New upstream version 21.15
Andreas Tille
6 years ago
| 0 | Script started on 2017-10-16 22:44:21+0200 | |
| 1 | ncq@hermes:~/Projekte/gm-git/gnumed/gnumed/server/bootstrap$ sudo ./bootstrap-latest.sh | |
| 2 | [sudo] Passwort für ncq: | |
| 3 | =========================================================== | |
| 4 | Bootstrapping latest GNUmed database. | |
| 5 | ||
| 6 | This will set up a GNUmed database of version v21 | |
| 7 | with the name "gnumed_v21". | |
| 8 | ||
| 9 | ------------------------------------------------ | |
| 10 | The database "gnumed_v2" already exists. | |
| 11 | Note that during bootstrapping this | |
| 12 | database will be OVERWRITTEN ! | |
| 13 | ||
| 14 | Do you really intend to bootstrap or did you | |
| 15 | rather want to *upgrade* from v20 to v21 ? | |
| 16 | ||
| 17 | (For upgrading you should run the | |
| 18 | upgrade script instead.) | |
| 19 | ||
| 20 | Continue bootstrapping (deletes databases) ? | |
| 21 | ||
| 22 | [yes / NO]: yes | |
| 23 | ||
| 24 | ------------------------------------------------ | |
| 25 | The database "gnumed_v3" already exists. | |
| 26 | Note that during bootstrapping this | |
| 27 | database will be OVERWRITTEN ! | |
| 28 | ||
| 29 | Do you really intend to bootstrap or did you | |
| 30 | rather want to *upgrade* from v20 to v21 ? | |
| 31 | ||
| 32 | (For upgrading you should run the | |
| 33 | upgrade script instead.) | |
| 34 | ||
| 35 | Continue bootstrapping (deletes databases) ? | |
| 36 | ||
| 37 | [yes / NO]: yes | |
| 38 | ||
| 39 | ------------------------------------------------ | |
| 40 | The database "gnumed_v4" already exists. | |
| 41 | Note that during bootstrapping this | |
| 42 | database will be OVERWRITTEN ! | |
| 43 | ||
| 44 | Do you really intend to bootstrap or did you | |
| 45 | rather want to *upgrade* from v20 to v21 ? | |
| 46 | ||
| 47 | (For upgrading you should run the | |
| 48 | upgrade script instead.) | |
| 49 | ||
| 50 | Continue bootstrapping (deletes databases) ? | |
| 51 | ||
| 52 | [yes / NO]: yes | |
| 53 | ||
| 54 | ------------------------------------------------ | |
| 55 | The database "gnumed_v5" already exists. | |
| 56 | Note that during bootstrapping this | |
| 57 | database will be OVERWRITTEN ! | |
| 58 | ||
| 59 | Do you really intend to bootstrap or did you | |
| 60 | rather want to *upgrade* from v20 to v21 ? | |
| 61 | ||
| 62 | (For upgrading you should run the | |
| 63 | upgrade script instead.) | |
| 64 | ||
| 65 | Continue bootstrapping (deletes databases) ? | |
| 66 | ||
| 67 | [yes / NO]: yes | |
| 68 | ||
| 69 | ------------------------------------------------ | |
| 70 | The database "gnumed_v6" already exists. | |
| 71 | Note that during bootstrapping this | |
| 72 | database will be OVERWRITTEN ! | |
| 73 | ||
| 74 | Do you really intend to bootstrap or did you | |
| 75 | rather want to *upgrade* from v20 to v21 ? | |
| 76 | ||
| 77 | (For upgrading you should run the | |
| 78 | upgrade script instead.) | |
| 79 | ||
| 80 | Continue bootstrapping (deletes databases) ? | |
| 81 | ||
| 82 | [yes / NO]: yes | |
| 83 | ||
| 84 | ------------------------------------------------ | |
| 85 | The database "gnumed_v7" already exists. | |
| 86 | Note that during bootstrapping this | |
| 87 | database will be OVERWRITTEN ! | |
| 88 | ||
| 89 | Do you really intend to bootstrap or did you | |
| 90 | rather want to *upgrade* from v20 to v21 ? | |
| 91 | ||
| 92 | (For upgrading you should run the | |
| 93 | upgrade script instead.) | |
| 94 | ||
| 95 | Continue bootstrapping (deletes databases) ? | |
| 96 | ||
| 97 | [yes / NO]: yes | |
| 98 | ||
| 99 | ------------------------------------------------ | |
| 100 | The database "gnumed_v8" already exists. | |
| 101 | Note that during bootstrapping this | |
| 102 | database will be OVERWRITTEN ! | |
| 103 | ||
| 104 | Do you really intend to bootstrap or did you | |
| 105 | rather want to *upgrade* from v20 to v21 ? | |
| 106 | ||
| 107 | (For upgrading you should run the | |
| 108 | upgrade script instead.) | |
| 109 | ||
| 110 | Continue bootstrapping (deletes databases) ? | |
| 111 | ||
| 112 | [yes / NO]: yes | |
| 113 | ||
| 114 | ------------------------------------------------ | |
| 115 | The database "gnumed_v9" already exists. | |
| 116 | Note that during bootstrapping this | |
| 117 | database will be OVERWRITTEN ! | |
| 118 | ||
| 119 | Do you really intend to bootstrap or did you | |
| 120 | rather want to *upgrade* from v20 to v21 ? | |
| 121 | ||
| 122 | (For upgrading you should run the | |
| 123 | upgrade script instead.) | |
| 124 | ||
| 125 | Continue bootstrapping (deletes databases) ? | |
| 126 | ||
| 127 | [yes / NO]: yes | |
| 128 | ||
| 129 | ------------------------------------------------ | |
| 130 | The database "gnumed_v10" already exists. | |
| 131 | Note that during bootstrapping this | |
| 132 | database will be OVERWRITTEN ! | |
| 133 | ||
| 134 | Do you really intend to bootstrap or did you | |
| 135 | rather want to *upgrade* from v20 to v21 ? | |
| 136 | ||
| 137 | (For upgrading you should run the | |
| 138 | upgrade script instead.) | |
| 139 | ||
| 140 | Continue bootstrapping (deletes databases) ? | |
| 141 | ||
| 142 | [yes / NO]: yes | |
| 143 | ||
| 144 | ------------------------------------------------ | |
| 145 | The database "gnumed_v11" already exists. | |
| 146 | Note that during bootstrapping this | |
| 147 | database will be OVERWRITTEN ! | |
| 148 | ||
| 149 | Do you really intend to bootstrap or did you | |
| 150 | rather want to *upgrade* from v20 to v21 ? | |
| 151 | ||
| 152 | (For upgrading you should run the | |
| 153 | upgrade script instead.) | |
| 154 | ||
| 155 | Continue bootstrapping (deletes databases) ? | |
| 156 | ||
| 157 | [yes / NO]: yes | |
| 158 | ||
| 159 | ------------------------------------------------ | |
| 160 | The database "gnumed_v12" already exists. | |
| 161 | Note that during bootstrapping this | |
| 162 | database will be OVERWRITTEN ! | |
| 163 | ||
| 164 | Do you really intend to bootstrap or did you | |
| 165 | rather want to *upgrade* from v20 to v21 ? | |
| 166 | ||
| 167 | (For upgrading you should run the | |
| 168 | upgrade script instead.) | |
| 169 | ||
| 170 | Continue bootstrapping (deletes databases) ? | |
| 171 | ||
| 172 | [yes / NO]: yes | |
| 173 | ||
| 174 | ------------------------------------------------ | |
| 175 | The database "gnumed_v13" already exists. | |
| 176 | Note that during bootstrapping this | |
| 177 | database will be OVERWRITTEN ! | |
| 178 | ||
| 179 | Do you really intend to bootstrap or did you | |
| 180 | rather want to *upgrade* from v20 to v21 ? | |
| 181 | ||
| 182 | (For upgrading you should run the | |
| 183 | upgrade script instead.) | |
| 184 | ||
| 185 | Continue bootstrapping (deletes databases) ? | |
| 186 | ||
| 187 | [yes / NO]: yes | |
| 188 | ||
| 189 | ------------------------------------------------ | |
| 190 | The database "gnumed_v14" already exists. | |
| 191 | Note that during bootstrapping this | |
| 192 | database will be OVERWRITTEN ! | |
| 193 | ||
| 194 | Do you really intend to bootstrap or did you | |
| 195 | rather want to *upgrade* from v20 to v21 ? | |
| 196 | ||
| 197 | (For upgrading you should run the | |
| 198 | upgrade script instead.) | |
| 199 | ||
| 200 | Continue bootstrapping (deletes databases) ? | |
| 201 | ||
| 202 | [yes / NO]: yes | |
| 203 | ||
| 204 | ------------------------------------------------ | |
| 205 | The database "gnumed_v15" already exists. | |
| 206 | Note that during bootstrapping this | |
| 207 | database will be OVERWRITTEN ! | |
| 208 | ||
| 209 | Do you really intend to bootstrap or did you | |
| 210 | rather want to *upgrade* from v20 to v21 ? | |
| 211 | ||
| 212 | (For upgrading you should run the | |
| 213 | upgrade script instead.) | |
| 214 | ||
| 215 | Continue bootstrapping (deletes databases) ? | |
| 216 | ||
| 217 | [yes / NO]: yes | |
| 218 | ||
| 219 | ------------------------------------------------ | |
| 220 | The database "gnumed_v16" already exists. | |
| 221 | Note that during bootstrapping this | |
| 222 | database will be OVERWRITTEN ! | |
| 223 | ||
| 224 | Do you really intend to bootstrap or did you | |
| 225 | rather want to *upgrade* from v20 to v21 ? | |
| 226 | ||
| 227 | (For upgrading you should run the | |
| 228 | upgrade script instead.) | |
| 229 | ||
| 230 | Continue bootstrapping (deletes databases) ? | |
| 231 | ||
| 232 | [yes / NO]: yes | |
| 233 | ||
| 234 | ------------------------------------------------ | |
| 235 | The database "gnumed_v17" already exists. | |
| 236 | Note that during bootstrapping this | |
| 237 | database will be OVERWRITTEN ! | |
| 238 | ||
| 239 | Do you really intend to bootstrap or did you | |
| 240 | rather want to *upgrade* from v20 to v21 ? | |
| 241 | ||
| 242 | (For upgrading you should run the | |
| 243 | upgrade script instead.) | |
| 244 | ||
| 245 | Continue bootstrapping (deletes databases) ? | |
| 246 | ||
| 247 | [yes / NO]: yes | |
| 248 | ||
| 249 | ------------------------------------------------ | |
| 250 | The database "gnumed_v18" already exists. | |
| 251 | Note that during bootstrapping this | |
| 252 | database will be OVERWRITTEN ! | |
| 253 | ||
| 254 | Do you really intend to bootstrap or did you | |
| 255 | rather want to *upgrade* from v20 to v21 ? | |
| 256 | ||
| 257 | (For upgrading you should run the | |
| 258 | upgrade script instead.) | |
| 259 | ||
| 260 | Continue bootstrapping (deletes databases) ? | |
| 261 | ||
| 262 | [yes / NO]: yes | |
| 263 | ||
| 264 | ------------------------------------------------ | |
| 265 | The database "gnumed_v19" already exists. | |
| 266 | Note that during bootstrapping this | |
| 267 | database will be OVERWRITTEN ! | |
| 268 | ||
| 269 | Do you really intend to bootstrap or did you | |
| 270 | rather want to *upgrade* from v20 to v21 ? | |
| 271 | ||
| 272 | (For upgrading you should run the | |
| 273 | upgrade script instead.) | |
| 274 | ||
| 275 | Continue bootstrapping (deletes databases) ? | |
| 276 | ||
| 277 | [yes / NO]: yes | |
| 278 | ||
| 279 | ------------------------------------------------ | |
| 280 | The database "gnumed_v20" already exists. | |
| 281 | Note that during bootstrapping this | |
| 282 | database will be OVERWRITTEN ! | |
| 283 | ||
| 284 | Do you really intend to bootstrap or did you | |
| 285 | rather want to *upgrade* from v20 to v21 ? | |
| 286 | ||
| 287 | (For upgrading you should run the | |
| 288 | upgrade script instead.) | |
| 289 | ||
| 290 | Continue bootstrapping (deletes databases) ? | |
| 291 | ||
| 292 | [yes / NO]: yes | |
| 293 | ||
| 294 | ------------------------------------------------ | |
| 295 | The database "gnumed_v21" already exists. | |
| 296 | Note that during bootstrapping this | |
| 297 | database will be OVERWRITTEN ! | |
| 298 | ||
| 299 | Do you really intend to bootstrap or did you | |
| 300 | rather want to *upgrade* from v20 to v21 ? | |
| 301 | ||
| 302 | (For upgrading you should run the | |
| 303 | upgrade script instead.) | |
| 304 | ||
| 305 | Continue bootstrapping (deletes databases) ? | |
| 306 | ||
| 307 | [yes / NO]: yes | |
| 308 | Adjusting PYTHONPATH ... | |
| 309 | ======================================= | |
| 310 | Bootstrapping GNUmed database system... | |
| 311 | ======================================= | |
| 312 | You are about to install the following parts of GNUmed: | |
| 313 | ------------------------------------------------------- | |
| 314 | bundle "config" in <gnumed_v2> (or overridden) on <> | |
| 315 | bundle "reference" in <gnumed_v2> (or overridden) on <> | |
| 316 | bundle "demographics" in <gnumed_v2> (or overridden) on <> | |
| 317 | bundle "clinical" in <gnumed_v2> (or overridden) on <> | |
| 318 | bundle "documents" in <gnumed_v2> (or overridden) on <> | |
| 319 | bundle "office" in <gnumed_v2> (or overridden) on <> | |
| 320 | ------------------------------------------------------- | |
| 321 | This will set up a monolithic GNUmed backend with all bundles | |
| 322 | in one database named [gnumed]. It will contain the core schema | |
| 323 | without country or language-specific components. Those will | |
| 324 | have to be added by using one of the bootstrap-XX.conf file | |
| 325 | where XX represents the ISO country code. | |
| 326 | ||
| 327 | Currently this file will also import the test accounts which | |
| 328 | MUST be removed prior to real use. | |
| 329 | ||
| 330 | ==> bootstrapping "config" ... | |
| 331 | ==> dropping pre-existing target database [gnumed_v2] ... | |
| 332 | ==> cloning [template1] (7997 kB) as target database [gnumed_v2] ... | |
| 333 | ==> reindexing target database (can take a while) ... | |
| 334 | ==> transferring users ... | |
| 335 | ... skipped (unconfigured) | |
| 336 | ==> bootstrapping "reference" ... | |
| 337 | ==> bootstrapping "demographics" ... | |
| 338 | ==> bootstrapping "clinical" ... | |
| 339 | ==> bootstrapping "documents" ... | |
| 340 | ==> bootstrapping "office" ... | |
| 341 | ==> setting up auditing ... | |
| 342 | ==> setting up encounter/episode FKs and IDXs ... | |
| 343 | ==> upgrading reference data sets ... | |
| 344 | ... skipped (no scripts to run) | |
| 345 | You are about to install the following parts of GNUmed: | |
| 346 | ------------------------------------------------------- | |
| 347 | bundle "demographics-de" in <gnumed_v2> (or overridden) on <> | |
| 348 | bundle "clinical-de" in <gnumed_v2> (or overridden) on <> | |
| 349 | bundle "reference-de" in <gnumed_v2> (or overridden) on <> | |
| 350 | bundle "Uebersetzung" in <gnumed_v2> (or overridden) on <> | |
| 351 | ------------------------------------------------------- | |
| 352 | Dieses Skript installiert Daten in ein GNUmed-Datenbanksystem, | |
| 353 | mit denen GNUmed fuer Deutschland angepasst wird. | |
| 354 | ||
| 355 | Die Datenbankstruktur muss bereits in einer GNUmed-Datenbank | |
| 356 | installiert sein, ebenso muss mindestens der Nutzer gm-dbo | |
| 357 | bereits existieren. | |
| 358 | ==> bootstrapping "demographics-de" ... | |
| 359 | ==> bootstrapping "clinical-de" ... | |
| 360 | ==> bootstrapping "reference-de" ... | |
| 361 | ==> bootstrapping "Uebersetzung" ... | |
| 362 | ==> setting up auditing ... | |
| 363 | ... skipped (disabled) | |
| 364 | ==> setting up encounter/episode FKs and IDXs ... | |
| 365 | ==> upgrading reference data sets ... | |
| 366 | ... skipped (no scripts to run) | |
| 367 | You are about to install the following parts of GNUmed: | |
| 368 | ------------------------------------------------------- | |
| 369 | bundle "demographics-es" in <gnumed_v2> (or overridden) on <> | |
| 370 | ------------------------------------------------------- | |
| 371 | ||
| 372 | Este script instala en la base de datos de GNUmed las informaciones | |
| 373 | especificas para su uso en Espana (provincias). | |
| 374 | ||
| 375 | Como requisitos, el esquema debe haber sido previamente instalado | |
| 376 | en la base de datos "gnumed" y, al menos, el usuario "gm-dbo" debe | |
| 377 | haber sido creado. | |
| 378 | ||
| 379 | ==> bootstrapping "demographics-es" ... | |
| 380 | ==> setting up auditing ... | |
| 381 | ... skipped (disabled) | |
| 382 | ==> setting up encounter/episode FKs and IDXs ... | |
| 383 | ==> upgrading reference data sets ... | |
| 384 | ... skipped (no scripts to run) | |
| 385 | You are about to install the following parts of GNUmed: | |
| 386 | ------------------------------------------------------- | |
| 387 | bundle "demographics-ca" in <gnumed_v2> (or overridden) on <> | |
| 388 | ------------------------------------------------------- | |
| 389 | This script installs data into a GNUmed database system in | |
| 390 | order to localise GNUmed for Canada. | |
| 391 | ||
| 392 | The core database schema must have been imported into a database | |
| 393 | "gnumed" already. Also, the user gm-dbo must exist. | |
| 394 | ||
| 395 | ==> bootstrapping "demographics-ca" ... | |
| 396 | ==> setting up auditing ... | |
| 397 | ... skipped (disabled) | |
| 398 | ==> setting up encounter/episode FKs and IDXs ... | |
| 399 | ==> upgrading reference data sets ... | |
| 400 | ... skipped (no scripts to run) | |
| 401 | You are about to install the following parts of GNUmed: | |
| 402 | ------------------------------------------------------- | |
| 403 | bundle "au-locale" in <gnumed_v2> (or overridden) on <> | |
| 404 | ------------------------------------------------------- | |
| 405 | This script installs data into a GNUmed database system in | |
| 406 | order to localise GNUmed for Australia. | |
| 407 | ||
| 408 | The core database schema must have been imported into a database | |
| 409 | "gnumed" already. Also, the user gm-dbo must exist. | |
| 410 | ||
| 411 | ==> bootstrapping "au-locale" ... | |
| 412 | ==> setting up auditing ... | |
| 413 | ... skipped (disabled) | |
| 414 | ==> setting up encounter/episode FKs and IDXs ... | |
| 415 | ==> upgrading reference data sets ... | |
| 416 | ... skipped (no scripts to run) | |
| 417 | You are about to install the following parts of GNUmed: | |
| 418 | ------------------------------------------------------- | |
| 419 | bundle "test data" in <gnumed_v2> (or overridden) on <> | |
| 420 | ------------------------------------------------------- | |
| 421 | This script installs test data into an existing GNUmed database | |
| 422 | named "gnumed". Also, the database owner "gm-dbo" must exist | |
| 423 | already. | |
| 424 | ==> bootstrapping "test data" ... | |
| 425 | ==> setting up auditing ... | |
| 426 | ... skipped (disabled) | |
| 427 | ==> setting up encounter/episode FKs and IDXs ... | |
| 428 | ==> upgrading reference data sets ... | |
| 429 | ... skipped (no scripts to run) | |
| 430 | ==> setting up auditing ... | |
| 431 | ... skipped (disabled) | |
| 432 | ==> setting up encounter/episode FKs and IDXs ... | |
| 433 | ==> upgrading reference data sets ... | |
| 434 | ... skipped (no scripts to run) | |
| 435 | You are about to install the following parts of GNUmed: | |
| 436 | ------------------------------------------------------- | |
| 437 | bundle "v2-v3-static" in <gnumed_v3> (or overridden) on <> | |
| 438 | bundle "v2-v3-dynamic" in <gnumed_v3> (or overridden) on <> | |
| 439 | ------------------------------------------------------- | |
| 440 | This will update an existing GNUmed version 2 | |
| 441 | database to the version 3 schema. It does not do | |
| 442 | any harm to the data contained within. | |
| 443 | ||
| 444 | The existing database is cloned first. The copy is | |
| 445 | then modified. The original database remains unchanged. | |
| 446 | ==> bootstrapping "v2-v3-static" ... | |
| 447 | ==> dropping pre-existing target database [gnumed_v3] ... | |
| 448 | ==> cloning [gnumed_v2] (21 MB) as target database [gnumed_v3] ... | |
| 449 | ==> reindexing target database (can take a while) ... | |
| 450 | ==> transferring users ... | |
| 451 | ... skipped (unconfigured) | |
| 452 | ==> bootstrapping "v2-v3-dynamic" ... | |
| 453 | ==> setting up auditing ... | |
| 454 | ... skipped (disabled) | |
| 455 | ==> setting up encounter/episode FKs and IDXs ... | |
| 456 | ==> upgrading reference data sets ... | |
| 457 | ... skipped (no scripts to run) | |
| 458 | You are about to install the following parts of GNUmed: | |
| 459 | ------------------------------------------------------- | |
| 460 | bundle "v3-v4-static" in <gnumed_v4> (or overridden) on <> | |
| 461 | bundle "v3-v4-dynamic" in <gnumed_v4> (or overridden) on <> | |
| 462 | ------------------------------------------------------- | |
| 463 | This will update an existing GNUmed version 3 | |
| 464 | database to the version 4 schema. It does not do | |
| 465 | any harm to the data contained within. | |
| 466 | ||
| 467 | The existing database is cloned first. The copy is | |
| 468 | then modified. The original database remains unchanged. | |
| 469 | ==> bootstrapping "v3-v4-static" ... | |
| 470 | ==> dropping pre-existing target database [gnumed_v4] ... | |
| 471 | ==> cloning [gnumed_v3] (21 MB) as target database [gnumed_v4] ... | |
| 472 | ==> reindexing target database (can take a while) ... | |
| 473 | ==> transferring users ... | |
| 474 | ... skipped (unconfigured) | |
| 475 | ==> bootstrapping "v3-v4-dynamic" ... | |
| 476 | ==> setting up auditing ... | |
| 477 | ... skipped (disabled) | |
| 478 | ==> setting up encounter/episode FKs and IDXs ... | |
| 479 | ==> upgrading reference data sets ... | |
| 480 | ... skipped (no scripts to run) | |
| 481 | You are about to install the following parts of GNUmed: | |
| 482 | ------------------------------------------------------- | |
| 483 | bundle "v4-v5-static" in <gnumed_v5> (or overridden) on <> | |
| 484 | bundle "v4-v5-dynamic" in <gnumed_v5> (or overridden) on <> | |
| 485 | ------------------------------------------------------- | |
| 486 | This will update an existing GNUmed version 4 | |
| 487 | database to the version 5 schema. It does not do | |
| 488 | any harm to the data contained within. | |
| 489 | ||
| 490 | The existing database is cloned first. The copy is | |
| 491 | then modified. The original database remains unchanged. | |
| 492 | ==> bootstrapping "v4-v5-static" ... | |
| 493 | ==> dropping pre-existing target database [gnumed_v5] ... | |
| 494 | ==> cloning [gnumed_v4] (21 MB) as target database [gnumed_v5] ... | |
| 495 | ==> reindexing target database (can take a while) ... | |
| 496 | ==> transferring users ... | |
| 497 | ... skipped (unconfigured) | |
| 498 | ==> bootstrapping "v4-v5-dynamic" ... | |
| 499 | ==> setting up auditing ... | |
| 500 | ... skipped (disabled) | |
| 501 | ==> setting up encounter/episode FKs and IDXs ... | |
| 502 | ==> upgrading reference data sets ... | |
| 503 | ... skipped (no scripts to run) | |
| 504 | You are about to install the following parts of GNUmed: | |
| 505 | ------------------------------------------------------- | |
| 506 | bundle "v5-v6-static" in <gnumed_v6> (or overridden) on <> | |
| 507 | bundle "v5-v6-dynamic" in <gnumed_v6> (or overridden) on <> | |
| 508 | ------------------------------------------------------- | |
| 509 | This will update an existing GNUmed version 5 | |
| 510 | database to the version 6 schema. It does not do | |
| 511 | any harm to the data contained within. | |
| 512 | ||
| 513 | The existing database is cloned first. The copy is | |
| 514 | then modified. The original database remains unchanged. | |
| 515 | ==> bootstrapping "v5-v6-static" ... | |
| 516 | ==> dropping pre-existing target database [gnumed_v6] ... | |
| 517 | ==> cloning [gnumed_v5] (21 MB) as target database [gnumed_v6] ... | |
| 518 | ==> reindexing target database (can take a while) ... | |
| 519 | ==> transferring users ... | |
| 520 | ==> bootstrapping "v5-v6-dynamic" ... | |
| 521 | ==> setting up auditing ... | |
| 522 | ... skipped (disabled) | |
| 523 | ==> setting up encounter/episode FKs and IDXs ... | |
| 524 | ==> upgrading reference data sets ... | |
| 525 | ... skipped (no scripts to run) | |
| 526 | You are about to install the following parts of GNUmed: | |
| 527 | ------------------------------------------------------- | |
| 528 | bundle "v6-v7-static" in <gnumed_v7> (or overridden) on <> | |
| 529 | bundle "v6-v7-dynamic" in <gnumed_v7> (or overridden) on <> | |
| 530 | ------------------------------------------------------- | |
| 531 | This will update an existing GNUmed version 6 | |
| 532 | database to the version 7 schema. It does not do | |
| 533 | any harm to the data contained within. | |
| 534 | ||
| 535 | The existing database is cloned first. The copy is | |
| 536 | then modified. The original database remains unchanged. | |
| 537 | ==> bootstrapping "v6-v7-static" ... | |
| 538 | ==> dropping pre-existing target database [gnumed_v7] ... | |
| 539 | ==> cloning [gnumed_v6] (21 MB) as target database [gnumed_v7] ... | |
| 540 | ==> reindexing target database (can take a while) ... | |
| 541 | ==> transferring users ... | |
| 542 | ==> bootstrapping "v6-v7-dynamic" ... | |
| 543 | ==> setting up auditing ... | |
| 544 | ... skipped (disabled) | |
| 545 | ==> setting up encounter/episode FKs and IDXs ... | |
| 546 | ==> upgrading reference data sets ... | |
| 547 | You are about to install the following parts of GNUmed: | |
| 548 | ------------------------------------------------------- | |
| 549 | bundle "v7-v8-static" in <gnumed_v8> (or overridden) on <> | |
| 550 | bundle "v7-v8-dynamic" in <gnumed_v8> (or overridden) on <> | |
| 551 | ------------------------------------------------------- | |
| 552 | This will update an existing GNUmed version 7 | |
| 553 | database to the version 8 schema. It does not do | |
| 554 | any harm to the data contained within. | |
| 555 | ||
| 556 | The existing database is cloned first. The copy is | |
| 557 | then modified. The original database remains unchanged. | |
| 558 | ==> bootstrapping "v7-v8-static" ... | |
| 559 | ==> dropping pre-existing target database [gnumed_v8] ... | |
| 560 | ==> cloning [gnumed_v7] (21 MB) as target database [gnumed_v8] ... | |
| 561 | ==> reindexing target database (can take a while) ... | |
| 562 | ==> transferring users ... | |
| 563 | ==> bootstrapping "v7-v8-dynamic" ... | |
| 564 | ==> setting up auditing ... | |
| 565 | ==> setting up encounter/episode FKs and IDXs ... | |
| 566 | ==> upgrading reference data sets ... | |
| 567 | ... skipped (no scripts to run) | |
| 568 | You are about to install the following parts of GNUmed: | |
| 569 | ------------------------------------------------------- | |
| 570 | bundle "v8-v9-static" in <gnumed_v9> (or overridden) on <> | |
| 571 | bundle "v8-v9-dynamic" in <gnumed_v9> (or overridden) on <> | |
| 572 | ------------------------------------------------------- | |
| 573 | This will update an existing GNUmed version 8 | |
| 574 | database to the version 9 schema. It does not do | |
| 575 | any harm to the data contained within. | |
| 576 | ||
| 577 | The existing database is cloned first. The copy is | |
| 578 | then modified. The original database remains unchanged. | |
| 579 | ==> bootstrapping "v8-v9-static" ... | |
| 580 | ==> dropping pre-existing target database [gnumed_v9] ... | |
| 581 | ==> cloning [gnumed_v8] (22 MB) as target database [gnumed_v9] ... | |
| 582 | ==> reindexing target database (can take a while) ... | |
| 583 | ==> transferring users ... | |
| 584 | ==> bootstrapping "v8-v9-dynamic" ... | |
| 585 | ==> setting up auditing ... | |
| 586 | ==> setting up encounter/episode FKs and IDXs ... | |
| 587 | ==> upgrading reference data sets ... | |
| 588 | ... skipped (no scripts to run) | |
| 589 | You are about to install the following parts of GNUmed: | |
| 590 | ------------------------------------------------------- | |
| 591 | bundle "v9-v10-static" in <gnumed_v10> (or overridden) on <> | |
| 592 | bundle "v9-v10-dynamic" in <gnumed_v10> (or overridden) on <> | |
| 593 | bundle "v10-fixups" in <gnumed_v10> (or overridden) on <> | |
| 594 | ------------------------------------------------------- | |
| 595 | This will update an existing GNUmed version 9 | |
| 596 | database to the version 10 schema. It does not do | |
| 597 | any harm to the data contained within. | |
| 598 | ||
| 599 | The existing database is cloned first. The copy is | |
| 600 | then modified. The original database remains unchanged. | |
| 601 | ==> bootstrapping "v9-v10-static" ... | |
| 602 | ==> dropping pre-existing target database [gnumed_v10] ... | |
| 603 | ==> cloning [gnumed_v9] (22 MB) as target database [gnumed_v10] ... | |
| 604 | ==> reindexing target database (can take a while) ... | |
| 605 | ==> transferring users ... | |
| 606 | ==> bootstrapping "v9-v10-dynamic" ... | |
| 607 | ==> bootstrapping "v10-fixups" ... | |
| 608 | ==> setting up auditing ... | |
| 609 | ... skipped (disabled) | |
| 610 | ==> setting up encounter/episode FKs and IDXs ... | |
| 611 | ==> upgrading reference data sets ... | |
| 612 | ... skipped (no scripts to run) | |
| 613 | You are about to install the following parts of GNUmed: | |
| 614 | ------------------------------------------------------- | |
| 615 | bundle "v10_fixups-pre_v11" in <gnumed_v11> (or overridden) on <> | |
| 616 | bundle "v10-v11-static" in <gnumed_v11> (or overridden) on <> | |
| 617 | bundle "v10-v11-dynamic" in <gnumed_v11> (or overridden) on <> | |
| 618 | bundle "v11-fixups" in <gnumed_v11> (or overridden) on <> | |
| 619 | bundle "v11-test_data" in <gnumed_v11> (or overridden) on <> | |
| 620 | ------------------------------------------------------- | |
| 621 | This will update an existing GNUmed version 10 | |
| 622 | database to the version 11 schema. It does not do | |
| 623 | any harm to the data contained within. | |
| 624 | ||
| 625 | The existing database will be cloned first. The copy is | |
| 626 | then modified. The original database remains unchanged. | |
| 627 | ==> bootstrapping "v10_fixups-pre_v11" ... | |
| 628 | ==> dropping pre-existing target database [gnumed_v11] ... | |
| 629 | ==> cloning [gnumed_v10] (23 MB) as target database [gnumed_v11] ... | |
| 630 | ==> reindexing target database (can take a while) ... | |
| 631 | ==> transferring users ... | |
| 632 | ==> bootstrapping "v10-v11-static" ... | |
| 633 | ==> bootstrapping "v10-v11-dynamic" ... | |
| 634 | ==> bootstrapping "v11-fixups" ... | |
| 635 | ==> bootstrapping "v11-test_data" ... | |
| 636 | ==> setting up auditing ... | |
| 637 | ==> setting up encounter/episode FKs and IDXs ... | |
| 638 | ==> upgrading reference data sets ... | |
| 639 | ... skipped (no scripts to run) | |
| 640 | You are about to install the following parts of GNUmed: | |
| 641 | ------------------------------------------------------- | |
| 642 | bundle "v11_fixups-pre_v12" in <gnumed_v12> (or overridden) on <> | |
| 643 | bundle "v11-v12-static" in <gnumed_v12> (or overridden) on <> | |
| 644 | bundle "v11-v12-dynamic" in <gnumed_v12> (or overridden) on <> | |
| 645 | ------------------------------------------------------- | |
| 646 | This will update an existing GNUmed version 11 | |
| 647 | database to the version 12 schema. It does not do | |
| 648 | any harm to the data contained within. | |
| 649 | ||
| 650 | The existing database will be cloned first. The copy is | |
| 651 | then modified. The original database remains unchanged. | |
| 652 | ==> bootstrapping "v11_fixups-pre_v12" ... | |
| 653 | ==> dropping pre-existing target database [gnumed_v12] ... | |
| 654 | ==> cloning [gnumed_v11] (24 MB) as target database [gnumed_v12] ... | |
| 655 | ==> reindexing target database (can take a while) ... | |
| 656 | ==> transferring users ... | |
| 657 | ==> bootstrapping "v11-v12-static" ... | |
| 658 | ==> bootstrapping "v11-v12-dynamic" ... | |
| 659 | ==> setting up auditing ... | |
| 660 | ==> setting up encounter/episode FKs and IDXs ... | |
| 661 | ==> upgrading reference data sets ... | |
| 662 | You are about to install the following parts of GNUmed: | |
| 663 | ------------------------------------------------------- | |
| 664 | bundle "v12-v13-static" in <gnumed_v13> (or overridden) on <> | |
| 665 | bundle "v12-v13-dynamic" in <gnumed_v13> (or overridden) on <> | |
| 666 | ------------------------------------------------------- | |
| 667 | This will update an existing GNUmed version 12 | |
| 668 | database to the version 13 schema. It does not do | |
| 669 | any harm to the data contained within. | |
| 670 | ||
| 671 | The existing database will be cloned first. The copy is | |
| 672 | then modified. The original database remains unchanged. | |
| 673 | ==> bootstrapping "v12-v13-static" ... | |
| 674 | ==> dropping pre-existing target database [gnumed_v13] ... | |
| 675 | ==> cloning [gnumed_v12] (25 MB) as target database [gnumed_v13] ... | |
| 676 | ==> reindexing target database (can take a while) ... | |
| 677 | ==> transferring users ... | |
| 678 | ==> bootstrapping "v12-v13-dynamic" ... | |
| 679 | ==> setting up auditing ... | |
| 680 | ==> setting up encounter/episode FKs and IDXs ... | |
| 681 | ==> upgrading reference data sets ... | |
| 682 | You are about to install the following parts of GNUmed: | |
| 683 | ------------------------------------------------------- | |
| 684 | bundle "pg_8.3_v14-pre_conversion_fixups" in <gnumed_v14> (or overridden) on <> | |
| 685 | bundle "v13-v14-static" in <gnumed_v14> (or overridden) on <> | |
| 686 | bundle "v13-v14-dynamic" in <gnumed_v14> (or overridden) on <> | |
| 687 | ------------------------------------------------------- | |
| 688 | This will update an existing GNUmed version 13 | |
| 689 | database to the version 14 schema. It does not do | |
| 690 | any harm to the data contained within. | |
| 691 | ||
| 692 | The existing database will be cloned first. The copy is | |
| 693 | then modified. The original database remains unchanged. | |
| 694 | ==> bootstrapping "pg_8.3_v14-pre_conversion_fixups" ... | |
| 695 | ==> dropping pre-existing target database [gnumed_v14] ... | |
| 696 | ==> cloning [gnumed_v13] (36 MB) as target database [gnumed_v14] ... | |
| 697 | ==> reindexing target database (can take a while) ... | |
| 698 | ==> transferring users ... | |
| 699 | ==> bootstrapping "v13-v14-static" ... | |
| 700 | ==> bootstrapping "v13-v14-dynamic" ... | |
| 701 | ==> setting up auditing ... | |
| 702 | ==> setting up encounter/episode FKs and IDXs ... | |
| 703 | ==> upgrading reference data sets ... | |
| 704 | You are about to install the following parts of GNUmed: | |
| 705 | ------------------------------------------------------- | |
| 706 | bundle "v14-v15-static" in <gnumed_v15> (or overridden) on <> | |
| 707 | bundle "v14-v15-dynamic" in <gnumed_v15> (or overridden) on <> | |
| 708 | bundle "v15-fixups" in <gnumed_v15> (or overridden) on <> | |
| 709 | ------------------------------------------------------- | |
| 710 | This will update an existing GNUmed version 14 | |
| 711 | database to the version 15 schema. It does not do | |
| 712 | any harm to the data contained within. | |
| 713 | ||
| 714 | The existing database will be cloned first. The copy is | |
| 715 | then modified. The original database remains unchanged. | |
| 716 | ==> bootstrapping "v14-v15-static" ... | |
| 717 | ==> dropping pre-existing target database [gnumed_v15] ... | |
| 718 | ==> cloning [gnumed_v14] (37 MB) as target database [gnumed_v15] ... | |
| 719 | ==> reindexing target database (can take a while) ... | |
| 720 | ==> transferring users ... | |
| 721 | ==> bootstrapping "v14-v15-dynamic" ... | |
| 722 | ==> bootstrapping "v15-fixups" ... | |
| 723 | ==> setting up auditing ... | |
| 724 | ==> setting up encounter/episode FKs and IDXs ... | |
| 725 | ==> upgrading reference data sets ... | |
| 726 | You are about to install the following parts of GNUmed: | |
| 727 | ------------------------------------------------------- | |
| 728 | bundle "v15_fixups-pre_v16" in <gnumed_v16> (or overridden) on <> | |
| 729 | bundle "v15-v16-static" in <gnumed_v16> (or overridden) on <> | |
| 730 | bundle "v15-v16-dynamic" in <gnumed_v16> (or overridden) on <> | |
| 731 | bundle "v16-fixups" in <gnumed_v16> (or overridden) on <> | |
| 732 | ------------------------------------------------------- | |
| 733 | This will update an existing GNUmed version 15 | |
| 734 | database to the version 16 schema. It does not do | |
| 735 | any harm to the data contained within. | |
| 736 | ||
| 737 | The existing database will be cloned first. The copy is | |
| 738 | then modified. The original database remains unchanged. | |
| 739 | ==> bootstrapping "v15_fixups-pre_v16" ... | |
| 740 | ==> dropping pre-existing target database [gnumed_v16] ... | |
| 741 | ==> cloning [gnumed_v15] (41 MB) as target database [gnumed_v16] ... | |
| 742 | ==> reindexing target database (can take a while) ... | |
| 743 | ==> transferring users ... | |
| 744 | ==> bootstrapping "v15-v16-static" ... | |
| 745 | ==> bootstrapping "v15-v16-dynamic" ... | |
| 746 | ==> bootstrapping "v16-fixups" ... | |
| 747 | ==> setting up auditing ... | |
| 748 | ==> setting up encounter/episode FKs and IDXs ... | |
| 749 | ==> upgrading reference data sets ... | |
| 750 | You are about to install the following parts of GNUmed: | |
| 751 | ------------------------------------------------------- | |
| 752 | bundle "v16_fixups-pre_v17" in <gnumed_v17> (or overridden) on <> | |
| 753 | bundle "v16-v17-static" in <gnumed_v17> (or overridden) on <> | |
| 754 | bundle "v16-v17-dynamic" in <gnumed_v17> (or overridden) on <> | |
| 755 | bundle "v17-fixups" in <gnumed_v17> (or overridden) on <> | |
| 756 | ------------------------------------------------------- | |
| 757 | This will update an existing GNUmed version 16 | |
| 758 | database to the version 17 schema. It does not do | |
| 759 | any harm to the data contained within. | |
| 760 | ||
| 761 | The existing database will be cloned first. The copy is | |
| 762 | then modified. The original database remains unchanged. | |
| 763 | ==> bootstrapping "v16_fixups-pre_v17" ... | |
| 764 | ==> dropping pre-existing target database [gnumed_v17] ... | |
| 765 | ==> cloning [gnumed_v16] (44 MB) as target database [gnumed_v17] ... | |
| 766 | ==> reindexing target database (can take a while) ... | |
| 767 | ==> transferring users ... | |
| 768 | ==> bootstrapping "v16-v17-static" ... | |
| 769 | ==> bootstrapping "v16-v17-dynamic" ... | |
| 770 | ==> bootstrapping "v17-fixups" ... | |
| 771 | ==> setting up auditing ... | |
| 772 | ==> setting up encounter/episode FKs and IDXs ... | |
| 773 | ==> upgrading reference data sets ... | |
| 774 | You are about to install the following parts of GNUmed: | |
| 775 | ------------------------------------------------------- | |
| 776 | bundle "v17_fixups-pre_v18" in <gnumed_v18> (or overridden) on <> | |
| 777 | bundle "v17-v18-static" in <gnumed_v18> (or overridden) on <> | |
| 778 | bundle "v17-v18-dynamic" in <gnumed_v18> (or overridden) on <> | |
| 779 | bundle "v18-fixups" in <gnumed_v18> (or overridden) on <> | |
| 780 | ------------------------------------------------------- | |
| 781 | This will update an existing GNUmed version 17 | |
| 782 | database to the version 18 schema. It does not do | |
| 783 | any harm to the data contained within. | |
| 784 | ||
| 785 | The existing database will be cloned first. The copy is | |
| 786 | then modified. The original database remains unchanged. | |
| 787 | ==> bootstrapping "v17_fixups-pre_v18" ... | |
| 788 | ==> dropping pre-existing target database [gnumed_v18] ... | |
| 789 | ==> cloning [gnumed_v17] (45 MB) as target database [gnumed_v18] ... | |
| 790 | ==> reindexing target database (can take a while) ... | |
| 791 | ==> transferring users ... | |
| 792 | ==> bootstrapping "v17-v18-static" ... | |
| 793 | ==> bootstrapping "v17-v18-dynamic" ... | |
| 794 | ==> bootstrapping "v18-fixups" ... | |
| 795 | ==> setting up auditing ... | |
| 796 | ==> setting up encounter/episode FKs and IDXs ... | |
| 797 | ==> upgrading reference data sets ... | |
| 798 | You are about to install the following parts of GNUmed: | |
| 799 | ------------------------------------------------------- | |
| 800 | bundle "v18_fixups-pre_v19" in <gnumed_v19> (or overridden) on <> | |
| 801 | bundle "v18-v19-static" in <gnumed_v19> (or overridden) on <> | |
| 802 | bundle "v18-v19-dynamic" in <gnumed_v19> (or overridden) on <> | |
| 803 | bundle "v19-fixups" in <gnumed_v19> (or overridden) on <> | |
| 804 | ------------------------------------------------------- | |
| 805 | This will update an existing GNUmed version 18 | |
| 806 | database to the version 19 schema. It does not do | |
| 807 | any harm to the data contained within. | |
| 808 | ||
| 809 | The existing database will be cloned first. The copy is | |
| 810 | then modified. The original database remains unchanged. | |
| 811 | ||
| 812 | ************************************************************ | |
| 813 | * Before upgrading your existing v18 database to the * | |
| 814 | * v19 schema it is very advisable to make sure you * | |
| 815 | * have created - using the 1.3 client against the v18 * | |
| 816 | * database -- an organization and a unit thereof to * | |
| 817 | * serve as your praxis and praxis location. During the * | |
| 818 | * very first start of the 1.4 client you will be asked * | |
| 819 | * which organization/unit represents your praxis/location. * | |
| 820 | ************************************************************ | |
| 821 | ||
| 822 | ==> bootstrapping "v18_fixups-pre_v19" ... | |
| 823 | ==> dropping pre-existing target database [gnumed_v19] ... | |
| 824 | ==> cloning [gnumed_v18] (52 MB) as target database [gnumed_v19] ... | |
| 825 | ==> reindexing target database (can take a while) ... | |
| 826 | ==> transferring users ... | |
| 827 | ==> bootstrapping "v18-v19-static" ... | |
| 828 | ==> bootstrapping "v18-v19-dynamic" ... | |
| 829 | ==> bootstrapping "v19-fixups" ... | |
| 830 | ==> setting up auditing ... | |
| 831 | ==> setting up encounter/episode FKs and IDXs ... | |
| 832 | ==> setting up generic notifications ... | |
| 833 | ==> upgrading reference data sets ... | |
| 834 | You are about to install the following parts of GNUmed: | |
| 835 | ------------------------------------------------------- | |
| 836 | bundle "v19_fixups-pre_v20" in <gnumed_v20> (or overridden) on <> | |
| 837 | bundle "v19-v20-static" in <gnumed_v20> (or overridden) on <> | |
| 838 | bundle "v19-v20-dynamic" in <gnumed_v20> (or overridden) on <> | |
| 839 | bundle "v20-fixups" in <gnumed_v20> (or overridden) on <> | |
| 840 | ------------------------------------------------------- | |
| 841 | This will update an existing GNUmed version 19 | |
| 842 | database to the version 20 schema. It does not do | |
| 843 | any harm to the data contained within. | |
| 844 | ||
| 845 | The existing database will be cloned first. The copy is | |
| 846 | then modified. The original database remains unchanged. | |
| 847 | ==> bootstrapping "v19_fixups-pre_v20" ... | |
| 848 | ==> dropping pre-existing target database [gnumed_v20] ... | |
| 849 | ==> cloning [gnumed_v19] (68 MB) as target database [gnumed_v20] ... | |
| 850 | ==> reindexing target database (can take a while) ... | |
| 851 | ==> transferring users ... | |
| 852 | ==> bootstrapping "v19-v20-static" ... | |
| 853 | ==> bootstrapping "v19-v20-dynamic" ... | |
| 854 | ==> bootstrapping "v20-fixups" ... | |
| 855 | ==> setting up auditing ... | |
| 856 | ==> setting up encounter/episode FKs and IDXs ... | |
| 857 | ==> setting up encounter/episode FK sanity check triggers ... | |
| 858 | ==> setting up generic notifications ... | |
| 859 | ==> upgrading reference data sets ... | |
| 860 | You are about to install the following parts of GNUmed: | |
| 861 | ------------------------------------------------------- | |
| 862 | bundle "v20_fixups-pre_v21" in <gnumed_v21> (or overridden) on <> | |
| 863 | bundle "v20-v21-static" in <gnumed_v21> (or overridden) on <> | |
| 864 | bundle "v20-v21-dynamic" in <gnumed_v21> (or overridden) on <> | |
| 865 | bundle "v21-fixups" in <gnumed_v21> (or overridden) on <> | |
| 866 | ------------------------------------------------------- | |
| 867 | This will update an existing GNUmed version 20 | |
| 868 | database to the version 21 schema. It does not do | |
| 869 | any harm to the data contained within. | |
| 870 | ||
| 871 | The existing database will be cloned first. The copy is | |
| 872 | then modified. The original database remains unchanged. | |
| 873 | ==> bootstrapping "v20_fixups-pre_v21" ... | |
| 874 | ==> dropping pre-existing target database [gnumed_v21] ... | |
| 875 | ==> cloning [gnumed_v20] (69 MB) as target database [gnumed_v21] ... | |
| 876 | ==> reindexing target database (can take a while) ... | |
| 877 | ==> transferring users ... | |
| 878 | ==> bootstrapping "v20-v21-static" ... | |
| 879 | ==> bootstrapping "v20-v21-dynamic" ... | |
| 880 | ==> bootstrapping "v21-fixups" ... | |
| 881 | ==> setting up auditing ... | |
| 882 | ==> setting up encounter/episode FKs and IDXs ... | |
| 883 | ==> setting up encounter/episode FK sanity check triggers ... | |
| 884 | ==> setting up generic notifications ... | |
| 885 | ==> upgrading reference data sets ... | |
| 886 | ==> verifying target database schema ... | |
| 887 | ==> checking migrated data for plausibility ... | |
| 888 | Done bootstrapping GNUmed database: We very likely succeeded. | |
| 889 | log: /home/ncq/Projekte/gm-git/gnumed/gnumed/server/bootstrap/bootstrap-latest.log | |
| 890 | *** Error in `python': free(): invalid pointer: 0x00770b14 *** | |
| 891 | ======= Backtrace: ========= | |
| 892 | /lib/i386-linux-gnu/libc.so.6(+0x6738a)[0xb7ccc38a] | |
| 893 | /lib/i386-linux-gnu/libc.so.6(+0x6dfc7)[0xb7cd2fc7] | |
| 894 | /lib/i386-linux-gnu/libc.so.6(+0x6e806)[0xb7cd3806] | |
| 895 | python(PyObject_Free+0xfb)[0x44affb] | |
| 896 | python(+0x110b51)[0x534b51] | |
| 897 | python(+0x110b51)[0x534b51] | |
| 898 | python(+0x110b51)[0x534b51] | |
| 899 | python(+0xf3ea7)[0x517ea7] | |
| 900 | python(PyDict_SetItem+0x201)[0x4d4f81] | |
| 901 | python(_PyModule_Clear+0x150)[0x539630] | |
| 902 | python(PyImport_Cleanup+0x61d)[0x53927d] | |
| 903 | python(Py_Finalize+0x9d)[0x53635d] | |
| 904 | python(Py_Exit+0x14)[0x55cb24] | |
| 905 | python(+0x136102)[0x55a102] | |
| 906 | python(PyErr_PrintEx+0x35)[0x559975] | |
| 907 | python(+0x3dd41)[0x461d41] | |
| 908 | python(Py_Main+0x753)[0x4d2c83] | |
| 909 | python(main+0x1b)[0x4d251b] | |
| 910 | /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf6)[0xb7c7d286] | |
| 911 | python(+0xae3f3)[0x4d23f3] | |
| 912 | ======= Memory map: ======== | |
| 913 | 00424000-00763000 r-xp 00000000 08:01 6285092 /usr/bin/python2.7 | |
| 914 | 00763000-00764000 r--p 0033e000 08:01 6285092 /usr/bin/python2.7 | |
| 915 | 00764000-007c4000 rw-p 0033f000 08:01 6285092 /usr/bin/python2.7 | |
| 916 | 007c4000-007d9000 rw-p 00000000 00:00 0 | |
| 917 | 026f1000-02921000 rw-p 00000000 00:00 0 [heap] | |
| 918 | b6800000-b6821000 rw-p 00000000 00:00 0 | |
| 919 | b6821000-b6900000 ---p 00000000 00:00 0 | |
| 920 | b6995000-b69b0000 r-xp 00000000 08:01 8151085 /lib/i386-linux-gnu/libgcc_s.so.1 | |
| 921 | b69b0000-b69b1000 r--p 0001a000 08:01 8151085 /lib/i386-linux-gnu/libgcc_s.so.1 | |
| 922 | b69b1000-b69b2000 rw-p 0001b000 08:01 8151085 /lib/i386-linux-gnu/libgcc_s.so.1 | |
| 923 | b69f5000-b6b35000 rw-p 00000000 00:00 0 | |
| 924 | b6b35000-b6b40000 r-xp 00000000 08:01 8151337 /lib/i386-linux-gnu/libnss_files-2.24.so | |
| 925 | b6b40000-b6b41000 r--p 0000a000 08:01 8151337 /lib/i386-linux-gnu/libnss_files-2.24.so | |
| 926 | b6b41000-b6b42000 rw-p 0000b000 08:01 8151337 /lib/i386-linux-gnu/libnss_files-2.24.so | |
| 927 | b6b42000-b6b48000 rw-p 00000000 00:00 0 | |
| 928 | b6b48000-b6b53000 r-xp 00000000 08:01 8151339 /lib/i386-linux-gnu/libnss_nis-2.24.so | |
| 929 | b6b53000-b6b54000 r--p 0000a000 08:01 8151339 /lib/i386-linux-gnu/libnss_nis-2.24.so | |
| 930 | b6b54000-b6b55000 rw-p 0000b000 08:01 8151339 /lib/i386-linux-gnu/libnss_nis-2.24.so | |
| 931 | b6b64000-b6b6b000 r--p 00000000 08:01 6286752 /usr/share/locale/de/LC_MESSAGES/libpq5-10.mo | |
| 932 | b6b6b000-b6b72000 r--s 00000000 08:01 6903281 /usr/lib/i386-linux-gnu/gconv/gconv-modules.cache | |
| 933 | b6b72000-b6b98000 r--p 00000000 08:01 6288754 /usr/share/locale/de/LC_MESSAGES/libc.mo | |
| 934 | b6b98000-b6c98000 rw-p 00000000 00:00 0 | |
| 935 | b6c9e000-b6cb4000 r-xp 00000000 08:01 8151334 /lib/i386-linux-gnu/libnsl-2.24.so | |
| 936 | b6cb4000-b6cb5000 r--p 00016000 08:01 8151334 /lib/i386-linux-gnu/libnsl-2.24.so | |
| 937 | b6cb5000-b6cb6000 rw-p 00017000 08:01 8151334 /lib/i386-linux-gnu/libnsl-2.24.so | |
| 938 | b6cb6000-b6cb8000 rw-p 00000000 00:00 0 | |
| 939 | b6cb8000-b6cc0000 r-xp 00000000 08:01 8151335 /lib/i386-linux-gnu/libnss_compat-2.24.so | |
| 940 | b6cc0000-b6cc1000 r--p 00007000 08:01 8151335 /lib/i386-linux-gnu/libnss_compat-2.24.so | |
| 941 | b6cc1000-b6cc2000 rw-p 00008000 08:01 8151335 /lib/i386-linux-gnu/libnss_compat-2.24.so | |
| 942 | b6cc2000-b6d02000 rw-p 00000000 00:00 0 | |
| 943 | b6d02000-b6d09000 r-xp 00000000 08:01 6899491 /usr/lib/i386-linux-gnu/libffi.so.6.0.4 | |
| 944 | b6d09000-b6d0a000 r--p 00006000 08:01 6899491 /usr/lib/i386-linux-gnu/libffi.so.6.0.4 | |
| 945 | b6d0a000-b6d0b000 rw-p 00007000 08:01 6899491 /usr/lib/i386-linux-gnu/libffi.so.6.0.4 | |
| 946 | b6d0b000-b6d96000 r-xp 00000000 08:01 6899509 /usr/lib/i386-linux-gnu/libgmp.so.10.3.2 | |
| 947 | b6d96000-b6d97000 r--p 0008a000 08:01 6899509 /usr/lib/i386-linux-gnu/libgmp.so.10.3.2 | |
| 948 | b6d97000-b6d98000 rw-p 0008b000 08:01 6899509 /usr/lib/i386-linux-gnu/libgmp.so.10.3.2 | |
| 949 | b6d98000-b6dcc000 r-xp 00000000 08:01 6899139 /usr/lib/i386-linux-gnu/libhogweed.so.4.3 | |
| 950 | b6dcc000-b6dcd000 r--p 00033000 08:01 6899139 /usr/lib/i386-linux-gnu/libhogweed.so.4.3 | |
| 951 | b6dcd000-b6dce000 rw-p 00034000 08:01 6899139 /usr/lib/i386-linux-gnu/libhogweed.so.4.3 | |
| 952 | b6dce000-b6e08000 r-xp 00000000 08:01 6897991 /usr/lib/i386-linux-gnu/libnettle.so.6.3 | |
| 953 | b6e08000-b6e09000 ---p 0003a000 08:01 6897991 /usr/lib/i386-linux-gnu/libnettle.so.6.3 | |
| 954 | b6e09000-b6e0a000 r--p 0003a000 08:01 6897991 /usr/lib/i386-linux-gnu/libnettle.so.6.3 | |
| 955 | b6e0a000-b6e0b000 rw-p 0003b000 08:01 6897991 /usr/lib/i386-linux-gnu/libnettle.so.6.3 | |
| 956 | b6e0b000-b6e1e000 r-xp 00000000 08:01 6898338 /usr/lib/i386-linux-gnu/libtasn1.so.6.5.4 | |
| 957 | b6e1e000-b6e1f000 r--p 00012000 08:01 6898338 /usr/lib/i386-linux-gnu/libtasn1.so.6.5.4 | |
| 958 | b6e1f000-b6e20000 rw-p 00013000 08:01 6898338 /usr/lib/i386-linux-gnu/libtasn1.so.6.5.4 | |
| 959 | b6e20000-b6f8c000 r-xp 00000000 08:01 6899693 /usr/lib/i386-linux-gnu/libunistring.so.2.0.0 | |
| 960 | b6f8c000-b6f8d000 ---p 0016c000 08:01 6899693 /usr/lib/i386-linux-gnu/libunistring.so.2.0.0 | |
| 961 | b6f8d000-b6f8f000 r--p 0016c000 08:01 6899693 /usr/lib/i386-linux-gnu/libunistring.so.2.0.0 | |
| 962 | b6f8f000-b6f90000 rw-p 0016e000 08:01 6899693 /usr/lib/i386-linux-gnu/libunistring.so.2.0.0 | |
| 963 | b6f90000-b6fac000 r-xp 00000000 08:01 6899147 /usr/lib/i386-linux-gnu/libidn2.so.0.3.1 | |
| 964 | b6fac000-b6fad000 r--p 0001b000 08:01 6899147 /usr/lib/i386-linux-gnu/libidn2.so.0.3.1 | |
| 965 | b6fad000-b6fae000 rw-p 0001c000 08:01 6899147 /usr/lib/i386-linux-gnu/libidn2.so.0.3.1 | |
| 966 | b6fae000-b70fe000 r-xp 00000000 08:01 6899036 /usr/lib/i386-linux-gnu/libp11-kit.so.0.3.0 | |
| 967 | b70fe000-b7104000 r--p 0014f000 08:01 6899036 /usr/lib/i386-linux-gnu/libp11-kit.so.0.3.0 | |
| 968 | b7104000-b7109000 rw-p 00155000 08:01 6899036 /usr/lib/i386-linux-gnu/libp11-kit.so.0.3.0 | |
| 969 | b7109000-b710a000 rw-p 00000000 00:00 0 | |
| 970 | b710a000-b7299000 r-xp 00000000 08:01 6898093 /usr/lib/i386-linux-gnu/libgnutls.so.30.14.7 | |
| 971 | b7299000-b72a1000 r--p 0018e000 08:01 6898093 /usr/lib/i386-linux-gnu/libgnutls.so.30.14.7 | |
| 972 | b72a1000-b72a2000 rw-p 00196000 08:01 6898093 /usr/lib/i386-linux-gnu/libgnutls.so.30.14.7 | |
| 973 | b72a2000-b72a3000 rw-p 00000000 00:00 0 | |
| 974 | b72a3000-b72bf000 r-xp 00000000 08:01 6897853 /usr/lib/i386-linux-gnu/libsasl2.so.2.0.25 | |
| 975 | b72bf000-b72c0000 r--p 0001b000 08:01 6897853 /usr/lib/i386-linux-gnu/libsasl2.so.2.0.25 | |
| 976 | b72c0000-b72c1000 rw-p 0001c000 08:01 6897853 /usr/lib/i386-linux-gnu/libsasl2.so.2.0.25 | |
| 977 | b72c1000-b72d5000 r-xp 00000000 08:01 8151343 /lib/i386-linux-gnu/libresolv-2.24.so | |
| 978 | b72d5000-b72d6000 r--p 00013000 08:01 8151343 /lib/i386-linux-gnu/libresolv-2.24.so | |
| 979 | b72d6000-b72d7000 rw-p 00014000 08:01 8151343 /lib/i386-linux-gnu/libresolv-2.24.so | |
| 980 | b72d7000-b72d9000 rw-p 00000000 00:00 0 | |
| 981 | b72d9000-b730b000 r-xp 00000000 08:01 6898091 /usr/lib/i386-linux-gnu/libk5crypto.so.3.1 | |
| 982 | b730b000-b730c000 ---p 00032000 08:01 6898091 /usr/lib/i386-linux-gnu/libk5crypto.so.3.1 | |
| 983 | b730c000-b730d000 r--p 00032000 08:01 6898091 /usr/lib/i386-linux-gnu/libk5crypto.so.3.1 | |
| 984 | b730d000-b730e000 rw-p 00033000 08:01 6898091 /usr/lib/i386-linux-gnu/libk5crypto.so.3.1 | |
| 985 | b730e000-b730f000 rw-p 00000000 00:00 0 | |
| 986 | b730f000-b73e2000 r-xp 00000000 08:01 6898964 /usr/lib/i386-linux-gnu/libkrb5.so.3.3 | |
| 987 | b73e2000-b73e3000 ---p 000d3000 08:01 6898964 /usr/lib/i386-linux-gnu/libkrb5.so.3.3 | |
| 988 | b73e3000-b73e9000 r--p 000d3000 08:01 6898964 /usr/lib/i386-linux-gnu/libkrb5.so.3.3 | |
| 989 | b73e9000-b73eb000 rw-p 000d9000 08:01 6898964 /usr/lib/i386-linux-gnu/libkrb5.so.3.3 | |
| 990 | b73eb000-b7441000 r-xp 00000000 08:01 6899719 /usr/lib/i386-linux-gnu/libldap_r-2.4.so.2.10.8 | |
| 991 | b7441000-b7442000 ---p 00056000 08:01 6899719 /usr/lib/i386-linux-gnu/libldap_r-2.4.so.2.10.8 | |
| 992 | b7442000-b7443000 r--p 00056000 08:01 6899719 /usr/lib/i386-linux-gnu/libldap_r-2.4.so.2.10.8 | |
| 993 | b7443000-b7444000 rw-p 00057000 08:01 6899719 /usr/lib/i386-linux-gnu/libldap_r-2.4.so.2.10.8 | |
| 994 | b7444000-b7445000 rw-p 00000000 00:00 0 | |
| 995 | b7445000-b7495000 r-xp 00000000 08:01 6898215 /usr/lib/i386-linux-gnu/libgssapi_krb5.so.2.2 | |
| 996 | b7495000-b7496000 r--p 0004f000 08:01 6898215 /usr/lib/i386-linux-gnu/libgssapi_krb5.so.2.2 | |
| 997 | b7496000-b7497000 rw-p 00050000 08:01 6898215 /usr/lib/i386-linux-gnu/libgssapi_krb5.so.2.2 | |
| 998 | b7497000-b74e1000 r-xp 00000000 08:01 6899474 /usr/lib/i386-linux-gnu/libpq.so.5.10 | |
| 999 | b74e1000-b74e3000 r--p 00049000 08:01 6899474 /usr/lib/i386-linux-gnu/libpq.so.5.10 | |
| 1000 | b74e3000-b74e4000 rw-p 0004b000 08:01 6899474 /usr/lib/i386-linux-gnu/libpq.so.5.10 | |
| 1001 | b74e8000-b74ed000 r-xp 00000000 08:01 6365428 /usr/lib/python2.7/dist-packages/faulthandler.i386-linux-gnu.so | |
| 1002 | b74ed000-b74ee000 r--p 00004000 08:01 6365428 /usr/lib/python2.7/dist-packages/faulthandler.i386-linux-gnu.so | |
| 1003 | b74ee000-b74ef000 rw-p 00005000 08:01 6365428 /usr/lib/python2.7/dist-packages/faulthandler.i386-linux-gnu.so | |
| 1004 | b74ef000-b74f6000 r-xp 00000000 08:01 6367548 /usr/lib/python2.7/lib-dynload/_csv.i386-linux-gnu.so | |
| 1005 | b74f6000-b74f7000 r--p 00006000 08:01 6367548 /usr/lib/python2.7/lib-dynload/_csv.i386-linux-gnu.so | |
| 1006 | b74f7000-b74f9000 rw-p 00007000 08:01 6367548 /usr/lib/python2.7/lib-dynload/_csv.i386-linux-gnu.so | |
| 1007 | b74f9000-b750c000 r-xp 00000000 08:01 6367559 /usr/lib/python2.7/lib-dynload/_json.i386-linux-gnu.so | |
| 1008 | b750c000-b750d000 r--p 00012000 08:01 6367559 /usr/lib/python2.7/lib-dynload/_json.i386-linux-gnu.so | |
| 1009 | b750d000-b750e000 rw-p 00013000 08:01 6367559 /usr/lib/python2.7/lib-dynload/_json.i386-linux-gnu.so | |
| 1010 | b750e000-b7523000 r-xp 00000000 08:01 6367569 /usr/lib/python2.7/lib-dynload/_ssl.i386-linux-gnu.so | |
| 1011 | b7523000-b7524000 r--p 00014000 08:01 6367569 /usr/lib/python2.7/lib-dynload/_ssl.i386-linux-gnu.so | |
| 1012 | b7524000-b7527000 rw-p 00015000 08:01 6367569 /usr/lib/python2.7/lib-dynload/_ssl.i386-linux-gnu.so | |
| 1013 | b7527000-b7559000 r-xp 00000000 08:01 6479968 /usr/lib/python2.7/dist-packages/psycopg2/_psycopg.i386-linux-gnu.so | |
| 1014 | b7559000-b755a000 r--p 00031000 08:01 6479968 /usr/lib/python2.7/dist-packages/psycopg2/_psycopg.i386-linux-gnu.so | |
| 1015 | b755a000-b755e000 rw-p 00032000 08:01 6479968 /usr/lib/python2.7/dist-packages/psycopg2/_psycopg.i386-linux-gnu.so | |
| 1016 | b755e000-b756e000 r-xp 00000000 08:01 8151113 /lib/i386-linux-gnu/libbz2.so.1.0.4 | |
| 1017 | b756e000-b756f000 r--p 0000f000 08:01 8151113 /lib/i386-linux-gnu/libbz2.so.1.0.4 | |
| 1018 | b756f000-b7570000 rw-p 00010000 08:01 8151113 /lib/i386-linux-gnu/libbz2.so.1.0.4 | |
| 1019 | b7576000-b7584000 r-xp 00000000 08:01 6897979 /usr/lib/i386-linux-gnu/liblber-2.4.so.2.10.8 | |
| 1020 | b7584000-b7585000 r--p 0000d000 08:01 6897979 /usr/lib/i386-linux-gnu/liblber-2.4.so.2.10.8 | |
| 1021 | b7585000-b7586000 rw-p 0000e000 08:01 6897979 /usr/lib/i386-linux-gnu/liblber-2.4.so.2.10.8 | |
| 1022 | b7586000-b7589000 r-xp 00000000 08:01 8151178 /lib/i386-linux-gnu/libkeyutils.so.1.5 | |
| 1023 | b7589000-b758a000 r--p 00002000 08:01 8151178 /lib/i386-linux-gnu/libkeyutils.so.1.5 | |
| 1024 | b758a000-b758b000 rw-p 00003000 08:01 8151178 /lib/i386-linux-gnu/libkeyutils.so.1.5 | |
| 1025 | b758b000-b7596000 r-xp 00000000 08:01 6899192 /usr/lib/i386-linux-gnu/libkrb5support.so.0.1 | |
| 1026 | b7596000-b7597000 r--p 0000a000 08:01 6899192 /usr/lib/i386-linux-gnu/libkrb5support.so.0.1 | |
| 1027 | b7597000-b7598000 rw-p 0000b000 08:01 6899192 /usr/lib/i386-linux-gnu/libkrb5support.so.0.1 | |
| 1028 | b7598000-b759f000 r-xp 00000000 08:01 8151344 /lib/i386-linux-gnu/librt-2.24.so | |
| 1029 | b759f000-b75a0000 r--p 00006000 08:01 8151344 /lib/i386-linux-gnu/librt-2.24.so | |
| 1030 | b75a0000-b75a1000 rw-p 00007000 08:01 8151344 /lib/i386-linux-gnu/librt-2.24.so | |
| 1031 | b75a1000-b75b1000 r-xp 00000000 08:01 6570027 /usr/lib/python2.7/dist-packages/mx/DateTime/mxDateTime/mxDateTime.so | |
| 1032 | b75b1000-b75b2000 r--p 0000f000 08:01 6570027 /usr/lib/python2.7/dist-packages/mx/DateTime/mxDateTime/mxDateTime.so | |
| 1033 | b75b2000-b75b3000 rw-p 00010000 08:01 6570027 /usr/lib/python2.7/dist-packages/mx/DateTime/mxDateTime/mxDateTime.so | |
| 1034 | b75b3000-b77fe000 r-xp 00000000 08:01 6897994 /usr/lib/i386-linux-gnu/libcrypto.so.1.1 | |
| 1035 | b77fe000-b77ff000 ---p 0024b000 08:01 6897994 /usr/lib/i386-linux-gnu/libcrypto.so.1.1 | |
| 1036 | b77ff000-b7810000 r--p 0024b000 08:01 6897994 /usr/lib/i386-linux-gnu/libcrypto.so.1.1 | |
| 1037 | b7810000-b7817000 rw-p 0025c000 08:01 6897994 /usr/lib/i386-linux-gnu/libcrypto.so.1.1 | |
| 1038 | b7817000-b781a000 rw-p 00000000 00:00 0 | |
| 1039 | b781a000-b7881000 r-xp 00000000 08:01 6899137 /usr/lib/i386-linux-gnu/libssl.so.1.1 | |
| 1040 | b7881000-b7884000 r--p 00066000 08:01 6899137 /usr/lib/i386-linux-gnu/libssl.so.1.1 | |
| 1041 | b7884000-b7888000 rw-p 00069000 08:01 6899137 /usr/lib/i386-linux-gnu/libssl.so.1.1 | |
| 1042 | b7888000-b7988000 rw-p 00000000 00:00 0 | |
| 1043 | b798a000-b798d000 r-xp 00000000 08:01 8151240 /lib/i386-linux-gnu/libcom_err.so.2.1 | |
| 1044 | b798d000-b798e000 r--p 00002000 08:01 8151240 /lib/i386-linux-gnu/libcom_err.so.2.1 | |
| 1045 | b798e000-b798f000 rw-p 00003000 08:01 8151240 /lib/i386-linux-gnu/libcom_err.so.2.1 | |
| 1046 | b798f000-b7998000 r-xp 00000000 08:01 6367575 /usr/lib/python2.7/lib-dynload/bz2.i386-linux-gnu.so | |
| 1047 | b7998000-b7999000 r--p 00008000 08:01 6367575 /usr/lib/python2.7/lib-dynload/bz2.i386-linux-gnu.so | |
| 1048 | b7999000-b799b000 rw-p 00009000 08:01 6367575 /usr/lib/python2.7/lib-dynload/bz2.i386-linux-gnu.so | |
| 1049 | b799b000-b79fc000 rw-p 00000000 00:00 0 | |
| 1050 | b79fc000-b7a00000 r-xp 00000000 08:01 6367555 /usr/lib/python2.7/lib-dynload/_hashlib.i386-linux-gnu.so | |
| 1051 | b7a00000-b7a01000 r--p 00003000 08:01 6367555 /usr/lib/python2.7/lib-dynload/_hashlib.i386-linux-gnu.so | |
| 1052 | b7a01000-b7a02000 rw-p 00004000 08:01 6367555 /usr/lib/python2.7/lib-dynload/_hashlib.i386-linux-gnu.so | |
| 1053 | b7a02000-b7a05000 r-xp 00000000 08:01 6367622 /usr/lib/python2.7/lib-dynload/termios.i386-linux-gnu.so | |
| 1054 | b7a05000-b7a06000 r--p 00002000 08:01 6367622 /usr/lib/python2.7/lib-dynload/termios.i386-linux-gnu.so | |
| 1055 | b7a06000-b7a08000 rw-p 00003000 08:01 6367622 /usr/lib/python2.7/lib-dynload/termios.i386-linux-gnu.so | |
| 1056 | b7a08000-b7a48000 rw-p 00000000 00:00 0 | |
| 1057 | b7a48000-b7be3000 r--p 00000000 08:01 6299936 /usr/lib/locale/locale-archive | |
| 1058 | b7be3000-b7c65000 rw-p 00000000 00:00 0 | |
| 1059 | b7c65000-b7e16000 r-xp 00000000 08:01 8151265 /lib/i386-linux-gnu/libc-2.24.so | |
| 1060 | b7e16000-b7e18000 r--p 001b0000 08:01 8151265 /lib/i386-linux-gnu/libc-2.24.so | |
| 1061 | b7e18000-b7e19000 rw-p 001b2000 08:01 8151265 /lib/i386-linux-gnu/libc-2.24.so | |
| 1062 | b7e19000-b7e1c000 rw-p 00000000 00:00 0 | |
| 1063 | b7e1c000-b7e6f000 r-xp 00000000 08:01 8151332 /lib/i386-linux-gnu/libm-2.24.so | |
| 1064 | b7e6f000-b7e70000 r--p 00052000 08:01 8151332 /lib/i386-linux-gnu/libm-2.24.so | |
| 1065 | b7e70000-b7e71000 rw-p 00053000 08:01 8151332 /lib/i386-linux-gnu/libm-2.24.so | |
| 1066 | b7e71000-b7e8a000 r-xp 00000000 08:01 8151148 /lib/i386-linux-gnu/libz.so.1.2.8 | |
| 1067 | b7e8a000-b7e8b000 r--p 00018000 08:01 8151148 /lib/i386-linux-gnu/libz.so.1.2.8 | |
| 1068 | b7e8b000-b7e8c000 rw-p 00019000 08:01 8151148 /lib/i386-linux-gnu/libz.so.1.2.8 | |
| 1069 | b7e8c000-b7e8e000 r-xp 00000000 08:01 8151355 /lib/i386-linux-gnu/libutil-2.24.so | |
| 1070 | b7e8e000-b7e8f000 r--p 00001000 08:01 8151355 /lib/i386-linux-gnu/libutil-2.24.so | |
| 1071 | b7e8f000-b7e90000 rw-p 00002000 08:01 8151355 /lib/i386-linux-gnu/libutil-2.24.so | |
| 1072 | b7e90000-b7e93000 r-xp 00000000 08:01 8151331 /lib/i386-linux-gnu/libdl-2.24.so | |
| 1073 | b7e93000-b7e94000 r--p 00002000 08:01 8151331 /lib/i386-linux-gnu/libdl-2.24.so | |
| 1074 | b7e94000-b7e95000 rw-p 00003000 08:01 8151331 /lib/i386-linux-gnu/libdl-2.24.so | |
| 1075 | b7e95000-b7eae000 r-xp 00000000 08:01 8151342 /lib/i386-linux-gnu/libpthread-2.24.so | |
| 1076 | b7eae000-b7eaf000 r--p 00018000 08:01 8151342 /lib/i386-linux-gnu/libpthread-2.24.so | |
| 1077 | b7eaf000-b7eb0000 rw-p 00019000 08:01 8151342 /lib/i386-linux-gnu/libpthread-2.24.so | |
| 1078 | b7eb0000-b7eb2000 rw-p 00000000 00:00 0 | |
| 1079 | b7eb4000-b7ef8000 rw-p 00000000 00:00 0 | |
| 1080 | b7ef8000-b7efb000 r--p 00000000 00:00 0 [vvar] | |
| 1081 | b7efb000-b7efd000 r-xp 00000000 00:00 0 [vdso] | |
| 1082 | b7efd000-b7f20000 r-xp 00000000 08:01 8151050 /lib/i386-linux-gnu/ld-2.24.so | |
| 1083 | b7f20000-b7f21000 r--p 00022000 08:01 8151050 /lib/i386-linux-gnu/ld-2.24.so | |
| 1084 | b7f21000-b7f22000 rw-p 00023000 08:01 8151050 /lib/i386-linux-gnu/ld-2.24.so | |
| 1085 | bf9f5000-bfa16000 rw-p 00000000 00:00 0 [stack] | |
| 1086 | Fatal Python error: Aborted | |
| 1087 | ||
| 1088 | Current thread 0xb7c63d00 (most recent call first): | |
| 1089 | ./bootstrap-latest.sh: Zeile 80: 20984 Abgebrochen ./bootstrap_gm_db_system.py --log-file=${LOG} --conf-file=${CONF} --${QUIET} | |
| 1090 | Bootstrapping "gnumed_v21" did not finish successfully (134). Aborting. | |
| 1091 | ||
| 1092 | Sie haben neue Post in /var/mail/ncq. | |
| 1093 | ncq@hermes:~/Projekte/gm-git/gnumed/gnumed/server/bootstrap$ exit | |
| 1094 | exit | |
| 1095 | ||
| 1096 | Script done on 2017-10-16 23:18:46+0200 |
| 77 | 77 | LOG="${GM_LOG_BASE}/bootstrap-latest.log" |
| 78 | 78 | CONF="bootstrap-latest.conf" |
| 79 | 79 | ./bootstrap_gm_db_system.py --log-file=${LOG} --conf-file=${CONF} --${QUIET} |
| 80 | if test "$?" != "0" ; then | |
| 81 | echo "Bootstrapping \"gnumed_v${VER}\" did not finish successfully. Aborting." | |
| 80 | #gdb --args /usr/bin/python2.7-dbg ./bootstrap_gm_db_system.py --log-file=${LOG} --conf-file=${CONF} --${QUIET} | |
| 81 | RESULT="$?" | |
| 82 | if test "${RESULT}" != "0" ; then | |
| 83 | echo "Bootstrapping \"gnumed_v${VER}\" did not finish successfully (${RESULT}). Aborting." | |
| 82 | 84 | read |
| 83 | 85 | exit 1 |
| 84 | 86 | fi |
| 0 | 0 | #!/usr/bin/env python |
| 1 | ||
| 2 | """GNUmed schema installation. | |
| 1 | ##!/usr/bin/python2.7-dbg | |
| 2 | ||
| 3 | u"""GNUmed schema installation. | |
| 3 | 4 | |
| 4 | 5 | This script bootstraps a GNUmed database system. |
| 5 | 6 | |
| 24 | 25 | --log-file= |
| 25 | 26 | --conf-file= |
| 26 | 27 | |
| 27 | Requires psycopg 2.7 ! | |
| 28 | Requires psycopg 2.7.3 ! | |
| 28 | 29 | """ |
| 29 | 30 | #================================================================== |
| 30 | 31 | # TODO |
| 81 | 82 | except ImportError: |
| 82 | 83 | print """Please make sure the GNUmed Python modules are in the Python path !""" |
| 83 | 84 | raise |
| 84 | from Gnumed.pycommon import gmCfg2, gmPsql, gmPG2, gmTools, gmI18N | |
| 85 | from Gnumed.pycommon import gmCfg2 | |
| 86 | from Gnumed.pycommon import gmPsql | |
| 87 | from Gnumed.pycommon import gmPG2 | |
| 88 | from Gnumed.pycommon import gmTools | |
| 89 | from Gnumed.pycommon import gmI18N | |
| 85 | 90 | from Gnumed.pycommon.gmExceptions import ConstructorError |
| 86 | 91 | |
| 87 | 92 | |
| 91 | 96 | |
| 92 | 97 | |
| 93 | 98 | _log = logging.getLogger('gm.bootstrapper') |
| 99 | ||
| 100 | try: | |
| 101 | import faulthandler | |
| 102 | #faulthandler.enable(file = gmLog2._logfile) | |
| 103 | faulthandler.enable() | |
| 104 | except ImportError: | |
| 105 | _log.error(u'<faulthandler> not available') | |
| 106 | ||
| 94 | 107 | _cfg = gmCfg2.gmCfgData() |
| 95 | 108 | |
| 96 | 109 | |
| 97 | _interactive = False | |
| 110 | _interactive = None | |
| 98 | 111 | _bootstrapped_servers = {} |
| 99 | 112 | _bootstrapped_dbs = {} |
| 100 | 113 | _dbowner = None |
| 204 | 217 | try: |
| 205 | 218 | cursor.execute(cmd, args) |
| 206 | 219 | except: |
| 207 | _log.exception(">>>[%s]<<< failed for user [%s]", cmd, user) | |
| 220 | _log.exception(u">>>[%s]<<< failed for user [%s]", cmd, user) | |
| 208 | 221 | return None |
| 209 | 222 | res = cursor.fetchone() |
| 210 | 223 | if cursor.rowcount == 1: |
| 211 | _log.info("user [%s] exists", user) | |
| 212 | return True | |
| 213 | _log.info("user [%s] does not exist", user) | |
| 224 | _log.info(u"user [%s] exists", user) | |
| 225 | return True | |
| 226 | _log.info(u"user [%s] does not exist", user) | |
| 214 | 227 | return None |
| 215 | 228 | #------------------------------------------------------------------ |
| 216 | 229 | def db_group_exists(cursor=None, group=None): |
| 219 | 232 | try: |
| 220 | 233 | cursor.execute(cmd, args) |
| 221 | 234 | except: |
| 222 | _log.exception(">>>[%s]<<< failed for group [%s]", cmd, group) | |
| 235 | _log.exception(u">>>[%s]<<< failed for group [%s]", cmd, group) | |
| 223 | 236 | return False |
| 224 | 237 | rows = cursor.fetchall() |
| 225 | 238 | if len(rows) > 0: |
| 226 | _log.info("group [%s] exists" % group) | |
| 227 | return True | |
| 228 | _log.info("group [%s] does not exist" % group) | |
| 239 | _log.info(u"group [%s] exists" % group) | |
| 240 | return True | |
| 241 | _log.info(u"group [%s] does not exist" % group) | |
| 229 | 242 | return False |
| 230 | 243 | #------------------------------------------------------------------ |
| 231 | 244 | def create_db_group(cursor=None, group=None): |
| 238 | 251 | try: |
| 239 | 252 | cursor.execute(cmd) |
| 240 | 253 | except: |
| 241 | _log.exception(">>>[%s]<<< failed for group [%s]", cmd, group) | |
| 254 | _log.exception(u">>>[%s]<<< failed for group [%s]", cmd, group) | |
| 242 | 255 | return False |
| 243 | 256 | |
| 244 | 257 | # paranoia is good |
| 265 | 278 | passwd = '' |
| 266 | 279 | |
| 267 | 280 | dsn = gmPG2.make_psycopg2_dsn(database=db, host=host, port=port, user=user, password=passwd) |
| 268 | _log.info("trying DB connection to %s on %s as %s", db, host or 'localhost', user) | |
| 281 | _log.info(u"trying DB connection to %s on %s as %s", db, host or 'localhost', user) | |
| 269 | 282 | try: |
| 270 | 283 | conn = gmPG2.get_connection(dsn=dsn, readonly=False, pooled=False, verbose=True, connection_name = conn_name) |
| 271 | 284 | except: |
| 276 | 289 | cached_passwd[user] = passwd |
| 277 | 290 | conn_ref_count.append(conn) |
| 278 | 291 | |
| 279 | _log.info('successfully connected') | |
| 292 | _log.info(u'successfully connected') | |
| 280 | 293 | return conn |
| 281 | 294 | |
| 282 | 295 | #================================================================== |
| 301 | 314 | # this means the user does not need a password |
| 302 | 315 | # but connects via IDENT or TRUST |
| 303 | 316 | if self.password is None: |
| 304 | _log.info('password not defined, assuming connect via IDENT/TRUST') | |
| 317 | _log.info(u'password not defined, assuming connect via IDENT/TRUST') | |
| 305 | 318 | # defined but empty: |
| 306 | 319 | # this means to ask the user if interactive |
| 307 | 320 | elif self.password == '': |
| 316 | 329 | #================================================================== |
| 317 | 330 | class db_server: |
| 318 | 331 | def __init__(self, aSrv_alias, auth_group): |
| 319 | _log.info("bootstrapping server [%s]" % aSrv_alias) | |
| 332 | _log.info(u"bootstrapping server [%s]" % aSrv_alias) | |
| 320 | 333 | |
| 321 | 334 | global _bootstrapped_servers |
| 322 | 335 | |
| 323 | 336 | if _bootstrapped_servers.has_key(aSrv_alias): |
| 324 | _log.info("server [%s] already bootstrapped" % aSrv_alias) | |
| 337 | _log.info(u"server [%s] already bootstrapped" % aSrv_alias) | |
| 325 | 338 | return None |
| 326 | 339 | |
| 327 | 340 | self.alias = aSrv_alias |
| 334 | 347 | |
| 335 | 348 | _bootstrapped_servers[self.alias] = self |
| 336 | 349 | |
| 337 | _log.info('done bootstrapping server [%s]', aSrv_alias) | |
| 350 | _log.info(u'done bootstrapping server [%s]', aSrv_alias) | |
| 338 | 351 | #-------------------------------------------------------------- |
| 339 | 352 | def __bootstrap(self): |
| 340 | 353 | self.superuser = user(anAlias = cfg_get(self.section, "super user alias")) |
| 341 | 354 | |
| 342 | 355 | # connect to server level template database |
| 343 | 356 | if not self.__connect_superuser_to_srv_template(): |
| 344 | _log.error("Cannot connect to server template database.") | |
| 357 | _log.error(u"Cannot connect to server template database.") | |
| 345 | 358 | return None |
| 346 | 359 | |
| 347 | 360 | # add users/groups |
| 348 | 361 | if not self.__bootstrap_db_users(): |
| 349 | _log.error("Cannot bootstrap database users.") | |
| 362 | _log.error(u"Cannot bootstrap database users.") | |
| 350 | 363 | return None |
| 351 | 364 | |
| 352 | 365 | self.conn.close() |
| 353 | 366 | return True |
| 354 | 367 | #-------------------------------------------------------------- |
| 355 | 368 | def __connect_superuser_to_srv_template(self): |
| 356 | _log.info("connecting to server template database") | |
| 369 | _log.info(u"connecting to server template database") | |
| 357 | 370 | |
| 358 | 371 | # sanity checks |
| 359 | 372 | self.template_db = cfg_get(self.section, "template database") |
| 360 | 373 | if self.template_db is None: |
| 361 | _log.error("Need to know the template database name.") | |
| 374 | _log.error(u"Need to know the template database name.") | |
| 362 | 375 | return None |
| 363 | 376 | |
| 364 | 377 | self.name = cfg_get(self.section, "name") |
| 365 | 378 | if self.name is None: |
| 366 | _log.error("Need to know the server name.") | |
| 379 | _log.error(u"Need to know the server name.") | |
| 367 | 380 | return None |
| 368 | 381 | |
| 369 | 382 | env_var = 'GM_DB_PORT' |
| 370 | 383 | self.port = os.getenv(env_var) |
| 371 | 384 | if self.port is None: |
| 372 | _log.info('environment variable [%s] is not set, using database port from config file' % env_var) | |
| 385 | _log.info(u'environment variable [%s] is not set, using database port from config file' % env_var) | |
| 373 | 386 | self.port = cfg_get(self.section, "port") |
| 374 | 387 | else: |
| 375 | _log.info('using database port [%s] from environment variable [%s]' % (self.port, env_var)) | |
| 388 | _log.info(u'using database port [%s] from environment variable [%s]' % (self.port, env_var)) | |
| 376 | 389 | if self.port is None: |
| 377 | _log.error("Need to know the database server port address.") | |
| 390 | _log.error(u"Need to know the database server port address.") | |
| 378 | 391 | return None |
| 379 | 392 | |
| 380 | 393 | if self.conn is not None: |
| 383 | 396 | |
| 384 | 397 | self.conn = connect(self.name, self.port, self.template_db, self.superuser.name, self.superuser.password, conn_name = u'root@template.server') |
| 385 | 398 | if self.conn is None: |
| 386 | _log.error('Cannot connect.') | |
| 399 | _log.error(u'Cannot connect.') | |
| 387 | 400 | return None |
| 388 | 401 | |
| 389 | 402 | self.conn.cookie = 'db_server.__connect_superuser_to_srv_template' |
| 393 | 406 | curs.execute(u"select setting from pg_settings where name = 'lc_ctype'") |
| 394 | 407 | data = curs.fetchall() |
| 395 | 408 | lc_ctype = data[0][0] |
| 396 | _log.info('template database LC_CTYPE is [%s]', lc_ctype) | |
| 409 | _log.info(u'template database LC_CTYPE is [%s]', lc_ctype) | |
| 397 | 410 | lc_ctype = lc_ctype.lower() |
| 398 | 411 | if lc_ctype in ['c', 'posix']: |
| 399 | 412 | _log.warning('while this cluster setting allows to store databases') |
| 401 | 414 | _log.warning('sorting etc, hence it is not recommended for use') |
| 402 | 415 | _log.warning('(although it will, technically, work)') |
| 403 | 416 | elif not (lc_ctype.endswith('.utf-8') or lc_ctype.endswith('.utf8')): |
| 404 | _log.error('LC_CTYPE does not end in .UTF-8 or .UTF8') | |
| 417 | _log.error(u'LC_CTYPE does not end in .UTF-8 or .UTF8') | |
| 405 | 418 | curs.execute(u"show server_encoding") |
| 406 | 419 | data = curs.fetchall() |
| 407 | 420 | srv_enc = data[0][0] |
| 408 | _log.info('server_encoding is [%s]', srv_enc) | |
| 421 | _log.info(u'server_encoding is [%s]', srv_enc) | |
| 409 | 422 | srv_enc = srv_enc.lower() |
| 410 | 423 | if not srv_enc in ['utf8', 'utf-8']: |
| 411 | _log.error('cluster encoding incompatible with utf8 encoded databases but') | |
| 412 | _log.error('for GNUmed installation the cluster must accept this encoding') | |
| 413 | _log.error('you may need to re-initdb or create a new cluster') | |
| 424 | _log.error(u'cluster encoding incompatible with utf8 encoded databases but') | |
| 425 | _log.error(u'for GNUmed installation the cluster must accept this encoding') | |
| 426 | _log.error(u'you may need to re-initdb or create a new cluster') | |
| 414 | 427 | return None |
| 415 | _log.info('server encoding seems compatible despite not being reported in LC_CTYPE') | |
| 428 | _log.info(u'server encoding seems compatible despite not being reported in LC_CTYPE') | |
| 416 | 429 | |
| 417 | 430 | # make sure we get english messages |
| 418 | 431 | curs.execute(u"set lc_messages to 'C'") |
| 419 | 432 | curs.close() |
| 420 | 433 | |
| 421 | _log.info("successfully connected to template database [%s]" % self.template_db) | |
| 434 | _log.info(u"successfully connected to template database [%s]" % self.template_db) | |
| 422 | 435 | return True |
| 423 | 436 | #-------------------------------------------------------------- |
| 424 | 437 | # user and group related |
| 425 | 438 | #-------------------------------------------------------------- |
| 426 | 439 | def __bootstrap_db_users(self): |
| 427 | _log.info("bootstrapping database users and groups") | |
| 440 | _log.info(u"bootstrapping database users and groups") | |
| 428 | 441 | |
| 429 | 442 | # insert standard groups |
| 430 | 443 | if not self.__create_groups(): |
| 431 | _log.error("Cannot create GNUmed standard groups.") | |
| 444 | _log.error(u"Cannot create GNUmed standard groups.") | |
| 432 | 445 | return None |
| 433 | 446 | |
| 434 | 447 | # create GNUmed owner |
| 435 | 448 | if self.__create_dbowner() is None: |
| 436 | _log.error("Cannot install GNUmed database owner.") | |
| 449 | _log.error(u"Cannot install GNUmed database owner.") | |
| 437 | 450 | return None |
| 438 | 451 | |
| 439 | 452 | # if not _import_schema(group=self.section, schema_opt='schema', conn=self.conn): |
| 440 | # _log.error("Cannot import schema definition for server [%s] into database [%s]." % (self.name, self.template_db)) | |
| 453 | # _log.error(u"Cannot import schema definition for server [%s] into database [%s]." % (self.name, self.template_db)) | |
| 441 | 454 | # return None |
| 442 | 455 | |
| 443 | 456 | return True |
| 447 | 460 | |
| 448 | 461 | dbowner_alias = cfg_get("GnuMed defaults", "database owner alias") |
| 449 | 462 | if dbowner_alias is None: |
| 450 | _log.error("Cannot load GNUmed database owner name from config file.") | |
| 463 | _log.error(u"Cannot load GNUmed database owner name from config file.") | |
| 451 | 464 | return None |
| 452 | 465 | |
| 453 | 466 | cursor = self.conn.cursor() |
| 468 | 481 | try: |
| 469 | 482 | cursor.execute(cmd) |
| 470 | 483 | except: |
| 471 | _log.error(">>>[%s]<<< failed." % cmd) | |
| 472 | _log.exception("Cannot add GNUmed database owner [%s] to groups [gm-logins] and [%s]." % (name, self.auth_group)) | |
| 484 | _log.error(u">>>[%s]<<< failed." % cmd) | |
| 485 | _log.exception(u"Cannot add GNUmed database owner [%s] to groups [gm-logins] and [%s]." % (name, self.auth_group)) | |
| 473 | 486 | cursor.close() |
| 474 | 487 | return False |
| 475 | 488 | self.conn.commit() |
| 478 | 491 | return True |
| 479 | 492 | |
| 480 | 493 | print_msg (( |
| 481 | """The database owner [%s] will be created. | |
| 494 | u"""The database owner [%s] will be created. | |
| 482 | 495 | |
| 483 | 496 | You will have to provide a new password for it |
| 484 | 497 | unless it is pre-defined in the configuration file. |
| 491 | 504 | try: |
| 492 | 505 | cursor.execute(cmd) |
| 493 | 506 | except: |
| 494 | _log.error(">>>[%s]<<< failed." % cmd) | |
| 495 | _log.exception("Cannot create GNUmed database owner [%s]." % _dbowner.name) | |
| 507 | _log.error(u">>>[%s]<<< failed." % cmd) | |
| 508 | _log.exception(u"Cannot create GNUmed database owner [%s]." % _dbowner.name) | |
| 496 | 509 | cursor.close() |
| 497 | 510 | return None |
| 498 | 511 | |
| 514 | 527 | |
| 515 | 528 | groups = cfg_get(section, "groups") |
| 516 | 529 | if groups is None: |
| 517 | _log.error("Cannot load GNUmed group names from config file (section [%s])." % section) | |
| 530 | _log.error(u"Cannot load GNUmed group names from config file (section [%s])." % section) | |
| 518 | 531 | groups = [self.auth_group] |
| 519 | 532 | else: |
| 520 | 533 | groups.append(self.auth_group) |
| 531 | 544 | #================================================================== |
| 532 | 545 | class database: |
| 533 | 546 | def __init__(self, aDB_alias): |
| 534 | _log.info("bootstrapping database [%s]" % aDB_alias) | |
| 547 | _log.info(u"bootstrapping database [%s]" % aDB_alias) | |
| 535 | 548 | |
| 536 | 549 | self.section = "database %s" % aDB_alias |
| 537 | 550 | |
| 540 | 553 | if overrider is not None: |
| 541 | 554 | self.name = os.getenv(overrider) |
| 542 | 555 | if self.name is None: |
| 543 | _log.info('environment variable [%s] is not set, using database name from config file' % overrider) | |
| 556 | _log.info(u'environment variable [%s] is not set, using database name from config file' % overrider) | |
| 544 | 557 | self.name = cfg_get(self.section, 'name') |
| 545 | 558 | else: |
| 546 | 559 | self.name = cfg_get(self.section, 'name') |
| 547 | 560 | |
| 548 | 561 | if self.name is None or str(self.name).strip() == '': |
| 549 | _log.error("Need to know database name.") | |
| 562 | _log.error(u"Need to know database name.") | |
| 550 | 563 | raise ConstructorError, "database.__init__(): Cannot bootstrap database." |
| 551 | 564 | |
| 552 | 565 | # already bootstrapped ? |
| 553 | 566 | global _bootstrapped_dbs |
| 554 | 567 | if _bootstrapped_dbs.has_key(aDB_alias): |
| 555 | 568 | if _bootstrapped_dbs[aDB_alias].name == self.name: |
| 556 | _log.info("database [%s] already bootstrapped", self.name) | |
| 569 | _log.info(u"database [%s] already bootstrapped", self.name) | |
| 557 | 570 | return None |
| 558 | 571 | |
| 559 | 572 | # no, so bootstrap from scratch |
| 560 | _log.info('bootstrapping database [%s] alias "%s"', self.name, aDB_alias) | |
| 573 | _log.info(u'bootstrapping database [%s] alias "%s"', self.name, aDB_alias) | |
| 561 | 574 | |
| 562 | 575 | for db in _bootstrapped_dbs.values(): |
| 563 | 576 | if db.conn.closed == 0: |
| 567 | 580 | |
| 568 | 581 | self.server_alias = cfg_get(self.section, "server alias") |
| 569 | 582 | if self.server_alias is None: |
| 570 | _log.error("Server alias missing.") | |
| 583 | _log.error(u"Server alias missing.") | |
| 571 | 584 | raise ConstructorError, "database.__init__(): Cannot bootstrap database." |
| 572 | 585 | |
| 573 | 586 | self.template_db = cfg_get(self.section, "template database") |
| 574 | 587 | if self.template_db is None: |
| 575 | _log.error("Template database name missing.") | |
| 588 | _log.error(u"Template database name missing.") | |
| 576 | 589 | raise ConstructorError, "database.__init__(): Cannot bootstrap database." |
| 577 | 590 | |
| 578 | 591 | # make sure server is bootstrapped |
| 595 | 608 | _dbowner = user(anAlias = cfg_get("GnuMed defaults", "database owner alias")) |
| 596 | 609 | |
| 597 | 610 | if _dbowner is None: |
| 598 | _log.error("Cannot load GNUmed database owner name from config file.") | |
| 599 | return None | |
| 600 | ||
| 601 | # get owner | |
| 611 | _log.error(u"Cannot load GNUmed database owner name from config file.") | |
| 612 | return None | |
| 613 | ||
| 602 | 614 | self.owner = _dbowner |
| 603 | 615 | |
| 604 | 616 | # connect as owner to template |
| 605 | 617 | if not self.__connect_superuser_to_template(): |
| 606 | _log.error("Cannot connect to template database.") | |
| 618 | _log.error(u"Cannot connect to template database.") | |
| 607 | 619 | return False |
| 608 | 620 | |
| 609 | 621 | # make sure db exists |
| 610 | 622 | if not self.__create_db(): |
| 611 | _log.error("Cannot create database.") | |
| 623 | _log.error(u"Cannot create database.") | |
| 612 | 624 | return False |
| 613 | 625 | |
| 614 | 626 | # reconnect as superuser to db |
| 615 | 627 | if not self.__connect_superuser_to_db(): |
| 616 | _log.error("Cannot connect to database.") | |
| 628 | _log.error(u"Cannot connect to database.") | |
| 617 | 629 | return None |
| 618 | 630 | |
| 619 | 631 | # create authentication group |
| 620 | _log.info('creating database-specific authentication group role') | |
| 632 | _log.info(u'creating database-specific authentication group role') | |
| 621 | 633 | curs = self.conn.cursor() |
| 622 | 634 | if not create_db_group(cursor = curs, group = self.name): |
| 623 | 635 | curs.close() |
| 624 | _log.error('cannot create authentication group role') | |
| 636 | _log.error(u'cannot create authentication group role') | |
| 625 | 637 | return False |
| 626 | 638 | self.conn.commit() |
| 627 | 639 | curs.close() |
| 630 | 642 | curs = self.conn.cursor() |
| 631 | 643 | if not db_group_exists(cursor = curs, group = self.name): |
| 632 | 644 | curs.close() |
| 633 | _log.error('cannot find authentication group role') | |
| 645 | _log.error(u'cannot find authentication group role') | |
| 634 | 646 | return False |
| 635 | 647 | curs.close() |
| 636 | 648 | |
| 637 | 649 | # reindex db so upgrade doesn't fail on broken index |
| 638 | 650 | if not self.reindex_all(): |
| 639 | _log.error('cannot REINDEX cloned target database') | |
| 651 | _log.error(u'cannot REINDEX cloned target database') | |
| 640 | 652 | return False |
| 641 | 653 | |
| 642 | 654 | tmp = cfg_get(self.section, 'superuser schema') |
| 643 | 655 | if tmp is not None: |
| 644 | 656 | if not _import_schema(group=self.section, schema_opt='superuser schema', conn=self.conn): |
| 645 | _log.error("cannot import schema definition for database [%s]" % (self.name)) | |
| 657 | _log.error(u"cannot import schema definition for database [%s]" % (self.name)) | |
| 646 | 658 | return False |
| 647 | 659 | del tmp |
| 648 | 660 | |
| 649 | 661 | # transfer users |
| 650 | 662 | if not self.transfer_users(): |
| 651 | _log.error("Cannot transfer users from old to new database.") | |
| 663 | _log.error(u"Cannot transfer users from old to new database.") | |
| 652 | 664 | return False |
| 653 | 665 | |
| 654 | 666 | # reconnect as owner to db |
| 655 | 667 | if not self.__connect_owner_to_db(): |
| 656 | _log.error("Cannot connect to database.") | |
| 668 | _log.error(u"Cannot connect to database.") | |
| 657 | 669 | return None |
| 658 | 670 | if not _import_schema(group=self.section, schema_opt='schema', conn=self.conn): |
| 659 | _log.error("cannot import schema definition for database [%s]" % (self.name)) | |
| 671 | _log.error(u"cannot import schema definition for database [%s]" % (self.name)) | |
| 660 | 672 | return None |
| 661 | 673 | |
| 662 | 674 | # don't close this here, the connection will |
| 710 | 722 | # we need English messages to detect errors |
| 711 | 723 | curs.execute(u"set lc_messages to 'C'") |
| 712 | 724 | curs.execute(u"alter database %s set lc_messages to 'C'" % self.name) |
| 713 | # we need inheritance or else things will fail miserably | |
| 714 | curs.execute("alter database %s set sql_inheritance to on" % self.name) | |
| 715 | 725 | # we want READ ONLY default transactions for maximum patient data safety |
| 716 | 726 | curs.execute("alter database %s set default_transaction_read_only to on" % self.name) |
| 717 | 727 | # we want checking of function bodies |
| 718 | 728 | curs.execute("alter database %s set check_function_bodies to on" % self.name) |
| 729 | # we want checking of data checksums if available | |
| 730 | curs.execute("alter database %s set ignore_checksum_failure to off" % self.name) | |
| 719 | 731 | curs.close() |
| 720 | 732 | self.conn.commit() |
| 721 | 733 | |
| 722 | # we want checking of data checksums if available | |
| 723 | # remove exception handler when 9.3 is default | |
| 734 | # we need inheritance or else things will fail miserably | |
| 724 | 735 | curs = self.conn.cursor() |
| 725 | 736 | try: |
| 726 | curs.execute("alter database %s set ignore_checksum_failure to off" % self.name) | |
| 737 | curs.execute("alter database %s set sql_inheritance to DEFAULT" % self.name) | |
| 727 | 738 | except: |
| 728 | _log.exception('PostgreSQL version < 9.3 does not support <ignore_checksum_failure>') | |
| 739 | _log.exception(u'PG 10 hardwired for sql_inheritance') | |
| 729 | 740 | curs.close() |
| 741 | self.conn.commit() | |
| 730 | 742 | |
| 731 | 743 | # we want to track commit timestamps if available |
| 732 | 744 | # remove exception handler when 9.5 is default |
| 734 | 746 | try: |
| 735 | 747 | curs.execute("alter database %s set track_commit_timestamp to on" % self.name) |
| 736 | 748 | except: |
| 737 | _log.exception('PostgreSQL version < 9.5 does not support <track_commit_timestamp> OR <track_commit_timestamp> cannot be set at runtime') | |
| 749 | _log.exception(u'PostgreSQL version < 9.5 does not support <track_commit_timestamp> OR <track_commit_timestamp> cannot be set at runtime') | |
| 738 | 750 | curs.close() |
| 739 | ||
| 740 | 751 | self.conn.commit() |
| 741 | 752 | |
| 742 | 753 | curs = self.conn.cursor() |
| 748 | 759 | #-------------------------------------------------------------- |
| 749 | 760 | def __connect_owner_to_db(self): |
| 750 | 761 | |
| 762 | _log.debug(u'__connect_owner_to_db') | |
| 763 | ||
| 751 | 764 | # reconnect as superuser to db |
| 752 | 765 | if not self.__connect_superuser_to_db(): |
| 753 | _log.error("Cannot connect to database.") | |
| 766 | _log.error(u"Cannot connect to database.") | |
| 754 | 767 | return False |
| 755 | 768 | |
| 756 | 769 | self.conn.cookie = 'database.__connect_owner_to_db via database.__connect_superuser_to_db' |
| 770 | ||
| 771 | _log.debug(u'setting session authorization to user %s', self.owner.name) | |
| 757 | 772 | |
| 758 | 773 | curs = self.conn.cursor() |
| 759 | 774 | cmd = "set session authorization %(usr)s" |
| 770 | 785 | try: |
| 771 | 786 | aCursor.execute(cmd) |
| 772 | 787 | except: |
| 773 | _log.exception(">>>[%s]<<< failed." % cmd) | |
| 788 | _log.exception(u">>>[%s]<<< failed." % cmd) | |
| 774 | 789 | return None |
| 775 | 790 | |
| 776 | 791 | res = aCursor.fetchall() |
| 777 | 792 | tmp = aCursor.rowcount |
| 778 | 793 | aCursor.close() |
| 779 | 794 | if tmp == 1: |
| 780 | _log.info("Database [%s] exists." % self.name) | |
| 795 | _log.info(u"Database [%s] exists." % self.name) | |
| 781 | 796 | return True |
| 782 | 797 | |
| 783 | _log.info("Database [%s] does not exist." % self.name) | |
| 798 | _log.info(u"Database [%s] does not exist." % self.name) | |
| 784 | 799 | return None |
| 785 | 800 | #-------------------------------------------------------------- |
| 786 | 801 | def __create_db(self): |
| 792 | 807 | else: |
| 793 | 808 | converted, version = gmTools.input2int(template_version.lstrip('v'), 0) |
| 794 | 809 | if not converted: |
| 795 | _log.error('invalid template database definition: %s', template_version) | |
| 810 | _log.error(u'invalid template database definition: %s', template_version) | |
| 796 | 811 | return False |
| 797 | 812 | if not gmPG2.database_schema_compatible(link_obj = self.conn, version = version): |
| 798 | _log.error('invalid [%s] schema structure in GNUmed template database [%s]', template_version, self.template_db) | |
| 813 | _log.error(u'invalid [%s] schema structure in GNUmed template database [%s]', template_version, self.template_db) | |
| 799 | 814 | return False |
| 800 | 815 | |
| 801 | 816 | # check for target database |
| 803 | 818 | drop_existing = bool(int(cfg_get(self.section, 'drop target database'))) |
| 804 | 819 | if drop_existing: |
| 805 | 820 | print_msg("==> dropping pre-existing target database [%s] ..." % self.name) |
| 806 | _log.info('trying to drop target database') | |
| 821 | _log.info(u'trying to drop target database') | |
| 807 | 822 | cmd = 'DROP DATABASE "%s"' % self.name |
| 808 | _log.debug('committing existing connection before setting autocommit') | |
| 823 | _log.debug(u'committing existing connection before setting autocommit') | |
| 809 | 824 | self.conn.commit() |
| 810 | _log.debug('setting autocommit to TRUE') | |
| 825 | _log.debug(u'setting autocommit to TRUE') | |
| 811 | 826 | self.conn.autocommit = True |
| 812 | 827 | self.conn.readonly = False |
| 813 | 828 | cursor = self.conn.cursor() |
| 814 | 829 | try: |
| 815 | 830 | cursor.execute(u'SET default_transaction_read_only TO OFF') |
| 816 | _log.debug('running SQL: %s', cmd) | |
| 831 | _log.debug(u'running SQL: %s', cmd) | |
| 817 | 832 | cursor.execute(cmd) |
| 818 | 833 | except: |
| 819 | _log.exception(">>>[%s]<<< failed" % cmd) | |
| 834 | _log.exception(u">>>[%s]<<< failed" % cmd) | |
| 820 | 835 | _log.debug(u'conn state after failed DROP: %s', gmPG2.capture_conn_state(self.conn)) |
| 821 | 836 | return False |
| 822 | 837 | finally: |
| 827 | 842 | if use_existing: |
| 828 | 843 | # FIXME: verify that database is owned by "gm-dbo" |
| 829 | 844 | print_msg("==> using pre-existing target database [%s] ..." % self.name) |
| 830 | _log.info('using existing database [%s]', self.name) | |
| 845 | _log.info(u'using existing database [%s]', self.name) | |
| 831 | 846 | return True |
| 832 | 847 | else: |
| 833 | _log.info('not using existing database [%s]', self.name) | |
| 848 | _log.info(u'not using existing database [%s]', self.name) | |
| 834 | 849 | return False |
| 835 | 850 | |
| 836 | 851 | tablespace = cfg_get(self.section, 'tablespace') |
| 868 | 883 | cursor.execute(u'SET default_transaction_read_only TO OFF') |
| 869 | 884 | cursor.execute(create_db_cmd) |
| 870 | 885 | except: |
| 871 | _log.exception(">>>[%s]<<< failed" % create_db_cmd) | |
| 886 | _log.exception(u">>>[%s]<<< failed" % create_db_cmd) | |
| 872 | 887 | return False |
| 873 | 888 | finally: |
| 874 | 889 | cursor.close() |
| 876 | 891 | |
| 877 | 892 | if not self.__db_exists(): |
| 878 | 893 | return None |
| 879 | _log.info("Successfully created GNUmed database [%s]." % self.name) | |
| 894 | _log.info(u"Successfully created GNUmed database [%s]." % self.name) | |
| 880 | 895 | |
| 881 | 896 | return True |
| 882 | 897 | |
| 893 | 908 | |
| 894 | 909 | no_of_queries, remainder = divmod(len(plausibility_queries), 2) |
| 895 | 910 | if remainder != 0: |
| 896 | _log.error('odd number of plausibility queries defined, aborting') | |
| 911 | _log.error(u'odd number of plausibility queries defined, aborting') | |
| 897 | 912 | print_msg(" ... failed (configuration error)") |
| 898 | 913 | return False |
| 899 | 914 | |
| 920 | 935 | for idx in range(no_of_queries): |
| 921 | 936 | check_def = plausibility_queries[idx*2] |
| 922 | 937 | if check_def.startswith('--'): |
| 923 | _log.debug('skipped: %s', check_def) | |
| 938 | _log.debug(u'skipped: %s', check_def) | |
| 924 | 939 | continue |
| 925 | 940 | |
| 926 | 941 | tag = u'?' |
| 975 | 990 | target_conn.close() |
| 976 | 991 | |
| 977 | 992 | return all_tests_successful |
| 993 | ||
| 978 | 994 | #-------------------------------------------------------------- |
| 979 | 995 | def check_holy_auth_line(self): |
| 980 | 996 | |
| 988 | 1004 | self.server.superuser.name, |
| 989 | 1005 | self.server.superuser.password |
| 990 | 1006 | ) |
| 991 | conn.cookie = 'holy auth check connection' | |
| 1007 | conn.cookie = u'holy auth check connection' | |
| 992 | 1008 | |
| 993 | 1009 | cmd = u"select setting from pg_settings where name = 'hba_file'" |
| 994 | 1010 | rows, idx = gmPG2.run_ro_queries(link_obj = conn, queries = [{'cmd': cmd}]) |
| 995 | 1011 | conn.close() |
| 996 | 1012 | if len(rows) == 0: |
| 997 | _log.info('cannot check pg_hba.conf for authentication information - not detectable in pg_settings') | |
| 1013 | _log.info(u'cannot check pg_hba.conf for authentication information - not detectable in pg_settings') | |
| 998 | 1014 | return |
| 999 | 1015 | |
| 1000 | 1016 | hba_file = rows[0][0] |
| 1001 | _log.info('hba file: %s', hba_file) | |
| 1017 | _log.info(u'hba file: %s', hba_file) | |
| 1002 | 1018 | |
| 1003 | 1019 | try: |
| 1004 | 1020 | f = io.open(hba_file, mode = 'rt').close() |
| 1005 | 1021 | except Exception: |
| 1006 | _log.exception('cannot check pg_hba.conf for authentication information - not readable') | |
| 1022 | _log.exception(u'cannot check pg_hba.conf for authentication information - not readable') | |
| 1007 | 1023 | return |
| 1008 | 1024 | |
| 1009 | 1025 | found_holy_line = False |
| 1010 | 1026 | for line in fileinput.input(hba_file): |
| 1011 | 1027 | if regex.match(holy_pattern, line) is not None: |
| 1012 | 1028 | found_holy_line = True |
| 1013 | _log.info('found standard GNUmed authentication directive in pg_hba.conf') | |
| 1014 | _log.info('[%s]', line) | |
| 1015 | _log.info('it may still be in the wrong place, though, so double-check if clients cannot connect') | |
| 1029 | _log.info(u'found standard GNUmed authentication directive in pg_hba.conf') | |
| 1030 | _log.info(u'[%s]', line) | |
| 1031 | _log.info(u'it may still be in the wrong place, though, so double-check if clients cannot connect') | |
| 1016 | 1032 | break |
| 1017 | 1033 | |
| 1018 | 1034 | if not found_holy_line: |
| 1019 | _log.info('did not find active standard GNUmed authentication directive in pg_hba.conf') | |
| 1020 | _log.info('regex: %s' % holy_pattern) | |
| 1035 | _log.info(u'did not find active standard GNUmed authentication directive in pg_hba.conf') | |
| 1036 | _log.info(u'regex: %s' % holy_pattern) | |
| 1021 | 1037 | |
| 1022 | 1038 | found_holy_line_inactive = False |
| 1023 | 1039 | for line in fileinput.input(hba_file): |
| 1024 | 1040 | if regex.match(holy_pattern_inactive, line) is not None: |
| 1025 | 1041 | found_holy_line_inactive = True |
| 1026 | _log.info('found inactive standard GNUmed authentication directive in pg_hba.conf') | |
| 1027 | _log.info('[%s]', line) | |
| 1028 | _log.info('it may still be in the wrong place, though, so double-check if clients cannot connect') | |
| 1042 | _log.info(u'found inactive standard GNUmed authentication directive in pg_hba.conf') | |
| 1043 | _log.info(u'[%s]', line) | |
| 1044 | _log.info(u'it may still be in the wrong place, though, so double-check if clients cannot connect') | |
| 1029 | 1045 | break |
| 1030 | 1046 | if not found_holy_line_inactive: |
| 1031 | _log.info('did not find inactive standard GNUmed authentication directive in pg_hba.conf either') | |
| 1032 | _log.info('regex: %s' % holy_pattern_inactive) | |
| 1033 | ||
| 1034 | _log.info('bootstrapping is likely to have succeeded but clients probably cannot connect yet') | |
| 1047 | _log.info(u'did not find inactive standard GNUmed authentication directive in pg_hba.conf either') | |
| 1048 | _log.info(u'regex: %s' % holy_pattern_inactive) | |
| 1049 | ||
| 1050 | _log.info(u'bootstrapping is likely to have succeeded but clients probably cannot connect yet') | |
| 1035 | 1051 | print_msg('==> sanity checking PostgreSQL authentication settings ...') |
| 1036 | 1052 | print_msg('') |
| 1037 | 1053 | print_msg('Note that even after successfully bootstrapping the GNUmed ') |
| 1059 | 1075 | |
| 1060 | 1076 | import_scripts = cfg_get(self.section, "data import scripts") |
| 1061 | 1077 | if (import_scripts is None) or (len(import_scripts) == 0): |
| 1062 | _log.info('skipped data import: no scripts to run') | |
| 1078 | _log.info(u'skipped data import: no scripts to run') | |
| 1063 | 1079 | print_msg(" ... skipped (no scripts to run)") |
| 1064 | 1080 | return True |
| 1065 | 1081 | |
| 1074 | 1090 | script = gmTools.import_module_from_directory(module_path = script_base_dir, module_name = import_script, always_remove_path = True) |
| 1075 | 1091 | except ImportError: |
| 1076 | 1092 | print_msg(" ... failed (cannot load script [%s])" % import_script) |
| 1077 | _log.error('cannot load data set import script [%s/%s]' % (script_base_dir, import_script)) | |
| 1093 | _log.error(u'cannot load data set import script [%s/%s]' % (script_base_dir, import_script)) | |
| 1078 | 1094 | return False |
| 1079 | 1095 | |
| 1080 | 1096 | try: |
| 1081 | 1097 | script.run(conn = self.conn) |
| 1082 | 1098 | except: |
| 1083 | 1099 | print_msg(" ... failed (cannot run script [%s])" % import_script) |
| 1084 | _log.exception('cannot run import script [%s]' % import_script) | |
| 1100 | _log.exception(u'cannot run import script [%s]' % import_script) | |
| 1085 | 1101 | return False |
| 1086 | 1102 | |
| 1087 | 1103 | if import_script.endswith('.py'): |
| 1092 | 1108 | del script |
| 1093 | 1109 | gc.collect() |
| 1094 | 1110 | except: |
| 1095 | _log.exception('cannot remove data import script module [%s], hoping for the best', import_script) | |
| 1111 | _log.exception(u'cannot remove data import script module [%s], hoping for the best', import_script) | |
| 1096 | 1112 | |
| 1097 | 1113 | return True |
| 1098 | 1114 | |
| 1104 | 1120 | target_version = cfg_get(self.section, 'target version') |
| 1105 | 1121 | if target_version == 'devel': |
| 1106 | 1122 | print_msg(" ... skipped (devel version)") |
| 1107 | _log.info('result schema hash: %s', gmPG2.get_schema_hash(link_obj = self.conn)) | |
| 1123 | _log.info(u'result schema hash: %s', gmPG2.get_schema_hash(link_obj = self.conn)) | |
| 1108 | 1124 | _log.warning('testing/development only, not failing due to invalid target database identity hash') |
| 1109 | 1125 | return True |
| 1110 | 1126 | converted, version = gmTools.input2int(target_version.lstrip('v'), 2) |
| 1111 | 1127 | if not converted: |
| 1112 | _log.error('cannot convert target database version: %s', target_version) | |
| 1128 | _log.error(u'cannot convert target database version: %s', target_version) | |
| 1113 | 1129 | print_msg(" ... failed (invalid target version specification)") |
| 1114 | 1130 | return False |
| 1115 | 1131 | if gmPG2.database_schema_compatible(link_obj = self.conn, version = version): |
| 1116 | _log.info('database identity hash properly verified') | |
| 1132 | _log.info(u'database identity hash properly verified') | |
| 1117 | 1133 | return True |
| 1118 | _log.error('target database identity hash invalid') | |
| 1134 | _log.error(u'target database identity hash invalid') | |
| 1119 | 1135 | print_msg(" ... failed (hash mismatch)") |
| 1120 | 1136 | return False |
| 1121 | 1137 | |
| 1134 | 1150 | print_msg(" ... skipped") |
| 1135 | 1151 | return True |
| 1136 | 1152 | |
| 1137 | _log.info('REINDEXing cloned target database so upgrade does not fail in case of a broken index') | |
| 1138 | _log.info('this may potentially take "quite a long time" depending on how much data there is in the database') | |
| 1139 | _log.info('you may want to monitor the PostgreSQL log for signs of progress') | |
| 1153 | _log.info(u'REINDEXing cloned target database so upgrade does not fail in case of a broken index') | |
| 1154 | _log.info(u'this may potentially take "quite a long time" depending on how much data there is in the database') | |
| 1155 | _log.info(u'you may want to monitor the PostgreSQL log for signs of progress') | |
| 1140 | 1156 | |
| 1141 | 1157 | self.conn.commit() |
| 1142 | 1158 | self.conn.set_session(readonly = False, autocommit = True) |
| 1146 | 1162 | try: |
| 1147 | 1163 | curs_outer.execute(cmd) |
| 1148 | 1164 | except: |
| 1149 | _log.exception(">>>[%s]<<< failed" % cmd) | |
| 1165 | _log.exception(u">>>[%s]<<< failed" % cmd) | |
| 1150 | 1166 | # re-attempt w/o VERBOSE |
| 1151 | _log.info('attempting REINDEXing without VERBOSE') | |
| 1167 | _log.info(u'attempting REINDEXing without VERBOSE') | |
| 1152 | 1168 | curs_inner = self.conn.cursor() |
| 1153 | 1169 | cmd = 'REINDEX DATABASE %s' % self.name |
| 1154 | 1170 | try: |
| 1155 | 1171 | curs_inner.execute(cmd) |
| 1156 | 1172 | except: |
| 1157 | _log.exception(">>>[%s]<<< failed" % cmd) | |
| 1173 | _log.exception(u">>>[%s]<<< failed" % cmd) | |
| 1158 | 1174 | return False |
| 1159 | 1175 | finally: |
| 1160 | 1176 | curs_inner.close() |
| 1170 | 1186 | print_msg("==> transferring users ...") |
| 1171 | 1187 | do_user_transfer = cfg_get(self.section, 'transfer users') |
| 1172 | 1188 | if do_user_transfer is None: |
| 1173 | _log.info('user transfer not defined') | |
| 1189 | _log.info(u'user transfer not defined') | |
| 1174 | 1190 | print_msg(" ... skipped (unconfigured)") |
| 1175 | 1191 | return True |
| 1176 | 1192 | do_user_transfer = int(do_user_transfer) |
| 1177 | 1193 | if not do_user_transfer: |
| 1178 | _log.info('configured to not transfer users') | |
| 1194 | _log.info(u'configured to not transfer users') | |
| 1179 | 1195 | print_msg(" ... skipped (disabled)") |
| 1180 | 1196 | return True |
| 1181 | 1197 | |
| 1184 | 1200 | rows, idx = gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}], end_tx = True, return_data = True) |
| 1185 | 1201 | except gmPG2.dbapi.ProgrammingError: |
| 1186 | 1202 | # maybe an old database |
| 1187 | _log.info('problem running gm.transfer_users(), trying gm_transfer_users()') | |
| 1203 | _log.info(u'problem running gm.transfer_users(), trying gm_transfer_users()') | |
| 1188 | 1204 | cmd = u"select gm_transfer_users('%s'::text)" % self.template_db |
| 1189 | 1205 | rows, idx = gmPG2.run_rw_queries(link_obj = self.conn, queries = [{'cmd': cmd}], end_tx = True, return_data = True) |
| 1190 | 1206 | |
| 1191 | 1207 | if rows[0][0]: |
| 1192 | _log.info('users properly transferred from [%s] to [%s]' % (self.template_db, self.name)) | |
| 1208 | _log.info(u'users properly transferred from [%s] to [%s]' % (self.template_db, self.name)) | |
| 1193 | 1209 | return True |
| 1194 | _log.error('error transferring user from [%s] to [%s]' % (self.template_db, self.name)) | |
| 1210 | _log.error(u'error transferring user from [%s] to [%s]' % (self.template_db, self.name)) | |
| 1195 | 1211 | print_msg(" ... failed") |
| 1196 | 1212 | return False |
| 1197 | 1213 | |
| 1227 | 1243 | audit_schema = gmAuditSchemaGenerator.create_audit_ddl(curs) |
| 1228 | 1244 | curs.close() |
| 1229 | 1245 | if audit_schema is None: |
| 1230 | _log.error('cannot generate audit trail schema for GNUmed database [%s]' % self.name) | |
| 1246 | _log.error(u'cannot generate audit trail schema for GNUmed database [%s]' % self.name) | |
| 1231 | 1247 | return None |
| 1232 | 1248 | # write schema to file |
| 1233 | 1249 | tmpfile = os.path.join(tempfile.gettempdir(), 'audit-trail-schema.sql') |
| 1239 | 1255 | # import auditing schema |
| 1240 | 1256 | psql = gmPsql.Psql(self.conn) |
| 1241 | 1257 | if psql.run(tmpfile) != 0: |
| 1242 | _log.error("cannot import audit schema definition for database [%s]" % (self.name)) | |
| 1258 | _log.error(u"cannot import audit schema definition for database [%s]" % (self.name)) | |
| 1243 | 1259 | return None |
| 1244 | 1260 | |
| 1245 | 1261 | if _keep_temp_files: |
| 1248 | 1264 | try: |
| 1249 | 1265 | os.remove(tmpfile) |
| 1250 | 1266 | except Exception: |
| 1251 | _log.exception('cannot remove audit trail schema file [%s]' % tmpfile) | |
| 1267 | _log.exception(u'cannot remove audit trail schema file [%s]' % tmpfile) | |
| 1252 | 1268 | return True |
| 1253 | 1269 | |
| 1254 | 1270 | #-------------------------------------------------------------- |
| 1257 | 1273 | # setup clin.clin_root_item child tables FK's |
| 1258 | 1274 | print_msg("==> setting up encounter/episode FKs and IDXs ...") |
| 1259 | 1275 | child_tables = gmPG2.get_child_tables(link_obj = self.conn, schema = 'clin', table = 'clin_root_item') |
| 1260 | _log.info('clin.clin_root_item child tables:') | |
| 1276 | _log.info(u'clin.clin_root_item child tables:') | |
| 1261 | 1277 | for child in child_tables: |
| 1262 | _log.info('%s.%s', child['namespace'], child['table']) | |
| 1278 | _log.info(u'%s.%s', child['namespace'], child['table']) | |
| 1263 | 1279 | for child in child_tables: |
| 1264 | 1280 | # .fk_episode |
| 1265 | 1281 | FKs = gmPG2.get_foreign_key_names ( |
| 1272 | 1288 | target_column = 'pk', |
| 1273 | 1289 | ) |
| 1274 | 1290 | if len(FKs) > 0: |
| 1275 | _log.info('%s FK(s) exist:', len(FKs)) | |
| 1291 | _log.info(u'%s FK(s) exist:', len(FKs)) | |
| 1276 | 1292 | for idx in range(len(FKs)): |
| 1277 | 1293 | FK = FKs[idx] |
| 1278 | 1294 | _log.info(u' #%s = %s.%s: %s.%s.%s -> %s.%s.%s', idx + 1, FK['constraint_schema'], FK['constraint_name'], FK['source_schema'], FK['source_table'], FK['source_column'], FK['target_schema'], FK['target_table'], FK['target_column']) |
| 1279 | 1295 | else: |
| 1280 | _log.info('adding FK: %s.%s.fk_episode -> clin.episode.pk', child['namespace'], child['table']) | |
| 1296 | _log.info(u'adding FK: %s.%s.fk_episode -> clin.episode.pk', child['namespace'], child['table']) | |
| 1281 | 1297 | cmd = SQL_add_foreign_key % { |
| 1282 | 1298 | 'src_schema': child['namespace'], |
| 1283 | 1299 | 'src_tbl': child['table'], |
| 1315 | 1331 | target_column = 'pk' |
| 1316 | 1332 | ) |
| 1317 | 1333 | if len(FKs) > 0: |
| 1318 | _log.info('%s FK(s) exist:', len(FKs)) | |
| 1334 | _log.info(u'%s FK(s) exist:', len(FKs)) | |
| 1319 | 1335 | for idx in range(len(FKs)): |
| 1320 | 1336 | FK = FKs[idx] |
| 1321 | 1337 | _log.info(u' #%s = %s.%s: %s.%s.%s -> %s.%s.%s', idx + 1, FK['constraint_schema'], FK['constraint_name'], FK['source_schema'], FK['source_table'], FK['source_column'], FK['target_schema'], FK['target_table'], FK['target_column']) |
| 1322 | 1338 | else: |
| 1323 | _log.info('adding FK: %s.%s.fk_encounter -> clin.encounter.pk', child['namespace'], child['table']) | |
| 1339 | _log.info(u'adding FK: %s.%s.fk_encounter -> clin.encounter.pk', child['namespace'], child['table']) | |
| 1324 | 1340 | cmd = SQL_add_foreign_key % { |
| 1325 | 1341 | 'src_schema': child['namespace'], |
| 1326 | 1342 | 'src_tbl': child['table'], |
| 1352 | 1368 | # re-create fk_encounter/fk_episode sanity check triggers on all tables |
| 1353 | 1369 | if gmPG2.function_exists(link_obj = curs, schema = u'gm', function = u'create_all_enc_epi_sanity_check_triggers'): |
| 1354 | 1370 | print_msg("==> setting up encounter/episode FK sanity check triggers ...") |
| 1355 | _log.debug('attempting to set up sanity check triggers on all tables linking to encounter AND episode') | |
| 1371 | _log.debug(u'attempting to set up sanity check triggers on all tables linking to encounter AND episode') | |
| 1356 | 1372 | cmd = u'select gm.create_all_enc_epi_sanity_check_triggers()' |
| 1357 | 1373 | curs.execute(cmd) |
| 1358 | 1374 | result = curs.fetchone() |
| 1359 | 1375 | if result[0] is False: |
| 1360 | _log.error('error creating sanity check triggers on all tables linking to clin.encounter AND clin.episode') | |
| 1376 | _log.error(u'error creating sanity check triggers on all tables linking to clin.encounter AND clin.episode') | |
| 1361 | 1377 | curs.close() |
| 1362 | 1378 | return None |
| 1363 | 1379 | |
| 1364 | 1380 | # always re-create generic super signal (if exists) |
| 1365 | 1381 | if gmPG2.function_exists(link_obj = curs, schema = u'gm', function = u'create_all_table_mod_triggers'): |
| 1366 | 1382 | print_msg("==> setting up generic notifications ...") |
| 1367 | _log.debug('attempting to create generic modification announcement triggers on all registered tables') | |
| 1383 | _log.debug(u'attempting to create generic modification announcement triggers on all registered tables') | |
| 1368 | 1384 | |
| 1369 | 1385 | cmd = u"SELECT gm.create_all_table_mod_triggers(True::boolean)" |
| 1370 | 1386 | curs.execute(cmd) |
| 1371 | 1387 | result = curs.fetchone() |
| 1372 | 1388 | curs.close() |
| 1373 | 1389 | if result[0] is False: |
| 1374 | _log.error('cannot create generic modification announcement triggers on all tables') | |
| 1390 | _log.error(u'cannot create generic modification announcement triggers on all tables') | |
| 1375 | 1391 | return None |
| 1376 | 1392 | |
| 1377 | 1393 | self.conn.commit() |
| 1388 | 1404 | self.section = "bundle %s" % aBundleAlias |
| 1389 | 1405 | #-------------------------------------------------------------- |
| 1390 | 1406 | def bootstrap(self): |
| 1391 | _log.info("bootstrapping bundle [%s]" % self.alias) | |
| 1407 | _log.info(u"bootstrapping bundle [%s]" % self.alias) | |
| 1392 | 1408 | |
| 1393 | 1409 | # load bundle definition |
| 1394 | 1410 | database_alias = cfg_get(self.section, "database alias") |
| 1395 | 1411 | if database_alias is None: |
| 1396 | _log.error("Need to know database name to install bundle [%s]." % self.alias) | |
| 1412 | _log.error(u"Need to know database name to install bundle [%s]." % self.alias) | |
| 1397 | 1413 | return None |
| 1398 | 1414 | # bootstrap database |
| 1399 | 1415 | try: |
| 1405 | 1421 | |
| 1406 | 1422 | # check PostgreSQL version |
| 1407 | 1423 | if not self.__verify_pg_version(): |
| 1408 | _log.error("Wrong PostgreSQL version.") | |
| 1424 | _log.error(u"Wrong PostgreSQL version.") | |
| 1409 | 1425 | return None |
| 1410 | 1426 | |
| 1411 | 1427 | # import schema |
| 1412 | 1428 | if not _import_schema(group=self.section, schema_opt='schema', conn=self.db.conn): |
| 1413 | _log.error("Cannot import schema definition for bundle [%s] into database [%s]." % (self.alias, database_alias)) | |
| 1429 | _log.error(u"Cannot import schema definition for bundle [%s] into database [%s]." % (self.alias, database_alias)) | |
| 1414 | 1430 | return None |
| 1415 | 1431 | |
| 1416 | 1432 | return True |
| 1420 | 1436 | |
| 1421 | 1437 | required_version = cfg_get(self.section, "minimum postgresql version") |
| 1422 | 1438 | if required_version is None: |
| 1423 | _log.error("Cannot load minimum required PostgreSQL version from config file.") | |
| 1424 | return None | |
| 1425 | ||
| 1426 | _log.info("minimum required PostgreSQL version: %s" % required_version) | |
| 1439 | _log.error(u"Cannot load minimum required PostgreSQL version from config file.") | |
| 1440 | return None | |
| 1441 | ||
| 1442 | _log.info(u"minimum required PostgreSQL version: %s" % required_version) | |
| 1427 | 1443 | |
| 1428 | 1444 | converted, pg_ver = gmTools.input2decimal(gmPG2.postgresql_version) |
| 1429 | 1445 | if not converted: |
| 1430 | _log.error('error checking PostgreSQL version') | |
| 1446 | _log.error(u'error checking PostgreSQL version') | |
| 1431 | 1447 | return None |
| 1432 | 1448 | converted, req_version = gmTools.input2decimal(required_version) |
| 1433 | 1449 | if not converted: |
| 1434 | _log.error('error checking PostgreSQL version') | |
| 1435 | _log.error('required: %s', required_version) | |
| 1450 | _log.error(u'error checking PostgreSQL version') | |
| 1451 | _log.error(u'required: %s', required_version) | |
| 1436 | 1452 | return None |
| 1437 | 1453 | if pg_ver < req_version: |
| 1438 | _log.error("Reported live PostgreSQL version [%s] is smaller than the required minimum version [%s]." % (gmPG2.postgresql_version, required_version)) | |
| 1439 | return None | |
| 1440 | ||
| 1441 | _log.info("installed PostgreSQL version: %s - this is fine with me" % gmPG2.postgresql_version) | |
| 1454 | _log.error(u"Reported live PostgreSQL version [%s] is smaller than the required minimum version [%s]." % (gmPG2.postgresql_version, required_version)) | |
| 1455 | return None | |
| 1456 | ||
| 1457 | _log.info(u"installed PostgreSQL version: %s - this is fine with me" % gmPG2.postgresql_version) | |
| 1442 | 1458 | return True |
| 1443 | 1459 | #================================================================== |
| 1444 | 1460 | def bootstrap_bundles(): |
| 1483 | 1499 | try: |
| 1484 | 1500 | aCurs.execute(aQuery) |
| 1485 | 1501 | except: |
| 1486 | _log.exception(">>>%s<<< failed" % aQuery) | |
| 1502 | _log.exception(u">>>%s<<< failed" % aQuery) | |
| 1487 | 1503 | return False |
| 1488 | 1504 | else: |
| 1489 | 1505 | try: |
| 1490 | 1506 | aCurs.execute(aQuery, args) |
| 1491 | 1507 | except: |
| 1492 | _log.exception(">>>%s<<< failed" % aQuery) | |
| 1508 | _log.exception(u">>>%s<<< failed" % aQuery) | |
| 1493 | 1509 | _log.error(str(args)) |
| 1494 | 1510 | return False |
| 1495 | 1511 | return True |
| 1512 | ||
| 1496 | 1513 | #------------------------------------------------------------------ |
| 1497 | 1514 | def ask_for_confirmation(): |
| 1498 | 1515 | bundles = cfg_get("installation", "bundles") |
| 1500 | 1517 | return True |
| 1501 | 1518 | if len(bundles) == 0: |
| 1502 | 1519 | return True |
| 1520 | ||
| 1503 | 1521 | if not _interactive: |
| 1504 | 1522 | print_msg("You are about to install the following parts of GNUmed:") |
| 1505 | 1523 | print_msg("-------------------------------------------------------") |
| 1514 | 1532 | if desc is not None: |
| 1515 | 1533 | for line in desc: |
| 1516 | 1534 | print_msg(line) |
| 1517 | else: | |
| 1518 | print "You are about to install the following parts of GNUmed:" | |
| 1519 | print "-------------------------------------------------------" | |
| 1520 | for bundle in bundles: | |
| 1521 | db_alias = cfg_get("bundle %s" % bundle, "database alias") | |
| 1522 | db_name = cfg_get("database %s" % db_alias, "name") | |
| 1523 | srv_alias = cfg_get("database %s" % db_alias, "server alias") | |
| 1524 | srv_name = cfg_get("server %s" % srv_alias, "name") | |
| 1525 | print 'bundle "%s" in <%s> (or overridden) on <%s>' % (bundle, db_name, srv_name) | |
| 1526 | print "-------------------------------------------------------" | |
| 1527 | desc = cfg_get("installation", "description") | |
| 1528 | if desc is not None: | |
| 1529 | for line in desc: | |
| 1530 | print line | |
| 1531 | ||
| 1532 | print "Do you really want to install this database setup ?" | |
| 1533 | answer = raw_input("Type yes or no: ") | |
| 1534 | if answer == "yes": | |
| 1535 | return True | |
| 1536 | else: | |
| 1537 | return None | |
| 1538 | return True | |
| 1535 | return True | |
| 1536 | ||
| 1537 | print "You are about to install the following parts of GNUmed:" | |
| 1538 | print "-------------------------------------------------------" | |
| 1539 | for bundle in bundles: | |
| 1540 | db_alias = cfg_get("bundle %s" % bundle, "database alias") | |
| 1541 | db_name = cfg_get("database %s" % db_alias, "name") | |
| 1542 | srv_alias = cfg_get("database %s" % db_alias, "server alias") | |
| 1543 | srv_name = cfg_get("server %s" % srv_alias, "name") | |
| 1544 | print 'bundle "%s" in <%s> (or overridden) on <%s>' % (bundle, db_name, srv_name) | |
| 1545 | print "-------------------------------------------------------" | |
| 1546 | desc = cfg_get("installation", "description") | |
| 1547 | if desc is not None: | |
| 1548 | for line in desc: | |
| 1549 | print line | |
| 1550 | ||
| 1551 | print "Do you really want to install this database setup ?" | |
| 1552 | answer = raw_input("Type yes or no: ") | |
| 1553 | if answer == "yes": | |
| 1554 | return True | |
| 1555 | return None | |
| 1539 | 1556 | |
| 1540 | 1557 | #-------------------------------------------------------------- |
| 1541 | 1558 | def _import_schema (group=None, schema_opt="schema", conn=None): |
| 1542 | 1559 | # load schema |
| 1543 | 1560 | schema_files = cfg_get(group, schema_opt) |
| 1544 | 1561 | if schema_files is None: |
| 1545 | _log.error("Need to know schema definition to install it.") | |
| 1562 | _log.error(u"Need to know schema definition to install it.") | |
| 1546 | 1563 | return None |
| 1547 | 1564 | |
| 1548 | 1565 | schema_base_dir = cfg_get(group, "schema base directory") |
| 1568 | 1585 | continue |
| 1569 | 1586 | full_path = os.path.join(schema_base_dir, filename) |
| 1570 | 1587 | if psql.run(full_path) == 0: |
| 1571 | #_log.info('success') | |
| 1588 | #_log.info(u'success') | |
| 1572 | 1589 | continue |
| 1573 | 1590 | _log.error(u'failure') |
| 1574 | 1591 | return None |
| 1585 | 1602 | print ' ', gmLog2._logfile_name |
| 1586 | 1603 | print '' |
| 1587 | 1604 | |
| 1588 | _log.error(aMsg) | |
| 1589 | _log.info("shutdown") | |
| 1605 | _log.error(unicode(aMsg, errors = 'replace')) | |
| 1606 | _log.info(u'shutdown') | |
| 1590 | 1607 | sys.exit(1) |
| 1608 | ||
| 1591 | 1609 | #------------------------------------------------------------------ |
| 1592 | 1610 | def print_msg(msg=None): |
| 1593 | 1611 | if quiet: |
| 1594 | 1612 | return |
| 1595 | 1613 | print msg |
| 1614 | ||
| 1596 | 1615 | #----------------------------------------------------------------- |
| 1597 | 1616 | def become_pg_demon_user(): |
| 1598 | 1617 | """Become "postgres" user. |
| 1614 | 1633 | |
| 1615 | 1634 | try: |
| 1616 | 1635 | running_as = pwd.getpwuid(os.getuid())[0] |
| 1617 | _log.info('running as user [%s]' % running_as) | |
| 1636 | _log.info(u'running as user [%s]' % running_as) | |
| 1618 | 1637 | except: |
| 1619 | 1638 | running_as = None |
| 1620 | 1639 | |
| 1634 | 1653 | return None |
| 1635 | 1654 | |
| 1636 | 1655 | if os.getuid() == 0: # we are the super-user |
| 1637 | _log.info('switching to UNIX user [%s]' % pg_demon_user_passwd_line[0]) | |
| 1656 | _log.info(u'switching to UNIX user [%s]' % pg_demon_user_passwd_line[0]) | |
| 1638 | 1657 | os.setuid(pg_demon_user_passwd_line[2]) |
| 1639 | 1658 | gmPG2.log_auth_environment() |
| 1640 | 1659 | |
| 1641 | 1660 | elif running_as == pg_demon_user_passwd_line[0]: # we are the postgres user already |
| 1642 | _log.info('I already am the UNIX user [%s]' % pg_demon_user_passwd_line[0]) | |
| 1661 | _log.info(u'I already am the UNIX user [%s]' % pg_demon_user_passwd_line[0]) | |
| 1643 | 1662 | |
| 1644 | 1663 | else: |
| 1645 | 1664 | _log.warning('not running as root or postgres, cannot become postmaster demon user') |
| 1646 | 1665 | _log.warning('may have trouble connecting as gm-dbo if IDENT auth is forced upon us') |
| 1647 | 1666 | if _interactive: |
| 1648 | 1667 | print_msg("WARNING: This script may not work if not running as the system administrator.") |
| 1668 | ||
| 1649 | 1669 | #============================================================================== |
| 1650 | 1670 | def cfg_get(group=None, option=None): |
| 1651 | 1671 | return _cfg.get ( |
| 1653 | 1673 | option = option, |
| 1654 | 1674 | source_order = [('file', 'return')] |
| 1655 | 1675 | ) |
| 1676 | ||
| 1656 | 1677 | #================================================================== |
| 1657 | 1678 | def handle_cfg(): |
| 1658 | 1679 | """Bootstrap the source 'file' in _cfg.""" |
| 1659 | 1680 | |
| 1660 | _log.info('config file: %s', _cfg.source_files['file']) | |
| 1681 | _log.info(u'config file: %s', _cfg.source_files['file']) | |
| 1661 | 1682 | |
| 1662 | 1683 | become_pg_demon_user() |
| 1663 | 1684 | |
| 1664 | tmp = cfg_get("installation", "interactive") | |
| 1665 | 1685 | global _interactive |
| 1666 | if tmp == "yes": | |
| 1667 | _interactive = True | |
| 1668 | elif tmp == "no": | |
| 1669 | _interactive = False | |
| 1686 | ||
| 1687 | if _interactive is None: | |
| 1688 | tmp = cfg_get("installation", "interactive") | |
| 1689 | if tmp == "no": | |
| 1690 | _interactive = False | |
| 1691 | else: | |
| 1692 | _interactive = True | |
| 1670 | 1693 | |
| 1671 | 1694 | tmp = cfg_get('installation', 'keep temp files') |
| 1672 | 1695 | if tmp == "yes": |
| 1703 | 1726 | # get initial conf file from CLI |
| 1704 | 1727 | cfg_file = _cfg.get(option = '--conf-file', source_order = [('cli', 'return')]) |
| 1705 | 1728 | if cfg_file is None: |
| 1706 | _log.error("no config file specified on command line") | |
| 1729 | _log.error(u"no config file specified on command line") | |
| 1707 | 1730 | exit_with_msg('Cannot bootstrap without config file. Use --conf-file=<FILE>.') |
| 1708 | 1731 | |
| 1709 | _log.info('initial config file: %s', cfg_file) | |
| 1732 | _log.info(u'initial config file: %s', cfg_file) | |
| 1710 | 1733 | |
| 1711 | 1734 | # read that conf file |
| 1712 | 1735 | _cfg.add_file_source ( |
| 1722 | 1745 | ) |
| 1723 | 1746 | |
| 1724 | 1747 | if cfg_files is None: |
| 1725 | _log.info('single-shot config file') | |
| 1748 | _log.info(u'single-shot config file') | |
| 1726 | 1749 | handle_cfg() |
| 1727 | 1750 | else: |
| 1728 | _log.info('aggregation of config files') | |
| 1751 | _log.info(u'aggregation of config files') | |
| 1752 | tmp = cfg_get("installation", "interactive") | |
| 1753 | global _interactive | |
| 1754 | if tmp == "no": | |
| 1755 | _interactive = False | |
| 1756 | else: | |
| 1757 | _interactive = True | |
| 1729 | 1758 | for cfg_file in cfg_files: |
| 1730 | 1759 | # read that conf file |
| 1731 | 1760 | _cfg.add_file_source ( |
| 1749 | 1778 | |
| 1750 | 1779 | db.check_holy_auth_line() |
| 1751 | 1780 | |
| 1781 | _log.info(u"shutdown") | |
| 1782 | print("Done bootstrapping GNUmed database: We very likely succeeded.") | |
| 1783 | print 'log:', gmLog2._logfile_name | |
| 1784 | ||
| 1785 | #================================================================== | |
| 1786 | if __name__ != "__main__": | |
| 1787 | print "This currently is not intended to be used as a module." | |
| 1788 | sys.exit(1) | |
| 1789 | ||
| 1790 | ||
| 1791 | gmI18N.activate_locale() | |
| 1792 | gmLog2.set_string_encoding() | |
| 1793 | ||
| 1794 | _log.info(u'startup') | |
| 1795 | ||
| 1796 | try: | |
| 1797 | main() | |
| 1798 | except StandardError: | |
| 1799 | _log.exception(u'unhandled exception caught, shutting down connections') | |
| 1800 | exit_with_msg(u'Bootstrapping failed: unhandled exception occurred') | |
| 1801 | finally: | |
| 1752 | 1802 | for conn in conn_ref_count: |
| 1753 | 1803 | if conn.closed == 0: |
| 1754 | _log.warning('open connection detected: %s', conn.cookie) | |
| 1755 | _log.warning('%s', conn) | |
| 1756 | _log.warning('closing connection') | |
| 1804 | _log.warning(u'open connection detected: %s', conn.cookie) | |
| 1805 | _log.warning(u'%s', conn) | |
| 1806 | _log.warning(u'closing connection') | |
| 1757 | 1807 | conn.close() |
| 1758 | ||
| 1759 | _log.info("shutdown") | |
| 1760 | print("Done bootstrapping GNUmed database: We very likely succeeded.") | |
| 1761 | print 'log:', gmLog2._logfile_name | |
| 1762 | ||
| 1763 | #================================================================== | |
| 1764 | if __name__ == "__main__": | |
| 1765 | ||
| 1766 | gmI18N.activate_locale() | |
| 1767 | gmLog2.set_string_encoding() | |
| 1768 | ||
| 1769 | _log.info("startup") | |
| 1770 | ||
| 1771 | try: | |
| 1772 | main() | |
| 1773 | except Exception: | |
| 1774 | for c in conn_ref_count: | |
| 1775 | if c.closed == 0: | |
| 1776 | print 'closing open connection from:', c.cookie | |
| 1777 | print c | |
| 1778 | c.close() | |
| 1779 | _log.exception('unhandled exception caught') | |
| 1780 | exit_with_msg("Bootstrapping failed: unhandled exception occurred") | |
| 1781 | ||
| 1782 | sys.exit(0) | |
| 1783 | else: | |
| 1784 | print "This currently is not intended to be used as a module." | |
| 1785 | sys.exit(1) | |
| 1808 | del conn | |
| 1809 | del conn_ref_count | |
| 1810 | ||
| 1811 | _log.info(u'after main, before sys.exit(0)') | |
| 1812 | ||
| 1813 | sys.exit(0) | |
| 1814 | ||
| 1786 | 1815 | |
| 1787 | 1816 | #================================================================== |
| 1788 | 1817 | # pipe = popen2.Popen3(cmd, 1==1) |
| 1799 | 1828 | # tmp = pipe.fromchild.read() |
| 1800 | 1829 | # lines = tmp.split("\n") |
| 1801 | 1830 | # for line in lines: |
| 1802 | # _log.debug("child stdout: [%s]" % line, gmLog.lCooked) | |
| 1831 | # _log.debug(u"child stdout: [%s]" % line, gmLog.lCooked) | |
| 1803 | 1832 | # tmp = pipe.childerr.read() |
| 1804 | 1833 | # lines = tmp.split("\n") |
| 1805 | 1834 | # for line in lines: |
| 1806 | # _log.error("child stderr: [%s]" % line, gmLog.lCooked) | |
| 1835 | # _log.error(u"child stderr: [%s]" % line, gmLog.lCooked) | |
| 1807 | 1836 | |
| 1808 | 1837 | # pipe.fromchild.close() |
| 1809 | 1838 | # pipe.childerr.close() |
| 1810 | 1839 | # del pipe |
| 1811 | 1840 | |
| 1812 | 1841 | #================================================================== |
| 1813 | ||
| 26 | 26 | minimum postgresql version = 9.2 |
| 27 | 27 | schema base directory = ../sql/v20-v21/fixups/ |
| 28 | 28 | schema = $schema$ |
| 29 | v21-db-sql_inheritance-fixup.sql | |
| 30 | v21-audit-add_table_for_audit-fixup.sql | |
| 31 | v21-i18n-lang_funcs-fixup.sql | |
| 29 | 32 | v21-previously-missing-array_agg-fixup.sql |
| 30 | 33 | v21-dem-view_grants-fixup.sql |
| 31 | 34 | ../dynamic/v21-release_notes-dynamic.sql |
| 37 | 40 | v21-ref-auto_hint-smoking_status-fixup.sql |
| 38 | 41 | v21-ref-GKV_CU-fixup.sql |
| 39 | 42 | v21-clin-get_hints_for_patient-fixup.sql |
| 43 | v21-clin-v_substance_intakes-fixup.sql | |
| 40 | 44 | v21-notifications-dynamic.sql |
| 41 | 45 | v21-clin-uppercase_soap_cat-fixup.sql |
| 42 | 46 | v21-dem-identity-fixup.sql |
| 118 | 118 | minimum postgresql version = 9.2 |
| 119 | 119 | schema base directory = ../sql/v20-v21/fixups/ |
| 120 | 120 | schema = $schema$ |
| 121 | v21-db-sql_inheritance-fixup.sql | |
| 122 | v21-audit-add_table_for_audit-fixup.sql | |
| 123 | v21-i18n-lang_funcs-fixup.sql | |
| 121 | 124 | v21-previously-missing-array_agg-fixup.sql |
| 122 | 125 | v21-dem-view_grants-fixup.sql |
| 123 | 126 | v21-ref-auto_hint-tetanus_STIKO.sql |
| 128 | 131 | v21-ref-auto_hint-smoking_status-fixup.sql |
| 129 | 132 | v21-ref-GKV_CU-fixup.sql |
| 130 | 133 | v21-clin-get_hints_for_patient-fixup.sql |
| 134 | v21-clin-v_substance_intakes-fixup.sql | |
| 131 | 135 | v21-notifications-dynamic.sql |
| 132 | 136 | v21-clin-uppercase_soap_cat-fixup.sql |
| 133 | 137 | v21-dem-identity-fixup.sql |
| 111 | 111 | <body> |
| 112 | 112 | |
| 113 | 113 | <!-- Primary Index --> |
| 114 | <p><br><br>Dumped on 2017-08-31</p> | |
| 114 | <p><br><br>Dumped on 2017-10-28</p> | |
| 115 | 115 | <h1><a name="index">Index of database - gnumed_v21</a></h1> |
| 116 | 116 | <ul> |
| 117 | 117 |
| 50 | 50 | echo "alter database ${TARGET_DB} set lc_messages to 'C';" >> $SQL_FILE |
| 51 | 51 | echo "alter database ${TARGET_DB} set password_encryption to 'on';" >> $SQL_FILE |
| 52 | 52 | echo "alter database ${TARGET_DB} set synchronous_commit to 'on';" >> $SQL_FILE |
| 53 | echo "alter database ${TARGET_DB} set sql_inheritance to 'on';" >> $SQL_FILE | |
| 54 | 53 | echo "alter database ${TARGET_DB} set check_function_bodies to 'on';" >> $SQL_FILE |
| 54 | echo "-- starting with 9.3:" >> $SQL_FILE | |
| 55 | echo "alter database ${TARGET_DB} set ignore_checksum_failure to 'off';" >> $SQL_FILE | |
| 56 | ||
| 55 | 57 | echo "" >> $SQL_FILE |
| 56 | echo "-- starting with 9.3 (remove when 9.3 is required):" >> $SQL_FILE | |
| 57 | echo "\unset ON_ERROR_STOP" >> $SQL_FILE | |
| 58 | echo "alter database ${TARGET_DB} set ignore_checksum_failure to 'off'; -- comment out if the script fails" >> $SQL_FILE | |
| 59 | echo "\set ON_ERROR_STOP 1" >> $SQL_FILE | |
| 60 | echo "" >> $SQL_FILE | |
| 61 | echo "-- < PG 9.0 only:" >> $SQL_FILE | |
| 62 | echo "--\unset ON_ERROR_STOP" >> $SQL_FILE | |
| 63 | echo "--alter database ${TARGET_DB} set regex_flavor to 'advanced';" >> $SQL_FILE | |
| 64 | echo "--\set ON_ERROR_STOP 1" >> $SQL_FILE | |
| 58 | echo "-- PG < 10 only:" >> $SQL_FILE | |
| 59 | echo "--alter database ${TARGET_DB} set sql_inheritance to 'on';" >> $SQL_FILE | |
| 65 | 60 | |
| 66 | 61 | echo "" >> $SQL_FILE |
| 67 | 62 | echo "-- the following can only be set at server start" >> $SQL_FILE |
| 45 | 45 | if (prop == 'mimetype') and (val != worst_case): |
| 46 | 46 | return val |
| 47 | 47 | except ImportError: |
| 48 | _log.debug('module <extractor> (python wrapper for libextractor) not installed') | |
| 49 | ||
| 48 | _log.debug(u'module <extractor> (python wrapper for libextractor) not installed') | |
| 49 | except OSError as exc: | |
| 50 | # winerror 126, errno 22 | |
| 51 | if exc.errno == 22: | |
| 52 | _log.exception(u'module <extractor> (python wrapper for libextractor) not installed') | |
| 53 | else: | |
| 54 | raise | |
| 50 | 55 | ret_code = -1 |
| 51 | 56 | |
| 52 | 57 | # 2) use "file" system command |
| 384 | 389 | |
| 385 | 390 | #_get_system_startfile_cmd(filename) |
| 386 | 391 | #print(_system_startfile_cmd) |
| 387 | #print(guess_mimetype(filename)) | |
| 392 | print(guess_mimetype(filename)) | |
| 388 | 393 | #print(get_viewer_cmd(guess_mimetype(filename), filename)) |
| 389 | 394 | #print(guess_ext_by_mimetype(mimetype=filename)) |
| 390 | 395 | #call_viewer_on_file(aFile = filename, block=None) |
| 391 | status, desc = describe_file(filename) | |
| 392 | print status | |
| 393 | print desc | |
| 396 | ||
| 397 | #status, desc = describe_file(filename) | |
| 398 | #print status | |
| 399 | #print desc | |
| 1548 | 1548 | conn_status = u'%s (%s)' % (conn.status, map_psyco_conn_status2str[conn.status]) |
| 1549 | 1549 | if conn.closed != 0: |
| 1550 | 1550 | conn_status = u'undefined (%s)' % conn_status |
| 1551 | try: | |
| 1552 | conn_deferrable = conn.deferrable | |
| 1553 | except AttributeError: | |
| 1554 | conn_deferrable = u'unavailable' | |
| 1551 | 1555 | |
| 1552 | 1556 | d = { |
| 1553 | 1557 | u'identity': id(conn), |
| 1559 | 1563 | u'autocommit': conn.autocommit, |
| 1560 | 1564 | u'isolation level (psyco)': isolation_level, |
| 1561 | 1565 | u'async': conn.async, |
| 1562 | u'deferrable': conn.deferrable, | |
| 1566 | u'deferrable': conn_deferrable, | |
| 1563 | 1567 | u'transaction status': u'%s (%s)' % (tx_status, map_psyco_tx_status2str[tx_status]), |
| 1564 | 1568 | u'connection status': conn_status, |
| 1565 | 1569 | u'executing async op': conn.isexecuting(), |
| 1596 | 1600 | isolation_level = u'tx aborted or unknown, cannot retrieve' |
| 1597 | 1601 | else: |
| 1598 | 1602 | isolation_level = conn.isolation_level |
| 1603 | try: | |
| 1604 | conn_deferrable = conn.deferrable | |
| 1605 | except AttributeError: | |
| 1606 | conn_deferrable = u'unavailable' | |
| 1599 | 1607 | |
| 1600 | 1608 | if cursor.query is None: |
| 1601 | 1609 | query = u'<no query>' |
| 1637 | 1645 | isolation_level, |
| 1638 | 1646 | conn.encoding, |
| 1639 | 1647 | conn.async, |
| 1640 | conn.deferrable, | |
| 1648 | conn_deferrable, | |
| 1641 | 1649 | conn.readonly, |
| 1642 | 1650 | map_psyco_tx_status2str[tx_status], |
| 1643 | 1651 | map_psyco_conn_status2str[conn.status], |
| 1852 | 1860 | if verbose: |
| 1853 | 1861 | _log.debug(capture_cursor_state(curs)) |
| 1854 | 1862 | for notice in notices_accessor.notices: |
| 1855 | _log.debug(notice.strip(u'\n').strip(u'\r')) | |
| 1863 | _log.debug(unicode(notice, 'utf8', 'replace').strip(u'\n').strip(u'\r')) | |
| 1856 | 1864 | del notices_accessor.notices[:] |
| 1857 | 1865 | # DB related exceptions |
| 1858 | 1866 | except dbapi.Error as pg_exc: |
| 1867 | 1875 | continue |
| 1868 | 1876 | _log.error(u'PG diags %s: %s', prop, val) |
| 1869 | 1877 | for notice in notices_accessor.notices: |
| 1870 | _log.error(notice.strip(u'\n').strip(u'\r')) | |
| 1878 | _log.error(unicode(notice, 'utf8', 'replace').strip(u'\n').strip(u'\r')) | |
| 1871 | 1879 | del notices_accessor.notices[:] |
| 1872 | 1880 | pg_exc = make_pg_exception_fields_unicode(pg_exc) |
| 1873 | 1881 | _log.error(u'PG error code: %s', pg_exc.pgcode) |
| 1911 | 1919 | _log.exception('error running query in RW connection') |
| 1912 | 1920 | _log.error(capture_cursor_state(curs)) |
| 1913 | 1921 | for notice in notices_accessor.notices: |
| 1914 | _log.debug(notice.strip(u'\n').strip(u'\r')) | |
| 1922 | _log.debug(unicode(notice, 'utf8', 'replace').strip(u'\n').strip(u'\r')) | |
| 1915 | 1923 | del notices_accessor.notices[:] |
| 1916 | 1924 | gmLog2.log_stack_trace() |
| 1917 | 1925 | try: |
| 2288 | 2296 | |
| 2289 | 2297 | options2check = { |
| 2290 | 2298 | # setting: [expected value, risk, fatal?] |
| 2291 | u'allow_system_table_mods': [u'off', u'system breakage', False], | |
| 2292 | u'check_function_bodies': [u'on', u'suboptimal error detection', False], | |
| 2293 | u'datestyle': [u'ISO', u'faulty timestamp parsing', True], | |
| 2294 | u'default_transaction_isolation': [u'read committed', u'faulty database reads', True], | |
| 2295 | u'default_transaction_read_only': [u'on', u'accidental database writes', False], | |
| 2296 | u'fsync': [u'on', u'data loss/corruption', True], | |
| 2297 | u'full_page_writes': [u'on', u'data loss/corruption', False], | |
| 2298 | u'lc_messages': [u'C', u'suboptimal error detection', False], | |
| 2299 | u'password_encryption': [u'on', u'breach of confidentiality', False], | |
| 2300 | #u'regex_flavor': [u'advanced', u'query breakage', False], # 9.0 doesn't support this anymore, default now advanced anyway | |
| 2301 | u'synchronous_commit': [u'on', u'data loss/corruption', False], | |
| 2302 | u'sql_inheritance': [u'on', u'query breakage, data loss/corruption', True], | |
| 2303 | u'ignore_checksum_failure': [u'off', u'data loss/corruption', False], # starting with PG 9.3 | |
| 2304 | u'track_commit_timestamp': [u'on', u'suboptimal auditing', False] # starting with PG 9.3 | |
| 2299 | u'allow_system_table_mods': [[u'off'], u'system breakage', False], | |
| 2300 | u'check_function_bodies': [[u'on'], u'suboptimal error detection', False], | |
| 2301 | u'datestyle': [[u'ISO'], u'faulty timestamp parsing', True], | |
| 2302 | u'default_transaction_isolation': [[u'read committed'], u'faulty database reads', True], | |
| 2303 | u'default_transaction_read_only': [[u'on'], u'accidental database writes', False], | |
| 2304 | u'fsync': [[u'on'], u'data loss/corruption', True], | |
| 2305 | u'full_page_writes': [[u'on'], u'data loss/corruption', False], | |
| 2306 | u'lc_messages': [[u'C'], u'suboptimal error detection', False], | |
| 2307 | u'password_encryption': [[u'on', u'md5', u'scram-sha-256'], u'breach of confidentiality', False], | |
| 2308 | #u'regex_flavor': [[u'advanced'], u'query breakage', False], # 9.0 doesn't support this anymore, default now advanced anyway | |
| 2309 | u'synchronous_commit': [[u'on'], u'data loss/corruption', False], | |
| 2310 | u'sql_inheritance': [[u'on'], u'query breakage, data loss/corruption', True], # IF returned (<PG10): better be ON, if NOT returned (PG10): hardwired | |
| 2311 | u'ignore_checksum_failure': [[u'off'], u'data loss/corruption', False], # starting with PG 9.3 | |
| 2312 | u'track_commit_timestamp': [[u'on'], u'suboptimal auditing', False] # starting with PG 9.3 | |
| 2305 | 2313 | } |
| 2306 | 2314 | |
| 2307 | 2315 | from Gnumed.pycommon import gmCfg2 |
| 2308 | 2316 | _cfg = gmCfg2.gmCfgData() |
| 2309 | 2317 | if _cfg.get(option = u'hipaa'): |
| 2310 | options2check[u'log_connections'] = [u'on', u'non-compliance with HIPAA', True] | |
| 2311 | options2check[u'log_disconnections'] = [u'on', u'non-compliance with HIPAA', True] | |
| 2318 | options2check[u'log_connections'] = [[u'on'], u'non-compliance with HIPAA', True] | |
| 2319 | options2check[u'log_disconnections'] = [[u'on'], u'non-compliance with HIPAA', True] | |
| 2312 | 2320 | else: |
| 2313 | options2check[u'log_connections'] = [u'on', u'non-compliance with HIPAA', None] | |
| 2314 | options2check[u'log_disconnections'] = [u'on', u'non-compliance with HIPAA', None] | |
| 2321 | options2check[u'log_connections'] = [[u'on'], u'non-compliance with HIPAA', None] | |
| 2322 | options2check[u'log_disconnections'] = [[u'on'], u'non-compliance with HIPAA', None] | |
| 2315 | 2323 | |
| 2316 | 2324 | cmd = u"SELECT name, setting from pg_settings where name in %(settings)s" |
| 2317 | 2325 | rows, idx = run_ro_queries ( |
| 2326 | 2334 | for row in rows: |
| 2327 | 2335 | option = row['name'] |
| 2328 | 2336 | value_found = row['setting'] |
| 2329 | value_expected = options2check[option][0] | |
| 2337 | values_expected = options2check[option][0] | |
| 2330 | 2338 | risk = options2check[option][1] |
| 2331 | 2339 | fatal_setting = options2check[option][2] |
| 2332 | if value_found != value_expected: | |
| 2340 | if value_found not in values_expected: | |
| 2333 | 2341 | if fatal_setting is True: |
| 2334 | 2342 | found_error = True |
| 2335 | 2343 | elif fatal_setting is False: |
| 2341 | 2349 | raise ValueError(u'invalid database configuration sanity check') |
| 2342 | 2350 | msg.append(_(' option [%s]: %s') % (option, value_found)) |
| 2343 | 2351 | msg.append(_(' risk: %s') % risk) |
| 2344 | _log.warning('PG option [%s] set to [%s], expected [%s], risk: <%s>' % (option, value_found, value_expected, risk)) | |
| 2352 | _log.warning('PG option [%s] set to [%s], expected %s, risk: <%s>' % (option, value_found, values_expected, risk)) | |
| 2345 | 2353 | |
| 2346 | 2354 | if found_error: |
| 2347 | 2355 | return 2, u'\n'.join(msg) |
| 2489 | 2497 | |
| 2490 | 2498 | def getquoted(self): |
| 2491 | 2499 | return _timestamp_template % self.__dt.isoformat() |
| 2492 | ||
| 2493 | ## remove for 0.9 | |
| 2494 | ## ---------------------------------------------------------------------- | |
| 2495 | ##class cAdapterMxDateTime(object): | |
| 2496 | ## | |
| 2497 | ## def __init__(self, dt): | |
| 2498 | ## if dt.tz == '???': | |
| 2499 | ## _log.info('[%s]: no time zone string available in (%s), assuming local time zone', self.__class__.__name__, dt) | |
| 2500 | ## self.__dt = dt | |
| 2501 | ## | |
| 2502 | ## def getquoted(self): | |
| 2503 | ## # under some locale settings the mx.DateTime ISO formatter | |
| 2504 | ## # will insert "," into the ISO string, | |
| 2505 | ## # while this is allowed per the ISO8601 spec PostgreSQL | |
| 2506 | ## # cannot currently handle that, | |
| 2507 | ## # so map those "," to "." to make things work: | |
| 2508 | ## return mxDT.ISO.str(self.__dt).replace(',', '.') | |
| 2509 | ## | |
| 2510 | ## ---------------------------------------------------------------------- | |
| 2511 | ## PostgreSQL -> Python | |
| 2512 | ## ---------------------------------------------------------------------- | |
| 2513 | 2500 | |
| 2514 | 2501 | #======================================================================= |
| 2515 | 2502 | # main |
| 8 | 8 | __license__ = "GPL v2 or later (details at http://www.gnu.org)" |
| 9 | 9 | |
| 10 | 10 | # stdlib |
| 11 | import sys, os, string, re, urllib2, logging, io | |
| 11 | import sys | |
| 12 | import os | |
| 13 | import re | |
| 14 | import logging | |
| 15 | import io | |
| 12 | 16 | |
| 13 | 17 | |
| 14 | 18 | _log = logging.getLogger('gm.bootstrapper') |
| 15 | 19 | |
| 16 | 20 | unformattable_error_id = 12345 |
| 17 | #=================================================================== | |
| 18 | def shellrun (cmd): | |
| 19 | """ | |
| 20 | runs the shell command and returns a string | |
| 21 | """ | |
| 22 | stdin, stdout = os.popen4 (cmd.group (1)) | |
| 23 | r = stdout.read () | |
| 24 | stdout.close() | |
| 25 | stdin.close() | |
| 26 | return r | |
| 27 | #------------------------------------------------------------------- | |
| 28 | def shell(str): | |
| 29 | """ | |
| 30 | performs backtick shell extension in a string | |
| 31 | """ | |
| 32 | return re.sub (r"`(.*)`", shellrun, str) | |
| 33 | 21 | |
| 34 | 22 | #=================================================================== |
| 35 | 23 | class Psql: |
| 39 | 27 | db : the interpreter to connect to, must be a DBAPI compliant interface |
| 40 | 28 | """ |
| 41 | 29 | self.conn = conn |
| 42 | self.vars = {'ON_ERROR_STOP':None} | |
| 30 | self.vars = {'ON_ERROR_STOP': None} | |
| 43 | 31 | |
| 44 | 32 | #--------------------------------------------------------------- |
| 45 | def match (self, str): | |
| 46 | match = re.match (str, self.line) | |
| 33 | def match(self, pattern): | |
| 34 | match = re.match(pattern, self.line) | |
| 47 | 35 | if match is None: |
| 48 | ret = 0 | |
| 49 | else: | |
| 50 | ret = 1 | |
| 51 | self.groups = match.groups () | |
| 52 | return ret | |
| 36 | return 0 | |
| 37 | ||
| 38 | self.groups = match.groups() | |
| 39 | return 1 | |
| 53 | 40 | |
| 54 | 41 | #--------------------------------------------------------------- |
| 55 | 42 | def fmt_msg(self, aMsg): |
| 73 | 60 | filename: a file, containg semicolon-separated SQL commands |
| 74 | 61 | """ |
| 75 | 62 | _log.debug('processing [%s]', filename) |
| 76 | if re.match ("http://.*", filename) or re.match ("ftp://.*", filename) or re.match ("gopher://.*", filename): | |
| 77 | try: | |
| 78 | self.file = urllib2.urlopen (filename) | |
| 79 | except URLError: | |
| 80 | _log.error(u"cannot access [%s]", filename) | |
| 81 | return 1 | |
| 63 | curs = self.conn.cursor() | |
| 64 | curs.execute(u'show session authorization') | |
| 65 | start_auth = curs.fetchall()[0][0] | |
| 66 | curs.close() | |
| 67 | _log.debug(u'session auth: %s', start_auth) | |
| 68 | ||
| 69 | if os.access (filename, os.R_OK): | |
| 70 | sql_file = io.open(filename, mode = 'rt', encoding = 'utf8') | |
| 82 | 71 | else: |
| 83 | if os.access (filename, os.R_OK): | |
| 84 | self.file = io.open(filename, mode = 'rt', encoding = 'utf8') | |
| 85 | else: | |
| 86 | _log.error(u"cannot open file [%s]", filename) | |
| 87 | return 1 | |
| 72 | _log.error(u"cannot open file [%s]", filename) | |
| 73 | return 1 | |
| 88 | 74 | |
| 89 | 75 | self.lineno = 0 |
| 90 | 76 | self.filename = filename |
| 93 | 79 | curr_cmd = '' |
| 94 | 80 | curs = self.conn.cursor() |
| 95 | 81 | |
| 96 | for self.line in self.file.readlines(): | |
| 82 | for self.line in sql_file.readlines(): | |
| 97 | 83 | self.lineno += 1 |
| 98 | 84 | if len(self.line.strip()) == 0: |
| 99 | 85 | continue |
| 100 | 86 | |
| 101 | # \echo | |
| 102 | if self.match (r"^\\echo (.*)"): | |
| 103 | _log.info(self.fmt_msg(shell(self.groups[0]))) | |
| 104 | continue | |
| 105 | ||
| 106 | # \qecho | |
| 107 | if self.match (r"^\\qecho (.*)"): | |
| 108 | _log.info(self.fmt_msg(shell (self.groups[0]))) | |
| 109 | continue | |
| 110 | ||
| 111 | # \q | |
| 112 | if self.match (r"^\\q"): | |
| 113 | _log.warning(self.fmt_msg(u"script terminated by \\q")) | |
| 114 | return 0 | |
| 115 | ||
| 116 | 87 | # \set |
| 117 | if self.match (r"^\\set (\S+) (\S+)"): | |
| 118 | self.vars[self.groups[0]] = shell (self.groups[1]) | |
| 88 | if self.match(r"^\\set (\S+) (\S+)"): | |
| 89 | _log.debug(u'"\set" found: %s', self.groups) | |
| 90 | self.vars[self.groups[0]] = self.groups[1] | |
| 119 | 91 | if self.groups[0] == 'ON_ERROR_STOP': |
| 120 | self.vars['ON_ERROR_STOP'] = int (self.vars['ON_ERROR_STOP']) | |
| 92 | # adjusting from string to int so that "1" -> 1 -> True | |
| 93 | self.vars['ON_ERROR_STOP'] = int(self.vars['ON_ERROR_STOP']) | |
| 121 | 94 | continue |
| 122 | 95 | |
| 123 | 96 | # \unset |
| 141 | 114 | if this_char == "'": |
| 142 | 115 | in_string = not in_string |
| 143 | 116 | |
| 144 | # detect -- style comments | |
| 117 | # detect "--"-style comments | |
| 145 | 118 | if this_char == '-' and next_char == '-' and not in_string: |
| 146 | 119 | break |
| 147 | 120 | |
| 151 | 124 | if this_char == ')' and not in_string: |
| 152 | 125 | bracketlevel -= 1 |
| 153 | 126 | |
| 154 | # found end of command, not inside string, not inside bracket ? | |
| 155 | if not (not in_string and (bracketlevel == 0) and (this_char == ';')): | |
| 127 | # have we: | |
| 128 | # - found end of command ? | |
| 129 | # - are not inside a string ? | |
| 130 | # - are not inside bracket pair ? | |
| 131 | if not ((in_string is False) and (bracketlevel == 0) and (this_char == ';')): | |
| 156 | 132 | curr_cmd += this_char |
| 157 | 133 | else: |
| 158 | try: | |
| 159 | if curr_cmd.strip() != '': | |
| 160 | curs.execute (curr_cmd) | |
| 161 | except Exception as error: | |
| 162 | _log.exception(curr_cmd) | |
| 163 | if re.match (r"^NOTICE:.*", str(error)): | |
| 164 | _log.warning(self.fmt_msg(error)) | |
| 165 | else: | |
| 166 | _log.error(self.fmt_msg(error)) | |
| 167 | if hasattr(error, 'diag'): | |
| 168 | for prop in dir(error.diag): | |
| 169 | if prop.startswith(u'__'): | |
| 170 | continue | |
| 171 | val = getattr(error.diag, prop) | |
| 172 | if val is None: | |
| 173 | continue | |
| 174 | _log.error(u'PG diags %s: %s', prop, val) | |
| 175 | if self.vars['ON_ERROR_STOP']: | |
| 176 | self.conn.commit() | |
| 177 | curs.close() | |
| 178 | return 1 | |
| 134 | if curr_cmd.strip() != '': | |
| 135 | try: | |
| 136 | curs.execute(curr_cmd) | |
| 137 | try: | |
| 138 | data = curs.fetchall() | |
| 139 | _log.debug(u'cursor data: %s', data) | |
| 140 | except StandardError: # actually: psycopg2.ProgrammingError but no handle | |
| 141 | pass | |
| 142 | except Exception as error: | |
| 143 | _log.exception(curr_cmd) | |
| 144 | if re.match(r"^NOTICE:.*", str(error)): | |
| 145 | _log.warning(self.fmt_msg(error)) | |
| 146 | else: | |
| 147 | _log.error(self.fmt_msg(error)) | |
| 148 | if hasattr(error, 'diag'): | |
| 149 | for prop in dir(error.diag): | |
| 150 | if prop.startswith(u'__'): | |
| 151 | continue | |
| 152 | val = getattr(error.diag, prop) | |
| 153 | if val is None: | |
| 154 | continue | |
| 155 | _log.error(u'PG diags %s: %s', prop, val) | |
| 156 | if self.vars['ON_ERROR_STOP']: | |
| 157 | self.conn.commit() | |
| 158 | curs.close() | |
| 159 | return 1 | |
| 179 | 160 | |
| 180 | 161 | self.conn.commit() |
| 181 | 162 | curs.close() |
| 183 | 164 | curr_cmd = '' |
| 184 | 165 | |
| 185 | 166 | this_char = next_char |
| 186 | ||
| 187 | 167 | # end of loop over chars |
| 188 | 168 | |
| 189 | 169 | # end of loop over lines |
| 190 | 170 | self.conn.commit() |
| 171 | curs.execute(u'show session authorization') | |
| 172 | end_auth = curs.fetchall()[0][0] | |
| 191 | 173 | curs.close() |
| 174 | _log.debug(u'session auth after sql file processing: %s', end_auth) | |
| 175 | if start_auth != end_auth: | |
| 176 | _log.error('session auth changed before/after processing sql file') | |
| 177 | ||
| 192 | 178 | return 0 |
| 193 | 179 | |
| 194 | 180 | #=================================================================== |
| 202 | 188 | sys.exit() |
| 203 | 189 | |
| 204 | 190 | #from pyPgSQL import PgSQL |
| 205 | conn = PgSQL.connect (user='gm-dbo', database = 'gnumed') | |
| 206 | psql = Psql (conn) | |
| 207 | psql.run (sys.argv[1]) | |
| 208 | conn.close () | |
| 191 | conn = PgSQL.connect(user='gm-dbo', database = 'gnumed') | |
| 192 | psql = Psql(conn) | |
| 193 | psql.run(sys.argv[1]) | |
| 194 | conn.close() | |
| 47 | 47 | |
| 48 | 48 | -- =================================================================== |
| 49 | 49 | create or replace function audit.add_table_for_audit(name, name) |
| 50 | returns unknown | |
| 50 | returns boolean | |
| 51 | 51 | language 'plpgsql' |
| 52 | 52 | security definer |
| 53 | 53 | as ' |
| 86 | 86 | |
| 87 | 87 | |
| 88 | 88 | create or replace function audit.add_table_for_audit(name) |
| 89 | returns unknown | |
| 89 | returns boolean | |
| 90 | 90 | language SQL |
| 91 | 91 | security definer |
| 92 | 92 | as ' |
| 161 | 161 | |
| 162 | 162 | -- ============================================= |
| 163 | 163 | create or replace function i18n.set_curr_lang(text) |
| 164 | returns unknown | |
| 164 | returns boolean | |
| 165 | 165 | language 'plpgsql' |
| 166 | 166 | security definer |
| 167 | 167 | as ' |
| 185 | 185 | |
| 186 | 186 | -- ============================================= |
| 187 | 187 | create or replace function i18n.force_curr_lang(text) |
| 188 | returns unknown | |
| 188 | returns boolean | |
| 189 | 189 | language 'plpgsql' |
| 190 | 190 | security definer |
| 191 | 191 | as ' |
| 259 | 259 | -- ============================================= |
| 260 | 260 | -- do simple schema revision tracking |
| 261 | 261 | select log_script_insertion('$RCSfile: gmI18N-dynamic.sql,v $', '$Revision: 1.5 $'); |
| 262 | ||
| 263 | -- ============================================= | |
| 264 | -- $Log: gmI18N-dynamic.sql,v $ | |
| 265 | -- Revision 1.5 2006-07-24 14:18:52 ncq | |
| 266 | -- - add comment | |
| 267 | -- | |
| 268 | -- Revision 1.4 2006/07/01 15:22:03 ncq | |
| 269 | -- - do not hard-fail set_curr_lang() | |
| 270 | -- | |
| 271 | -- Revision 1.3 2006/02/06 13:18:27 ncq | |
| 272 | -- - quote user when column name | |
| 273 | -- | |
| 274 | -- Revision 1.2 2006/01/10 08:44:22 ncq | |
| 275 | -- - drop index does not require "on" | |
| 276 | -- | |
| 277 | -- Revision 1.1 2006/01/09 13:42:29 ncq | |
| 278 | -- - factor out dynamic stuff | |
| 279 | -- - move into schema "i18n" (except for _()) | |
| 280 | -- | |
| 281 | -- Revision 1.23 2005/09/19 16:38:51 ncq | |
| 282 | -- - adjust to removed is_core from gm_schema_revision | |
| 283 | -- | |
| 284 | -- Revision 1.22 2005/07/14 21:31:42 ncq | |
| 285 | -- - partially use improved schema revision tracking | |
| 286 | -- | |
| 287 | -- Revision 1.21 2005/07/04 11:42:24 ncq | |
| 288 | -- - fix _(text, text) | |
| 289 | -- | |
| 290 | -- Revision 1.20 2005/03/31 20:08:38 ncq | |
| 291 | -- - add i18n_upd_tx() for safe update of translations | |
| 292 | -- | |
| 293 | -- Revision 1.19 2005/03/01 20:38:19 ncq | |
| 294 | -- - varchar -> text | |
| 295 | -- | |
| 296 | -- Revision 1.18 2005/02/03 20:28:25 ncq | |
| 297 | -- - improved comments | |
| 298 | -- - added _(text, text) | |
| 299 | -- | |
| 300 | -- Revision 1.17 2005/02/01 16:52:50 ncq | |
| 301 | -- - added force_curr_lang() | |
| 302 | -- | |
| 303 | -- Revision 1.16 2004/07/17 20:57:53 ncq | |
| 304 | -- - don't use user/_user workaround anymore as we dropped supporting | |
| 305 | -- it (but we did NOT drop supporting readonly connections on > 7.3) | |
| 306 | -- | |
| 307 | -- Revision 1.15 2003/12/29 15:40:42 uid66147 | |
| 308 | -- - added not null | |
| 309 | -- - added v_missing_translations | |
| 310 | -- | |
| 311 | -- Revision 1.14 2003/06/10 09:58:11 ncq | |
| 312 | -- - i18n() inserts strings into i18n_keys, not _(), fix comment to that effect | |
| 313 | -- | |
| 314 | -- Revision 1.13 2003/05/12 12:43:39 ncq | |
| 315 | -- - gmI18N, gmServices and gmSchemaRevision are imported globally at the | |
| 316 | -- database level now, don't include them in individual schema file anymore | |
| 317 | -- | |
| 318 | -- Revision 1.12 2003/05/02 15:06:44 ncq | |
| 319 | -- - fix comment | |
| 320 | -- | |
| 321 | -- Revision 1.11 2003/04/23 08:36:00 michaelb | |
| 322 | -- made i18n_curr_lang longer still (11 to 15) | |
| 323 | -- | |
| 324 | -- Revision 1.9 2003/02/04 13:22:01 ncq | |
| 325 | -- - refined set_curr_lang to only work if translations available | |
| 326 | -- - also auto-set for both "user" and "_user" | |
| 327 | -- | |
| 328 | -- Revision 1.8 2003/02/04 12:22:52 ncq | |
| 329 | -- - valid until in create user cannot do a sub-query :-( | |
| 330 | -- - columns "owner" should really be of type "name" if defaulting to "CURRENT_USER" | |
| 331 | -- - new functions set_curr_lang(*) | |
| 332 | -- | |
| 333 | -- Revision 1.7 2003/01/24 14:16:18 ncq | |
| 334 | -- - don't drop functions repeatedly since that will kill views created earlier | |
| 335 | -- | |
| 336 | -- Revision 1.6 2003/01/20 20:21:53 ncq | |
| 337 | -- - keep the last useful bit from i18n.sql as documentation | |
| 338 | -- | |
| 339 | -- Revision 1.5 2003/01/20 19:42:47 ncq | |
| 340 | -- - simplified creation of translating view a lot | |
| 341 | -- | |
| 342 | -- Revision 1.4 2003/01/17 00:24:33 ncq | |
| 343 | -- - add a few access right definitions | |
| 344 | -- | |
| 345 | -- Revision 1.3 2003/01/05 13:05:51 ncq | |
| 346 | -- - schema_revision -> gm_schema_revision | |
| 347 | -- | |
| 348 | -- Revision 1.2 2003/01/04 10:30:26 ncq | |
| 349 | -- - better documentation | |
| 350 | -- - insert default english "translation" into i18n_translations | |
| 351 | -- | |
| 352 | -- Revision 1.1 2003/01/01 17:41:57 ncq | |
| 353 | -- - improved database i18n | |
| 354 | -- | |
| 57 | 57 | -- ============================================= |
| 58 | 58 | -- do simple schema revision tracking |
| 59 | 59 | select log_script_insertion('$RCSfile: gmI18N.sql,v $', '$Revision: 1.25 $'); |
| 60 | ||
| 61 | -- ============================================= | |
| 62 | -- $Log: gmI18N.sql,v $ | |
| 63 | -- Revision 1.25 2006-02-10 14:06:40 ncq | |
| 64 | -- - proper script insertion logging | |
| 65 | -- | |
| 66 | -- Revision 1.24 2006/01/09 13:42:29 ncq | |
| 67 | -- - factor out dynamic stuff | |
| 68 | -- - move into schema "i18n" (except for _()) | |
| 69 | -- | |
| 70 | -- Revision 1.23 2005/09/19 16:38:51 ncq | |
| 71 | -- - adjust to removed is_core from gm_schema_revision | |
| 72 | -- | |
| 73 | -- Revision 1.22 2005/07/14 21:31:42 ncq | |
| 74 | -- - partially use improved schema revision tracking | |
| 75 | -- | |
| 76 | -- Revision 1.21 2005/07/04 11:42:24 ncq | |
| 77 | -- - fix _(text, text) | |
| 78 | -- | |
| 79 | -- Revision 1.20 2005/03/31 20:08:38 ncq | |
| 80 | -- - add i18n_upd_tx() for safe update of translations | |
| 81 | -- | |
| 82 | -- Revision 1.19 2005/03/01 20:38:19 ncq | |
| 83 | -- - varchar -> text | |
| 84 | -- | |
| 85 | -- Revision 1.18 2005/02/03 20:28:25 ncq | |
| 86 | -- - improved comments | |
| 87 | -- - added _(text, text) | |
| 88 | -- | |
| 89 | -- Revision 1.17 2005/02/01 16:52:50 ncq | |
| 90 | -- - added force_curr_lang() | |
| 91 | -- | |
| 92 | -- Revision 1.16 2004/07/17 20:57:53 ncq | |
| 93 | -- - don't use user/_user workaround anymore as we dropped supporting | |
| 94 | -- it (but we did NOT drop supporting readonly connections on > 7.3) | |
| 95 | -- | |
| 96 | -- Revision 1.15 2003/12/29 15:40:42 uid66147 | |
| 97 | -- - added not null | |
| 98 | -- - added v_missing_translations | |
| 99 | -- | |
| 100 | -- Revision 1.14 2003/06/10 09:58:11 ncq | |
| 101 | -- - i18n() inserts strings into i18n_keys, not _(), fix comment to that effect | |
| 102 | -- | |
| 103 | -- Revision 1.13 2003/05/12 12:43:39 ncq | |
| 104 | -- - gmI18N, gmServices and gmSchemaRevision are imported globally at the | |
| 105 | -- database level now, don't include them in individual schema file anymore | |
| 106 | -- | |
| 107 | -- Revision 1.12 2003/05/02 15:06:44 ncq | |
| 108 | -- - fix comment | |
| 109 | -- | |
| 110 | -- Revision 1.11 2003/04/23 08:36:00 michaelb | |
| 111 | -- made i18n_curr_lang longer still (11 to 15) | |
| 112 | -- | |
| 113 | -- Revision 1.9 2003/02/04 13:22:01 ncq | |
| 114 | -- - refined set_curr_lang to only work if translations available | |
| 115 | -- - also auto-set for both "user" and "_user" | |
| 116 | -- | |
| 117 | -- Revision 1.8 2003/02/04 12:22:52 ncq | |
| 118 | -- - valid until in create user cannot do a sub-query :-( | |
| 119 | -- - columns "owner" should really be of type "name" if defaulting to "CURRENT_USER" | |
| 120 | -- - new functions set_curr_lang(*) | |
| 121 | -- | |
| 122 | -- Revision 1.7 2003/01/24 14:16:18 ncq | |
| 123 | -- - don't drop functions repeatedly since that will kill views created earlier | |
| 124 | -- | |
| 125 | -- Revision 1.6 2003/01/20 20:21:53 ncq | |
| 126 | -- - keep the last useful bit from i18n.sql as documentation | |
| 127 | -- | |
| 128 | -- Revision 1.5 2003/01/20 19:42:47 ncq | |
| 129 | -- - simplified creation of translating view a lot | |
| 130 | -- | |
| 131 | -- Revision 1.4 2003/01/17 00:24:33 ncq | |
| 132 | -- - add a few access right definitions | |
| 133 | -- | |
| 134 | -- Revision 1.3 2003/01/05 13:05:51 ncq | |
| 135 | -- - schema_revision -> gm_schema_revision | |
| 136 | -- | |
| 137 | -- Revision 1.2 2003/01/04 10:30:26 ncq | |
| 138 | -- - better documentation | |
| 139 | -- - insert default english "translation" into i18n_translations | |
| 140 | -- | |
| 141 | -- Revision 1.1 2003/01/01 17:41:57 ncq | |
| 142 | -- - improved database i18n | |
| 143 | -- |
| 19 | 19 | |
| 20 | 20 | |
| 21 | 21 | create or replace function i18n.force_curr_lang(text, name) |
| 22 | returns unknown | |
| 22 | returns boolean | |
| 23 | 23 | language 'plpgsql' |
| 24 | 24 | security definer |
| 25 | 25 | as E' |
| 40 | 40 | |
| 41 | 41 | -- ============================================= |
| 42 | 42 | create or replace function i18n.force_curr_lang(text) |
| 43 | returns unknown | |
| 43 | returns boolean | |
| 44 | 44 | language 'plpgsql' |
| 45 | 45 | as ' |
| 46 | 46 | DECLARE |
| 120 | 120 | (select fk_patient from clin.encounter where pk = c_si.fk_encounter) |
| 121 | 121 | as pk_patient, |
| 122 | 122 | c_si.soap_cat, |
| 123 | null | |
| 123 | null::text | |
| 124 | 124 | as brand, |
| 125 | 125 | c_si.preparation, |
| 126 | 126 | r_cs.description |
| 130 | 130 | as unit, |
| 131 | 131 | r_cs.atc_code |
| 132 | 132 | as atc_substance, |
| 133 | null | |
| 133 | null::text | |
| 134 | 134 | as atc_brand, |
| 135 | null | |
| 135 | null::text | |
| 136 | 136 | as external_code_brand, |
| 137 | null | |
| 137 | null::text | |
| 138 | 138 | as external_code_type_brand, |
| 139 | 139 | |
| 140 | 140 | c_si.clin_when |
| 150 | 150 | as episode, |
| 151 | 151 | c_si.narrative |
| 152 | 152 | as notes, |
| 153 | null | |
| 153 | null::boolean | |
| 154 | 154 | as fake_brand, |
| 155 | 155 | -- currently active ? |
| 156 | 156 | case |
| 176 | 176 | else null |
| 177 | 177 | end::boolean |
| 178 | 178 | as seems_inactive, |
| 179 | null | |
| 179 | null::integer | |
| 180 | 180 | as pk_brand, |
| 181 | null | |
| 181 | null::integer | |
| 182 | 182 | as pk_data_source, |
| 183 | 183 | r_cs.pk |
| 184 | 184 | as pk_substance, |
| 185 | null | |
| 185 | null::integer | |
| 186 | 186 | as pk_drug_component, |
| 187 | 187 | c_si.fk_encounter |
| 188 | 188 | as pk_encounter, |
| 13 | 13 | ALTER DATABASE gnumed_v16 |
| 14 | 14 | SET default_transaction_isolation to 'read committed'; |
| 15 | 15 | |
| 16 | ALTER DATABASE gnumed_v16 | |
| 17 | SET sql_inheritance to 'on'; | |
| 16 | -- does not exist on PG10 anymore, so can't be set if bootstrapping on PG10 | |
| 17 | --ALTER DATABASE gnumed_v16 | |
| 18 | -- SET sql_inheritance to 'on'; | |
| 18 | 19 | |
| 19 | 20 | -- -------------------------------------------------------------- |
| 20 | 21 | select gm.log_script_insertion('v16-db-default_settings.sql', 'v16'); |
| 21 | ||
| 22 | -- ==============================================================⏎ |
| 122 | 122 | (select fk_patient from clin.encounter where pk = c_si.fk_encounter) |
| 123 | 123 | as pk_patient, |
| 124 | 124 | c_si.soap_cat, |
| 125 | null | |
| 125 | null::text | |
| 126 | 126 | as brand, |
| 127 | 127 | c_si.preparation, |
| 128 | 128 | r_cs.description |
| 132 | 132 | as unit, |
| 133 | 133 | r_cs.atc_code |
| 134 | 134 | as atc_substance, |
| 135 | null | |
| 135 | null::text | |
| 136 | 136 | as atc_brand, |
| 137 | null | |
| 137 | null::text | |
| 138 | 138 | as external_code_brand, |
| 139 | null | |
| 139 | null::text | |
| 140 | 140 | as external_code_type_brand, |
| 141 | 141 | |
| 142 | 142 | c_si.clin_when |
| 154 | 154 | as health_issue, |
| 155 | 155 | c_si.narrative |
| 156 | 156 | as notes, |
| 157 | null | |
| 157 | null::boolean | |
| 158 | 158 | as fake_brand, |
| 159 | 159 | -- currently active ? |
| 160 | 160 | case |
| 180 | 180 | else null |
| 181 | 181 | end::boolean |
| 182 | 182 | as seems_inactive, |
| 183 | null | |
| 183 | null::integer | |
| 184 | 184 | as pk_brand, |
| 185 | null | |
| 185 | null::integer | |
| 186 | 186 | as pk_data_source, |
| 187 | 187 | r_cs.pk |
| 188 | 188 | as pk_substance, |
| 189 | null | |
| 189 | null::integer | |
| 190 | 190 | as pk_drug_component, |
| 191 | 191 | c_si.fk_encounter |
| 192 | 192 | as pk_encounter, |
| 7 | 7 | \set ON_ERROR_STOP 1 |
| 8 | 8 | |
| 9 | 9 | -- -------------------------------------------------------------- |
| 10 | \unset ON_ERROR_STOP | |
| 11 | 10 | -- very old: |
| 12 | alter table blobs.doc_obj drop constraint "$1" cascade; | |
| 11 | alter table blobs.doc_obj drop constraint if exists "$1" cascade; | |
| 13 | 12 | -- medium age: |
| 14 | alter table blobs.doc_obj drop constraint doc_obj_doc_id_fkey cascade; | |
| 13 | alter table blobs.doc_obj drop constraint if exists doc_obj_doc_id_fkey cascade; | |
| 15 | 14 | -- current: |
| 16 | alter table blobs.doc_obj drop constraint doc_obj_fk_doc_fkey cascade; | |
| 17 | \set ON_ERROR_STOP 1 | |
| 15 | alter table blobs.doc_obj drop constraint if exists doc_obj_fk_doc_fkey cascade; | |
| 18 | 16 | |
| 19 | 17 | -- recreate: |
| 20 | 18 | alter table blobs.doc_obj |
| 5 | 5 | -- |
| 6 | 6 | -- ============================================================== |
| 7 | 7 | \set ON_ERROR_STOP 1 |
| 8 | set check_function_bodies to on; | |
| 9 | ||
| 10 | --set default_transaction_read_only to off; | |
| 11 | 8 | |
| 12 | 9 | -- -------------------------------------------------------------- |
| 13 | 10 | \unset ON_ERROR_STOP |
| 14 | 14 | |
| 15 | 15 | \unset ON_ERROR_STOP |
| 16 | 16 | |
| 17 | set client_encoding 'utf8'; | |
| 17 | set client_encoding to 'utf8'; | |
| 18 | 18 | |
| 19 | 19 | select i18n.upd_tx(quote_literal(E'fr'), quote_literal(E'British Columbia'), quote_literal(E'Colombie-Britannique')); |
| 20 | 20 | select i18n.upd_tx(quote_literal(E'fr'), quote_literal(E'New Brunswick'), quote_literal(E'Nouveau-Brunswick')); |
| 14 | 14 | |
| 15 | 15 | \unset ON_ERROR_STOP |
| 16 | 16 | |
| 17 | set client_encoding 'utf8'; | |
| 17 | set client_encoding to 'utf8'; | |
| 18 | 18 | |
| 19 | 19 | select i18n.upd_tx(quote_literal(E'ru'), quote_literal(E'cause of death'), quote_literal(E'причина смерти')); |
| 20 | 20 | select i18n.upd_tx(quote_literal(E'ru_RU'), quote_literal(E'Abakan'), quote_literal(E'Абакан')); |
| 128 | 128 | (select fk_patient from clin.encounter where pk = c_si.fk_encounter) |
| 129 | 129 | as pk_patient, |
| 130 | 130 | c_si.soap_cat, |
| 131 | null | |
| 131 | null::text | |
| 132 | 132 | as brand, |
| 133 | 133 | c_si.preparation, |
| 134 | 134 | r_cs.description |
| 138 | 138 | as unit, |
| 139 | 139 | r_cs.atc_code |
| 140 | 140 | as atc_substance, |
| 141 | null | |
| 141 | null::text | |
| 142 | 142 | as atc_brand, |
| 143 | null | |
| 143 | null::text | |
| 144 | 144 | as external_code_brand, |
| 145 | null | |
| 145 | null::text | |
| 146 | 146 | as external_code_type_brand, |
| 147 | 147 | |
| 148 | 148 | c_si.clin_when |
| 160 | 160 | as health_issue, |
| 161 | 161 | c_si.narrative |
| 162 | 162 | as notes, |
| 163 | null | |
| 163 | null::boolean | |
| 164 | 164 | as fake_brand, |
| 165 | 165 | -- currently active ? |
| 166 | 166 | case |
| 186 | 186 | else null |
| 187 | 187 | end::boolean |
| 188 | 188 | as seems_inactive, |
| 189 | null | |
| 189 | null::integer | |
| 190 | 190 | as pk_brand, |
| 191 | null | |
| 191 | null::integer | |
| 192 | 192 | as pk_data_source, |
| 193 | 193 | r_cs.pk |
| 194 | 194 | as pk_substance, |
| 195 | null | |
| 195 | null::integer | |
| 196 | 196 | as pk_drug_component, |
| 197 | 197 | c_si.fk_encounter |
| 198 | 198 | as pk_encounter, |
| 138 | 138 | (select fk_patient from clin.encounter where pk = c_si.fk_encounter) |
| 139 | 139 | as pk_patient, |
| 140 | 140 | c_si.soap_cat, |
| 141 | null | |
| 141 | null::text | |
| 142 | 142 | as brand, |
| 143 | 143 | c_si.preparation, |
| 144 | 144 | r_cs.description |
| 148 | 148 | as unit, |
| 149 | 149 | r_cs.atc_code |
| 150 | 150 | as atc_substance, |
| 151 | null | |
| 151 | null::text | |
| 152 | 152 | as atc_brand, |
| 153 | null | |
| 153 | null::text | |
| 154 | 154 | as external_code_brand, |
| 155 | null | |
| 155 | null::text | |
| 156 | 156 | as external_code_type_brand, |
| 157 | 157 | |
| 158 | 158 | -- uncertainty of start |
| 191 | 191 | as health_issue, |
| 192 | 192 | c_si.narrative |
| 193 | 193 | as notes, |
| 194 | null | |
| 194 | null::boolean | |
| 195 | 195 | as fake_brand, |
| 196 | 196 | -- currently active ? |
| 197 | 197 | case |
| 217 | 217 | else null |
| 218 | 218 | end::boolean |
| 219 | 219 | as seems_inactive, |
| 220 | null | |
| 220 | null::integer | |
| 221 | 221 | as pk_brand, |
| 222 | null | |
| 222 | null::integer | |
| 223 | 223 | as pk_data_source, |
| 224 | 224 | r_cs.pk |
| 225 | 225 | as pk_substance, |
| 226 | null | |
| 226 | null::integer | |
| 227 | 227 | as pk_drug_component, |
| 228 | 228 | c_si.fk_encounter |
| 229 | 229 | as pk_encounter, |
| 415 | 415 | ; |
| 416 | 416 | |
| 417 | 417 | -- -------------------------------------------------------------- |
| 418 | select gm.log_script_insertion('v21-clin-v_substance_intakes.sql', '21.0'); | |
| 418 | select gm.log_script_insertion('v21-clin-v_substance_intakes.sql', '21.15'); | |
| 16 | 16 | ) VALUES ( |
| 17 | 17 | (select pk from dem.staff where db_user = 'any-doc'), |
| 18 | 18 | (select pk_type from dem.v_inbox_item_type where type = 'memo' and category = 'administrative'), |
| 19 | 'Release Notes for GNUmed 1.6.14 (database v21.14)', | |
| 20 | 'GNUmed 1.6.14 Release Notes: | |
| 19 | 'Release Notes for GNUmed 1.6.15 (database v21.15)', | |
| 20 | 'GNUmed 1.6.15 Release Notes: | |
| 21 | 21 | |
| 22 | 1.6.14 | |
| 22 | 1.6.15 | |
| 23 | 23 | |
| 24 | FIX: exception when having issues with calculating eGFR in medication plugin | |
| 25 | FIX: exception on disabling identity [thanks Marc] | |
| 26 | FIX: exception on adding archived documents to export area | |
| 27 | FIX: Orthanc DICOM patient ID modification | |
| 28 | FIX: faulty file drop target declarations | |
| 24 | FIX: exception on tooltipping patient overview inbox item | |
| 25 | FIX: exception in cursor/connection state logging w/ older psycopg2s | |
| 26 | FIX: exception on import error inside portable app | |
| 29 | 27 | |
| 30 | IMPROVED: saving of export area items | |
| 31 | IMPROVED: patient display in provider inbox | |
| 32 | IMPROVED: copy document to export area from document plugin | |
| 33 | IMPROVED: Orthanc modification dialog title | |
| 34 | IMPROVED: imported documents deletion confirmation | |
| 35 | IMPROVED: patient media metadata | |
| 28 | IMPROVED: use Dicom[RequestingPhysician] if available | |
| 29 | IMPROVED: user visible rendering of raw DICOM strings | |
| 30 | IMPROVED: baptize SCRAM for PG passwords in settings check | |
| 31 | ||
| 32 | 21.15 | |
| 33 | ||
| 34 | FIX: handle SQL_INHERITANCE in a way compatible with PG10 | |
| 35 | FIX: untyped UNIONs not tolerated by PG10 anymore | |
| 36 | FIX: RETURNS UNKNOWN functions not tolerated by PG10 anymore | |
| 37 | ||
| 38 | IMPROVED: script to adjust db settings | |
| 36 | 39 | '); |
| 37 | 40 | |
| 38 | 41 | -- -------------------------------------------------------------- |
| 39 | select gm.log_script_insertion('v21-release_notes-dynamic.sql', '21.14'); | |
| 42 | select gm.log_script_insertion('v21-release_notes-dynamic.sql', '21.15'); |
| 0 | -- GNUmed auditing functionality | |
| 1 | -- =================================================================== | |
| 2 | -- license: GPL v2 or later | |
| 3 | -- author: Karsten Hilbert | |
| 4 | ||
| 5 | -- =================================================================== | |
| 6 | -- force terminate + exit(3) on errors if non-interactive | |
| 7 | \set ON_ERROR_STOP 1 | |
| 8 | ||
| 9 | -- -------------------------------------------------------------- | |
| 10 | create or replace function audit.add_table_for_audit(name, name) | |
| 11 | returns boolean | |
| 12 | language 'plpgsql' | |
| 13 | security definer | |
| 14 | as ' | |
| 15 | DECLARE | |
| 16 | _relnamespace alias for $1; | |
| 17 | _relname ALIAS FOR $2; | |
| 18 | dummy RECORD; | |
| 19 | tmp text; | |
| 20 | BEGIN | |
| 21 | -- does table exist ? | |
| 22 | select relname into dummy from pg_class where | |
| 23 | relname = _relname and | |
| 24 | relnamespace = (select oid from pg_namespace where nspname = _relnamespace) | |
| 25 | ; | |
| 26 | if not found then | |
| 27 | tmp := _relnamespace || ''.'' || _relname; | |
| 28 | raise exception ''audit.add_table_for_audit: Table [%] does not exist.'', tmp; | |
| 29 | return false; | |
| 30 | end if; | |
| 31 | -- already queued for auditing ? | |
| 32 | select 1 into dummy from audit.audited_tables where table_name = _relname and schema = _relnamespace; | |
| 33 | if found then | |
| 34 | return true; | |
| 35 | end if; | |
| 36 | -- add definition | |
| 37 | insert into audit.audited_tables ( | |
| 38 | schema, table_name | |
| 39 | ) values ( | |
| 40 | _relnamespace, _relname | |
| 41 | ); | |
| 42 | return true; | |
| 43 | END;'; | |
| 44 | ||
| 45 | comment on function audit.add_table_for_audit (name, name) is | |
| 46 | 'sanity-checking convenience function for marking tables for auditing'; | |
| 47 | ||
| 48 | ||
| 49 | create or replace function audit.add_table_for_audit(name) | |
| 50 | returns boolean | |
| 51 | language SQL | |
| 52 | security definer | |
| 53 | as ' | |
| 54 | select audit.add_table_for_audit(''public'', $1);'; | |
| 55 | ||
| 56 | comment on function audit.add_table_for_audit(name) is | |
| 57 | 'sanity-checking convenience function for marking tables | |
| 58 | for auditing, schema is always "public"'; | |
| 59 | ||
| 60 | -- -------------------------------------------------------------- | |
| 61 | select gm.log_script_insertion('v21-audit-add_table_for_audit-fixup.sql', '21.15'); |
| 0 | -- ============================================================== | |
| 1 | -- GNUmed database schema change script | |
| 2 | -- | |
| 3 | -- License: GPL v2 or later | |
| 4 | -- Author: karsten.hilbert@gmx.net | |
| 5 | -- | |
| 6 | -- ============================================================== | |
| 7 | \set ON_ERROR_STOP 1 | |
| 8 | --set default_transaction_read_only to off; | |
| 9 | ||
| 10 | -- -------------------------------------------------------------- | |
| 11 | drop view if exists clin.v_nonbrand_intakes cascade; | |
| 12 | ||
| 13 | create view clin.v_nonbrand_intakes as | |
| 14 | select | |
| 15 | c_si.pk | |
| 16 | as pk_substance_intake, | |
| 17 | (select fk_patient from clin.encounter where pk = c_si.fk_encounter) | |
| 18 | as pk_patient, | |
| 19 | c_si.soap_cat, | |
| 20 | null::text | |
| 21 | as brand, | |
| 22 | c_si.preparation, | |
| 23 | r_cs.description | |
| 24 | as substance, | |
| 25 | r_cs.amount, | |
| 26 | r_cs.unit | |
| 27 | as unit, | |
| 28 | r_cs.atc_code | |
| 29 | as atc_substance, | |
| 30 | null::text | |
| 31 | as atc_brand, | |
| 32 | null::text | |
| 33 | as external_code_brand, | |
| 34 | null::text | |
| 35 | as external_code_type_brand, | |
| 36 | ||
| 37 | -- uncertainty of start | |
| 38 | case | |
| 39 | when c_si.comment_on_start = '?' then null | |
| 40 | else c_si.clin_when | |
| 41 | end::timestamp with time zone | |
| 42 | as started, | |
| 43 | c_si.comment_on_start, | |
| 44 | case | |
| 45 | when c_si.comment_on_start = '?' then true | |
| 46 | else false | |
| 47 | end::boolean | |
| 48 | as start_is_unknown, | |
| 49 | case | |
| 50 | when c_si.comment_on_start is null then false | |
| 51 | else true | |
| 52 | end::boolean | |
| 53 | as start_is_approximate, | |
| 54 | c_si.intake_is_approved_of, | |
| 55 | c_si.harmful_use_type, | |
| 56 | CASE | |
| 57 | WHEN c_si.harmful_use_type IS NULL THEN NULL::timestamp with time zone | |
| 58 | ELSE c_enc.started | |
| 59 | END | |
| 60 | AS last_checked_when, | |
| 61 | c_si.schedule, | |
| 62 | c_si.duration, | |
| 63 | c_si.discontinued, | |
| 64 | c_si.discontinue_reason, | |
| 65 | c_si.is_long_term, | |
| 66 | c_si.aim, | |
| 67 | cep.description | |
| 68 | as episode, | |
| 69 | c_hi.description | |
| 70 | as health_issue, | |
| 71 | c_si.narrative | |
| 72 | as notes, | |
| 73 | null::boolean | |
| 74 | as fake_brand, | |
| 75 | -- currently active ? | |
| 76 | case | |
| 77 | -- no discontinue date documented so assumed active | |
| 78 | when c_si.discontinued is null then true | |
| 79 | -- else not active (constraints guarantee that .discontinued > clin_when and < current_timestamp) | |
| 80 | else false | |
| 81 | end::boolean | |
| 82 | as is_currently_active, | |
| 83 | -- seems inactive ? | |
| 84 | case | |
| 85 | when c_si.discontinued is not null then true | |
| 86 | -- from here on discontinued is NULL | |
| 87 | when c_si.clin_when is null then | |
| 88 | case | |
| 89 | when c_si.is_long_term is true then false | |
| 90 | else null | |
| 91 | end | |
| 92 | -- from here clin_when is NOT null | |
| 93 | when (c_si.clin_when > current_timestamp) is true then true | |
| 94 | when ((c_si.clin_when + c_si.duration) < current_timestamp) is true then true | |
| 95 | when ((c_si.clin_when + c_si.duration) > current_timestamp) is true then false | |
| 96 | else null | |
| 97 | end::boolean | |
| 98 | as seems_inactive, | |
| 99 | null::integer | |
| 100 | as pk_brand, | |
| 101 | null::integer | |
| 102 | as pk_data_source, | |
| 103 | r_cs.pk | |
| 104 | as pk_substance, | |
| 105 | null::integer | |
| 106 | as pk_drug_component, | |
| 107 | c_si.fk_encounter | |
| 108 | as pk_encounter, | |
| 109 | c_si.fk_episode | |
| 110 | as pk_episode, | |
| 111 | cep.fk_health_issue | |
| 112 | as pk_health_issue, | |
| 113 | c_si.modified_when, | |
| 114 | c_si.modified_by, | |
| 115 | c_si.row_version | |
| 116 | as row_version, | |
| 117 | c_si.xmin | |
| 118 | as xmin_substance_intake | |
| 119 | from | |
| 120 | clin.substance_intake c_si | |
| 121 | inner join ref.consumable_substance r_cs on (c_si.fk_substance = r_cs.pk) | |
| 122 | left join clin.episode cep on (c_si.fk_episode = cep.pk) | |
| 123 | left join clin.health_issue c_hi on (c_hi.pk = cep.fk_health_issue) | |
| 124 | left join clin.encounter c_enc on (c_si.fk_encounter = c_enc.pk) | |
| 125 | where | |
| 126 | c_si.fk_drug_component IS NULL | |
| 127 | ; | |
| 128 | ||
| 129 | grant select on clin.v_nonbrand_intakes to group "gm-doctors"; | |
| 130 | ||
| 131 | -- -------------------------------------------------------------- | |
| 132 | drop view if exists clin.v_substance_intakes cascade; | |
| 133 | ||
| 134 | create view clin.v_substance_intakes as | |
| 135 | select * from clin.v_brand_intakes | |
| 136 | union all | |
| 137 | select * from clin.v_nonbrand_intakes | |
| 138 | ; | |
| 139 | ||
| 140 | grant select on clin.v_substance_intakes to group "gm-doctors"; | |
| 141 | ||
| 142 | -- -------------------------------------------------------------- | |
| 143 | select gm.log_script_insertion('v21-clin-v_substance_intakes-fixup.sql', '21.15'); |
| 0 | -- ============================================================== | |
| 1 | -- GNUmed database schema change script | |
| 2 | -- | |
| 3 | -- License: GPL v2 or later | |
| 4 | -- Author: karsten.hilbert@gmx.net | |
| 5 | -- | |
| 6 | -- ============================================================== | |
| 7 | \set ON_ERROR_STOP 1 | |
| 8 | --set default_transaction_read_only to off; | |
| 9 | ||
| 10 | -- -------------------------------------------------------------- | |
| 11 | select 'no-op SELECT such that the bootstrapper is run and forces SQL_INHERITANCE back to DEFAULT if on PG <10'; | |
| 12 | ||
| 13 | -- -------------------------------------------------------------- | |
| 14 | select gm.log_script_insertion('v21-db-sql_inheritance-fixup.sql', '21.15'); |
| 0 | -- ====================================================== | |
| 1 | -- GNUmed fixed string internationalisation (SQL gettext) | |
| 2 | -- ====================================================== | |
| 3 | -- force terminate + exit(3) on errors if non-interactive | |
| 4 | \set ON_ERROR_STOP 1 | |
| 5 | ||
| 6 | -- ============================================= | |
| 7 | create or replace function i18n.set_curr_lang(text) | |
| 8 | returns boolean | |
| 9 | language 'plpgsql' | |
| 10 | security definer | |
| 11 | as ' | |
| 12 | DECLARE | |
| 13 | _lang ALIAS FOR $1; | |
| 14 | BEGIN | |
| 15 | if exists(select pk from i18n.translations where lang = _lang) then | |
| 16 | delete from i18n.curr_lang where user = CURRENT_USER; | |
| 17 | insert into i18n.curr_lang (lang) values (_lang); | |
| 18 | return true; | |
| 19 | end if; | |
| 20 | raise notice ''Cannot set current language to [%]. No translations available.'', _lang; | |
| 21 | return false; | |
| 22 | END; | |
| 23 | '; | |
| 24 | ||
| 25 | comment on function i18n.set_curr_lang(text) is | |
| 26 | 'set preferred language: | |
| 27 | - for "current user" | |
| 28 | - only if translations for this language are available'; | |
| 29 | ||
| 30 | -- ============================================= | |
| 31 | create or replace function i18n.force_curr_lang(text) | |
| 32 | returns boolean | |
| 33 | language 'plpgsql' | |
| 34 | security definer | |
| 35 | as ' | |
| 36 | DECLARE | |
| 37 | _lang ALIAS FOR $1; | |
| 38 | BEGIN | |
| 39 | raise notice ''Forcing current language to [%] without checking for translations..'', _lang; | |
| 40 | delete from i18n.curr_lang where user = CURRENT_USER; | |
| 41 | insert into i18n.curr_lang(lang) values (_lang); | |
| 42 | return 1; | |
| 43 | END; | |
| 44 | '; | |
| 45 | ||
| 46 | comment on function i18n.force_curr_lang(text) is | |
| 47 | 'force preferred language to some language: | |
| 48 | - for "current user"'; | |
| 49 | ||
| 50 | -- -------------------------------------------------------------- | |
| 51 | select gm.log_script_insertion('v21-i18n-lang_funcs-fixup.sql', '21.15'); |