Coverage for common/constants.py: 87%

1"""

2crate_anon/common/constants.py

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

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

9 This file is part of CRATE.

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

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

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

14 (at your option) any later version.

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

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

18 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

19 GNU General Public License for more details.

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

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

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

26**Constants used throughout CRATE.**

28"""

30import os

33# =============================================================================

34# Plain constants

35# =============================================================================

37CRATE_DOCS_URL = "https://crateanon.readthedocs.io/"

39DEMO_NLP_INPUT_TERMINATOR = "STOP"

40DEMO_NLP_OUTPUT_TERMINATOR = "END_OF_NLP_OUTPUT_RECORD"

42EXIT_FAILURE = 1

43EXIT_SUCCESS = 0

45JSON_INDENT = 4

47JSON_SEPARATORS_COMPACT = (",", ":")

48# ... see https://docs.python.org/3/library/json.html

50LOWER_CASE_STRINGS_MEANING_TRUE = ["true", "1", "t", "y", "yes"]

52# Is this program running on readthedocs.org?

53ON_READTHEDOCS = os.environ.get("READTHEDOCS") == "True"

55NoneType = type(None) # for isinstance, sometimes

58# =============================================================================

59# Constant creation

60# =============================================================================

63def mebibytes(mb: int) -> int:

64 """

65 Takes a parameter in mebibytes (1024^2 bytes) and returns the number of

66 bytes.

67 """

68 return mb * 1024 * 1024

71# =============================================================================

72# Directories within CRATE

73# =============================================================================

76class CratePath:

77 """

78 Directories within the CRATE Python package.

79 """

81 CRATE_ANON_DIR = os.path.abspath(

82 os.path.join(

83 os.path.dirname(

84 os.path.abspath(__file__)

85 ), # this directory, common

86 os.pardir, # parent, crate_anon

87 )

88 )

89 CRATEWEB_DIR = os.path.join(CRATE_ANON_DIR, "crateweb")

90 STATIC_SRC_DIR = os.path.join(CRATEWEB_DIR, "static")

91 NLP_MANAGER_DIR = os.path.join(CRATE_ANON_DIR, "nlp_manager")

92 JAVA_CLASSES_DIR = os.path.join(NLP_MANAGER_DIR, "compiled_nlp_classes")

93 NLPRP_DIR = os.path.join(CRATE_ANON_DIR, "nlprp")

96# =============================================================================

97# DockerConstants

98# =============================================================================

100

101class DockerConstants:

102 """

103 Constants for the Docker environment.

104 """

105

106 # Directories

107 DOCKER_CRATE_ROOT_DIR = "/crate"

108 CONFIG_DIR = os.path.join(DOCKER_CRATE_ROOT_DIR, "cfg")

109 FILES_DIR = os.path.join(DOCKER_CRATE_ROOT_DIR, "files")

110 STATIC_DIR = os.path.join(DOCKER_CRATE_ROOT_DIR, "static")

111 TMP_DIR = os.path.join(DOCKER_CRATE_ROOT_DIR, "tmp")

112 VENV_DIR = os.path.join(DOCKER_CRATE_ROOT_DIR, "venv")

113

114 HOST = "0.0.0.0"

115 # ... not "localhost" or "127.0.0.1"; see

116 # https://nickjanetakis.com/blog/docker-tip-54-fixing-connection-reset-by-peer-or-similar-errors # noqa: E501

117

118

119# =============================================================================

120# Environment variables

121# =============================================================================

122

123

124class EnvVar:

125 """

126 Environment variable names.

127 """

128

129 CRATE_GATE_PLUGIN_FILE = "CRATE_GATE_PLUGIN_FILE"

130 # ... environment variable whose presence shows that we are generating

131 # docs.

132 GATE_HOME = "GATE_HOME"

133 GENERATING_CRATE_DOCS = "GENERATING_CRATE_DOCS"

134 JAVA_HOME = "JAVA_HOME"

135 KCL_KCONNECT_DIR = "KCL_KCONNECT_DIR"

136 KCL_LEWY_BODY_DIAGNOSIS_DIR = "KCL_LEWY_BODY_DIAGNOSIS_DIR"

137 KCL_PHARMACOTHERAPY_DIR = "KCL_PHARMACOTHERAPY_DIR"

138 MEDEX_HOME = "MEDEX_HOME"

139 PATH = "PATH"

140 RUNNING_TESTS = "RUNNING_TESTS"

141 RUN_WITHOUT_CONFIG = "CRATE_RUN_WITHOUT_LOCAL_SETTINGS"

142

143

144# =============================================================================

145# CRATE top-level commands

146# =============================================================================

147

148

149class CrateCommand:

150 """

151 Top-level commands within CRATE, recorded here to ensure consistency.

152 However, see also crate/installer/installer.py, which duplicates some

153 (because the full Python environment is not then available).

154 """

155

156 # Preprocessing

157 AUTOIMPORTDB = "crate_autoimport_db"

158 FETCH_WORDLISTS = "crate_fetch_wordlists"

159 POSTCODES = "crate_postcodes"

160 PREPROCESS_PCMIS = "crate_preprocess_pcmis"

161 PREPROCESS_RIO = "crate_preprocess_rio"

162 PREPROCESS_SYSTMONE = "crate_preprocess_systmone"

163

164 # Linkage

165 BULK_HASH = "crate_bulk_hash"

166 FUZZY_ID_MATCH = "crate_fuzzy_id_match"

167

168 # Anonymisation

169 ANON_CHECK_TEXT_EXTRACTOR = "crate_anon_check_text_extractor"

170 ANON_DEMO_CONFIG = "crate_anon_demo_config"

171 ANON_DRAFT_DD = "crate_anon_draft_dd"

172 ANON_SHOW_COUNTS = "crate_anon_show_counts"

173 ANON_SUMMARIZE_DD = "crate_anon_summarize_dd"

174 ANONYMISE = "crate_anonymise"

175 ANONYMISE_MULTIPROCESS = "crate_anonymise_multiprocess"

176 MAKE_DEMO_DATABASE = "crate_make_demo_database"

177 RESEARCHER_REPORT = "crate_researcher_report"

178 SUBSET_DB = "crate_subset_db"

179 TEST_ANONYMISATION = "crate_test_anonymisation"

180 TEST_EXTRACT_TEXT = "crate_test_extract_text"

181

182 # NLP

183 NLP = "crate_nlp"

184 NLP_BUILD_GATE_JAVA_INTERFACE = "crate_nlp_build_gate_java_interface"

185 NLP_BUILD_MEDEX_ITSELF = "crate_nlp_build_medex_itself"

186 NLP_BUILD_MEDEX_JAVA_INTERFACE = "crate_nlp_build_medex_java_interface"

187 NLP_MULTIPROCESS = "crate_nlp_multiprocess"

188 NLP_PREPARE_YMLS_FOR_BIOYODIE = "crate_nlp_prepare_ymls_for_bioyodie"

189 NLP_WRITE_GATE_AUTO_INSTALL_XML = "crate_nlp_write_gate_auto_install_xml"

190 RUN_CRATE_NLP_DEMO = "crate_run_crate_nlp_demo"

191 RUN_GATE_ANNIE_DEMO = "crate_run_gate_annie_demo"

192 RUN_GATE_KCL_KCONNECT_DEMO = "crate_run_gate_kcl_kconnect_demo"

193 RUN_GATE_KCL_LEWY_DEMO = "crate_run_gate_kcl_lewy_demo"

194 RUN_GATE_KCL_PHARMACOTHERAPY_DEMO = (

195 "crate_run_gate_kcl_pharmacotherapy_demo"

196 )

197 SHOW_CRATE_GATE_PIPELINE_OPTIONS = "crate_show_crate_gate_pipeline_options"

198 SHOW_CRATE_MEDEX_PIPELINE_OPTIONS = (

199 "crate_show_crate_medex_pipeline_options"

200 )

201

202 # Web site

203 CELERY_STATUS = "crate_celery_status"

204 DJANGO_MANAGE = "crate_django_manage"

205 EMAIL_RDBM = "crate_email_rdbm"

206 GENERATE_NEW_DJANGO_SECRET_KEY = "crate_generate_new_django_secret_key"

207 LAUNCH_CELERY = "crate_launch_celery"

208 LAUNCH_FLOWER = "crate_launch_flower"

209 PRINT_DEMO_CRATEWEB_CONFIG = "crate_print_demo_crateweb_config"

210 WINDOWS_SERVICE = "crate_windows_service"

211 LAUNCH_CHERRYPY_SERVER = "crate_launch_cherrypy_server"

212 LAUNCH_DJANGO_SERVER = "crate_launch_django_server"

213

214 # NLP web server

215 NLP_WEBSERVER_GENERATE_ENCRYPTION_KEY = (

216 "crate_nlp_webserver_generate_encryption_key"

217 )

218 NLP_WEBSERVER_INITIALIZE_DB = "crate_nlp_webserver_initialize_db"

219 NLP_WEBSERVER_LAUNCH_CELERY = "crate_nlp_webserver_launch_celery"

220 NLP_WEBSERVER_LAUNCH_FLOWER = "crate_nlp_webserver_launch_flower"

221 NLP_WEBSERVER_LAUNCH_GUNICORN = "crate_nlp_webserver_launch_gunicorn"

222 NLP_WEBSERVER_MANAGE_USERS = "crate_nlp_webserver_manage_users"

223 NLP_WEBSERVER_PRINT_DEMO = "crate_nlp_webserver_print_demo"

224 NLP_WEBSERVER_PSERVE = "crate_nlp_webserver_pserve"

225

226 # Testing

227 TEST_DATABASE_CONNECTION = "crate_test_database_connection"

228

229

230# =============================================================================

231# HelpUrl

232# =============================================================================

233

234

235class HelpUrl:

236 """

237 Makes help URLs, for an approximation to context-sensitive help within the

238 web site.

239

240 Note that in Django's template syntax,

241

242 .. code-block:: none

243

244 {{ HelpUrl.main }}

245

246 gets translated to

247

248 .. code-block:: python

249

250 HelpUrl.main()

251

252 i.e. further brackets are unnecessary (and an error). See:

253

254 - https://docs.djangoproject.com/en/2.2/topics/templates/#variables

255

256 ... "If a variable resolves to a callable, the template system will call it

257 with no arguments and use its result instead of the callable."

258

259 """

260

261 @staticmethod

262 def make_url(

263 location: str, language: str = "en", version: str = "latest"

264 ) -> str:

265 """

266 Make a CRATE help URL.

267

268 Args:

269 location: location within docs

270 language: language (default ``en``)

271 version: version (default ``latest``)

272 """

273 return f"{CRATE_DOCS_URL}{language}/{version}/{location}"

274

275 @classmethod

276 def main(cls) -> str:

277 return cls.make_url("")

278

279 @classmethod

280 def website(cls) -> str:

281 return cls.make_url("website_using/index.html")

282

283 @classmethod

284 def find_text_anywhere(cls) -> str:

285 return cls.make_url(

286 "website_using/clinician_privileged.html#clinician-privileged-find-text-anywhere" # noqa: E501

287 )

288

289 @classmethod

290 def clinician_lookup_rid(cls) -> str:

291 return cls.make_url(

292 "website_using/clinician_privileged.html#look-up-research-id-from-patient-id" # noqa: E501

293 )

294

295 @classmethod

296 def clinician_submit_contact_request(cls) -> str:

297 return cls.make_url(

298 "website_using/clinician_privileged.html#submit-patient-contact-request" # noqa: E501

299 )

300

301 @classmethod

302 def querybuilder(cls) -> str:

303 return cls.make_url(

304 "website_using/research_queries.html#query-builder"

305 )

306

307 @classmethod

308 def sql(cls) -> str:

309 return cls.make_url(

310 "website_using/research_queries.html#research-query-sql"

311 )

312

313 @classmethod

314 def highlighting(cls) -> str:

315 return cls.make_url(

316 "website_using/research_queries.html#highlighting-text-in-results"

317 )

318

319 @classmethod

320 def results(cls) -> str:

321 return cls.make_url(

322 "website_using/research_queries.html#results-table-view"

323 )

324

325 @classmethod

326 def patient_explorer(cls) -> str:

327 return cls.make_url("website_using/patient_explorer.html")

328

329 @classmethod

330 def sqlhelper_find_text_anywhere(cls) -> str:

331 return cls.make_url(

332 "website_using/sql_helpers.html#find-text-anywhere"

333 )

334

335 @classmethod

336 def sqlhelper_find_drugs_anywhere(cls) -> str:

337 return cls.make_url(

338 "website_using/sql_helpers.html#find-drugs-of-a-given-type-anywhere" # noqa: E501

339 )

340

341 @classmethod

342 def sitewide_queries(cls) -> str:

343 return cls.make_url("website_using/site_queries.html")

344

345 @classmethod

346 def research_db_structure(cls) -> str:

347 return cls.make_url("website_using/database_structure.html")

348

349 @classmethod

350 def submit_contact_request(cls) -> str:

351 return cls.make_url(

352 "website_using/contact_patients.html#submit-a-contact-request"

353 )

354

355 @classmethod

356 def rdbm(cls) -> str:

357 return cls.make_url("website_using/rdbm_admin.html")

358

359 @classmethod

360 def developer(cls) -> str:

361 return cls.make_url("website_using/developer_admin.html")

362

363 @classmethod

364 def user_settings(cls) -> str:

365 return cls.make_url(

366 "website_using/clinician_researcher_overview.html#your-settings"

367 )

368

369 @classmethod

370 def about_crate(cls) -> str:

371 return cls.make_url(

372 "website_using/clinician_researcher_overview.html#about-crate"

373 )

374

375 @classmethod

376 def archive(cls) -> str:

377 return cls.make_url("website_using/archive.html")

378

379

380# =============================================================================

381# More plain constants

382# =============================================================================

383

384# Will we run without a config file?

385RUNNING_WITHOUT_CONFIG = ON_READTHEDOCS or (

386 EnvVar.RUN_WITHOUT_CONFIG in os.environ

387 and os.environ[EnvVar.RUN_WITHOUT_CONFIG].lower()

388 in LOWER_CASE_STRINGS_MEANING_TRUE

389)