def getArtDbPath(datasetName):
""" return the sqlite database name with meta info of a dataset """
dataDir = pubConf.resolveTextDir(datasetName, mustFind=False)
if dataDir==None:
return None
dbPath = join(dataDir, "articles.db")
return dbPath
def resolveDatasetDesc(descs):
" resolve a comma-sep list of dataset identifiers like pmc or elsevier to a list of directories "
dirs = []
for desc in descs.split(","):
descDir = pubConf.resolveTextDir(desc)
if descDir == None:
raise Exception("Unknown dataset: %s" % desc)
dirs.append(descDir)
return dirs
def resolveDatasetDesc(descs):
" resolve a comma-sep list of dataset identifiers like pmc or elsevier to a list of directories "
dirs = []
for desc in descs.split(','):
descDir = pubConf.resolveTextDir(desc)
if descDir == None:
raise Exception("Unknown dataset: %s" % desc)
dirs.append(descDir)
return dirs
def __init__(self, dataset):
self.dataset = dataset
self.textDir = pubConf.resolveTextDir(dataset)
if self.textDir == None:
raise Exception("dataset %s can not be resolved to a directory" % dataset)
self.pubMapBaseDir = pubConf.pubMapBaseDir
maxCommon.mustExistDir(pubConf.pubMapBaseDir, makeDir=True)
self._defineBatchDirectories()
def findFiles(dataset):
""" return all basenames for .gz files in datasets.
inDir can be a list of datasetnames, a file or a directory with datasetnames """
#assert(type(datasets)==types.ListType)
fnames = []
dataDir = pubConf.resolveTextDir(dataset)
if dataDir==None:
raise Exception("error in input data spec")
fnames.extend(glob.glob(join(dataDir, "*.articles.gz")))
if len(fnames)==0:
raise Exception("Could not find any *.articles.gz files in %s"% dataDir)
return fnames
def __init__(self, dataset):
self.markerCountsBase = MARKERCOUNTSBASE
self.markerDirBase = MARKERDIRBASE
self.pubMapBaseDir = pubConf.pubMapBaseDir
maxCommon.mustExistDir(pubConf.pubMapBaseDir, makeDir=True)
self.dataset = dataset
if "," in dataset:
logging.debug("comma in dataset description, deferring config")
return
self.textDir = pubConf.resolveTextDir(dataset)
if self.textDir==None:
raise Exception("dataset %s can not be resolved to a directory" % dataset)
self._defineBatchDirectories()
def getAllUpdateIds(datasets):
" collect all available text dataset updateIds for all datasets "
textUpdateIds = {}
for dataset in datasets:
textDir = pubConf.resolveTextDir(dataset)
updateFname = join(textDir, "updates.tab")
logging.debug("Reading %s" % updateFname)
updateIds = []
for row in maxCommon.iterTsvRows(updateFname):
updateIds.append(row.updateId)
textUpdateIds[dataset] = updateIds
return textUpdateIds
# also save to file, so we don't have to do this again
outFname = join(batchDir, "updateIds.json")
json.dumps(textUpdateIds, open(outFname, "w"), sort_keys=True, indent=4, )
return textUpdateIds
def getAllUpdateIds(datasets):
" collect all available text dataset updateIds for all datasets "
textUpdateIds = {}
for dataset in datasets:
textDir = pubConf.resolveTextDir(dataset)
updateFname = join(textDir, "updates.tab")
logging.debug("Reading %s" % updateFname)
updateIds = []
for row in maxCommon.iterTsvRows(updateFname):
updateIds.append(row.updateId)
textUpdateIds[dataset] = updateIds
return textUpdateIds
# also save to file, so we don't have to do this again
outFname = join(batchDir, "updateIds.json")
json.dumps(
textUpdateIds,
open(outFname, "w"),
sort_keys=True,
indent=4,
)
return textUpdateIds
def __init__(self, dataset, outDir):
self.markerCountsBase = MARKERCOUNTSBASE
self.markerDirBase = MARKERDIRBASE
assert(outDir!=None and outDir!="")
self.pubMapBaseDir = outDir
maxCommon.mustExistDir(self.pubMapBaseDir, makeDir=True)
logging.debug("Main pipeline outdir is %s" % outDir)
self.dataset = dataset
if "," in dataset:
logging.debug("comma in dataset description, deferring config")
return
self.textDir = pubConf.resolveTextDir(dataset)
if self.textDir==None:
raise Exception("dataset %s can not be resolved to a directory" % dataset)
# base dir for dataset
self.baseDir = join(self.pubMapBaseDir, self.dataset)
self.batchId = self._findCurrentBatchDir()
self.batchDir = join(self.baseDirBatches, str(self.batchId))
self._defineBatchDirectories()
def addPmids(datasetString):
" for a given dataset, add the pmids from the pubFingerprint output file to the article files "
#datasetString = args[0]
textDir = pubConf.resolveTextDir(datasetString)
logging.info("Changing article files in %s" % textDir)
aToPfn = join(textDir, pubConf.idFname)
logging.info("Reading art -> pmid mapping from %s" % aToPfn)
artToPmid = parseIdFname(aToPfn)
fnames = glob.glob(join(textDir, "*.articles.gz"))
logging.info("Running on %d article files" % len(fnames))
pm = maxCommon.ProgressMeter(len(fnames), stepCount=100)
updateSqliteIds(textDir, artToPmid.items())
#sys.exit(0)
logging.info("Updating tab sep files")
for fname in fnames:
# write headers
newFname = join(pubConf.TEMPDIR, basename(fname))
logging.debug("reading %s, writing %s" % (fname, newFname))
newF = gzip.open(newFname, "w")
newF.write(gzip.open(fname).readline())
# write rows, replacing pmids on the way
for row in maxCommon.iterTsvRows(fname):
artId = int(row.articleId)
if int(row.articleId) in artToPmid:
row = row._replace(pmid=artToPmid[artId])
newF.write((u'\t'.join(row)).encode("utf8"))
newF.write("\n")
newF.close()
# rename old, move over the new one
shutil.move(fname, fname+".bak")
shutil.move(newFname, fname)
pm.taskCompleted()
def addPmids(datasetString):
" for a given dataset, add the pmids from the pubFingerprint output file to the article files "
#datasetString = args[0]
textDir = pubConf.resolveTextDir(datasetString)
logging.info("Changing article files in %s" % textDir)
aToPfn = join(textDir, pubConf.idFname)
logging.info("Reading art -> pmid mapping from %s" % aToPfn)
artToPmid = parseIdFname(aToPfn)
fnames = glob.glob(join(textDir, "*.articles.gz"))
logging.info("Running on %d article files" % len(fnames))
pm = maxCommon.ProgressMeter(len(fnames), stepCount=100)
updateSqliteIds(textDir, artToPmid.items())
#sys.exit(0)
logging.info("Updating tab sep files")
for fname in fnames:
# write headers
newFname = join(pubConf.TEMPDIR, basename(fname))
logging.debug("reading %s, writing %s" % (fname, newFname))
newF = gzip.open(newFname, "w")
newF.write(gzip.open(fname).readline())
# write rows, replacing pmids on the way
for row in maxCommon.iterTsvRows(fname):
artId = int(row.articleId)
if int(row.articleId) in artToPmid:
row = row._replace(pmid=artToPmid[artId])
newF.write((u'\t'.join(row)).encode("utf8"))
newF.write("\n")
newF.close()
# rename old, move over the new one
shutil.move(fname, fname + ".bak")
shutil.move(newFname, fname)
pm.taskCompleted()
def getArtDbPath(datasetName):
" return the sqlite database name with meta info of a dataset "
dataDir = pubConf.resolveTextDir(datasetName)
dbPath = join(dataDir, "articles.db")
return dbPath
def __init__(self):
textDir = pubConf.resolveTextDir("medline")
fname = join(textDir, FINGERPRINTFNAME)
self.db = pubGeneric.openKeyValDb(fname)
self.noPrints = []
self.noMatches = []
def filterCmd(inSpec, searchSpec, outSpec, options):
outDir = pubConf.resolveTextDir(outSpec)
assert(outDir!=None)
maxCommon.mustBeEmptyDir(outDir)
return submitJobs(inSpec, searchSpec, outDir)
def filterCmd(inSpec, searchSpec, outSpec, options):
outDir = pubConf.resolveTextDir(outSpec)
assert (outDir != None)
maxCommon.mustBeEmptyDir(outDir)
return submitJobs(inSpec, searchSpec, outDir)
def __init__(self):
textDir = pubConf.resolveTextDir("medline")
fname = join(textDir, FINGERPRINTFNAME)
self.db = pubGeneric.openKeyValDb(fname)
self.noPrints = []
self.noMatches = []
