Strabon: 014379fdddf2 scripts/strabon

Strabon

view scripts/strabon @ 1426:014379fdddf2

fixed the tests of geof:distance and geof:buffer, that had wrong results due to the
conversion of the resulting geometry to the srid 3857.
The results are validated using PostGIS, where in the case of buffer there are
small differences in the precision.
Moreover, in the case of BufferMetresTest, there was no point in having as distance
1m, because the geometry did not change, so i added 55000 metres instead (about 0.5 degrees).

author	Stella Giannakopoulou <sgian@di.uoa.gr>
date	Wed Sep 24 17:43:53 2014 +0300 (2014-09-24)
parents	b58aa113f25e
children	da14a303bf2c

line source

1 #!/bin/bash

3 #

4 # This Source Code Form is subject to the terms of the Mozilla Public

5 # License, v. 2.0. If a copy of the MPL was not distributed with this

6 # file, You can obtain one at http://mozilla.org/MPL/2.0/.

7 #

9 #

10 # http://www.strabon.di.uoa.gr/

11 #

13 #

14 # Script for running the main classes of Strabon. The main classes of Strabon comprises

15 # QueryOp, , UpdateOp, StoreOp, and DescribeOp.

16 #

17 # Author: Charalampos (Babis) Nikolaou <charnik@di.uoa.gr>

18 #

20 # command name

21 CMD="$(basename ${0})"

23 # absolute directory name of this command

24 LOC="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"

26 RUNTIME="${LOC}/../runtime"

28 # runtime package

29 PKG="eu.earthobservatory.runtime"

31 # the underlying database to use (one of `postgis' or `monetdb')

32 DATABASE="postgis"

34 # the main class to run

35 CLASS=

37 # the hostname at which the database runs

38 HOST="localhost"

40 # the port at which the database listens

41 PORT=

43 # the database name to connect to

44 DB="strabon"

46 # the username for the database connection

47 DBUSER=

49 # the password for the database connection

50 DBPASS=

52 # the query to run

53 QUERY=

55 # the RDF format of the files to store (defaults to ntriples)

56 FORMAT="ntriples"

58 # true to force deletion of locked table, false otherwise

59 FORCE_DELETE="false"

61 # the URI of the named graph into which the RDF files shall be stored

62 NAMED_GRAPH=

64 # true when inference is enabled

65 INFERENCE=

67 # predefined queries

68 QUERY_SIZE="SELECT (COUNT(*) as ?C) WHERE {?s ?p ?o}"

69 QUERY_GETALL="SELECT * WHERE {?s ?p ?o}"

70 QUERY_DELETEALL="DELETE {?s ?p ?o} WHERE {?s ?p ?o}"

71 QUERY_HOTSPOT_SIZE="SELECT (COUNT(*) as ?C) WHERE {?h <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://teleios.di.uoa.gr/ontologies/noaOntology.owl#Hotspot>}"

72 QUERY_EXPORT="CONSTRUCT {?s ?p ?o} WHERE {?s ?p ?o}"

74 # debug option for log4j configuration:

75 #-Dlog4j.debug

76 #-Dlog4j.configuration=\"${RUNTIME}/log4j.properties\"

78 # further options for java

79 JAVA_OPTS=

81 # base max memory memory

82 BASE_MEMORY=1024

84 # more memory

85 MORE_MEMORY="-Xms512M -Xmx1024M"

87 # much more memory

88 MMORE_MEMORY="-Xms512M -Xmx1536M"

90 # flag for not setting the memory limit more than once

91 MEMORY_INCREASED=false

93 # just print what shall be executed

94 DEBUG=false

96 # if true, DEBUG has been set in command line,

97 # so it must not be overidden

98 DEBUG_SAVE=false

100 # Filename containing the prefixes to be included in SPARQL queries

101 PREFIXES_FILE="${LOC}/prefixes.sparql"

102

103 # configuration file for the Strabon connection

104 STRABON_CONF="${HOME}/.strabon"

105

106 function help() {

107 echo "Usage: ${CMD} [OPTIONS] COMMAND ARGS"

108 echo

109 echo "Interface to execute the main classes of Strabon, such as QueryOp, StoreOp, UpdateOp, DescribeOp, etc."

110 echo

111 echo " COMMAND : one of \`query', \`update', \`store', \`describe', or \`help'"

112 echo " ARGS : arguments according to selected command"

113 echo

114 echo "OPTIONS can be any of the following (variable names and values are case sensitive)"

115 echo " -d : don't run, just print what shall be executed"

116 echo " Variable for configuration file: \`DEBUG'"

117 echo " Values: \`true' or \`false'"

118 echo " -m : use more memory \`${MORE_MEMORY}' (useful in \"out of memory exceptions\")"

119 echo " -M : use much more memory \`${MMORE_MEMORY}' (useful in \"out of memory exceptions\")"

120 echo " -MM MULT : use MULT * ${BASE_MEMORY} MB of memory (useful in \"out of memory exceptions\")"

121 echo " -i : include URI prefixes in the SPARQL query. Prefixes are taken from file"

122 echo " \`prefixes.sparql'"

123 echo " -e DATABASE : the database engine to connect (one of \`postgis' (default) or \`monetdb')"

124 echo " Variable for configuration file: \`DATABASE'"

125 echo " Values: \`postgis' or \`monetdb'"

126 echo " -db DB : the database to connect to (defaults to \`${DB}')"

127 echo " Variable for configuration file: \`DB'"

128 echo " -p PORT : the port to use for the database connection"

129 echo " : (defaults to 5432 for postgis and 50000 for monetdb)"

130 echo " Variable for configuration file: \`PORT'"

131 echo " -h HOSTNAME : the hostname to use for the database connection (defaults to \`${HOST}')"

132 echo " Variable for configuration file: \`HOST'"

133 echo " -u USERNAME : the username for the database connection"

134 echo " (defaults to \`postgres' for postgis and \`monetdb' for monetdb)"

135 echo " Variable for configuration file: \`DBUSER'"

136 echo " -pass PASS : the password for the database connection"

137 echo " (defaults to \`postgres' for postgis and \`monetdb' for monetdb)"

138 echo " Variable for configuration file: \`DBPASS'"

139 echo " -c FILE : configuration file to use for the connection (defaults to \`${STRABON_CONF}')."

140 echo " If the default configuration file exists, it is read. Options specified in the"

141 echo " command line override their values already set by the configuration file."

142 }

143

144 function help_query() {

145 echo "Usage: ${CMD} query [OPTIONS] SPARQL_QUERY [RESULT_FORMAT]"

146 echo

147 echo "Execute a SPARQL query on Strabon."

148 echo

149 echo " SPARQL_QUERY : the SPARQL query to execute or an alias name such as the following:"

150 echo " size: returns the number of triples"

151 echo " all: returns all triples"

152 echo " hotspots: returns the number of hotspots"

153 echo " RESULT_FORMAT : the format of the result. Possible values are \`???' (default), \`xml'"

154 echo " \`html', \`kml', \`kmz', or \`geojson'"

155 echo

156 echo "OPTIONS can be one of the following"

157 echo " --force-delete : forces deletion of \"locked\" table (e.g., when Strabon has been"

158 echo " ungracefully shutdown)"

159 }

160

161 function help_update() {

162 echo "Usage: ${CMD} update SPARQL_UPDATE"

163 echo

164 echo "Execute a SPARQL Update query on Strabon."

165 echo

166 echo " SPARQL_UPDATE : the SPARQL update query to execute or an alias name such as the"

167 echo " the following:"

168 echo " clear: deletes all triples"

169 }

170

171 function help_store() {

172 echo "Usage: ${CMD} store [OPTIONS] FILE..."

173 echo

174 echo "Store RDF documents in Strabon."

175 echo

176 echo " FILE : the file containing the RDF document to store. It can be a filename or a URL,"

177 echo " (i.e., file:///tmp/file.nt, http://www.example.org/file.nt,"

178 echo " ftp://www.example.org/file.nt, etc.)."

179 echo

180 echo "OPTIONS can be one of the following"

181 echo " -f FORMAT : the RDF format of the files to store. The format can be one of the following:"

182 echo " \`ntriples' (default), \`n3', \`rdfxml', or \`turtle'."

183 echo " -g NAMED_GRAPH : the URI of the named graph into which the RDF files shall be stored"

184 echo " (defaults to the default graph)."

185 echo " --inference : enables inference."

186 }

187

188 function help_describe() {

189 echo "Usage: ${CMD} describe DESCRIBE_QUERY [RESULT_FORMAT]"

190 echo

191 echo "Execute a SPARQL DESCRIBE query on Strabon."

192 echo

193 echo " DESCRIBE_QUERY : the SPARQL DESCRIBE query to execute or an alias name such as the following:"

194 echo " export: returns all triples stored in the database"

195 echo " RESULT_FORMAT : the format of the result. Possible values are \`N-Triples', "

196 echo " \`RDM/XML', \`N3', \`TURTLE', \`TRIG', \`TRIX', and \`BinaryRDF'"

197 echo " (defaults to N-Triples)"

198 }

199

200 # read configuration script first

201 if test -e "${STRABON_CONF}"; then

202 . ${STRABON_CONF}

203 fi

204

205 if ${DEBUG}; then

206 echo "${CMD}: debug is ON (from configuration file ${STRABON_CONF})"

207 fi

208

209 # read script options

210 while test $# -gt 0 -a "X${1:0:1}" == "X-"; do

211 case "${1}" in

212 --help)

213 help

214 exit 0

215 ;;

216 -d)

217 shift

218 if ! ${DEBUG}; then

219 echo "${CMD}: debug is ON"

220 fi

221 DEBUG=true

222 DEBUG_SAVE=true

223 ;;

224 -m)

225 if ! ${MEMORY_INCREASED}; then

226 JAVA_OPTS="${JAVA_OPTS} ${MORE_MEMORY}"

227 MEMORY_INCREASED=true

228 else

229 echo "${CMD}: memory has already been increased; option \`${1}' will be ignored."

230 fi

231 shift

232 ;;

233 -M)

234 if ! ${MEMORY_INCREASED}; then

235 JAVA_OPTS="${JAVA_OPTS} ${MMORE_MEMORY}"

236 MEMORY_INCREASED=true

237 else

238 echo "${CMD}: memory has already been increased; option \`${1}' will be ignored."

239 fi

240 shift

241 ;;

242 -MM)

243 shift

244 if ! test $# -gt 1; then

245 help

246 exit 1

247 fi

248 MULT=${1}

249

250 if ! ${MEMORY_INCREASED}; then

251 JAVA_OPTS="${JAVA_OPTS} -Xms512M -Xmx$((${MULT}*${BASE_MEMORY}))M"

252 MEMORY_INCREASED=true

253 else

254 echo "${CMD}: memory has already been increased; option \`${1}' will be ignored."

255 fi

256 shift

257 ;;

258 -i)

259 shift

260 PREFIXES="$(cat ${PREFIXES_FILE})

261 "

262 ;;

263 -e)

264 shift

265 if ! test $# -gt 1; then

266 help

267 exit 1

268 fi

269

270 DATABASE=${1}

271 case "${DATABASE}" in

272 monetdb|postgis)

273 shift

274 ;;

275 postgis)

276 shift

277 ;;

278 *)

279 echo "${CMD}: invalid database engine"

280 echo "${CMD}: valid database engines are \`postgis' or \`monetdb'"

281 exit 2

282 ;;

283 esac

284 ;;

285 -db)

286 shift

287 if ! test $# -gt 1; then

288 help

289 exit 1

290 fi

291 DB="${1}"

292 shift

293 ;;

294 -p)

295 shift

296 if ! test $# -gt 1; then

297 help

298 exit 1

299 fi

300 PORT=${1}

301 shift

302 ;;

303 -h)

304 shift

305 if ! test $# -gt 1; then

306 help

307 exit 1

308 fi

309 HOST=${1}

310 shift

311 ;;

312 -u)

313 shift

314 if ! test $# -gt 1; then

315 help

316 exit 1

317 fi

318 DBUSER=${1}

319 shift

320 ;;

321 -pass)

322 shift

323 if ! test $# -gt 1; then

324 help

325 exit 1

326 fi

327 DBPASS=${1}

328 shift

329 ;;

330 -c)

331 shift

332 if ! test $# -gt 1; then

333 help

334 exit 1

335 fi

336

337 STRABON_CONF="${1}"

338 if ! test -e "${STRABON_CONF}"; then

339 echo "${CMD}: configuration file \"${1}\" does not exist"

340 exit 1

341 else

342 # if true, then debug has been set ON in command line

343 if $DEBUG; then

344 echo "${CMD}: Reading configuration file \"${STRABON_CONF}\""

345 fi

346

347 . ${STRABON_CONF}

348

349 if $DEBUG_SAVE; then

350 # restore debug value set on command line

351 DEBUG=true

352 fi

353 shift

354 fi

355 ;;

356 -*)

357 echo "${CMD}: unknown option \"${1}\""

358 help

359 exit 1

360 ;;

361 esac

362 done

363

364 # set defaults

365 case "${DATABASE}" in

366 postgis)

367 if test -z "${PORT}";

368 then

369 PORT=5432

370 fi

371

372 if test -z "${DBUSER}";

373 then

374 DBUSER="postgres"

375 fi

376

377 if test -z "${DBPASS}";

378 then

379 DBPASS="postgres"

380 fi

381 ;;

382 monetdb)

383 if test -z "${PORT}";

384 then

385 PORT=50000

386 fi

387

388 if test -z "${DBUSER}";

389 then

390 DBUSER="monetdb"

391 fi

392

393 if test -z "${DBPASS}";

394 then

395 DBPASS="monetdb"

396 fi

397 ;;

398 esac

399

400 # print configuration/options

401 if ${DEBUG}; then

402 echo "${CMD}: printing database connection details"

403 echo " Database Engine : ${DATABASE}"

404 echo " Database Name : ${DB}"

405 echo " Hostname : ${HOST}"

406 echo " Port : ${PORT}"

407 echo " Username : ${DBUSER}"

408 echo " Password : ${DBPASS}"

409 fi

410

411 # determine command to execute

412 case "${1}" in

413 help)

414 shift

415 if test $# -ge 1; then

416 case "${1}" in

417 query)

418 help_query

419 ;;

420 update)

421 help_update

422 ;;

423 store)

424 help_store

425 ;;

426 describe)

427 help_describe

428 ;;

429 *)

430 help

431 ;;

432 esac

433 exit 1

434 fi

435 help

436 exit 0

437 ;;

438 query)

439 CLASS="QueryOp"

440 shift

441 if ! test $# -ge 1; then

442 help_query

443 exit 1

444 fi

445

446 # check whether force deletion of locked table has been specified

447 if test "${1}" = "--force-delete"; then

448 shift

449 FORCE_DELETE="true"

450 fi

451

452 QUERY="${1}"

453 shift

454

455 # check for predefined queries

456 case "${QUERY}" in

457 size)

458 QUERY="${QUERY_SIZE}"

459 ;;

460 hotspots)

461 QUERY="${QUERY_HOTSPOT_SIZE}"

462 ;;

463 all)

464 QUERY="${QUERY_GETALL}"

465 ;;

466 esac

467

468 # check for format of result

469 if test $# -gt 0; then

470 RESULT_FORMAT="${1}"

471 shift

472 case "${RESULT_FORMAT}" in

474 ;;

475 *)

476 echo "${CMD}: invalid result format \"${RESULT_FORMAT}\""

477 echo "${CMD}: valid formats are \`???' (default), \`xml', \`html', \`kml', \`kmz', or \`geojson'"

478 exit 2

479 ;;

480 esac

481 fi

482 ;;

483 update)

484 CLASS="UpdateOp"

485 shift

486 if ! test $# -eq 1; then

487 help_update

488 exit 1

489 fi

490 QUERY="${1}"

491

492 # check for predefined queries

493 case "${QUERY}" in

494 clear)

495 QUERY="${QUERY_DELETEALL}"

496 ;;

497 esac

498 ;;

499 store)

500 CLASS="StoreOp"

501 shift

502 if ! test $# -ge 1; then

503 help_store

504 exit 1

505 fi

506

507 while test $# -gt 0 -a "X${1:0:1}" == "X-"; do

508 # check whether format is specified

509 if test "${1}" = "-f"; then

510 shift

511 if ! test $# -ge 1; then

512 echo "${CMD}: Option -f requires an RDF format (\`ntriples', \`n3', \`rdfxml', or \`turtle')"

513 exit 2

514 else

515 FORMAT="${1}"

516 case "${FORMAT}" in

517 [nN][tT][rR][iI][pP][lL][eE][sS]|[nN]3|[rR][dD][fF][xX][mM][lL]|[tT][uU][rR][tT][lL][eE])

518 shift

519 ;;

520 *)

521 echo "${CMD}: invalid RDF format \"${FORMAT}\"."

522 echo "${CMD}: valid RDF formats are \`ntriples', \`n3', \`rdfxml', or \`turtle'"

523 exit 2

524 ;;

525 esac

526 fi

527 fi

528

529 # check whether a named graph is specified

530 if test "${1}" = "-g"; then

531 shift

532 if ! test $# -ge 1; then

533 echo "${CMD}: Option -g requires a URI argument"

534 exit 2

535 else

536 NAMED_GRAPH="-g ${1}"

537 shift

538 fi

539 fi

540

541 # check whether inference is enabled

542 if test "${1}" = "--inference"; then

543 shift

544 INFERENCE="-i true"

545 fi

546

547 done

548

549 # if no files are given

550 if ! test $# -ge 1; then

551 help_store

552 exit 1

553 fi

554

555 # do not make an assignment of the files to QUERY

556 # handle the case of storing multiple files afterwards

557 # QUERY="${@}"

558 ;;

559 describe)

560 CLASS="DescribeOp"

561 shift

562 if ! test $# -ge 1; then

563 help_describe

564 exit 1

565 fi

566 QUERY="${1}"

567 shift

568

569 # check for predefined queries

570 case "${QUERY}" in

571 export)

572 QUERY="${QUERY_EXPORT}"

573 ;;

574 esac

575

576 # check for format of result

577 if test $# -gt 0; then

578 RESULT_FORMAT="${1}"

579 shift

580 case "${RESULT_FORMAT}" in

582 ;;

583 *)

584 echo "${CMD}: invalid result format \"${RESULT_FORMAT}\""

585 echo "${CMD}: valid formats are \`N-Triples', \`RDM/XML', \`N3', \`TURTLE', \`TRIG', \`TRIX', and \`BinaryRDF'"

586 exit 2

587 ;;

588 esac

589 fi

590 ;;

591 "")

592 help

593 exit 1

594 ;;

595 *)

596 help

597 echo

598 echo "${CMD}: unknown command \"${1}\"."

599 exit 1

600 ;;

601 esac

602

603 # compile command to execute

604 if test "${CLASS}" = "StoreOp"; then

605 STRABON_EXEC=

606 for file in "${@}"; do

607 # check whether a relative path was given

608 if ! test "${file:0:7}" == "file://" -o "${file:0:7}" == "http://" -o "${file:0:1}" == "/"; then

609 file="$(pwd)/${file}"

610 fi

611

612 STRABON_EXEC="${STRABON_EXEC}(cd ${RUNTIME} && java ${JAVA_OPTS} -cp ./target/\*:. ${PKG}.${DATABASE}.${CLASS} ${HOST} ${PORT} ${DB} ${DBUSER} ${DBPASS} \"${file}\" -f ${FORMAT} ${NAMED_GRAPH} ${INFERENCE});

613 "

614 done

615 elif test "${CLASS}" = "QueryOp"; then

616 STRABON_EXEC="(cd ${RUNTIME} && java ${JAVA_OPTS} -cp ./target/\*:. ${PKG}.${DATABASE}.${CLASS} ${HOST} ${PORT} ${DB} ${DBUSER} ${DBPASS} \"${PREFIXES}${QUERY}\" ${FORCE_DELETE} ${RESULT_FORMAT})"

617 else

618 STRABON_EXEC="(cd ${RUNTIME} && java ${JAVA_OPTS} -cp ./target/\*:. ${PKG}.${DATABASE}.${CLASS} ${HOST} ${PORT} ${DB} ${DBUSER} ${DBPASS} \"${PREFIXES}${QUERY}\" ${RESULT_FORMAT})"

619 fi

620

621 # execute command or debug

622 if ${DEBUG}; then

623 echo "${CMD}: printing command for execution"

624 echo "${STRABON_EXEC}"

625 else

626 eval "${STRABON_EXEC}"

627 fi