BPRS-E
796 BPRS1962_SCALE = "bprs1962_scale"
797 # no observable/procedure
799 # CAGE
800 CAGE_SCALE = "cage_scale"
801 CAGE_SCORE = "cage_observable_score"
802 CAGE_PROCEDURE_ASSESSMENT = "cage_procedure_assessment"
804 # CAPE-42: none
805 # CAPS: none
806 # Cardinal RN, Expectation-Detection: none
807 # CBI-R: none
808 # CECA-Q3: none
809 # CESD, CESD-R: none
810 # CGI, CGI-I, CGI-SCH: none
811 # CIS-R: none
813 # CIWA-Ar
814 CIWA_AR_SCALE = "ciwa_ar_scale"
815 CIWA_AR_SCORE = "ciwa_ar_observable_score"
816 CIWA_AR_PROCEDURE_ASSESSMENT = "ciwa_ar_procedure_assessment"
818 # Clinical: progress note
819 PROGRESS_NOTE_PROCEDURE = "progress_note_procedure"
820 CLINICAL_NOTE = "clinical_note"
822 # Clinical: photograph
823 PHOTOGRAPH_PROCEDURE = "photograph_procedure"
824 PHOTOGRAPH_PHYSICAL_OBJECT = "photograph_physical_object"
826 # Clinical: psychiatric clerking
827 # ... "location": not obvious
828 # ... "contact type" is an AoMRC heading, but I'm not sure the observable
829 # entity of "Initial contact type" is right.
830 PSYCHIATRIC_ASSESSMENT_PROCEDURE = "psychiatric_assessment_procedure"
832 PSYCLERK_REASON_FOR_REFERRAL = "psyclerk_reason_for_referral"
833 PSYCLERK_PRESENTING_ISSUE = "psyclerk_presenting_issue"
834 PSYCLERK_SYSTEMS_REVIEW = "psyclerk_systems_review"
835 PSYCLERK_COLLATERAL_HISTORY = "psyclerk_collateral_history"
837 PSYCLERK_PAST_MEDICAL_SURGICAL_MENTAL_HEALTH_HISTORY = "psyclerk_past_medical_surgical_mental_health_history" # noqa
838 PSYCLERK_PROCEDURES = "psyclerk_procedures"
839 PSYCLERK_ALLERGIES_ADVERSE_REACTIONS = "psyclerk_allergies_adverse_reactions" # noqa
840 PSYCLERK_MEDICATIONS_MEDICAL_DEVICES = "psyclerk_medications_medical_devices" # noqa
841 PSYCLERK_DRUG_SUBSTANCE_USE = "psyclerk_drug_substance_use"
842 PSYCLERK_FAMILY_HISTORY = "psyclerk_family_history"
843 PSYCLERK_DEVELOPMENTAL_HISTORY = "psyclerk_developmental_history"
844 PSYCLERK_SOCIAL_PERSONAL_HISTORY = "psyclerk_social_personal_history"
845 PSYCLERK_PERSONALITY = "psyclerk_personality"
846 PSYCLERK_PRISON_RECORD_CRIMINAL_ACTIVITY = "psyclerk_prison_record_criminal_activity" # noqa
847 PSYCLERK_SOCIAL_HISTORY_BASELINE = "psyclerk_social_history_baseline"
849 PSYCLERK_MSE_APPEARANCE = "psyclerk_mse_appearance"
850 PSYCLERK_MSE_BEHAVIOUR = "psyclerk_mse_behaviour"
851 PSYCLERK_MSE_SPEECH = "psyclerk_mse_speech"
852 PSYCLERK_MSE_MOOD = "psyclerk_mse_mood"
853 PSYCLERK_MSE_AFFECT = "psyclerk_mse_affect"
854 PSYCLERK_MSE_THOUGHT = "psyclerk_mse_thought"
855 PSYCLERK_MSE_PERCEPTION = "psyclerk_mse_perception"
856 PSYCLERK_MSE_COGNITION = "psyclerk_mse_cognition"
857 PSYCLERK_MSE_INSIGHT = "psyclerk_mse_insight"
859 PSYCLERK_PHYSEXAM_GENERAL = "psyclerk_physexam_general"
860 PSYCLERK_PHYSEXAM_CARDIOVASCULAR = "psyclerk_physexam_cardiovascular"
861 PSYCLERK_PHYSEXAM_RESPIRATORY = "psyclerk_physexam_respiratory"
862 PSYCLERK_PHYSEXAM_ABDOMINAL = "psyclerk_physexam_abdominal"
863 PSYCLERK_PHYSEXAM_NEUROLOGICAL = "psyclerk_physexam_neurological"
865 PSYCLERK_ASSESSMENT_SCALES = "psyclerk_assessment_scales"
866 PSYCLERK_INVESTIGATIONS_RESULTS = "psyclerk_investigations_results"
868 PSYCLERK_SAFETY_ALERTS = "psyclerk_safety_alerts"
869 PSYCLERK_RISK_ASSESSMENT = "psyclerk_risk_assessment"
870 PSYCLERK_RELEVANT_LEGAL_INFORMATION = "psyclerk_relevant_legal_information"
872 PSYCLERK_CURRENT_PROBLEMS = "psyclerk_current_problems"
873 PSYCLERK_PATIENT_CARER_CONCERNS = "psyclerk_patient_carer_concerns"
874 PSYCLERK_CLINICAL_NARRATIVE = "psyclerk_clinical_narrative"
875 PSYCLERK_MANAGEMENT_PLAN = "psyclerk_management_plan"
876 PSYCLERK_INFORMATION_GIVEN = "psyclerk_information_given"
878 # CPFT/CUH LPS: none
879 # COPE: none
881 # CORE-10
882 CORE10_SCALE = "core10_scale"
883 CORE10_SCORE = "core10_observable_score"
884 CORE10_PROCEDURE_ASSESSMENT = "core10_procedure_assessment"
886 # DAD: none
888 # DAST
889 DAST_SCALE = "dast_scale"
890 # I think the similarly named codes represent urine screening.
892 # Deakin JB, antibody: none
893 # Demo questionnaire: none
894 # DEMQOL, DEMQOL-Proxy: none
895 # Distress Thermometer: none
897 # EQ-5D-5L
898 EQ5D5L_SCALE = "eq5d5l_scale"
899 EQ5D5L_INDEX_VALUE = "eq5d5l_observable_index_value"
900 EQ5D5L_PAIN_DISCOMFORT_SCORE = "eq5d5l_observable_pain_discomfort_score"
901 EQ5D5L_USUAL_ACTIVITIES_SCORE = "eq5d5l_observable_usual_activities_score"
902 EQ5D5L_ANXIETY_DEPRESSION_SCORE = "eq5d5l_observable_anxiety_depression_score" # noqa
903 EQ5D5L_MOBILITY_SCORE = "eq5d5l_observable_mobility_score"
904 EQ5D5L_SELF_CARE_SCORE = "eq5d5l_observable_self_care_score"
905 EQ5D5L_PROCEDURE_ASSESSMENT = "eq5d5l_procedure_assessment"
907 # FACT-G: none
909 # FAST: none
910 FAST_SCALE = "fast_scale"
911 FAST_SCORE = "fast_observable_score"
912 FAST_PROCEDURE_ASSESSMENT = "fast_procedure_assessment"
914 # IRAC: none
915 # FFT: none
917 # Patient Satisfaction Scale
918 # Not sure. See XML
920 # Referrer Satisfaction Scale (patient-specific, survey): none
921 # Frontotemporal Dementia Rating Scale: none
923 # GAD-7
924 GAD7_SCALE = "gad7_scale"
925 GAD7_SCORE = "gad7_observable_score"
926 GAD7_PROCEDURE_ASSESSMENT = "gad7_procedure_assessment"
928 # GAF
929 GAF_SCALE = "gaf_scale"
930 # no observable/procedure
932 # GDS-15
933 GDS15_SCALE = "gds15_scale"
934 GDS15_SCORE = "gds15_observable_score"
935 GDS15_PROCEDURE_ASSESSMENT = "gds15_procedure_assessment"
937 # UK GMC Patient Questionnaire: none
939 # HADS, HADS-respondent
940 HADS_SCALE = "hads_scale"
941 HADS_ANXIETY_SCORE = "hads_observable_anxiety_score"
942 HADS_DEPRESSION_SCORE = "hads_observable_depression_score"
943 HADS_PROCEDURE_ASSESSMENT = "hads_procedure_assessment"
945 # HAMA: none
947 # HAMD
948 HAMD_SCALE = "hamd_scale"
949 HAMD_SCORE = "hamd_observable_score"
950 HAMD_PROCEDURE_ASSESSMENT = "hamd_procedure_assessment"
952 # HAMD-7: none
954 # HoNOS, HoNOS-65+, HoNOSCA, etc. (there are others too)
955 HONOSCA_SCALE = "honos_childrenadolescents_scale"
956 HONOSCA_SECTION_A_SCALE = "honos_childrenadolescents_section_a_scale"
957 HONOSCA_SECTION_B_SCALE = "honos_childrenadolescents_section_b_scale"
958 HONOSCA_SCORE = "honos_childrenadolescents_observable_score"
959 HONOSCA_SECTION_A_SCORE = "honos_childrenadolescents_observable_section_a_score" # noqa
960 HONOSCA_SECTION_B_SCORE = "honos_childrenadolescents_observable_section_b_score" # noqa
961 HONOSCA_SECTION_A_PLUS_B_SCORE = "honos_childrenadolescents_observable_section_a_plus_b_score" # noqa
962 HONOSCA_PROCEDURE_ASSESSMENT = "honos_childrenadolescents_procedure_assessment" # noqa
963 #
964 HONOS65_SCALE = "honos_olderadults_scale"
965 HONOS65_SCORE = "honos_olderadults_observable_score"
966 HONOS65_PROCEDURE_ASSESSMENT = "honos_olderadults_procedure_assessment"
967 #
968 HONOSWA_SCALE = "honos_workingage_scale"
969 HONOSWA_SUBSCALE_1_OVERACTIVE = "honos_workingage_subscale_1_overactive"
970 HONOSWA_SUBSCALE_2_SELFINJURY = "honos_workingage_subscale_2_selfinjury"
971 HONOSWA_SUBSCALE_3_SUBSTANCE = "honos_workingage_subscale_3_substance"
972 HONOSWA_SUBSCALE_4_COGNITIVE = "honos_workingage_subscale_4_cognitive"
973 HONOSWA_SUBSCALE_5_PHYSICAL = "honos_workingage_subscale_5_physical"
974 HONOSWA_SUBSCALE_6_PSYCHOSIS = "honos_workingage_subscale_6_psychosis"
975 HONOSWA_SUBSCALE_7_DEPRESSION = "honos_workingage_subscale_7_depression"
976 HONOSWA_SUBSCALE_8_OTHERMENTAL = "honos_workingage_subscale_8_othermental"
977 HONOSWA_SUBSCALE_9_RELATIONSHIPS = "honos_workingage_subscale_9_relationships" # noqa
978 HONOSWA_SUBSCALE_10_ADL = "honos_workingage_subscale_10_adl"
979 HONOSWA_SUBSCALE_11_LIVINGCONDITIONS = "honos_workingage_subscale_11_livingconditions" # noqa
980 HONOSWA_SUBSCALE_12_OCCUPATION = "honos_workingage_subscale_12_occupation"
981 HONOSWA_SCORE = "honos_workingage_observable_score"
982 HONOSWA_1_OVERACTIVE_SCORE = "honos_workingage_observable_1_overactive_score" # noqa
983 HONOSWA_2_SELFINJURY_SCORE = "honos_workingage_observable_2_selfinjury_score" # noqa
984 HONOSWA_3_SUBSTANCE_SCORE = "honos_workingage_observable_3_substance_score"
985 HONOSWA_4_COGNITIVE_SCORE = "honos_workingage_observable_4_cognitive_score"
986 HONOSWA_5_PHYSICAL_SCORE = "honos_workingage_observable_5_physical_score"
987 HONOSWA_6_PSYCHOSIS_SCORE = "honos_workingage_observable_6_psychosis_score"
988 HONOSWA_7_DEPRESSION_SCORE = "honos_workingage_observable_7_depression_score" # noqa
989 HONOSWA_8_OTHERMENTAL_SCORE = "honos_workingage_observable_8_othermental_score" # noqa
990 HONOSWA_9_RELATIONSHIPS_SCORE = "honos_workingage_observable_9_relationships_score" # noqa
991 HONOSWA_10_ADL_SCORE = "honos_workingage_observable_10_adl_score"
992 HONOSWA_11_LIVINGCONDITIONS_SCORE = "honos_workingage_observable_11_livingconditions_score" # noqa
993 HONOSWA_12_OCCUPATION_SCORE = "honos_workingage_observable_12_occupation_score" # noqa
994 HONOSWA_PROCEDURE_ASSESSMENT = "honos_workingage_procedure_assessment"
996 # ICD-9-CM: see below; separate file
998 # ICD-10: see below; separate file
1000 # IDED3D: none
1002 # IES-R
1003 IESR_SCALE = "iesr_scale"
1004 IESR_SCORE = "iesr_observable_score"
1005 IESR_PROCEDURE_ASSESSMENT = "iesr_procedure_assessment"
1007 # INECO Frontal Screening: none
1008 # Khandaker G, Insight: none
1010 # MAST, SMAST
1011 MAST_SCALE = "mast_scale"
1012 MAST_SCORE = "mast_observable_score"
1013 MAST_PROCEDURE_ASSESSMENT = "mast_procedure_assessment"
1015 SMAST_SCALE = "smast_scale"
1016 # SMAST: no observable/procedure
1018 # MDS-UPDRS
1019 UPDRS_SCALE = "updrs_scale"
1020 # MDS-UPDRS: no observable/procedure
1022 # MoCA
1023 MOCA_SCALE = "moca_scale"
1024 MOCA_SCORE = "moca_observable_score"
1025 MOCA_PROCEDURE_ASSESSMENT = "moca_procedure_assessment"
1027 # NART
1028 NART_SCALE = "nart_scale"
1029 NART_SCORE = "nart_observable_score"
1030 NART_PROCEDURE_ASSESSMENT = "nart_procedure_assessment"
1032 # NPI-Q: none
1034 # PANSS
1035 PANSS_SCALE = "panss_scale"
1036 # PANSS: no observable/procedure
1038 # PCL and variants: none
1040 # PDSS
1041 PDSS_SCALE = "pdss_scale"
1042 PDSS_SCORE = "pdss_observable_score"
1043 # PDSS: no procedure
1045 # "Perinatal" and "scale": none
1047 # PHQ-9
1048 PHQ9_FINDING_NEGATIVE_SCREENING_FOR_DEPRESSION = "phq9_finding_negative_screening_for_depression" # noqa
1049 PHQ9_FINDING_POSITIVE_SCREENING_FOR_DEPRESSION = "phq9_finding_positive_screening_for_depression" # noqa
1050 PHQ9_SCORE = "phq9_observable_score"
1051 PHQ9_PROCEDURE_DEPRESSION_SCREENING = "phq9_procedure_depression_screening" # noqa
1052 PHQ9_SCALE = "phq9_scale" # https://snomedbrowser.com/Codes/Details/758711000000105 # noqa
1054 # PHQ-15
1055 PHQ15_SCORE = "phq15_observable_score"
1056 PHQ15_PROCEDURE = "phq15_procedure_assessment"
1057 PHQ15_SCALE = "phq15_scale"
1059 # PIIOS or "parent infant scale": none
1061 # PSWQ
1062 PSWQ_SCALE = "pswq_scale"
1063 PSWQ_SCORE = "pswq_observable_score"
1064 PSWQ_PROCEDURE_ASSESSMENT = "pswq_procedure_assessment"
1066 # QOL-Basic, QOL-SG
1067 # Unsure, but there is this:
1068 QOL_SCALE = "qol_scale"
1069 # ... with no observable/procedure
1071 # RAND-36: none directly
1073 # SLUMS: none
1075 # WEMWBS, SWEMWBS
1076 WEMWBS_SCALE = "wemwbs_scale"
1077 WEMWBS_SCORE = "wemwbs_observable_score"
1078 WEMWBS_PROCEDURE_ASSESSMENT = "wemwbs_procedure_assessment"
1079 #
1080 SWEMWBS_SCALE = "swemwbs_scale"
1081 SWEMWBS_SCORE = "swemwbs_observable_score"
1082 SWEMWBS_PROCEDURE_ASSESSMENT = "swemwbs_procedure_assessment"
1084 # WSAS
1085 WSAS_SCALE = "wsas_scale"
1086 WSAS_SCORE = "wsas_observable_score"
1087 WSAS_WORK_SCORE = "wsas_observable_work_score"
1088 WSAS_RELATIONSHIPS_SCORE = "wsas_observable_relationships_score"
1089 WSAS_HOME_MANAGEMENT_SCORE = "wsas_observable_home_management_score"
1090 WSAS_SOCIAL_LEISURE_SCORE = "wsas_observable_social_leisure_score"
1091 WSAS_PRIVATE_LEISURE_SCORE = "wsas_observable_private_leisure_score"
1092 WSAS_PROCEDURE_ASSESSMENT = "wsas_procedure_assessment"
1094 # Y-BOCS, Y-BOCS-SC: none
1095 # ZBI: none
1098# -----------------------------------------------------------------------------
1099# Perform the lookup
1100# -----------------------------------------------------------------------------
1102VALID_SNOMED_LOOKUPS = set([getattr(SnomedLookup, k) for k in dir(SnomedLookup)
1103 if not k.startswith("_")])
1106@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1107def get_all_task_snomed_concepts(xml_filename: str) \
1108 -> Dict[str, SnomedConcept]:
1109 """
1110 Reads in all SNOMED-CT codes for CamCOPS tasks, from the custom CamCOPS XML
1111 file for this.
1113 Args:
1114 xml_filename: XML filename to read
1116 Returns:
1117 dict: maps lookup strings to :class:`SnomedConcept` objects
1119 """
1120 xml_concepts = get_snomed_concepts_from_xml(xml_filename)
1121 camcops_concepts = {} # type: Dict[str, SnomedConcept]
1122 identifiers_seen = set() # type: Set[int]
1123 for lookup, concepts in xml_concepts.items():
1124 # Check it
1125 if lookup not in VALID_SNOMED_LOOKUPS:
1126 log.debug("Ignoring unknown SNOMED-CT lookup: {!r}", lookup)
1127 continue
1128 assert len(concepts) == 1, (
1129 f"More than one SNOMED-CT concept for lookup: {lookup!r}"
1130 )
1131 concept = concepts[0]
1132 assert concept.identifier not in identifiers_seen, (
1133 f"Duplicate SNOMED-CT identifier: {concept.identifier!r}")
1134 identifiers_seen.add(concept.identifier)
1135 # Stash it
1136 camcops_concepts[lookup] = concept
1137 # Check if any are missing
1138 missing = sorted(list(VALID_SNOMED_LOOKUPS - set(camcops_concepts.keys())))
1139 if missing:
1140 raise ValueError(
1141 f"The following SNOMED-CT concepts required by CamCOPS are "
1142 f"missing from the XML ({xml_filename!r}): {missing!r}")
1143 # Done
1144 return camcops_concepts
1147# =============================================================================
1148# UMLS ICD-9-CM
1149# =============================================================================
1151class UmlsIcd9SnomedRow(object):
1152 """
1153 Simple information-holding class for a row of the ICD-9-CM TSV file, from
1154 https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html.
1156 NOT CURRENTLY USED.
1157 """
1158 HEADER = [
1159 "ICD_CODE", "ICD_NAME", "IS_CURRENT_ICD", "IP_USAGE", "OP_USAGE",
1160 "AVG_USAGE", "IS_NEC", "SNOMED_CID", "SNOMED_FSN", "IS_1-1MAP",
1161 "CORE_USAGE", "IN_CORE",
1162 ]
1164 @staticmethod
1165 def to_float(x: str) -> Optional[float]:
1166 return None if x == "NULL" else float(x)
1168 def __init__(self,
1169 icd_code: str,
1170 icd_name: str,
1171 is_current_icd: str,
1172 ip_usage: str,
1173 op_usage: str,
1174 avg_usage: str,
1175 is_nec: str,
1176 snomed_cid: str,
1177 snomed_fsn: str,
1178 is_one_to_one_map: str,
1179 core_usage: str,
1180 in_core: str) -> None:
1181 """
1182 Argument order is important.
1184 Args:
1185 icd_code: ICD-9-CM code
1186 icd_name: Name of ICD-9-CM entity
1187 is_current_icd: ?
1188 ip_usage: ?
1189 op_usage: ?
1190 avg_usage: ?
1191 is_nec: ?
1192 snomed_cid: SNOMED-CT concept ID
1193 snomed_fsn: SNOMED-CT fully specified name
1194 is_one_to_one_map: ?; possibly always true in this dataset but not
1195 true in a broader dataset including things other than 1:1
1196 mappings?
1197 core_usage: ?
1198 in_core: ?
1199 """
1200 self.icd_code = icd_code
1201 self.icd_name = icd_name
1202 self.is_current_icd = bool(int(is_current_icd))
1203 self.ip_usage = self.to_float(ip_usage)
1204 self.op_usage = self.to_float(op_usage)
1205 self.avg_usage = self.to_float(avg_usage)
1206 self.is_nec = bool(int(is_nec))
1207 self.snomed_cid = int(snomed_cid)
1208 self.snomed_fsn = snomed_fsn
1209 self.is_one_to_one_map = bool(int(is_one_to_one_map))
1210 self.core_usage = self.to_float(core_usage)
1211 self.in_core = bool(int(in_core))
1213 def __repr__(self) -> str:
1214 return simple_repr(self, [
1215 "icd_code", "icd_name", "is_current_icd", "ip_usage", "op_usage",
1216 "avg_usage", "is_nec",
1217 "snomed_cid", "snomed_fsn",
1218 "is_one_to_one_map", "core_usage", "in_core",
1219 ])
1221 def snomed_concept(self) -> SnomedConcept:
1222 """
1223 Returns the associated SNOMED-CT concept.
1224 """
1225 return SnomedConcept(self.snomed_cid, self.snomed_fsn)
1227 def __str__(self) -> str:
1228 return (
1229 f"ICD-9-CM {self.icd_code} ({self.icd_name}) "
1230 f"-> SNOMED-CT {self.snomed_concept()}"
1231 )
1234@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1235def get_all_icd9cm_snomed_concepts_from_umls(
1236 tsv_filename: str) -> Dict[str, SnomedConcept]:
1237 """
1238 Reads in all ICD-9-CM SNOMED-CT codes that are supported by the client,
1239 from the UMLS data file, from
1240 https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html.
1242 Args:
1243 tsv_filename: TSV filename to read
1245 Returns:
1246 dict: maps lookup strings to :class:`SnomedConcept` objects
1248 NOT CURRENTLY USED.
1249 """
1250 log.info("Loading SNOMED-CT ICD-9-CM codes from file: {}", tsv_filename)
1251 concepts = {} # type: Dict[str, SnomedConcept]
1252 with open(tsv_filename, 'r') as tsvin:
1253 reader = csv.reader(tsvin, delimiter="\t")
1254 header = next(reader, None)
1255 if header != UmlsIcd9SnomedRow.HEADER:
1256 raise ValueError(
1257 f"ICD-9-CM TSV file has unexpected header: {header!r}; "
1258 f"expected {UmlsIcd9SnomedRow.HEADER!r}")
1259 for row in reader:
1260 entry = UmlsIcd9SnomedRow(*row)
1261 if entry.icd_code not in CLIENT_ICD9CM_CODES:
1262 continue
1263 if not entry.is_one_to_one_map:
1264 continue
1265 if entry.icd_code in concepts:
1266 log.warning(
1267 "Duplicate ICD-9-CM code found in SNOMED file {!r}: {!r}",
1268 tsv_filename, entry.icd_code)
1269 continue
1270 concept = entry.snomed_concept()
1271 # log.debug("{}", entry)
1272 concepts[entry.icd_code] = concept
1273 missing = CLIENT_ICD9CM_CODES - set(concepts.keys())
1274 if missing:
1275 log.info("No SNOMED-CT codes for ICD-9-CM codes: {}",
1276 ", ".join(sorted(missing)))
1277 return concepts
1280# =============================================================================
1281# UMLS ICD-10
1282# =============================================================================
1284class UmlsSnomedToIcd10Row(object):
1285 """
1286 Simple information-holding class for a row of the ICD-10-CM TSV file from
1287 https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html.
1289 However, that is unhelpful (many to one).
1291 NOT CURRENTLY USED.
1292 """
1293 HEADER = [
1294 "id", "effectiveTime", "active", "moduleId", "refsetId",
1295 "referencedComponentId", "referencedComponentName", "mapGroup",
1296 "mapPriority", "mapRule", "mapAdvice", "mapTarget", "mapTargetName",
1297 "correlationId", "mapCategoryId", "mapCategoryName",
1298 ]
1299 MAP_GOOD = "MAP SOURCE CONCEPT IS PROPERLY CLASSIFIED"
1301 def __init__(self,
1302 row_id: str,
1303 effective_time: str,
1304 active: str,
1305 module_id: str,
1306 refset_id: str,
1307 referenced_component_id: str,
1308 referenced_component_name: str,
1309 map_group: str,
1310 map_priority: str,
1311 map_rule: str,
1312 map_advice: str,
1313 map_target: str,
1314 map_target_name: str,
1315 correlation_id: str,
1316 map_category_id: str,
1317 map_category_name: str) -> None:
1318 """
1319 Argument order is important.
1321 Args:
1322 row_id: UUID format or similar
1323 effective_time: date in YYYYMMDD format
1324 active: ?
1325 module_id: ?
1326 refset_id: ?
1327 referenced_component_id: SNOMED-CT concept ID
1328 referenced_component_name: SNOMED-CT concept name
1329 map_group: ?; e.g. 1
1330 map_priority: ? but e.g. 1, 2; correlates with map_rule
1331 map_rule: ?; e.g. "TRUE"; "OTHERWISE TRUE"
1332 map_advice: ?, but e.g. "ALWAYS F32.2" or "ALWAYS F32.2 |
1333 DESCENDANTS NOT EXHAUSTIVELY MAPPED"
1334 map_target: ICD-10 code
1335 map_target_name: ICD-10 name
1336 correlation_id: a SNOMED-CT concept for the mapping, e.g.
1337 447561005 = "SNOMED CT source code to target map code
1338 correlation not specified (foundation metadata concept)"
1339 map_category_id: a SNOMED-CT concept for the mapping, e.g.
1340 447637006 = "Map source concept is properly classified
1341 (foundation metadata concept)"
1342 map_category_name: SNOMED-CT name corresponding to map_category_id,
1343 e.g. "MAP SOURCE CONCEPT IS PROPERLY CLASSIFIED"
1344 """
1345 self.row_id = row_id
1346 self.effective_time = effective_time
1347 self.active = bool(int(active))
1348 self.module_id = int(module_id)
1349 self.refset_id = int(refset_id)
1350 self.referenced_component_id = int(referenced_component_id)
1351 self.referenced_component_name = referenced_component_name
1352 self.map_group = int(map_group)
1353 self.map_priority = int(map_priority)
1354 self.map_rule = map_rule
1355 self.map_advice = map_advice
1356 self.map_target = map_target
1357 self.map_target_name = map_target_name
1358 self.correlation_id = int(correlation_id)
1359 self.map_category_id = int(map_category_id)
1360 self.map_category_name = map_category_name
1362 def __repr__(self) -> str:
1363 return simple_repr(self, [
1364 "row_id", "effective_time", "active", "module_id", "refset_id",
1365 "referenced_component_id", "referenced_component_name",
1366 "map_group", "map_priority", "map_rule", "map_advice",
1367 "map_target", "map_target_name",
1368 "correlation_id", "map_category_id", "map_category_name",
1369 ])
1371 def snomed_concept(self) -> SnomedConcept:
1372 """
1373 Returns the associated SNOMED-CT concept.
1374 """
1375 return SnomedConcept(self.referenced_component_id,
1376 self.referenced_component_name)
1378 @property
1379 def icd_code(self) -> str:
1380 return self.map_target
1382 @property
1383 def icd_name(self) -> str:
1384 return self.map_target_name
1386 def __str__(self) -> str:
1387 return (
1388 f"ICD-10 {self.icd_code} ({self.icd_name}) "
1389 f"-> SNOMED-CT {self.snomed_concept()}"
1390 )
1393def get_all_icd10_snomed_concepts_from_umls(
1394 tsv_filename: str) -> Dict[str, SnomedConcept]:
1395 """
1396 Reads in all ICD-10 SNOMED-CT codes that are supported by the client,
1397 from the UMLS data file, from
1398 https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html.
1400 Args:
1401 tsv_filename: TSV filename to read
1403 Returns:
1404 dict: maps lookup strings to :class:`SnomedConcept` objects
1406 NOT CURRENTLY USED.
1407 """
1408 log.info("Loading SNOMED-CT ICD-10-CM codes from file: {}", tsv_filename)
1409 concepts = {} # type: Dict[str, SnomedConcept]
1410 with open(tsv_filename, 'r') as tsvin:
1411 reader = csv.reader(tsvin, delimiter="\t")
1412 header = next(reader, None)
1413 if header != UmlsSnomedToIcd10Row.HEADER:
1414 raise ValueError(
1415 f"ICD-9-CM TSV file has unexpected header: {header!r}; "
1416 f"expected {UmlsSnomedToIcd10Row.HEADER!r}")
1417 for row in reader:
1418 entry = UmlsSnomedToIcd10Row(*row)
1419 if entry.icd_code not in CLIENT_ICD10_CODES:
1420 continue
1421 if entry.icd_code in concepts:
1422 log.warning(
1423 "Duplicate ICD-10-CM code found in SNOMED file {!r}: {!r}",
1424 tsv_filename, entry.icd_code)
1425 continue
1426 concept = entry.snomed_concept()
1427 # log.debug("{}", entry)
1428 concepts[entry.icd_code] = concept
1429 missing = CLIENT_ICD10_CODES - set(concepts.keys())
1430 if missing:
1431 log.info("No SNOMED-CT codes for ICD-10 codes: {}",
1432 ", ".join(sorted(missing)))
1433 return concepts
1436# =============================================================================
1437# Athena OHDSI mapping
1438# =============================================================================
1440# -----------------------------------------------------------------------------
1441# Fetch ICD-9-CM and ICD-10 codes (shared for fewer passes through the files)
1442# -----------------------------------------------------------------------------
1444def get_icd9cm_icd10_snomed_concepts_from_athena(
1445 athena_concept_tsv_filename: str,
1446 athena_concept_relationship_tsv_filename: str) \
1447 -> Tuple[Dict[str, List[SnomedConcept]],
1448 Dict[str, List[SnomedConcept]]]:
1449 """
1450 Takes Athena concept and concept-relationship files, and fetches details
1451 of SNOMED-CT code for all ICD-9-CM and ICD-10[-CM] codes used by CamCOPS.
1453 A bit of human review is required; this is probably preferable to using
1454 gensim or some other automatic similarity check.
1456 Args:
1457 athena_concept_tsv_filename:
1458 path to ``CONCEPT.csv`` (a tab-separated value file)
1459 athena_concept_relationship_tsv_filename:
1460 path to ``CONCEPT_RELATIONSHIP.csv`` (a tab-separated value file)
1462 Returns:
1463 tuple: ``icd9cm, icd10``, where each is a dictionary mapping ICD codes
1464 to a list of mapped :class:`SnomedConcept` objects.
1466 """
1467 athena_icd_concepts = get_athena_concepts(
1468 tsv_filename=athena_concept_tsv_filename,
1469 vocabulary_ids={AthenaVocabularyId.ICD9CM, AthenaVocabularyId.ICD10CM},
1470 concept_codes=CLIENT_ICD9CM_CODES | CLIENT_ICD10_CODES,
1471 )
1472 athena_icd_concepts.sort(key=lambda x: x.concept_code)
1473 relationships = get_athena_concept_relationships(
1474 tsv_filename=athena_concept_relationship_tsv_filename,
1475 concept_id_1_values=set(x.concept_id for x in athena_icd_concepts),
1476 relationship_id_values={AthenaRelationshipId.MAPS_TO}
1477 )
1478 athena_snomed_concepts = get_athena_concepts(
1479 tsv_filename=athena_concept_tsv_filename,
1480 vocabulary_ids={AthenaVocabularyId.SNOMED},
1481 concept_ids=set(x.concept_id_2 for x in relationships)
1482 )
1483 snomed_concepts_icd9 = OrderedDict() # type: Dict[str, List[SnomedConcept]] # noqa
1484 snomed_concepts_icd10 = OrderedDict() # type: Dict[str, List[SnomedConcept]] # noqa
1485 for icd in athena_icd_concepts:
1486 target = (
1487 snomed_concepts_icd9
1488 if icd.vocabulary_id == AthenaVocabularyId.ICD9CM
1489 else snomed_concepts_icd10
1490 )
1491 icd_code = icd.concept_code
1492 # log.debug("Processing icd = {}", icd)
1493 possible_snomed = [] # type: List[AthenaConceptRow]
1494 for rel in relationships:
1495 if rel.concept_id_1 != icd.concept_id:
1496 continue
1497 # log.debug("Processing rel = {}", rel)
1498 for snomed in athena_snomed_concepts:
1499 if snomed.concept_id != rel.concept_id_2:
1500 continue
1501 # log.debug("Processing snomed = {}", snomed)
1502 possible_snomed.append(snomed)
1503 if possible_snomed:
1504 sclist = [
1505 SnomedConcept.create(s.snomed_concept())
1506 for s in possible_snomed
1507 ]
1508 sclist.sort(key=lambda sc: sc.identifier)
1509 log.debug("Mapping {} -> {}", icd, sclist)
1510 target[icd_code] = sclist
1511 else:
1512 log.debug("No SNOMED code found for {}", icd)
1513 return snomed_concepts_icd9, snomed_concepts_icd10
1516# -----------------------------------------------------------------------------
1517# Fetch codes from Athena data set and write them to CamCOPS XML
1518# -----------------------------------------------------------------------------
1520def send_athena_icd_snomed_to_xml(
1521 athena_concept_tsv_filename: str,
1522 athena_concept_relationship_tsv_filename: str,
1523 icd9_xml_filename: str,
1524 icd10_xml_filename) -> None:
1525 """
1526 Reads SNOMED-CT codes for ICD-9-CM and ICD10 from Athena OHDSI files, and
1527 writes
1529 Args:
1530 athena_concept_tsv_filename:
1531 path to ``CONCEPT.csv`` (a tab-separated value file)
1532 athena_concept_relationship_tsv_filename:
1533 path to ``CONCEPT_RELATIONSHIP.csv`` (a tab-separated value file)
1534 icd9_xml_filename:
1535 ICD-9 XML filename to write
1536 icd10_xml_filename:
1537 ICD-10 XML filename to write
1538 """
1539 icd9, icd10 = get_icd9cm_icd10_snomed_concepts_from_athena(
1540 athena_concept_tsv_filename=athena_concept_tsv_filename,
1541 athena_concept_relationship_tsv_filename=athena_concept_relationship_tsv_filename # noqa
1542 )
1543 write_snomed_concepts_to_xml(icd9_xml_filename, icd9)
1544 write_snomed_concepts_to_xml(icd10_xml_filename, icd10)
1547# -----------------------------------------------------------------------------
1548# Fetch data from XML
1549# -----------------------------------------------------------------------------
1551def get_multiple_snomed_concepts_from_xml(xml_filename: str,
1552 valid_lookups: Set[str] = None,
1553 require_all: bool = False) \
1554 -> Dict[str, List[SnomedConcept]]:
1555 """
1556 Reads in all SNOMED-CT codes for ICD-9 or ICD-10, from the custom CamCOPS
1557 XML file for this (made by e.g. :func:`send_athena_icd_snomed_to_xml`).
1559 Args:
1560 xml_filename: XML filename to read
1561 valid_lookups: possible lookup values
1562 require_all: require that ``valid_lookups`` is truthy and that all
1563 values in it are present in the XML
1565 Returns:
1566 dict: maps lookup strings to lists of :class:`SnomedConcept` objects
1568 """
1569 valid_lookups = set(valid_lookups or []) # type: Set[str]
1570 xml_concepts = get_snomed_concepts_from_xml(xml_filename)
1571 camcops_concepts = {} # type: Dict[str, List[SnomedConcept]]
1572 for lookup, concepts in xml_concepts.items():
1573 # Check it
1574 if valid_lookups and lookup not in valid_lookups:
1575 log.debug("Ignoring unknown SNOMED-CT lookup: {!r}", lookup)
1576 continue
1577 # Stash it
1578 camcops_concepts[lookup] = concepts
1579 if require_all:
1580 # Check if any are missing
1581 assert valid_lookups, "require_all specified but valid_lookups missing"
1582 if valid_lookups:
1583 missing = sorted(list(valid_lookups - set(camcops_concepts.keys())))
1584 if missing:
1585 msg = (
1586 f'The following {"required " if require_all else ""}'
1587 f'SNOMED-CT concepts are missing from the XML '
1588 f'({xml_filename!r}): {missing!r}'
1589 )
1590 if require_all:
1591 log.critical(msg)
1592 raise ValueError(msg)
1593 else:
1594 log.debug(msg)
1595 # Done
1596 return camcops_concepts
1599@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1600def get_icd9_snomed_concepts_from_xml(xml_filename: str) \
1601 -> Dict[str, List[SnomedConcept]]:
1602 """
1603 Reads in all ICD-9-CM SNOMED-CT codes from a custom CamCOPS XML file.
1605 Args:
1606 xml_filename: filename to read
1608 Returns:
1609 dict: maps ICD-9-CM codes to lists of :class:`SnomedConcept` objects
1610 """
1611 return get_multiple_snomed_concepts_from_xml(xml_filename,
1612 CLIENT_ICD9CM_CODES)
1615@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1616def get_icd10_snomed_concepts_from_xml(xml_filename: str) \
1617 -> Dict[str, List[SnomedConcept]]:
1618 """
1619 Reads in all ICD-10 SNOMED-CT codes from a custom CamCOPS XML file.
1621 Args:
1622 xml_filename: filename to read
1624 Returns:
1625 dict: maps ICD-10 codes to lists of :class:`SnomedConcept` objects
1626 """
1627 return get_multiple_snomed_concepts_from_xml(xml_filename,
1628 CLIENT_ICD10_CODES)