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, University of Cambridge, Department of Psychiatry.
9 Created by Rudolf Cardinal (rnc1001@cam.ac.uk).
11 This file is part of CamCOPS.
13 CamCOPS is free software: you can redistribute it and/or modify
14 it under the terms of the GNU General Public License as published by
15 the Free Software Foundation, either version 3 of the License, or
16 (at your option) any later version.
18 CamCOPS is distributed in the hope that it will be useful,
19 but WITHOUT ANY WARRANTY; without even the implied warranty of
20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 GNU General Public License for more details.
23 You should have received a copy of the GNU General Public License
24 along with CamCOPS. If not, see <https://www.gnu.org/licenses/>.
26===============================================================================
28**CamCOPS code to support SNOMED-CT.**
30Note that the licensing arrangements for SNOMED-CT mean that the actual codes
31must be separate (and not part of the CamCOPS code). See the documentation.
33Some tests:
35.. code-block:: python
37 import logging
38 from cardinal_pythonlib.logs import main_only_quicksetup_rootlogger
39 from camcops_server.cc_modules.cc_request import get_command_line_request
40 from camcops_server.cc_modules.cc_snomed import *
41 from camcops_server.tasks.phq9 import Phq9
42 main_only_quicksetup_rootlogger(level=logging.DEBUG)
43 req = get_command_line_request()
45 # ---------------------------------------------------------------------
46 # Read the XML, etc.
47 # ---------------------------------------------------------------------
49 print(VALID_SNOMED_LOOKUPS)
50 concepts = get_all_snomed_concepts(req.config.snomed_xml_filename)
52 # ---------------------------------------------------------------------
53 # Test a task, and loading SNOMED data from XML via the CamCOPS config
54 # ---------------------------------------------------------------------
56 phq9 = Phq9()
57 print("\n".join(str(x) for x in phq9.get_snomed_codes(req)))
58 phq9.q1 = 2
59 phq9.q2 = 2
60 phq9.q3 = 2
61 phq9.q4 = 2
62 phq9.q5 = 2
63 phq9.q6 = 2
64 phq9.q7 = 2
65 phq9.q8 = 2
66 phq9.q9 = 2
67 phq9.q10 = 2
68 print("\n".join(repr(x) for x in phq9.get_snomed_codes(req)))
69 print("\n".join(str(x) for x in phq9.get_snomed_codes(req)))
71Note diagnostic coding maps:
73- https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html
74- https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html
76Other testing:
78.. code-block:: bash
80 camcops_server dev_cli --verbose
82.. code-block:: python
84 from camcops_server.cc_modules.cc_snomed import *
86 athena_concepts = get_athena_concepts(config.athena_concept_tsv_filename)
87 relationships = get_athena_concept_relationships(config.athena_concept_relationship_tsv_filename)
88 rel_ids = set(r.relationship_id for r in relationships)
89 icd9, icd10 = get_icd9cm_icd10_snomed_concepts(config.athena_concept_tsv_filename, config.athena_concept_relationship_tsv_filename)
91 ac = get_athena_concepts(config.athena_concept_tsv_filename, vocabulary_ids=[AthenaVocabularyId.SNOMED], concept_codes=["4303690"])
93Regarding temporal coding:
95- SNOMED CT has some concepts relating to time (e.g. "time aspect", "single
96 point in time", "date of birth", "date of event", "time (property)", "time
97 (attribute)"). HOWEVER, note that SNOMED-CT isn't intended for recording
98 event dates:
100 - https://confluence.ihtsdotools.org/display/DOCRSG/3.5.+Safely+representing+the+context+of+recorded+codes
102 "Contextual information that is not represented by SNOMED CT
104 Clinical statements that contain SNOMED CT Concept representations will
105 be associated with some information which is not intended to be
106 represented using SNOMED CT:
108 - Dates, times of an activity of recording and activity;
109 - Quantitative information including ranges and durations;
110 - Identifiers or names of authors, providers of information or other
111 parties involved in a recorded activity.
112 - SNOMED CT is not intended to represent this information. Appropriate
113 constructs in a standardized or proprietary record architecture
114 should be used to relate this information to SNOMED CT encoded
115 clinical statements."
117 - https://confluence.ihtsdotools.org/display/DOCRSG/3.4.+Record+architectures%2C+structures+and+semantics
119 "Using SNOMED CT in standard architectures
121 ...
123 Each health record component has the potential to include:
125 - Dates and times of actual and planned events.
126 - Associations with people, organizations, devices and other entities
127 that participate or are used in relations to a recorded event or
128 plan.
129 - Codes or other representations that name or provide the semantic
130 information container, link, or statement:
132 - SNOMED CT fulfills this role in a structured health record.
134 - Additional data including text, numeric values, images and other
135 digital data."
137- That explains why the grammar has no explanation of how to represent
138 dates/times, perhaps!
140""" # noqa
142from collections import OrderedDict
143import csv
144import logging
145from typing import Dict, List, Optional, Set, Tuple, Union
146import xml.etree.cElementTree as ElementTree
148from cardinal_pythonlib.athena_ohdsi import (
149 AthenaConceptRow,
150 AthenaRelationshipId,
151 AthenaVocabularyId,
152 get_athena_concept_relationships,
153 get_athena_concepts,
154)
155from cardinal_pythonlib.logs import BraceStyleAdapter
156from cardinal_pythonlib.reprfunc import simple_repr
158# noinspection PyUnresolvedReferences
159from cardinal_pythonlib.snomed import ( # noqa: F401
160 SnomedAttribute,
161 SnomedAttributeGroup,
162 SnomedAttributeSet,
163 SnomedConcept as SnomedConceptCardinalPythonlib,
164 SnomedExpression as SnomedExpressionCardinalPythonlib,
165 SnomedFocusConcept,
166 SnomedRefinement,
167 SnomedValue,
168)
170from camcops_server.cc_modules.cc_cache import cache_region_static, fkg
171from camcops_server.cc_modules.cc_xml import XmlDataTypes, XmlElement
173log = BraceStyleAdapter(logging.getLogger(__name__))
176# =============================================================================
177# Constants
178# =============================================================================
180# -----------------------------------------------------------------------------
181# Internal
182# -----------------------------------------------------------------------------
184SNOMED_XML_NAME = "snomed_ct_expression"
186# -----------------------------------------------------------------------------
187# ICD-9-CM; from the client: camcops --print_icd9_codes
188# -----------------------------------------------------------------------------
190CLIENT_ICD9CM_CODES = set(
191 """
192290.0 290.1 290.10 290.11 290.12 290.13 290.2 290.20 290.21 290.3 290.4 290.40
193290.41 290.42 290.43 290.8 290.9 291.0 291.1 291.2 291.3 291.4 291.5 291.8
194291.81 291.82 291.89 291.9 292.0 292.1 292.11 292.12 292.2 292.8 292.81 292.82
195292.83 292.84 292.85 292.89 292.9 293.0 293.1 293.8 293.81 293.82 293.83 293.84
196293.89 293.9 294.0 294.1 294.10 294.11 294.2 294.20 294.21 294.8 294.9 295.0
197295.00 295.01 295.02 295.03 295.04 295.05 295.1 295.10 295.11 295.12 295.13
198295.14 295.15 295.2 295.20 295.21 295.22 295.23 295.24 295.25 295.3 295.30
199295.31 295.32 295.33 295.34 295.35 295.4 295.40 295.41 295.42 295.43 295.44
200295.45 295.5 295.50 295.51 295.52 295.53 295.54 295.55 295.6 295.60 295.61
201295.62 295.63 295.64 295.65 295.7 295.70 295.71 295.72 295.73 295.74 295.75
202295.8 295.80 295.81 295.82 295.83 295.84 295.85 295.9 295.90 295.91 295.92
203295.93 295.94 295.95 296.0 296.00 296.01 296.02 296.03 296.04 296.05 296.06
204296.1 296.10 296.11 296.12 296.13 296.14 296.15 296.16 296.2 296.20 296.21
205296.22 296.23 296.24 296.25 296.26 296.3 296.30 296.31 296.32 296.33 296.34
206296.35 296.36 296.4 296.40 296.41 296.42 296.43 296.44 296.45 296.46 296.5
207296.50 296.51 296.52 296.53 296.54 296.55 296.56 296.6 296.60 296.61 296.62
208296.63 296.64 296.65 296.66 296.7 296.8 296.80 296.81 296.82 296.89 296.9
209296.90 296.99 297.0 297.1 297.2 297.3 297.8 297.9 298.0 298.1 298.2 298.3 298.4
210298.8 298.9 299.0 299.00 299.01 299.1 299.10 299.11 299.8 299.80 299.81 299.9
211299.90 299.91 300.0 300.00 300.01 300.02 300.09 300.1 300.10 300.11 300.12
212300.13 300.14 300.15 300.16 300.19 300.2 300.20 300.21 300.22 300.23 300.29
213300.3 300.4 300.5 300.6 300.7 300.8 300.81 300.82 300.89 300.9 301.0 301.1
214301.10 301.11 301.12 301.13 301.2 301.20 301.21 301.22 301.3 301.4 301.5 301.50
215301.51 301.59 301.6 301.7 301.8 301.81 301.82 301.83 301.84 301.89 301.9 302.0
216302.1 302.2 302.3 302.4 302.5 302.50 302.51 302.52 302.53 302.6 302.7 302.70
217302.71 302.72 302.73 302.74 302.75 302.76 302.79 302.8 302.81 302.82 302.83
218302.84 302.85 302.89 302.9 303.0 303.00 303.01 303.02 303.03 303.0x 303.9
219303.90 303.91 303.92 303.93 304.0 304.00 304.01 304.02 304.03 304.1 304.10
220304.11 304.12 304.13 304.2 304.20 304.21 304.22 304.23 304.3 304.30 304.31
221304.32 304.33 304.4 304.40 304.41 304.42 304.43 304.5 304.50 304.51 304.52
222304.53 304.6 304.60 304.61 304.62 304.63 304.7 304.70 304.71 304.72 304.73
223304.8 304.80 304.81 304.82 304.83 304.9 304.90 304.91 304.92 304.93 305.0
224305.00 305.01 305.02 305.03 305.0x 305.1 305.10 305.11 305.12 305.13 305.2
225305.20 305.21 305.22 305.23 305.2x 305.3 305.30 305.31 305.32 305.33 305.3x
226305.4 305.40 305.41 305.42 305.43 305.4x 305.5 305.50 305.51 305.52 305.53
227305.5x 305.6 305.60 305.61 305.62 305.63 305.6x 305.7 305.70 305.71 305.72
228305.73 305.7x 305.8 305.80 305.81 305.82 305.83 305.8x 305.9 305.90 305.91
229305.92 305.93 305.9x 306.0 306.1 306.2 306.3 306.4 306.50 306.51 306.52 306.53
230306.59 306.6 306.7 306.8 306.9 307.0 307.1 307.2 307.20 307.21 307.22 307.23
231307.3 307.4 307.40 307.41 307.42 307.43 307.44 307.45 307.46 307.47 307.48
232307.49 307.5 307.50 307.51 307.52 307.53 307.54 307.59 307.6 307.7 307.8 307.80
233307.81 307.89 307.9 308.0 308.1 308.2 308.3 308.4 308.9 309.0 309.1 309.2
234309.21 309.22 309.23 309.24 309.28 309.29 309.3 309.4 309.8 309.81 309.82
235309.83 309.89 309.9 310.0 310.1 310.2 310.8 310.81 310.89 310.9 311 312.0
236312.00 312.01 312.02 312.03 312.1 312.10 312.11 312.12 312.13 312.2 312.20
237312.21 312.22 312.23 312.3 312.30 312.31 312.32 312.33 312.34 312.35 312.39
238312.4 312.8 312.81 312.82 312.89 312.9 313.0 313.1 313.2 313.21 313.22 313.23
239313.3 313.8 313.81 313.82 313.83 313.89 313.9 314.0 314.00 314.01 314.1 314.2
240314.8 314.9 315.0 315.00 315.01 315.02 315.09 315.1 315.2 315.3 315.31 315.32
241315.34 315.35 315.39 315.4 315.5 315.8 315.9 316 317 318.0 318.1 318.2 319
242V71.09
243""".split()
244)
246# -----------------------------------------------------------------------------
247# ICD-10; from the client: camcops --print_icd10_codes
248# -----------------------------------------------------------------------------
250CLIENT_ICD10_CODES = set(
251 """
252F00 F00.0 F00.00 F00.000 F00.001 F00.002 F00.01 F00.010 F00.011 F00.012 F00.02
253F00.020 F00.021 F00.022 F00.03 F00.030 F00.031 F00.032 F00.04 F00.040 F00.041
254F00.042 F00.1 F00.10 F00.100 F00.101 F00.102 F00.11 F00.110 F00.111 F00.112
255F00.12 F00.120 F00.121 F00.122 F00.13 F00.130 F00.131 F00.132 F00.14 F00.140
256F00.141 F00.142 F00.2 F00.20 F00.200 F00.201 F00.202 F00.21 F00.210 F00.211
257F00.212 F00.22 F00.220 F00.221 F00.222 F00.23 F00.230 F00.231 F00.232 F00.24
258F00.240 F00.241 F00.242 F00.9 F00.90 F00.900 F00.901 F00.902 F00.91 F00.910
259F00.911 F00.912 F00.92 F00.920 F00.921 F00.922 F00.93 F00.930 F00.931 F00.932
260F00.94 F00.940 F00.941 F00.942 F01 F01.0 F01.00 F01.000 F01.001 F01.002 F01.01
261F01.010 F01.011 F01.012 F01.02 F01.020 F01.021 F01.022 F01.03 F01.030 F01.031
262F01.032 F01.04 F01.040 F01.041 F01.042 F01.1 F01.10 F01.100 F01.101 F01.102
263F01.11 F01.110 F01.111 F01.112 F01.12 F01.120 F01.121 F01.122 F01.13 F01.130
264F01.131 F01.132 F01.14 F01.140 F01.141 F01.142 F01.2 F01.20 F01.200 F01.201
265F01.202 F01.21 F01.210 F01.211 F01.212 F01.22 F01.220 F01.221 F01.222 F01.23
266F01.230 F01.231 F01.232 F01.24 F01.240 F01.241 F01.242 F01.3 F01.30 F01.300
267F01.301 F01.302 F01.31 F01.310 F01.311 F01.312 F01.32 F01.320 F01.321 F01.322
268F01.33 F01.330 F01.331 F01.332 F01.34 F01.340 F01.341 F01.342 F01.8 F01.80
269F01.800 F01.801 F01.802 F01.81 F01.810 F01.811 F01.812 F01.82 F01.820 F01.821
270F01.822 F01.83 F01.830 F01.831 F01.832 F01.84 F01.840 F01.841 F01.842 F01.9
271F01.90 F01.900 F01.901 F01.902 F01.91 F01.910 F01.911 F01.912 F01.92 F01.920
272F01.921 F01.922 F01.93 F01.930 F01.931 F01.932 F01.94 F01.940 F01.941 F01.942
273F02 F02.0 F02.00 F02.000 F02.001 F02.002 F02.01 F02.010 F02.011 F02.012 F02.02
274F02.020 F02.021 F02.022 F02.03 F02.030 F02.031 F02.032 F02.04 F02.040 F02.041
275F02.042 F02.1 F02.10 F02.100 F02.101 F02.102 F02.11 F02.110 F02.111 F02.112
276F02.12 F02.120 F02.121 F02.122 F02.13 F02.130 F02.131 F02.132 F02.14 F02.140
277F02.141 F02.142 F02.2 F02.20 F02.200 F02.201 F02.202 F02.21 F02.210 F02.211
278F02.212 F02.22 F02.220 F02.221 F02.222 F02.23 F02.230 F02.231 F02.232 F02.24
279F02.240 F02.241 F02.242 F02.3 F02.30 F02.300 F02.301 F02.302 F02.31 F02.310
280F02.311 F02.312 F02.32 F02.320 F02.321 F02.322 F02.33 F02.330 F02.331 F02.332
281F02.34 F02.340 F02.341 F02.342 F02.4 F02.40 F02.400 F02.401 F02.402 F02.41
282F02.410 F02.411 F02.412 F02.42 F02.420 F02.421 F02.422 F02.43 F02.430 F02.431
283F02.432 F02.44 F02.440 F02.441 F02.442 F02.8 F02.80 F02.800 F02.801 F02.802
284F02.81 F02.810 F02.811 F02.812 F02.82 F02.820 F02.821 F02.822 F02.83 F02.830
285F02.831 F02.832 F02.84 F02.840 F02.841 F02.842 F03 F03.0 F03.00 F03.000 F03.001
286F03.002 F03.01 F03.010 F03.011 F03.012 F03.02 F03.020 F03.021 F03.022 F03.03
287F03.030 F03.031 F03.032 F03.04 F03.040 F03.041 F03.042 F04 F05 F05.0 F05.1
288F05.8 F05.9 F06 F06.0 F06.1 F06.2 F06.3 F06.4 F06.5 F06.6 F06.7 F06.8 F06.9 F07
289F07.0 F07.1 F07.2 F07.8 F07.9 F09 F10 F10.0 F10.00 F10.01 F10.02 F10.03 F10.04
290F10.05 F10.06 F10.07 F10.1 F10.2 F10.20 F10.200 F10.201 F10.202 F10.21 F10.22
291F10.23 F10.24 F10.241 F10.242 F10.25 F10.26 F10.3 F10.30 F10.31 F10.4 F10.40
292F10.41 F10.5 F10.50 F10.51 F10.52 F10.53 F10.54 F10.55 F10.56 F10.6 F10.7
293F10.70 F10.71 F10.72 F10.73 F10.74 F10.75 F10.8 F10.9 F11 F11.0 F11.00 F11.01
294F11.02 F11.03 F11.04 F11.05 F11.06 F11.1 F11.2 F11.20 F11.200 F11.201 F11.202
295F11.21 F11.22 F11.23 F11.24 F11.241 F11.242 F11.25 F11.26 F11.3 F11.30 F11.31
296F11.4 F11.40 F11.41 F11.5 F11.50 F11.51 F11.52 F11.53 F11.54 F11.55 F11.56
297F11.6 F11.7 F11.70 F11.71 F11.72 F11.73 F11.74 F11.75 F11.8 F11.9 F12 F12.0
298F12.00 F12.01 F12.02 F12.03 F12.04 F12.05 F12.06 F12.1 F12.2 F12.20 F12.200
299F12.201 F12.202 F12.21 F12.22 F12.23 F12.24 F12.241 F12.242 F12.25 F12.26 F12.3
300F12.30 F12.31 F12.4 F12.40 F12.41 F12.5 F12.50 F12.51 F12.52 F12.53 F12.54
301F12.55 F12.56 F12.6 F12.7 F12.70 F12.71 F12.72 F12.73 F12.74 F12.75 F12.8 F12.9
302F13 F13.0 F13.00 F13.01 F13.02 F13.03 F13.04 F13.05 F13.06 F13.1 F13.2 F13.20
303F13.200 F13.201 F13.202 F13.21 F13.22 F13.23 F13.24 F13.241 F13.242 F13.25
304F13.26 F13.3 F13.30 F13.31 F13.4 F13.40 F13.41 F13.5 F13.50 F13.51 F13.52
305F13.53 F13.54 F13.55 F13.56 F13.6 F13.7 F13.70 F13.71 F13.72 F13.73 F13.74
306F13.75 F13.8 F13.9 F14 F14.0 F14.00 F14.01 F14.02 F14.03 F14.04 F14.05 F14.06
307F14.1 F14.2 F14.20 F14.200 F14.201 F14.202 F14.21 F14.22 F14.23 F14.24 F14.241
308F14.242 F14.25 F14.26 F14.3 F14.30 F14.31 F14.4 F14.40 F14.41 F14.5 F14.50
309F14.51 F14.52 F14.53 F14.54 F14.55 F14.56 F14.6 F14.7 F14.70 F14.71 F14.72
310F14.73 F14.74 F14.75 F14.8 F14.9 F15 F15.0 F15.00 F15.01 F15.02 F15.03 F15.04
311F15.05 F15.06 F15.1 F15.2 F15.20 F15.200 F15.201 F15.202 F15.21 F15.22 F15.23
312F15.24 F15.241 F15.242 F15.25 F15.26 F15.3 F15.30 F15.31 F15.4 F15.40 F15.41
313F15.5 F15.50 F15.51 F15.52 F15.53 F15.54 F15.55 F15.56 F15.6 F15.7 F15.70
314F15.71 F15.72 F15.73 F15.74 F15.75 F15.8 F15.9 F16 F16.0 F16.00 F16.01 F16.02
315F16.03 F16.04 F16.05 F16.06 F16.1 F16.2 F16.20 F16.200 F16.201 F16.202 F16.21
316F16.22 F16.23 F16.24 F16.241 F16.242 F16.25 F16.26 F16.3 F16.30 F16.31 F16.4
317F16.40 F16.41 F16.5 F16.50 F16.51 F16.52 F16.53 F16.54 F16.55 F16.56 F16.6
318F16.7 F16.70 F16.71 F16.72 F16.73 F16.74 F16.75 F16.8 F16.9 F17 F17.0 F17.00
319F17.01 F17.02 F17.03 F17.04 F17.05 F17.06 F17.1 F17.2 F17.20 F17.200 F17.201
320F17.202 F17.21 F17.22 F17.23 F17.24 F17.241 F17.242 F17.25 F17.26 F17.3 F17.30
321F17.31 F17.4 F17.40 F17.41 F17.5 F17.50 F17.51 F17.52 F17.53 F17.54 F17.55
322F17.56 F17.6 F17.7 F17.70 F17.71 F17.72 F17.73 F17.74 F17.75 F17.8 F17.9 F18
323F18.0 F18.00 F18.01 F18.02 F18.03 F18.04 F18.05 F18.06 F18.1 F18.2 F18.20
324F18.200 F18.201 F18.202 F18.21 F18.22 F18.23 F18.24 F18.241 F18.242 F18.25
325F18.26 F18.3 F18.30 F18.31 F18.4 F18.40 F18.41 F18.5 F18.50 F18.51 F18.52
326F18.53 F18.54 F18.55 F18.56 F18.6 F18.7 F18.70 F18.71 F18.72 F18.73 F18.74
327F18.75 F18.8 F18.9 F19 F19.0 F19.00 F19.01 F19.02 F19.03 F19.04 F19.05 F19.06
328F19.1 F19.2 F19.20 F19.200 F19.201 F19.202 F19.21 F19.22 F19.23 F19.24 F19.241
329F19.242 F19.25 F19.26 F19.3 F19.30 F19.31 F19.4 F19.40 F19.41 F19.5 F19.50
330F19.51 F19.52 F19.53 F19.54 F19.55 F19.56 F19.6 F19.7 F19.70 F19.71 F19.72
331F19.73 F19.74 F19.75 F19.8 F19.9 F20 F20.0 F20.1 F20.2 F20.3 F20.4 F20.5 F20.6
332F20.8 F20.9 F21 F22 F22.0 F22.8 F22.9 F23 F23.0 F23.1 F23.2 F23.3 F23.8 F23.9
333F23.90 F23.91 F24 F25 F25.0 F25.00 F25.01 F25.1 F25.10 F25.11 F25.2 F25.20
334F25.21 F25.8 F25.80 F25.81 F25.9 F25.90 F25.91 F28 F29 F30 F30.0 F30.1 F30.2
335F30.20 F30.21 F30.8 F30.9 F31 F31.0 F31.1 F31.2 F31.20 F31.21 F31.3 F31.30
336F31.31 F31.4 F31.5 F31.50 F31.51 F31.6 F31.7 F31.8 F31.9 F32 F32.0 F32.00
337F32.01 F32.1 F32.10 F32.11 F32.2 F32.3 F32.30 F32.31 F32.8 F32.9 F33 F33.0
338F33.00 F33.01 F33.1 F33.10 F33.11 F33.2 F33.3 F33.30 F33.31 F33.4 F33.8 F33.9
339F34 F34.0 F34.1 F34.8 F34.9 F38 F38.0 F38.00 F38.1 F38.10 F38.8 F39 F40 F40.0
340F40.00 F40.01 F40.1 F40.2 F40.8 F40.9 F41 F41.0 F41.00 F41.01 F41.1 F41.2 F41.3
341F41.8 F41.9 F42 F42.0 F42.1 F42.2 F42.8 F42.9 F43 F43.0 F43.00 F43.01 F43.02
342F43.1 F43.2 F43.20 F43.21 F43.22 F43.23 F43.24 F43.25 F43.28 F43.8 F43.9 F44
343F44.0 F44.1 F44.2 F44.3 F44.4 F44.5 F44.6 F44.7 F44.8 F44.80 F44.81 F44.82
344F44.88 F44.9 F45 F45.0 F45.1 F45.2 F45.3 F45.30 F45.31 F45.32 F45.33 F45.34
345F45.38 F45.4 F45.8 F45.9 F48 F48.0 F48.1 F48.8 F48.9 F50 F50.0 F50.1 F50.2
346F50.3 F50.4 F50.5 F50.8 F50.9 F51 F51.0 F51.1 F51.2 F51.3 F51.4 F51.5 F51.8
347F51.9 F52 F52.0 F52.1 F52.10 F52.11 F52.2 F52.3 F52.4 F52.5 F52.6 F52.7 F52.8
348F52.9 F53 F53.0 F53.1 F53.8 F53.9 F54 F55 F59 F60 F60.0 F60.1 F60.2 F60.3
349F60.30 F60.31 F60.4 F60.5 F60.6 F60.7 F60.8 F60.9 F61 F62 F62.0 F62.1 F62.8
350F62.9 F63 F63.0 F63.1 F63.2 F63.3 F63.8 F63.9 F64 F64.0 F64.1 F64.2 F64.8 F64.9
351F65 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
352F66.8 F66.9 F66.90 F66.91 F66.92 F66.98 F68 F68.0 F68.1 F68.8 F69 F70 F70.0
353F70.1 F70.8 F70.9 F71 F71.0 F71.1 F71.8 F71.9 F72 F72.0 F72.1 F72.8 F72.9 F73
354F73.0 F73.1 F73.8 F73.9 F78 F78.0 F78.1 F78.8 F78.9 F79 F79.0 F79.1 F79.8 F79.9
355F80 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
356F82 F83 F84 F84.0 F84.1 F84.10 F84.11 F84.12 F84.2 F84.3 F84.4 F84.5 F84.8
357F84.9 F88 F89 F90 F90.0 F90.1 F90.8 F90.9 F91 F91.0 F91.1 F91.2 F91.3 F91.8
358F91.9 F92 F92.0 F92.8 F92.9 F93 F93.0 F93.1 F93.2 F93.3 F93.8 F93.80 F93.9 F94
359F94.0 F94.1 F94.2 F94.8 F94.9 F95 F95.0 F95.1 F95.2 F95.8 F95.9 F98 F98.0
360F98.00 F98.01 F98.02 F98.1 F98.10 F98.11 F98.12 F98.2 F98.3 F98.4 F98.40 F98.41
361F98.42 F98.5 F98.6 F98.8 F98.9 F99 R40 R40.0 R40.1 R40.2 R41 R41.0 R41.1 R41.2
362R41.3 R41.8 R42 R43 R43.0 R43.1 R43.2 R43.8 R44 R44.0 R44.1 R44.2 R44.3 R44.8
363R45 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
364R46.3 R46.4 R46.5 R46.6 R46.7 R46.8 X60 X60.0 X60.00 X60.01 X60.02 X60.03
365X60.04 X60.08 X60.09 X60.1 X60.10 X60.11 X60.12 X60.13 X60.14 X60.18 X60.19
366X60.2 X60.20 X60.21 X60.22 X60.23 X60.24 X60.28 X60.29 X60.3 X60.30 X60.31
367X60.32 X60.33 X60.34 X60.38 X60.39 X60.4 X60.40 X60.41 X60.42 X60.43 X60.44
368X60.48 X60.49 X60.5 X60.50 X60.51 X60.52 X60.53 X60.54 X60.58 X60.59 X60.6
369X60.60 X60.61 X60.62 X60.63 X60.64 X60.68 X60.69 X60.7 X60.70 X60.71 X60.72
370X60.73 X60.74 X60.78 X60.79 X60.8 X60.80 X60.81 X60.82 X60.83 X60.84 X60.88
371X60.89 X60.9 X60.90 X60.91 X60.92 X60.93 X60.94 X60.98 X60.99 X61 X61.0 X61.00
372X61.01 X61.02 X61.03 X61.04 X61.08 X61.09 X61.1 X61.10 X61.11 X61.12 X61.13
373X61.14 X61.18 X61.19 X61.2 X61.20 X61.21 X61.22 X61.23 X61.24 X61.28 X61.29
374X61.3 X61.30 X61.31 X61.32 X61.33 X61.34 X61.38 X61.39 X61.4 X61.40 X61.41
375X61.42 X61.43 X61.44 X61.48 X61.49 X61.5 X61.50 X61.51 X61.52 X61.53 X61.54
376X61.58 X61.59 X61.6 X61.60 X61.61 X61.62 X61.63 X61.64 X61.68 X61.69 X61.7
377X61.70 X61.71 X61.72 X61.73 X61.74 X61.78 X61.79 X61.8 X61.80 X61.81 X61.82
378X61.83 X61.84 X61.88 X61.89 X61.9 X61.90 X61.91 X61.92 X61.93 X61.94 X61.98
379X61.99 X62 X62.0 X62.00 X62.01 X62.02 X62.03 X62.04 X62.08 X62.09 X62.1 X62.10
380X62.11 X62.12 X62.13 X62.14 X62.18 X62.19 X62.2 X62.20 X62.21 X62.22 X62.23
381X62.24 X62.28 X62.29 X62.3 X62.30 X62.31 X62.32 X62.33 X62.34 X62.38 X62.39
382X62.4 X62.40 X62.41 X62.42 X62.43 X62.44 X62.48 X62.49 X62.5 X62.50 X62.51
383X62.52 X62.53 X62.54 X62.58 X62.59 X62.6 X62.60 X62.61 X62.62 X62.63 X62.64
384X62.68 X62.69 X62.7 X62.70 X62.71 X62.72 X62.73 X62.74 X62.78 X62.79 X62.8
385X62.80 X62.81 X62.82 X62.83 X62.84 X62.88 X62.89 X62.9 X62.90 X62.91 X62.92
386X62.93 X62.94 X62.98 X62.99 X63 X63.0 X63.00 X63.01 X63.02 X63.03 X63.04 X63.08
387X63.09 X63.1 X63.10 X63.11 X63.12 X63.13 X63.14 X63.18 X63.19 X63.2 X63.20
388X63.21 X63.22 X63.23 X63.24 X63.28 X63.29 X63.3 X63.30 X63.31 X63.32 X63.33
389X63.34 X63.38 X63.39 X63.4 X63.40 X63.41 X63.42 X63.43 X63.44 X63.48 X63.49
390X63.5 X63.50 X63.51 X63.52 X63.53 X63.54 X63.58 X63.59 X63.6 X63.60 X63.61
391X63.62 X63.63 X63.64 X63.68 X63.69 X63.7 X63.70 X63.71 X63.72 X63.73 X63.74
392X63.78 X63.79 X63.8 X63.80 X63.81 X63.82 X63.83 X63.84 X63.88 X63.89 X63.9
393X63.90 X63.91 X63.92 X63.93 X63.94 X63.98 X63.99 X64 X64.0 X64.00 X64.01 X64.02
394X64.03 X64.04 X64.08 X64.09 X64.1 X64.10 X64.11 X64.12 X64.13 X64.14 X64.18
395X64.19 X64.2 X64.20 X64.21 X64.22 X64.23 X64.24 X64.28 X64.29 X64.3 X64.30
396X64.31 X64.32 X64.33 X64.34 X64.38 X64.39 X64.4 X64.40 X64.41 X64.42 X64.43
397X64.44 X64.48 X64.49 X64.5 X64.50 X64.51 X64.52 X64.53 X64.54 X64.58 X64.59
398X64.6 X64.60 X64.61 X64.62 X64.63 X64.64 X64.68 X64.69 X64.7 X64.70 X64.71
399X64.72 X64.73 X64.74 X64.78 X64.79 X64.8 X64.80 X64.81 X64.82 X64.83 X64.84
400X64.88 X64.89 X64.9 X64.90 X64.91 X64.92 X64.93 X64.94 X64.98 X64.99 X65 X65.0
401X65.00 X65.01 X65.02 X65.03 X65.04 X65.08 X65.09 X65.1 X65.10 X65.11 X65.12
402X65.13 X65.14 X65.18 X65.19 X65.2 X65.20 X65.21 X65.22 X65.23 X65.24 X65.28
403X65.29 X65.3 X65.30 X65.31 X65.32 X65.33 X65.34 X65.38 X65.39 X65.4 X65.40
404X65.41 X65.42 X65.43 X65.44 X65.48 X65.49 X65.5 X65.50 X65.51 X65.52 X65.53
405X65.54 X65.58 X65.59 X65.6 X65.60 X65.61 X65.62 X65.63 X65.64 X65.68 X65.69
406X65.7 X65.70 X65.71 X65.72 X65.73 X65.74 X65.78 X65.79 X65.8 X65.80 X65.81
407X65.82 X65.83 X65.84 X65.88 X65.89 X65.9 X65.90 X65.91 X65.92 X65.93 X65.94
408X65.98 X65.99 X66 X66.0 X66.00 X66.01 X66.02 X66.03 X66.04 X66.08 X66.09 X66.1
409X66.10 X66.11 X66.12 X66.13 X66.14 X66.18 X66.19 X66.2 X66.20 X66.21 X66.22
410X66.23 X66.24 X66.28 X66.29 X66.3 X66.30 X66.31 X66.32 X66.33 X66.34 X66.38
411X66.39 X66.4 X66.40 X66.41 X66.42 X66.43 X66.44 X66.48 X66.49 X66.5 X66.50
412X66.51 X66.52 X66.53 X66.54 X66.58 X66.59 X66.6 X66.60 X66.61 X66.62 X66.63
413X66.64 X66.68 X66.69 X66.7 X66.70 X66.71 X66.72 X66.73 X66.74 X66.78 X66.79
414X66.8 X66.80 X66.81 X66.82 X66.83 X66.84 X66.88 X66.89 X66.9 X66.90 X66.91
415X66.92 X66.93 X66.94 X66.98 X66.99 X67 X67.0 X67.00 X67.01 X67.02 X67.03 X67.04
416X67.08 X67.09 X67.1 X67.10 X67.11 X67.12 X67.13 X67.14 X67.18 X67.19 X67.2
417X67.20 X67.21 X67.22 X67.23 X67.24 X67.28 X67.29 X67.3 X67.30 X67.31 X67.32
418X67.33 X67.34 X67.38 X67.39 X67.4 X67.40 X67.41 X67.42 X67.43 X67.44 X67.48
419X67.49 X67.5 X67.50 X67.51 X67.52 X67.53 X67.54 X67.58 X67.59 X67.6 X67.60
420X67.61 X67.62 X67.63 X67.64 X67.68 X67.69 X67.7 X67.70 X67.71 X67.72 X67.73
421X67.74 X67.78 X67.79 X67.8 X67.80 X67.81 X67.82 X67.83 X67.84 X67.88 X67.89
422X67.9 X67.90 X67.91 X67.92 X67.93 X67.94 X67.98 X67.99 X68 X68.0 X68.00 X68.01
423X68.02 X68.03 X68.04 X68.08 X68.09 X68.1 X68.10 X68.11 X68.12 X68.13 X68.14
424X68.18 X68.19 X68.2 X68.20 X68.21 X68.22 X68.23 X68.24 X68.28 X68.29 X68.3
425X68.30 X68.31 X68.32 X68.33 X68.34 X68.38 X68.39 X68.4 X68.40 X68.41 X68.42
426X68.43 X68.44 X68.48 X68.49 X68.5 X68.50 X68.51 X68.52 X68.53 X68.54 X68.58
427X68.59 X68.6 X68.60 X68.61 X68.62 X68.63 X68.64 X68.68 X68.69 X68.7 X68.70
428X68.71 X68.72 X68.73 X68.74 X68.78 X68.79 X68.8 X68.80 X68.81 X68.82 X68.83
429X68.84 X68.88 X68.89 X68.9 X68.90 X68.91 X68.92 X68.93 X68.94 X68.98 X68.99 X69
430X69.0 X69.00 X69.01 X69.02 X69.03 X69.04 X69.08 X69.09 X69.1 X69.10 X69.11
431X69.12 X69.13 X69.14 X69.18 X69.19 X69.2 X69.20 X69.21 X69.22 X69.23 X69.24
432X69.28 X69.29 X69.3 X69.30 X69.31 X69.32 X69.33 X69.34 X69.38 X69.39 X69.4
433X69.40 X69.41 X69.42 X69.43 X69.44 X69.48 X69.49 X69.5 X69.50 X69.51 X69.52
434X69.53 X69.54 X69.58 X69.59 X69.6 X69.60 X69.61 X69.62 X69.63 X69.64 X69.68
435X69.69 X69.7 X69.70 X69.71 X69.72 X69.73 X69.74 X69.78 X69.79 X69.8 X69.80
436X69.81 X69.82 X69.83 X69.84 X69.88 X69.89 X69.9 X69.90 X69.91 X69.92 X69.93
437X69.94 X69.98 X69.99 X70 X70.0 X70.00 X70.01 X70.02 X70.03 X70.04 X70.08 X70.09
438X70.1 X70.10 X70.11 X70.12 X70.13 X70.14 X70.18 X70.19 X70.2 X70.20 X70.21
439X70.22 X70.23 X70.24 X70.28 X70.29 X70.3 X70.30 X70.31 X70.32 X70.33 X70.34
440X70.38 X70.39 X70.4 X70.40 X70.41 X70.42 X70.43 X70.44 X70.48 X70.49 X70.5
441X70.50 X70.51 X70.52 X70.53 X70.54 X70.58 X70.59 X70.6 X70.60 X70.61 X70.62
442X70.63 X70.64 X70.68 X70.69 X70.7 X70.70 X70.71 X70.72 X70.73 X70.74 X70.78
443X70.79 X70.8 X70.80 X70.81 X70.82 X70.83 X70.84 X70.88 X70.89 X70.9 X70.90
444X70.91 X70.92 X70.93 X70.94 X70.98 X70.99 X71 X71.0 X71.00 X71.01 X71.02 X71.03
445X71.04 X71.08 X71.09 X71.1 X71.10 X71.11 X71.12 X71.13 X71.14 X71.18 X71.19
446X71.2 X71.20 X71.21 X71.22 X71.23 X71.24 X71.28 X71.29 X71.3 X71.30 X71.31
447X71.32 X71.33 X71.34 X71.38 X71.39 X71.4 X71.40 X71.41 X71.42 X71.43 X71.44
448X71.48 X71.49 X71.5 X71.50 X71.51 X71.52 X71.53 X71.54 X71.58 X71.59 X71.6
449X71.60 X71.61 X71.62 X71.63 X71.64 X71.68 X71.69 X71.7 X71.70 X71.71 X71.72
450X71.73 X71.74 X71.78 X71.79 X71.8 X71.80 X71.81 X71.82 X71.83 X71.84 X71.88
451X71.89 X71.9 X71.90 X71.91 X71.92 X71.93 X71.94 X71.98 X71.99 X72 X72.0 X72.00
452X72.01 X72.02 X72.03 X72.04 X72.08 X72.09 X72.1 X72.10 X72.11 X72.12 X72.13
453X72.14 X72.18 X72.19 X72.2 X72.20 X72.21 X72.22 X72.23 X72.24 X72.28 X72.29
454X72.3 X72.30 X72.31 X72.32 X72.33 X72.34 X72.38 X72.39 X72.4 X72.40 X72.41
455X72.42 X72.43 X72.44 X72.48 X72.49 X72.5 X72.50 X72.51 X72.52 X72.53 X72.54
456X72.58 X72.59 X72.6 X72.60 X72.61 X72.62 X72.63 X72.64 X72.68 X72.69 X72.7
457X72.70 X72.71 X72.72 X72.73 X72.74 X72.78 X72.79 X72.8 X72.80 X72.81 X72.82
458X72.83 X72.84 X72.88 X72.89 X72.9 X72.90 X72.91 X72.92 X72.93 X72.94 X72.98
459X72.99 X73 X73.0 X73.00 X73.01 X73.02 X73.03 X73.04 X73.08 X73.09 X73.1 X73.10
460X73.11 X73.12 X73.13 X73.14 X73.18 X73.19 X73.2 X73.20 X73.21 X73.22 X73.23
461X73.24 X73.28 X73.29 X73.3 X73.30 X73.31 X73.32 X73.33 X73.34 X73.38 X73.39
462X73.4 X73.40 X73.41 X73.42 X73.43 X73.44 X73.48 X73.49 X73.5 X73.50 X73.51
463X73.52 X73.53 X73.54 X73.58 X73.59 X73.6 X73.60 X73.61 X73.62 X73.63 X73.64
464X73.68 X73.69 X73.7 X73.70 X73.71 X73.72 X73.73 X73.74 X73.78 X73.79 X73.8
465X73.80 X73.81 X73.82 X73.83 X73.84 X73.88 X73.89 X73.9 X73.90 X73.91 X73.92
466X73.93 X73.94 X73.98 X73.99 X74 X74.0 X74.00 X74.01 X74.02 X74.03 X74.04 X74.08
467X74.09 X74.1 X74.10 X74.11 X74.12 X74.13 X74.14 X74.18 X74.19 X74.2 X74.20
468X74.21 X74.22 X74.23 X74.24 X74.28 X74.29 X74.3 X74.30 X74.31 X74.32 X74.33
469X74.34 X74.38 X74.39 X74.4 X74.40 X74.41 X74.42 X74.43 X74.44 X74.48 X74.49
470X74.5 X74.50 X74.51 X74.52 X74.53 X74.54 X74.58 X74.59 X74.6 X74.60 X74.61
471X74.62 X74.63 X74.64 X74.68 X74.69 X74.7 X74.70 X74.71 X74.72 X74.73 X74.74
472X74.78 X74.79 X74.8 X74.80 X74.81 X74.82 X74.83 X74.84 X74.88 X74.89 X74.9
473X74.90 X74.91 X74.92 X74.93 X74.94 X74.98 X74.99 X75 X75.0 X75.00 X75.01 X75.02
474X75.03 X75.04 X75.08 X75.09 X75.1 X75.10 X75.11 X75.12 X75.13 X75.14 X75.18
475X75.19 X75.2 X75.20 X75.21 X75.22 X75.23 X75.24 X75.28 X75.29 X75.3 X75.30
476X75.31 X75.32 X75.33 X75.34 X75.38 X75.39 X75.4 X75.40 X75.41 X75.42 X75.43
477X75.44 X75.48 X75.49 X75.5 X75.50 X75.51 X75.52 X75.53 X75.54 X75.58 X75.59
478X75.6 X75.60 X75.61 X75.62 X75.63 X75.64 X75.68 X75.69 X75.7 X75.70 X75.71
479X75.72 X75.73 X75.74 X75.78 X75.79 X75.8 X75.80 X75.81 X75.82 X75.83 X75.84
480X75.88 X75.89 X75.9 X75.90 X75.91 X75.92 X75.93 X75.94 X75.98 X75.99 X76 X76.0
481X76.00 X76.01 X76.02 X76.03 X76.04 X76.08 X76.09 X76.1 X76.10 X76.11 X76.12
482X76.13 X76.14 X76.18 X76.19 X76.2 X76.20 X76.21 X76.22 X76.23 X76.24 X76.28
483X76.29 X76.3 X76.30 X76.31 X76.32 X76.33 X76.34 X76.38 X76.39 X76.4 X76.40
484X76.41 X76.42 X76.43 X76.44 X76.48 X76.49 X76.5 X76.50 X76.51 X76.52 X76.53
485X76.54 X76.58 X76.59 X76.6 X76.60 X76.61 X76.62 X76.63 X76.64 X76.68 X76.69
486X76.7 X76.70 X76.71 X76.72 X76.73 X76.74 X76.78 X76.79 X76.8 X76.80 X76.81
487X76.82 X76.83 X76.84 X76.88 X76.89 X76.9 X76.90 X76.91 X76.92 X76.93 X76.94
488X76.98 X76.99 X77 X77.0 X77.00 X77.01 X77.02 X77.03 X77.04 X77.08 X77.09 X77.1
489X77.10 X77.11 X77.12 X77.13 X77.14 X77.18 X77.19 X77.2 X77.20 X77.21 X77.22
490X77.23 X77.24 X77.28 X77.29 X77.3 X77.30 X77.31 X77.32 X77.33 X77.34 X77.38
491X77.39 X77.4 X77.40 X77.41 X77.42 X77.43 X77.44 X77.48 X77.49 X77.5 X77.50
492X77.51 X77.52 X77.53 X77.54 X77.58 X77.59 X77.6 X77.60 X77.61 X77.62 X77.63
493X77.64 X77.68 X77.69 X77.7 X77.70 X77.71 X77.72 X77.73 X77.74 X77.78 X77.79
494X77.8 X77.80 X77.81 X77.82 X77.83 X77.84 X77.88 X77.89 X77.9 X77.90 X77.91
495X77.92 X77.93 X77.94 X77.98 X77.99 X78 X78.0 X78.00 X78.01 X78.02 X78.03 X78.04
496X78.08 X78.09 X78.1 X78.10 X78.11 X78.12 X78.13 X78.14 X78.18 X78.19 X78.2
497X78.20 X78.21 X78.22 X78.23 X78.24 X78.28 X78.29 X78.3 X78.30 X78.31 X78.32
498X78.33 X78.34 X78.38 X78.39 X78.4 X78.40 X78.41 X78.42 X78.43 X78.44 X78.48
499X78.49 X78.5 X78.50 X78.51 X78.52 X78.53 X78.54 X78.58 X78.59 X78.6 X78.60
500X78.61 X78.62 X78.63 X78.64 X78.68 X78.69 X78.7 X78.70 X78.71 X78.72 X78.73
501X78.74 X78.78 X78.79 X78.8 X78.80 X78.81 X78.82 X78.83 X78.84 X78.88 X78.89
502X78.9 X78.90 X78.91 X78.92 X78.93 X78.94 X78.98 X78.99 X79 X79.0 X79.00 X79.01
503X79.02 X79.03 X79.04 X79.08 X79.09 X79.1 X79.10 X79.11 X79.12 X79.13 X79.14
504X79.18 X79.19 X79.2 X79.20 X79.21 X79.22 X79.23 X79.24 X79.28 X79.29 X79.3
505X79.30 X79.31 X79.32 X79.33 X79.34 X79.38 X79.39 X79.4 X79.40 X79.41 X79.42
506X79.43 X79.44 X79.48 X79.49 X79.5 X79.50 X79.51 X79.52 X79.53 X79.54 X79.58
507X79.59 X79.6 X79.60 X79.61 X79.62 X79.63 X79.64 X79.68 X79.69 X79.7 X79.70
508X79.71 X79.72 X79.73 X79.74 X79.78 X79.79 X79.8 X79.80 X79.81 X79.82 X79.83
509X79.84 X79.88 X79.89 X79.9 X79.90 X79.91 X79.92 X79.93 X79.94 X79.98 X79.99 X80
510X80.0 X80.00 X80.01 X80.02 X80.03 X80.04 X80.08 X80.09 X80.1 X80.10 X80.11
511X80.12 X80.13 X80.14 X80.18 X80.19 X80.2 X80.20 X80.21 X80.22 X80.23 X80.24
512X80.28 X80.29 X80.3 X80.30 X80.31 X80.32 X80.33 X80.34 X80.38 X80.39 X80.4
513X80.40 X80.41 X80.42 X80.43 X80.44 X80.48 X80.49 X80.5 X80.50 X80.51 X80.52
514X80.53 X80.54 X80.58 X80.59 X80.6 X80.60 X80.61 X80.62 X80.63 X80.64 X80.68
515X80.69 X80.7 X80.70 X80.71 X80.72 X80.73 X80.74 X80.78 X80.79 X80.8 X80.80
516X80.81 X80.82 X80.83 X80.84 X80.88 X80.89 X80.9 X80.90 X80.91 X80.92 X80.93
517X80.94 X80.98 X80.99 X81 X81.0 X81.00 X81.01 X81.02 X81.03 X81.04 X81.08 X81.09
518X81.1 X81.10 X81.11 X81.12 X81.13 X81.14 X81.18 X81.19 X81.2 X81.20 X81.21
519X81.22 X81.23 X81.24 X81.28 X81.29 X81.3 X81.30 X81.31 X81.32 X81.33 X81.34
520X81.38 X81.39 X81.4 X81.40 X81.41 X81.42 X81.43 X81.44 X81.48 X81.49 X81.5
521X81.50 X81.51 X81.52 X81.53 X81.54 X81.58 X81.59 X81.6 X81.60 X81.61 X81.62
522X81.63 X81.64 X81.68 X81.69 X81.7 X81.70 X81.71 X81.72 X81.73 X81.74 X81.78
523X81.79 X81.8 X81.80 X81.81 X81.82 X81.83 X81.84 X81.88 X81.89 X81.9 X81.90
524X81.91 X81.92 X81.93 X81.94 X81.98 X81.99 X82 X82.0 X82.00 X82.01 X82.02 X82.03
525X82.04 X82.08 X82.09 X82.1 X82.10 X82.11 X82.12 X82.13 X82.14 X82.18 X82.19
526X82.2 X82.20 X82.21 X82.22 X82.23 X82.24 X82.28 X82.29 X82.3 X82.30 X82.31
527X82.32 X82.33 X82.34 X82.38 X82.39 X82.4 X82.40 X82.41 X82.42 X82.43 X82.44
528X82.48 X82.49 X82.5 X82.50 X82.51 X82.52 X82.53 X82.54 X82.58 X82.59 X82.6
529X82.60 X82.61 X82.62 X82.63 X82.64 X82.68 X82.69 X82.7 X82.70 X82.71 X82.72
530X82.73 X82.74 X82.78 X82.79 X82.8 X82.80 X82.81 X82.82 X82.83 X82.84 X82.88
531X82.89 X82.9 X82.90 X82.91 X82.92 X82.93 X82.94 X82.98 X82.99 X83 X83.0 X83.00
532X83.01 X83.02 X83.03 X83.04 X83.08 X83.09 X83.1 X83.10 X83.11 X83.12 X83.13
533X83.14 X83.18 X83.19 X83.2 X83.20 X83.21 X83.22 X83.23 X83.24 X83.28 X83.29
534X83.3 X83.30 X83.31 X83.32 X83.33 X83.34 X83.38 X83.39 X83.4 X83.40 X83.41
535X83.42 X83.43 X83.44 X83.48 X83.49 X83.5 X83.50 X83.51 X83.52 X83.53 X83.54
536X83.58 X83.59 X83.6 X83.60 X83.61 X83.62 X83.63 X83.64 X83.68 X83.69 X83.7
537X83.70 X83.71 X83.72 X83.73 X83.74 X83.78 X83.79 X83.8 X83.80 X83.81 X83.82
538X83.83 X83.84 X83.88 X83.89 X83.9 X83.90 X83.91 X83.92 X83.93 X83.94 X83.98
539X83.99 X84 X84.0 X84.00 X84.01 X84.02 X84.03 X84.04 X84.08 X84.09 X84.1 X84.10
540X84.11 X84.12 X84.13 X84.14 X84.18 X84.19 X84.2 X84.20 X84.21 X84.22 X84.23
541X84.24 X84.28 X84.29 X84.3 X84.30 X84.31 X84.32 X84.33 X84.34 X84.38 X84.39
542X84.4 X84.40 X84.41 X84.42 X84.43 X84.44 X84.48 X84.49 X84.5 X84.50 X84.51
543X84.52 X84.53 X84.54 X84.58 X84.59 X84.6 X84.60 X84.61 X84.62 X84.63 X84.64
544X84.68 X84.69 X84.7 X84.70 X84.71 X84.72 X84.73 X84.74 X84.78 X84.79 X84.8
545X84.80 X84.81 X84.82 X84.83 X84.84 X84.88 X84.89 X84.9 X84.90 X84.91 X84.92
546X84.93 X84.94 X84.98 X84.99 Z00.4 Z03.2 Z71.1
547""".split()
548)
551# =============================================================================
552# The SnomedConcept class, amended
553# =============================================================================
556class SnomedConcept(SnomedConceptCardinalPythonlib):
557 @classmethod
558 def create(
559 cls, concept: SnomedConceptCardinalPythonlib
560 ) -> "SnomedConcept":
561 """
562 Creates a CamCOPS-friendly
563 :class:`camcops_server.cc_modules.cc_snomed.SnomedConcept` from a
564 :class:`cardinal_pythonlib.snomed.SnomedConcept`.
566 The result has extra methods.
567 """
568 return SnomedConcept(identifier=concept.identifier, term=concept.term)
570 def xml_element(self, longform: bool = True) -> XmlElement:
571 """
572 Returns a :class:`camcops_server.cc_modules.cc_xml.XmlElement` for this
573 SNOMED-CT object.
575 Args:
576 longform: print SNOMED-CT concepts in long form?
577 """
578 return XmlElement(
579 name=SNOMED_XML_NAME,
580 value=self.as_string(longform),
581 datatype=XmlDataTypes.STRING,
582 )
585# =============================================================================
586# The SnomedExpression class, amended
587# =============================================================================
590class SnomedExpression(SnomedExpressionCardinalPythonlib):
591 def xml_element(self, longform: bool = True) -> XmlElement:
592 """
593 Returns a :class:`camcops_server.cc_modules.cc_xml.XmlElement` for this
594 SNOMED-CT object.
596 Args:
597 longform: print SNOMED-CT expressions in long form?
598 """
599 return XmlElement(
600 name=SNOMED_XML_NAME,
601 value=self.as_string(longform),
602 datatype=XmlDataTypes.STRING,
603 )
606# =============================================================================
607# The CamCOPS XML file format for SNOMED-CT
608# =============================================================================
610ROOT_TAG = "snomed_concepts"
611CONCEPT_TAG = "concept"
612LOOKUP_TAG = "lookup"
613LOOKUP_NAME_ATTR = "name"
614LOOKUP_ATTR = "lookup"
615ID_TAG = "id"
616TERM_TAG = "term"
617AUTOGEN_COMMENT = (
618 "Autogenerated XML (see camcops_server.cc_modules.cc_snomed.py); do not "
619 "edit"
620)
623def get_snomed_concepts_from_xml(
624 xml_filename: str,
625) -> Dict[str, Union[SnomedConcept, List[SnomedConcept]]]:
626 """
627 Reads in all SNOMED-CT concepts from an XML file according to the CamCOPS
628 format.
630 Args:
631 xml_filename: XML filename to read
633 Returns:
634 dict: mapping each lookup code found to a list of
635 :class:`SnomedConcept` objects
637 """
638 log.info("Reading SNOMED-CT XML file: {}", xml_filename)
639 parser = ElementTree.XMLParser(encoding="UTF-8")
640 tree = ElementTree.parse(xml_filename, parser=parser)
641 root = tree.getroot()
642 all_concepts = {} # type: Dict[str, List[SnomedConcept]]
643 find_lookup = "./{tag}[@{attr}]".format(
644 tag=LOOKUP_TAG, attr=LOOKUP_NAME_ATTR
645 )
646 find_concept = "./{tag}".format(tag=CONCEPT_TAG)
647 find_id_in_concept = "./{tag}".format(tag=ID_TAG)
648 find_name_in_concept = "./{tag}".format(tag=TERM_TAG)
649 for lookuproot in root.findall(find_lookup):
650 # Extract info from the XML
651 lookupname = lookuproot.attrib.get(LOOKUP_NAME_ATTR)
652 for conceptroot in lookuproot.findall(find_concept):
653 id_node = conceptroot.find(find_id_in_concept)
654 identifier = int(id_node.text)
655 name_node = conceptroot.find(find_name_in_concept)
656 name = name_node.text or ""
657 # Stash it
658 concept = SnomedConcept(identifier, name)
659 concepts_for_lookup = all_concepts.setdefault(lookupname, [])
660 concepts_for_lookup.append(concept)
661 # Done
662 return all_concepts
665def write_snomed_concepts_to_xml(
666 xml_filename: str,
667 concepts: Dict[str, List[SnomedConcept]],
668 comment: str = AUTOGEN_COMMENT,
669) -> None:
670 """
671 Writes SNOMED-CT concepts to an XML file in the CamCOPS format.
673 Args:
674 xml_filename: XML filename to write
675 concepts: dictionary mapping lookup codes to a list of
676 :class:`SnomedConcept` objects
677 comment: comment for XML file
678 """
679 # https://stackoverflow.com/questions/3605680/creating-a-simple-xml-file-using-python
680 root = ElementTree.Element(ROOT_TAG)
681 comment_element = ElementTree.Comment(comment)
682 root.insert(0, comment_element)
683 for lookup, concepts_for_lookup in concepts.items():
684 l_el = ElementTree.SubElement(
685 root, LOOKUP_TAG, {LOOKUP_NAME_ATTR: lookup}
686 )
687 for concept in concepts_for_lookup:
688 c_el = ElementTree.SubElement(l_el, CONCEPT_TAG)
689 i_el = ElementTree.SubElement(c_el, ID_TAG)
690 i_el.text = str(concept.identifier)
691 n_el = ElementTree.SubElement(c_el, TERM_TAG)
692 n_el.text = concept.term
693 tree = ElementTree.ElementTree(root)
694 log.info("Writing to {!r}", xml_filename)
695 tree.write(xml_filename)
698# =============================================================================
699# SNOMED-CT concepts for CamCOPS tasks
700# =============================================================================
702# -----------------------------------------------------------------------------
703# CamCOPS lookup codes for SNOMED-CT concepts
704# -----------------------------------------------------------------------------
707class SnomedLookup(object):
708 """
709 We're not allowed to embed SNOMED-CT codes in the CamCOPS code. Therefore,
710 within CamCOPS, we use string constants represented in this class. If the
711 local institution is allowed (e.g. in the UK, as below), then it can
712 install additional data.
714 - UK license:
715 https://isd.digital.nhs.uk/trud3/user/guest/group/0/pack/26/subpack/101/licences
717 - To find codes: https://termbrowser.nhs.uk/
719 Abbreviations:
721 - "Finding" is not abbreviated
722 - "Obs" or "observable" is short for "observable entity"
723 - "Procedure" is not abbreviated
724 - "Scale" is short for "assessment scale"
725 - "Situation" is not abbreviated
727 Variable names are designed for clear code. Value strings are designed for
728 clear XML that matches SNOMED-CT, in the format TASK_CONCEPTTYPE_NAME.
730 """ # noqa
732 # https://snomedbrowser.com/Codes/Details/XXX # noqa
734 # -------------------------------------------------------------------------
735 # SNOMED-CT core concepts
736 # -------------------------------------------------------------------------
738 # Base concepts
739 OBSERVABLE_ENTITY = "observable_entity"
741 # Abstract physical quantities
742 MASS = "mass"
743 LENGTH = "length"
745 # Saying "units"
746 UNIT_OF_MEASURE = "unit_of_measure"
748 # Base physical units
749 KILOGRAM = "kilogram"
750 METRE = "metre"
751 CENTIMETRE = "centimetre"
753 # Compound physical units
754 KG_PER_SQ_M = "kilogram_per_square_metre"
756 # -------------------------------------------------------------------------
757 # Scales
758 # -------------------------------------------------------------------------
760 # ACE-R
761 ACE_R_SCALE = "ace_r_scale"
762 ACE_R_SUBSCALE_ATTENTION_ORIENTATION = (
763 "ace_r_subscale_attention_orientation"
764 )
765 ACE_R_SUBSCALE_FLUENCY = "ace_r_subscale_fluency"
766 ACE_R_SUBSCALE_LANGUAGE = "ace_r_subscale_language"
767 ACE_R_SUBSCALE_MEMORY = "ace_r_subscale_memory"
768 ACE_R_SUBSCALE_VISUOSPATIAL = "ace_r_subscale_visuospatial"
769 ACE_R_SCORE = "ace_r_observable_score"
770 ACE_R_SUBSCORE_ATTENTION_ORIENTATION = (
771 "ace_r_observable_subscore_attention_orientation"
772 )
773 ACE_R_SUBSCORE_FLUENCY = "ace_r_observable_subscore_fluency"
774 ACE_R_SUBSCORE_LANGUAGE = "ace_r_observable_subscore_language"
775 ACE_R_SUBSCORE_MEMORY = "ace_r_observable_subscore_memory"
776 ACE_R_SUBSCORE_VISUOSPATIAL = "ace_r_observable_subscore_visuospatial"
777 ACE_R_PROCEDURE_ASSESSMENT = "ace_r_procedure_assessment"
778 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_ATTENTION_ORIENTATION = (
779 "ace_r_procedure_assessment_subscale_attention_orientation"
780 )
781 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_FLUENCY = (
782 "ace_r_procedure_assessment_subscale_fluency"
783 )
784 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_LANGUAGE = (
785 "ace_r_procedure_assessment_subscale_language"
786 )
787 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_MEMORY = (
788 "ace_r_procedure_assessment_subscale_memory"
789 )
790 ACE_R_PROCEDURE_ASSESSMENT_SUBSCALE_VISUOSPATIAL = (
791 "ace_r_procedure_assessment_subscale_visuospatial"
792 )
794 # AIMS
795 AIMS_SCALE = "aims_scale"
796 AIMS_TOTAL_SCORE = "aims_observable_total_score"
797 AIMS_PROCEDURE_ASSESSMENT = "aims_procedure_assessment"
799 # AUDIT, AUDIT-C
800 AUDIT_SCALE = "audit_scale"
801 AUDIT_SCORE = "audit_observable_score"
802 AUDIT_PROCEDURE_ASSESSMENT = "audit_procedure_assessment"
803 AUDITC_SCALE = "auditc_scale"
804 AUDITC_SCORE = "auditc_observable_score"
805 AUDITC_PROCEDURE_ASSESSMENT = "auditc_procedure_assessment"
807 # BADLS
808 BADLS_SCALE = "badls_scale"
809 BADLS_SCORE = "badls_observable_score"
810 BADLS_PROCEDURE_ASSESSMENT = "badls_procedure_assessment"
812 # BDI
813 BDI_SCALE = "bdi_scale"
814 BDI_SCORE = "bdi_observable_score"
815 BDI_PROCEDURE_ASSESSMENT = "bdi_procedure_assessment"
816 BDI_II_SCORE = "bdi_ii_observable_score"
817 BDI_II_PROCEDURE_ASSESSMENT = "bdi_ii_procedure_assessment"
819 # BMI
820 BMI_OBSERVABLE = "bmi_observable"
821 BMI_PROCEDURE_MEASUREMENT = "bmi_procedure_measurement"
822 BODY_HEIGHT_OBSERVABLE = "body_height_observable"
823 BODY_WEIGHT_OBSERVABLE = "body_weight_observable"
824 WAIST_CIRCUMFERENCE_PROCEDURE_MEASUREMENT = (
825 "waist_circumference_procedure_measurement"
826 )
827 WAIST_CIRCUMFERENCE_OBSERVABLE = "waist_circumference_observable"
829 # BPRS, BPRS-E
830 BPRS1962_SCALE = "bprs1962_scale"
831 # no observable/procedure
833 # CAGE
834 CAGE_SCALE = "cage_scale"
835 CAGE_SCORE = "cage_observable_score"
836 CAGE_PROCEDURE_ASSESSMENT = "cage_procedure_assessment"
838 # CAPE-42: none
839 # CAPS: none
840 # Cardinal RN, Expectation-Detection: none
841 # CBI-R: none
842 # CECA-Q3: none
843 # CESD, CESD-R: none
844 # CGI, CGI-I, CGI-SCH: none
845 # CIS-R: none
847 # CIWA-Ar
848 CIWA_AR_SCALE = "ciwa_ar_scale"
849 CIWA_AR_SCORE = "ciwa_ar_observable_score"
850 CIWA_AR_PROCEDURE_ASSESSMENT = "ciwa_ar_procedure_assessment"
852 # Clinical: progress note
853 PROGRESS_NOTE_PROCEDURE = "progress_note_procedure"
854 CLINICAL_NOTE = "clinical_note"
856 # Clinical: photograph
857 PHOTOGRAPH_PROCEDURE = "photograph_procedure"
858 PHOTOGRAPH_PHYSICAL_OBJECT = "photograph_physical_object"
860 # Clinical: psychiatric clerking
861 # ... "location": not obvious
862 # ... "contact type" is an AoMRC heading, but I'm not sure the observable
863 # entity of "Initial contact type" is right.
864 #
865 # Deprecated between v20191001 and v20210929:
866 # PSYCHIATRIC_ASSESSMENT_PROCEDURE = "psychiatric_assessment_procedure"
867 DIAGNOSTIC_PSYCHIATRIC_INTERVIEW_PROCEDURE = (
868 "diagnostic_psychiatric_interview_procedure"
869 )
871 PSYCLERK_REASON_FOR_REFERRAL = "psyclerk_reason_for_referral"
872 PSYCLERK_PRESENTING_ISSUE = "psyclerk_presenting_issue"
873 PSYCLERK_SYSTEMS_REVIEW = "psyclerk_systems_review"
874 PSYCLERK_COLLATERAL_HISTORY = "psyclerk_collateral_history"
876 PSYCLERK_PAST_MEDICAL_SURGICAL_MENTAL_HEALTH_HISTORY = (
877 "psyclerk_past_medical_surgical_mental_health_history"
878 )
879 PSYCLERK_PROCEDURES = "psyclerk_procedures"
880 PSYCLERK_ALLERGIES_ADVERSE_REACTIONS = (
881 "psyclerk_allergies_adverse_reactions"
882 )
883 PSYCLERK_MEDICATIONS_MEDICAL_DEVICES = (
884 "psyclerk_medications_medical_devices"
885 )
886 PSYCLERK_DRUG_SUBSTANCE_USE = "psyclerk_drug_substance_use"
887 PSYCLERK_FAMILY_HISTORY = "psyclerk_family_history"
888 PSYCLERK_DEVELOPMENTAL_HISTORY = "psyclerk_developmental_history"
889 PSYCLERK_SOCIAL_PERSONAL_HISTORY = "psyclerk_social_personal_history"
890 PSYCLERK_PERSONALITY = "psyclerk_personality"
891 PSYCLERK_PRISON_RECORD_CRIMINAL_ACTIVITY = (
892 "psyclerk_prison_record_criminal_activity"
893 )
894 PSYCLERK_SOCIAL_HISTORY_BASELINE = "psyclerk_social_history_baseline"
896 PSYCLERK_MSE_APPEARANCE = "psyclerk_mse_appearance"
897 PSYCLERK_MSE_BEHAVIOUR = "psyclerk_mse_behaviour"
898 PSYCLERK_MSE_SPEECH = "psyclerk_mse_speech"
899 PSYCLERK_MSE_MOOD = "psyclerk_mse_mood"
900 PSYCLERK_MSE_AFFECT = "psyclerk_mse_affect"
901 PSYCLERK_MSE_THOUGHT = "psyclerk_mse_thought"
902 PSYCLERK_MSE_PERCEPTION = "psyclerk_mse_perception"
903 PSYCLERK_MSE_COGNITION = "psyclerk_mse_cognition"
904 PSYCLERK_MSE_INSIGHT = "psyclerk_mse_insight"
906 PSYCLERK_PHYSEXAM_GENERAL = "psyclerk_physexam_general"
907 PSYCLERK_PHYSEXAM_CARDIOVASCULAR = "psyclerk_physexam_cardiovascular"
908 PSYCLERK_PHYSEXAM_RESPIRATORY = "psyclerk_physexam_respiratory"
909 PSYCLERK_PHYSEXAM_ABDOMINAL = "psyclerk_physexam_abdominal"
910 PSYCLERK_PHYSEXAM_NEUROLOGICAL = "psyclerk_physexam_neurological"
912 PSYCLERK_ASSESSMENT_SCALES = "psyclerk_assessment_scales"
913 PSYCLERK_INVESTIGATIONS_RESULTS = "psyclerk_investigations_results"
915 PSYCLERK_SAFETY_ALERTS = "psyclerk_safety_alerts"
916 PSYCLERK_RISK_ASSESSMENT = "psyclerk_risk_assessment"
917 PSYCLERK_RELEVANT_LEGAL_INFORMATION = "psyclerk_relevant_legal_information"
919 PSYCLERK_CURRENT_PROBLEMS = "psyclerk_current_problems"
920 PSYCLERK_PATIENT_CARER_CONCERNS = "psyclerk_patient_carer_concerns"
921 PSYCLERK_CLINICAL_NARRATIVE = "psyclerk_clinical_narrative"
922 PSYCLERK_MANAGEMENT_PLAN = "psyclerk_management_plan"
923 PSYCLERK_INFORMATION_GIVEN = "psyclerk_information_given"
925 # CPFT/CUH LPS: none
926 # COPE: none
928 # CORE-10
929 CORE10_SCALE = "core10_scale"
930 CORE10_SCORE = "core10_observable_score"
931 CORE10_PROCEDURE_ASSESSMENT = "core10_procedure_assessment"
933 # DAD: none
935 # DAST
936 DAST_SCALE = "dast_scale"
937 # I think the similarly named codes represent urine screening.
939 # Deakin JB, antibody: none
940 # Demo questionnaire: none
941 # DEMQOL, DEMQOL-Proxy: none
942 # Distress Thermometer: none
944 # EQ-5D-5L
945 EQ5D5L_SCALE = "eq5d5l_scale"
946 EQ5D5L_INDEX_VALUE = "eq5d5l_observable_index_value"
947 EQ5D5L_PAIN_DISCOMFORT_SCORE = "eq5d5l_observable_pain_discomfort_score"
948 EQ5D5L_USUAL_ACTIVITIES_SCORE = "eq5d5l_observable_usual_activities_score"
949 EQ5D5L_ANXIETY_DEPRESSION_SCORE = (
950 "eq5d5l_observable_anxiety_depression_score"
951 )
952 EQ5D5L_MOBILITY_SCORE = "eq5d5l_observable_mobility_score"
953 EQ5D5L_SELF_CARE_SCORE = "eq5d5l_observable_self_care_score"
954 EQ5D5L_PROCEDURE_ASSESSMENT = "eq5d5l_procedure_assessment"
956 # FACT-G: none
958 # FAST: none
959 FAST_SCALE = "fast_scale"
960 FAST_SCORE = "fast_observable_score"
961 FAST_PROCEDURE_ASSESSMENT = "fast_procedure_assessment"
963 # IRAC: none
964 # FFT: none
966 # Patient Satisfaction Scale
967 # Not sure. See XML
969 # Referrer Satisfaction Scale (patient-specific, survey): none
970 # Frontotemporal Dementia Rating Scale: none
972 # GAD-7
973 GAD7_SCALE = "gad7_scale"
974 GAD7_SCORE = "gad7_observable_score"
975 GAD7_PROCEDURE_ASSESSMENT = "gad7_procedure_assessment"
977 # GAF
978 GAF_SCALE = "gaf_scale"
979 # no observable/procedure
981 # GDS-15
982 GDS15_SCALE = "gds15_scale"
983 GDS15_SCORE = "gds15_observable_score"
984 GDS15_PROCEDURE_ASSESSMENT = "gds15_procedure_assessment"
986 # UK GMC Patient Questionnaire: none
988 # HADS, HADS-respondent
989 HADS_SCALE = "hads_scale"
990 HADS_ANXIETY_SCORE = "hads_observable_anxiety_score"
991 HADS_DEPRESSION_SCORE = "hads_observable_depression_score"
992 HADS_PROCEDURE_ASSESSMENT = "hads_procedure_assessment"
994 # HAMA: none
996 # HAMD
997 HAMD_SCALE = "hamd_scale"
998 HAMD_SCORE = "hamd_observable_score"
999 HAMD_PROCEDURE_ASSESSMENT = "hamd_procedure_assessment"
1001 # HAMD-7: none
1003 # HoNOS, HoNOS-65+, HoNOSCA, etc. (there are others too)
1004 HONOSCA_SCALE = "honos_childrenadolescents_scale"
1005 HONOSCA_SECTION_A_SCALE = "honos_childrenadolescents_section_a_scale"
1006 HONOSCA_SECTION_B_SCALE = "honos_childrenadolescents_section_b_scale"
1007 HONOSCA_SCORE = "honos_childrenadolescents_observable_score"
1008 HONOSCA_SECTION_A_SCORE = (
1009 "honos_childrenadolescents_observable_section_a_score"
1010 )
1011 HONOSCA_SECTION_B_SCORE = (
1012 "honos_childrenadolescents_observable_section_b_score"
1013 )
1014 HONOSCA_SECTION_A_PLUS_B_SCORE = (
1015 "honos_childrenadolescents_observable_section_a_plus_b_score"
1016 )
1017 HONOSCA_PROCEDURE_ASSESSMENT = (
1018 "honos_childrenadolescents_procedure_assessment"
1019 )
1020 #
1021 HONOS65_SCALE = "honos_olderadults_scale"
1022 HONOS65_SCORE = "honos_olderadults_observable_score"
1023 HONOS65_PROCEDURE_ASSESSMENT = "honos_olderadults_procedure_assessment"
1024 #
1025 HONOSWA_SCALE = "honos_workingage_scale"
1026 HONOSWA_SUBSCALE_1_OVERACTIVE = "honos_workingage_subscale_1_overactive"
1027 HONOSWA_SUBSCALE_2_SELFINJURY = "honos_workingage_subscale_2_selfinjury"
1028 HONOSWA_SUBSCALE_3_SUBSTANCE = "honos_workingage_subscale_3_substance"
1029 HONOSWA_SUBSCALE_4_COGNITIVE = "honos_workingage_subscale_4_cognitive"
1030 HONOSWA_SUBSCALE_5_PHYSICAL = "honos_workingage_subscale_5_physical"
1031 HONOSWA_SUBSCALE_6_PSYCHOSIS = "honos_workingage_subscale_6_psychosis"
1032 HONOSWA_SUBSCALE_7_DEPRESSION = "honos_workingage_subscale_7_depression"
1033 HONOSWA_SUBSCALE_8_OTHERMENTAL = "honos_workingage_subscale_8_othermental"
1034 HONOSWA_SUBSCALE_9_RELATIONSHIPS = (
1035 "honos_workingage_subscale_9_relationships"
1036 )
1037 HONOSWA_SUBSCALE_10_ADL = "honos_workingage_subscale_10_adl"
1038 HONOSWA_SUBSCALE_11_LIVINGCONDITIONS = (
1039 "honos_workingage_subscale_11_livingconditions"
1040 )
1041 HONOSWA_SUBSCALE_12_OCCUPATION = "honos_workingage_subscale_12_occupation"
1042 HONOSWA_SCORE = "honos_workingage_observable_score"
1043 HONOSWA_1_OVERACTIVE_SCORE = (
1044 "honos_workingage_observable_1_overactive_score"
1045 )
1046 HONOSWA_2_SELFINJURY_SCORE = (
1047 "honos_workingage_observable_2_selfinjury_score"
1048 )
1049 HONOSWA_3_SUBSTANCE_SCORE = "honos_workingage_observable_3_substance_score"
1050 HONOSWA_4_COGNITIVE_SCORE = "honos_workingage_observable_4_cognitive_score"
1051 HONOSWA_5_PHYSICAL_SCORE = "honos_workingage_observable_5_physical_score"
1052 HONOSWA_6_PSYCHOSIS_SCORE = "honos_workingage_observable_6_psychosis_score"
1053 HONOSWA_7_DEPRESSION_SCORE = (
1054 "honos_workingage_observable_7_depression_score"
1055 )
1056 HONOSWA_8_OTHERMENTAL_SCORE = (
1057 "honos_workingage_observable_8_othermental_score"
1058 )
1059 HONOSWA_9_RELATIONSHIPS_SCORE = (
1060 "honos_workingage_observable_9_relationships_score"
1061 )
1062 HONOSWA_10_ADL_SCORE = "honos_workingage_observable_10_adl_score"
1063 HONOSWA_11_LIVINGCONDITIONS_SCORE = (
1064 "honos_workingage_observable_11_livingconditions_score"
1065 )
1066 HONOSWA_12_OCCUPATION_SCORE = (
1067 "honos_workingage_observable_12_occupation_score"
1068 )
1069 HONOSWA_PROCEDURE_ASSESSMENT = "honos_workingage_procedure_assessment"
1071 # ICD-9-CM: see below; separate file
1073 # ICD-10: see below; separate file
1075 # IDED3D: none
1077 # IES-R
1078 IESR_SCALE = "iesr_scale"
1079 IESR_SCORE = "iesr_observable_score"
1080 IESR_PROCEDURE_ASSESSMENT = "iesr_procedure_assessment"
1082 # INECO Frontal Screening: none
1083 # Khandaker G, Insight: none
1085 # MAST, SMAST
1086 MAST_SCALE = "mast_scale"
1087 MAST_SCORE = "mast_observable_score"
1088 MAST_PROCEDURE_ASSESSMENT = "mast_procedure_assessment"
1090 SMAST_SCALE = "smast_scale"
1091 # SMAST: no observable/procedure
1093 # MDS-UPDRS
1094 UPDRS_SCALE = "updrs_scale"
1095 # MDS-UPDRS: no observable/procedure
1097 # MoCA
1098 MOCA_SCALE = "moca_scale"
1099 MOCA_SCORE = "moca_observable_score"
1100 MOCA_PROCEDURE_ASSESSMENT = "moca_procedure_assessment"
1102 # NART
1103 NART_SCALE = "nart_scale"
1104 NART_SCORE = "nart_observable_score"
1105 NART_PROCEDURE_ASSESSMENT = "nart_procedure_assessment"
1107 # NPI-Q: none
1109 # PANSS
1110 PANSS_SCALE = "panss_scale"
1111 # PANSS: no observable/procedure
1113 # PCL and variants: none
1115 # PDSS
1116 PDSS_SCALE = "pdss_scale"
1117 PDSS_SCORE = "pdss_observable_score"
1118 # PDSS: no procedure
1120 # "Perinatal" and "scale": none
1122 # PHQ-9
1123 PHQ9_FINDING_NEGATIVE_SCREENING_FOR_DEPRESSION = (
1124 "phq9_finding_negative_screening_for_depression"
1125 )
1126 PHQ9_FINDING_POSITIVE_SCREENING_FOR_DEPRESSION = (
1127 "phq9_finding_positive_screening_for_depression"
1128 )
1129 PHQ9_SCORE = "phq9_observable_score"
1130 PHQ9_PROCEDURE_DEPRESSION_SCREENING = "phq9_procedure_depression_screening"
1131 PHQ9_SCALE = (
1132 "phq9_scale" # https://snomedbrowser.com/Codes/Details/758711000000105
1133 )
1135 # PHQ-15
1136 PHQ15_SCORE = "phq15_observable_score"
1137 PHQ15_PROCEDURE = "phq15_procedure_assessment"
1138 PHQ15_SCALE = "phq15_scale"
1140 # PIIOS or "parent infant scale": none
1142 # PSWQ
1143 PSWQ_SCALE = "pswq_scale"
1144 PSWQ_SCORE = "pswq_observable_score"
1145 PSWQ_PROCEDURE_ASSESSMENT = "pswq_procedure_assessment"
1147 # QOL-Basic, QOL-SG
1148 # Unsure, but there is this:
1149 QOL_SCALE = "qol_scale"
1150 # ... with no observable/procedure
1152 # RAND-36: none directly
1154 # SLUMS: none
1156 # WEMWBS, SWEMWBS
1157 WEMWBS_SCALE = "wemwbs_scale"
1158 WEMWBS_SCORE = "wemwbs_observable_score"
1159 WEMWBS_PROCEDURE_ASSESSMENT = "wemwbs_procedure_assessment"
1160 #
1161 SWEMWBS_SCALE = "swemwbs_scale"
1162 SWEMWBS_SCORE = "swemwbs_observable_score"
1163 SWEMWBS_PROCEDURE_ASSESSMENT = "swemwbs_procedure_assessment"
1165 # WSAS
1166 WSAS_SCALE = "wsas_scale"
1167 WSAS_SCORE = "wsas_observable_score"
1168 WSAS_WORK_SCORE = "wsas_observable_work_score"
1169 WSAS_RELATIONSHIPS_SCORE = "wsas_observable_relationships_score"
1170 WSAS_HOME_MANAGEMENT_SCORE = "wsas_observable_home_management_score"
1171 WSAS_SOCIAL_LEISURE_SCORE = "wsas_observable_social_leisure_score"
1172 WSAS_PRIVATE_LEISURE_SCORE = "wsas_observable_private_leisure_score"
1173 WSAS_PROCEDURE_ASSESSMENT = "wsas_procedure_assessment"
1175 # Y-BOCS, Y-BOCS-SC: none
1176 # ZBI: none
1179# -----------------------------------------------------------------------------
1180# Perform the lookup
1181# -----------------------------------------------------------------------------
1183VALID_SNOMED_LOOKUPS = set(
1184 [
1185 getattr(SnomedLookup, k)
1186 for k in dir(SnomedLookup)
1187 if not k.startswith("_")
1188 ]
1189)
1192@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1193def get_all_task_snomed_concepts(
1194 xml_filename: str,
1195) -> Dict[str, SnomedConcept]:
1196 """
1197 Reads in all SNOMED-CT codes for CamCOPS tasks, from the custom CamCOPS XML
1198 file for this.
1200 Args:
1201 xml_filename: XML filename to read
1203 Returns:
1204 dict: maps lookup strings to :class:`SnomedConcept` objects
1206 """
1207 xml_concepts = get_snomed_concepts_from_xml(xml_filename)
1208 camcops_concepts = {} # type: Dict[str, SnomedConcept]
1209 identifiers_seen = set() # type: Set[int]
1210 for lookup, concepts in xml_concepts.items():
1211 # Check it
1212 if lookup not in VALID_SNOMED_LOOKUPS:
1213 log.debug("Ignoring unknown SNOMED-CT lookup: {!r}", lookup)
1214 continue
1215 assert (
1216 len(concepts) == 1
1217 ), f"More than one SNOMED-CT concept for lookup: {lookup!r}"
1218 concept = concepts[0]
1219 assert (
1220 concept.identifier not in identifiers_seen
1221 ), f"Duplicate SNOMED-CT identifier: {concept.identifier!r}"
1222 identifiers_seen.add(concept.identifier)
1223 # Stash it
1224 camcops_concepts[lookup] = concept
1225 # Check if any are missing
1226 missing = sorted(list(VALID_SNOMED_LOOKUPS - set(camcops_concepts.keys())))
1227 if missing:
1228 raise ValueError(
1229 f"The following SNOMED-CT concepts required by CamCOPS are "
1230 f"missing from the XML ({xml_filename}): {missing!r}"
1231 )
1232 # Done
1233 return camcops_concepts
1236# =============================================================================
1237# UMLS ICD-9-CM
1238# =============================================================================
1241class UmlsIcd9SnomedRow(object):
1242 """
1243 Simple information-holding class for a row of the ICD-9-CM TSV file, from
1244 https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html.
1246 NOT CURRENTLY USED.
1247 """
1249 HEADER = [
1250 "ICD_CODE",
1251 "ICD_NAME",
1252 "IS_CURRENT_ICD",
1253 "IP_USAGE",
1254 "OP_USAGE",
1255 "AVG_USAGE",
1256 "IS_NEC",
1257 "SNOMED_CID",
1258 "SNOMED_FSN",
1259 "IS_1-1MAP",
1260 "CORE_USAGE",
1261 "IN_CORE",
1262 ]
1264 @staticmethod
1265 def to_float(x: str) -> Optional[float]:
1266 return None if x == "NULL" else float(x)
1268 def __init__(
1269 self,
1270 icd_code: str,
1271 icd_name: str,
1272 is_current_icd: str,
1273 ip_usage: str,
1274 op_usage: str,
1275 avg_usage: str,
1276 is_nec: str,
1277 snomed_cid: str,
1278 snomed_fsn: str,
1279 is_one_to_one_map: str,
1280 core_usage: str,
1281 in_core: str,
1282 ) -> None:
1283 """
1284 Argument order is important.
1286 Args:
1287 icd_code: ICD-9-CM code
1288 icd_name: Name of ICD-9-CM entity
1289 is_current_icd: ?
1290 ip_usage: ?
1291 op_usage: ?
1292 avg_usage: ?
1293 is_nec: ?
1294 snomed_cid: SNOMED-CT concept ID
1295 snomed_fsn: SNOMED-CT fully specified name
1296 is_one_to_one_map: ?; possibly always true in this dataset but not
1297 true in a broader dataset including things other than 1:1
1298 mappings?
1299 core_usage: ?
1300 in_core: ?
1301 """
1302 self.icd_code = icd_code
1303 self.icd_name = icd_name
1304 self.is_current_icd = bool(int(is_current_icd))
1305 self.ip_usage = self.to_float(ip_usage)
1306 self.op_usage = self.to_float(op_usage)
1307 self.avg_usage = self.to_float(avg_usage)
1308 self.is_nec = bool(int(is_nec))
1309 self.snomed_cid = int(snomed_cid)
1310 self.snomed_fsn = snomed_fsn
1311 self.is_one_to_one_map = bool(int(is_one_to_one_map))
1312 self.core_usage = self.to_float(core_usage)
1313 self.in_core = bool(int(in_core))
1315 def __repr__(self) -> str:
1316 return simple_repr(
1317 self,
1318 [
1319 "icd_code",
1320 "icd_name",
1321 "is_current_icd",
1322 "ip_usage",
1323 "op_usage",
1324 "avg_usage",
1325 "is_nec",
1326 "snomed_cid",
1327 "snomed_fsn",
1328 "is_one_to_one_map",
1329 "core_usage",
1330 "in_core",
1331 ],
1332 )
1334 def snomed_concept(self) -> SnomedConcept:
1335 """
1336 Returns the associated SNOMED-CT concept.
1337 """
1338 return SnomedConcept(self.snomed_cid, self.snomed_fsn)
1340 def __str__(self) -> str:
1341 return (
1342 f"ICD-9-CM {self.icd_code} ({self.icd_name}) "
1343 f"-> SNOMED-CT {self.snomed_concept()}"
1344 )
1347@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1348def get_all_icd9cm_snomed_concepts_from_umls(
1349 tsv_filename: str,
1350) -> Dict[str, SnomedConcept]:
1351 """
1352 Reads in all ICD-9-CM SNOMED-CT codes that are supported by the client,
1353 from the UMLS data file, from
1354 https://www.nlm.nih.gov/research/umls/mapping_projects/icd9cm_to_snomedct.html.
1356 Args:
1357 tsv_filename: TSV filename to read
1359 Returns:
1360 dict: maps lookup strings to :class:`SnomedConcept` objects
1362 NOT CURRENTLY USED.
1363 """
1364 log.info("Loading SNOMED-CT ICD-9-CM codes from file: {}", tsv_filename)
1365 concepts = {} # type: Dict[str, SnomedConcept]
1366 with open(tsv_filename, "r") as tsvin:
1367 reader = csv.reader(tsvin, delimiter="\t")
1368 header = next(reader, None)
1369 if header != UmlsIcd9SnomedRow.HEADER:
1370 raise ValueError(
1371 f"ICD-9-CM TSV file has unexpected header: {header!r}; "
1372 f"expected {UmlsIcd9SnomedRow.HEADER!r}"
1373 )
1374 for row in reader:
1375 entry = UmlsIcd9SnomedRow(*row)
1376 if entry.icd_code not in CLIENT_ICD9CM_CODES:
1377 continue
1378 if not entry.is_one_to_one_map:
1379 continue
1380 if entry.icd_code in concepts:
1381 log.warning(
1382 "Duplicate ICD-9-CM code found in SNOMED file "
1383 "{!r}: {!r}",
1384 tsv_filename,
1385 entry.icd_code,
1386 )
1387 continue
1388 concept = entry.snomed_concept()
1389 # log.debug("{}", entry)
1390 concepts[entry.icd_code] = concept
1391 missing = CLIENT_ICD9CM_CODES - set(concepts.keys())
1392 if missing:
1393 log.info(
1394 "No SNOMED-CT codes for ICD-9-CM codes: {}",
1395 ", ".join(sorted(missing)),
1396 )
1397 return concepts
1400# =============================================================================
1401# UMLS ICD-10
1402# =============================================================================
1405class UmlsSnomedToIcd10Row(object):
1406 """
1407 Simple information-holding class for a row of the ICD-10-CM TSV file from
1408 https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html.
1410 However, that is unhelpful (many to one).
1412 NOT CURRENTLY USED.
1413 """
1415 HEADER = [
1416 "id",
1417 "effectiveTime",
1418 "active",
1419 "moduleId",
1420 "refsetId",
1421 "referencedComponentId",
1422 "referencedComponentName",
1423 "mapGroup",
1424 "mapPriority",
1425 "mapRule",
1426 "mapAdvice",
1427 "mapTarget",
1428 "mapTargetName",
1429 "correlationId",
1430 "mapCategoryId",
1431 "mapCategoryName",
1432 ]
1433 MAP_GOOD = "MAP SOURCE CONCEPT IS PROPERLY CLASSIFIED"
1435 def __init__(
1436 self,
1437 row_id: str,
1438 effective_time: str,
1439 active: str,
1440 module_id: str,
1441 refset_id: str,
1442 referenced_component_id: str,
1443 referenced_component_name: str,
1444 map_group: str,
1445 map_priority: str,
1446 map_rule: str,
1447 map_advice: str,
1448 map_target: str,
1449 map_target_name: str,
1450 correlation_id: str,
1451 map_category_id: str,
1452 map_category_name: str,
1453 ) -> None:
1454 """
1455 Argument order is important.
1457 Args:
1458 row_id: UUID format or similar
1459 effective_time: date in YYYYMMDD format
1460 active: ?
1461 module_id: ?
1462 refset_id: ?
1463 referenced_component_id: SNOMED-CT concept ID
1464 referenced_component_name: SNOMED-CT concept name
1465 map_group: ?; e.g. 1
1466 map_priority: ? but e.g. 1, 2; correlates with map_rule
1467 map_rule: ?; e.g. "TRUE"; "OTHERWISE TRUE"
1468 map_advice: ?, but e.g. "ALWAYS F32.2" or "ALWAYS F32.2 |
1469 DESCENDANTS NOT EXHAUSTIVELY MAPPED"
1470 map_target: ICD-10 code
1471 map_target_name: ICD-10 name
1472 correlation_id: a SNOMED-CT concept for the mapping, e.g.
1473 447561005 = "SNOMED CT source code to target map code
1474 correlation not specified (foundation metadata concept)"
1475 map_category_id: a SNOMED-CT concept for the mapping, e.g.
1476 447637006 = "Map source concept is properly classified
1477 (foundation metadata concept)"
1478 map_category_name: SNOMED-CT name corresponding to map_category_id,
1479 e.g. "MAP SOURCE CONCEPT IS PROPERLY CLASSIFIED"
1480 """
1481 self.row_id = row_id
1482 self.effective_time = effective_time
1483 self.active = bool(int(active))
1484 self.module_id = int(module_id)
1485 self.refset_id = int(refset_id)
1486 self.referenced_component_id = int(referenced_component_id)
1487 self.referenced_component_name = referenced_component_name
1488 self.map_group = int(map_group)
1489 self.map_priority = int(map_priority)
1490 self.map_rule = map_rule
1491 self.map_advice = map_advice
1492 self.map_target = map_target
1493 self.map_target_name = map_target_name
1494 self.correlation_id = int(correlation_id)
1495 self.map_category_id = int(map_category_id)
1496 self.map_category_name = map_category_name
1498 def __repr__(self) -> str:
1499 return simple_repr(
1500 self,
1501 [
1502 "row_id",
1503 "effective_time",
1504 "active",
1505 "module_id",
1506 "refset_id",
1507 "referenced_component_id",
1508 "referenced_component_name",
1509 "map_group",
1510 "map_priority",
1511 "map_rule",
1512 "map_advice",
1513 "map_target",
1514 "map_target_name",
1515 "correlation_id",
1516 "map_category_id",
1517 "map_category_name",
1518 ],
1519 )
1521 def snomed_concept(self) -> SnomedConcept:
1522 """
1523 Returns the associated SNOMED-CT concept.
1524 """
1525 return SnomedConcept(
1526 self.referenced_component_id, self.referenced_component_name
1527 )
1529 @property
1530 def icd_code(self) -> str:
1531 return self.map_target
1533 @property
1534 def icd_name(self) -> str:
1535 return self.map_target_name
1537 def __str__(self) -> str:
1538 return (
1539 f"ICD-10 {self.icd_code} ({self.icd_name}) "
1540 f"-> SNOMED-CT {self.snomed_concept()}"
1541 )
1544def get_all_icd10_snomed_concepts_from_umls(
1545 tsv_filename: str,
1546) -> Dict[str, SnomedConcept]:
1547 """
1548 Reads in all ICD-10 SNOMED-CT codes that are supported by the client,
1549 from the UMLS data file, from
1550 https://www.nlm.nih.gov/research/umls/mapping_projects/snomedct_to_icd10cm.html.
1552 Args:
1553 tsv_filename: TSV filename to read
1555 Returns:
1556 dict: maps lookup strings to :class:`SnomedConcept` objects
1558 NOT CURRENTLY USED.
1559 """
1560 log.info("Loading SNOMED-CT ICD-10-CM codes from file: {}", tsv_filename)
1561 concepts = {} # type: Dict[str, SnomedConcept]
1562 with open(tsv_filename, "r") as tsvin:
1563 reader = csv.reader(tsvin, delimiter="\t")
1564 header = next(reader, None)
1565 if header != UmlsSnomedToIcd10Row.HEADER:
1566 raise ValueError(
1567 f"ICD-9-CM TSV file has unexpected header: {header!r}; "
1568 f"expected {UmlsSnomedToIcd10Row.HEADER!r}"
1569 )
1570 for row in reader:
1571 entry = UmlsSnomedToIcd10Row(*row)
1572 if entry.icd_code not in CLIENT_ICD10_CODES:
1573 continue
1574 if entry.icd_code in concepts:
1575 log.warning(
1576 "Duplicate ICD-10-CM code found in SNOMED file "
1577 "{!r}: {!r}",
1578 tsv_filename,
1579 entry.icd_code,
1580 )
1581 continue
1582 concept = entry.snomed_concept()
1583 # log.debug("{}", entry)
1584 concepts[entry.icd_code] = concept
1585 missing = CLIENT_ICD10_CODES - set(concepts.keys())
1586 if missing:
1587 log.info(
1588 "No SNOMED-CT codes for ICD-10 codes: {}",
1589 ", ".join(sorted(missing)),
1590 )
1591 return concepts
1594# =============================================================================
1595# Athena OHDSI mapping
1596# =============================================================================
1598# -----------------------------------------------------------------------------
1599# Fetch ICD-9-CM and ICD-10 codes (shared for fewer passes through the files)
1600# -----------------------------------------------------------------------------
1603def get_icd9cm_icd10_snomed_concepts_from_athena(
1604 athena_concept_tsv_filename: str,
1605 athena_concept_relationship_tsv_filename: str,
1606) -> Tuple[Dict[str, List[SnomedConcept]], Dict[str, List[SnomedConcept]]]:
1607 """
1608 Takes Athena concept and concept-relationship files, and fetches details
1609 of SNOMED-CT code for all ICD-9-CM and ICD-10[-CM] codes used by CamCOPS.
1611 A bit of human review is required; this is probably preferable to using
1612 gensim or some other automatic similarity check.
1614 Args:
1615 athena_concept_tsv_filename:
1616 path to ``CONCEPT.csv`` (a tab-separated value file)
1617 athena_concept_relationship_tsv_filename:
1618 path to ``CONCEPT_RELATIONSHIP.csv`` (a tab-separated value file)
1620 Returns:
1621 tuple: ``icd9cm, icd10``, where each is a dictionary mapping ICD codes
1622 to a list of mapped :class:`SnomedConcept` objects.
1624 """
1625 athena_icd_concepts = get_athena_concepts(
1626 tsv_filename=athena_concept_tsv_filename,
1627 vocabulary_ids={AthenaVocabularyId.ICD9CM, AthenaVocabularyId.ICD10CM},
1628 concept_codes=CLIENT_ICD9CM_CODES | CLIENT_ICD10_CODES,
1629 )
1630 athena_icd_concepts.sort(key=lambda x: x.concept_code)
1631 relationships = get_athena_concept_relationships(
1632 tsv_filename=athena_concept_relationship_tsv_filename,
1633 concept_id_1_values=set(x.concept_id for x in athena_icd_concepts),
1634 relationship_id_values={AthenaRelationshipId.MAPS_TO},
1635 )
1636 athena_snomed_concepts = get_athena_concepts(
1637 tsv_filename=athena_concept_tsv_filename,
1638 vocabulary_ids={AthenaVocabularyId.SNOMED},
1639 concept_ids=set(x.concept_id_2 for x in relationships),
1640 )
1641 snomed_concepts_icd9 = (
1642 OrderedDict()
1643 ) # type: Dict[str, List[SnomedConcept]] # noqa
1644 snomed_concepts_icd10 = (
1645 OrderedDict()
1646 ) # type: Dict[str, List[SnomedConcept]] # noqa
1647 for icd in athena_icd_concepts:
1648 target = (
1649 snomed_concepts_icd9
1650 if icd.vocabulary_id == AthenaVocabularyId.ICD9CM
1651 else snomed_concepts_icd10
1652 )
1653 icd_code = icd.concept_code
1654 # log.debug("Processing icd = {}", icd)
1655 possible_snomed = [] # type: List[AthenaConceptRow]
1656 for rel in relationships:
1657 if rel.concept_id_1 != icd.concept_id:
1658 continue
1659 # log.debug("Processing rel = {}", rel)
1660 for snomed in athena_snomed_concepts:
1661 if snomed.concept_id != rel.concept_id_2:
1662 continue
1663 # log.debug("Processing snomed = {}", snomed)
1664 possible_snomed.append(snomed)
1665 if possible_snomed:
1666 sclist = [
1667 SnomedConcept.create(s.snomed_concept())
1668 for s in possible_snomed
1669 ]
1670 sclist.sort(key=lambda sc: sc.identifier)
1671 log.debug("Mapping {} -> {}", icd, sclist)
1672 target[icd_code] = sclist
1673 else:
1674 log.debug("No SNOMED code found for {}", icd)
1675 return snomed_concepts_icd9, snomed_concepts_icd10
1678# -----------------------------------------------------------------------------
1679# Fetch codes from Athena data set and write them to CamCOPS XML
1680# -----------------------------------------------------------------------------
1683def send_athena_icd_snomed_to_xml(
1684 athena_concept_tsv_filename: str,
1685 athena_concept_relationship_tsv_filename: str,
1686 icd9_xml_filename: str,
1687 icd10_xml_filename,
1688) -> None:
1689 """
1690 Reads SNOMED-CT codes for ICD-9-CM and ICD10 from Athena OHDSI files, and
1691 writes
1693 Args:
1694 athena_concept_tsv_filename:
1695 path to ``CONCEPT.csv`` (a tab-separated value file)
1696 athena_concept_relationship_tsv_filename:
1697 path to ``CONCEPT_RELATIONSHIP.csv`` (a tab-separated value file)
1698 icd9_xml_filename:
1699 ICD-9 XML filename to write
1700 icd10_xml_filename:
1701 ICD-10 XML filename to write
1702 """
1703 icd9, icd10 = get_icd9cm_icd10_snomed_concepts_from_athena(
1704 athena_concept_tsv_filename=athena_concept_tsv_filename,
1705 athena_concept_relationship_tsv_filename=athena_concept_relationship_tsv_filename, # noqa
1706 )
1707 write_snomed_concepts_to_xml(icd9_xml_filename, icd9)
1708 write_snomed_concepts_to_xml(icd10_xml_filename, icd10)
1711# -----------------------------------------------------------------------------
1712# Fetch data from XML
1713# -----------------------------------------------------------------------------
1716def get_multiple_snomed_concepts_from_xml(
1717 xml_filename: str,
1718 valid_lookups: Set[str] = None,
1719 require_all: bool = False,
1720) -> Dict[str, List[SnomedConcept]]:
1721 """
1722 Reads in all SNOMED-CT codes for ICD-9 or ICD-10, from the custom CamCOPS
1723 XML file for this (made by e.g. :func:`send_athena_icd_snomed_to_xml`).
1725 Args:
1726 xml_filename: XML filename to read
1727 valid_lookups: possible lookup values
1728 require_all: require that ``valid_lookups`` is truthy and that all
1729 values in it are present in the XML
1731 Returns:
1732 dict: maps lookup strings to lists of :class:`SnomedConcept` objects
1734 """
1735 valid_lookups = set(valid_lookups or []) # type: Set[str]
1736 xml_concepts = get_snomed_concepts_from_xml(xml_filename)
1737 camcops_concepts = {} # type: Dict[str, List[SnomedConcept]]
1738 for lookup, concepts in xml_concepts.items():
1739 # Check it
1740 if valid_lookups and lookup not in valid_lookups:
1741 log.debug("Ignoring unknown SNOMED-CT lookup: {!r}", lookup)
1742 continue
1743 # Stash it
1744 camcops_concepts[lookup] = concepts
1745 if require_all:
1746 # Check if any are missing
1747 assert valid_lookups, "require_all specified but valid_lookups missing"
1748 if valid_lookups:
1749 missing = sorted(list(valid_lookups - set(camcops_concepts.keys())))
1750 if missing:
1751 msg = (
1752 f'The following {"required " if require_all else ""}'
1753 f"SNOMED-CT concepts are missing from the XML "
1754 f"({xml_filename!r}): {missing!r}"
1755 )
1756 if require_all:
1757 log.critical(msg)
1758 raise ValueError(msg)
1759 else:
1760 log.debug(msg)
1761 # Done
1762 return camcops_concepts
1765@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1766def get_icd9_snomed_concepts_from_xml(
1767 xml_filename: str,
1768) -> Dict[str, List[SnomedConcept]]:
1769 """
1770 Reads in all ICD-9-CM SNOMED-CT codes from a custom CamCOPS XML file.
1772 Args:
1773 xml_filename: filename to read
1775 Returns:
1776 dict: maps ICD-9-CM codes to lists of :class:`SnomedConcept` objects
1777 """
1778 return get_multiple_snomed_concepts_from_xml(
1779 xml_filename, CLIENT_ICD9CM_CODES
1780 )
1783@cache_region_static.cache_on_arguments(function_key_generator=fkg)
1784def get_icd10_snomed_concepts_from_xml(
1785 xml_filename: str,
1786) -> Dict[str, List[SnomedConcept]]:
1787 """
1788 Reads in all ICD-10 SNOMED-CT codes from a custom CamCOPS XML file.
1790 Args:
1791 xml_filename: filename to read
1793 Returns:
1794 dict: maps ICD-10 codes to lists of :class:`SnomedConcept` objects
1795 """
1796 return get_multiple_snomed_concepts_from_xml(
1797 xml_filename, CLIENT_ICD10_CODES
1798 )