def createChunksSubmitJobs(inDir, outDir, minId, runner, chunkSize):
""" submit jobs to convert zip and disk files from inDir to outDir
split files into chunks and submit chunks to cluster system
write first to temporary dir, and copy over at end of all jobs
This is based on pubConvElsevier.py
"""
maxCommon.mustExistDir(outDir)
updateId, minId, alreadyDoneFiles = pubStore.parseUpdatesTab(outDir, minId)
assert(chunkSize!=None)
finalOutDir= outDir
outDir = tempfile.mktemp(dir = outDir, prefix = "springerUpdate.tmp.")
os.mkdir(outDir)
# getting filenames from the disk
diskDir = join(inDir, "disk")
if int(updateId)==0 and isdir(diskDir):
inDiskFiles = parseDiskFnames(diskDir)
else:
logging.info("Not first update or no directory %s, not parsing files from springer disk" % diskDir)
# getting filenames from the updates
zipDir = join(inDir, "updates")
inZipFiles = os.listdir(zipDir)
inZipFiles = [x for x in inZipFiles if x.endswith(".zip")]
logging.info("Found %d update zip files" % len(inZipFiles))
# keep order of input files for first run
if len(alreadyDoneFiles)==0:
processFiles = inDiskFiles+inZipFiles
else:
processFiles = set(inZipFiles).difference(alreadyDoneFiles)
if len(processFiles)==0:
logging.info("All updates done, not converting anything")
return None
else:
logging.info("Total number of files to convert: %d" % (len(processFiles)))
indexFilename = join(outDir, "%d_index.tab" % updateId)
maxArticleId = createIndexFile(zipDir, processFiles, indexFilename, updateId, minId, chunkSize)
indexSplitDir = join(outDir, "indexFiles")
pubStore.splitTabFileOnChunkId(indexFilename, indexSplitDir)
idFname = concatDois(finalOutDir, outDir, "doneArticles.tab")
submitJobs(runner, zipDir, indexSplitDir, idFname, outDir)
pubGeneric.concatDelIdFiles(outDir, finalOutDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(outDir, finalOutDir, "%d.log" % updateId)
# cleanup, move over, remove whole temp dir
if isdir(indexSplitDir): # necessary? how could it not be there?
logging.info("Deleting directory %s" % indexSplitDir)
shutil.rmtree(indexSplitDir) # got sometimes exception here...
pubStore.moveFiles(outDir, finalOutDir)
shutil.rmtree(outDir)
pubStore.appendToUpdatesTxt(finalOutDir, updateId, maxArticleId, processFiles)
def createChunksSubmitJobs(inDir, outDir, minId, runner, chunkSize):
tmpDir = pubGeneric.makeTempDir("bingData", tmpDir=outDir)
#maxCommon.delOnExit(tmpDir)
maxCommon.mustExistDir(outDir)
updateId, minId, alreadyDoneFiles = pubStore.parseUpdatesTab(outDir, minId)
# get all .gz.index files, remove the already done files
inFnames = glob.glob(join(inDir, "*.index.gz"))
inBaseNames = set([basename(x) for x in inFnames])
todoBasenames = inBaseNames - set(alreadyDoneFiles)
todoFnames = [join(inDir, x) for x in todoBasenames]
if len(todoFnames) == 0:
logging.info("All input files already converted")
return
indexFilename = join(outDir, "%d_index.tab" % updateId)
indexFile = open(indexFilename, "w")
headers = ["articleId", "tsvFile", "url", "offset"]
indexFile.write("\t".join(headers))
indexFile.write("\n")
# read them and create a big index file:
# with tsvname, url, offset
numId = minId
doneUrls = set()
for fname in todoFnames:
baseName = basename(fname)
for line in gzip.open(fname):
url, offset = line.rstrip("\n").split("\t")
assert (offset.isdigit())
if "\t" in url or "\n" in url:
logging.info("tab or NL in url %s, skipping" % url)
continue
if url in doneUrls:
logging.info("Already did %s" % url)
continue
baseName = baseName.replace(".index.gz", ".gz")
row = [str(numId), baseName, url, offset]
indexFile.write("\t".join(row))
indexFile.write("\n")
numId += 1
indexFile.close()
# split the index file into chunks, one per job
chunkIds = pubStore.splitTabFileOnChunkId(indexFilename,
tmpDir,
chunkSize=chunkSize)
idFname = pubGeneric.concatIdentifiers(outDir, tmpDir, "doneArticles.tab")
# submit one conversion job per chunk
submitConvertJobs(runner, inDir, updateId, chunkIds, tmpDir, idFname,
tmpDir)
pubGeneric.concatDelIdFiles(tmpDir, outDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(tmpDir, outDir, "%d.log" % updateId)
pubStore.moveFiles(tmpDir, outDir)
shutil.rmtree(tmpDir)
pubStore.appendToUpdatesTxt(outDir, updateId, numId, todoBasenames)
def createChunksSubmitJobs(inDir, outDir, minId, runner, chunkSize):
tmpDir = pubGeneric.makeTempDir("bingData", tmpDir=outDir)
#maxCommon.delOnExit(tmpDir)
maxCommon.mustExistDir(outDir)
updateId, minId, alreadyDoneFiles = pubStore.parseUpdatesTab(outDir, minId)
# get all .gz.index files, remove the already done files
inFnames = glob.glob(join(inDir, "*.index.gz"))
inBaseNames = set([basename(x) for x in inFnames])
todoBasenames = inBaseNames - set(alreadyDoneFiles)
todoFnames = [join(inDir, x) for x in todoBasenames]
if len(todoFnames)==0:
logging.info("All input files already converted")
return
indexFilename = join(outDir, "%d_index.tab" % updateId)
indexFile = open(indexFilename, "w")
headers = ["articleId", "tsvFile", "url", "offset"]
indexFile.write("\t".join(headers))
indexFile.write("\n")
# read them and create a big index file:
# with tsvname, url, offset
numId = minId
doneUrls = set()
for fname in todoFnames:
baseName = basename(fname)
for line in gzip.open(fname):
url, offset = line.rstrip("\n").split("\t")
assert(offset.isdigit())
if "\t" in url or "\n" in url:
logging.info("tab or NL in url %s, skipping" % url)
continue
if url in doneUrls:
logging.info("Already did %s" % url)
continue
baseName = baseName.replace(".index.gz", ".gz")
row = [str(numId), baseName, url, offset]
indexFile.write("\t".join(row))
indexFile.write("\n")
numId+=1
indexFile.close()
# split the index file into chunks, one per job
chunkIds = pubStore.splitTabFileOnChunkId(indexFilename, tmpDir, chunkSize=chunkSize)
idFname = pubGeneric.concatIdentifiers(outDir, tmpDir, "doneArticles.tab")
# submit one conversion job per chunk
submitConvertJobs(runner, inDir, updateId, chunkIds, tmpDir, idFname, tmpDir)
pubGeneric.concatDelIdFiles(tmpDir, outDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(tmpDir, outDir, "%d.log" % updateId)
pubStore.moveFiles(tmpDir, outDir)
shutil.rmtree(tmpDir)
pubStore.appendToUpdatesTxt(outDir, updateId, numId, todoBasenames)
def createChunksSubmitJobs(inDir, outDir, minId, runner, chunkSize):
""" convert Consyn ZIP files from inDir to outDir
split files into chunks and submit chunks to cluster system
write first to temporary dir, and copy over at end of all jobs
"""
maxCommon.mustExistDir(outDir)
updateId, minId, alreadyDoneFiles = pubStore.parseUpdatesTab(outDir, minId)
if chunkSize == None:
chunkSize = pubStore.guessChunkSize(outDir)
assert (chunkSize != None)
# build into temporary dir, fail if it exists
# it should not exist, otherwise something is wrong
finalOutDir = outDir
#outDir = tempfile.mktemp(dir = outDir, prefix = "elsevierUpdate%s.tmp." % str(updateId))
buildDir = join(outDir, "build")
os.mkdir(buildDir)
inFiles = os.listdir(inDir)
inFiles = [x for x in inFiles if x.endswith(".ZIP")]
# keep order of input of input files for first run
if len(alreadyDoneFiles) != 0:
processFiles = set(inFiles).difference(alreadyDoneFiles)
else:
processFiles = inFiles
if len(processFiles) == 0:
logging.info("All updates done, not converting anything")
os.rmdir(buildDir)
return None
indexFilename = join(buildDir, "%d_index.tab" % updateId)
maxArticleId = createIndexFile(inDir, processFiles, indexFilename,
updateId, minId, chunkSize)
indexSplitDir = indexFilename + ".tmp.split"
chunkIds = pubStore.splitTabFileOnChunkId(indexFilename, indexSplitDir)
idFname = pubGeneric.concatIdentifiers(finalOutDir, indexSplitDir,
"doneArticles.tab")
submitJobs(runner, inDir, chunkIds, indexSplitDir, idFname, buildDir)
pubGeneric.concatDelIdFiles(buildDir, finalOutDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(buildDir, finalOutDir, "%d.log" % updateId)
if isdir(indexSplitDir): # necessary? how could it not be there?
logging.info("Deleting directory %s" % indexSplitDir)
shutil.rmtree(indexSplitDir) # got sometimes exception here...
pubStore.moveFiles(buildDir, finalOutDir)
shutil.rmtree(buildDir)
pubStore.appendToUpdatesTxt(finalOutDir, updateId, maxArticleId,
processFiles)
def createChunksSubmitJobs(inDir, outDir, minId, runner, chunkSize):
""" convert Consyn ZIP files from inDir to outDir
split files into chunks and submit chunks to cluster system
write first to temporary dir, and copy over at end of all jobs
"""
maxCommon.mustExistDir(outDir)
updateId, minId, alreadyDoneFiles = pubStore.parseUpdatesTab(outDir, minId)
if chunkSize==None:
chunkSize = pubStore.guessChunkSize(outDir)
assert(chunkSize!=None)
# build into temporary dir, fail if it exists
# it should not exist, otherwise something is wrong
finalOutDir= outDir
#outDir = tempfile.mktemp(dir = outDir, prefix = "elsevierUpdate%s.tmp." % str(updateId))
buildDir = join(outDir, "build")
os.mkdir(buildDir)
inFiles = os.listdir(inDir)
inFiles = [x for x in inFiles if x.endswith(".ZIP")]
# keep order of input of input files for first run
if len(alreadyDoneFiles)!=0:
processFiles = set(inFiles).difference(alreadyDoneFiles)
else:
processFiles = inFiles
if len(processFiles)==0:
logging.info("All updates done, not converting anything")
os.rmdir(buildDir)
return None
indexFilename = join(buildDir, "%d_index.tab" % updateId)
maxArticleId = createIndexFile(inDir, processFiles, indexFilename, updateId, minId, chunkSize)
indexSplitDir = indexFilename+".tmp.split"
chunkIds = pubStore.splitTabFileOnChunkId(indexFilename, indexSplitDir)
idFname = pubGeneric.concatIdentifiers(finalOutDir, indexSplitDir, "doneArticles.tab")
submitJobs(runner, inDir, chunkIds, indexSplitDir, idFname, buildDir)
pubGeneric.concatDelIdFiles(buildDir, finalOutDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(buildDir, finalOutDir, "%d.log" % updateId)
if isdir(indexSplitDir): # necessary? how could it not be there?
logging.info("Deleting directory %s" % indexSplitDir)
shutil.rmtree(indexSplitDir) # got sometimes exception here...
pubStore.moveFiles(buildDir, finalOutDir)
shutil.rmtree(buildDir)
pubStore.appendToUpdatesTxt(finalOutDir, updateId, maxArticleId, processFiles)
def finishUp(finalOutDir):
" do the final post-batch processing "
buildDir = pubGeneric.makeBuildDir(finalOutDir, mustExist=True)
minId = pubConf.identifierStart["springer"]
pubGeneric.concatDelIdFiles(buildDir, finalOutDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(buildDir, finalOutDir, "%d.log" % updateId)
# cleanup, move over, remove whole temp dir
if isdir(indexSplitDir): # necessary? how could it not be there?
logging.info("Deleting directory %s" % indexSplitDir)
shutil.rmtree(indexSplitDir) # got sometimes exception here...
pubStore.moveFiles(buildDir, finalOutDir)
shutil.rmtree(buildDir)
pubStore.appendToUpdatesTxt(finalOutDir, updateId, maxArticleId, processFiles)
pubStore.updateSqlite(finalOutDir)
def finishUp(finalOutDir):
" do the final post-batch processing "
buildDir = pubGeneric.makeBuildDir(finalOutDir, mustExist=True)
minId = pubConf.identifierStart["springer"]
pubGeneric.concatDelIdFiles(buildDir, finalOutDir, "%d_ids.tab" % updateId)
pubGeneric.concatDelLogs(buildDir, finalOutDir, "%d.log" % updateId)
# cleanup, move over, remove whole temp dir
if isdir(indexSplitDir): # necessary? how could it not be there?
logging.info("Deleting directory %s" % indexSplitDir)
shutil.rmtree(indexSplitDir) # got sometimes exception here...
pubStore.moveFiles(buildDir, finalOutDir)
shutil.rmtree(buildDir)
pubStore.appendToUpdatesTxt(finalOutDir, updateId, maxArticleId, processFiles)
pubStore.updateSqlite(finalOutDir)