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How to use update_file method in lisa
Best Python code snippet using lisa_python
update_test_data.py
Source:update_test_data.py 
...62 if not ServiceCheck.service_ok():63 print('Not updating test data as services are unavailable.')64 sys.exit(1)65 pool = LocalSessionThreadPool()66 def update_file(filepath, url, process_fn=None):67 pool.execute(update_file_real, (filepath, url, process_fn))68 # types/boring69 update_file('types/boring/boring.xml',70 build_dov_url('data/boring/2004-103984.xml'))71 update_file(72 'types/boring/wfsgetfeature.xml',73 build_dov_url(74 'geoserver/ows?service=WFS'75 '&version=2.0.0&request=GetFeature&typeName=dov-pub:Boringen'76 '&maxFeatures=1&CQL_Filter=fiche=%27' +77 build_dov_url('data/boring/2004-103984%27')))78 update_file(79 'types/boring/feature.xml',80 build_dov_url(81 'geoserver/ows?service=WFS'82 '&version=2.0.0&request=GetFeature&typeName=dov-pub:Boringen'83 '&maxFeatures=1&CQL_Filter=fiche=%27' +84 build_dov_url('data/boring/2004-103984%27')),85 get_first_featuremember)86 update_file(87 'types/boring/fc_featurecatalogue.xml',88 build_dov_url(89 'geonetwork/srv/dut/csw'90 '?Service=CSW&Request=GetRecordById&Version=2.0.2'91 '&outputSchema=http://www.isotc211.org/2005/gfc'92 '&elementSetName=full&id=c0cbd397-520f-4ee1-aca7'93 '-d70e271eeed6'))94 update_file(95 'types/boring/md_metadata.xml',96 build_dov_url(97 'geonetwork/srv/dut/csw'98 '?Service=CSW&Request=GetRecordById&Version=2.0.2'99 '&outputSchema=http://www.isotc211.org/2005/gmd'100 '&elementSetName=full&id=4e20bf9c-3a5c-42be-b5b6'101 '-bef6214d1fa7'))102 update_file(103 'types/boring/wfsdescribefeaturetype.xml',104 build_dov_url(105 'geoserver/dov-pub/Boringen'106 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))107 for xsd_schema in Boring.get_xsd_schemas():108 update_file(109 'types/boring/xsd_{}.xml'.format(xsd_schema.split('/')[-1]),110 xsd_schema)111 # types/sondering112 update_file('types/sondering/sondering.xml',113 build_dov_url('data/sondering/2002-018435.xml'))114 update_file(115 'types/sondering/wfsgetfeature.xml',116 build_dov_url(117 'geoserver/ows?service=WFS'118 '&version=2.0.0&request=GetFeature&typeName=dov-pub'119 ':Sonderingen&maxFeatures=1&CQL_Filter=fiche=%27' +120 build_dov_url('data/sondering/2002-018435%27')))121 update_file(122 'types/sondering/feature.xml',123 build_dov_url(124 'geoserver/ows?service=WFS'125 '&version=2.0.0&request=GetFeature&typeName=dov-pub'126 ':Sonderingen&maxFeatures=1&CQL_Filter=fiche=%27' +127 build_dov_url('data/sondering/2002-018435%27')),128 get_first_featuremember)129 update_file(130 'types/sondering/fc_featurecatalogue.xml',131 build_dov_url(132 'geonetwork/srv/dut/csw'133 '?Service=CSW&Request=GetRecordById&Version=2.0.2'134 '&outputSchema=http://www.isotc211.org/2005/gfc'135 '&elementSetName=full&id=bd539ba5-5f4d-4c43-9662'136 '-51c16caea351'))137 update_file(138 'types/sondering/md_metadata.xml',139 build_dov_url(140 'geonetwork/srv/dut/csw'141 '?Service=CSW&Request=GetRecordById&Version=2.0.2'142 '&outputSchema=http://www.isotc211.org/2005/gmd'143 '&elementSetName=full&id=b397faec-1b64-4854-8000'144 '-2375edb3b1a8'))145 update_file(146 'types/sondering/wfsdescribefeaturetype.xml',147 build_dov_url(148 'geoserver/dov-pub/Sonderingen'149 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))150 for xsd_schema in Sondering.get_xsd_schemas():151 update_file(152 'types/sondering/xsd_{}.xml'.format(xsd_schema.split('/')[-1]),153 xsd_schema)154 # types/interpretaties/informele_stratigrafie155 update_file('types/interpretaties/informele_stratigrafie'156 '/informele_stratigrafie.xml',157 build_dov_url('data/interpretatie/1962-101692.xml'))158 update_file(159 'types/interpretaties/informele_stratigrafie'160 '/wfsgetfeature.xml',161 build_dov_url(162 'geoserver/ows?service=WFS'163 '&version=2.0.0&request=GetFeature&typeName=interpretaties'164 ':informele_stratigrafie&maxFeatures=1&CQL_Filter'165 '=Interpretatiefiche=%27') +166 build_dov_url(167 'data'168 '/interpretatie/1962-101692%27'))169 update_file(170 'types/interpretaties/informele_stratigrafie/feature.xml',171 build_dov_url(172 'geoserver/ows?service=WFS'173 '&version=2.0.0&request=GetFeature&typeName=interpretaties'174 ':informele_stratigrafie&maxFeatures=1&CQL_Filter'175 '=Interpretatiefiche=%27') +176 build_dov_url(177 'data'178 '/interpretatie/1962-101692%27'),179 get_first_featuremember)180 update_file(181 'types/interpretaties/informele_stratigrafie/fc_featurecatalogue.xml',182 build_dov_url(183 'geonetwork/srv/dut/csw'184 '?Service=CSW&Request=GetRecordById&Version=2.0.2'185 '&outputSchema=http://www.isotc211.org/2005/gfc'186 '&elementSetName=full&id=b6c651f9-5972-4252-ae10-ad69ad08e78d'))187 update_file(188 'types/interpretaties/informele_stratigrafie/md_metadata.xml',189 build_dov_url(190 'geonetwork/srv/dut/csw'191 '?Service=CSW&Request=GetRecordById&Version=2.0.2'192 '&outputSchema=http://www.isotc211.org/2005/gmd'193 '&elementSetName=full&id=bd171ea4-2509-478d-a21c'194 '-c2728d3a9051'))195 update_file(196 'types/interpretaties/informele_stratigrafie/wfsdescribefeaturetype'197 '.xml', build_dov_url(198 'geoserver/interpretaties'199 '/informele_stratigrafie/ows?service=wfs&version=2.0.0&request'200 '=DescribeFeatureType'))201 for xsd_schema in InformeleStratigrafie.get_xsd_schemas():202 update_file(203 'types/interpretaties/informele_stratigrafie/xsd_%s.xml' %204 xsd_schema.split('/')[-1], xsd_schema)205 # types/interpretaties/formele_stratigrafie206 update_file('types/interpretaties/formele_stratigrafie'207 '/formele_stratigrafie.xml',208 build_dov_url('data/interpretatie/2011-249333.xml'))209 update_file(210 'types/interpretaties/formele_stratigrafie'211 '/wfsgetfeature.xml',212 build_dov_url(213 'geoserver/ows?service=WFS'214 '&version=2.0.0&request=GetFeature&typeName=interpretaties'215 ':formele_stratigrafie&maxFeatures=1&CQL_Filter'216 '=Interpretatiefiche=%27') +217 build_dov_url(218 'data'219 '/interpretatie/2011-249333%27'))220 update_file(221 'types/interpretaties/formele_stratigrafie/feature.xml',222 build_dov_url(223 'geoserver/ows?service=WFS'224 '&version=2.0.0&request=GetFeature&typeName=interpretaties'225 ':formele_stratigrafie&maxFeatures=1&CQL_Filter'226 '=Interpretatiefiche=%27') +227 build_dov_url(228 'data'229 '/interpretatie/2011-249333%27'),230 get_first_featuremember)231 update_file(232 'types/interpretaties/formele_stratigrafie/fc_featurecatalogue.xml',233 build_dov_url(234 'geonetwork/srv/dut/csw'235 '?Service=CSW&Request=GetRecordById&Version=2.0.2'236 '&outputSchema=http://www.isotc211.org/2005/gfc'237 '&elementSetName=full&id=68405b5d-51e6-44d0-b634-b580bc2f9eb6'))238 update_file(239 'types/interpretaties/formele_stratigrafie/md_metadata.xml',240 build_dov_url(241 'geonetwork/srv/dut/csw'242 '?Service=CSW&Request=GetRecordById&Version=2.0.2'243 '&outputSchema=http://www.isotc211.org/2005/gmd'244 '&elementSetName=full&id=212af8cd-bffd-423c-9d2b'245 '-69c544ab3b04'))246 update_file(247 'types/interpretaties/formele_stratigrafie/wfsdescribefeaturetype'248 '.xml', build_dov_url(249 'geoserver/interpretaties'250 '/formele_stratigrafie/ows?service=wfs&version=2.0.0&request'251 '=DescribeFeatureType'))252 for xsd_schema in FormeleStratigrafie.get_xsd_schemas():253 update_file(254 'types/interpretaties/formele_stratigrafie/xsd_%s.xml' %255 xsd_schema.split('/')[-1], xsd_schema)256 # types/interpretaties/hydrogeologische_stratigrafie257 update_file('types/interpretaties/hydrogeologische_stratigrafie'258 '/hydrogeologische_stratigrafie.xml',259 build_dov_url('data/interpretatie/2001-186543.xml'))260 update_file(261 'types/interpretaties/hydrogeologische_stratigrafie'262 '/wfsgetfeature.xml',263 build_dov_url(264 'geoserver/ows?service=WFS'265 '&version=2.0.0&request=GetFeature&typeName=interpretaties'266 ':hydrogeologische_stratigrafie&maxFeatures=1&CQL_Filter'267 '=Interpretatiefiche=%27') +268 build_dov_url(269 'data'270 '/interpretatie/2001-186543%27'))271 update_file(272 'types/interpretaties/hydrogeologische_stratigrafie'273 '/feature.xml',274 build_dov_url(275 'geoserver/ows?service=WFS'276 '&version=2.0.0&request=GetFeature&typeName=interpretaties'277 ':hydrogeologische_stratigrafie&maxFeatures=1&CQL_Filter'278 '=Interpretatiefiche=%27') +279 build_dov_url(280 'data/'281 'interpretatie/2001-186543%27'),282 get_first_featuremember)283 update_file(284 'types/interpretaties/hydrogeologische_stratigrafie/'285 'fc_featurecatalogue.xml', build_dov_url(286 'geonetwork/srv/dut/csw'287 '?Service=CSW&Request=GetRecordById&Version=2.0.2'288 '&outputSchema=http://www.isotc211.org/2005/gfc'289 '&elementSetName=full&id=b89e72de-35a9-4bca-8d0b-712d1e881ea6'))290 update_file(291 'types/interpretaties/hydrogeologische_stratigrafie/'292 'md_metadata.xml', build_dov_url(293 'geonetwork/srv/dut/csw'294 '?Service=CSW&Request=GetRecordById&Version=2.0.2'295 '&outputSchema=http://www.isotc211.org/2005/gmd'296 '&elementSetName=full&id=25c5d9fa-c2ba-4184-b796'297 '-fde790e73d39'))298 update_file(299 'types/interpretaties/hydrogeologische_stratigrafie/'300 'wfsdescribefeaturetype.xml', build_dov_url(301 'geoserver/interpretaties'302 '/hydrogeologische_stratigrafie/ows?service=wfs&version=2.0.0'303 '&request=DescribeFeatureType'))304 for xsd_schema in HydrogeologischeStratigrafie.get_xsd_schemas():305 update_file(306 'types/interpretaties/hydrogeologische_stratigrafie/xsd_%s.xml' %307 xsd_schema.split('/')[-1], xsd_schema)308 # types/interpretaties/lithologische_beschrijvingen309 update_file('types/interpretaties/lithologische_beschrijvingen'310 '/lithologische_beschrijvingen.xml',311 build_dov_url('data/interpretatie/1958-003925.xml'))312 update_file(313 'types/interpretaties/lithologische_beschrijvingen'314 '/wfsgetfeature.xml',315 build_dov_url(316 'geoserver/ows?service=WFS'317 '&version=2.0.0&request=GetFeature&typeName=interpretaties'318 ':lithologische_beschrijvingen&maxFeatures=1&CQL_Filter'319 '=Interpretatiefiche=%27') +320 build_dov_url(321 'data'322 '/interpretatie/1958-003925%27'))323 update_file(324 'types/interpretaties/lithologische_beschrijvingen/feature.xml',325 build_dov_url(326 'geoserver/ows?service=WFS'327 '&version=2.0.0&request=GetFeature&typeName=interpretaties'328 ':lithologische_beschrijvingen&maxFeatures=1&CQL_Filter'329 '=Interpretatiefiche=%27') +330 build_dov_url(331 'data'332 '/interpretatie/1958-003925%27'),333 get_first_featuremember)334 update_file(335 'types/interpretaties/lithologische_beschrijvingen/'336 'fc_featurecatalogue.xml',337 build_dov_url(338 'geonetwork/srv/dut/csw'339 '?Service=CSW&Request=GetRecordById&Version=2.0.2'340 '&outputSchema=http://www.isotc211.org/2005/gfc'341 '&elementSetName=full&id=2450d592-29bc-4970-a89f-a7b14bd38dc2'))342 update_file(343 'types/interpretaties/lithologische_beschrijvingen/md_metadata.xml',344 build_dov_url(345 'geonetwork/srv/dut/csw'346 '?Service=CSW&Request=GetRecordById&Version=2.0.2'347 '&outputSchema=http://www.isotc211.org/2005/gmd'348 '&elementSetName=full&id=45b5610e-9a66-42bd-b920'349 '-af099e399f3b'))350 update_file(351 'types/interpretaties/lithologische_beschrijvingen/'352 'wfsdescribefeaturetype.xml', build_dov_url(353 'geoserver/interpretaties'354 '/lithologische_beschrijvingen/ows?service=wfs&version=2.0.0'355 '&request=DescribeFeatureType'))356 for xsd_schema in LithologischeBeschrijvingen.get_xsd_schemas():357 update_file(358 'types/interpretaties/lithologische_beschrijvingen/xsd_%s.xml' %359 xsd_schema.split('/')[-1], xsd_schema)360 # types/interpretaties/gecodeerde_lithologie361 update_file('types/interpretaties/gecodeerde_lithologie'362 '/gecodeerde_lithologie.xml',363 build_dov_url('data/interpretatie/2001-046845.xml'))364 update_file(365 'types/interpretaties/gecodeerde_lithologie'366 '/wfsgetfeature.xml',367 build_dov_url(368 'geoserver/ows?service=WFS'369 '&version=2.0.0&request=GetFeature&typeName=interpretaties'370 ':gecodeerde_lithologie&maxFeatures=1&CQL_Filter'371 '=Interpretatiefiche=%27') +372 build_dov_url(373 'data'374 '/interpretatie/2001-046845%27'))375 update_file(376 'types/interpretaties/gecodeerde_lithologie/feature.xml',377 build_dov_url(378 'geoserver/ows?service=WFS'379 '&version=2.0.0&request=GetFeature&typeName=interpretaties'380 ':gecodeerde_lithologie&maxFeatures=1&CQL_Filter'381 '=Interpretatiefiche=%27') +382 build_dov_url(383 'data'384 '/interpretatie/2001-046845%27'),385 get_first_featuremember)386 update_file(387 'types/interpretaties/gecodeerde_lithologie/fc_featurecatalogue.xml',388 build_dov_url(389 'geonetwork/srv/dut/csw'390 '?Service=CSW&Request=GetRecordById&Version=2.0.2'391 '&outputSchema=http://www.isotc211.org/2005/gfc'392 '&elementSetName=full&id=0032241d-8920-415e-b1d8-fa0a48154904'))393 update_file(394 'types/interpretaties/gecodeerde_lithologie/md_metadata.xml',395 build_dov_url(396 'geonetwork/srv/dut/csw'397 '?Service=CSW&Request=GetRecordById&Version=2.0.2'398 '&outputSchema=http://www.isotc211.org/2005/gmd'399 '&elementSetName=full&id=35d630e4-9145-46f9-b7dc'400 '-da290a0adc55'))401 update_file(402 'types/interpretaties/gecodeerde_lithologie/wfsdescribefeaturetype'403 '.xml', build_dov_url(404 'geoserver/interpretaties'405 '/gecodeerde_lithologie/ows?service=wfs&version=2.0.0&request'406 '=DescribeFeatureType'))407 for xsd_schema in GecodeerdeLithologie.get_xsd_schemas():408 update_file(409 'types/interpretaties/gecodeerde_lithologie/xsd_%s.xml' %410 xsd_schema.split('/')[-1], xsd_schema)411 # types/interpretaties/geotechnische_codering412 update_file('types/interpretaties/geotechnische_codering'413 '/geotechnische_codering.xml',414 build_dov_url('data/interpretatie/2016-298511.xml'))415 update_file(416 'types/interpretaties/geotechnische_codering'417 '/wfsgetfeature.xml',418 build_dov_url(419 'geoserver/ows?service=WFS'420 '&version=2.0.0&request=GetFeature&typeName=interpretaties'421 ':geotechnische_coderingen&maxFeatures=1&CQL_Filter'422 '=Interpretatiefiche=%27') +423 build_dov_url(424 'data'425 '/interpretatie/2016-298511%27'))426 update_file(427 'types/interpretaties/geotechnische_codering/feature.xml',428 build_dov_url(429 'geoserver/ows?service=WFS'430 '&version=2.0.0&request=GetFeature&typeName=interpretaties'431 ':geotechnische_coderingen&maxFeatures=1&CQL_Filter'432 '=Interpretatiefiche=%27') +433 build_dov_url(434 'data'435 '/interpretatie/2016-298511%27'),436 get_first_featuremember)437 update_file(438 'types/interpretaties/geotechnische_codering/fc_featurecatalogue.xml',439 build_dov_url(440 'geonetwork/srv/dut/csw'441 '?Service=CSW&Request=GetRecordById&Version=2.0.2'442 '&outputSchema=http://www.isotc211.org/2005/gfc'443 '&elementSetName=full&id=85404aa6-2d88-46f6-ae5a-575aece71efd'))444 update_file(445 'types/interpretaties/geotechnische_codering/md_metadata.xml',446 build_dov_url(447 'geonetwork/srv/dut/csw'448 '?Service=CSW&Request=GetRecordById&Version=2.0.2'449 '&outputSchema=http://www.isotc211.org/2005/gmd'450 '&elementSetName=full&id=6a3dc5d4-0744-4d9c-85ce'451 '-da50913851cc'))452 update_file(453 'types/interpretaties/geotechnische_codering/wfsdescribefeaturetype'454 '.xml', build_dov_url(455 'geoserver/interpretaties'456 '/geotechnische_coderingen/ows?service=wfs&version=2.0.0&request'457 '=DescribeFeatureType'))458 for xsd_schema in GeotechnischeCodering.get_xsd_schemas():459 update_file(460 'types/interpretaties/geotechnische_codering/xsd_%s.xml' %461 xsd_schema.split('/')[-1], xsd_schema)462 # types/interpretaties/informele_hydrogeologische_stratigrafie463 update_file('types/interpretaties/informele_hydrogeologische_stratigrafie'464 '/informele_hydrogeologische_stratigrafie.xml',465 build_dov_url('data/interpretatie/2003-297774.xml'))466 update_file(467 'types/interpretaties/informele_hydrogeologische_stratigrafie'468 '/wfsgetfeature.xml',469 build_dov_url(470 'geoserver/ows?service=WFS'471 '&version=2.0.0&request=GetFeature&typeName=interpretaties'472 ':informele_hydrogeologische_stratigrafie&maxFeatures=1'473 '&CQL_Filter=Interpretatiefiche=%27') +474 build_dov_url(475 'data'476 '/interpretatie/2003-297774%27'))477 update_file(478 'types/interpretaties/informele_hydrogeologische_stratigrafie'479 '/feature.xml',480 build_dov_url(481 'geoserver/ows?service=WFS'482 '&version=2.0.0&request=GetFeature&typeName=interpretaties'483 ':informele_hydrogeologische_stratigrafie&maxFeatures=1'484 '&CQL_Filter=Interpretatiefiche=%27') +485 build_dov_url(486 'data'487 '/interpretatie/2003-297774%27'),488 get_first_featuremember)489 update_file(490 'types/interpretaties/informele_hydrogeologische_stratigrafie'491 '/fc_featurecatalogue.xml',492 build_dov_url(493 'geonetwork/srv/dut/csw'494 '?Service=CSW&Request=GetRecordById&Version=2.0.2'495 '&outputSchema=http://www.isotc211.org/2005/gfc'496 '&elementSetName=full&id=69f71840-bd29-4b59-9b02-4e36aafaa041'))497 update_file(498 'types/interpretaties/informele_hydrogeologische_stratigrafie'499 '/md_metadata.xml',500 build_dov_url(501 'geonetwork/srv/dut/csw'502 '?Service=CSW&Request=GetRecordById&Version=2.0.2'503 '&outputSchema=http://www.isotc211.org/2005/gmd'504 '&elementSetName=full'505 '&id=ca1d704a-cdee-4968-aa65-9c353863e4b1'))506 update_file(507 'types/interpretaties/informele_hydrogeologische_stratigrafie/'508 'wfsdescribefeaturetype.xml', build_dov_url(509 'geoserver/interpretaties'510 '/informele_hydrogeologische_stratigrafie/'511 'ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))512 for xsd_schema in InformeleHydrogeologischeStratigrafie.get_xsd_schemas():513 update_file(514 'types/interpretaties/informele_hydrogeologische_stratigrafie/'515 'xsd_%s.xml' % xsd_schema.split('/')[-1], xsd_schema)516 # types/grondwaterfilter517 update_file('types/grondwaterfilter/grondwaterfilter.xml',518 build_dov_url('data/filter/2003-004471.xml'))519 update_file('types/grondwaterfilter/wfsgetfeature.xml',520 build_dov_url('geoserver/ows?service=WFS'521 '&version=2.0.0&request=GetFeature&typeName='522 'gw_meetnetten:meetnetten&maxFeatures=1&'523 'CQL_Filter=filterfiche=%27' + build_dov_url(524 'data/filter/2003-004471%27')))525 update_file('types/grondwaterfilter/feature.xml',526 build_dov_url('geoserver/ows?service=WFS'527 '&version=2.0.0&request=GetFeature&typeName='528 'gw_meetnetten:meetnetten&maxFeatures=1&'529 'CQL_Filter=filterfiche=%27' + build_dov_url(530 'data/filter/2003-004471%27')),531 get_first_featuremember)532 update_file(533 'types/grondwaterfilter/fc_featurecatalogue.xml',534 build_dov_url(535 'geonetwork/srv/dut/csw'536 '?Service=CSW&Request=GetRecordById&Version=2.0.2'537 '&outputSchema=http://www.isotc211.org/2005/gfc'538 '&elementSetName=full&id=b142965f-b2aa-429e-86ff'539 '-a7cb0e065d48'))540 update_file(541 'types/grondwaterfilter/md_metadata.xml',542 build_dov_url(543 'geonetwork/srv/dut/csw'544 '?Service=CSW&Request=GetRecordById&Version=2.0.2'545 '&outputSchema=http://www.isotc211.org/2005/gmd'546 '&elementSetName=full&id=6c39d716-aecc-4fbc-bac8'547 '-4f05a49a78d5'))548 update_file('types/grondwaterfilter/wfsdescribefeaturetype.xml',549 build_dov_url('geoserver/gw_meetnetten/'550 'meetnetten/ows?service=wfs&version=2.0.0&'551 'request=DescribeFeatureType'))552 for xsd_schema in GrondwaterFilter.get_xsd_schemas():553 update_file(554 'types/grondwaterfilter/xsd_%s.xml' % xsd_schema.split('/')[-1],555 xsd_schema)556 update_file('types/grondwaterfilter/grondwaterfilter_geenpeilmeting.xml',557 build_dov_url('data/filter/1976-101132.xml'))558 update_file('types/grondwaterfilter/wfsgetfeature_geenpeilmeting.xml',559 build_dov_url('geoserver/ows?service=WFS'560 '&version=2.0.0&request=GetFeature&typeName='561 'gw_meetnetten:meetnetten&maxFeatures=1&'562 'CQL_Filter=filterfiche=%27' + build_dov_url(563 'data/filter/1976-101132%27')))564 update_file('types/grondwaterfilter/feature_geenpeilmeting.xml',565 build_dov_url('geoserver/ows?service=WFS'566 '&version=2.0.0&request=GetFeature&typeName='567 'gw_meetnetten:meetnetten&maxFeatures=1&'568 'CQL_Filter=filterfiche=%27' + build_dov_url(569 'data/filter/1976-101132%27')),570 get_first_featuremember)571 # types/grondwatermonster572 update_file('types/grondwatermonster/grondwatermonster.xml',573 build_dov_url('data/watermonster/2006-115684.xml'))574 update_file(575 'types/grondwatermonster/wfsgetfeature.xml',576 build_dov_url(577 'geoserver/ows?service=WFS'578 '&version=2.0.0&request=GetFeature&typeName='579 'gw_meetnetten:grondwatermonsters&maxFeatures=1&'580 'CQL_Filter=grondwatermonsterfiche=%27' +581 build_dov_url('data/watermonster/2006-115684') +582 '%27'))583 update_file(584 'types/grondwatermonster/feature.xml',585 build_dov_url(586 'geoserver/ows?service=WFS'587 '&version=2.0.0&request=GetFeature&typeName='588 'gw_meetnetten:grondwatermonsters&maxFeatures=1&'589 'CQL_Filter=grondwatermonsterfiche=%27' +590 build_dov_url('data/watermonster/2006-115684') +591 '%27'),592 get_first_featuremember)593 update_file(594 'types/grondwatermonster/fc_featurecatalogue.xml',595 build_dov_url(596 'geonetwork/srv/dut/csw'597 '?Service=CSW&Request=GetRecordById&Version=2.0.2'598 '&outputSchema=http://www.isotc211.org/2005/gfc'599 '&elementSetName=full&'600 'id=639c9612-4bbb-4826-86fd-fec9afd49bf7'))601 update_file(602 'types/grondwatermonster/md_metadata.xml',603 build_dov_url(604 'geonetwork/srv/dut/csw'605 '?Service=CSW&Request=GetRecordById&Version=2.0.2'606 '&outputSchema=http://www.isotc211.org/2005/gmd'607 '&elementSetName=full&'608 'id=0b378716-39fb-4151-96c5-2021672f4762'))609 update_file(610 'types/grondwatermonster/wfsdescribefeaturetype.xml',611 build_dov_url(612 'geoserver/gw_meetnetten/'613 'grondwatermonsters/ows?service=wfs&version=2.0.0&'614 'request=DescribeFeatureType'))615 for xsd_schema in GrondwaterMonster.get_xsd_schemas():616 update_file(617 'types/grondwatermonster/xsd_%s.xml' % xsd_schema.split('/')[-1],618 xsd_schema)619 # util/owsutil620 update_file(621 'util/owsutil/fc_featurecatalogue_notfound.xml',622 build_dov_url(623 'geonetwork/srv/dut/csw'624 '?Service=CSW&Request=GetRecordById&Version=2.0.2'625 '&outputSchema=http://www.isotc211.org/2005/gfc'626 '&elementSetName=full&id=badfc000-0000-0000-0000'627 '-badfc00badfc'))628 update_file('util/owsutil/wfscapabilities.xml',629 build_dov_url('geoserver/wfs?request'630 '=getcapabilities&service=wfs&version=2.0.0'))631 # types/interpretaties/quartaire_stratigrafie632 update_file('types/interpretaties/quartaire_stratigrafie'633 '/quartaire_stratigrafie.xml',634 build_dov_url('data/interpretatie/1999-057087.xml'))635 update_file(636 'types/interpretaties/quartaire_stratigrafie'637 '/wfsgetfeature.xml',638 build_dov_url(639 'geoserver/ows?service=WFS'640 '&version=2.0.0&request=GetFeature&typeName=interpretaties'641 ':quartaire_stratigrafie&maxFeatures=1&CQL_Filter'642 '=Interpretatiefiche=%27') +643 build_dov_url(644 'data'645 '/interpretatie/1999-057087%27'))646 update_file(647 'types/interpretaties/quartaire_stratigrafie/feature.xml',648 build_dov_url(649 'geoserver/ows?service=WFS'650 '&version=2.0.0&request=GetFeature&typeName=interpretaties'651 ':quartaire_stratigrafie&maxFeatures=1&CQL_Filter'652 '=Interpretatiefiche=%27') +653 build_dov_url(654 'data'655 '/interpretatie/1999-057087%27'),656 get_first_featuremember)657 update_file(658 'types/interpretaties/quartaire_stratigrafie/fc_featurecatalogue.xml',659 build_dov_url(660 'geonetwork/srv/dut/csw'661 '?Service=CSW&Request=GetRecordById&Version=2.0.2'662 '&outputSchema=http://www.isotc211.org/2005/gfc'663 '&elementSetName=full&id=d40ef884-3278-45db-ad69-2c2a8c3981c3'))664 update_file(665 'types/interpretaties/quartaire_stratigrafie/md_metadata.xml',666 build_dov_url(667 'geonetwork/srv/dut/csw'668 '?Service=CSW&Request=GetRecordById&Version=2.0.2'669 '&outputSchema=http://www.isotc211.org/2005/gmd'670 '&elementSetName=full&id=8b204ed6-e44c-4567-bbe8'671 '-bd427eba082c'))672 update_file(673 'types/interpretaties/quartaire_stratigrafie/wfsdescribefeaturetype'674 '.xml', build_dov_url(675 'geoserver/interpretaties'676 '/quartaire_stratigrafie/ows?service=wfs&version=2.0.0&request'677 '=DescribeFeatureType'))678 for xsd_schema in QuartairStratigrafie.get_xsd_schemas():679 update_file(680 'types/interpretaties/quartaire_stratigrafie/xsd_%s.xml' %681 xsd_schema.split('/')[-1], xsd_schema)682 # types/grondmonster683 update_file('types/grondmonster/grondmonster.xml',684 build_dov_url('data/grondmonster/2018-211728.xml'))685 update_file(686 'types/grondmonster/wfsgetfeature.xml',687 build_dov_url(688 'geoserver/ows?service=WFS'689 '&version=2.0.0&request=GetFeature&typeName='690 'boringen:grondmonsters&maxFeatures=1&CQL_Filter'691 '=grondmonsterfiche=%27' +692 build_dov_url(693 'data'694 '/grondmonster/2018-211728') +695 '%27'))696 update_file(697 'types/grondmonster/feature.xml',698 build_dov_url(699 'geoserver/ows?service=WFS'700 '&version=2.0.0&request=GetFeature&typeName='701 'boringen:grondmonsters&maxFeatures=1&CQL_Filter'702 '=grondmonsterfiche=%27' +703 build_dov_url(704 'data'705 '/grondmonster/2018-211728') +706 '%27'),707 get_first_featuremember)708 update_file(709 'types/grondmonster/fc_featurecatalogue.xml',710 build_dov_url(711 'geonetwork/srv/dut/csw'712 '?Service=CSW&Request=GetRecordById&Version=2.0.2'713 '&outputSchema=http://www.isotc211.org/2005/gfc'714 '&elementSetName=full&id=b9338fb5-fc9c-4229-858b-06a5fa3ee49d'))715 update_file(716 'types/grondmonster/md_metadata.xml',717 build_dov_url(718 'geonetwork/srv/dut/csw'719 '?Service=CSW&Request=GetRecordById&Version=2.0.2'720 '&outputSchema=http://www.isotc211.org/2005/gmd'721 '&elementSetName=full&'722 'id=6edeab46-2cfc-4aa2-ae03-307d772f34ae'))723 update_file(724 'types/grondmonster/wfsdescribefeaturetype'725 '.xml',726 build_dov_url('geoserver/boringen'727 '/grondmonsters/ows?service=wfs&version=2.0.0&request'728 '=DescribeFeatureType'))729 for xsd_schema in Grondmonster.get_xsd_schemas():730 update_file(731 'types/grondmonster/xsd_%s.xml' %732 xsd_schema.split('/')[-1], xsd_schema)733 # types/bodemlocatie734 update_file('types/bodemlocatie/bodemlocatie.xml',735 build_dov_url('data/bodemlocatie/2011-000002.xml'))736 update_file(737 'types/bodemlocatie/wfsgetfeature.xml',738 build_dov_url(739 'geoserver/ows?service=WFS'740 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemlocaties'741 '&maxFeatures=1&CQL_Filter=Bodemlocatiefiche=%27' +742 build_dov_url('data/bodemlocatie/2011-000002%27')))743 update_file(744 'types/bodemlocatie/feature.xml',745 build_dov_url(746 'geoserver/ows?service=WFS'747 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemlocaties'748 '&maxFeatures=1&CQL_Filter=Bodemlocatiefiche=%27' +749 build_dov_url('data/bodemlocatie/2011-000002%27')),750 get_first_featuremember)751 update_file(752 'types/bodemlocatie/fc_featurecatalogue.xml',753 build_dov_url(754 'geonetwork/srv/dut/csw'755 '?Service=CSW&Request=GetRecordById&Version=2.0.2'756 '&outputSchema=http://www.isotc211.org/2005/gfc'757 '&elementSetName=full&id=89d4f9a1-0474-4ade-b30f-442c31d17dc6'))758 update_file(759 'types/bodemlocatie/md_metadata.xml',760 build_dov_url(761 'geonetwork/srv/dut/csw'762 '?Service=CSW&Request=GetRecordById&Version=2.0.2'763 '&outputSchema=http://www.isotc211.org/2005/gmd'764 '&elementSetName=full&id=3f507fd9-24c0-40ab-9328-29f0dff571fe'))765 update_file(766 'types/bodemlocatie/wfsdescribefeaturetype.xml',767 build_dov_url(768 'geoserver/bodem/bodemlocaties'769 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))770 for xsd_schema in Bodemlocatie.get_xsd_schemas():771 update_file(772 'types/bodemlocatie/xsd_{}.xml'.format(xsd_schema.split('/')[-1]),773 xsd_schema)774 # types/bodemdiepteinterval775 update_file(776 'types/bodemdiepteinterval/wfsgetfeature.xml',777 build_dov_url(778 'geoserver/ows?service=WFS'779 '&version=2.0.0&request=GetFeature&typeName='780 'bodem:bodemdiepteintervallen&maxFeatures=1&'781 'CQL_Filter=Diepteintervalfiche=%27' +782 build_dov_url('data/bodemdiepteinterval/2018-000004%27')))783 update_file(784 'types/bodemdiepteinterval/feature.xml',785 build_dov_url(786 'geoserver/ows?service=WFS'787 '&version=2.0.0&request=GetFeature&typeName='788 'bodem:bodemdiepteintervallen&maxFeatures=1&'789 'CQL_Filter=Diepteintervalfiche=%27' +790 build_dov_url('data/bodemdiepteinterval/2018-000004%27')),791 get_first_featuremember)792 update_file(793 'types/bodemdiepteinterval/fc_featurecatalogue.xml',794 build_dov_url(795 'geonetwork/srv/dut/csw'796 '?Service=CSW&Request=GetRecordById&Version=2.0.2'797 '&outputSchema=http://www.isotc211.org/2005/gfc'798 '&elementSetName=full&id=859ad05d-d6fc-4850-b040-1bdac3641ff5'))799 update_file(800 'types/bodemdiepteinterval/md_metadata.xml',801 build_dov_url(802 'geonetwork/srv/dut/csw'803 '?Service=CSW&Request=GetRecordById&Version=2.0.2'804 '&outputSchema=http://www.isotc211.org/2005/gmd'805 '&elementSetName=full&id=96a1127f-d7d0-4a33-b24c-04d982b63dce'))806 update_file(807 'types/bodemdiepteinterval/wfsdescribefeaturetype.xml',808 build_dov_url(809 'geoserver/bodem/bodemdiepteintervallen'810 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))811 for xsd_schema in Bodemdiepteinterval.get_xsd_schemas():812 update_file(813 'types/bodemdiepteinterval/xsd_{}.xml'.format(814 xsd_schema.split('/')[-1]),815 xsd_schema)816 # types/bodemobservatie817 update_file('types/bodemobservatie/bodemobservatie.xml',818 build_dov_url('data/bodemobservatie/2019-001221.xml'))819 update_file(820 'types/bodemobservatie/wfsgetfeature.xml',821 build_dov_url(822 'geoserver/ows?service=WFS'823 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemobservaties'824 '&maxFeatures=1&CQL_Filter=Bodemobservatiefiche=%27' +825 build_dov_url('data/bodemobservatie/2019-001221%27')))826 update_file(827 'types/bodemobservatie/feature.xml',828 build_dov_url(829 'geoserver/ows?service=WFS'830 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemobservaties'831 '&maxFeatures=1&CQL_Filter=Bodemobservatiefiche=%27' +832 build_dov_url('data/bodemobservatie/2019-001221%27')),833 get_first_featuremember)834 update_file(835 'types/bodemobservatie/fc_featurecatalogue.xml',836 build_dov_url(837 'geonetwork/srv/dut/csw'838 '?Service=CSW&Request=GetRecordById&Version=2.0.2'839 '&outputSchema=http://www.isotc211.org/2005/gfc'840 '&elementSetName=full&id=44df1272-6b57-471b-9f7a-2dc82f760137'))841 update_file(842 'types/bodemobservatie/md_metadata.xml',843 build_dov_url(844 'geonetwork/srv/dut/csw'845 '?Service=CSW&Request=GetRecordById&Version=2.0.2'846 '&outputSchema=http://www.isotc211.org/2005/gmd'847 '&elementSetName=full&id=dd327fef-62c7-4980-9788-9fac047a1553'))848 update_file(849 'types/bodemobservatie/wfsdescribefeaturetype.xml',850 build_dov_url(851 'geoserver/bodem/bodemobservaties'852 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))853 for xsd_schema in Bodemobservatie.get_xsd_schemas():854 update_file(855 'types/bodemobservatie/xsd_{}.xml'.format(856 xsd_schema.split('/')[-1]),857 xsd_schema)858 # types/bodemmonster859 update_file('types/bodemmonster/bodemmonster.xml',860 build_dov_url('data/bodemmonster/2015-211807.xml'))861 update_file(862 'types/bodemmonster/wfsgetfeature.xml',863 build_dov_url(864 'geoserver/ows?service=WFS'865 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemmonsters'866 '&maxFeatures=1&CQL_Filter=Bodemmonsterfiche=%27' +867 build_dov_url('data/bodemmonster/2015-211807%27')))868 update_file(869 'types/bodemmonster/feature.xml',870 build_dov_url(871 'geoserver/ows?service=WFS'872 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemmonsters'873 '&maxFeatures=1&CQL_Filter=Bodemmonsterfiche=%27' +874 build_dov_url('data/bodemmonster/2015-211807%27')),875 get_first_featuremember)876 update_file(877 'types/bodemmonster/fc_featurecatalogue.xml',878 build_dov_url(879 'geonetwork/srv/dut/csw'880 '?Service=CSW&Request=GetRecordById&Version=2.0.2'881 '&outputSchema=http://www.isotc211.org/2005/gfc'882 '&elementSetName=full&id=7d69c092-fa5a-4399-86ed-003877f5899e'))883 update_file(884 'types/bodemmonster/md_metadata.xml',885 build_dov_url(886 'geonetwork/srv/dut/csw'887 '?Service=CSW&Request=GetRecordById&Version=2.0.2'888 '&outputSchema=http://www.isotc211.org/2005/gmd'889 '&elementSetName=full&id=ff1902b2-7ba2-46be-ba8c-bfcf893444c2'))890 update_file(891 'types/bodemmonster/wfsdescribefeaturetype.xml',892 build_dov_url(893 'geoserver/bodem/bodemmonsters'894 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))895 for xsd_schema in Bodemmonster.get_xsd_schemas():896 update_file(897 'types/bodemmonster/xsd_{}.xml'.format(xsd_schema.split('/')[-1]),898 xsd_schema)899 # types/bodemsite900 update_file('types/bodemsite/bodemsite.xml',901 build_dov_url('data/bodemsite/2013-000180.xml'))902 update_file(903 'types/bodemsite/wfsgetfeature.xml',904 build_dov_url(905 'geoserver/ows?service=WFS'906 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemsites'907 '&maxFeatures=1&CQL_Filter=Bodemsitefiche=%27' +908 build_dov_url('data/bodemsite/2013-000180%27')))909 update_file(910 'types/bodemsite/feature.xml',911 build_dov_url(912 'geoserver/ows?service=WFS'913 '&version=2.0.0&request=GetFeature&typeName=bodem:bodemsites'914 '&maxFeatures=1&CQL_Filter=Bodemsitefiche=%27' +915 build_dov_url('data/bodemsite/2013-000180%27')),916 get_first_featuremember)917 update_file(918 'types/bodemsite/fc_featurecatalogue.xml',919 build_dov_url(920 'geonetwork/srv/dut/csw'921 '?Service=CSW&Request=GetRecordById&Version=2.0.2'922 '&outputSchema=http://www.isotc211.org/2005/gfc'923 '&elementSetName=full&id=955d4bc8-9d78-4af6-9782-85698caae0aa'))924 update_file(925 'types/bodemsite/md_metadata.xml',926 build_dov_url(927 'geonetwork/srv/dut/csw'928 '?Service=CSW&Request=GetRecordById&Version=2.0.2'929 '&outputSchema=http://www.isotc211.org/2005/gmd'930 '&elementSetName=full&id=27142078-f0d0-46e3-b97e-2ffc2c6bdd41'))931 update_file(932 'types/bodemsite/wfsdescribefeaturetype.xml',933 build_dov_url(934 'geoserver/bodem/bodemsites'935 '/ows?service=wfs&version=2.0.0&request=DescribeFeatureType'))936 for xsd_schema in Bodemsite.get_xsd_schemas():937 update_file(938 'types/bodemsite/xsd_{}.xml'.format(xsd_schema.split('/')[-1]),939 xsd_schema)940 # types/bodemclassificatie941 update_file(942 'types/bodemclassificatie/wfsgetfeature.xml',943 build_dov_url(944 'geoserver/ows?service=WFS'945 '&version=2.0.0&request=GetFeature&typeName='946 'bodem:bodemclassificaties&maxFeatures=1&'947 'CQL_Filter=Bodemclassificatiefiche=%27' +948 build_dov_url('data/belgischebodemclassificatie/2018-000146%27')))949 update_file(950 'types/bodemclassificatie/feature.xml',951 build_dov_url(952 'geoserver/ows?service=WFS'953 '&version=2.0.0&request=GetFeature&typeName='954 'bodem:bodemclassificaties&maxFeatures=1&'955 'CQL_Filter=Bodemclassificatiefiche=%27' +956 build_dov_url('data/belgischebodemclassificatie/2018-000146%27')),957 get_first_featuremember)958 update_file(959 'types/bodemclassificatie/fc_featurecatalogue.xml',960 build_dov_url('geonetwork/srv/dut/csw'961 '?Service=CSW&Request=GetRecordById&Version=2.0.2'962 '&outputSchema=http://www.isotc211.org/2005/gfc'963 '&elementSetName=full&'964 'id=9ace8d74-8daa-461f-86bb-273573bc7fa9'))965 update_file('types/bodemclassificatie/md_metadata.xml',966 build_dov_url(967 'geonetwork/srv/dut/csw'968 '?Service=CSW&Request=GetRecordById&Version=2.0.2'969 '&outputSchema=http://www.isotc211.org/2005/gmd'970 '&elementSetName=full&'971 'id=7f668812-edc3-464b-870c-08e964f884b6'))972 update_file('types/bodemclassificatie/wfsdescribefeaturetype.xml',973 build_dov_url(974 'geoserver/bodem/bodemclassificaties'975 '/ows?service=wfs&version=2.0.0'976 '&request=DescribeFeatureType'))977 for xsd_schema in Bodemclassificatie.get_xsd_schemas():978 update_file(979 'types/bodemclassificatie/xsd_%s.xml' %980 xsd_schema.split('/')[-1], xsd_schema)981 # types/gw_vergunningen982 update_file(983 'types/grondwatervergunning/wfsgetfeature.xml',984 build_dov_url(985 'geoserver/ows?service=WFS'986 '&version=2.0.0&request=GetFeature&typeName='987 'gw_vergunningen:alle_verg&maxFeatures=1&CQL_Filter'988 '=id=38598'))989 update_file(990 'types/grondwatervergunning/feature.xml',991 build_dov_url(992 'geoserver/ows?service=WFS'993 '&version=2.0.0&request=GetFeature&typeName='994 'gw_vergunningen:alle_verg&maxFeatures=1&CQL_Filter'995 '=id=38598'), get_first_featuremember)996 update_file(997 'types/grondwatervergunning/fc_featurecatalogue.xml',998 build_dov_url('geonetwork/srv/dut/csw'999 '?Service=CSW&Request=GetRecordById&Version=2.0.2'1000 '&outputSchema=http://www.isotc211.org/2005/gfc'1001 '&elementSetName=full&id=5e605651-'1002 '6b2e-406f-863f-d2eda4d3e534'))1003 update_file('types/grondwatervergunning/md_metadata.xml',1004 build_dov_url(1005 'geonetwork/srv/dut/csw'1006 '?Service=CSW&Request=GetRecordById&Version=2.0.2'1007 '&outputSchema=http://www.isotc211.org/2005/gmd'1008 '&elementSetName=full&id=1b8d9dce-40b2-450c-81ed-'1009 'decb453b3143'))1010 update_file('types/grondwatervergunning/wfsdescribefeaturetype.xml',1011 build_dov_url(1012 'geoserver/gw_vergunningen/alle_verg'1013 '/ows?service=wfs&version=2.0.0'1014 '&request=DescribeFeatureType'))1015 for xsd_schema in GrondwaterVergunning.get_xsd_schemas():1016 update_file(1017 'types/grondwatervergunning/xsd_%s.xml' %1018 xsd_schema.split('/')[-1], xsd_schema)1019 for r in pool.join():1020 if r.get_error() is not None:1021 sys.stdout.write('{}: {}\n'.format(1022 type(r.get_error()).__name__, r.get_error()))1023 sys.exit(1)1024 else:1025 output, failed = r.get_result()1026 sys.stdout.write(output)1027 if failed:...
pubmed_updater.py
Source:pubmed_updater.py
1from data_load.base.data_source_processor import DataSourceProcessor2from data_load.base.data_source_xml import XMLDataSource3from data_load.pubmed.pubmed_relationship_processor import PubmedRelationshipProcessor4from data_load.base.constants import API_URL, ID_PUBMED5from data_load.base.utils.export_doc_ids import get_doc_ids6import data_load.base.utils.file_utils as file_utils7import os8import json9import time10import requests11# from config import *12from email_client import EmailClient13from prospective_citations import FindProspectiveCitations14ALL_PUBMED_IDS_FILE = 'all_pubmed_ids.json'15DIR_DOCS_WITH_NEW_CITATION = 'docs_with_new_citations'16DIR_DOCS_CITATION_HISTORY = 'docs_citation_history'17DIR_PROSPECTS = 'prospects'18DIR_UPDATE_SUMMARY = 'update_summary'19class PubmedUpdater(object):20 def __init__(self, load_manager):21 self.load_manager = load_manager22 # self.file_summaries = {}23 self.existing_pubmed_ids = {}24 # self.docs_with_new_citations = {}25 def get_existing_pmids(self):26 load_config = self.load_manager.get_load_config()27 self.existing_pubmed_ids = get_doc_ids(server=load_config.server,28 src_index=load_config.index,29 src_type=load_config.type,30 dest_dir=load_config.other_files_directory(),31 dest_file_name=ALL_PUBMED_IDS_FILE)32 load_config.logger().info('Existing pmid count: ' + str(len(self.existing_pubmed_ids)))33 def clean_up_data_source_summary(self, data_source_summary):34 updated_ids = data_source_summary['updated_ids']35 indexed_ids = data_source_summary['indexed_ids']36 filtered_indexed_ids = {}37 for pmid in indexed_ids:38 if pmid in self.existing_pubmed_ids:39 updated_ids[pmid] = 040 else:41 filtered_indexed_ids[pmid] = 042 data_source_summary['updated_ids'] = updated_ids43 data_source_summary['indexed_ids'] = filtered_indexed_ids44 return data_source_summary45 def process_file(self, update_file):46 file_name = os.path.basename(update_file)47 load_config = self.load_manager.get_load_config()48 load_config.data_source_name = file_name.split('.')[0]49 load_config.logger().info('Processing file: ' + str(file_name))50 load_config.process_count = 451 data_processor = DataSourceProcessor(52 load_config, XMLDataSource(update_file, 2))53 data_processor.run()54 # Get data load summary55 data_source_summary = data_processor.get_combined_data_source_summary()56 57 # Clean up updated vs indexed ids58 data_source_summary = self.clean_up_data_source_summary(data_source_summary)59 # Save update summary60 self.save_update_summary(data_source_summary, update_file)61 return data_source_summary62 # Process relationships63 # self.process_relationships(update_file, data_source_summary)64 def process_relationships(self, update_file):65 file_name = os.path.basename(update_file)66 data_source_summary = self.load_update_summary(update_file)67 68 load_config = self.load_manager.get_load_config()69 load_config.data_source_name = file_name.split('.')[0] + '_relations'70 load_config.process_count = 471 load_config.append_relations = True72 load_config.source = ''73 74 # print 'Processing relationships......'75 load_config.logger().info('Processing relationships: ' + str(file_name))76 data_processor = PubmedRelationshipProcessor(load_config, XMLDataSource(update_file, 2), data_source_summary)77 data_processor.run()78 79 docs_with_new_citations = data_processor.get_docs_with_new_citations()80 # Save docs with new citations81 self.save_docs_with_new_citations(docs_with_new_citations, update_file)82 # Save docs citation history83 docs_citations_history = data_processor.get_citations_history()84 self.save_docs_citations_history(docs_citations_history, update_file)85 return docs_with_new_citations86 def save_new_pmids(self, update_files):87 load_config = self.load_manager.get_load_config()88 self.existing_pubmed_ids = file_utils.load_file(load_config.other_files_directory(), ALL_PUBMED_IDS_FILE)89 update_summary = self.generate_update_summary(update_files)90 for update_file in update_summary:91 update_summary_for_file = update_summary[update_file]92 articles_processed = update_summary_for_file['articles_processed']93 for _id in articles_processed:94 self.existing_pubmed_ids[_id] = None95 file_utils.save_file(load_config.other_files_directory(), ALL_PUBMED_IDS_FILE, self.existing_pubmed_ids)96 def get_update_records_directory(self, sub_directory=None):97 load_config = self.load_manager.get_load_config()98 other_files_directory = load_config.other_files_directory()99 100 update_records_directory = other_files_directory + '/' + 'update_records'101 if sub_directory is not None:102 update_records_directory += '/' + sub_directory103 file_utils.make_directory(update_records_directory)104 return update_records_directory105 def save_update_summary(self, update_summary, update_file):106 update_record_file_name = self.get_update_summary_file_name(update_file)107 file_utils.save_file(self.get_update_records_directory(DIR_UPDATE_SUMMARY), update_record_file_name, update_summary) 108 def load_update_summary(self, update_file):109 update_record_file_name = self.get_update_summary_file_name(update_file)110 # print 'update_record_file_name', update_record_file_name111 return file_utils.load_file(self.get_update_records_directory(DIR_UPDATE_SUMMARY), update_record_file_name)112 def save_docs_with_new_citations(self, docs_with_new_citations, update_file):113 update_record_file_name = self.get_docs_with_new_citations_file_name(update_file)114 file_utils.save_file(self.get_update_records_directory(DIR_DOCS_WITH_NEW_CITATION), update_record_file_name, docs_with_new_citations) 115 def load_docs_with_new_citations(self, update_file):116 update_record_file_name = self.get_docs_with_new_citations_file_name(update_file)117 return file_utils.load_file(self.get_update_records_directory(DIR_DOCS_WITH_NEW_CITATION), update_record_file_name) 118 def save_docs_citations_history(self, doc_citations_history, update_file):119 update_record_file_name = self.get_docs_citations_history_file_name(update_file)120 file_utils.save_file(self.get_update_records_directory(DIR_DOCS_CITATION_HISTORY), update_record_file_name, doc_citations_history) 121 def get_update_file_name(self, update_file):122 file_name = os.path.basename(update_file)123 name = file_name.split('.')[0]124 return name125 def get_update_summary_file_name(self, update_file):126 name = self.get_update_file_name(update_file)127 file_name = 'update_summary_' + name + '.json'128 return file_name129 def get_docs_with_new_citations_file_name(self, update_file):130 name = self.get_update_file_name(update_file)131 file_name = 'docs_with_new_citations_' + name + '.json'132 return file_name133 def get_docs_citations_history_file_name(self, update_file):134 name = self.get_update_file_name(update_file)135 file_name = 'docs_citations_history_' + name + '.json'136 return file_name137 def get_new_pmids_per_file(self, update_files):138 new_pmids_per_file = {}139 for update_file in update_files:140 indexed_ids = {}141 data_source_summary = self.load_update_summary(update_file)142 batch_indexed_ids = data_source_summary['indexed_ids']143 for _id in batch_indexed_ids:144 if _id not in self.existing_pubmed_ids:145 indexed_ids[_id] = 0146 new_pmids_per_file[update_file] = indexed_ids147 # print 'New pmids', len(indexed_ids)148 return new_pmids_per_file149 def get_total_updated_ids(self, update_files):150 total_updated_ids_per_file = {}151 for update_file in update_files:152 # indexed_ids = {}153 updated_ids = {}154 data_source_summary = self.load_update_summary(update_file)155 batch_indexed_ids = data_source_summary['indexed_ids']156 batch_updated_ids = data_source_summary['updated_ids']157 for _id in batch_indexed_ids:158 updated_ids[_id] = _id159 for _id in batch_updated_ids:160 updated_ids[_id] = _id161 total_updated_ids_per_file[update_file] = updated_ids162 # print 'Total updated pmids', total_updated_ids163 return total_updated_ids_per_file164 def generate_update_summary(self, update_files):165 # Update stats166 total_updated_ids_per_file = self.get_total_updated_ids(update_files)167 new_pmids_per_file = self.get_new_pmids_per_file(update_files)168 update_data = {}169 for update_file in update_files:170 total_updated_ids = {}171 new_pmids = {}172 if update_file in total_updated_ids_per_file:173 total_updated_ids = total_updated_ids_per_file[update_file]174 if update_file in new_pmids_per_file:175 new_pmids = new_pmids_per_file[update_file]176 update_data[update_file] = {177 'articles_processed': total_updated_ids,178 'new_articles': new_pmids179 }180 return update_data181 def get_docs_with_new_citations(self, update_files):182 # Merge docs with new citations from different update files183 docs_with_new_citations = {}184 for update_file in update_files:185 docs_with_new_citations_for_update_file = self.load_docs_with_new_citations(update_file)186 for pmid in docs_with_new_citations_for_update_file:187 if pmid not in docs_with_new_citations:188 docs_with_new_citations[pmid] = []189 new_citations = docs_with_new_citations_for_update_file[pmid]190 docs_with_new_citations[pmid].extend(new_citations)191 192 return docs_with_new_citations193 ...
list.py
Source:list.py
1# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other2# Spack Project Developers. See the top-level COPYRIGHT file for details.3#4# SPDX-License-Identifier: (Apache-2.0 OR MIT)5import pytest6from spack.main import SpackCommand7list = SpackCommand('list')8def test_list():9 output = list()10 assert 'cloverleaf3d' in output11 assert 'hdf5' in output12def test_list_filter():13 output = list('py-*')14 assert 'py-numpy' in output15 assert 'perl-file-copy-recursive' not in output16 output = list('py-')17 assert 'py-numpy' in output18 assert 'perl-file-copy-recursive' in output19@pytest.mark.maybeslow20def test_list_search_description():21 output = list('--search-description', 'xml')22 assert 'expat' in output23def test_list_tags():24 output = list('--tags', 'proxy-app')25 assert 'cloverleaf3d' in output26 assert 'hdf5' not in output27def test_list_format_name_only():28 output = list('--format', 'name_only')29 assert 'cloverleaf3d' in output30 assert 'hdf5' in output31@pytest.mark.maybeslow32def test_list_format_version_json():33 output = list('--format', 'version_json')34 assert ' {"name": "cloverleaf3d",' in output35 assert ' {"name": "hdf5",' in output36 import json37 json.loads(output)38@pytest.mark.maybeslow39def test_list_format_html():40 output = list('--format', 'html')41 assert '<div class="section" id="cloverleaf3d">' in output42 assert '<h1>cloverleaf3d' in output43 assert '<div class="section" id="hdf5">' in output44 assert '<h1>hdf5' in output45def test_list_update(tmpdir):46 update_file = tmpdir.join('output')47 # not yet created when list is run48 list('--update', str(update_file))49 assert update_file.exists()50 with update_file.open() as f:51 assert f.read()52 # created but older than any package53 with update_file.open('w') as f:54 f.write('empty\n')55 update_file.setmtime(0)56 list('--update', str(update_file))57 assert update_file.exists()58 with update_file.open() as f:59 assert f.read() != 'empty\n'60 # newer than any packages61 with update_file.open('w') as f:62 f.write('empty\n')63 list('--update', str(update_file))64 assert update_file.exists()65 with update_file.open() as f:...
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