| 1 | #!/usr/bin/env python |
|---|
| 2 | ''' |
|---|
| 3 | Main script to do the document ingest from the OAI harvested files to the |
|---|
| 4 | discovery postgres DB. NB, can be ran for all datacentres using the run_all_ingest.py script |
|---|
| 5 | or can specify an individual datacentre to run the ingester on. |
|---|
| 6 | As well as doing the ingest, a backup directory is created to store the created moles files. |
|---|
| 7 | ''' |
|---|
| 8 | import os, sys, string, getopt, logging, re, pkg_resources |
|---|
| 9 | from time import strftime |
|---|
| 10 | from SchemaNameSpace import SchemaNameSpace |
|---|
| 11 | from ndg.common.src.lib.ndgresources import ndgResources |
|---|
| 12 | import ndg.common.src.lib.fileutilities as FileUtilities |
|---|
| 13 | from ndg.common.src.clients.reldb.postgres.postgresclient import PostgresClient as pgc |
|---|
| 14 | from Utilities import idget, IngestTracking |
|---|
| 15 | from Utilities import DatasetBasicParameters_MEDIN_v01,DatasetBasicParameters_Original |
|---|
| 16 | from Utilities import ndgRedirectTransform,redirectUrlChanger |
|---|
| 17 | from DeleteRecord import DeleteRecord |
|---|
| 18 | import datetime,time |
|---|
| 19 | from ndg.common.src.models.ndgObject import ndgObject |
|---|
| 20 | from ndg.common.src.lib.ndgresources import ndgResources |
|---|
| 21 | from AbstractFormatIngester_original import AbstractFormatIngesterOriginal |
|---|
| 22 | from ndg.common.src.models.ndgObject import ndgObject |
|---|
| 23 | |
|---|
| 24 | SAXON_JAR_FILE = '/disks/glue1/sdonegan/NDG3_workspace/buildouts/oai_document_ingester_MEDIN/ingestAutomation-upgrade/OAIBatch/lib/saxon9.jar' |
|---|
| 25 | |
|---|
| 26 | |
|---|
| 27 | class AbstractDocumentIngester(object): |
|---|
| 28 | ''' |
|---|
| 29 | Class to handle the ingest of files from the OAI harvester to the discovery service postgres DB |
|---|
| 30 | - including running the various transforms and parsings to get all doc types and spatiotemporal |
|---|
| 31 | data in the correct form in the DB |
|---|
| 32 | ''' |
|---|
| 33 | lineSeparator = "------------------------------" |
|---|
| 34 | |
|---|
| 35 | # The directory to put things for a tape backup (should already exist) |
|---|
| 36 | BACKUP_DIR = '/disks/glue1/oaiBackup/' |
|---|
| 37 | |
|---|
| 38 | #keep ndg3beta service for testing MEDIN upgrades |
|---|
| 39 | NDG_redirect_URL = 'http://ndg3beta.badc.rl.ac.uk/URL_redirect_NDG3/ndgURLredirect/redirect?url=' |
|---|
| 40 | |
|---|
| 41 | |
|---|
| 42 | #NDG_redirect_URL = 'http://triton.badc.rl.ac.uk/URL_redirect_NDG3/ndgURLredirect/redirect?url=' |
|---|
| 43 | |
|---|
| 44 | |
|---|
| 45 | |
|---|
| 46 | def _setupCmdLineOptions(self): |
|---|
| 47 | ''' |
|---|
| 48 | Determine the logging level to use and configure this appropriately |
|---|
| 49 | @return args: any input arguments - excluding options |
|---|
| 50 | ''' |
|---|
| 51 | |
|---|
| 52 | # check for verbose option |
|---|
| 53 | |
|---|
| 54 | try: |
|---|
| 55 | opts, args = getopt.getopt(sys.argv[1:], "vd") |
|---|
| 56 | except getopt.GetoptError, err: |
|---|
| 57 | # print help information and exit: |
|---|
| 58 | print str(err) # will print something like "option -a not recognized" |
|---|
| 59 | sys.exit(2) |
|---|
| 60 | |
|---|
| 61 | if len(args) < 1: |
|---|
| 62 | self.usage() |
|---|
| 63 | |
|---|
| 64 | loggingLevel = logging.WARNING |
|---|
| 65 | for o, a in opts: |
|---|
| 66 | if o == "-v": |
|---|
| 67 | print " - Verbose mode ON" |
|---|
| 68 | loggingLevel = logging.INFO |
|---|
| 69 | elif o == "-d": |
|---|
| 70 | print " - Debug mode ON" |
|---|
| 71 | loggingLevel = logging.DEBUG |
|---|
| 72 | |
|---|
| 73 | |
|---|
| 74 | # set up any keywords on the object |
|---|
| 75 | # NB, be careful to keep the instance variables the same name as the keywords! (not also feed keywords also in here) |
|---|
| 76 | for arg in args: |
|---|
| 77 | |
|---|
| 78 | keywordArgs=['ingestFromDate','interval','individualFile','interval','ingestFromDate','eXistDBHostname','eXistPortNo','dataCentrePoll'] |
|---|
| 79 | |
|---|
| 80 | |
|---|
| 81 | |
|---|
| 82 | bits = arg.split('=') |
|---|
| 83 | if len(bits) == 2: |
|---|
| 84 | if bits[0] == keywordArgs[0]: |
|---|
| 85 | self.setIngestFromDate(bits[1]) |
|---|
| 86 | elif bits[0] == keywordArgs[1]: |
|---|
| 87 | self.setPollInterval(bits[1]) |
|---|
| 88 | elif bits[0] == keywordArgs[2]: |
|---|
| 89 | print " - Running in single file ingestion mode!" |
|---|
| 90 | self.setIndFileToIngest(bits[1]) |
|---|
| 91 | elif bits[0] not in keywordArgs: |
|---|
| 92 | print "\nWARNING: invalid keyword supplied (%s)! \n"%bits[0] |
|---|
| 93 | sys.exit(2) |
|---|
| 94 | else: |
|---|
| 95 | setattr(self, bits[0], bits[1]) |
|---|
| 96 | |
|---|
| 97 | print self.lineSeparator |
|---|
| 98 | |
|---|
| 99 | # NB, this is a slight fudge as cannot get the detailed logging to work |
|---|
| 100 | # without setting up a new logger here - which means we get two loggers |
|---|
| 101 | # outputing data. The initial call to logging needs to be tracked down |
|---|
| 102 | # and configured correctly, so this can be avoided... |
|---|
| 103 | # self.logger = logging.getLogger() |
|---|
| 104 | # self.logger.setLevel(loggingLevel) |
|---|
| 105 | |
|---|
| 106 | # create console handler and set level to debug |
|---|
| 107 | # ch = logging.StreamHandler() |
|---|
| 108 | # ch.setLevel(loggingLevel) |
|---|
| 109 | # create formatter |
|---|
| 110 | # formatter = logging.Formatter('%(asctime)s %(filename)s:%(lineno)d %(levelname)s %(message)s') |
|---|
| 111 | # add formatter to ch |
|---|
| 112 | # ch.setFormatter(formatter) |
|---|
| 113 | # add ch to logger |
|---|
| 114 | # self.logger.addHandler(ch) |
|---|
| 115 | return args |
|---|
| 116 | |
|---|
| 117 | |
|---|
| 118 | def getID(self, filename): |
|---|
| 119 | ''' |
|---|
| 120 | Gets the identifier out of an input metadata xml record. |
|---|
| 121 | @param filename - name of document file being processed |
|---|
| 122 | @return: ID - id to use to refer to the document |
|---|
| 123 | ''' |
|---|
| 124 | logging.info("Retrieving identifier for metadata record " + filename) |
|---|
| 125 | xml=file(filename).read() |
|---|
| 126 | ID = idget(xml) |
|---|
| 127 | return ID |
|---|
| 128 | |
|---|
| 129 | |
|---|
| 130 | |
|---|
| 131 | |
|---|
| 132 | |
|---|
| 133 | def getConfigDetails(self, datacentre): |
|---|
| 134 | ''' |
|---|
| 135 | Get the harvested records directory and groups for this datacentre from the |
|---|
| 136 | datacentre specific config file. The harvested records directory depends on the |
|---|
| 137 | datacentres OAI base url, the set and format. These have to be know up-front. |
|---|
| 138 | The groups denote which 'portal groups' they belong to - for limiting searches to |
|---|
| 139 | say NERC-only datacentres records. |
|---|
| 140 | Groups are added to the intermediate MOLES when it is created. |
|---|
| 141 | @param datacentre: datacentre to use when looking up config file |
|---|
| 142 | ''' |
|---|
| 143 | # initialise the variables to retrieve from the config file |
|---|
| 144 | self._harvest_home = "" |
|---|
| 145 | self._datacentre_groups = "" |
|---|
| 146 | self._datacentre_format = "" |
|---|
| 147 | self._datacentre_namespace = "" |
|---|
| 148 | self._NDG_dataProvider = False |
|---|
| 149 | |
|---|
| 150 | datacentre_config_filename = 'datacentre_config/' + datacentre + "_config.properties" |
|---|
| 151 | logging.info("Retrieving data from datacentre config file, " + datacentre_config_filename) |
|---|
| 152 | |
|---|
| 153 | |
|---|
| 154 | #file = pkg_resources.resource_string('OAIBatch', datacentre_config_filename) |
|---|
| 155 | file = open(datacentre_config_filename,"r") |
|---|
| 156 | |
|---|
| 157 | for line in file.readlines(): |
|---|
| 158 | words = line.split() |
|---|
| 159 | if len(words) == 0: |
|---|
| 160 | continue |
|---|
| 161 | elif words[0] == 'host_path': |
|---|
| 162 | self._harvest_home = words[1].rstrip() |
|---|
| 163 | elif words[0] == 'groups': |
|---|
| 164 | self._datacentre_groups = words[1:] |
|---|
| 165 | elif words[0] == 'format': |
|---|
| 166 | self._datacentre_format = words[1] |
|---|
| 167 | elif words[0] == 'namespace': |
|---|
| 168 | self._datacentre_namespace = words[1] |
|---|
| 169 | elif words[0] == 'NDG_dataProvider': |
|---|
| 170 | self._NDG_dataProvider = True |
|---|
| 171 | |
|---|
| 172 | if self._harvest_home == "": |
|---|
| 173 | sys.exit("Failed at getting harvested records directory stage. datacentre config file tried = %s" %datacentre_config_filename) |
|---|
| 174 | |
|---|
| 175 | logging.info("harvested records are in " + self._harvest_home) |
|---|
| 176 | |
|---|
| 177 | if self._datacentre_groups == "": |
|---|
| 178 | logging.info("No groups/keywords set for datacentre " + datacentre) |
|---|
| 179 | else: |
|---|
| 180 | logging.info("datacentre groups/keywords: " + str(self._datacentre_groups)) |
|---|
| 181 | |
|---|
| 182 | if self._datacentre_format == "": |
|---|
| 183 | sys.exit("Failed at stage: getting datacentre format. datacentre config file tried = %s" %datacentre_config_filename) |
|---|
| 184 | |
|---|
| 185 | logging.info("format being harvested: " + self._datacentre_format) |
|---|
| 186 | |
|---|
| 187 | if self._datacentre_namespace == "": |
|---|
| 188 | sys.exit("Failed at stage: getting datacentre namespace. datacentre config file tried = %s" %datacentre_config_filename) |
|---|
| 189 | |
|---|
| 190 | logging.info("datacentre namespace: " + self._datacentre_namespace) |
|---|
| 191 | |
|---|
| 192 | if self._NDG_dataProvider: |
|---|
| 193 | logging.info("Datacentre classified as an NDG data provider") |
|---|
| 194 | else: |
|---|
| 195 | logging.info("Datacentre is not classified as an NDG data provider") |
|---|
| 196 | logging.info(self.lineSeparator) |
|---|
| 197 | |
|---|
| 198 | |
|---|
| 199 | def convertDIFtoISO(self,metadataFileLoc,repositoryName,metadataID,metadataFilename): |
|---|
| 200 | ''' |
|---|
| 201 | New to MEDIN ingest Upgrade: |
|---|
| 202 | This converts the still supported DIF to ISO format - all extractions will come from ISO, |
|---|
| 203 | whether original ISO format or conversions to ISO. |
|---|
| 204 | |
|---|
| 205 | Uses the new "dif2stubISO" xquery |
|---|
| 206 | ''' |
|---|
| 207 | xQueryType = 'dif2stubISO' |
|---|
| 208 | |
|---|
| 209 | self._repository_local_id = repositoryName #'neodc.nerc.ac.uk' |
|---|
| 210 | self.discovery_id = metadataID |
|---|
| 211 | self._local_id = metadataFilename |
|---|
| 212 | self._repository = repositoryName #'neodc.nerc.ac.uk' |
|---|
| 213 | |
|---|
| 214 | self.xqueryLib = ndgResources() |
|---|
| 215 | xquery = self.xqueryLib.createXQuery(xQueryType,metadataFileLoc, self._repository_local_id, self._local_id) |
|---|
| 216 | |
|---|
| 217 | # sort out the input ID stuff |
|---|
| 218 | xquery=xquery.replace('Input_Entry_ID', self.discovery_id) |
|---|
| 219 | xquery=xquery.replace('repository_localid', self._repository) |
|---|
| 220 | |
|---|
| 221 | # strip out the eXist reference to the libraries; these files should be available in the |
|---|
| 222 | # running dir - as set up by oai_ingest.py |
|---|
| 223 | xquery=xquery.replace('xmldb:exist:///db/xqueryLib/Vocabs/', '') |
|---|
| 224 | xquery=xquery.replace('xmldb:exist:///db/xqueryLib/Utilities/', '') |
|---|
| 225 | |
|---|
| 226 | # write the query to file, to make it easier to input |
|---|
| 227 | # NB, running directly at the command line leads to problems with the interpretation of $ characters |
|---|
| 228 | xqFile = "currentQuery" + xQueryType + ".xq" |
|---|
| 229 | |
|---|
| 230 | FileUtilities.createFile(xqFile, xquery) |
|---|
| 231 | |
|---|
| 232 | # ensure the jar file is available - NB, this may be running from a different |
|---|
| 233 | # location - e.g. the OAIInfoEditor.lib.harvester - and this won't have the |
|---|
| 234 | # saxon file directly on its filesystem |
|---|
| 235 | |
|---|
| 236 | #jarFile = pkg_resources.resource_filename('OAIBatch', SAXON_JAR_FILE) |
|---|
| 237 | jarFile = SAXON_JAR_FILE |
|---|
| 238 | # Now do the transform |
|---|
| 239 | os.putenv ('PATH', ':/usr/java/jdk1.5.0_03/bin:/usr/java/jdk1.5.0_03:/usr/java/jdk1.5.0_03/lib/tools.jar:/usr/local/WSClients/OAIBatch:/usr/local/exist-client/bin:/bin:/usr/bin:.') |
|---|
| 240 | xqCommand = "java -cp %s net.sf.saxon.Query %s !omit-xml-declaration=yes" %(jarFile, xqFile) |
|---|
| 241 | |
|---|
| 242 | logging.debug("Running saxon command: " + xqCommand) |
|---|
| 243 | pipe = os.popen(xqCommand + " 2>&1") |
|---|
| 244 | output = pipe.read() |
|---|
| 245 | status = pipe.close() |
|---|
| 246 | |
|---|
| 247 | if status is not None: |
|---|
| 248 | raise SystemError, 'Failed at running the XQuery' |
|---|
| 249 | |
|---|
| 250 | |
|---|
| 251 | # now remove the temp xquery file |
|---|
| 252 | '''status = os.unlink(xqFile) |
|---|
| 253 | if status is not None: |
|---|
| 254 | raise OSError, 'Failed to remove the temporary xquery file, ' + xqFile''' |
|---|
| 255 | |
|---|
| 256 | logging.info("Transform completed successfully") |
|---|
| 257 | |
|---|
| 258 | return output |
|---|
| 259 | |
|---|
| 260 | |
|---|
| 261 | |
|---|
| 262 | def _convertIngestFiles(self, originals_dir, discovery_dir, stubIso_dir, format): |
|---|
| 263 | ''' |
|---|
| 264 | Processes/renames the files (changed 08/01/07 to get id from inside file) |
|---|
| 265 | - also replace any namespace declarations with a standard one which we know works in NDG |
|---|
| 266 | NB, this copies files from the original dir to the discovery dir |
|---|
| 267 | @param originals_dir: directory to convert files from |
|---|
| 268 | @param discovery_dir: directory in which converted files will end up |
|---|
| 269 | @return numfilesproc: counter of number of files processed |
|---|
| 270 | ''' |
|---|
| 271 | numfilesproc = 0 |
|---|
| 272 | |
|---|
| 273 | self.inputFileOrigFinal = {} |
|---|
| 274 | |
|---|
| 275 | logging.info(self.lineSeparator) |
|---|
| 276 | logging.info("Renaming files:") |
|---|
| 277 | |
|---|
| 278 | for filename in os.listdir(originals_dir): |
|---|
| 279 | |
|---|
| 280 | if not filename.endswith('.xml'): |
|---|
| 281 | logging.warning('File %s is not xml format. Not processed' %(filename)) |
|---|
| 282 | continue |
|---|
| 283 | |
|---|
| 284 | original_filename = originals_dir + filename |
|---|
| 285 | |
|---|
| 286 | |
|---|
| 287 | #convert urls within original xml input file to NDG redirect URLS |
|---|
| 288 | #call new class in Utilities.py --will replace original file... |
|---|
| 289 | redirectUrlChanger(original_filename,original_filename,self._datacentre_format, self.NDG_redirect_URL) |
|---|
| 290 | |
|---|
| 291 | if format == 'DIF': |
|---|
| 292 | |
|---|
| 293 | #NOTE MDIP now deprecated!! easier to leave all those crappy dif or mdip code but will mainly be replaced anyway |
|---|
| 294 | |
|---|
| 295 | logging.info("Converting DIF to stub ISO...") |
|---|
| 296 | |
|---|
| 297 | #gets the metadata id from the xml |
|---|
| 298 | metadataID=self.getID(original_filename) |
|---|
| 299 | |
|---|
| 300 | repositoryName = self._datacentre_namespace |
|---|
| 301 | |
|---|
| 302 | #get the name of the file to be used in the xquery |
|---|
| 303 | metadataFilename = filename.replace('.xml', '') |
|---|
| 304 | |
|---|
| 305 | #where is the file to be ingested located? |
|---|
| 306 | metadataFileLoc = originals_dir |
|---|
| 307 | |
|---|
| 308 | #generate a new stubISO filename |
|---|
| 309 | isoFormat= "stubISO" |
|---|
| 310 | |
|---|
| 311 | if self._NDG_dataProvider: |
|---|
| 312 | |
|---|
| 313 | #changed so new new NDG3 discovery can pick up Discoveru View URL's correctly? (why should it be different to previous?) |
|---|
| 314 | new_filename = discovery_dir + self._datacentre_namespace + "__" + isoFormat + "__"+ metadataFilename.replace(":", "-")+".xml" |
|---|
| 315 | new_filename_short = self._datacentre_namespace + "__" + isoFormat + "__" + metadataFilename.replace(":", "-")+".xml" |
|---|
| 316 | |
|---|
| 317 | else: |
|---|
| 318 | |
|---|
| 319 | ident = ident.replace(":", "-") |
|---|
| 320 | ident = ident.replace("/", "-") |
|---|
| 321 | |
|---|
| 322 | new_filename = discovery_dir + "/" +self._datacentre_namespace+ "__"+ isoFormat + "__"+ ident +".xml" |
|---|
| 323 | new_filename_short = self._datacentre_namespace+ "__"+ isoFormat + "__"+ ident +".xml" |
|---|
| 324 | |
|---|
| 325 | |
|---|
| 326 | self.isoXML = self.convertDIFtoISO(metadataFileLoc,repositoryName,metadataID,metadataFilename) |
|---|
| 327 | |
|---|
| 328 | #now create this stub ISO file on system so can access it |
|---|
| 329 | self.stubIsoFile = stubIso_dir + new_filename_short |
|---|
| 330 | FileUtilities.createFile(self.stubIsoFile, self.isoXML) |
|---|
| 331 | logging.info("Stub ISO file created - at %s" %stubIso_dir) |
|---|
| 332 | |
|---|
| 333 | #elif format == 'MEDIN_v0.1': |
|---|
| 334 | |
|---|
| 335 | #basicParameters=DatasetBasicParameters_MEDIN_v01(original_filename,self._datacentre_format) |
|---|
| 336 | |
|---|
| 337 | |
|---|
| 338 | logging.info("original file = " + original_filename) |
|---|
| 339 | logging.info("newfile = " + new_filename) |
|---|
| 340 | |
|---|
| 341 | #create list of all ORIGINAL filenames for ingest reporting (use actual filename) |
|---|
| 342 | #this links a derived filename in processing dir with original filename |
|---|
| 343 | #get basic filename from the path+filename passed to this function to use as key |
|---|
| 344 | self.inputFileOrigFinal[new_filename_short]=filename |
|---|
| 345 | |
|---|
| 346 | # now correct any namespace issues |
|---|
| 347 | try: |
|---|
| 348 | SchemaNameSpace(original_filename, new_filename, self._datacentre_format) |
|---|
| 349 | except Exception, detail: |
|---|
| 350 | logging.error("SchemaNameSpace failed on file %s" %original_filename) |
|---|
| 351 | logging.error("Detail: %s" %detail) |
|---|
| 352 | logging.info("Continue with next file") |
|---|
| 353 | continue |
|---|
| 354 | numfilesproc += 1 |
|---|
| 355 | |
|---|
| 356 | logging.info("File renaming and converting completed") |
|---|
| 357 | logging.info(self.lineSeparator) |
|---|
| 358 | |
|---|
| 359 | return numfilesproc |
|---|
| 360 | |
|---|
| 361 | |
|---|
| 362 | def _getPostgresDBConnection(self): |
|---|
| 363 | ''' |
|---|
| 364 | Get the default postgres DB connection - by reading in data from the db config file |
|---|
| 365 | ''' |
|---|
| 366 | |
|---|
| 367 | logging.debug("Setting up connection to postgres DB") |
|---|
| 368 | self.pgc = pgc(configFile = '/usr/local/ndg-oai-info-editor/ingest.config') |
|---|
| 369 | logging.info("Postgres DB connection now set up") |
|---|
| 370 | |
|---|
| 371 | |
|---|
| 372 | |
|---|
| 373 | def _backupAndCleanData(self): |
|---|
| 374 | ''' |
|---|
| 375 | Back up ingested data for specified data centre, then clean any of |
|---|
| 376 | the ingest dirs |
|---|
| 377 | ''' |
|---|
| 378 | logging.info("Backing up ingested data") |
|---|
| 379 | this_backupdir = self.BACKUP_DIR + self.dataCentre + "_" + \ |
|---|
| 380 | strftime("%y%m%d_%H%M") + "_originals/" |
|---|
| 381 | |
|---|
| 382 | #FileUtilities.makeBackUp(self.originals_dir, this_backupdir) |
|---|
| 383 | logging.info("Data backed up - now clearing ingest directories") |
|---|
| 384 | #Clear out the original harvest records area and discovery dir |
|---|
| 385 | #FileUtilities.cleanDir(self.originals_dir) |
|---|
| 386 | #FileUtilities.cleanDir(self.discovery_dir) |
|---|
| 387 | logging.info("Ingest directories cleared") |
|---|
| 388 | |
|---|
| 389 | |
|---|
| 390 | def _setupDataCentreDirs(self): |
|---|
| 391 | ''' |
|---|
| 392 | Set up directories appropriate for the current data centre |
|---|
| 393 | ''' |
|---|
| 394 | logging.info("Setting up ingest directories for data centre, '%s'" %self.dataCentre) |
|---|
| 395 | data_dir = self._base_dir + "data/" + self.dataCentre # dir relating to the specified dataCentre docs |
|---|
| 396 | |
|---|
| 397 | # the following dirs define where the specific documents should go |
|---|
| 398 | self.originals_dir = data_dir + "/oai/originals/" |
|---|
| 399 | self.discovery_dir = data_dir + "/discovery/" |
|---|
| 400 | self.stubISO_dir = data_dir + "/stub_iso/" |
|---|
| 401 | |
|---|
| 402 | # Create/clear the 'in' and 'out' directories |
|---|
| 403 | FileUtilities.setUpDir(self.originals_dir) |
|---|
| 404 | FileUtilities.setUpDir(self.discovery_dir) |
|---|
| 405 | FileUtilities.setUpDir(self.stubISO_dir) |
|---|
| 406 | |
|---|
| 407 | logging.info("Ingest directories for data centre set up") |
|---|
| 408 | |
|---|
| 409 | |
|---|
| 410 | def _convertAndIngestFiles(self, originals_dir, discovery_dir, datacentre, feed, format): |
|---|
| 411 | ''' |
|---|
| 412 | Convert files from originals dir to discovery one, then |
|---|
| 413 | ingest, backup and clean |
|---|
| 414 | @param originals_dir: directory to ingest docs from |
|---|
| 415 | @param discovery_dir: directory to use to process ingested docs |
|---|
| 416 | @param feed: boolean, False if calling func is feedDocumentIngester, True - all other |
|---|
| 417 | ''' |
|---|
| 418 | |
|---|
| 419 | numfilesproc = self._convertIngestFiles(self.originals_dir, self.discovery_dir, self.stubISO_dir, format) |
|---|
| 420 | |
|---|
| 421 | filenames = os.listdir(self.discovery_dir) |
|---|
| 422 | |
|---|
| 423 | #generate a list of files ALREADY in database so can compare with what has been ingested |
|---|
| 424 | sqlCmd = "select discovery_id from original_document where discovery_id like '%" + self._datacentre_namespace + "%'" |
|---|
| 425 | |
|---|
| 426 | |
|---|
| 427 | filePresentListArr = self.pgc.runSQLCommand(sqlCmd) |
|---|
| 428 | filesPresentList=[] |
|---|
| 429 | if filePresentListArr: |
|---|
| 430 | for fileArr in filePresentListArr: |
|---|
| 431 | filesPresentList.append(fileArr[0]) |
|---|
| 432 | |
|---|
| 433 | #TODO - is above relevant - duplicating functionlaity? |
|---|
| 434 | |
|---|
| 435 | #create list to to hold files ingest failed on. |
|---|
| 436 | self.thisIngestMonitor = IngestTracking() |
|---|
| 437 | |
|---|
| 438 | #self.updateFailList = [] |
|---|
| 439 | #self.deletedFailList = [] |
|---|
| 440 | #no_problem_files = 0 |
|---|
| 441 | |
|---|
| 442 | for filename in filenames: |
|---|
| 443 | fullPath = self.discovery_dir + filename |
|---|
| 444 | |
|---|
| 445 | if os.path.isfile(fullPath): |
|---|
| 446 | |
|---|
| 447 | #ingest file intelligently according to input formatfilename,datacentre_format,datacentre_groups,datacentre_groups |
|---|
| 448 | if format == 'DIF' or format == 'MDIP': |
|---|
| 449 | |
|---|
| 450 | #thisIngestedID = ingestOriginal.addFileToPostgresDB_original(fullPath) |
|---|
| 451 | |
|---|
| 452 | |
|---|
| 453 | thisIngest = AbstractFormatIngesterOriginal() |
|---|
| 454 | thisIngestedID = thisIngest.ingest(fullPath,format,self._datacentre_groups,self._datacentre_namespace,self._xq,self.pgc,self.inputFileOrigFinal,self.thisIngestMonitor, self._NDG_dataProvider,self.stubIsoFile) |
|---|
| 455 | sys.exit() |
|---|
| 456 | |
|---|
| 457 | |
|---|
| 458 | elif format == 'MEDIN_v0.1': |
|---|
| 459 | thisIngestedID, errorMsg = AbstractFormatIngester.addFileToPostgresDB_Medin_v01(fullPath) |
|---|
| 460 | |
|---|
| 461 | #remove this filename from the list of files for this DC already in list (whats left over is to be deleted) |
|---|
| 462 | if (thisIngestedID != "") and (len(filesPresentList) != 0): |
|---|
| 463 | if thisIngestedID in filesPresentList: |
|---|
| 464 | filesPresentList.remove(thisIngestedID) |
|---|
| 465 | |
|---|
| 466 | #test loop through remaining items in filePresentList - in order to synchronise with ingest directory - these |
|---|
| 467 | #will need to be removed. |
|---|
| 468 | |
|---|
| 469 | #only do this if not in single file mode (or else wverything else gets deleted!) |
|---|
| 470 | if ((self.indFileToIngest == "") & (feed)): |
|---|
| 471 | for item in filesPresentList: |
|---|
| 472 | logging.info("NEED to DELETE : " + item + " IN ORDER TO SYNCHRONISE INGEST DIRECTORY WITH DATABASE CONTENTS") |
|---|
| 473 | DeleteRecord(item) |
|---|
| 474 | |
|---|
| 475 | #self.deletedFailList.append(item) |
|---|
| 476 | #self._no_files_deleted += 1 |
|---|
| 477 | self.thisIngestMonitor.appendDeletedList(item) |
|---|
| 478 | self.thisIngestMonitor.incrementDeletedFile() |
|---|
| 479 | |
|---|
| 480 | |
|---|
| 481 | self._backupAndCleanData() |
|---|
| 482 | |
|---|
| 483 | #at this stage put the reporting code in (will work for oai or atom feed) |
|---|
| 484 | #create a summary file for each data centre ingest |
|---|
| 485 | data_dir = self._base_dir + "data/" |
|---|
| 486 | recOpFileName = data_dir + datacentre + "_ingestSummary.txt" |
|---|
| 487 | recOpFile = open(recOpFileName,'w') |
|---|
| 488 | |
|---|
| 489 | logging.info("oai_document_ingest processing complete:") |
|---|
| 490 | |
|---|
| 491 | #Update log file details op on ingest to s atring which is THEN wrtten to a file, so as can return and email for info editor |
|---|
| 492 | message = "Ingest report for data centre: " + datacentre + "\n" |
|---|
| 493 | message = message + "Ingest date: " + str(datetime.datetime.now()) + "\n" |
|---|
| 494 | message = message + "Original metadata directory: " + self._harvest_home + "\n\n" |
|---|
| 495 | message = message + "TOTAL PROCESSED " + str(numfilesproc) + "\n" |
|---|
| 496 | message = message + "INGESTED (Created) " + str(self.thisIngestMonitor.getIngestedFileNum()) + "\n" |
|---|
| 497 | message = message + "INGESTED (Updated) " + str(self.thisIngestMonitor.getChangedFileNum()) + "\n" |
|---|
| 498 | message = message + "DELETED " + str(self.thisIngestMonitor.getDeletedFileNum()) + "\n" |
|---|
| 499 | message = message + "PROBLEM FILES " + str(self.thisIngestMonitor.getProblemFileNum()) + "\n" |
|---|
| 500 | |
|---|
| 501 | '''recOpFile.write("Ingest report for data centre: " + datacentre + "\n") |
|---|
| 502 | recOpFile.write("Ingest date: " + str(datetime.datetime.now()) + "\n") |
|---|
| 503 | recOpFile.write("Original metadata directory: " + self._harvest_home + "\n\n") |
|---|
| 504 | recOpFile.write("TOTAL PROCESSED " + str(numfilesproc) + "\n") |
|---|
| 505 | recOpFile.write("INGESTED (Created) " + str(self._no_files_changed) + "\n") |
|---|
| 506 | recOpFile.write("INGESTED (Updated) " + str(self._no_files_ingested) + "\n") |
|---|
| 507 | recOpFile.write("DELETED " + str(self._no_files_deleted) + "\n") |
|---|
| 508 | recOpFile.write("PROBLEM FILES " + str(self._no_problem_files) + "\n")''' |
|---|
| 509 | |
|---|
| 510 | |
|---|
| 511 | #for badFile in self.updateFailList: |
|---|
| 512 | for badFile in self.thisIngestMonitor.getFailList(): |
|---|
| 513 | #recOpFile.write("PROBLEM_FILE " + badFile + "\n") |
|---|
| 514 | message = message +"PROBLEM_FILE " + badFile + "\n" |
|---|
| 515 | |
|---|
| 516 | recOpFile.write(message) |
|---|
| 517 | |
|---|
| 518 | return numfilesproc, message |
|---|
| 519 | |
|---|
| 520 | |
|---|
| 521 | |
|---|
| 522 | def _setupXQueries(self): |
|---|
| 523 | ''' |
|---|
| 524 | Set up the required XQueries |
|---|
| 525 | - NB, extract the xquery libraries locally for easy reference |
|---|
| 526 | ''' |
|---|
| 527 | self._xq = ndgResources() |
|---|
| 528 | for libFile in self._xq.xqlib: |
|---|
| 529 | # NB, we don't want the full path to the files - just the filename |
|---|
| 530 | fileName = libFile.split('/')[-1] |
|---|
| 531 | FileUtilities.createFile(fileName, self._xq.xqlib[libFile]) |
|---|
